---
_id: '7783'
abstract:
- lang: eng
text: The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource
to better understand the genetic landscapes underlying quantitative traits. However,
such DGRP studies have so far only focused on nuclear genetic variants. To address
this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229
variants including 21 indels and 7 frameshifts. We used our mitochondrial variation
data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing
important population structure at the mitochondrial level. We further examined
whether this population structure was reflected on the nuclear genome by screening
for the presence of potential mito-nuclear genetic incompatibilities in the form
of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear
variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the
highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl).
Intriguingly, downstream phenotypic analyses did not uncover major fitness effects
associated with these GRDs, suggesting that a large number of mito-nuclear GRDs
may reflect population structure at the mitochondrial level rather than actual
genomic incompatibilities. This is further supported by the GRD landscape showing
particular large genomic regions associated with a single mitochondrial haplotype.
Next, we explored the functional relevance of the detected mitochondrial haplotypes
through an association analysis on a set of 259 assembled, non-correlating DGRP
phenotypes. We found multiple significant associations with stress- and metabolism-related
phenotypes, including food intake in males. We validated the latter observation
by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines
to low food intake ones. In conclusion, our study uncovered important mitochondrial
population structure and haplotype-specific metabolic variation in the DGRP, thus
demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype
relationship studies.
article_processing_charge: No
author:
- first_name: Roel P.J.
full_name: Bevers, Roel P.J.
last_name: Bevers
- first_name: Maria
full_name: Litovchenko, Maria
last_name: Litovchenko
- first_name: Adamandia
full_name: Kapopoulou, Adamandia
last_name: Kapopoulou
- first_name: Virginie S.
full_name: Braman, Virginie S.
last_name: Braman
- first_name: Matthew Richard
full_name: Robinson, Matthew Richard
id: E5D42276-F5DA-11E9-8E24-6303E6697425
last_name: Robinson
orcid: 0000-0001-8982-8813
- first_name: Johan
full_name: Auwerx, Johan
last_name: Auwerx
- first_name: Brian
full_name: Hollis, Brian
last_name: Hollis
- first_name: Bart
full_name: Deplancke, Bart
last_name: Deplancke
citation:
ama: Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Extensive mitochondrial population
structure and haplotype-specific phenotypic variation in the Drosophila Genetic
Reference Panel. bioRxiv. 2018.
apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson,
M. R., Auwerx, J., … Deplancke, B. (2018). Extensive mitochondrial population
structure and haplotype-specific phenotypic variation in the Drosophila Genetic
Reference Panel. bioRxiv. Cold Spring Harbor Laboratory.
chicago: Bevers, Roel P.J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S.
Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke.
“Extensive Mitochondrial Population Structure and Haplotype-Specific Phenotypic
Variation in the Drosophila Genetic Reference Panel.” BioRxiv. Cold Spring
Harbor Laboratory, 2018.
ieee: R. P. J. Bevers et al., “Extensive mitochondrial population structure
and haplotype-specific phenotypic variation in the Drosophila Genetic Reference
Panel,” bioRxiv. Cold Spring Harbor Laboratory, 2018.
ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J,
Hollis B, Deplancke B. 2018. Extensive mitochondrial population structure and
haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel.
bioRxiv, .
mla: Bevers, Roel P. J., et al. “Extensive Mitochondrial Population Structure and
Haplotype-Specific Phenotypic Variation in the Drosophila Genetic Reference Panel.”
BioRxiv, Cold Spring Harbor Laboratory, 2018.
short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson,
J. Auwerx, B. Hollis, B. Deplancke, BioRxiv (2018).
date_created: 2020-04-30T13:09:37Z
date_published: 2018-11-09T00:00:00Z
date_updated: 2021-01-12T08:15:30Z
day: '09'
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/466771 '
month: '11'
oa: 1
oa_version: Preprint
page: '49'
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
status: public
title: Extensive mitochondrial population structure and haplotype-specific phenotypic
variation in the Drosophila Genetic Reference Panel
type: preprint
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '6001'
abstract:
- lang: eng
text: "The concurrent memory reclamation problem is that of devising a way for a
deallocating thread to verify that no other concurrent threads hold references
to a memory block being deallocated. To date, in the absence of automatic garbage
collection, there is no satisfactory solution to this problem; existing tracking
methods like hazard pointers, reference counters, or epoch-based techniques like
RCU are either prohibitively expensive or require significant programming expertise
to the extent that implementing them efficiently can be worthy of a publication.
None of the existing techniques are automatic or even semi-automated.\r\nIn this
article, we take a new approach to concurrent memory reclamation. Instead of manually
tracking access to memory locations as done in techniques like hazard pointers,
or restricting shared accesses to specific epoch boundaries as in RCU, our algorithm,
called ThreadScan, leverages operating system signaling to automatically detect
which memory locations are being accessed by concurrent threads.\r\nInitial empirical
evidence shows that ThreadScan scales surprisingly well and requires negligible
programming effort beyond the standard use of Malloc and Free."
article_number: '18'
author:
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
- first_name: William
full_name: Leiserson, William
last_name: Leiserson
- first_name: Alexander
full_name: Matveev, Alexander
last_name: Matveev
- first_name: Nir
full_name: Shavit, Nir
last_name: Shavit
citation:
ama: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. ThreadScan: Automatic and
scalable memory reclamation. ACM Transactions on Parallel Computing. 2018;4(4).
doi:10.1145/3201897'
apa: 'Alistarh, D.-A., Leiserson, W., Matveev, A., & Shavit, N. (2018). ThreadScan:
Automatic and scalable memory reclamation. ACM Transactions on Parallel Computing.
