---
_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.
date_created: 2019-04-09T14:37:06Z
date_published: 2019-02-04T00:00:00Z
date_updated: 2023-09-08T11:43:03Z
day: '04'
ddc:
- '575'
degree_awarded: PhD
department:
- _id: JiFr
doi: 10.15479/at:ista:th1075
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language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
page: '138'
publication_identifier:
issn:
- 2663-337X
publication_status: published
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '11222'
acknowledgement: This work was supported by the ERC and EU Horizon 2020 (ERC 692692;
MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).
article_number: A3.27
article_processing_charge: No
author:
- first_name: Olena
full_name: Kim, Olena
id: 3F8ABDDA-F248-11E8-B48F-1D18A9856A87
last_name: Kim
- first_name: Carolina
full_name: Borges Merjane, Carolina
id: 4305C450-F248-11E8-B48F-1D18A9856A87
last_name: Borges Merjane
orcid: 0000-0003-0005-401X
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
citation:
ama: 'Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle
pool in hippocampal mossy fiber terminals by electron microscopy. In: Intrinsic
Activity. Vol 7. Austrian Pharmacological Society; 2019. doi:10.25006/ia.7.s1-a3.27'
apa: 'Kim, O., Borges Merjane, C., & Jonas, P. M. (2019). Functional analysis
of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy.
In Intrinsic Activity (Vol. 7). Innsbruck, Austria: Austrian Pharmacological
Society. https://doi.org/10.25006/ia.7.s1-a3.27'
chicago: Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis
of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.”
In Intrinsic Activity, Vol. 7. Austrian Pharmacological Society, 2019.
https://doi.org/10.25006/ia.7.s1-a3.27.
ieee: O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked
vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in
Intrinsic Activity, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1.
ista: 'Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked
vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic
Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological
Society vol. 7, A3.27.'
mla: Kim, Olena, et al. “Functional Analysis of the Docked Vesicle Pool in Hippocampal
Mossy Fiber Terminals by Electron Microscopy.” Intrinsic Activity, vol.
7, no. Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:10.25006/ia.7.s1-a3.27.
short: O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian
Pharmacological Society, 2019.
conference:
end_date: 2019-09-27
location: Innsbruck, Austria
name: 'ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological
Society'
start_date: 2019-09-25
date_created: 2022-04-20T15:06:05Z
date_published: 2019-09-11T00:00:00Z
date_updated: 2024-03-27T23:30:07Z
day: '11'
department:
- _id: PeJo
doi: 10.25006/ia.7.s1-a3.27
ec_funded: 1
intvolume: ' 7'
issue: Suppl. 1
keyword:
- hippocampus
- mossy fibers
- readily releasable pool
- electron microscopy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.intrinsicactivity.org/2019/7/S1/A3.27/
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 25B7EB9E-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '692692'
name: Biophysics and circuit function of a giant cortical glumatergic synapse
- _id: 25BAF7B2-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '708497'
name: Presynaptic calcium channels distribution and impact on coupling at the hippocampal
mossy fiber synapse
- _id: 25C3DBB6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: W01205
name: Zellkommunikation in Gesundheit und Krankheit
- _id: 25C5A090-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z00312
name: The Wittgenstein Prize
publication: Intrinsic Activity
publication_identifier:
issn:
- 2309-8503
publication_status: published
publisher: Austrian Pharmacological Society
quality_controlled: '1'
related_material:
record:
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relation: dissertation_contains
status: public
status: public
title: Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals
by electron microscopy
type: conference_abstract
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 7
year: '2019'
...
---
_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.'
date_created: 2019-10-14T16:54:52Z
date_published: 2019-10-09T00:00:00Z
date_updated: 2023-09-13T08:50:57Z
day: '9'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: MiSi
doi: 10.15479/AT:ISTA:6947
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has_accepted_license: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: '142'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '664'
relation: part_of_dissertation
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- id: '402'
relation: part_of_dissertation
status: public
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_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.
date_created: 2019-09-06T06:54:16Z
date_published: 2019-09-09T00:00:00Z
date_updated: 2023-09-19T10:01:12Z
day: '09'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6849
file:
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content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: drangel
date_created: 2019-09-09T13:09:45Z
date_updated: 2021-02-10T23:30:09Z
embargo_to: open_access
file_id: '6865'
file_name: Thesis_Damaris_Rangel_source.docx
file_size: 18253100
relation: source_file
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checksum: 59c73be40eeaa1c4db24067270151555
content_type: application/pdf
creator: drangel
date_created: 2019-09-09T13:09:52Z
date_updated: 2020-09-11T22:30:04Z
embargo: 2020-09-10
file_id: '6866'
file_name: Thesis_Damaris_Rangel_pdfa.pdf
file_size: 2160109
relation: main_file
request_a_copy: 0
file_date_updated: 2021-02-10T23:30:09Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '97'
publication_identifier:
isbn:
- '9783990780039'
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
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
- 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.
