---
_id: '799'
abstract:
- lang: eng
text: Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly
distributing various membrane proteins to their destination. Polarly localized
auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported
between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular
trafficking of PIN1 protein is sensitive to a fungal toxin brefeldin A (BFA),
which is known to inhibit guanine-nucleotide exchange factors for ADP ribosylation
factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive
trafficking pathway have not been revealed fully. In a previous study, we have
identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective
3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular
PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF
GEFs, BIG2. Fluorescent proteins tagged BEN3/BIG2 co-localized with markers for
TGN / early endosome (EE). Inspection of conditionally induced de novo synthesized
PIN1 confirmed that its secretion to the PM is BFA-sensitive and established BEN3/BIG2
as a crucial component of this BFA action at the level of TGN/EE. Furthermore,
ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF
GEF BEN1/MIN7. Taken together our results suggest that BEN3/BIG2 is an ARF GEF
component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.
article_number: 1801-1811
article_processing_charge: No
author:
- first_name: Saeko
full_name: Kitakura, Saeko
last_name: Kitakura
- first_name: Maciek
full_name: Adamowski, Maciek
id: 45F536D2-F248-11E8-B48F-1D18A9856A87
last_name: Adamowski
orcid: 0000-0001-6463-5257
- first_name: Yuki
full_name: Matsuura, Yuki
last_name: Matsuura
- first_name: Luca
full_name: Santuari, Luca
last_name: Santuari
- first_name: Hirotaka
full_name: Kouno, Hirotaka
last_name: Kouno
- first_name: Kohei
full_name: Arima, Kohei
last_name: Arima
- first_name: Christian
full_name: Hardtke, Christian
last_name: Hardtke
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Tatsuo
full_name: Kakimoto, Tatsuo
last_name: Kakimoto
- first_name: Hirokazu
full_name: Tanaka, Hirokazu
last_name: Tanaka
citation:
ama: Kitakura S, Adamowski M, Matsuura Y, et al. BEN3/BIG2 ARF GEF is involved in
brefeldin a-sensitive trafficking at the trans-Golgi network/early endosome in
Arabidopsis thaliana. Plant and Cell Physiology. 2017;58(10). doi:10.1093/pcp/pcx118
apa: Kitakura, S., Adamowski, M., Matsuura, Y., Santuari, L., Kouno, H., Arima,
K., … Tanaka, H. (2017). BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive
trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana.
Plant and Cell Physiology. Oxford University Press. https://doi.org/10.1093/pcp/pcx118
chicago: Kitakura, Saeko, Maciek Adamowski, Yuki Matsuura, Luca Santuari, Hirotaka
Kouno, Kohei Arima, Christian Hardtke, Jiří Friml, Tatsuo Kakimoto, and Hirokazu
Tanaka. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive Trafficking at
the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.” Plant and
Cell Physiology. Oxford University Press, 2017. https://doi.org/10.1093/pcp/pcx118.
ieee: S. Kitakura et al., “BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive
trafficking at the trans-Golgi network/early endosome in Arabidopsis thaliana,”
Plant and Cell Physiology, vol. 58, no. 10. Oxford University Press, 2017.
ista: Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke
C, Friml J, Kakimoto T, Tanaka H. 2017. BEN3/BIG2 ARF GEF is involved in brefeldin
a-sensitive trafficking at the trans-Golgi network/early endosome in Arabidopsis
thaliana. Plant and Cell Physiology. 58(10), 1801–1811.
mla: Kitakura, Saeko, et al. “BEN3/BIG2 ARF GEF Is Involved in Brefeldin a-Sensitive
Trafficking at the Trans-Golgi Network/Early Endosome in Arabidopsis Thaliana.”
Plant and Cell Physiology, vol. 58, no. 10, 1801–1811, Oxford University
Press, 2017, doi:10.1093/pcp/pcx118.
short: S. Kitakura, M. Adamowski, Y. Matsuura, L. Santuari, H. Kouno, K. Arima,
C. Hardtke, J. Friml, T. Kakimoto, H. Tanaka, Plant and Cell Physiology 58 (2017).
date_created: 2018-12-11T11:48:34Z
date_published: 2017-08-21T00:00:00Z
date_updated: 2023-09-27T11:00:19Z
day: '21'
ddc:
- '581'
department:
- _id: JiFr
doi: 10.1093/pcp/pcx118
external_id:
isi:
- '000413220400019'
pmid:
- '29016942'
file:
- access_level: open_access
checksum: bd3e3a94d55416739cbb19624bb977f8
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:52:34Z
date_updated: 2020-07-14T12:48:06Z
file_id: '6333'
file_name: 2017_PlantCellPhysio_Kitakura.pdf
file_size: 1352913
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 58'
isi: 1
issue: '10'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Plant and Cell Physiology
publication_identifier:
issn:
- '00320781'
publication_status: published
publisher: Oxford University Press
publist_id: '6854'
pubrep_id: '1009'
quality_controlled: '1'
scopus_import: '1'
status: public
title: BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-Golgi
network/early endosome in Arabidopsis thaliana
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 58
year: '2017'
...
---
_id: '800'
abstract:
- lang: eng
text: Gamma oscillations (30–150 Hz) in neuronal networks are associated with the
processing and recall of information. We measured local field potentials in the
dentate gyrus of freely moving mice and found that gamma activity occurs in bursts,
which are highly heterogeneous in their spatial extensions, ranging from focal
to global coherent events. Synaptic communication among perisomatic-inhibitory
interneurons (PIIs) is thought to play an important role in the generation of
hippocampal gamma patterns. However, how neuronal circuits can generate synchronous
oscillations at different spatial scales is unknown. We analyzed paired recordings
in dentate gyrus slices and show that synaptic signaling at interneuron-interneuron
synapses is distance dependent. Synaptic strength declines whereas the duration
of inhibitory signals increases with axonal distance among interconnected PIIs.
Using neuronal network modeling, we show that distance-dependent inhibition generates
multiple highly synchronous focal gamma bursts allowing the network to process
complex inputs in parallel in flexibly organized neuronal centers.
article_number: '758'
article_processing_charge: No
author:
- first_name: Michael
full_name: Strüber, Michael
last_name: Strüber
- first_name: Jonas
full_name: Sauer, Jonas
last_name: Sauer
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: Marlene
full_name: Bartos, Marlene
last_name: Bartos
citation:
ama: Strüber M, Sauer J, Jonas PM, Bartos M. Distance-dependent inhibition facilitates
focality of gamma oscillations in the dentate gyrus. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-00936-3
apa: Strüber, M., Sauer, J., Jonas, P. M., & Bartos, M. (2017). Distance-dependent
inhibition facilitates focality of gamma oscillations in the dentate gyrus. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00936-3
chicago: Strüber, Michael, Jonas Sauer, Peter M Jonas, and Marlene Bartos. “Distance-Dependent
Inhibition Facilitates Focality of Gamma Oscillations in the Dentate Gyrus.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00936-3.
ieee: M. Strüber, J. Sauer, P. M. Jonas, and M. Bartos, “Distance-dependent inhibition
facilitates focality of gamma oscillations in the dentate gyrus,” Nature Communications,
vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Strüber M, Sauer J, Jonas PM, Bartos M. 2017. Distance-dependent inhibition
facilitates focality of gamma oscillations in the dentate gyrus. Nature Communications.
8(1), 758.
mla: Strüber, Michael, et al. “Distance-Dependent Inhibition Facilitates Focality
of Gamma Oscillations in the Dentate Gyrus.” Nature Communications, vol.
8, no. 1, 758, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00936-3.
short: M. Strüber, J. Sauer, P.M. Jonas, M. Bartos, Nature Communications 8 (2017).
date_created: 2018-12-11T11:48:34Z
date_published: 2017-10-02T00:00:00Z
date_updated: 2023-09-27T10:59:41Z
day: '02'
ddc:
- '571'
department:
- _id: PeJo
doi: 10.1038/s41467-017-00936-3
ec_funded: 1
external_id:
isi:
- '000412053100004'
file:
- access_level: open_access
checksum: 7e2c7621afd5f802338e92e8619f024d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:17Z
date_updated: 2020-07-14T12:48:07Z
file_id: '5135'
file_name: IST-2017-914-v1+1_s41467-017-00936-3.pdf
file_size: 4261832
relation: main_file
file_date_updated: 2020-07-14T12:48:07Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
project:
- _id: 25C0F108-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '268548'
name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6853'
pubrep_id: '914'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Distance-dependent inhibition facilitates focality of gamma oscillations in
the dentate gyrus
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '8016'
abstract:
- lang: eng
text: Long-term modifications of neuronal connections are critical for reliable
memory storage in the brain. However, their locus of expression—pre- or postsynaptic—is
highly variable. Here we introduce a theoretical framework in which long-term
plasticity performs an optimization of the postsynaptic response statistics toward
a given mean with minimal variance. Consequently, the state of the synapse at
the time of plasticity induction determines the ratio of pre- and postsynaptic
modifications. Our theory explains the experimentally observed expression loci
of the hippocampal and neocortical synaptic potentiation studies we examined.
Moreover, the theory predicts presynaptic expression of long-term depression,
consistent with experimental observations. At inhibitory synapses, the theory
suggests a statistically efficient excitatory-inhibitory balance in which changes
in inhibitory postsynaptic response statistics specifically target the mean excitation.
Our results provide a unifying theory for understanding the expression mechanisms
and functions of long-term synaptic transmission plasticity.
article_processing_charge: No
article_type: original
author:
- first_name: Rui Ponte
full_name: Costa, Rui Ponte
last_name: Costa
- first_name: Zahid
full_name: Padamsey, Zahid
last_name: Padamsey
- first_name: James A.
full_name: D’Amour, James A.
last_name: D’Amour
- first_name: Nigel J.
full_name: Emptage, Nigel J.
last_name: Emptage
- first_name: Robert C.
full_name: Froemke, Robert C.
last_name: Froemke
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. Synaptic
transmission optimization predicts expression loci of long-term plasticity. Neuron.