Association for Computing Machinery. https://doi.org/10.1145/3201897'
chicago: 'Alistarh, Dan-Adrian, William Leiserson, Alexander Matveev, and Nir Shavit.
“ThreadScan: Automatic and Scalable Memory Reclamation.” ACM Transactions on
Parallel Computing. Association for Computing Machinery, 2018. https://doi.org/10.1145/3201897.'
ieee: 'D.-A. Alistarh, W. Leiserson, A. Matveev, and N. Shavit, “ThreadScan: Automatic
and scalable memory reclamation,” ACM Transactions on Parallel Computing,
vol. 4, no. 4. Association for Computing Machinery, 2018.'
ista: 'Alistarh D-A, Leiserson W, Matveev A, Shavit N. 2018. ThreadScan: Automatic
and scalable memory reclamation. ACM Transactions on Parallel Computing. 4(4),
18.'
mla: 'Alistarh, Dan-Adrian, et al. “ThreadScan: Automatic and Scalable Memory Reclamation.”
ACM Transactions on Parallel Computing, vol. 4, no. 4, 18, Association
for Computing Machinery, 2018, doi:10.1145/3201897.'
short: D.-A. Alistarh, W. Leiserson, A. Matveev, N. Shavit, ACM Transactions on
Parallel Computing 4 (2018).
date_created: 2019-02-14T13:24:11Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-02-23T13:17:54Z
day: '01'
department:
- _id: DaAl
doi: 10.1145/3201897
intvolume: ' 4'
issue: '4'
language:
- iso: eng
month: '09'
oa_version: None
publication: ACM Transactions on Parallel Computing
publication_identifier:
issn:
- 2329-4949
publication_status: published
publisher: Association for Computing Machinery
quality_controlled: '1'
related_material:
record:
- id: '779'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: 'ThreadScan: Automatic and scalable memory reclamation'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2018'
...
---
_id: '7812'
abstract:
- lang: eng
text: Deep neural networks (DNNs) continue to make significant advances, solving
tasks from image classification to translation or reinforcement learning. One
aspect of the field receiving considerable attention is efficiently executing
deep models in resource-constrained environments, such as mobile or embedded devices.
This paper focuses on this problem, and proposes two new compression methods,
which jointly leverage weight quantization and distillation of larger teacher
networks into smaller student networks. The first method we propose is called
quantized distillation and leverages distillation during the training process,
by incorporating distillation loss, expressed with respect to the teacher, into
the training of a student network whose weights are quantized to a limited set
of levels. The second method, differentiable quantization, optimizes the location
of quantization points through stochastic gradient descent, to better fit the
behavior of the teacher model. We validate both methods through experiments on
convolutional and recurrent architectures. We show that quantized shallow students
can reach similar accuracy levels to full-precision teacher models, while providing
order of magnitude compression, and inference speedup that is linear in the depth
reduction. In sum, our results enable DNNs for resource-constrained environments
to leverage architecture and accuracy advances developed on more powerful devices.
article_processing_charge: No
author:
- first_name: Antonio
full_name: Polino, Antonio
last_name: Polino
- first_name: Razvan
full_name: Pascanu, Razvan
last_name: Pascanu
- first_name: Dan-Adrian
full_name: Alistarh, Dan-Adrian
id: 4A899BFC-F248-11E8-B48F-1D18A9856A87
last_name: Alistarh
orcid: 0000-0003-3650-940X
citation:
ama: 'Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and
quantization. In: 6th International Conference on Learning Representations.
; 2018.'
apa: Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via
distillation and quantization. In 6th International Conference on Learning
Representations. Vancouver, Canada.
chicago: Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression
via Distillation and Quantization.” In 6th International Conference on Learning
Representations, 2018.
ieee: A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation
and quantization,” in 6th International Conference on Learning Representations,
Vancouver, Canada, 2018.
ista: 'Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation
and quantization. 6th International Conference on Learning Representations. ICLR:
International Conference on Learning Representations.'
mla: Polino, Antonio, et al. “Model Compression via Distillation and Quantization.”
6th International Conference on Learning Representations, 2018.
short: A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference
on Learning Representations, 2018.
conference:
end_date: 2018-05-03
location: Vancouver, Canada
name: 'ICLR: International Conference on Learning Representations'
start_date: 2018-04-30
date_created: 2020-05-10T22:00:51Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-02-23T13:18:41Z
day: '01'
ddc:
- '000'
department:
- _id: DaAl
external_id:
arxiv:
- '1802.05668'
file:
- access_level: open_access
checksum: a4336c167978e81891970e4e4517a8c3
content_type: application/pdf
creator: dernst
date_created: 2020-05-26T13:02:00Z
date_updated: 2020-07-14T12:48:03Z
file_id: '7894'
file_name: 2018_ICLR_Polino.pdf
file_size: 308339
relation: main_file
file_date_updated: 2020-07-14T12:48:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: 6th International Conference on Learning Representations
publication_status: published
quality_controlled: '1'
scopus_import: 1
status: public
title: Model compression via distillation and quantization
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '7983'
abstract:
- lang: ger
text: 'Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten
an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien,
und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden
und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen
>3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung
detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2
+ O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und
wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir,
dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in
einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird.
Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit
von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu
verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie
basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität
von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.'
article_processing_charge: No
article_type: original
author:
- first_name: Nika
full_name: Mahne, Nika
last_name: Mahne
- first_name: Sara E.
full_name: Renfrew, Sara E.
last_name: Renfrew
- first_name: Bryan D.
full_name: McCloskey, Bryan D.
last_name: McCloskey
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
citation:
ama: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. Elektrochemische Oxidation
von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie.
2018;130(19):5627-5631. doi:10.1002/ange.201802277
apa: Mahne, N., Renfrew, S. E., McCloskey, B. D., & Freunberger, S. A. (2018).
Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff.
Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.201802277
chicago: Mahne, Nika, Sara E. Renfrew, Bryan D. McCloskey, and Stefan Alexander
Freunberger. “Elektrochemische Oxidation von Lithiumcarbonat Generiert Singulett-Sauerstoff.”
Angewandte Chemie. Wiley, 2018. https://doi.org/10.1002/ange.201802277.
ieee: N. Mahne, S. E. Renfrew, B. D. McCloskey, and S. A. Freunberger, “Elektrochemische
Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff,” Angewandte Chemie,
vol. 130, no. 19. Wiley, pp. 5627–5631, 2018.
ista: Mahne N, Renfrew SE, McCloskey BD, Freunberger SA. 2018. Elektrochemische
Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff. Angewandte Chemie.
130(19), 5627–5631.
mla: Mahne, Nika, et al. “Elektrochemische Oxidation von Lithiumcarbonat Generiert
Singulett-Sauerstoff.” Angewandte Chemie, vol. 130, no. 19, Wiley, 2018,
pp. 5627–31, doi:10.1002/ange.201802277.
short: N. Mahne, S.E. Renfrew, B.D. McCloskey, S.A. Freunberger, Angewandte Chemie
130 (2018) 5627–5631.
date_created: 2020-06-19T08:33:24Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2021-01-12T08:16:21Z
day: '04'
ddc:
- '540'
doi: 10.1002/ange.201802277
extern: '1'
file:
- access_level: open_access
checksum: 81506e0f7079e1e3591f3cd9f626bf67
content_type: application/pdf
creator: dernst
date_created: 2020-06-19T11:58:06Z
date_updated: 2020-07-14T12:48:06Z
file_id: '7988'
file_name: 2018_AngChemieDT_Mahne.pdf
file_size: 674789
relation: main_file
file_date_updated: 2020-07-14T12:48:06Z
has_accepted_license: '1'
intvolume: ' 130'
issue: '19'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 5627-5631
publication: Angewandte Chemie
publication_identifier:
issn:
- 0044-8249
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 130
year: '2018'
...
---
_id: '8015'
abstract:
- lang: eng
text: 'The neural code of cortical processing remains uncracked; however, it must
necessarily rely on faithful signal propagation between cortical areas. In this
issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation
balanced by local inhibition can enable reliable signal propagation in data-constrained
network models of macaque cortex. '
article_processing_charge: No
article_type: original
author:
- first_name: Jake P.
full_name: Stroud, Jake P.
last_name: Stroud
- 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: 'Stroud JP, Vogels TP. Cortical signal propagation: Balance, amplify, transmit.
Neuron. 2018;98(1):8-9. doi:10.1016/j.neuron.2018.03.028'
apa: 'Stroud, J. P., & Vogels, T. P. (2018). Cortical signal propagation: Balance,
amplify, transmit. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.03.028'
chicago: 'Stroud, Jake P., and Tim P Vogels. “Cortical Signal Propagation: Balance,
Amplify, Transmit.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.03.028.'
ieee: 'J. P. Stroud and T. P. Vogels, “Cortical signal propagation: Balance, amplify,
transmit,” Neuron, vol. 98, no. 1. Elsevier, pp. 8–9, 2018.'
ista: 'Stroud JP, Vogels TP. 2018. Cortical signal propagation: Balance, amplify,
transmit. Neuron. 98(1), 8–9.'
mla: 'Stroud, Jake P., and Tim P. Vogels. “Cortical Signal Propagation: Balance,
Amplify, Transmit.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 8–9, doi:10.1016/j.neuron.2018.03.028.'
short: J.P. Stroud, T.P. Vogels, Neuron 98 (2018) 8–9.
date_created: 2020-06-25T12:53:39Z
date_published: 2018-04-04T00:00:00Z
date_updated: 2021-01-12T08:16:31Z
day: '04'
doi: 10.1016/j.neuron.2018.03.028
extern: '1'
external_id:
pmid:
- '29621492'
intvolume: ' 98'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.neuron.2018.03.028
month: '04'
oa: 1
oa_version: Published Version
page: 8-9
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Cortical signal propagation: Balance, amplify, transmit'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 98
year: '2018'
...
---
_id: '8073'
abstract:
- lang: eng
text: Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support
the generation of complex movements. Although recent neuronal-network models capture
many qualitative aspects of M1 dynamics, they can generate only a few distinct
movements. Additionally, it is unclear how M1 efficiently controls movements over
a wide range of shapes and speeds. We demonstrate that modulation of neuronal
input–output gains in recurrent neuronal-network models with a fixed architecture
can dramatically reorganize neuronal activity and thus downstream muscle outputs.
