---
_id: '7391'
abstract:
- lang: eng
text: Electron microscopy (EM) is a technology that enables visualization of single
proteins at a nanometer resolution. However, current protein analysis by EM mainly
relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised
by large size of antibody, precluding precise detection of protein location in
biological samples. Here, we develop a specific chemical labeling method for EM
detection of proteins at single-molecular level. Rational design of α-helical
peptide tag and probe structure provided a complementary reaction pair that enabled
specific cysteine conjugation of the tag. The developed chemical labeling with
gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency
and detectability of high-density clusters of tag-fused G protein-coupled receptors
in freeze-fracture replicas compared with immunogold labeling. Furthermore, in
ultrathin sections, the spatial resolution of the chemical labeling was significantly
higher than that of antibody-mediated labeling. These results demonstrate substantial
advantages of the chemical labeling approach for single protein visualization
by EM.
article_processing_charge: No
article_type: original
author:
- first_name: Shigekazu
full_name: Tabata, Shigekazu
id: 4427179E-F248-11E8-B48F-1D18A9856A87
last_name: Tabata
- first_name: Marijo
full_name: Jevtic, Marijo
id: 4BE3BC94-F248-11E8-B48F-1D18A9856A87
last_name: Jevtic
- first_name: Nobutaka
full_name: Kurashige, Nobutaka
last_name: Kurashige
- first_name: Hirokazu
full_name: Fuchida, Hirokazu
last_name: Fuchida
- first_name: Munetsugu
full_name: Kido, Munetsugu
last_name: Kido
- first_name: Kazushi
full_name: Tani, Kazushi
last_name: Tani
- first_name: Naoki
full_name: Zenmyo, Naoki
last_name: Zenmyo
- first_name: Shohei
full_name: Uchinomiya, Shohei
last_name: Uchinomiya
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Makoto
full_name: Itakura, Makoto
last_name: Itakura
- first_name: Itaru
full_name: Hamachi, Itaru
last_name: Hamachi
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Akio
full_name: Ojida, Akio
last_name: Ojida
citation:
ama: Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single
membrane proteins by a specific chemical labeling. iScience. 2019;22(12):256-268.
doi:10.1016/j.isci.2019.11.025
apa: Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida,
A. (2019). Electron microscopic detection of single membrane proteins by a specific
chemical labeling. IScience. Elsevier. https://doi.org/10.1016/j.isci.2019.11.025
chicago: Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida,
Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection
of Single Membrane Proteins by a Specific Chemical Labeling.” IScience.
Elsevier, 2019. https://doi.org/10.1016/j.isci.2019.11.025.
ieee: S. Tabata et al., “Electron microscopic detection of single membrane
proteins by a specific chemical labeling,” iScience, vol. 22, no. 12. Elsevier,
pp. 256–268, 2019.
ista: Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya
S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic
detection of single membrane proteins by a specific chemical labeling. iScience.
22(12), 256–268.
mla: Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane
Proteins by a Specific Chemical Labeling.” IScience, vol. 22, no. 12, Elsevier,
2019, pp. 256–68, doi:10.1016/j.isci.2019.11.025.
short: S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo,
S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience
22 (2019) 256–268.
corr_author: '1'
date_created: 2020-01-29T15:56:56Z
date_published: 2019-12-20T00:00:00Z
date_updated: 2026-04-28T22:30:32Z
day: '20'
ddc:
- '570'
department:
- _id: RySh
doi: 10.1016/j.isci.2019.11.025
ec_funded: 1
external_id:
isi:
- '000504652000020'
pmid:
- '31786521'
file:
- access_level: open_access
checksum: f3e90056a49f09b205b1c4f8c739ffd1
content_type: application/pdf
creator: dernst
date_created: 2020-02-04T10:48:36Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7448'
file_name: 2019_iScience_Tabata.pdf
file_size: 7197776
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 22'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 256-268
pmid: 1
project:
- _id: 25CA28EA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '694539'
name: 'In situ analysis of single channel subunit composition in neurons: physiological
implication in synaptic plasticity and behaviour'
- _id: 25CBA828-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '720270'
name: Human Brain Project Specific Grant Agreement 1
publication: iScience
publication_identifier:
issn:
- 2589-0042
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '11393'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Electron microscopic detection of single membrane proteins by a specific chemical
labeling
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 22
year: '2019'
...
---
_id: '6194'
abstract:
- lang: eng
text: Grid cells with their rigid hexagonal firing fields are thought to provide
an invariant metric to the hippocampal cognitive map, yet environmental geometrical
features have recently been shown to distort the grid structure. Given that the
hippocampal role goes beyond space, we tested the influence of nonspatial information
on the grid organization. We trained rats to daily learn three new reward locations
on a cheeseboard maze while recording from the medial entorhinal cortex and the
hippocampal CA1 region. Many grid fields moved toward goal location, leading to
long-lasting deformations of the entorhinal map. Therefore, distortions in the
grid structure contribute to goal representation during both learning and recall,
which demonstrates that grid cells participate in mnemonic coding and do not merely
provide a simple metric of space.
article_processing_charge: No
article_type: original
author:
- first_name: Charlotte N.
full_name: Boccara, Charlotte N.
id: 3FC06552-F248-11E8-B48F-1D18A9856A87
last_name: Boccara
orcid: 0000-0001-7237-5109
- first_name: Michele
full_name: Nardin, Michele
id: 30BD0376-F248-11E8-B48F-1D18A9856A87
last_name: Nardin
orcid: 0000-0001-8849-6570
- first_name: Federico
full_name: Stella, Federico
id: 39AF1E74-F248-11E8-B48F-1D18A9856A87
last_name: Stella
orcid: 0000-0001-9439-3148
- first_name: Joseph
full_name: O'Neill, Joseph
id: 426376DC-F248-11E8-B48F-1D18A9856A87
last_name: O'Neill
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive
map is attracted to goals. Science. 2019;363(6434):1443-1447. doi:10.1126/science.aav4837
apa: Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., & Csicsvari, J. L.
(2019). The entorhinal cognitive map is attracted to goals. Science. American
Association for the Advancement of Science. https://doi.org/10.1126/science.aav4837
chicago: Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill,
and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.”
Science. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/science.aav4837.
ieee: C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The
entorhinal cognitive map is attracted to goals,” Science, vol. 363, no.
6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.
ista: Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal
cognitive map is attracted to goals. Science. 363(6434), 1443–1447.
mla: Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to
Goals.” Science, vol. 363, no. 6434, American Association for the Advancement
of Science, 2019, pp. 1443–47, doi:10.1126/science.aav4837.
short: C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363
(2019) 1443–1447.
date_created: 2019-04-04T08:39:30Z
date_published: 2019-03-29T00:00:00Z
date_updated: 2026-04-28T22:30:34Z
day: '29'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1126/science.aav4837
ec_funded: 1
external_id:
isi:
- '000462738000034'
file:
- access_level: open_access
checksum: 5e6b16742cde10a560cfaf2130764da1
content_type: application/pdf
creator: dernst
date_created: 2020-05-14T09:11:10Z
date_updated: 2020-07-14T12:47:23Z
file_id: '7826'
file_name: 2019_Science_Boccara.pdf
file_size: 9045923
relation: main_file
file_date_updated: 2020-07-14T12:47:23Z
has_accepted_license: '1'
intvolume: ' 363'
isi: 1
issue: '6434'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1443-1447
project:
- _id: 257A4776-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281511'
name: Memory-related information processing in neuronal circuits of the hippocampus
and entorhinal cortex
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/
record:
- id: '6062'
relation: popular_science
status: public
- id: '11932'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The entorhinal cognitive map is attracted to goals
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 363
year: '2019'
...
---
OA_place: publisher
_id: '6891'
abstract:
- lang: eng
text: "While cells of mesenchymal or epithelial origin perform their effector functions
in a purely anchorage dependent manner, cells derived from the hematopoietic lineage
are not committed to operate only within a specific niche. Instead, these cells
are able to function autonomously of the molecular composition in a broad range
of tissue compartments. By this means, cells of the hematopoietic lineage retain
the capacity to disseminate into connective tissue and recirculate between organs,
building the foundation for essential processes such as tissue regeneration or
immune surveillance. \r\nCells of the immune system, specifically leukocytes,
are extraordinarily good at performing this task. These cells are able to flexibly
shift their mode of migration between an adhesion-mediated and an adhesion-independent
manner, instantaneously accommodating for any changes in molecular composition
of the external scaffold. The key component driving directed leukocyte migration
is the chemokine receptor 7, which guides the cell along gradients of chemokine
ligand. Therefore, the physical destination of migrating leukocytes is purely
deterministic, i.e. given by global directional cues such as chemokine gradients.