2017;96(1):177-189.e7. doi:10.1016/j.neuron.2017.09.021
apa: Costa, R. P., Padamsey, Z., D’Amour, J. A., Emptage, N. J., Froemke, R. C.,
& Vogels, T. P. (2017). Synaptic transmission optimization predicts expression
loci of long-term plasticity. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2017.09.021
chicago: Costa, Rui Ponte, Zahid Padamsey, James A. D’Amour, Nigel J. Emptage, Robert
C. Froemke, and Tim P Vogels. “Synaptic Transmission Optimization Predicts Expression
Loci of Long-Term Plasticity.” Neuron. Elsevier, 2017. https://doi.org/10.1016/j.neuron.2017.09.021.
ieee: R. P. Costa, Z. Padamsey, J. A. D’Amour, N. J. Emptage, R. C. Froemke, and
T. P. Vogels, “Synaptic transmission optimization predicts expression loci of
long-term plasticity,” Neuron, vol. 96, no. 1. Elsevier, p. 177–189.e7,
2017.
ista: Costa RP, Padamsey Z, D’Amour JA, Emptage NJ, Froemke RC, Vogels TP. 2017.
Synaptic transmission optimization predicts expression loci of long-term plasticity.
Neuron. 96(1), 177–189.e7.
mla: Costa, Rui Ponte, et al. “Synaptic Transmission Optimization Predicts Expression
Loci of Long-Term Plasticity.” Neuron, vol. 96, no. 1, Elsevier, 2017,
p. 177–189.e7, doi:10.1016/j.neuron.2017.09.021.
short: R.P. Costa, Z. Padamsey, J.A. D’Amour, N.J. Emptage, R.C. Froemke, T.P. Vogels,
Neuron 96 (2017) 177–189.e7.
date_created: 2020-06-25T12:54:46Z
date_published: 2017-09-27T00:00:00Z
date_updated: 2021-01-12T08:16:32Z
day: '27'
ddc:
- '570'
doi: 10.1016/j.neuron.2017.09.021
extern: '1'
external_id:
pmid:
- '28957667'
file:
- access_level: open_access
checksum: 49fbca2821066c0965bd5678b32b6b48
content_type: application/pdf
creator: cziletti
date_created: 2020-07-09T09:42:49Z
date_updated: 2020-07-14T12:48:08Z
file_id: '8103'
file_name: 2017_Neuron_Costa.pdf
file_size: 7140149
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 96'
issue: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 177-189.e7
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Synaptic transmission optimization predicts expression loci of long-term plasticity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 96
year: '2017'
...
---
_id: '8017'
abstract:
- lang: eng
text: nhibitory neurons, although relatively few in number, exert powerful control
over brain circuits. They stabilize network activity in the face of strong feedback
excitation and actively engage in computations. Recent studies reveal the importance
of a precise balance of excitation and inhibition in neural circuits, which often
requires exquisite fine-tuning of inhibitory connections. We review inhibitory
synaptic plasticity and its roles in shaping both feedforward and feedback control.
We discuss the necessity of complex, codependent plasticity mechanisms to build
nontrivial, functioning networks, and we end by summarizing experimental evidence
of such interactions.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- first_name: Everton J.
full_name: Agnes, Everton J.
last_name: Agnes
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Hennequin G, Agnes EJ, Vogels TP. Inhibitory plasticity: Balance, control,
and codependence. Annual Review of Neuroscience. 2017;40(1):557-579. doi:10.1146/annurev-neuro-072116-031005'
apa: 'Hennequin, G., Agnes, E. J., & Vogels, T. P. (2017). Inhibitory plasticity:
Balance, control, and codependence. Annual Review of Neuroscience. Annual
Reviews. https://doi.org/10.1146/annurev-neuro-072116-031005'
chicago: 'Hennequin, Guillaume, Everton J. Agnes, and Tim P Vogels. “Inhibitory
Plasticity: Balance, Control, and Codependence.” Annual Review of Neuroscience.
Annual Reviews, 2017. https://doi.org/10.1146/annurev-neuro-072116-031005.'
ieee: 'G. Hennequin, E. J. Agnes, and T. P. Vogels, “Inhibitory plasticity: Balance,
control, and codependence,” Annual Review of Neuroscience, vol. 40, no.
1. Annual Reviews, pp. 557–579, 2017.'
ista: 'Hennequin G, Agnes EJ, Vogels TP. 2017. Inhibitory plasticity: Balance, control,
and codependence. Annual Review of Neuroscience. 40(1), 557–579.'
mla: 'Hennequin, Guillaume, et al. “Inhibitory Plasticity: Balance, Control, and
Codependence.” Annual Review of Neuroscience, vol. 40, no. 1, Annual Reviews,
2017, pp. 557–79, doi:10.1146/annurev-neuro-072116-031005.'
short: G. Hennequin, E.J. Agnes, T.P. Vogels, Annual Review of Neuroscience 40 (2017)
557–579.
date_created: 2020-06-25T12:55:53Z
date_published: 2017-07-01T00:00:00Z
date_updated: 2021-01-12T08:16:32Z
day: '01'
doi: 10.1146/annurev-neuro-072116-031005
extern: '1'
external_id:
pmid:
- '28598717'
intvolume: ' 40'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 557-579
pmid: 1
publication: Annual Review of Neuroscience
publication_identifier:
issn:
- 0147-006X
- 1545-4126
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
status: public
title: 'Inhibitory plasticity: Balance, control, and codependence'
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 40
year: '2017'
...
---
_id: '8018'
abstract:
- lang: eng
text: 'Nervous systems use excitatory cell assemblies to encode and represent sensory
percepts. Similarly, synaptically connected cell assemblies or "engrams" are thought
to represent memories of past experience. Multiple lines of recent evidence indicate
that brain systems create and use inhibitory replicas of excitatory representations
for important cognitive functions. Such matched "inhibitory engrams" can form
through homeostatic potentiation of inhibition onto postsynaptic cells that show
increased levels of excitation. Inhibitory engrams can reduce behavioral responses
to familiar stimuli, thereby resulting in behavioral habituation. In addition,
by preventing inappropriate activation of excitatory memory engrams, inhibitory
engrams can make memories quiescent, stored in a latent form that is available
for context-relevant activation. In neural networks with balanced excitatory and
inhibitory engrams, the release of innate responses and recall of associative
memories can occur through focused disinhibition. Understanding mechanisms that
regulate the formation and expression of inhibitory engrams in vivo may help not
only to explain key features of cognition but also to provide insight into transdiagnostic
traits associated with psychiatric conditions such as autism, schizophrenia, and
posttraumatic stress disorder. '
article_processing_charge: No
article_type: original
author:
- first_name: Helen C.
full_name: Barron, Helen C.
last_name: Barron
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Timothy E.
full_name: Behrens, Timothy E.
last_name: Behrens
- first_name: Mani
full_name: Ramaswami, Mani
last_name: Ramaswami
citation:
ama: Barron HC, Vogels TP, Behrens TE, Ramaswami M. Inhibitory engrams in perception
and memory. Proceedings of the National Academy of Sciences. 2017;114(26):6666-6674.
doi:10.1073/pnas.1701812114
apa: Barron, H. C., Vogels, T. P., Behrens, T. E., & Ramaswami, M. (2017). Inhibitory
engrams in perception and memory. Proceedings of the National Academy of Sciences.
Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1701812114
chicago: Barron, Helen C., Tim P Vogels, Timothy E. Behrens, and Mani Ramaswami.
“Inhibitory Engrams in Perception and Memory.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1701812114.
ieee: H. C. Barron, T. P. Vogels, T. E. Behrens, and M. Ramaswami, “Inhibitory engrams
in perception and memory,” Proceedings of the National Academy of Sciences,
vol. 114, no. 26. Proceedings of the National Academy of Sciences, pp. 6666–6674,
2017.
ista: Barron HC, Vogels TP, Behrens TE, Ramaswami M. 2017. Inhibitory engrams in
perception and memory. Proceedings of the National Academy of Sciences. 114(26),
6666–6674.
mla: Barron, Helen C., et al. “Inhibitory Engrams in Perception and Memory.” Proceedings
of the National Academy of Sciences, vol. 114, no. 26, Proceedings of the
National Academy of Sciences, 2017, pp. 6666–74, doi:10.1073/pnas.1701812114.
short: H.C. Barron, T.P. Vogels, T.E. Behrens, M. Ramaswami, Proceedings of the
National Academy of Sciences 114 (2017) 6666–6674.
date_created: 2020-06-25T12:56:58Z
date_published: 2017-06-27T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '27'
doi: 10.1073/pnas.1701812114
extern: '1'
external_id:
pmid:
- '28611219'
intvolume: ' 114'
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495250/
month: '06'
oa: 1
oa_version: Published Version
page: 6666-6674
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Inhibitory engrams in perception and memory
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 114
year: '2017'
...
---
_id: '8019'
abstract:
- lang: eng
text: Synaptic plasticity is essential for the function of neural systems. It sets
up initial circuitry and adjusts connection strengths according to the maintenance
requirements of its host networks. Like all things biological, synaptic plasticity
must rely on genetic programs to provide the molecular components of its machinery
to integrate ongoing, often multi-sensory experience without destabilising effects.
Because of its fundamental importance to healthy behaviour, understanding plasticity
is thought to hold the key to understanding the brain. There are innumerable ways
to approach this topic and a complete review of its status quo would be impossible.