Consistent with the observation of diffuse neuromodulatory projections to M1,
a relatively small number of modulatory control units provide sufficient flexibility
to adjust high-dimensional network activity using a simple reward-based learning
rule. Furthermore, it is possible to assemble novel movements from previously
learned primitives, and one can separately change movement speed while preserving
movement shape. Our results provide a new perspective on the role of modulatory
systems in controlling recurrent cortical activity.
article_processing_charge: No
article_type: original
author:
- first_name: Jake P.
full_name: Stroud, Jake P.
last_name: Stroud
- first_name: Mason A.
full_name: Porter, Mason A.
last_name: Porter
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- 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: Stroud JP, Porter MA, Hennequin G, Vogels TP. Motor primitives in space and
time via targeted gain modulation in cortical networks. Nature Neuroscience.
2018;21(12):1774-1783. doi:10.1038/s41593-018-0276-0
apa: Stroud, J. P., Porter, M. A., Hennequin, G., & Vogels, T. P. (2018). Motor
primitives in space and time via targeted gain modulation in cortical networks.
Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-018-0276-0
chicago: Stroud, Jake P., Mason A. Porter, Guillaume Hennequin, and Tim P Vogels.
“Motor Primitives in Space and Time via Targeted Gain Modulation in Cortical Networks.”
Nature Neuroscience. Springer Nature, 2018. https://doi.org/10.1038/s41593-018-0276-0.
ieee: J. P. Stroud, M. A. Porter, G. Hennequin, and T. P. Vogels, “Motor primitives
in space and time via targeted gain modulation in cortical networks,” Nature
Neuroscience, vol. 21, no. 12. Springer Nature, pp. 1774–1783, 2018.
ista: Stroud JP, Porter MA, Hennequin G, Vogels TP. 2018. Motor primitives in space
and time via targeted gain modulation in cortical networks. Nature Neuroscience.
21(12), 1774–1783.
mla: Stroud, Jake P., et al. “Motor Primitives in Space and Time via Targeted Gain
Modulation in Cortical Networks.” Nature Neuroscience, vol. 21, no. 12,
Springer Nature, 2018, pp. 1774–83, doi:10.1038/s41593-018-0276-0.
short: J.P. Stroud, M.A. Porter, G. Hennequin, T.P. Vogels, Nature Neuroscience
21 (2018) 1774–1783.
date_created: 2020-06-30T13:18:02Z
date_published: 2018-12-01T00:00:00Z
date_updated: 2021-01-12T08:16:46Z
day: '01'
doi: 10.1038/s41593-018-0276-0
extern: '1'
external_id:
pmid:
- '30482949'
intvolume: ' 21'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276991/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1774-1783
pmid: 1
publication: Nature Neuroscience
publication_identifier:
issn:
- 1097-6256
- 1546-1726
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41593-018-0307-x
status: public
title: Motor primitives in space and time via targeted gain modulation in cortical
networks
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 21
year: '2018'
...
---
_id: '8231'
article_processing_charge: No
article_type: letter_note
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: Josef
full_name: Singer, Josef
last_name: Singer
- first_name: Kristina M.
full_name: Ilieva, Kristina M.
last_name: Ilieva
- first_name: Miroslawa
full_name: Matz, Miroslawa
last_name: Matz
- first_name: Ina
full_name: Herrmann, Ina
last_name: Herrmann
- first_name: Edzard
full_name: Spillner, Edzard
last_name: Spillner
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: 'Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine
anticancer IgE against the epidermal growth factor receptor. Journal of Allergy
and Clinical Immunology. 2018;142(3):973-976.e11. doi:10.1016/j.jaci.2018.04.021'
apa: 'Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E.,
… Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE
against the epidermal growth factor receptor. Journal of Allergy and Clinical
Immunology. Elsevier. https://doi.org/10.1016/j.jaci.2018.04.021'
chicago: 'Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann,
Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology:
Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.”
Journal of Allergy and Clinical Immunology. Elsevier, 2018. https://doi.org/10.1016/j.jaci.2018.04.021.'
ieee: 'J. Singer et al., “AllergoOncology: Generating a canine anticancer
IgE against the epidermal growth factor receptor,” Journal of Allergy and Clinical
Immunology, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.'
ista: 'Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis
SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE
against the epidermal growth factor receptor. Journal of Allergy and Clinical
Immunology. 142(3), 973–976.e11.'
mla: 'Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE
against the Epidermal Growth Factor Receptor.” Journal of Allergy and Clinical
Immunology, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:10.1016/j.jaci.2018.04.021.'
short: J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N.
Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142
(2018) 973–976.e11.
date_created: 2020-08-10T11:51:36Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2021-01-12T08:17:37Z
day: '01'
doi: 10.1016/j.jaci.2018.04.021
extern: '1'
intvolume: ' 142'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jaci.2018.04.021
month: '09'
oa: 1
oa_version: Published Version
page: 973-976.e11
publication: Journal of Allergy and Clinical Immunology
publication_identifier:
issn:
- 0091-6749
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'AllergoOncology: Generating a canine anticancer IgE against the epidermal
growth factor receptor'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 142
year: '2018'
...
---
_id: '8234'
abstract:
- lang: eng
text: Molecular imaging probes such as PET-tracers have the potential to improve
the accuracy of tumor characterization by directly visualizing the biochemical
situation. Thus, molecular changes can be detected early before morphological
manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed
in colon cancer cell lines and human colorectal cancer (CRC), suggesting this
receptor as a tumor marker. The aim of this preclinical study was the evaluation
of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging.