date_created: 2019-04-28T21:59:14Z
date_published: 2019-05-02T00:00:00Z
date_updated: 2024-03-27T23:30:10Z
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:
- '10974172'
issn:
- '00928674'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
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.
date_created: 2019-10-14T07:00:24Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2024-03-27T23:30:11Z
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: '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.
date_created: 2020-01-29T15:56:56Z
date_published: 2019-12-20T00:00:00Z
date_updated: 2024-03-27T23:30:13Z
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'
issue: '12'
language:
- iso: eng
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 (HBP SGA 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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 22
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
- 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: 2024-03-27T23:30:14Z
day: '12'
ddc:
- '572'
department:
- _id: LeSa
doi: 10.1038/s41586-019-1519-2
ec_funded: 1
external_id:
isi:
- '000485415400061'
pmid:
- '31462775'
file:
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checksum: 52728cda5210a3e9b74cc204e8aed3d5
content_type: application/pdf
creator: lsazanov
date_created: 2020-11-26T16:33:44Z
date_updated: 2020-11-26T16:33:44Z
file_id: '8821'
file_name: Manuscript_final_acc_withFigs_SI_opt_red.pdf
file_size: 3066206
relation: main_file
success: 1
file_date_updated: 2020-11-26T16:33:44Z
has_accepted_license: '1'
intvolume: ' 573'
isi: 1
issue: '7773'
language:
- iso: eng
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'
...
---
_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: 2024-03-27T23:30:16Z
day: '29'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1126/science.aav4837
ec_funded: 1
external_id:
isi:
- '000462738000034'
file:
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content_type: application/pdf
creator: dernst
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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
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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'
...
---
_id: '7132'
abstract:
- lang: eng
text: "A major challenge in neuroscience research is to dissect the circuits that
orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian
species, such as microbial opsins, have been successfully transplanted to specific
neuronal targets to override their natural communication patterns. The goal of
our work is to manipulate synaptic communication in a manner that closely incorporates
the functional intricacies of synapses by preserving temporal encoding (i.e. the
firing pattern of the presynaptic neuron) and connectivity (i.e. target specific
synapses rather than specific neurons). Our strategy to achieve this goal builds
on the use of non-mammalian transplants to create a synthetic synapse. The mode
of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN)
into synaptic vesicles by means of a genetically targeted transporter selective
for the SN. Upon natural vesicular release, exposure of the SN to the synaptic
cleft will modify the post-synaptic potential through an orthogonal ligand gated
ion channel. To achieve this goal we have functionally characterized a mixed cationic
methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally
characterize a synthetic transporter in isolated synaptic vesicles without the
need for transgenic animals, identified and extracted multiple prokaryotic uptake
systems that are substrate specific for methionine (Met), and established a primary/cell
line co-culture system that would allow future combinatorial testing of this orthogonal
transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a
unique opportunity to manipulate synaptic communication while maintaining the
electrophysiological integrity of the pre-synaptic cell. In this way, information
may be preserved that was generated in upstream circuits and that could be essential
for concerted function and information processing."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Catherine
full_name: Mckenzie, Catherine
id: 3EEDE19A-F248-11E8-B48F-1D18A9856A87
last_name: Mckenzie
citation:
ama: Mckenzie C. Design and characterization of methods and biological components
to realize synthetic neurotransmission. 2019. doi:10.15479/at:ista:7132
apa: Mckenzie, C. (2019). Design and characterization of methods and biological
components to realize synthetic neurotransmission. Institute of Science and
Technology Austria. https://doi.org/10.15479/at:ista:7132
chicago: Mckenzie, Catherine. “Design and Characterization of Methods and Biological
Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/at:ista:7132.
ieee: C. Mckenzie, “Design and characterization of methods and biological components
to realize synthetic neurotransmission,” Institute of Science and Technology Austria,
2019.
ista: Mckenzie C. 2019. Design and characterization of methods and biological components
to realize synthetic neurotransmission. Institute of Science and Technology Austria.
mla: Mckenzie, Catherine. Design and Characterization of Methods and Biological
Components to Realize Synthetic Neurotransmission. Institute of Science and
Technology Austria, 2019, doi:10.15479/at:ista:7132.
short: C. Mckenzie, Design and Characterization of Methods and Biological Components
to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria,
2019.