In the current issue we dig into some of the finer points of synaptic plasticity,
starting small, at the level of genes, and slowly zooming out to synapses, populations
of synapses, and finally entire systems and brain regions. At each level, we tried
to represent different perspectives, different systems, and approaches to the
same questions to give a broad sampling of how synaptic plasticity is being studied.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Leslie C
full_name: Griffith, Leslie C
last_name: Griffith
citation:
ama: 'Vogels TP, Griffith LC. Editorial overview: Neurobiology of learning and plasticity
2017. Current Opinion in Neurobiology. 2017;43:A1-A5. doi:10.1016/j.conb.2017.04.002'
apa: 'Vogels, T. P., & Griffith, L. C. (2017). Editorial overview: Neurobiology
of learning and plasticity 2017. Current Opinion in Neurobiology. Elsevier.
https://doi.org/10.1016/j.conb.2017.04.002'
chicago: 'Vogels, Tim P, and Leslie C Griffith. “Editorial Overview: Neurobiology
of Learning and Plasticity 2017.” Current Opinion in Neurobiology. Elsevier,
2017. https://doi.org/10.1016/j.conb.2017.04.002.'
ieee: 'T. P. Vogels and L. C. Griffith, “Editorial overview: Neurobiology of learning
and plasticity 2017,” Current Opinion in Neurobiology, vol. 43. Elsevier,
pp. A1–A5, 2017.'
ista: 'Vogels TP, Griffith LC. 2017. Editorial overview: Neurobiology of learning
and plasticity 2017. Current Opinion in Neurobiology. 43, A1–A5.'
mla: 'Vogels, Tim P., and Leslie C. Griffith. “Editorial Overview: Neurobiology
of Learning and Plasticity 2017.” Current Opinion in Neurobiology, vol.
43, Elsevier, 2017, pp. A1–5, doi:10.1016/j.conb.2017.04.002.'
short: T.P. Vogels, L.C. Griffith, Current Opinion in Neurobiology 43 (2017) A1–A5.
date_created: 2020-06-25T13:03:30Z
date_published: 2017-04-17T00:00:00Z
date_updated: 2021-01-12T08:16:33Z
day: '17'
doi: 10.1016/j.conb.2017.04.002
extern: '1'
external_id:
pmid:
- '28427877'
intvolume: ' 43'
language:
- iso: eng
month: '04'
oa_version: None
page: A1-A5
pmid: 1
publication: Current Opinion in Neurobiology
publication_identifier:
issn:
- 0959-4388
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Editorial overview: Neurobiology of learning and plasticity 2017'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 43
year: '2017'
...
---
_id: '803'
abstract:
- lang: eng
text: Eukaryotic cells store their chromosomes in a single nucleus. This is important
to maintain genomic integrity, as chromosomes packaged into separate nuclei (micronuclei)
are prone to massive DNA damage. During mitosis, higher eukaryotes disassemble
their nucleus and release individualized chromosomes for segregation. How numerous
chromosomes subsequently reform a single nucleus has remained unclear. Using image-based
screening of human cells, we identified barrier-to-autointegration factor (BAF)
as a key factor guiding membranes to form a single nucleus. Unexpectedly, nuclear
assembly does not require BAF?s association with inner nuclear membrane proteins
but instead relies on BAF?s ability to bridge distant DNA sites. Live-cell imaging
and in vitro reconstitution showed that BAF enriches around the mitotic chromosome
ensemble to induce a densely cross-bridged chromatin layer that is mechanically
stiff and limits membranes to the surface. Our study reveals that BAF-mediated
changes in chromosome mechanics underlie nuclear assembly with broad implications
for proper genome function.
acknowledged_ssus:
- _id: Bio
article_processing_charge: No
author:
- first_name: Matthias
full_name: Samwer, Matthias
last_name: Samwer
- first_name: Maximilian
full_name: Schneider, Maximilian
last_name: Schneider
- first_name: Rudolf
full_name: Hoefler, Rudolf
last_name: Hoefler
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Julian
full_name: Jude, Julian
last_name: Jude
- first_name: Johannes
full_name: Zuber, Johannes
last_name: Zuber
- first_name: Daniel
full_name: Gerlic, Daniel
last_name: Gerlic
citation:
ama: Samwer M, Schneider M, Hoefler R, et al. DNA cross-bridging shapes a single
nucleus from a set of mitotic chromosomes. Cell. 2017;170(5):956-972. doi:10.1016/j.cell.2017.07.038
apa: Samwer, M., Schneider, M., Hoefler, R., Schmalhorst, P. S., Jude, J., Zuber,
J., & Gerlic, D. (2017). DNA cross-bridging shapes a single nucleus from a
set of mitotic chromosomes. Cell. Cell Press. https://doi.org/10.1016/j.cell.2017.07.038
chicago: Samwer, Matthias, Maximilian Schneider, Rudolf Hoefler, Philipp S Schmalhorst,
Julian Jude, Johannes Zuber, and Daniel Gerlic. “DNA Cross-Bridging Shapes a Single
Nucleus from a Set of Mitotic Chromosomes.” Cell. Cell Press, 2017. https://doi.org/10.1016/j.cell.2017.07.038.
ieee: M. Samwer et al., “DNA cross-bridging shapes a single nucleus from
a set of mitotic chromosomes,” Cell, vol. 170, no. 5. Cell Press, pp. 956–972,
2017.
ista: Samwer M, Schneider M, Hoefler R, Schmalhorst PS, Jude J, Zuber J, Gerlic
D. 2017. DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes.
Cell. 170(5), 956–972.
mla: Samwer, Matthias, et al. “DNA Cross-Bridging Shapes a Single Nucleus from a
Set of Mitotic Chromosomes.” Cell, vol. 170, no. 5, Cell Press, 2017, pp.
956–72, doi:10.1016/j.cell.2017.07.038.
short: M. Samwer, M. Schneider, R. Hoefler, P.S. Schmalhorst, J. Jude, J. Zuber,
D. Gerlic, Cell 170 (2017) 956–972.
date_created: 2018-12-11T11:48:35Z
date_published: 2017-08-24T00:00:00Z
date_updated: 2023-09-27T10:59:14Z
day: '24'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1016/j.cell.2017.07.038
external_id:
isi:
- '000408372400014'
file:
- access_level: open_access
checksum: 64897b0c5373f22273f598e4672c60ff
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:45:40Z
date_updated: 2020-07-14T12:48:08Z
file_id: '5852'
file_name: 2017_Cell_Samwer.pdf
file_size: 17666637
relation: main_file
file_date_updated: 2020-07-14T12:48:08Z
has_accepted_license: '1'
intvolume: ' 170'
isi: 1
issue: '5'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 956 - 972
publication: Cell
publication_identifier:
issn:
- '00928674'
publication_status: published
publisher: Cell Press
publist_id: '6848'
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA cross-bridging shapes a single nucleus from a set of mitotic chromosomes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 170
year: '2017'
...
---
_id: '804'
abstract:
- lang: eng
text: Polysaccharides (carbohydrates) are key regulators of a large number of cell
biological processes. However, precise biochemical or genetic manipulation of
these often complex structures is laborious and hampers experimental structure–function
studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool
to generate and test hypotheses on saccharide function. Yet, currently used MD
force fields often overestimate the aggregation propensity of polysaccharides,
affecting the usability of those simulations. Here we tested MARTINI, a popular
coarse-grained (CG) force field for biological macromolecules, for its ability
to accurately represent molecular forces between saccharides. To this end, we
calculated a thermodynamic solution property, the second virial coefficient of
the osmotic pressure (B22). Comparison with light scattering experiments revealed
a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing
at an imbalance of the nonbonded solute–solute, solute–water, and water–water
interactions. This finding also applies to smaller oligosaccharides which were
all found to aggregate in simulations even at moderate concentrations, well below
their solubility limit. Finally, we explored the influence of the Lennard-Jones
(LJ) interaction between saccharide molecules and propose a simple scaling of
the LJ interaction strength that makes MARTINI more reliable for the simulation
of saccharides.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: P.S.S. was supported by research fellowship 2811/1-1 from the German
Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF
187-2013 and Grant GC65-32 from the Interdisciplinary Centre for Mathematical and
Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje
Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions
and the IST Austria Scientific Computing Facility for support.
article_processing_charge: No
author:
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Felix
full_name: Deluweit, Felix
last_name: Deluweit
- first_name: Roger
full_name: Scherrers, Roger
last_name: Scherrers
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
citation:
ama: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming
the limitations of the MARTINI force field in simulations of polysaccharides.
Journal of Chemical Theory and Computation. 2017;13(10):5039-5053. doi:10.1021/acs.jctc.7b00374
apa: Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &
Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in
simulations of polysaccharides. Journal of Chemical Theory and Computation.
American Chemical Society. https://doi.org/10.1021/acs.jctc.7b00374
chicago: Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J
Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force
Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation.
American Chemical Society, 2017. https://doi.org/10.1021/acs.jctc.7b00374.
ieee: P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M.
K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations
of polysaccharides,” Journal of Chemical Theory and Computation, vol. 13,
no. 10. American Chemical Society, pp. 5039–5053, 2017.
ista: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017.
Overcoming the limitations of the MARTINI force field in simulations of polysaccharides.
Journal of Chemical Theory and Computation. 13(10), 5039–5053.
mla: Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI
Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory
and Computation, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53,
doi:10.1021/acs.jctc.7b00374.
short: P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora,
Journal of Chemical Theory and Computation 13 (2017) 5039–5053.
date_created: 2018-12-11T11:48:35Z
date_published: 2017-10-10T00:00:00Z
date_updated: 2023-09-27T10:58:45Z
day: '10'
department:
- _id: CaHe
doi: 10.1021/acs.jctc.7b00374
external_id:
isi:
- '000412965700036'
intvolume: ' 13'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.03773
month: '10'
oa: 1
oa_version: Submitted Version
page: 5039 - 5053
publication: Journal of Chemical Theory and Computation
publication_identifier:
issn:
- '15499618'
publication_status: published
publisher: American Chemical Society
publist_id: '6847'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming the limitations of the MARTINI force field in simulations of polysaccharides
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2017'
...
---
_id: '805'
abstract:
- lang: eng
text: During corticogenesis, distinct classes of neurons are born from progenitor
cells located in the ventricular and subventricular zones, from where they migrate
towards the pial surface to assemble into highly organized layer-specific circuits.