First, affinity and selectivity of FE@SUPPY and its metabolites were determined,
proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell
line HT-29 was characterized regarding its hA3AR expression and was subsequently
chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as
a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher
accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy
colon tissue from the same patient. Nevertheless, first in vivo studies using
HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation
of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY
in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize
hA3ARs using FE@SUPPY.
article_number: '1269830'
article_processing_charge: No
article_type: original
author:
- first_name: T.
full_name: Balber, T.
last_name: Balber
- first_name: Judit
full_name: Singer, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Singer
orcid: 0000-0002-8777-3502
- first_name: N.
full_name: Berroterán-Infante, N.
last_name: Berroterán-Infante
- first_name: M.
full_name: Dumanic, M.
last_name: Dumanic
- first_name: L.
full_name: Fetty, L.
last_name: Fetty
- first_name: J.
full_name: Fazekas-Singer, J.
last_name: Fazekas-Singer
orcid: 0000-0002-8777-3502
- first_name: C.
full_name: Vraka, C.
last_name: Vraka
- first_name: L.
full_name: Nics, L.
last_name: Nics
- first_name: M.
full_name: Bergmann, M.
last_name: Bergmann
- first_name: K.
full_name: Pallitsch, K.
last_name: Pallitsch
- first_name: H.
full_name: Spreitzer, H.
last_name: Spreitzer
- first_name: W.
full_name: Wadsak, W.
last_name: Wadsak
orcid: 0000-0003-4479-8053
- first_name: M.
full_name: Hacker, M.
last_name: Hacker
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
- first_name: H.
full_name: Viernstein, H.
last_name: Viernstein
- first_name: M.
full_name: Mitterhauser, M.
last_name: Mitterhauser
orcid: 0000-0003-3173-5272
citation:
ama: 'Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and
in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft
model for colorectal cancer. Contrast Media & Molecular Imaging. 2018;2018.
doi:10.1155/2018/1269830'
apa: 'Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer,
J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of
[18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal
cancer. Contrast Media & Molecular Imaging. Hindawi. https://doi.org/10.1155/2018/1269830'
chicago: 'Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty,
J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation
of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for
Colorectal Cancer.” Contrast Media & Molecular Imaging. Hindawi, 2018.
https://doi.org/10.1155/2018/1269830.'
ieee: 'T. Balber et al., “Preclinical in vitro and in vivo evaluation of
[18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal
cancer,” Contrast Media & Molecular Imaging, vol. 2018. Hindawi, 2018.'
ista: 'Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer
J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M,
Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and
in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft
model for colorectal cancer. Contrast Media & Molecular Imaging. 2018, 1269830.'
mla: 'Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY
for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.”
Contrast Media & Molecular Imaging, vol. 2018, 1269830, Hindawi, 2018,
doi:10.1155/2018/1269830.'
short: T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer,
C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker,
E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media & Molecular
Imaging 2018 (2018).
date_created: 2020-08-10T11:53:07Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2021-01-12T08:17:38Z
day: '13'
doi: 10.1155/2018/1269830
extern: '1'
intvolume: ' 2018'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1155/2018/1269830
month: '02'
oa: 1
oa_version: Published Version
publication: Contrast Media & Molecular Imaging
publication_identifier:
issn:
- 1555-4309
- 1555-4317
publication_status: published
publisher: Hindawi
quality_controlled: '1'
status: public
title: 'Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET
imaging: Limitations of a xenograft model for colorectal cancer'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2018
year: '2018'
...
---
_id: '8232'
abstract:
- lang: eng
text: 'Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in
EGFR expressing cancers including lung, colon, head and neck, and bladder cancers,
however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is
a highly selective tumor treatment that employs an antibody-photo-absorber conjugate
which is activated by NIR light. NIR-PIT is in clinical trials in patients with
recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However,
its use has otherwise been restricted to mouse models. This is an effort to explore
larger animal models with NIR-PIT. We describe the use of a recombinant canine
anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber,
IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell
lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate
showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing
cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation
of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing
mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700
i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light
exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared
with the other groups (p < 0.001), and significantly prolonged survival was achieved
(p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with
can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including
invasive transitional cell carcinoma in pet dogs, that could provide a pathway
to translation to humans.'
article_processing_charge: No
article_type: original
author:
- first_name: Tadanobu
full_name: Nagaya, Tadanobu
last_name: Nagaya
- first_name: Shuhei
full_name: Okuyama, Shuhei
last_name: Okuyama
- first_name: Fusa
full_name: Ogata, Fusa
last_name: Ogata
- first_name: Yasuhiro
full_name: Maruoka, Yasuhiro
last_name: Maruoka
- first_name: Deborah W.
full_name: Knapp, Deborah W.
last_name: Knapp
- first_name: Sophia N.
full_name: Karagiannis, Sophia N.
last_name: Karagiannis
- 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: Peter L.
full_name: Choyke, Peter L.
last_name: Choyke
- first_name: Amy K.
full_name: LeBlanc, Amy K.
last_name: LeBlanc
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Hisataka
full_name: Kobayashi, Hisataka
last_name: Kobayashi
citation:
ama: Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting
bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody.
Oncotarget. 2018;9:19026-19038. doi:10.18632/oncotarget.24876
apa: Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis,
S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder
cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget.