date_created: 2019-11-27T09:07:14Z
date_published: 2019-06-27T00:00:00Z
date_updated: 2024-03-27T23:30:21Z
day: '27'
ddc:
- '571'
- '573'
degree_awarded: PhD
department:
- _id: HaJa
doi: 10.15479/at:ista:7132
file:
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date_created: 2019-11-27T09:06:10Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7133'
file_name: McKenzie PhD Thesis August 2018 - Corrected Final.docx
file_size: 5054633
relation: source_file
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checksum: 140dfb5e3df7edca34f4b6fcc55d876f
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date_created: 2019-11-27T09:06:10Z
date_updated: 2020-07-14T12:47:50Z
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file_name: McKenzie PhD Thesis August 2018 - Corrected Final.pdf
file_size: 3231837
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
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language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '95'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6266'
relation: old_edition
status: public
status: public
supervisor:
- first_name: Harald L
full_name: Janovjak, Harald L
id: 33BA6C30-F248-11E8-B48F-1D18A9856A87
last_name: Janovjak
orcid: 0000-0002-8023-9315
title: Design and characterization of methods and biological components to realize
synthetic neurotransmission
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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: 2024-03-27T23:30:22Z
day: '01'
ddc:
- '570'
department:
- _id: JoCs
doi: 10.1002/hipo.23076
ec_funded: 1
external_id:
isi:
- '000480635400003'
file:
- access_level: open_access
checksum: 5e8de271ca04aef92a5de42d6aac4404
content_type: application/pdf
creator: dernst
date_created: 2019-02-11T10:42:51Z
date_updated: 2020-07-14T12:47:13Z
file_id: '5950'
file_name: 2019_Hippocampus_Kaefer.pdf
file_size: 2132893
relation: main_file
file_date_updated: 2020-07-14T12:47:13Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '9'
language:
- iso: eng
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'
...
---
_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.
date_created: 2019-08-21T15:00:57Z
date_published: 2019-08-24T00:00:00Z
date_updated: 2023-09-07T13:01:42Z
day: '24'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: JoCs
doi: 10.15479/AT:ISTA:6825
file:
- access_level: open_access
checksum: 2664420e332a33338568f4f3bfc59287
content_type: application/pdf
creator: kkaefer
date_created: 2019-09-03T08:07:13Z
date_updated: 2020-09-06T22:30:03Z
embargo: 2020-09-05
file_id: '6846'
file_name: Thesis_Kaefer_PDFA.pdf
file_size: 3205202
relation: main_file
request_a_copy: 0
- access_level: closed
checksum: 9a154eab6f07aa590a3d2651dc0d926a
content_type: application/zip
creator: kkaefer
date_created: 2019-09-03T08:07:17Z
date_updated: 2020-09-15T22:30:05Z
embargo_to: open_access
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month: '08'
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page: '89'
publication_identifier:
issn:
- 2663-337X
publication_status: published
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
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: 2024-03-27T23:30:22Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.7554/eLife.42014
external_id:
isi:
- '000473588700001'
pmid:
- '31169497'
file:
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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
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intvolume: ' 8'
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month: '06'
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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: '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
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.).
date_created: 2021-10-01T12:14:51Z
date_published: 2019-10-13T00:00:00Z
date_updated: 2024-03-27T23:30:26Z
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: submitted
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: '6187'
abstract:
- lang: eng
text: Aberrant display of the truncated core1 O-glycan T-antigen is a common feature
of human cancer cells that correlates with metastasis. Here we show that T-antigen
in Drosophila melanogaster macrophages is involved in their developmentally programmed
tissue invasion. Higher macrophage T-antigen levels require an atypical major
facilitator superfamily (MFS) member that we named Minerva which enables macrophage
dissemination and invasion. We characterize for the first time the T and Tn glycoform
O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva
increases the presence of T-antigen on proteins in pathways previously linked
to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required
for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the
minerva mutant’s migration and T-antigen glycosylation defects. We thus identify
a key conserved regulator that orchestrates O-glycosylation on a protein subset
to activate a program governing migration steps important for both development
and cancer metastasis.