However, the precise and coordinated transcriptional network activity defining
neuronal identity is still not understood. Here, we show that genetic depletion
of the basic helix-loop-helix (bHLH) transcription factor E2A splice variant E47
increased the number of Tbr1-positive deep layer and Satb2-positive upper layer
neurons at E14.5, while depletion of the alternatively spliced E12 variant did
not affect layer-specific neurogenesis. While ChIP-Seq identified a big overlap
for E12- and E47-specific binding sites in embryonic NSCs, including sites at
the cyclin-dependent kinase inhibitor (CDKI) Cdkn1c gene locus, RNA-Seq revealed
a unique transcriptional regulation by each splice variant. E47 activated the
expression of the CDKI Cdkn1c through binding to a distal enhancer. Finally, overexpression
of E47 in embryonic NSCs in vitro impaired neurite outgrowth and E47 overexpression
in vivo by in utero electroporation disturbed proper layer-specific neurogenesis
and upregulated p57(KIP2) expression. Overall, this study identified E2A target
genes in embryonic NSCs and demonstrates that E47 regulates neuronal differentiation
via p57(KIP2).
article_processing_charge: No
author:
- first_name: Sabrina
full_name: Pfurr, Sabrina
last_name: Pfurr
- first_name: Yu
full_name: Chu, Yu
last_name: Chu
- first_name: Christian
full_name: Bohrer, Christian
last_name: Bohrer
- first_name: Franziska
full_name: Greulich, Franziska
last_name: Greulich
- first_name: Robert J
full_name: Beattie, Robert J
id: 2E26DF60-F248-11E8-B48F-1D18A9856A87
last_name: Beattie
orcid: 0000-0002-8483-8753
- first_name: Könül
full_name: Mammadzada, Könül
last_name: Mammadzada
- first_name: Miriam
full_name: Hils, Miriam
last_name: Hils
- first_name: Sebastian
full_name: Arnold, Sebastian
last_name: Arnold
- first_name: Verdon
full_name: Taylor, Verdon
last_name: Taylor
- first_name: Kristina
full_name: Schachtrup, Kristina
last_name: Schachtrup
- first_name: N Henriette
full_name: Uhlenhaut, N Henriette
last_name: Uhlenhaut
- first_name: Christian
full_name: Schachtrup, Christian
last_name: Schachtrup
citation:
ama: Pfurr S, Chu Y, Bohrer C, et al. The E2A splice variant E47 regulates the differentiation
of projection neurons via p57(KIP2) during cortical development. Development.
2017;144:3917-3931. doi:10.1242/dev.145698
apa: Pfurr, S., Chu, Y., Bohrer, C., Greulich, F., Beattie, R. J., Mammadzada, K.,
… Schachtrup, C. (2017). The E2A splice variant E47 regulates the differentiation
of projection neurons via p57(KIP2) during cortical development. Development.
Company of Biologists. https://doi.org/10.1242/dev.145698
chicago: Pfurr, Sabrina, Yu Chu, Christian Bohrer, Franziska Greulich, Robert J
Beattie, Könül Mammadzada, Miriam Hils, et al. “The E2A Splice Variant E47 Regulates
the Differentiation of Projection Neurons via P57(KIP2) during Cortical Development.”
Development. Company of Biologists, 2017. https://doi.org/10.1242/dev.145698.
ieee: S. Pfurr et al., “The E2A splice variant E47 regulates the differentiation
of projection neurons via p57(KIP2) during cortical development,” Development,
vol. 144. Company of Biologists, pp. 3917–3931, 2017.
ista: Pfurr S, Chu Y, Bohrer C, Greulich F, Beattie RJ, Mammadzada K, Hils M, Arnold
S, Taylor V, Schachtrup K, Uhlenhaut NH, Schachtrup C. 2017. The E2A splice variant
E47 regulates the differentiation of projection neurons via p57(KIP2) during cortical
development. Development. 144, 3917–3931.
mla: Pfurr, Sabrina, et al. “The E2A Splice Variant E47 Regulates the Differentiation
of Projection Neurons via P57(KIP2) during Cortical Development.” Development,
vol. 144, Company of Biologists, 2017, pp. 3917–31, doi:10.1242/dev.145698.
short: S. Pfurr, Y. Chu, C. Bohrer, F. Greulich, R.J. Beattie, K. Mammadzada, M.
Hils, S. Arnold, V. Taylor, K. Schachtrup, N.H. Uhlenhaut, C. Schachtrup, Development
144 (2017) 3917–3931.
date_created: 2018-12-11T11:48:36Z
date_published: 2017-10-31T00:00:00Z
date_updated: 2023-09-26T16:20:09Z
day: '31'
department:
- _id: SiHi
doi: 10.1242/dev.145698
external_id:
isi:
- '000414025600007'
intvolume: ' 144'
isi: 1
language:
- iso: eng
month: '10'
oa_version: None
page: 3917 - 3931
publication: Development
publication_status: published
publisher: Company of Biologists
publist_id: '6846'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The E2A splice variant E47 regulates the differentiation of projection neurons
via p57(KIP2) during cortical development
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 144
year: '2017'
...
---
_id: '807'
abstract:
- lang: eng
text: 'On January the 1st, 2016 a new agreement between 32 Austrian scientific libraries
and the publisher Springer took its effect: this deal covers accessing the licensed
content on the one hand, and publishing open access on the other hand. More than
1000 papers by Austrian authors were published open access at Springer in the
first year alone. The working group "Springer Compact Evaluierung" made
the data for these articles available via the platform OpenAPC and would like
to use this opportunity to give a short account of what this publishing agreement
actually entails and the working group intends to do.'
author:
- first_name: Magdalena
full_name: Andrae, Magdalena
last_name: Andrae
- first_name: Márton
full_name: Villányi, Márton
id: 3FFCCD3A-F248-11E8-B48F-1D18A9856A87
last_name: Villányi
orcid: 0000-0001-8126-0426
citation:
ama: Andrae M, Villányi M. Der Springer Compact-Deal – Ein erster Einblick in die
Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung Österreichischer
Bibliothekarinnen und Bibliothekare. 2017;70(2):274-280. doi:10.31263/voebm.v70i2.1898
apa: Andrae, M., & Villányi, M. (2017). Der Springer Compact-Deal – Ein erster
Einblick in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen Der
Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB. https://doi.org/10.31263/voebm.v70i2.1898
chicago: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein
Erster Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen
Der Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare. VÖB,
2017. https://doi.org/10.31263/voebm.v70i2.1898.
ieee: M. Andrae and M. Villányi, “Der Springer Compact-Deal – Ein erster Einblick
in die Evaluierung einer Offsetting-Vereinbarung,” Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare, vol. 70, no. 2. VÖB,
pp. 274–280, 2017.
ista: Andrae M, Villányi M. 2017. Der Springer Compact-Deal – Ein erster Einblick
in die Evaluierung einer Offsetting-Vereinbarung. Mitteilungen der Vereinigung
Österreichischer Bibliothekarinnen und Bibliothekare. 70(2), 274–280.
mla: Andrae, Magdalena, and Márton Villányi. “Der Springer Compact-Deal – Ein Erster
Einblick in Die Evaluierung Einer Offsetting-Vereinbarung.” Mitteilungen Der
Vereinigung Österreichischer Bibliothekarinnen Und Bibliothekare, vol. 70,
no. 2, VÖB, 2017, pp. 274–80, doi:10.31263/voebm.v70i2.1898.
short: M. Andrae, M. Villányi, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen
Und Bibliothekare 70 (2017) 274–280.
date_created: 2018-12-11T11:48:36Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2021-01-12T08:16:45Z
day: '01'
ddc:
- '020'
department:
- _id: E-Lib
doi: 10.31263/voebm.v70i2.1898
file:
- access_level: open_access
checksum: 558c18bcf5580d87dd371ec626d52075
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T13:39:26Z
date_updated: 2020-07-14T12:48:09Z
file_id: '5851'
file_name: 2017_VOEB_Andrae.pdf
file_size: 125065
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 70'
issue: '2'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 274 - 280
popular_science: '1'
publication: Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
publication_identifier:
issn:
- '10222588'
publication_status: published
publisher: VÖB
publist_id: '6843'
scopus_import: 1
status: public
title: Der Springer Compact-Deal – Ein erster Einblick in die Evaluierung einer Offsetting-Vereinbarung
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 70
year: '2017'
...
---
_id: '8075'
abstract:
- lang: eng
text: Ion channel models are the building blocks of computational neuron models.
Their biological fidelity is therefore crucial for the interpretation of simulations.
However, the number of published models, and the lack of standardization, make
the comparison of ion channel models with one another and with experimental data
difficult. Here, we present a framework for the automated large-scale classification
of ion channel models. Using annotated metadata and responses to a set of voltage-clamp
protocols, we assigned 2378 models of voltage- and calcium-gated ion channels
coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface
provides an interactive resource for the categorization of new and existing models
and experimental recordings. It enables quantitative comparisons of simulated
and/or measured ion channel kinetics, and facilitates field-wide standardization
of experimentally-constrained modeling.
article_number: e22152
article_processing_charge: No
article_type: original
author:
- first_name: William F
full_name: Podlaski, William F
last_name: Podlaski
- first_name: Alexander
full_name: Seeholzer, Alexander
last_name: Seeholzer
- first_name: Lukas N
full_name: Groschner, Lukas N
last_name: Groschner
- first_name: Gero
full_name: Miesenböck, Gero
last_name: Miesenböck
- first_name: Rajnish
full_name: Ranjan, Rajnish
last_name: Ranjan
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP.
Mapping the function of neuronal ion channels in model and experiment. eLife.