Impact Journals. https://doi.org/10.18632/oncotarget.24876
chicago: Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah
W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy
Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR)
Antibody.” Oncotarget. Impact Journals, 2018. https://doi.org/10.18632/oncotarget.24876.
ieee: T. Nagaya et al., “Near infrared photoimmunotherapy targeting bladder
cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” Oncotarget,
vol. 9. Impact Journals, pp. 19026–19038, 2018.
ista: Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer
J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy
targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR)
antibody. Oncotarget. 9, 19026–19038.
mla: Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder
Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget,
vol. 9, Impact Journals, 2018, pp. 19026–38, doi:10.18632/oncotarget.24876.
short: T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis,
J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget
9 (2018) 19026–19038.
date_created: 2020-08-10T11:52:54Z
date_published: 2018-04-10T00:00:00Z
date_updated: 2021-01-12T08:17:37Z
day: '10'
doi: 10.18632/oncotarget.24876
extern: '1'
intvolume: ' 9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.18632/oncotarget.24876
month: '04'
oa: 1
oa_version: Published Version
page: 19026-19038
publication: Oncotarget
publication_identifier:
eissn:
- 1949-2553
publication_status: published
publisher: Impact Journals
quality_controlled: '1'
status: public
title: Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal
growth factor receptor (EGFR) antibody
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '8233'
abstract:
- lang: eng
text: The M2a subtype of macrophages plays an important role in human immunoglobulin
E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very
little is known about these cells in the dog. Here we describe an in vitro method
to activate canine histiocytic DH82 cells and primary canine monocyte-derived
macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side
comparison, we compared the canine cells to human MDMs, and the human monocytic
cell line U937 activated towards M1 and M2a cells on the cellular and molecular
level. In analogy to activated human M2a cells, canine M2a, differentiated from
both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared
to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the
high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes
(IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog
species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated
in canine and human M1 cells (cell lines and MDMs). We suggest that our novel
in vitro method will be suitable in comparative allergology studies focussing
on macrophages.
article_processing_charge: No
article_type: original
author:
- first_name: Ina
full_name: Herrmann, Ina
last_name: Herrmann
- first_name: Jelena
full_name: Gotovina, Jelena
last_name: Gotovina
- 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: Michael B.
full_name: Fischer, Michael B.
last_name: Fischer
- first_name: Karin
full_name: Hufnagl, Karin
last_name: Hufnagl
- first_name: Rodolfo
full_name: Bianchini, Rodolfo
last_name: Bianchini
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
citation:
ama: Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human
macrophages be in vitro activated toward the M2a subtype relevant in allergy.
Developmental & Comparative Immunology. 2018;82(5):118-127. doi:10.1016/j.dci.2018.01.005
apa: Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini,
R., & Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages
be in vitro activated toward the M2a subtype relevant in allergy. Developmental
& Comparative Immunology. Elsevier. https://doi.org/10.1016/j.dci.2018.01.005
chicago: Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin
Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can
like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in
Allergy.” Developmental & Comparative Immunology. Elsevier, 2018. https://doi.org/10.1016/j.dci.2018.01.005.
ieee: I. Herrmann et al., “Canine macrophages can like human macrophages
be in vitro activated toward the M2a subtype relevant in allergy,” Developmental
& Comparative Immunology, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.
ista: Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim
E. 2018. Canine macrophages can like human macrophages be in vitro activated toward
the M2a subtype relevant in allergy. Developmental & Comparative Immunology.
82(5), 118–127.
mla: Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro
Activated toward the M2a Subtype Relevant in Allergy.” Developmental &
Comparative Immunology, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:10.1016/j.dci.2018.01.005.
short: I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini,
E. Jensen-Jarolim, Developmental & Comparative Immunology 82 (2018) 118–127.
date_created: 2020-08-10T11:53:01Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:17:38Z
day: '01'
doi: 10.1016/j.dci.2018.01.005
extern: '1'
intvolume: ' 82'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.dci.2018.01.005
month: '05'
oa: 1
oa_version: Published Version
page: 118-127
publication: Developmental & Comparative Immunology
publication_identifier:
issn:
- 0145-305X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Canine macrophages can like human macrophages be in vitro activated toward
the M2a subtype relevant in allergy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2018'
...
---
_id: '8262'
abstract:
- lang: eng
text: "Background: The genus Burkholderia consists of species that occupy remarkably
diverse ecological niches. Its best known members are important pathogens, B.
mallei and B. pseudomallei, which cause glanders and melioidosis, respectively.
Burkholderia genomes are unusual due to their multichromosomal organization, generally
comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic
analysis of 127 Burkholderia strains. The pan-genome is open with the saturation
to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements
indicate a strong avoidance of intra-replichore inversions that is likely caused
by selection against the transfer of large groups of genes between the leading
and the lagging strands. Translocated genes also tend to retain their position
in the leading or the lagging strand, and this selection is stronger for large
syntenies. Integrated reconstruction of chromosome rearrangements in the context
of strains phylogeny reveals parallel rearrangements that may indicate inversion-based
phase variation and integration of new genomic islands. In particular, we detected
parallel inversions in the second chromosomes of B. pseudomallei with breakpoints
formed by genes encoding membrane components of multidrug resistance complex,
that may be linked to a phase variation mechanism. Two genomic islands, spreading
horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions:
This study demonstrates the power of integrated analysis of pan-genomes, chromosome
rearrangements, and selection regimes. Non-random inversion patterns indicate
selective pressure, inversions are particularly frequent in a recent pathogen
B. mallei, and, together with periods of positive selection at other branches,
may indicate adaptation to new niches. One such adaptation could be a possible
phase variation mechanism in B. pseudomallei."
article_number: '965'
article_processing_charge: No
article_type: original
author:
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Elena V.
full_name: Moroz, Elena V.
last_name: Moroz
- first_name: Iakov I.
full_name: Davydov, Iakov I.
last_name: Davydov
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection
in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018;19. doi:10.1186/s12864-018-5245-1
apa: Bochkareva, O., Moroz, E. V., Davydov, I. I., & Gelfand, M. S. (2018).