acknowledged_ssus:
- _id: LifeSc
article_number: e41801
article_processing_charge: No
author:
- first_name: Katarina
full_name: Valosková, Katarina
id: 46F146FC-F248-11E8-B48F-1D18A9856A87
last_name: Valosková
- first_name: Julia
full_name: Biebl, Julia
id: 3CCBB46E-F248-11E8-B48F-1D18A9856A87
last_name: Biebl
- first_name: Marko
full_name: Roblek, Marko
id: 3047D808-F248-11E8-B48F-1D18A9856A87
last_name: Roblek
orcid: 0000-0001-9588-1389
- first_name: Shamsi
full_name: Emtenani, Shamsi
id: 49D32318-F248-11E8-B48F-1D18A9856A87
last_name: Emtenani
orcid: 0000-0001-6981-6938
- first_name: Attila
full_name: György, Attila
id: 3BCEDBE0-F248-11E8-B48F-1D18A9856A87
last_name: György
orcid: 0000-0002-1819-198X
- first_name: Michaela
full_name: Misova, Michaela
id: 495A3C32-F248-11E8-B48F-1D18A9856A87
last_name: Misova
orcid: 0000-0003-2427-6856
- first_name: Aparna
full_name: Ratheesh, Aparna
id: 2F064CFE-F248-11E8-B48F-1D18A9856A87
last_name: Ratheesh
orcid: 0000-0001-7190-0776
- first_name: Patricia
full_name: Rodrigues, Patricia
id: 2CE4065A-F248-11E8-B48F-1D18A9856A87
last_name: Rodrigues
- first_name: Katerina
full_name: Shkarina, Katerina
last_name: Shkarina
- first_name: Ida Signe Bohse
full_name: Larsen, Ida Signe Bohse
last_name: Larsen
- first_name: Sergey Y
full_name: Vakhrushev, Sergey Y
last_name: Vakhrushev
- first_name: Henrik
full_name: Clausen, Henrik
last_name: Clausen
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
citation:
ama: Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily
member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion.
eLife. 2019;8. doi:10.7554/elife.41801
apa: Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M.,
… Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates
a subset of O-glycosylation to aid macrophage tissue invasion. ELife. eLife
Sciences Publications. https://doi.org/10.7554/elife.41801
chicago: Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila
György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator
Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage
Tissue Invasion.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.41801.
ieee: K. Valosková et al., “A conserved major facilitator superfamily member
orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” eLife,
vol. 8. eLife Sciences Publications, 2019.
ista: Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh
A, Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE.
2019. A conserved major facilitator superfamily member orchestrates a subset of
O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.
mla: Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member
Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” ELife,
vol. 8, e41801, eLife Sciences Publications, 2019, doi:10.7554/elife.41801.
short: K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A.
Ratheesh, P. Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen,
D.E. Siekhaus, ELife 8 (2019).
date_created: 2019-03-28T13:37:45Z
date_published: 2019-03-26T00:00:00Z
date_updated: 2024-03-27T23:30:29Z
day: '26'
ddc:
- '570'
department:
- _id: DaSi
doi: 10.7554/elife.41801
ec_funded: 1
external_id:
isi:
- '000462530200001'
file:
- access_level: open_access
checksum: cc0d1a512559d52e7e7cb0e9b9854b40
content_type: application/pdf
creator: dernst
date_created: 2019-03-28T14:00:41Z
date_updated: 2020-07-14T12:47:23Z
file_id: '6188'
file_name: 2019_eLife_Valoskova.pdf
file_size: 4496017
relation: main_file
file_date_updated: 2020-07-14T12:47:23Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 253CDE40-B435-11E9-9278-68D0E5697425
grant_number: '24283'
name: Examination of the role of a MFS transporter in the migration of Drosophila
immune cells
- _id: 253B6E48-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P29638
name: The role of Drosophila TNF alpha in immune cell invasion
- _id: 2536F660-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '334077'
name: Investigating the role of transporters in invasive migration through junctions
- _id: 25388084-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329540'
name: 'Breaking barriers: Investigating the junctional and mechanobiological changes
underlying the ability of Drosophila immune cells to invade an epithelium'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/
record:
- id: '6530'
relation: dissertation_contains
- id: '8983'
relation: dissertation_contains
status: public
- id: '6546'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation
to aid macrophage tissue invasion
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: '6546'
abstract:
- lang: eng
text: "Invasive migration plays a crucial role not only during development and homeostasis
but also in pathological states, such as tumor metastasis. Drosophila macrophage
migration into the extended germband is an interesting system to study invasive
migration. It carries similarities to immune cell transmigration and cancer cell
invasion, therefore studying this process could also bring new understanding of
invasion in higher organisms. In our work, we uncover a highly conserved member
of the major facilitator family that plays a role in tissue invasion through regulation
of glycosylation on a subgroup of proteins and/or by aiding the precise timing
of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1
O-glycan T-antigen is a common feature of human cancer cells that correlates with
metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages
is involved in their developmentally programmed tissue invasion. Higher macrophage
T-antigen levels require an atypical major facilitator superfamily (MFS) member
that we named Minerva which enables macrophage dissemination and invasion. We
characterize for the first time the T and Tn glycoform O-glycoproteome of the
Drosophila melanogaster embryo, and determine that Minerva increases the presence
of T-antigen on proteins in pathways previously linked to cancer, most strongly
on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue
entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration
and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator
that orchestrates O-glycosylation on a protein subset to activate \r\na program
governing migration steps important for both development and cancer metastasis.