2017;6. doi:10.7554/elife.22152
apa: Podlaski, W. F., Seeholzer, A., Groschner, L. N., Miesenböck, G., Ranjan, R.,
& Vogels, T. P. (2017). Mapping the function of neuronal ion channels in model
and experiment. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.22152
chicago: Podlaski, William F, Alexander Seeholzer, Lukas N Groschner, Gero Miesenböck,
Rajnish Ranjan, and Tim P Vogels. “Mapping the Function of Neuronal Ion Channels
in Model and Experiment.” ELife. eLife Sciences Publications, Ltd, 2017.
https://doi.org/10.7554/elife.22152.
ieee: W. F. Podlaski, A. Seeholzer, L. N. Groschner, G. Miesenböck, R. Ranjan, and
T. P. Vogels, “Mapping the function of neuronal ion channels in model and experiment,”
eLife, vol. 6. eLife Sciences Publications, Ltd, 2017.
ista: Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP.
2017. Mapping the function of neuronal ion channels in model and experiment. eLife.
6, e22152.
mla: Podlaski, William F., et al. “Mapping the Function of Neuronal Ion Channels
in Model and Experiment.” ELife, vol. 6, e22152, eLife Sciences Publications,
Ltd, 2017, doi:10.7554/elife.22152.
short: W.F. Podlaski, A. Seeholzer, L.N. Groschner, G. Miesenböck, R. Ranjan, T.P.
Vogels, ELife 6 (2017).
date_created: 2020-06-30T13:32:18Z
date_published: 2017-03-06T00:00:00Z
date_updated: 2021-01-12T08:16:46Z
day: '06'
ddc:
- '570'
doi: 10.7554/elife.22152
extern: '1'
external_id:
pmid:
- '28267430'
file:
- access_level: open_access
checksum: e5c5a33bcb3ac38ad62df1010ab29040
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T12:08:40Z
date_updated: 2020-07-16T12:08:40Z
file_id: '8124'
file_name: 2017_elife_Podlaski.pdf
file_size: 16034505
relation: main_file
success: 1
file_date_updated: 2020-07-16T12:08:40Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications, Ltd
quality_controlled: '1'
status: public
title: Mapping the function of neuronal ion channels in model and experiment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 6
year: '2017'
...
---
_id: '8129'
abstract:
- lang: eng
text: "Cortical circuits exhibit intricate recurrent architectures that are remarkably
similar across different brain areas. Such stereotyped structure suggests the
existence of common computational principles. However, such principles have remained
largely elusive. Inspired by gated-memory networks, namely long short-term memory
networks (LSTMs), we introduce a recurrent neural network in which information
is gated through inhibitory cells that are subtractive (subLSTM). We propose a
natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical
microcircuits. Our empirical evaluation across sequential image classification
and language modelling tasks shows that subLSTM units can achieve similar performance
to LSTM units. These results suggest that cortical circuits can be optimised to
solve complex contextual problems and proposes a novel view on their computational
function.\r\nOverall our work provides a step towards unifying recurrent networks
as used in machine learning with their biological counterparts."
article_processing_charge: No
arxiv: 1
author:
- first_name: Rui Ponte
full_name: Costa, Rui Ponte
last_name: Costa
- first_name: Yannis M.
full_name: Assael, Yannis M.
last_name: Assael
- first_name: Brendan
full_name: Shillingford, Brendan
last_name: Shillingford
- first_name: Nando de
full_name: Freitas, Nando de
last_name: Freitas
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits
as gated-recurrent neural networks. In: Advances in Neural Information Processing
Systems. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283.'
apa: 'Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, & Vogels,
T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In Advances
in Neural Information Processing Systems (Vol. 30, pp. 272–283). Long Beach,
CA, United States: Neural Information Processing Systems Foundation.'
chicago: Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas,
and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.”
In Advances in Neural Information Processing Systems, 30:272–83. Neural
Information Processing Systems Foundation, 2017.
ieee: R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels,
“Cortical microcircuits as gated-recurrent neural networks,” in Advances in
Neural Information Processing Systems, Long Beach, CA, United States, 2017,
vol. 30, pp. 272–283.
ista: 'Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical
microcircuits as gated-recurrent neural networks. Advances in Neural Information
Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.'
mla: Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural
Networks.” Advances in Neural Information Processing Systems, vol. 30,
Neural Information Processing Systems Foundation, 2017, pp. 272–83.
short: R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:,
Advances in Neural Information Processing Systems, Neural Information Processing
Systems Foundation, 2017, pp. 272–283.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NIPS: Neural Information Processing System'
start_date: 2017-12-04
date_created: 2020-07-16T19:13:10Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:17:03Z
day: '01'
extern: '1'
external_id:
arxiv:
- '1711.02448'
intvolume: ' 30'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1711.02448
month: '12'
oa: 1
oa_version: Preprint
page: 272-283
publication: Advances in Neural Information Processing Systems
publication_identifier:
issn:
- '10495258'
publication_status: published
publisher: Neural Information Processing Systems Foundation
quality_controlled: '1'
status: public
title: Cortical microcircuits as gated-recurrent neural networks
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2017'
...
---
_id: '817'
abstract:
- lang: eng
text: Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular
complexes to be imaged in three-dimensions in their native environments. Cryo-electron
tomograms are reconstructed from projection images taken at defined tilt-angles.
In order to recover high-resolution information from cryo-electron tomograms,
it is necessary to measure and correct for the contrast transfer function (CTF)
of the microscope. Most commonly, this is performed using protocols that approximate
the sample as a two-dimensional (2D) plane. This approximation accounts for differences
in defocus and therefore CTF across the tilted sample. It does not account for
differences in defocus of objects at different heights within the sample; instead,
a 3D approach is required. Currently available approaches for 3D-CTF correction
are computationally expensive and have not been widely implemented. Here we simulate
the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and
present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF,
that is compatible with standard tomogram reconstruction workflows in IMOD. We
validate the approach on synthetic data and test it using subtomogram averaging
of real data. Consistent with our simulations, we find that 3D-CTF correction
allows high-resolution structures to be obtained with much smaller subtomogram
averaging datasets than are required using 2D-CTF. We also show that using equivalent
dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures.
We present a 3.4. Å resolution structure determined by subtomogram averaging.
author:
- first_name: Beata
full_name: Turoňová, Beata
last_name: Turoňová
- first_name: Florian
full_name: Schur, Florian
id: 48AD8942-F248-11E8-B48F-1D18A9856A87
last_name: Schur
orcid: 0000-0003-4790-8078
- first_name: William
full_name: Wan, William
last_name: Wan
- first_name: John
full_name: Briggs, John
last_name: Briggs
citation:
ama: Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron
tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal
of Structural Biology. 2017;199(3):187-195. doi:10.1016/j.jsb.2017.07.007
apa: Turoňová, B., Schur, F. K., Wan, W., & Briggs, J. (2017). Efficient 3D-CTF
correction for cryo-electron tomography using NovaCTF improves subtomogram averaging
resolution to 3.4Å. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2017.07.007
chicago: Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient
3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram
Averaging Resolution to 3.4Å.” Journal of Structural Biology. Academic
Press, 2017. https://doi.org/10.1016/j.jsb.2017.07.007.
ieee: B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction
for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
to 3.4Å,” Journal of Structural Biology, vol. 199, no. 3. Academic Press,
pp. 187–195, 2017.
ista: Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for
cryo-electron tomography using NovaCTF improves subtomogram averaging resolution
to 3.4Å. Journal of Structural Biology. 199(3), 187–195.
mla: Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography
Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” Journal of
Structural Biology, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:10.1016/j.jsb.2017.07.007.
short: B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology
199 (2017) 187–195.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-01T00:00:00Z
date_updated: 2021-01-12T08:17:16Z
day: '01'
ddc:
- '570'
doi: 10.1016/j.jsb.2017.07.007
extern: '1'
file:
- access_level: open_access
checksum: 7f2d4bbac767f9acc254d1a4114d181a
content_type: application/pdf
creator: kschuh
date_created: 2019-03-22T09:29:44Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6168'
file_name: 2017_Elsevier_Turonova.pdf
file_size: 1310009
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
intvolume: ' 199'
issue: '3'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 187-195
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '6832'
quality_controlled: '1'
status: public
title: Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves
subtomogram averaging resolution to 3.4Å
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 199
year: '2017'
...