\r\nNevertheless, these cells typically reside in three-dimensional scaffolds
of inhomogeneous complexity, raising the question whether cells are able to locally
discriminate between multiple optional migration routes. Current literature provides
evidence that leukocytes, specifically dendritic cells, do indeed probe their
surrounding by virtue of multiple explorative protrusions. However, it remains
enigmatic how these cells decide which one is the more favorable route to follow
and what are the key players involved in performing this task. Due to the heterogeneous
environment of most tissues, and the vast adaptability of migrating leukocytes,
at this time it is not clear to what extent leukocytes are able to optimize their
migratory strategy by adapting their level of adhesiveness. And, given the fact
that leukocyte migration is characterized by branched cell shapes in combination
with high migration velocities, it is reasonable to assume that these cells require
fine tuned shape maintenance mechanisms that tightly coordinate protrusion and
adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed
to elucidate how rapidly migrating leukocytes opt for an ideal migratory path
while maintaining a continuous cell shape and balancing adhesive forces to efficiently
navigate through complex microenvironments. \r\nThe results of this study unraveled
a role for the microtubule cytoskeleton in promoting the decision making process
during path finding and for the first time point towards a microtubule-mediated
function in cell shape maintenance of highly ramified cells such as dendritic
cells. Furthermore, we found that migrating low-adhesive leukocytes are able to
instantaneously adapt to increased tensile load by engaging adhesion receptors.
This response was only occurring tangential to the substrate while adhesive properties
in the vertical direction were not increased. As leukocytes are primed for rapid
migration velocities, these results demonstrate that leukocyte integrins are able
to confer a high level of traction forces parallel to the cell membrane along
the direction of migration without wasting energy in gluing the cell to the substrate.
\r\nThus, the data in the here presented thesis provide new insights into the
pivotal role of cytoskeletal dynamics and the mechanisms of force transduction
during leukocyte migration. \r\nThereby the here presented results help to further
define fundamental principles underlying leukocyte migration and open up potential
therapeutic avenues of clinical relevance.\r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
citation:
ama: Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019.
doi:10.15479/AT:ISTA:6891
apa: Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891
chicago: Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.”
Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891.
ieee: A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,”
Institute of Science and Technology Austria, 2019.
ista: Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration.
Institute of Science and Technology Austria.
mla: Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration.
Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891.
short: A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration,
Institute of Science and Technology Austria, 2019.
corr_author: '1'
date_created: 2019-09-19T08:19:44Z
date_published: 2019-07-24T00:00:00Z
date_updated: 2026-04-08T07:11:03Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
doi: 10.15479/AT:ISTA:6891
file:
- access_level: closed
checksum: 00d100d6468e31e583051e0a006b640c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: akopf
date_created: 2019-10-15T05:28:42Z
date_updated: 2020-10-17T22:30:03Z
embargo_to: open_access
file_id: '6950'
file_name: Kopf_PhD_Thesis.docx
file_size: 74735267
relation: source_file
- access_level: open_access
checksum: 5d1baa899993ae6ca81aebebe1797000
content_type: application/pdf
creator: akopf
date_created: 2019-10-15T05:28:47Z
date_updated: 2020-10-17T22:30:03Z
embargo: 2020-10-16
file_id: '6951'
file_name: Kopf_PhD_Thesis1.pdf
file_size: 52787224
relation: main_file
file_date_updated: 2020-10-17T22:30:03Z
has_accepted_license: '1'
keyword:
- cell biology
- immunology
- leukocyte
- migration
- microfluidics
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '171'
project:
- _id: 265E2996-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
publication_identifier:
eissn:
- 2663-337X
isbn:
- 978-3-99078-002-2
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
link:
- relation: press_release
url: https://ist.ac.at/en/news/feeling-like-a-cell/
record:
- id: '6877'
relation: part_of_dissertation
status: public
- id: '15'
relation: part_of_dissertation
status: public
- id: '6328'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: The implication of cytoskeletal dynamics on leukocyte migration
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
_id: '6328'
abstract:
- lang: eng
text: During metazoan development, immune surveillance and cancer dissemination,
cells migrate in complex three-dimensional microenvironments1,2,3. These spaces
are crowded by cells and extracellular matrix, generating mazes with differently
sized gaps that are typically smaller than the diameter of the migrating cell4,5.
Most mesenchymal and epithelial cells and some—but not all—cancer cells actively
generate their migratory path using pericellular tissue proteolysis6. By contrast,
amoeboid cells such as leukocytes use non-destructive strategies of locomotion7,
raising the question how these extremely fast cells navigate through dense tissues.
Here we reveal that leukocytes sample their immediate vicinity for large pore
sizes, and are thereby able to choose the path of least resistance. This allows
them to circumnavigate local obstacles while effectively following global directional
cues such as chemotactic gradients. Pore-size discrimination is facilitated by
frontward positioning of the nucleus, which enables the cells to use their bulkiest
compartment as a mechanical gauge. Once the nucleus and the closely associated
microtubule organizing centre pass the largest pore, cytoplasmic protrusions still
lingering in smaller pores are retracted. These retractions are coordinated by
dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence
and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning
in front of the microtubule organizing centre is a typical feature of amoeboid
migration, our findings link the fundamental organization of cellular polarity
to the strategy of locomotion.
acknowledged_ssus:
- _id: SSU
article_processing_charge: No
article_type: letter_note
author:
- first_name: Jörg
full_name: Renkawitz, Jörg
id: 3F0587C8-F248-11E8-B48F-1D18A9856A87
last_name: Renkawitz
orcid: 0000-0003-2856-3369
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Julian A
full_name: Stopp, Julian A
id: 489E3F00-F248-11E8-B48F-1D18A9856A87
last_name: Stopp
- first_name: Ingrid
full_name: de Vries, Ingrid
id: 4C7D837E-F248-11E8-B48F-1D18A9856A87
last_name: de Vries
- first_name: Meghan K.
full_name: Driscoll, Meghan K.
last_name: Driscoll
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Robert
full_name: Hauschild, Robert
id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
last_name: Hauschild
orcid: 0000-0001-9843-3522
- first_name: Erik S.
full_name: Welf, Erik S.
last_name: Welf
- first_name: Gaudenz
full_name: Danuser, Gaudenz
last_name: Danuser
- first_name: Reto
full_name: Fiolka, Reto
last_name: Fiolka
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid
migration along the path of least resistance. Nature. 2019;568:546-550.
doi:10.1038/s41586-019-1087-5
apa: Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin,
J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along
the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5
chicago: Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K.
Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates
Amoeboid Migration along the Path of Least Resistance.” Nature. Springer
Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5.
ieee: J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration
along the path of least resistance,” Nature, vol. 568. Springer Nature,
pp. 546–550, 2019.
ista: Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild
R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates
amoeboid migration along the path of least resistance. Nature. 568, 546–550.
mla: Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration
along the Path of Least Resistance.” Nature, vol. 568, Springer Nature,
2019, pp. 546–50, doi:10.1038/s41586-019-1087-5.
short: J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin,
R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.
date_created: 2019-04-17T06:52:28Z
date_published: 2019-04-25T00:00:00Z
date_updated: 2026-04-28T22:30:35Z
day: '25'
department:
- _id: MiSi
- _id: NanoFab
- _id: Bio
doi: 10.1038/s41586-019-1087-5
ec_funded: 1
external_id:
isi:
- '000465594200050'
pmid:
- '30944468'
intvolume: ' 568'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/
month: '04'
oa: 1
oa_version: Submitted Version
page: 546-550
pmid: 1
project:
- _id: 25A603A2-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '281556'
name: Cytoskeletal force generation and force transduction of migrating leukocytes
- _id: 25FE9508-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '724373'
name: Cellular Navigation Along Spatial Gradients
- _id: 265FAEBA-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01250-B20
name: Nano-Analytics of Cellular Systems
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25A48D24-B435-11E9-9278-68D0E5697425
grant_number: ALTF 1396-2014
name: Molecular and system level view of immune cell migration
publication: Nature
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/
record:
- id: '14697'
relation: dissertation_contains
status: public
- id: '6891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Nuclear positioning facilitates amoeboid migration along the path of least
resistance
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 568
year: '2019'
...