\r\n"
acknowledged_ssus:
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Katarina
full_name: Valosková, Katarina
id: 46F146FC-F248-11E8-B48F-1D18A9856A87
last_name: Valosková
citation:
ama: Valosková K. The role of a highly conserved major facilitator superfamily member
in Drosophila embryonic macrophage migration. 2019. doi:10.15479/AT:ISTA:6546
apa: Valosková, K. (2019). The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:6546
chicago: Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator
Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of
Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6546.
ieee: K. Valosková, “The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration,” Institute of Science and
Technology Austria, 2019.
ista: Valosková K. 2019. The role of a highly conserved major facilitator superfamily
member in Drosophila embryonic macrophage migration. Institute of Science and
Technology Austria.
mla: Valosková, Katarina. The Role of a Highly Conserved Major Facilitator Superfamily
Member in Drosophila Embryonic Macrophage Migration. Institute of Science
and Technology Austria, 2019, doi:10.15479/AT:ISTA:6546.
short: K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily
Member in Drosophila Embryonic Macrophage Migration, Institute of Science and
Technology Austria, 2019.
date_created: 2019-06-07T12:49:19Z
date_published: 2019-06-07T00:00:00Z
date_updated: 2023-09-19T10:15:54Z
day: '07'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: DaSi
doi: 10.15479/AT:ISTA:6546
file:
- access_level: closed
checksum: 68949c2d96210b45b981a23e9c9cd93c
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: khribikova
date_created: 2019-06-07T13:00:04Z
date_updated: 2020-07-14T12:47:33Z
embargo_to: open_access
file_id: '6549'
file_name: Katarina Valoskova_PhD thesis_final version.docx
file_size: 14110626
relation: source_file
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checksum: 555329cd76e196c96f5278c480ee2e6e
content_type: application/pdf
creator: khribikova
date_created: 2019-06-07T13:00:08Z
date_updated: 2021-02-11T11:17:14Z
embargo: 2020-06-07
file_id: '6550'
file_name: Katarina Valoskova_PhD thesis_final version.pdf
file_size: 10054156
relation: main_file
file_date_updated: 2021-02-11T11:17:14Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: '141'
project:
- _id: 253CDE40-B435-11E9-9278-68D0E5697425
grant_number: '24283'
name: Examination of the role of a MFS transporter in the migration of Drosophila
immune cells
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6187'
relation: part_of_dissertation
status: public
- id: '544'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
title: The role of a highly conserved major facilitator superfamily member in Drosophila
embryonic macrophage migration
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6363'
abstract:
- lang: eng
text: "Distinguishing between similar experiences is achieved by the brain
\ in a process called pattern separation. In the hippocampus, pattern
\ separation reduces the interference of memories and increases the storage
capacity by decorrelating similar inputs patterns of neuronal activity into
\ non-overlapping output firing patterns. Winners-take-all (WTA) mechanism
\ is a theoretical model for pattern separation in which a \"winner\"
\ cell suppresses the activity of the neighboring neurons through feedback
inhibition. However, if the network properties of the dentate gyrus support WTA
as a biologically conceivable model remains unknown. Here, we showed that the
connectivity rules of PV+interneurons and their synaptic properties are optimizedfor
efficient pattern separation. We found using multiple whole-cell in vitrorecordings
that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition,
a form of feedback inhibition in which a GC inhibits other GCs but not
\ itself through the activation of PV+interneurons. Thus, lateral inhibition
between GC–PV+interneurons was ~10 times more abundant than recurrent connections.
Furthermore, the GC–PV+interneuron connectivity was more spatially confined
\ but less abundant than PV+interneurons–GC connectivity, leading to an
\ asymmetrical distribution of excitatory and inhibitory connectivity. Our
network model of the dentate gyrus with incorporated real connectivity rules efficiently
decorrelates neuronal activity patterns using WTA as the primary mechanism.