---
_id: '818'
abstract:
- lang: eng
text: 'Antibiotics have diverse effects on bacteria, including massive changes in
bacterial gene expression. Whereas the gene expression changes under many antibiotics
have been measured, the temporal organization of these responses and their dependence
on the bacterial growth rate are unclear. As described in Chapter 1, we quantified
the temporal gene expression changes in the bacterium Escherichia coli in response
to the sudden exposure to antibiotics using a fluorescent reporter library and
a robotic system. Our data show temporally structured gene expression responses,
with response times for individual genes ranging from tens of minutes to several
hours. We observed that many stress response genes were activated in response
to antibiotics. As certain stress responses cross-protect bacteria from other
stressors, we then asked whether cellular responses to antibiotics have a similar
protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid
stress response protects bacteria from subsequent acid stress. We combined microfluidics
with time-lapse imaging to monitor survival, intracellular pH, and acid stress
response in single cells. This approach revealed that the variable expression
of the acid resistance operon gadBC strongly correlates with single-cell survival
time. Cells with higher gadBC expression following trimethoprim maintain higher
intracellular pH and survive the acid stress longer. Overall, we provide a way
to identify single-cell cross-protection between antibiotics and environmental
stressors from temporal gene expression data, and show how antibiotics can increase
bacterial fitness in changing environments. While gene expression changes to antibiotics
show a clear temporal structure at the population-level, it is unclear whether
this clear temporal order is followed by every single cell. Using dual-reporter
strains described in Chapter 3, we measured gene expression dynamics of promoter
pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that
the oxidative stress response and the DNA stress response showed little timing
variability and a clear temporal order under the antibiotic nitrofurantoin. In
contrast, the acid stress response under trimethoprim ran independently from all
other activated response programs including the DNA stress response, which showed
particularly high timing variability in this stress condition. In summary, this
approach provides insight into the temporal organization of gene expression programs
at the single-cell level and suggests dependencies between response programs and
the underlying variability-introducing mechanisms. Altogether, this work advances
our understanding of the diverse effects that antibiotics have on bacteria. These
results were obtained by taking into account gene expression dynamics, which allowed
us to identify general principles, molecular mechanisms, and dependencies between
genes. Our findings may have implications for infectious disease treatments, and
microbial communities in the human body and in nature. '
acknowledgement: 'First of all, I would like to express great gratitude to my PhD
supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom
to explore different scientific directions during this project, and follow the research
lines of my interest. I am thankful for constructive and often extensive discussions
and his support and commitment during the different stages of my PhD. I want to
thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest
and their valuable input to this project. Special thanks to Nassos for career guidance,
and for accepting me in his lab. A big thank you goes to the past, present and affiliated
members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová,
Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr,
Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed
working and discussing with you very much and I will miss our lengthy group meetings,
our inspiring journal clubs, and our common lunches. Special thanks to Bor for great
mental and professional support during the hard months of thesis writing, and to
Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial
Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and
collaborator Georg Rieckh for his enthusiasm and for getting so involved in these
projects, for his endurance and for his company throughout the years. Thanks to
the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular
I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange,
and enjoyable time together. Thanks to everybody who contributed to the cover for
Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh,
Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by
the graphic designer Martina Markus from the University of Cologne. Thanks to all
my office mates in the first floor Bertalanffy building throughout the years: for
ensuring a pleasant working atmosphere, and for your company! In general, I want
to thank all the people that make IST such a great environment, with the many possibilities
to shape our own social and research environment. I want to thank my family for
all kind of practical support during the years, and my second family in Argentina
for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being
great siblings, and to Helena and Valentin for the joy you brought to my life. My
deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and
for believing in me. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Karin
full_name: Mitosch, Karin
id: 39B66846-F248-11E8-B48F-1D18A9856A87
last_name: Mitosch
citation:
ama: Mitosch K. Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics. 2017. doi:10.15479/AT:ISTA:th_862
apa: Mitosch, K. (2017). Timing, variability and cross-protection in bacteria
– insights from dynamic gene expression responses to antibiotics. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_862
chicago: Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria –
Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of
Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_862.
ieee: K. Mitosch, “Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics,” Institute of Science and
Technology Austria, 2017.
ista: Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights
from dynamic gene expression responses to antibiotics. Institute of Science and
Technology Austria.
mla: Mitosch, Karin. Timing, Variability and Cross-Protection in Bacteria – Insights
from Dynamic Gene Expression Responses to Antibiotics. Institute of Science
and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_862.
short: K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights
from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and
Technology Austria, 2017.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-27T00:00:00Z
date_updated: 2023-09-07T12:00:26Z
day: '27'
ddc:
- '571'
- '579'
degree_awarded: PhD
department:
- _id: ToBo
doi: 10.15479/AT:ISTA:th_862
file:
- access_level: closed
checksum: da3993c5f90f59a8e8623cc31ad501dd
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: dernst
date_created: 2019-04-05T08:48:51Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6210'
file_name: Thesis_KarinMitosch.docx
file_size: 6331071
relation: source_file
- access_level: open_access
checksum: 24c3d9e51992f1b721f3df55aa13fcb8
content_type: application/pdf
creator: dernst
date_created: 2019-04-05T08:48:51Z
date_updated: 2020-07-14T12:48:09Z
file_id: '6211'
file_name: Thesis_KarinMitosch.pdf
file_size: 9289852
relation: main_file
file_date_updated: 2020-07-14T12:48:09Z
has_accepted_license: '1'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: '113'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6831'
pubrep_id: '862'
related_material:
record:
- id: '2001'
relation: part_of_dissertation
status: public
- id: '666'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
title: Timing, variability and cross-protection in bacteria – insights from dynamic
gene expression responses to antibiotics
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: '2017'
...
---
_id: '819'
abstract:
- lang: eng
text: 'Contagious diseases must transmit from infectious to susceptible hosts in
order to reproduce. Whilst vectored pathogens can rely on intermediaries to find
new hosts for them, many infectious pathogens require close contact or direct
interaction between hosts for transmission. Hence, this means that conspecifics
are often the main source of infection for most animals and so, in theory, animals
should avoid conspecifics to reduce their risk of infection. Of course, in reality
animals must interact with one another, as a bare minimum, to mate. However, being
social provides many additional benefits and group living has become a taxonomically
diverse and widespread trait. How then do social animals overcome the issue of
increased disease? Over the last few decades, the social insects (ants, termites
and some bees and wasps) have become a model system for studying disease in social
animals. On paper, a social insect colony should be particularly susceptible to
disease, given that they often contain thousands of potential hosts that are closely
related and frequently interact, as well as exhibiting stable environmental conditions
that encourage microbial growth. Yet, disease outbreaks appear to be rare and
attempts to eradicate pest species using pathogens have failed time and again.
Evolutionary biologists investigating this observation have discovered that the
reduced disease susceptibility in social insects is, in part, due to collectively
performed disease defences of the workers. These defences act like a “social immune
system” for the colony, resulting in a per capita decrease in disease, termed
social immunity. Our understanding of social immunity, and its importance in relation
to the immunological defences of each insect, continues to grow, but there remain
many open questions. In this thesis I have studied disease defence in garden ants.
In the first data chapter, I use the invasive garden ant, Lasius neglectus, to
investigate how colonies mitigate lethal infections and prevent them from spreading
systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour
that uses endogenously produced acidic poison to kill diseased brood and to prevent
the pathogen from replicating. In the second experimental chapter, I continue
to study the use of poison in invasive garden ant colonies, finding that it is
sprayed prophylactically within the nest. However, this spraying has negative
effects on developing pupae when they have had their cocoons artificially removed.
Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon
spinning in this species. In the next experimental chapter, I investigated how
colony founding black garden ant queens (Lasius niger) prevent disease when a
co-foundress dies. I show that ant queens prophylactically perform undertaking
behaviours, similar to those performed by the workers in mature nests. When a
co-foundress was infected, these undertaking behaviours improved the survival
of the healthy queen. In the final data chapter, I explored how immunocompetence
(measured as antifungal activity) changes as incipient black garden ant colonies
grow and mature, from the solitary queen phase to colonies with several hundred
workers. Queen and worker antifungal activity varied throughout this time period,
but despite social immunity, did not decrease as colonies matured. In addition
to the above data chapters, this thesis includes two co-authored reviews. In the
first, we examine the state of the art in the field of social immunity and how
it might develop in the future. In the second, we identify several challenges
and open questions in the study of disease defence in animals. We highlight how
social insects offer a unique model to tackle some of these problems, as disease
defence can be studied from the cell to the society. '
acknowledgement: "ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely
spoilt to work in a lab with such good resources and I must thank the wonderful
Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help
and keeping the lab up and running. You guys will probably be the most missed once
I realise just how much work you have been saving me! For the same reason, I must
say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding
my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you
will be sorely missed now that I will have to take this task on myself. Of course,
I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing
and being a constant source of guidance and inspiration. You have given me the perfect
balance of independence and supervision. I cannot thank you enough for creating
such a great working environment and allowing me the freedom to follow my own research
questions. I have had so many exceptional opportunities – attending and presenting
at conferences all over the world, inviting me to write the ARE with you, going
to workshops in Panama and Switzerland, and even organising our own PhD course –
that I often think I must have had the best PhD in the world. You have taught me
so much and made me a scientist. I sincerely hope we get the chance to work together
again in the future. Thank you for everything. I must also thank my PhD Committee,
Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout
the duration of my PhD. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Christopher
full_name: Pull, Christopher
id: 3C7F4840-F248-11E8-B48F-1D18A9856A87
last_name: Pull
orcid: 0000-0003-1122-3982
citation:
ama: Pull C. Disease defence in garden ants. 2017. doi:10.15479/AT:ISTA:th_861
apa: Pull, C. (2017). Disease defence in garden ants. Institute of Science
and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_861
chicago: Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science
and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_861.
ieee: C. Pull, “Disease defence in garden ants,” Institute of Science and Technology
Austria, 2017.
ista: Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology
Austria.
mla: Pull, Christopher. Disease Defence in Garden Ants. Institute of Science
and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_861.
short: C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology
Austria, 2017.
date_created: 2018-12-11T11:48:40Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-28T11:31:32Z
day: '26'
ddc:
- '576'
- '577'
- '578'
- '579'
- '590'
- '592'
degree_awarded: PhD
department:
- _id: SyCr
doi: 10.15479/AT:ISTA:th_861
file:
- access_level: closed
checksum: 4993cdd5382295758ecc3ecbd2a9aaff
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
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date_created: 2019-04-05T07:53:04Z
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relation: part_of_dissertation
status: public
- id: '806'
relation: part_of_dissertation
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- id: '734'
relation: part_of_dissertation
status: public
- id: '732'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Sylvia M
full_name: Cremer, Sylvia M
id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87
last_name: Cremer
orcid: 0000-0002-2193-3868
title: Disease defence in garden ants
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: '2017'
...
---
_id: '820'
abstract:
- lang: eng
text: "The lac operon is a classic model system for bacterial gene regulation, and
has been studied extensively in E. coli, a classic model organism. However, not
much is known about E. coli’s ecology and life outside the laboratory, in particular
in soil and water environments. The natural diversity of the lac operon outside
the laboratory, its role in the ecology of E. coli and the selection pressures
it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore
the genetic diversity, phylogenetic history and signatures of selection of the
lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia.