---
_id: '6713'
abstract:
- lang: eng
text: Evolutionary studies are often limited by missing data that are critical to
understanding the history of selection. Selection experiments, which reproduce
rapid evolution under controlled conditions, are excellent tools to study how
genomes evolve under selection. Here we present a genomic dissection of the Longshanks
selection experiment, in which mice were selectively bred over 20 generations
for longer tibiae relative to body mass, resulting in 13% longer tibiae in two
replicates. We synthesized evolutionary theory, genome sequences and molecular
genetics to understand the selection response and found that it involved both
polygenic adaptation and discrete loci of major effect, with the strongest loci
tending to be selected in parallel between replicates. We show that selection
may favor de-repression of bone growth through inactivating two limb enhancers
of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is
possible to connect individual base-pair changes to the overall selection response.
article_number: e42014
article_processing_charge: No
author:
- first_name: João Pl
full_name: Castro, João Pl
last_name: Castro
- first_name: Michelle N.
full_name: Yancoskie, Michelle N.
last_name: Yancoskie
- first_name: Marta
full_name: Marchini, Marta
last_name: Marchini
- first_name: Stefanie
full_name: Belohlavy, Stefanie
id: 43FE426A-F248-11E8-B48F-1D18A9856A87
last_name: Belohlavy
orcid: 0000-0002-9849-498X
- first_name: Layla
full_name: Hiramatsu, Layla
last_name: Hiramatsu
- first_name: Marek
full_name: Kučka, Marek
last_name: Kučka
- first_name: William H.
full_name: Beluch, William H.
last_name: Beluch
- first_name: Ronald
full_name: Naumann, Ronald
last_name: Naumann
- first_name: Isabella
full_name: Skuplik, Isabella
last_name: Skuplik
- first_name: John
full_name: Cobb, John
last_name: Cobb
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Campbell
full_name: Rolian, Campbell
last_name: Rolian
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
citation:
ama: Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis
of the Longshanks selection experiment for longer limbs in mice. eLife.
2019;8. doi:10.7554/eLife.42014
apa: Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L.,
Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks
selection experiment for longer limbs in mice. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.42014
chicago: Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy,
Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic
Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife.
eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.
ieee: J. P. Castro et al., “An integrative genomic analysis of the Longshanks
selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences
Publications, 2019.
ista: Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch
WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative
genomic analysis of the Longshanks selection experiment for longer limbs in mice.
eLife. 8, e42014.
mla: Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks
Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014,
eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.
short: J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M.
Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F.
Chan, ELife 8 (2019).
date_created: 2019-07-28T21:59:17Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2026-04-28T22:30:36Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.7554/eLife.42014
external_id:
isi:
- '000473588700001'
pmid:
- '31169497'
file:
- access_level: open_access
checksum: fa0936fe58f0d9e3f8e75038570e5a17
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-29T07:41:18Z
date_updated: 2020-07-14T12:47:38Z
file_id: '6721'
file_name: 2019_eLife_Castro.pdf
file_size: 6748249
relation: main_file
file_date_updated: 2020-07-14T12:47:38Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '9804'
relation: research_data
status: public
- id: '11388'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: An integrative genomic analysis of the Longshanks selection experiment for
longer limbs in mice
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '6877'
article_processing_charge: No
article_type: original
author:
- first_name: Aglaja
full_name: Kopf, Aglaja
id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
last_name: Kopf
orcid: 0000-0002-2187-6656
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
citation:
ama: Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. Cell.
2019;179(1):51-53. doi:10.1016/j.cell.2019.08.047
apa: Kopf, A., & Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic
debris. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.08.047
chicago: Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove
Apoptotic Debris.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.08.047.
ieee: A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,”
Cell, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.
ista: Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris.
Cell. 179(1), 51–53.
mla: Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic
Debris.” Cell, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:10.1016/j.cell.2019.08.047.
short: A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.
date_created: 2019-09-15T22:00:46Z
date_published: 2019-09-19T00:00:00Z
date_updated: 2026-04-28T22:30:35Z
day: '19'
department:
- _id: MiSi
doi: 10.1016/j.cell.2019.08.047
external_id:
isi:
- '000486618500011'
pmid:
- '31539498'
intvolume: ' 179'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 51-53
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '6891'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The neural crest pitches in to remove apoptotic debris
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 179
year: '2019'
...
---
_id: '6351'
abstract:
- lang: eng
text: "A process of restorative patterning in plant roots correctly replaces eliminated
cells to heal local injuries despite the absence of cell migration, which underpins
wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell
divisions and acquisition of specific cell identities. Plants regularly endure
wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary
abilities to restore their tissues after injuries. Here, we provide insight into
a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted
elimination of different cells in Arabidopsis root combined with live-imaging
tracking during vertical growth allowed analysis of the regeneration processes
in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated
their stem cell transcriptional programs. They accelerated their progression through
cell cycle, coordinately changed the cell division orientation, and ultimately
acquired de novo the correct cell fates to replace missing cells. These observations
highlight existence of unknown intercellular positional signaling and demonstrate
the capability of specified cells to re-acquire stem cell programs as a crucial
part of the plant-specific mechanism of wound healing."
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
author:
- first_name: Petra
full_name: Marhavá, Petra
id: 44E59624-F248-11E8-B48F-1D18A9856A87
last_name: Marhavá
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Saiko
full_name: Yoshida, Saiko
id: 2E46069C-F248-11E8-B48F-1D18A9856A87
last_name: Yoshida
orcid: 0000-0001-6111-9353
- first_name: Peter
full_name: Marhavy, Peter
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Eva
full_name: Benková, Eva
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation
of stem cell pathways for pattern restoration in plant wound healing. Cell.
2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015
apa: Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml,
J. (2019). Re-activation of stem cell pathways for pattern restoration in plant
wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015
chicago: Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková,
and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in
Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015.
ieee: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml,
“Re-activation of stem cell pathways for pattern restoration in plant wound healing,”
Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.
ista: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation
of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4),
957–969.e13.
mla: Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration
in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13,
doi:10.1016/j.cell.2019.04.015.
short: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell
177 (2019) 957–969.e13.
corr_author: '1'
date_created: 2019-04-28T21:59:14Z
date_published: 2019-05-02T00:00:00Z
date_updated: 2026-04-28T22:30:38Z
day: '02'
ddc:
- '570'
department:
- _id: JiFr
- _id: EvBe
doi: 10.1016/j.cell.2019.04.015
ec_funded: 1
external_id:
isi:
- '000466843000015'
pmid:
- '31051107'
file:
- access_level: open_access
checksum: 4ceba04a96a74f5092ec3ce2c579a0c7
content_type: application/pdf
creator: dernst
date_created: 2019-05-13T06:12:45Z
date_updated: 2020-07-14T12:47:28Z
file_id: '6411'
file_name: 2019_Cell_Marhava.pdf
file_size: 10272032
relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: ' 177'
isi: 1
issue: '4'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 957-969.e13
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Re-activation of stem cell pathways for pattern restoration in plant wound
healing
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: 177
year: '2019'
...
---
_id: '6943'
abstract:
- lang: eng
text: Plants as sessile organisms are constantly under attack by herbivores, rough
environmental situations, or mechanical pressure. These challenges often lead
to the induction of wounds or destruction of already specified and developed tissues.
Additionally, wounding makes plants vulnerable to invasion by pathogens, which
is why wound signalling often triggers specific defence responses. To stay competitive
or, eventually, survive under these circumstances, plants need to regenerate efficiently,
which in rigid, tissue migration-incompatible plant tissues requires post-embryonic
patterning and organogenesis. Now, several studies used laser-assisted single
cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we
discuss their findings and put them into context of a broader spectrum of wound
signalling, pathogen responses and tissue as well as organ regeneration.
article_processing_charge: No
article_type: original
author:
- first_name: Lukas
full_name: Hörmayer, Lukas
id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87
last_name: Hörmayer
orcid: 0000-0001-8295-2926
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing
and restorative patterning. Current Opinion in Plant Biology. 2019;52:124-130.
doi:10.1016/j.pbi.2019.08.006
apa: Hörmayer, L., & Friml, J. (2019). Targeted cell ablation-based insights
into wound healing and restorative patterning. Current Opinion in Plant Biology.
Elsevier. https://doi.org/10.1016/j.pbi.2019.08.006
chicago: Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights
into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology.
Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.08.006.
ieee: L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound
healing and restorative patterning,” Current Opinion in Plant Biology,
vol. 52. Elsevier, pp. 124–130, 2019.
ista: Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound
healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.
mla: Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into
Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology,
vol. 52, Elsevier, 2019, pp. 124–30, doi:10.1016/j.pbi.2019.08.006.
short: L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130.
corr_author: '1'
date_created: 2019-10-14T07:00:24Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2026-04-28T22:30:38Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.pbi.2019.08.006
ec_funded: 1
external_id:
isi:
- '000502890600017'
pmid:
- '31585333'
file:
- access_level: open_access
checksum: d6fd68a6e965f1efe3f0bf2d2070a616
content_type: application/pdf
creator: dernst
date_created: 2019-10-14T14:48:21Z
date_updated: 2020-07-14T12:47:45Z
file_id: '6946'
file_name: 2019_CurrentOpinionPlant_Hoermayer.pdf
file_size: 1659288
relation: main_file
file_date_updated: 2020-07-14T12:47:45Z
has_accepted_license: '1'
intvolume: ' 52'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 124-130
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Current Opinion in Plant Biology
publication_identifier:
issn:
- 1369-5266
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
record:
- id: '9992'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Targeted cell ablation-based insights into wound healing and restorative patterning
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 52
year: '2019'
...
---
_id: '10065'
abstract:
- lang: eng
text: We study double quantum dots in a Ge/SiGe heterostructure and test their maturity
towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability,
from two single quantum dots to a double quantum dot. We measure Pauli spin blockade
and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for
sensing charge transitions in the double quantum dot at interest. In conclusion,
Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit.
acknowledged_ssus:
- _id: M-Shop
- _id: NanoFab
acknowledgement: "We thank Matthias Brauns for helpful discussions and careful proofreading
of the manuscript. This project has received funding from the European Union’s Horizon
2020 research and innovation program under the Marie Sklodowska-Curie grant agreement
No 844511 and from the FWF project P30207. The research was supported by the Scientific
Service Units of IST Austria through resources provided by the MIBA machine shop
and the nanofabrication\r\nfacility."
article_number: '1910.05841'
article_processing_charge: No
arxiv: 1
author:
- first_name: Andrea C
full_name: Hofmann, Andrea C
id: 340F461A-F248-11E8-B48F-1D18A9856A87
last_name: Hofmann
- first_name: Daniel
full_name: Jirovec, Daniel
id: 4C473F58-F248-11E8-B48F-1D18A9856A87
last_name: Jirovec
orcid: 0000-0002-7197-4801
- first_name: Maxim
full_name: Borovkov, Maxim
last_name: Borovkov
- first_name: Ivan
full_name: Prieto Gonzalez, Ivan
id: 2A307FE2-F248-11E8-B48F-1D18A9856A87
last_name: Prieto Gonzalez
orcid: 0000-0002-7370-5357
- first_name: Andrea
full_name: Ballabio, Andrea
last_name: Ballabio
- first_name: Jacopo
full_name: Frigerio, Jacopo
last_name: Frigerio
- first_name: Daniel
full_name: Chrastina, Daniel
last_name: Chrastina
- first_name: Giovanni
full_name: Isella, Giovanni
last_name: Isella
- first_name: Georgios
full_name: Katsaros, Georgios
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
orcid: 0000-0001-8342-202X
citation:
ama: Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe
quantum dots as hosts for singlet-triplet qubits. arXiv. doi:10.48550/arXiv.1910.05841
apa: Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A.,
Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum
dots as hosts for singlet-triplet qubits. arXiv. https://doi.org/10.48550/arXiv.1910.05841
chicago: Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez,
Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios
Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet
Qubits.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1910.05841.
ieee: A. C. Hofmann et al., “Assessing the potential of Ge/SiGe quantum dots
as hosts for singlet-triplet qubits,” arXiv. .
ista: Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio
J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum
dots as hosts for singlet-triplet qubits. arXiv, 1910.05841.
mla: Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots
as Hosts for Singlet-Triplet Qubits.” ArXiv, 1910.05841, doi:10.48550/arXiv.1910.05841.
short: A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J.
Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).
corr_author: '1'
date_created: 2021-10-01T12:14:51Z
date_published: 2019-10-13T00:00:00Z
date_updated: 2026-04-28T22:30:39Z
day: '13'
department:
- _id: GeKa
doi: 10.48550/arXiv.1910.05841
ec_funded: 1
external_id:
arxiv:
- '1910.05841'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1910.05841
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 26A151DA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '844511'
name: Majorana bound states in Ge/SiGe heterostructures
- _id: 2641CE5E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P30207
name: Hole spin orbit qubits in Ge quantum wells
publication: arXiv
publication_status: draft
related_material:
record:
- id: '10058'
relation: dissertation_contains
status: public
status: public
title: Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet
qubits
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '6486'
abstract:
- lang: eng
text: Based on a novel control scheme, where a steady modification of the streamwise
velocity profile leads to complete relaminarization of initially fully turbulent
pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs
for such control. The custom-shaped honeycombs are used as stationary flow management
devices which generate specific modifications of the streamwise velocity profile.
Stereoscopic particle image velocimetry and pressure drop measurements are used
to investigate and capture the development of the relaminarizing flow downstream
these devices. We compare the performance of straight (constant length across
the radius of the pipe) honeycombs with custom-shaped ones (variable length across
the radius) and try to determine the optimal shape for maximal relaminarization
at minimal pressure loss. The optimally modified streamwise velocity profile is
found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization
is found to be of the order of 10,000. Consequently, the respective reduction
in skin friction downstream of the device is almost by a factor of 5. The break-even
point, where the additional pressure drop caused by the device is balanced by
the savings due to relaminarization and a net gain is obtained, corresponds to
a downstream stretch of distances as low as approximately 100 pipe diameters of
laminar flow.
acknowledged_ssus:
- _id: M-Shop
article_number: '111105'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed
shaped honeycombs. Journal of Fluids Engineering. 2019;141(11). doi:10.1115/1.4043494
apa: Kühnen, J., Scarselli, D., & Hof, B. (2019). Relaminarization of pipe flow
by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering.
ASME. https://doi.org/10.1115/1.4043494
chicago: Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe
Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering.
ASME, 2019. https://doi.org/10.1115/1.4043494.
ieee: J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means
of 3D-printed shaped honeycombs,” Journal of Fluids Engineering, vol. 141,
no. 11. ASME, 2019.
ista: Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means
of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.
mla: Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed
Shaped Honeycombs.” Journal of Fluids Engineering, vol. 141, no. 11, 111105,
ASME, 2019, doi:10.1115/1.4043494.
short: J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019).
date_created: 2019-05-26T21:59:13Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2026-04-28T22:30:44Z
day: '01'
department:
- _id: BjHo
doi: 10.1115/1.4043494
ec_funded: 1
external_id:
arxiv:
- '1809.07625'
isi:
- '000487748600005'
intvolume: ' 141'
isi: 1
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1809.07625
month: '11'
oa: 1
oa_version: Preprint
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
publication: Journal of Fluids Engineering
publication_identifier:
eissn:
- 1528-901X
issn:
- 0098-2202
publication_status: published
publisher: ASME
quality_controlled: '1'
related_material:
record:
- id: '7258'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Relaminarization of pipe flow by means of 3D-printed shaped honeycombs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 141
year: '2019'
...
---
_id: '6228'
abstract:
- lang: eng
text: Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number.
article_processing_charge: No
arxiv: 1
author:
- first_name: Davide
full_name: Scarselli, Davide
id: 40315C30-F248-11E8-B48F-1D18A9856A87
last_name: Scarselli
orcid: 0000-0001-5227-4271
- first_name: Jakob
full_name: Kühnen, Jakob
id: 3A47AE32-F248-11E8-B48F-1D18A9856A87
last_name: Kühnen
orcid: 0000-0003-4312-0179
- first_name: Björn
full_name: Hof, Björn
id: 3A374330-F248-11E8-B48F-1D18A9856A87
last_name: Hof
orcid: 0000-0003-2057-2754
citation:
ama: Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. Journal
of Fluid Mechanics. 2019;867:934-948. doi:10.1017/jfm.2019.191
apa: Scarselli, D., Kühnen, J., & Hof, B. (2019). Relaminarising pipe flow by
wall movement. Journal of Fluid Mechanics. Cambridge University Press.
https://doi.org/10.1017/jfm.2019.191
chicago: Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow
by Wall Movement.” Journal of Fluid Mechanics. Cambridge University Press,
2019. https://doi.org/10.1017/jfm.2019.191.
ieee: D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,”
Journal of Fluid Mechanics, vol. 867. Cambridge University Press, pp. 934–948,
2019.
ista: Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement.