\ This process relied on lateral inhibition, fast-signaling properties of
\ PV+interneurons and the asymmetrical distribution of excitatory and inhibitory
connectivity. Finally, we found that silencing the activity of PV+interneurons
in vivoleads to acute deficits in discrimination between similar environments,
suggesting that PV+interneuron networks are necessary for behavioral relevant
computations. Our results demonstrate that PV+interneurons possess unique
connectivity and fast signaling properties that confer to the dentate
\ gyrus network properties that allow the emergence of pattern separation. Thus,
our results contribute to the knowledge of how specific forms of network organization
underlie sophisticated types of information processing. \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: 'Claudia '
full_name: 'Espinoza Martinez, Claudia '
id: 31FFEE2E-F248-11E8-B48F-1D18A9856A87
last_name: Espinoza Martinez
orcid: 0000-0003-4710-2082
citation:
ama: Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation
in hippocampal microcircuits. 2019. doi:10.15479/AT:ISTA:6363
apa: Espinoza Martinez, C. (2019). Parvalbumin+ interneurons enable efficient
pattern separation in hippocampal microcircuits. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:6363
chicago: Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient
Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology
Austria, 2019. https://doi.org/10.15479/AT:ISTA:6363.
ieee: C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern
separation in hippocampal microcircuits,” Institute of Science and Technology
Austria, 2019.
ista: Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern
separation in hippocampal microcircuits. Institute of Science and Technology Austria.
mla: Espinoza Martinez, Claudia. Parvalbumin+ Interneurons Enable Efficient Pattern
Separation in Hippocampal Microcircuits. Institute of Science and Technology
Austria, 2019, doi:10.15479/AT:ISTA:6363.
short: C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern
Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria,
2019.
date_created: 2019-04-30T11:56:10Z
date_published: 2019-04-30T00:00:00Z
date_updated: 2023-09-15T12:03:48Z
day: '30'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: PeJo
doi: 10.15479/AT:ISTA:6363
file:
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content_type: application/pdf
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date_created: 2019-05-07T16:00:39Z
date_updated: 2021-02-11T11:17:15Z
embargo: 2020-05-09
file_id: '6389'
file_name: Espinozathesis_all2.pdf
file_size: 13966891
relation: main_file
- access_level: closed
checksum: f6aa819f127691a2b0fc21c76eb09746
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creator: cespinoza
date_created: 2019-05-07T16:00:48Z
date_updated: 2020-07-14T12:47:28Z
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file_id: '6390'
file_name: Espinoza_Thesis.docx
file_size: 11159900
relation: source_file
file_date_updated: 2021-02-11T11:17:15Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '140'
publication_identifier:
isbn:
- 978-3-99078-000-8
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '21'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
title: Parvalbumin+ interneurons enable efficient pattern separation in hippocampal
microcircuits
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6780'
abstract:
- lang: eng
text: "In this work, we consider the almost-sure termination problem for probabilistic
programs that asks whether a\r\ngiven probabilistic program terminates with probability
1. Scalable approaches for program analysis often\r\nrely on modularity as their
theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof
Floyd-Hoare logic provides the foundation for modular analysis. Extension of this
rule to almost-sure\r\ntermination of probabilistic programs is quite tricky,
and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic
variant cautiously addresses the key issue of integrability, we show that the
proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic
programs.\r\nBesides establishing unsoundness of the previous rule, our contributions
are as follows: First, we present a\r\nsound modular rule for almost-sure termination
of probabilistic programs. Our approach is based on a novel\r\nnotion of descent
supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat
are linear and show that they can be synthesized in polynomial time. Finally,
we present experimental\r\nresults on a variety of benchmarks and several natural
examples that model various types of nested while\r\nloops in probabilistic programs
and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination
property"
article_number: '129'
article_processing_charge: No
author:
- first_name: Mingzhang
full_name: Huang, Mingzhang
last_name: Huang
- first_name: Hongfei
full_name: Fu, Hongfei
last_name: Fu
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
citation:
ama: 'Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure
termination of probabilistic programs. In: Proceedings of the 34th ACM International
Conference on Object-Oriented Programming, Systems, Languages, and Applications
. Vol 3. ACM; 2019. doi:10.1145/3360555'
apa: 'Huang, M., Fu, H., Chatterjee, K., & Goharshady, A. K. (2019). Modular
verification for almost-sure termination of probabilistic programs. In Proceedings
of the 34th ACM International Conference on Object-Oriented Programming, Systems,
Languages, and Applications (Vol. 3). Athens, Greece: ACM. https://doi.org/10.1145/3360555'
chicago: Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar
Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic
Programs.” In Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications , Vol. 3. ACM, 2019. https://doi.org/10.1145/3360555.
ieee: M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification
for almost-sure termination of probabilistic programs,” in Proceedings of the
34th ACM International Conference on Object-Oriented Programming, Systems, Languages,
and Applications , Athens, Greece, 2019, vol. 3.
ista: 'Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for
almost-sure termination of probabilistic programs. Proceedings of the 34th ACM
International Conference on Object-Oriented Programming, Systems, Languages, and
Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications
vol. 3, 129.'
mla: Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination
of Probabilistic Programs.” Proceedings of the 34th ACM International Conference
on Object-Oriented Programming, Systems, Languages, and Applications , vol.