I found that complete lac operons were present in all isolates examined, which
in all but one case were functional. The lac operon phylogeny conformed to the
whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal
gene transfer as an explanation for the presence of functional lac operons in
these clades. All lac operon genes showed a signature of purifying selection;
this signature was strongest for the lacY gene. Lac operon genes of human and
environmental isolates showed similar signatures of selection, except the lacZ
gene, which showed a stronger signature of selection in environmental isolates.\r\nIn
Chapter Three, I try to identify the natural genetic variation relevant for phenotype
and fitness in the lac operon, comparing growth rate on lactose and LacZ activity
of the lac operons of these wild isolates in a common genetic background. Sequence
variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase
binding motif, predicted variation in LacZ activity at full induction, using a
thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation
in LacZ activity, nor RNA polymerase binding predicted by the model correlated
with variation in growth rate. Lac operons of human and environmental isolates
did not differ systematically in either growth rate on lactose or LacZ protein
activity, suggesting that these lac operons have been exposed to similar selection
pressures. We thus have no evidence that the phenotypic variation we measured
is relevant for fitness.\r\nTo start assessing the effect of genomic background
on the growth phenotype conferred by the lac operon, I compared growth on minimal
medium with lactose between lac operon constructs and the corresponding original
isolates, I found that maximal growth rate was determined by genomic background,
with almost all backgrounds conferring higher growth rates than lab strain K12
MG1655. However, I found no evidence that the lactose concentration at which growth
was half maximal depended on genomic background."
acknowledgement: "ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon
Bollback for giving me the chance to do this work, for sharing the ideas that lay
at the basis of this work, for his honesty and openness, showing himself to me as
a person and not just as a boss. Thanks to Nick Barton for his guidance at the last
stage, reading and commenting extensively on several versions of this manuscript,
and for his encouragement; thanks to both Jon and Nick for their kindness and patience.
Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be
in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter
my thesis committee at the last moment, and for his very sharp, helpful and relevant
comments during and after the defense. Thanks to my collaborators and discussion
partners: Anne Kupczok, for her guidance, ideas and discussions during the construction
of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh
for making me aware of the issue of parameter identifiability, suggesting how to
solve it, and for his unfortunate idea to start the plasmid enterprise in the first
place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments
on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting,
fast forwarding the analysis to turbo speed and making beautiful figures, and making
the discussion fun on top of it all; Vanessa Barone for her last minute comments,
especially on Chapter Three, providing a sharp and very helpful experimentalist
perspective at the last moment; Maros Pleska and Marjon de Vos for their comments
on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation
between growth rate and lactose concentration; Bor Kavcic for his input on growth
rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton,
Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific
environment to work in, as well as a lot of warmth and colour to everyday life.
And thanks to the friends I found here, to the people who were there for me and
to the people who changed my life, making it stranger and more beautiful than I
could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof,
Karin, Irene, Misha, Mato, Guillaume and Zanin. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Fabienne
full_name: Jesse, Fabienne
id: 4C8C26A4-F248-11E8-B48F-1D18A9856A87
last_name: Jesse
citation:
ama: Jesse F. The lac operon in the wild. 2017. doi:10.15479/AT:ISTA:th_857
apa: Jesse, F. (2017). The lac operon in the wild. Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:th_857
chicago: Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and
Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_857.
ieee: F. Jesse, “The lac operon in the wild,” Institute of Science and Technology
Austria, 2017.
ista: Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology
Austria.
mla: Jesse, Fabienne. The Lac Operon in the Wild. Institute of Science and
Technology Austria, 2017, doi:10.15479/AT:ISTA:th_857.
short: F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology
Austria, 2017.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-08-25T00:00:00Z
date_updated: 2023-09-07T12:01:21Z
day: '25'
ddc:
- '576'
- '577'
- '579'
degree_awarded: PhD
department:
- _id: JoBo
doi: 10.15479/AT:ISTA:th_857
ec_funded: 1
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language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: '87'
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6829'
pubrep_id: '857'
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
title: The lac operon in the wild
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: '2017'
...
---
_id: '821'
abstract:
- lang: eng
text: "This dissertation focuses on algorithmic aspects of program verification,
and presents modeling and complexity advances on several problems related to the\r\nstatic
analysis of programs, the stateless model checking of concurrent programs, and
the competitive analysis of real-time scheduling algorithms.\r\nOur contributions
can be broadly grouped into five categories.\r\n\r\nOur first contribution is
a set of new algorithms and data structures for the quantitative and data-flow
analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt
has been observed that the control-flow graphs of typical programs have special
structure, and are characterized as graphs of small treewidth.\r\nWe utilize this
structural property to provide faster algorithms for the quantitative and data-flow
analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic
treatment of the considered problem,\r\nwhere several interesting analyses, such
as the reachability, shortest path, and certain kind of data-flow analysis problems
follow as special cases. \r\nWe exploit the constant-treewidth property to obtain
algorithmic improvements for on-demand versions of the problems, \r\nand provide
data structures with various tradeoffs between the resources spent in the preprocessing
and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative
problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff,
minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur
second contribution is a set of algorithms for Dyck reachability with applications
to data-dependence analysis and alias analysis.\r\nIn particular, we develop an
optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous
in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we
develop an efficient algorithm for context-sensitive data-dependence analysis
via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library
code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in
almost linear time, after which the contribution of the library in the complexity
of the client analysis is (i)~linear in the number of call sites and (ii)~only
logarithmic in the size of the whole library, as opposed to linear in the size
of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix
Multiplication-hard in general, and the hardness also holds for graphs of constant
treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial
algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur
third contribution is the formalization and algorithmic treatment of the Quantitative
Interprocedural Analysis framework.\r\nIn this framework, the transitions of a
recursive program are annotated as good, bad or neutral, and receive a weight
which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative
Interprocedural Analysis problem asks to determine whether there exists an infinite
run of the program where the long-run ratio of the bad weights over the good weights
is above a given threshold.\r\nWe illustrate how several quantitative problems
related to static analysis of recursive programs can be instantiated in this framework,\r\nand
present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution
is a new dynamic partial-order reduction for the stateless model checking of concurrent
programs. Traditional approaches rely on the standard Mazurkiewicz equivalence
between traces, by means of partitioning the trace space into equivalence classes,
and attempting to explore a few representatives from each class.\r\nWe present
a new dynamic partial-order reduction method called the Data-centric Partial
Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between
traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning
of the trace space than any exploration method based on the standard Mazurkiewicz
equivalence.\r\nDepending on the program, the new partitioning can be even exponentially
coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored
class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic
verification techniques in the competitive analysis and synthesis of real-time
scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage
automata on infinite words to compute the competitive ratio of real-time schedulers
subject to various environmental constraints.\r\nOn the synthesis side, we introduce
a new instance of two-player mean-payoff partial-information games, and show\r\nhow
the synthesis of an optimal real-time scheduler can be reduced to computing winning
strategies in this new type of games."
acknowledgement: "First, I am thankful to my advisor, Krishnendu Chatterjee, for offering
me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide
range of interesting topics, as well as for his constant availability and continuous
support throughout my doctoral studies. I have had the privilege of collaborating
with, discussing and getting inspired by all members of my committee: Thomas A.
Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people
has been very instrumental both to the research carried out for this dissertation,
and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my
numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to
results on low-treewidth graphs presented here. I thank Alex Kößler for our\r\ndiscussions
on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration
on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our
initial discussions on partial order reduction techniques in stateless model checking.
I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful
collaborations on\r\ntopics outside the scope of this dissertation, as well as the
interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary
and Marek Chalupa, with whom I have shared my excitement on various research topics.
Together with my collaborators, I thank officemates and members of the Chatterjee
and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha
Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta, Arjun Radhakrishna,
\ Petr Novontý, Christian Hilbe, Jakob Ruess, Martin Chmelik,\r\nCezara Dragoi,
Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei
Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong,
Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey. Besides collaborations and
office spaces, with many of the above people I have been fortunate to share numerous
whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied
by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her
continuous assistance in matters\r\nthat often exceeded her official duties, and
who made my integration in Austria a smooth process."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Andreas
full_name: Pavlogiannis, Andreas
id: 49704004-F248-11E8-B48F-1D18A9856A87
last_name: Pavlogiannis
orcid: 0000-0002-8943-0722
citation:
ama: Pavlogiannis A. Algorithmic advances in program analysis and their applications.
2017. doi:10.15479/AT:ISTA:th_854
apa: Pavlogiannis, A. (2017). Algorithmic advances in program analysis and their
applications. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_854
chicago: Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their
Applications.” Institute of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:th_854.
ieee: A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,”
Institute of Science and Technology Austria, 2017.
ista: Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications.
Institute of Science and Technology Austria.
mla: Pavlogiannis, Andreas. Algorithmic Advances in Program Analysis and Their
Applications. Institute of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:th_854.
short: A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications,
Institute of Science and Technology Austria, 2017.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-07T12:01:59Z
day: '09'
ddc:
- '000'
degree_awarded: PhD
department:
- _id: KrCh
doi: 10.15479/AT:ISTA:th_854
ec_funded: 1
file:
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checksum: 3a3ec003f6ee73f41f82a544d63dfc77
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date_updated: 2020-07-14T12:48:10Z
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language:
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month: '08'
oa: 1
oa_version: Published Version
page: '418'
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal 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_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6828'
pubrep_id: '854'
related_material:
record:
- id: '1071'
relation: part_of_dissertation
status: public
- id: '1437'
relation: part_of_dissertation
status: public
- id: '1602'
relation: part_of_dissertation
status: public
- id: '1604'
relation: part_of_dissertation
status: public
- id: '1607'
relation: part_of_dissertation
status: public
- id: '1714'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
title: Algorithmic advances in program analysis and their applications
tmp:
image: /image/cc_by_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nd/4.0/legalcode
name: Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)
short: CC BY-ND (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '822'
abstract:
- lang: eng
text: 'Polymicrobial infections constitute small ecosystems that accommodate several
bacterial species. Commonly, these bacteria are investigated in isolation. However,
it is unknown to what extent the isolates interact and whether their interactions
alter bacterial growth and ecosystem resilience in the presence and absence of
antibiotics. We quantified the complete ecological interaction network for 72
bacterial isolates collected from 23 individuals diagnosed with polymicrobial
urinary tract infections and found that most interactions cluster based on evolutionary
relatedness. Statistical network analysis revealed that competitive and cooperative
reciprocal interactions are enriched in the global network, while cooperative
interactions are depleted in the individual host community networks. A population
dynamics model parameterized by our measurements suggests that interactions restrict
community stability, explaining the observed species diversity of these communities.