Journal of Fluid Mechanics. 867, 934–948.
mla: Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” Journal
of Fluid Mechanics, vol. 867, Cambridge University Press, 2019, pp. 934–48,
doi:10.1017/jfm.2019.191.
short: D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.
date_created: 2019-04-07T21:59:14Z
date_published: 2019-05-25T00:00:00Z
date_updated: 2026-04-28T22:30:44Z
day: '25'
department:
- _id: BjHo
doi: 10.1017/jfm.2019.191
ec_funded: 1
external_id:
arxiv:
- '1807.05357'
isi:
- '000462606100001'
intvolume: ' 867'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1807.05357
month: '05'
oa: 1
oa_version: Preprint
page: 934-948
project:
- _id: 25152F3A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '306589'
name: Decoding the complexity of turbulence at its origin
- _id: 25104D44-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '737549'
name: Eliminating turbulence in oil pipelines
publication: Journal of Fluid Mechanics
publication_identifier:
eissn:
- 1469-7645
issn:
- 0022-1120
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://doi.org/10.1017/jfm.2019.191
record:
- id: '7258'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Relaminarising pipe flow by wall movement
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 867
year: '2019'
...
---
_id: '6260'
abstract:
- lang: eng
text: Polar auxin transport plays a pivotal role in plant growth and development.
PIN auxin efflux carriers regulate directional auxin movement by establishing
local auxin maxima, minima, and gradients that drive multiple developmental processes
and responses to environmental signals. Auxin has been proposed to modulate its
own transport by regulating subcellular PIN trafficking via processes such as
clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further
investigated the mechanisms by which auxin affects PIN trafficking by screening
auxin analogs and identified pinstatic acid (PISA) as a positive modulator of
polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on
hypocotyl elongation and adventitious root formation via positive regulation of
auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN
accumulation at the cell surface by inhibiting PIN internalization from the plasma
membrane. This work demonstrates PISA to be a promising chemical tool to dissect
the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.
acknowledgement: "We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden
University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University
of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis
work was supported by the Ministry of Education, Culture, Sports, Science, and Technology
(Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology
and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.),
and the European Union’s Horizon2020 program (European Research Council grant agreement
no. 742985 to J.F.)."
article_processing_charge: No
article_type: original
author:
- first_name: A
full_name: Oochi, A
last_name: Oochi
- first_name: Jakub
full_name: Hajny, Jakub
id: 4800CC20-F248-11E8-B48F-1D18A9856A87
last_name: Hajny
orcid: 0000-0003-2140-7195
- first_name: K
full_name: Fukui, K
last_name: Fukui
- first_name: Y
full_name: Nakao, Y
last_name: Nakao
- first_name: Michelle C
full_name: Gallei, Michelle C
id: 35A03822-F248-11E8-B48F-1D18A9856A87
last_name: Gallei
orcid: 0000-0003-1286-7368
- first_name: M
full_name: Quareshy, M
last_name: Quareshy
- first_name: K
full_name: Takahashi, K
last_name: Takahashi
- first_name: T
full_name: Kinoshita, T
last_name: Kinoshita
- first_name: SR
full_name: Harborough, SR
last_name: Harborough
- first_name: S
full_name: Kepinski, S
last_name: Kepinski
- first_name: H
full_name: Kasahara, H
last_name: Kasahara
- first_name: RM
full_name: Napier, RM
last_name: Napier
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: KI
full_name: Hayashi, KI
last_name: Hayashi
citation:
ama: Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by
inhibiting PIN internalization. Plant Physiology. 2019;180(2):1152-1165.
doi:10.1104/pp.19.00201
apa: Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., …
Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN
internalization. Plant Physiology. ASPB. https://doi.org/10.1104/pp.19.00201
chicago: Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy,
K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN
Internalization.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.19.00201.
ieee: A. Oochi et al., “Pinstatic acid promotes auxin transport by inhibiting
PIN internalization,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 1152–1165,
2019.
ista: Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita
T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic
acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology.
180(2), 1152–1165.
mla: Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN
Internalization.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 1152–65,
doi:10.1104/pp.19.00201.
short: A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi,
T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K.
Hayashi, Plant Physiology 180 (2019) 1152–1165.
date_created: 2019-04-09T08:38:20Z
date_published: 2019-06-01T00:00:00Z
date_updated: 2026-04-28T22:30:46Z
day: '01'
department:
- _id: JiFr
doi: 10.1104/pp.19.00201
ec_funded: 1
external_id:
isi:
- '000470086100045'
pmid:
- '30936248'
intvolume: ' 180'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1104/pp.19.00201
month: '06'
oa: 1
oa_version: Published Version
page: 1152-1165
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742985'
name: Tracing Evolution of Auxin Transport and Polarity in Plants
publication: Plant Physiology
publication_identifier:
eissn:
- 1532-2548
issn:
- 0032-0889
publication_status: published
publisher: ASPB
quality_controlled: '1'
related_material:
record:
- id: '11626'
relation: dissertation_contains
status: public
- id: '8822'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Pinstatic acid promotes auxin transport by inhibiting PIN internalization
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 180
year: '2019'
...
---
OA_place: publisher
_id: '6435'
abstract:
- lang: eng
text: "Social insect colonies tend to have numerous members which function together
like a single organism in such harmony that the term ``super-organism'' is often
used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells
of a metazoan, while the sterile worker caste corresponds to somatic cells. The
worker castes, like tissues, are\r\nin charge of all functions of a living being,
besides reproduction. The establishment of new super-organismal units\r\n(i.e.
new colonies) is accomplished by the co-dependent castes. The term oftentimes
goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation,
nutrient regulation and gas exchange of a social insect colony. Furthermore, we
assert that the super-organism has an immune system, and benefits from ``social
immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists
to resolve the apparent discrepancy between the expected high frequency of disease
outbreak amongst numerous, closely related tightly-interacting hosts, living in
stable and microbially-rich environments, against the exceptionally scarce epidemic
accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly
of behaviours which have evolved to effectively keep the pathogenic enemies of
a colony at bay. The field of social immunity has drawn interest, as it becomes
increasingly urgent to stop\r\nthe collapse of pollinator species and curb the
growth of invasive pests. In the past decade, several mechanisms of\r\nsocial
immune responses have been dissected, but many more questions remain open.\r\n\r\nI
present my work in two experimental chapters. In the first, I use invasive garden
ants (*Lasius neglectus*) to study how pathogen load and its distribution among
nestmates affect the grooming response of the group. Any given group of ants will
carry out the same total grooming work, but will direct their grooming effort
towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation,
the highest risk of transmission does not stem from grooming highly contaminated
ants, but instead, we suggest that the grooming response likely minimizes spore
loss to the environment, reducing contamination from inadvertent pickup from the
substrate.\r\n\r\nThe second is a comparative developmental approach. I follow
black garden ant queens (*Lasius niger*) and their colonies from mating flight,
through hibernation for a year. Colonies which grow fast from the start, have
a lower chance of survival through hibernation, and those which survive grow at
a lower pace later. This is true for colonies of naive\r\nand challenged queens.
Early pathogen exposure of the queens changes colony dynamics in an unexpected
way: colonies from exposed queens are more likely to grow slowly and recover in
numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental
chapters, this thesis includes a co-authored published review on organisational\r\nimmunity,
where we enlist the experimental evidence and theoretical framework on which this
hypothesis is built,\r\nidentify the caveats and underline how the field is ripe
to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative
efforts, one to develop an image-based tracker, and the second to develop a classifier
for ant\r\nbehaviour."
acknowledged_ssus:
- _id: Bio
- _id: ScienComp
- _id: M-Shop
- _id: LifeSc
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Barbara E
full_name: Casillas Perez, Barbara E
id: 351ED2AA-F248-11E8-B48F-1D18A9856A87
last_name: Casillas Perez
citation:
ama: Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen.
2019. doi:10.15479/AT:ISTA:6435
apa: Casillas Perez, B. E. (2019). Collective defenses of garden ants against
a fungal pathogen. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6435
chicago: Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against
a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6435.
ieee: B. E. Casillas Perez, “Collective defenses of garden ants against a fungal
pathogen,” Institute of Science and Technology Austria, 2019.
ista: Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal
pathogen. Institute of Science and Technology Austria.
mla: Casillas Perez, Barbara E. Collective Defenses of Garden Ants against a
Fungal Pathogen. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6435.
short: B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal
Pathogen, Institute of Science and Technology Austria, 2019.
corr_author: '1'
date_created: 2019-05-13T08:58:35Z
date_published: 2019-05-07T00:00:00Z
date_updated: 2026-04-08T14:02:12Z
day: '07'
ddc:
- '570'
- '006'
- '578'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:6435
ec_funded: 1
file:
- access_level: open_access
checksum: 6daf2d2086111aa8fd3fbc919a3e2833
content_type: application/pdf
creator: casillas
date_created: 2019-05-13T09:16:20Z
date_updated: 2021-02-11T11:17:15Z
embargo: 2020-05-08
file_id: '6438'
file_name: tesisDoctoradoBC.pdf
file_size: 3895187
relation: main_file
- access_level: closed
checksum: 3d221aaff7559a7060230a1ff610594f
content_type: application/zip
creator: casillas
date_created: 2019-05-13T09:16:20Z
date_updated: 2020-07-14T12:47:30Z
embargo_to: open_access
file_id: '6439'
file_name: tesisDoctoradoBC.zip
file_size: 7365118
relation: source_file
file_date_updated: 2021-02-11T11:17:15Z
has_accepted_license: '1'
keyword:
- Social Immunity
- Sanitary care
- Social Insects
- Organisational Immunity
- Colony development
- Multi-target tracking
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '183'
project:
- _id: 2649B4DE-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771402'
name: Epidemics in ant societies on a chip
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1999'
relation: part_of_dissertation
status: public
status: public
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: Collective defenses of garden ants against a fungal pathogen
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
OA_place: publisher
_id: '6849'
abstract:
- lang: eng
text: 'Brain function is mediated by complex dynamical interactions between excitatory
and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons)
are one of the least studied types, despite being suspected to play important
roles in cognitive processes. We studied the network effects of optogenetic silencing
of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states.