3, 129, ACM, 2019, doi:10.1145/3360555.
short: M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the
34th ACM International Conference on Object-Oriented Programming, Systems, Languages,
and Applications , ACM, 2019.
conference:
end_date: 2019-10-25
location: Athens, Greece
name: 'OOPSLA: Object-oriented Programming, Systems, Languages and Applications'
start_date: 2019-10-23
date_created: 2019-08-09T09:54:20Z
date_published: 2019-10-01T00:00:00Z
date_updated: 2024-03-27T23:30:33Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1145/3360555
ec_funded: 1
external_id:
arxiv:
- '1901.06087'
file:
- access_level: open_access
checksum: 3482d8ace6fb4991eb7810e3b70f1b9f
content_type: application/pdf
creator: akafshda
date_created: 2019-08-12T15:40:57Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6807'
file_name: oopsla-2019.pdf
file_size: 1024643
relation: main_file
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checksum: 4e5a6fb2b59a75222a4e8335a5a60eac
content_type: application/pdf
creator: dernst
date_created: 2020-05-12T15:15:14Z
date_updated: 2020-07-14T12:47:40Z
file_id: '7821'
file_name: 2019_ACM_Huang.pdf
file_size: 538579
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 3'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
publication: 'Proceedings of the 34th ACM International Conference on Object-Oriented
Programming, Systems, Languages, and Applications '
publication_status: published
publisher: ACM
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
status: public
title: Modular verification for almost-sure termination of probabilistic programs
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 3
year: '2019'
...
---
_id: '6380'
abstract:
- lang: eng
text: 'There is a huge gap between the speeds of modern caches and main memories,
and therefore cache misses account for a considerable loss of efficiency in programs.
The predominant technique to address this issue has been Data Packing: data elements
that are frequently accessed within time proximity are packed into the same cache
block, thereby minimizing accesses to the main memory. We consider the algorithmic
problem of Data Packing on a two-level memory system. Given a reference sequence
R of accesses to data elements, the task is to partition the elements into cache
blocks such that the number of cache misses on R is minimized. The problem is
notoriously difficult: it is NP-hard even when the cache has size 1, and is hard
to approximate for any cache size larger than 4. Therefore, all existing techniques
for Data Packing are based on heuristics and lack theoretical guarantees. In this
work, we present the first positive theoretical results for Data Packing, along
with new and stronger negative results. We consider the problem under the lens
of the underlying access hypergraphs, which are hypergraphs of affinities between
the data elements, where the order of an access hypergraph corresponds to the
size of the affinity group. We study the problem parameterized by the treewidth
of access hypergraphs, which is a standard notion in graph theory to measure the
closeness of a graph to a tree. Our main results are as follows: We show there
is a number q* depending on the cache parameters such that (a) if the access hypergraph
of order q* has constant treewidth, then there is a linear-time algorithm for
Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph
of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy
depending on a single parameter, namely, the highest order among access hypegraphs
that have constant treewidth; and establish the optimal value q* of this parameter.
Finally, we present an experimental evaluation of a prototype implementation of
our algorithm. Our results demonstrate that, in practice, access hypergraphs of
many commonly-used algorithms have small treewidth. We compare our approach with
several state-of-the-art heuristic-based algorithms and show that our algorithm
leads to significantly fewer cache-misses. '
article_number: '53'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Nastaran
full_name: Okati, Nastaran
last_name: Okati
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
2019;3(POPL). doi:10.1145/3290366
apa: Chatterjee, K., Goharshady, A. K., Okati, N., & Pavlogiannis, A. (2019).
Efficient parameterized algorithms for data packing. Proceedings of the ACM
on Programming Languages. ACM. https://doi.org/10.1145/3290366
chicago: Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas
Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” Proceedings
of the ACM on Programming Languages. ACM, 2019. https://doi.org/10.1145/3290366.
ieee: K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient
parameterized algorithms for data packing,” Proceedings of the ACM on Programming
Languages, vol. 3, no. POPL. ACM, 2019.
ista: Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized
algorithms for data packing. Proceedings of the ACM on Programming Languages.
3(POPL), 53.
mla: Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data
Packing.” Proceedings of the ACM on Programming Languages, vol. 3, no.