We further show that the clinical isolates frequently protect each other from
clinically relevant antibiotics. Together, these results highlight that ecological
interactions are crucial for the growth and survival of bacteria in polymicrobial
infection communities and affect their assembly and resilience. '
article_processing_charge: No
author:
- first_name: Marjon
full_name: De Vos, Marjon
id: 3111FFAC-F248-11E8-B48F-1D18A9856A87
last_name: De Vos
- first_name: Marcin P
full_name: Zagórski, Marcin P
id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
last_name: Zagórski
orcid: 0000-0001-7896-7762
- first_name: Alan
full_name: Mcnally, Alan
last_name: Mcnally
- first_name: Mark Tobias
full_name: Bollenbach, Mark Tobias
id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87
last_name: Bollenbach
orcid: 0000-0003-4398-476X
citation:
ama: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological
stability, and collective antibiotic tolerance in polymicrobial infections. PNAS.
2017;114(40):10666-10671. doi:10.1073/pnas.1713372114
apa: de Vos, M., Zagórski, M. P., Mcnally, A., & Bollenbach, M. T. (2017). Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713372114
chicago: Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach.
“Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance
in Polymicrobial Infections.” PNAS. National Academy of Sciences, 2017.
https://doi.org/10.1073/pnas.1713372114.
ieee: M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction
networks, ecological stability, and collective antibiotic tolerance in polymicrobial
infections,” PNAS, vol. 114, no. 40. National Academy of Sciences, pp.
10666–10671, 2017.
ista: de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks,
ecological stability, and collective antibiotic tolerance in polymicrobial infections.
PNAS. 114(40), 10666–10671.
mla: de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective
Antibiotic Tolerance in Polymicrobial Infections.” PNAS, vol. 114, no.
40, National Academy of Sciences, 2017, pp. 10666–71, doi:10.1073/pnas.1713372114.
short: M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.
date_created: 2018-12-11T11:48:41Z
date_published: 2017-10-03T00:00:00Z
date_updated: 2023-09-26T16:18:48Z
day: '03'
department:
- _id: ToBo
doi: 10.1073/pnas.1713372114
ec_funded: 1
external_id:
isi:
- '000412130500061'
pmid:
- '28923953'
intvolume: ' 114'
isi: 1
issue: '40'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/
month: '10'
oa: 1
oa_version: Submitted Version
page: 10666 - 10671
pmid: 1
project:
- _id: 25E83C2C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '303507'
name: Optimality principles in responses to antibiotics
- _id: 25E9AF9E-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P27201-B22
name: Revealing the mechanisms underlying drug interactions
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '6827'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interaction networks, ecological stability, and collective antibiotic tolerance
in polymicrobial infections
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 114
year: '2017'
...
---
_id: '823'
abstract:
- lang: eng
text: The resolution of a linear system with positive integer variables is a basic
yet difficult computational problem with many applications. We consider sparse
uncorrelated random systems parametrised by the density c and the ratio α=N/M
between number of variables N and number of constraints M. By means of ensemble
calculations we show that the space of feasible solutions endows a Van-Der-Waals
phase diagram in the plane (c, α). We give numerical evidence that the associated
computational problems become more difficult across the critical point and in
particular in the coexistence region.
article_number: '093404'
article_processing_charge: No
author:
- first_name: Simona
full_name: Colabrese, Simona
last_name: Colabrese
- first_name: Daniele
full_name: De Martino, Daniele
id: 3FF5848A-F248-11E8-B48F-1D18A9856A87
last_name: De Martino
orcid: 0000-0002-5214-4706
- first_name: Luca
full_name: Leuzzi, Luca
last_name: Leuzzi
- first_name: Enzo
full_name: Marinari, Enzo
last_name: Marinari
citation:
ama: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer
linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017;2017(9). doi:10.1088/1742-5468/aa85c3'
apa: 'Colabrese, S., De Martino, D., Leuzzi, L., & Marinari, E. (2017). Phase
transitions in integer linear problems. Journal of Statistical Mechanics:
Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa85c3'
chicago: 'Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari.
“Phase Transitions in Integer Linear Problems.” Journal of Statistical Mechanics:
Theory and Experiment. IOPscience, 2017. https://doi.org/10.1088/1742-5468/aa85c3.'
ieee: 'S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions
in integer linear problems,” Journal of Statistical Mechanics: Theory and
Experiment, vol. 2017, no. 9. IOPscience, 2017.'
ista: 'Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions
in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment.
2017(9), 093404.'
mla: 'Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.”
Journal of Statistical Mechanics: Theory and Experiment, vol. 2017, no.
9, 093404, IOPscience, 2017, doi:10.1088/1742-5468/aa85c3.'
short: 'S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical
Mechanics: Theory and Experiment 2017 (2017).'
date_created: 2018-12-11T11:48:41Z
date_published: 2017-09-26T00:00:00Z
date_updated: 2023-09-26T16:18:12Z
day: '26'
department:
- _id: GaTk
doi: 10.1088/1742-5468/aa85c3
ec_funded: 1
external_id:
isi:
- '000411842900001'
intvolume: ' 2017'
isi: 1
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.06303
month: '09'
oa: 1
oa_version: Submitted Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: ' Journal of Statistical Mechanics: Theory and Experiment'
publication_identifier:
issn:
- '17425468'
publication_status: published
publisher: IOPscience
publist_id: '6826'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phase transitions in integer linear problems
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 2017
year: '2017'
...
---
_id: '8235'
abstract:
- lang: eng
text: Due to large homology of human and canine EGFR, dogs suffering from spontaneous
EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic
compounds can be developed for both human and veterinary patients. This study
describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with
potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG
was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc.
Successful coupling of 10 DTPA molecules per antibody on average was proven by
significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots.
Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained
its binding capacity towards human and canine EGFR in flow cytometry, immuno-
and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was
determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma
cells by a competition binding technique. Stability tests of the radiolabeled
compound identified TRIS buffered saline as the ideal formulation for short-term
storage with 87.11 ±6.04% intact compound being still detected 60 minutes post
radiolabeling. High stability, specificity and EGFR binding affinity pinpoint
towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the
first proof-of-concept diagnostic and therapeutic applications in canine cancer
patients.
article_processing_charge: No
article_type: original
author:
- first_name: Judit
full_name: Fazekas-Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: Neydher
full_name: Berroterán-Infante, Neydher
last_name: Berroterán-Infante
- first_name: Christina
full_name: Rami-Mark, Christina
last_name: Rami-Mark
- first_name: Monika
full_name: Dumanic, Monika
last_name: Dumanic
- first_name: Miroslawa
full_name: Matz, Miroslawa
last_name: Matz
- first_name: Michael
full_name: Willmann, Michael
last_name: Willmann
- first_name: Fritz
full_name: Andreae, Fritz
last_name: Andreae
- first_name: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Wolfgang
full_name: Wadsak, Wolfgang
last_name: Wadsak
- first_name: Markus
full_name: Mitterhauser, Markus
last_name: Mitterhauser
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Singer J, Berroterán-Infante N, Rami-Mark C, et al. Development of a radiolabeled
caninized anti-EGFR antibody for comparative oncology trials. Oncotarget.
2017;8:83128-83141. doi:10.18632/oncotarget.20914
apa: Singer, J., Berroterán-Infante, N., Rami-Mark, C., Dumanic, M., Matz, M., Willmann,
M., … Jensen-Jarolim, E. (2017). Development of a radiolabeled caninized anti-EGFR
antibody for comparative oncology trials. Oncotarget. Impact Journals.
https://doi.org/10.18632/oncotarget.20914
chicago: Singer, Judit, Neydher Berroterán-Infante, Christina Rami-Mark, Monika
Dumanic, Miroslawa Matz, Michael Willmann, Fritz Andreae, et al. “Development
of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.”
Oncotarget. Impact Journals, 2017. https://doi.org/10.18632/oncotarget.20914.
ieee: J. Singer et al., “Development of a radiolabeled caninized anti-EGFR
antibody for comparative oncology trials,” Oncotarget, vol. 8. Impact Journals,
pp. 83128–83141, 2017.
ista: Singer J, Berroterán-Infante N, Rami-Mark C, Dumanic M, Matz M, Willmann M,
Andreae F, Singer J, Wadsak W, Mitterhauser M, Jensen-Jarolim E. 2017. Development
of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials.
Oncotarget. 8, 83128–83141.
mla: Singer, Judit, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody
for Comparative Oncology Trials.” Oncotarget, vol. 8, Impact Journals,
2017, pp. 83128–41, doi:10.18632/oncotarget.20914.
short: J. Singer, N. Berroterán-Infante, C. Rami-Mark, M. Dumanic, M. Matz, M. Willmann,
F. Andreae, J. Singer, W. Wadsak, M. Mitterhauser, E. Jensen-Jarolim, Oncotarget
8 (2017) 83128–83141.
date_created: 2020-08-10T11:53:18Z
date_published: 2017-09-15T00:00:00Z
date_updated: 2021-01-12T08:17:39Z
day: '15'
doi: 10.18632/oncotarget.20914
extern: '1'
intvolume: ' 8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.18632/oncotarget.20914
month: '09'
oa: 1
oa_version: Published Version
page: 83128-83141
publication: Oncotarget
publication_identifier:
issn:
- 1949-2553
publication_status: published
publisher: Impact Journals
quality_controlled: '1'
status: public
title: Development of a radiolabeled caninized anti-EGFR antibody for comparative
oncology trials
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...