The cell firing pattern in response to light pulses allowed us to classify the
recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal
cell and interneurons, and the inhibited interneurons corresponding to the CCK
group. The light application, which inhibited the activity of CCK interneurons
triggered wider changes in the firing dynamics of cells. We observed rate changes
(i.e. remapping) of pyramidal cells during the exploration session in which the
light was applied relative to the previous control session that was not restricted
neither in time nor space to the light delivery. Also, the disinhibited pyramidal
cells had higher increase in bursting than in single spike firing rate as a result
of CCK silencing. In addition, the firing activity patterns during exploratory
periods were more weakly reactivated in sleep for those periods in which CCK-interneuron
were silenced than in the unaffected periods. Furthermore, light pulses during
sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK
neurons during exploration suppressed the reactivation of waking firing patterns
in sleep and CCK interneuron activity was also required during sleep for the normal
reactivation of waking patterns. These findings demonstrate the involvement of
CCK cells in reactivation-related memory consolidation. An important part of our
analysis was to test the relationship of the identified CCKinterneurons to brain
oscillations. Our findings showed that these cells exhibited different oscillatory
behaviour during anaesthesia and natural waking and sleep conditions. We showed
that: 1) Contrary to the past studies performed under anaesthesia, the identified
CCKinterneurons fired on the descending portion of the theta phase in waking exploration.
2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3)
Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons
increased around the peak activity of the sharp-wave ripple (SWR) events in natural
sleep, which is congruent with new reports about their functional connectivity.
We also found that light driven CCK-interneuron silencing altered the dynamics
on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted
their preferred theta phases when the light was applied, while interneurons responses
were less consistent. 2) As a population, pyramidal cells negatively shifted their
preferred activity during gamma oscillations, albeit we did not find gamma modulation
differences related to the light application when pyramidal cells were subdivided
into the disinhibited and unaffected groups. 3) During the peak of SWR events,
all but the CCK-interneurons had a reduction in their relative firing rate change
during the light application as compared to the change observed at SWR initiation.
Finally, regarding to the place field activity of the recorded pyramidal neurons,
we showed that the disinhibited pyramidal cells had reduced place field similarity,
coherence and spatial information, but only during the light application. The
mechanisms behind such observed behaviours might involve eCB signalling and plastic
changes in CCK-interneuron synapses. In conclusion, the observed changes related
to the light-mediated silencing of CCKinterneurons have unravelled characteristics
of this interneuron subpopulation that might change the understanding not only
of their particular network interactions, but also of the current theories about
the emergence of certain cognitive processes such as place coding needed for navigation
or hippocampus-dependent memory consolidation. '
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: M-Shop
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Dámaris K
full_name: Rangel Guerrero, Dámaris K
id: 4871BCE6-F248-11E8-B48F-1D18A9856A87
last_name: Rangel Guerrero
orcid: 0000-0002-8602-4374
citation:
ama: Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal
network dynamics. 2019. doi:10.15479/AT:ISTA:6849
apa: Rangel Guerrero, D. K. (2019). The role of CCK-interneurons in regulating
hippocampal network dynamics. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:6849
chicago: Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating
Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019.
https://doi.org/10.15479/AT:ISTA:6849.
ieee: D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal
network dynamics,” Institute of Science and Technology Austria, 2019.
ista: Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal
network dynamics. Institute of Science and Technology Austria.
mla: Rangel Guerrero, Dámaris K. The Role of CCK-Interneurons in Regulating Hippocampal
Network Dynamics. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6849.
short: D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal
Network Dynamics, Institute of Science and Technology Austria, 2019.
corr_author: '1'
date_created: 2019-09-06T06:54:16Z
date_published: 2019-09-09T00:00:00Z
date_updated: 2026-04-08T13:56:53Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6849
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related_material:
record:
- id: '5914'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: The role of CCK-interneurons in regulating hippocampal network dynamics
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
_id: '6848'
abstract:
- lang: eng
text: Proton-translocating transhydrogenase (also known as nicotinamide nucleotide
transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner
mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride
between NADH and NADP+, coupled to the translocation of one proton across the
membrane. Its main physiological function is the generation of NADPH, which is
a substrate in anabolic reactions and a regulator of oxidative status; however,
NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid
deficiency in humans and metabolic abnormalities in mice, similar to those observed
in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve
a rotation of around 180° of the entire NADP(H)-binding domain that alternately
participates in hydride transfer and proton-channel gating. However, owing to
the lack of high-resolution structures of intact NNT, the details of this process
remain unclear5,6. Here we present the cryo-electron microscopy structure of intact
mammalian NNT in different conformational states. We show how the NADP(H)-binding
domain opens the proton channel to the opposite sides of the membrane, and we
provide structures of these two states. We also describe the catalytically important
interfaces and linkers between the membrane and the soluble domains and their
roles in nucleotide exchange. These structures enable us to propose a revised
mechanism for a coupling process in NNT that is consistent with a large body of
previous biochemical work. Our results are relevant to the development of currently
unavailable NNT inhibitors, which may have therapeutic potential in ischaemia
reperfusion injury, metabolic syndrome and some cancers7,8,9.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: " We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their
assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing
was performed at the IST high-performance computing cluster.\r\nThis project has
received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement no. 665385."
article_processing_charge: No
article_type: letter_note
author:
- first_name: Domen
full_name: Kampjut, Domen
id: 37233050-F248-11E8-B48F-1D18A9856A87
last_name: Kampjut
orcid: 0000-0002-6018-3422
- first_name: Leonid A
full_name: Sazanov, Leonid A
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 2019;573(7773):291–295. doi:10.1038/s41586-019-1519-2
apa: Kampjut, D., & Sazanov, L. A. (2019). Structure and mechanism of mitochondrial
proton-translocating transhydrogenase. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1519-2
chicago: Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature. Springer Nature, 2019.
https://doi.org/10.1038/s41586-019-1519-2.
ieee: D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating
transhydrogenase,” Nature, vol. 573, no. 7773. Springer Nature, pp. 291–295,
2019.
ista: Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating
transhydrogenase. Nature. 573(7773), 291–295.
mla: Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial
Proton-Translocating Transhydrogenase.” Nature, vol. 573, no. 7773, Springer
Nature, 2019, pp. 291–295, doi:10.1038/s41586-019-1519-2.
short: D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.
date_created: 2019-09-04T06:21:41Z
date_published: 2019-09-12T00:00:00Z
date_updated: 2026-04-28T22:30:48Z
day: '12'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-019-1519-2
ec_funded: 1
external_id:
isi:
- '000485415400061'
pmid:
- '31462775'
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language:
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month: '09'
oa: 1
oa_version: Submitted Version
page: 291–295
pmid: 1
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/
record:
- id: '8340'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Structure and mechanism of mitochondrial proton-translocating transhydrogenase
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 573
year: '2019'
...
---
OA_place: publisher
_id: '6269'
abstract:
- lang: eng
text: 'Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking
that is constantly regulated for mediating developmental and physiological responses.
The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic
trafficking in the whole multicellular organ systems of Arabidopsis. The first
chapter of my thesis describes the search for new components involved in CME.
Tandem affinity purification was conducted using CLC and its interacting partners
were identified. Amongst the identified proteins were the Auxilin-likes1 and 2
(Axl1/2), putative uncoating factors, for which we made a full functional analysis.