Genome rearrangements and selection in multi-chromosome bacteria Burkholderia
spp. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-018-5245-1
chicago: Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand.
“Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia
Spp.” BMC Genomics. Springer Nature, 2018. https://doi.org/10.1186/s12864-018-5245-1.
ieee: O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements
and selection in multi-chromosome bacteria Burkholderia spp.,” BMC Genomics,
vol. 19. Springer Nature, 2018.
ista: Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements
and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19,
965.
mla: Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome
Bacteria Burkholderia Spp.” BMC Genomics, vol. 19, 965, Springer Nature,
2018, doi:10.1186/s12864-018-5245-1.
short: O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).
date_created: 2020-08-15T11:02:08Z
date_published: 2018-12-27T00:00:00Z
date_updated: 2023-02-23T13:28:52Z
day: '27'
doi: 10.1186/s12864-018-5245-1
extern: '1'
intvolume: ' 19'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s12864-018-5245-1
month: '12'
oa: 1
oa_version: Published Version
publication: BMC Genomics
publication_identifier:
issn:
- 1471-2164
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Genome rearrangements and selection in multi-chromosome bacteria Burkholderia
spp.
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 19
year: '2018'
...
---
_id: '8265'
abstract:
- lang: eng
text: Genome rearrangements have played an important role in the evolution of Yersinia
pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic
trees for Y. pestis based on sequence comparison have short internal branches
and low bootstrap supports as only a small number of nucleotide substitutions
have occurred. On the other hand, even a small number of genome rearrangements
may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic
trees based on genome rearrangements using several popular approaches such as
Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements
by inversions. We also reconciled phylogenetic trees for each of the three CRISPR
loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis
of contradictions between the obtained evolutionary trees yielded numerous parallel
inversions and gain/loss events. Our data indicate that an integrated analysis
of sequence-based and inversion-based trees enhances the resolution of phylogenetic
reconstruction. In contrast, reconstructions of strain relationships based on
solely CRISPR loci may not be reliable, as the history is obscured by large deletions,
obliterating the order of spacer gains. Similarly, numerous parallel gene losses
preclude reconstruction of phylogeny based on gene content.
article_number: e4545
article_processing_charge: No
article_type: original
author:
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
- first_name: Natalia O.
full_name: Dranenko, Natalia O.
last_name: Dranenko
- first_name: Elena S.
full_name: Ocheredko, Elena S.
last_name: Ocheredko
- first_name: German M.
full_name: Kanevsky, German M.
last_name: Kanevsky
- first_name: Yaroslav N.
full_name: Lozinsky, Yaroslav N.
last_name: Lozinsky
- first_name: Vera A.
full_name: Khalaycheva, Vera A.
last_name: Khalaycheva
- first_name: Irena I.
full_name: Artamonova, Irena I.
last_name: Artamonova
- first_name: Mikhail S.
full_name: Gelfand, Mikhail S.
last_name: Gelfand
citation:
ama: Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny
reconstruction in Yersinia pestis. PeerJ. 2018;6. doi:10.7717/peerj.4545
apa: Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky,
Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and
phylogeny reconstruction in Yersinia pestis. PeerJ. PeerJ. https://doi.org/10.7717/peerj.4545
chicago: Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky,
Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S.
Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.”
PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.4545.
ieee: O. Bochkareva et al., “Genome rearrangements and phylogeny reconstruction
in Yersinia pestis,” PeerJ, vol. 6. PeerJ, 2018.
ista: Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva
VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction
in Yersinia pestis. PeerJ. 6, e4545.
mla: Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction
in Yersinia Pestis.” PeerJ, vol. 6, e4545, PeerJ, 2018, doi:10.7717/peerj.4545.
short: O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky,
V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018).
date_created: 2020-08-15T11:08:23Z
date_published: 2018-03-27T00:00:00Z
date_updated: 2023-02-23T13:28:57Z
day: '27'
doi: 10.7717/peerj.4545
extern: '1'
external_id:
pmid:
- '29607260'
intvolume: ' 6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7717/peerj.4545
month: '03'
oa: 1
oa_version: Published Version
pmid: 1
publication: PeerJ
publication_identifier:
issn:
- 2167-8359
publication_status: published
publisher: PeerJ
quality_controlled: '1'
status: public
title: Genome rearrangements and phylogeny reconstruction in Yersinia pestis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2018'
...
---
_id: '8274'
abstract:
- lang: eng
text: 'Background/Aim: Our aim was to investigate the crosstalk between tumor and
immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation
in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human
BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral
blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes
(dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated
by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2
overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages,
was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with
dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29
human colon cancer cells and reduced production of COX2 in BT474 human mammary
cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated
with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion:
Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape
a tolerogenic tumor microenvironment in CMT.'
article_processing_charge: No
article_type: original
author:
- first_name: Maria Isabel
full_name: Carvalho, Maria Isabel
last_name: Carvalho
- first_name: Rodolfo
full_name: Bianchini, Rodolfo
last_name: Bianchini
- 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: Ina
full_name: Herrmann, Ina
last_name: Herrmann
- first_name: Irene
full_name: Flickinger, Irene
last_name: Flickinger
- first_name: Johann G.
full_name: Thalhammer, Johann G.
last_name: Thalhammer
- first_name: Isabel
full_name: Pires, Isabel
last_name: Pires
- first_name: Erika
full_name: Jensen-Jarolim, Erika
last_name: Jensen-Jarolim
- first_name: Felisbina L.