POPL, 53, ACM, 2019, doi:10.1145/3290366.
short: K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of
the ACM on Programming Languages 3 (2019).
date_created: 2019-05-06T12:18:17Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2024-03-27T23:30:33Z
day: '01'
ddc:
- '004'
department:
- _id: KrCh
doi: 10.1145/3290366
ec_funded: 1
file:
- access_level: open_access
checksum: c157752f96877b36685ad7063ada4524
content_type: application/pdf
creator: dernst
date_created: 2019-05-06T12:23:11Z
date_updated: 2020-07-14T12:47:29Z
file_id: '6381'
file_name: 2019_ACM_POPL_Chatterjee.pdf
file_size: 1294962
relation: main_file
file_date_updated: 2020-07-14T12:47:29Z
has_accepted_license: '1'
intvolume: ' 3'
issue: POPL
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Proceedings of the ACM on Programming Languages
publication_identifier:
issn:
- 2475-1421
publication_status: published
publisher: ACM
pubrep_id: '1056'
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
status: public
title: Efficient parameterized algorithms for data packing
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: 3
year: '2019'
...
---
_id: '6056'
abstract:
- lang: eng
text: In today's programmable blockchains, smart contracts are limited to being
deterministic and non-probabilistic. This lack of randomness is a consequential
limitation, given that a wide variety of real-world financial contracts, such
as casino games and lotteries, depend entirely on randomness. As a result, several
ad-hoc random number generation approaches have been developed to be used in smart
contracts. These include ideas such as using an oracle or relying on the block
hash. However, these approaches are manipulatable, i.e. their output can be tampered
with by parties who might not be neutral, such as the owner of the oracle or the
miners.We propose a novel game-theoretic approach for generating provably unmanipulatable
pseudorandom numbers on the blockchain. Our approach allows smart contracts to
access a trustworthy source of randomness that does not rely on potentially compromised
miners or oracles, hence enabling the creation of a new generation of smart contracts
that are not limited to being non-probabilistic and can be drawn from the much
more general class of probabilistic programs.
article_number: '8751326'
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Amir Kafshdar
full_name: Goharshady, Amir Kafshdar
id: 391365CE-F248-11E8-B48F-1D18A9856A87
last_name: Goharshady
orcid: 0000-0003-1702-6584
- first_name: Arash
full_name: Pourdamghani, Arash
last_name: Pourdamghani
citation:
ama: 'Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts:
Secure randomness on the blockchain. In: IEEE International Conference on Blockchain
and Cryptocurrency. IEEE; 2019. doi:10.1109/BLOC.2019.8751326'
apa: 'Chatterjee, K., Goharshady, A. K., & Pourdamghani, A. (2019). Probabilistic
smart contracts: Secure randomness on the blockchain. In IEEE International
Conference on Blockchain and Cryptocurrency. Seoul, Korea: IEEE. https://doi.org/10.1109/BLOC.2019.8751326'
chicago: 'Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani.
“Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In IEEE
International Conference on Blockchain and Cryptocurrency. IEEE, 2019. https://doi.org/10.1109/BLOC.2019.8751326.'
ieee: 'K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart
contracts: Secure randomness on the blockchain,” in IEEE International Conference
on Blockchain and Cryptocurrency, Seoul, Korea, 2019.'
ista: 'Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Probabilistic smart contracts:
Secure randomness on the blockchain. IEEE International Conference on Blockchain
and Cryptocurrency. IEEE International Conference on Blockchain and Cryptocurrency,
8751326.'
mla: 'Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness
on the Blockchain.” IEEE International Conference on Blockchain and Cryptocurrency,
8751326, IEEE, 2019, doi:10.1109/BLOC.2019.8751326.'
short: K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International
Conference on Blockchain and Cryptocurrency, IEEE, 2019.
conference:
end_date: 2019-05-17
location: Seoul, Korea
name: IEEE International Conference on Blockchain and Cryptocurrency
start_date: 2019-05-14
date_created: 2019-02-26T09:03:15Z
date_published: 2019-05-01T00:00:00Z
date_updated: 2024-03-27T23:30:33Z
day: '01'
department:
- _id: KrCh
doi: 10.1109/BLOC.2019.8751326
ec_funded: 1
external_id:
arxiv:
- '1902.07986'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1902.07986
month: '05'
oa: 1
oa_version: Preprint
project:
- _id: 25892FC0-B435-11E9-9278-68D0E5697425
grant_number: ICT15-003
name: Efficient Algorithms for Computer Aided Verification
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 266EEEC0-B435-11E9-9278-68D0E5697425
name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart
Contracts
- _id: 267066CE-B435-11E9-9278-68D0E5697425
name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies
publication: IEEE International Conference on Blockchain and Cryptocurrency
publication_status: published
publisher: IEEE
quality_controlled: '1'
related_material:
record:
- id: '8934'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: 'Probabilistic smart contracts: Secure randomness on the blockchain'
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2019'
...