Over-expression of Axl1/2 causes extreme modifications in the dynamics of the
machinery proteins and inhibition of endocytosis altogether. However the loss
of function of the axl1/2 did not present any cellular or physiological phenotype,
meaning Auxilin-likes do not form the major uncoating machinery. The second chapter
of my thesis describes the establishment/utilisation of techniques to capture
the dynamicity and the complexity of CME and post-endocytic trafficking. We have
studied the development of endocytic pits at the PM – specifically, the mode of
membrane remodeling during pit development and the role of actin in it, given
plant cells possess high turgor pressure. Utilizing the improved z-resolution
of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events
at the plasma membrane; and using particle detection software, we quantitatively
analysed all the endocytic trajectories in an unbiased way to obtain the endocytic
rate of the system. This together with the direct analysis of cargo internalisation
from the PM provided an estimate on the endocytic potential of the cell. We also
developed a methodology for ultrastructural analysis of different populations
of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed
protoplasts. Structural analysis, together with the intensity profile of CCSs
at the PM show that the mode of CCP development at the PM follows ‘Constant curvature
model’; meaning that clathrin polymerisation energy is a major contributing factor
of membrane remodeling. In addition, other analyses clearly show that actin is
not required for membrane remodeling during invagination or any other step of
CCP development, despite the prevalent high turgor pressure. However, actin is
essential in orchestrating the post-endocytic trafficking of CCVs facilitating
the EE formation. We also observed that the uncoating process post-endocytosis
is not immediate; an alternative mechanism of uncoating – Sequential multi-step
process – functions in the cell. Finally we also looked at one of the important
physiological stimuli modulating the process – hormone, auxin. auxin has been
known to influence CME before. We have made a detailed study on the concentration-time
based effect of auxin on the machinery proteins, CCP development, and the specificity
of cargoes endocytosed. To this end, we saw no general effect of auxin on CME
at earlier time points. However, very low concentration of IAA, such as 50nM,
accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory
control with high specificity to PIN2 could be essential in modulating its polarity. '
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Madhumitha
full_name: Narasimhan, Madhumitha
id: 44BF24D0-F248-11E8-B48F-1D18A9856A87
last_name: Narasimhan
orcid: 0000-0002-8600-0671
citation:
ama: Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and
their regulatory controls in plants . 2019. doi:10.15479/at:ista:th1075
apa: Narasimhan, M. (2019). Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants . Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:th1075
chicago: Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic
Trafficking and Their Regulatory Controls in Plants .” Institute of Science and
Technology Austria, 2019. https://doi.org/10.15479/at:ista:th1075.
ieee: M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants ,” Institute of Science and Technology
Austria, 2019.
ista: Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking
and their regulatory controls in plants . Institute of Science and Technology
Austria.
mla: Narasimhan, Madhumitha. Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking
and Their Regulatory Controls in Plants . Institute of Science and Technology
Austria, 2019, doi:10.15479/at:ista:th1075.
short: M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking
and Their Regulatory Controls in Plants , Institute of Science and Technology
Austria, 2019.
corr_author: '1'
date_created: 2019-04-09T14:37:06Z
date_published: 2019-02-04T00:00:00Z
date_updated: 2026-04-08T14:00:24Z
day: '04'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/at:ista:th1075
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- 2663-337X
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publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '412'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jiří
full_name: Friml, Jiří
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
title: 'Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory
controls in plants '
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
OA_place: publisher
_id: '6371'
abstract:
- lang: eng
text: "Decades of studies have revealed the mechanisms of gene regulation in molecular
detail. We make use of such well-described regulatory systems to explore how the
molecular mechanisms of protein-protein and protein-DNA interactions shape the
dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics
of protein-DNA binding determines the potential of regulatory networks to evolve
and adapt, which can be captured using a simple mathematical model. \r\nii) The
evolution of regulatory connections can lead to a significant amount of crosstalk
between binding proteins. We explore the effect of crosstalk on gene expression
from a target promoter, which seems to be modulated through binding competition
at non-specific DNA sites. \r\niii) We investigate how the very same biophysical
characteristics as in i) can generate significant fitness costs for cells through
global crosstalk, meaning non-specific DNA binding across the genomic background.
\r\niv) Binding competition between proteins at a target promoter is a prevailing
regulatory feature due to the prevalence of co-regulation at bacterial promoters.
However, the dynamics of these systems are not always straightforward to determine
even if the molecular mechanisms of regulation are known. A detailed model of
the biophysical interactions reveals that interference between the regulatory
proteins can constitute a new, generic form of system memory that records the
history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics
of protein-DNA binding can be harnessed to investigate the principles that shape
and ultimately limit cellular gene regulation. These results provide a basis for
studies of higher-level functionality, which arises from the underlying regulation.
\ \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Claudia
full_name: Igler, Claudia
id: 46613666-F248-11E8-B48F-1D18A9856A87
last_name: Igler
orcid: 0000-0001-7777-546X
citation:
ama: Igler C. On the nature of gene regulatory design - The biophysics of transcription
factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371
apa: Igler, C. (2019). On the nature of gene regulatory design - The biophysics
of transcription factor binding shapes gene regulation. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371
chicago: Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics
of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science
and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.
ieee: C. Igler, “On the nature of gene regulatory design - The biophysics of transcription
factor binding shapes gene regulation,” Institute of Science and Technology Austria,
2019.
ista: Igler C. 2019. On the nature of gene regulatory design - The biophysics of
transcription factor binding shapes gene regulation. Institute of Science and
Technology Austria.
mla: Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics
of Transcription Factor Binding Shapes Gene Regulation. Institute of Science
and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.
short: C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription
Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria,
2019.
corr_author: '1'
date_created: 2019-05-03T11:55:51Z
date_published: 2019-05-03T00:00:00Z
date_updated: 2026-04-08T13:56:27Z
day: '03'
ddc:
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- '579'
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department:
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doi: 10.15479/AT:ISTA:6371
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embargo_to: open_access
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file_size: 34644426
relation: source_file
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keyword:
- gene regulation
- biophysics
- transcription factor binding
- bacteria
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '152'
project:
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
grant_number: '24573'
name: Design principles underlying genetic switch architecture
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '67'
relation: part_of_dissertation
status: public
- id: '5585'
relation: popular_science
status: public
status: public
supervisor:
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
title: On the nature of gene regulatory design - The biophysics of transcription factor
binding shapes gene regulation
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
OA_place: publisher
_id: '6825'
abstract:
- lang: eng
text: "The solving of complex tasks requires the functions of more than one brain
area and their interaction. Whilst spatial navigation and memory is dependent
on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC).
To further examine the roles of the hippocampus and mPFC, we recorded their neural
activity during a task that depends on both of these brain regions.\r\nWith tetrodes,
we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC
neurons in Long-Evans rats performing a rule-switching task on the plus-maze.
The plus-maze task had a spatial component since it required navigation along
one of the two start arms and at the maze center a choice between one of the two
goal arms. Which goal contained a reward depended on the rule currently in place.
After an uncued rule change the animal had to abandon the old strategy and switch
to the new rule, testing cognitive flexibility. Investigating the coordination
of activity between the HPC and mPFC allows determination during which task stages
their interaction is required. Additionally, comparing neural activity patterns
in these two brain regions allows delineation of the specialized functions of
the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC
in terms of oscillatory interactions, rule coding and replay.\r\nWe found that
theta coherence between the HPC and mPFC is increased at the center and goals
of the maze, both when the rule was stable or has changed. Similar results were
found for locking of HPC and mPFC neurons to HPC theta oscillations. However,
no differences in HPC-mPFC theta coordination were observed between the spatially-
and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations
was not modulated by\r\nmaze position or rule type. We found that the HPC coded
for the two different rules with cofiring relationships between\r\ncell pairs.
However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective
firing in the mPFC generalized between the two start and two goal arms. With Bayesian
positional decoding, we found that the mPFC reactivated non-local positions during
awake immobility periods. Replay of these non-local positions could represent
entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore,
mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching
performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently
of each other. These results show that the mPFC can replay ordered patterns of
activity during awake immobility, possibly underlying its role in flexible behavior. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
citation:
ama: Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior.
2019. doi:10.15479/AT:ISTA:6825
apa: Käfer, K. (2019). The hippocampus and medial prefrontal cortex during flexible
behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6825
chicago: Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible
Behavior.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6825.
ieee: K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,”
Institute of Science and Technology Austria, 2019.
ista: Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible
behavior. Institute of Science and Technology Austria.
mla: Käfer, Karola. The Hippocampus and Medial Prefrontal Cortex during Flexible
Behavior. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6825.
short: K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior,
Institute of Science and Technology Austria, 2019.
corr_author: '1'
date_created: 2019-08-21T15:00:57Z
date_published: 2019-08-24T00:00:00Z
date_updated: 2026-04-08T13:56:14Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoCs
- _id: GradSch
doi: 10.15479/AT:ISTA:6825
file:
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file_size: 3205202
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oa: 1
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page: '89'
publication_identifier:
issn:
- 2663-337X
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publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '5949'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
title: The hippocampus and medial prefrontal cortex during flexible behavior
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...
---
_id: '5949'
abstract:
- lang: eng
text: Aberrant proteostasis of protein aggregation may lead to behavior disorders
including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations
that underlie CMI are not well understood. We recorded the local field potential
and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically
overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling
sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein
aggregation, disturbances in the dopaminergic system and attention-related deficits.
Recordings were performed during exploration of familiar and novel open field
environments and during sleep, allowing investigation of neuronal abnormalities
in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited
smaller place fields and decreased speed-modulation of their firing rates, demonstrating
altered spatial coding and deficits in encoding location-independent sensory inputs.
Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase
locking strength during novelty, limiting their phase coding ability. However,
their mean theta phases were more variable at the population level, reducing oscillatory
network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced
shift in their preferred theta and gamma firing phases, indicating deficits in
coding of novel environments with oscillatory firing. By combining single cell
and neuronal population analyses, we link DISC1 protein pathology with abnormal
hippocampal neural coding and network synchrony, and thereby gain a more comprehensive
understanding of CMI mechanisms.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Karola
full_name: Käfer, Karola
id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87
last_name: Käfer
- first_name: Hugo
full_name: Malagon-Vina, Hugo
last_name: Malagon-Vina
- first_name: Desiree
full_name: Dickerson, Desiree
id: 444EB89E-F248-11E8-B48F-1D18A9856A87
last_name: Dickerson
- first_name: Joseph
full_name: O'Neill, Joseph
last_name: O'Neill
- first_name: Svenja V.
full_name: Trossbach, Svenja V.
last_name: Trossbach
- first_name: Carsten
full_name: Korth, Carsten
last_name: Korth
- first_name: Jozsef L
full_name: Csicsvari, Jozsef L
id: 3FA14672-F248-11E8-B48F-1D18A9856A87
last_name: Csicsvari
orcid: 0000-0002-5193-4036
citation:
ama: Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression
disrupts hippocampal coding and oscillatory synchronization. Hippocampus.
2019;29(9):802-816. doi:10.1002/hipo.23076
apa: Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V.,
Korth, C., & Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression
disrupts hippocampal coding and oscillatory synchronization. Hippocampus.
Wiley. https://doi.org/10.1002/hipo.23076
chicago: Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja
V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia
1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.”
Hippocampus. Wiley, 2019. https://doi.org/10.1002/hipo.23076.
ieee: K. Käfer et al., “Disrupted-in-schizophrenia 1 overexpression disrupts
hippocampal coding and oscillatory synchronization,” Hippocampus, vol.
29, no. 9. Wiley, pp. 802–816, 2019.
ista: Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari
JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding
and oscillatory synchronization. Hippocampus. 29(9), 802–816.
mla: Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts
Hippocampal Coding and Oscillatory Synchronization.” Hippocampus, vol.
29, no. 9, Wiley, 2019, pp. 802–16, doi:10.1002/hipo.23076.
short: K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth,
J.L. Csicsvari, Hippocampus 29 (2019) 802–816.
date_created: 2019-02-10T22:59:18Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2026-04-28T22:30:49Z
day: '01'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1002/hipo.23076
ec_funded: 1
external_id:
isi:
- '000480635400003'
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checksum: 5e8de271ca04aef92a5de42d6aac4404
content_type: application/pdf
creator: dernst
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date_updated: 2020-07-14T12:47:13Z
file_id: '5950'
file_name: 2019_Hippocampus_Kaefer.pdf
file_size: 2132893
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intvolume: ' 29'
isi: 1
issue: '9'
language:
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month: '09'
oa: 1
oa_version: Published Version
page: 802-816
project:
- _id: 257BBB4C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '607616'
name: inter-and intracellular signalling in schizophrenia
publication: Hippocampus
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '6825'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and
oscillatory synchronization
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2019'
...
---
OA_place: publisher
_id: '6947'
abstract:
- lang: eng
text: Lymph nodes are es s ential organs of the immune s ys tem where adaptive
immune responses originate, and consist of various leukocyte populations and a
stromal backbone. Fibroblastic reticular cells (FRCs) are the main stromal cells
and form a sponge-like extracellular matrix network, called conduits , which they thems
elves enwrap and contract. Lymph, containing s oluble antigens , arrive
in lymph nodes via afferent lymphatic vessels that connect to the s ubcaps
ular s inus and conduit network. According to the current paradigm, the conduit network dis
tributes afferent lymph through lymph nodes and thus provides acces
s for immune cells to lymph-borne antigens. An elas tic caps ule s urrounds the organ and confines the
immune cells and FRC network. Lymph nodes are completely packed with lymphocytes and lymphocyte numbers directly dictates the
size of the organ. Although lymphocytes cons tantly enter and leave the lymph node, its s
ize remains remarkedly s table under homeostatic conditions. It is only
partly known how the cellularity and s ize of the lymph node is regulated and how the lymph node is
able to swell in inflammation. The role of the FRC network in lymph node s
welling and trans fer of fluids are inves tigated in this thes is. Furthermore, we s
tudied what trafficking routes are us ed by cancer cells in lymph nodes to form distal
metastases.We examined the role of a mechanical feedback in regulation of lymph node
swelling. Using parallel plate compression and UV-las er cutting experiments we dis
s ected the mechanical force dynamics of the whole lymph node, and individually
for FRCs and the caps ule. Physical forces generated by packed lymphocytes directly affect the tens
ion on the FRC network and capsule, which increases its resistance to swelling. This implies a feedback mechanism between tis
s ue pres s ure and ability of lymphocytes to enter the organ. Following inflammation, the lymph node swells
∼10 fold in two weeks . Yet, what is the role for tens ion on the FRC network and caps
ule, and how are lymphocytes able to enter in conditions that resist
swelling remain open ques tions . We s how that tens ion on the FRC network is important
to limit the swelling rate of the organ so that the FRC network can grow in a coordinated fashion.
This is illustrated by interfering with FRC contractility, which leads to faster
swelling rates and a dis organized FRC network in the inflamed lymph node.
Growth of the FRC network in turn is expected to releas e tens ion on thes
e s tructures and lowers the res is tance to swelling, thereby allowing
more lymphocytes to enter the organ and drive more swelling. Halt of swelling
coincides with a thickening of the caps ule, which forms a thick res
is tant band around the organ and lowers tens ion on the FRC network to form
a new force equilibrium.The FRC and conduit network are further believed to be a privileged s
ite of s oluble information within the lymph node, although many details remain uns
olved. We s how by 3D ultra-recons truction that FRCs and antigen pres
enting cells cover the s urface of conduit s ys tem for more than 99%
and we dis cus s the implications for s oluble information exchangeat the conduit
level.Finally, there is an ongoing debate in the cancer field whether and how
cancer cells in lymph nodes s eed dis tal metas tas es . We s how that cancer cells infus
ed into the lymph node can utilize trafficking routes of immune cells and rapidly migrate to blood vessels.
Once in the blood circulation, these cells are able to form metastases in
distal tissues.
acknowledged_ssus:
- _id: Bio
- _id: PreCl
- _id: EM-Fac
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Frank P
full_name: Assen, Frank P
id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87
last_name: Assen
orcid: 0000-0003-3470-6119
citation:
ama: 'Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility,
morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947'
apa: 'Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between
stroma contractility, morphology and lymphocyte trafficking. Institute of
Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947'
chicago: 'Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between
Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science
and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947.'
ieee: 'F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma
contractility, morphology and lymphocyte trafficking,” Institute of Science and
Technology Austria, 2019.'
ista: 'Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma
contractility, morphology and lymphocyte trafficking. Institute of Science and
Technology Austria.'
mla: 'Assen, Frank P. Lymph Node Mechanics: Deciphering the Interplay between
Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of
Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947.'
short: 'F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma
Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and
Technology Austria, 2019.'
corr_author: '1'
date_created: 2019-10-14T16:54:52Z
date_published: 2019-10-09T00:00:00Z
date_updated: 2026-04-08T14:01:50Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
doi: 10.15479/AT:ISTA:6947
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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language:
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publication_identifier:
issn:
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status: public
supervisor:
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full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
title: 'Lymph node mechanics: Deciphering the interplay between stroma contractility,
morphology and lymphocyte trafficking'
type: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2019'
...