full_name: Queiroga, Felisbina L.
last_name: Queiroga
citation:
ama: Carvalho MI, Bianchini R, Singer J, et al. Bidirectional regulation of COX-2
expression between cancer cells and macrophages. Anticancer Research. 2018;38(5):2811-2817.
doi:10.21873/anticanres.12525
apa: Carvalho, M. I., Bianchini, R., Singer, J., Herrmann, I., Flickinger, I., Thalhammer,
J. G., … Queiroga, F. L. (2018). Bidirectional regulation of COX-2 expression
between cancer cells and macrophages. Anticancer Research. International
Institute of Anticancer Research. https://doi.org/10.21873/anticanres.12525
chicago: Carvalho, Maria Isabel, Rodolfo Bianchini, Judit Singer, Ina Herrmann,
Irene Flickinger, Johann G. Thalhammer, Isabel Pires, Erika Jensen-Jarolim, and
Felisbina L. Queiroga. “Bidirectional Regulation of COX-2 Expression between Cancer
Cells and Macrophages.” Anticancer Research. International Institute of
Anticancer Research, 2018. https://doi.org/10.21873/anticanres.12525.
ieee: M. I. Carvalho et al., “Bidirectional regulation of COX-2 expression
between cancer cells and macrophages,” Anticancer Research, vol. 38, no.
5. International Institute of Anticancer Research, pp. 2811–2817, 2018.
ista: Carvalho MI, Bianchini R, Singer J, Herrmann I, Flickinger I, Thalhammer JG,
Pires I, Jensen-Jarolim E, Queiroga FL. 2018. Bidirectional regulation of COX-2
expression between cancer cells and macrophages. Anticancer Research. 38(5), 2811–2817.
mla: Carvalho, Maria Isabel, et al. “Bidirectional Regulation of COX-2 Expression
between Cancer Cells and Macrophages.” Anticancer Research, vol. 38, no.
5, International Institute of Anticancer Research, 2018, pp. 2811–17, doi:10.21873/anticanres.12525.
short: M.I. Carvalho, R. Bianchini, J. Singer, I. Herrmann, I. Flickinger, J.G.
Thalhammer, I. Pires, E. Jensen-Jarolim, F.L. Queiroga, Anticancer Research 38
(2018) 2811–2817.
date_created: 2020-08-17T07:13:55Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2021-01-12T08:17:52Z
day: '01'
doi: 10.21873/anticanres.12525
extern: '1'
intvolume: ' 38'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 2811-2817
publication: Anticancer Research
publication_identifier:
eissn:
- 1791-7530
issn:
- 0250-7005
publication_status: published
publisher: International Institute of Anticancer Research
quality_controlled: '1'
status: public
title: Bidirectional regulation of COX-2 expression between cancer cells and macrophages
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2018'
...
---
_id: '8298'
abstract:
- lang: eng
text: Sharding, or partitioning the system’s state so that different subsets of
participants handle it, is a proven approach to building distributed systems whose
total capacity scales horizontally with the number of participants. Many distributed
ledgers have adopted this approach to increase their performance, however, they
focus on the permissionless setting that assumes the existence of a strong adversary.
In this paper, we deploy channels for permissioned blockchains. Our first contribution
is to adapt sharding on asset-management applications for the permissioned setting,
while preserving liveness and safety even on transactions spanning across-channels.
Our second contribution is to leverage channels as a confidentiality boundary,
enabling different organizations and consortia to preserve their privacy within
their channels and still be part of a bigger collaborative ecosystem. To make
our system concrete we map it on top of Hyperledger Fabric.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Elli
full_name: Androulaki, Elli
last_name: Androulaki
- first_name: Christian
full_name: Cachin, Christian
last_name: Cachin
- first_name: Angelo
full_name: De Caro, Angelo
last_name: De Caro
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
citation:
ama: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. Channels: Horizontal
scaling and confidentiality on permissioned blockchains. In: Computer Security.
Vol 11098. Springer Nature; 2018:111-131. doi:10.1007/978-3-319-99073-6_6'
apa: 'Androulaki, E., Cachin, C., De Caro, A., & Kokoris Kogias, E. (2018).
Channels: Horizontal scaling and confidentiality on permissioned blockchains.
In Computer Security (Vol. 11098, pp. 111–131). Barcelona, Spain: Springer
Nature. https://doi.org/10.1007/978-3-319-99073-6_6'
chicago: 'Androulaki, Elli, Christian Cachin, Angelo De Caro, and Eleftherios Kokoris
Kogias. “Channels: Horizontal Scaling and Confidentiality on Permissioned Blockchains.”
In Computer Security, 11098:111–31. Springer Nature, 2018. https://doi.org/10.1007/978-3-319-99073-6_6.'
ieee: 'E. Androulaki, C. Cachin, A. De Caro, and E. Kokoris Kogias, “Channels: Horizontal
scaling and confidentiality on permissioned blockchains,” in Computer Security,
Barcelona, Spain, 2018, vol. 11098, pp. 111–131.'
ista: 'Androulaki E, Cachin C, De Caro A, Kokoris Kogias E. 2018. Channels: Horizontal
scaling and confidentiality on permissioned blockchains. Computer Security. ESORICS:
European Symposium on Research in Computer Security, LNCS, vol. 11098, 111–131.'
mla: 'Androulaki, Elli, et al. “Channels: Horizontal Scaling and Confidentiality
on Permissioned Blockchains.” Computer Security, vol. 11098, Springer Nature,
2018, pp. 111–31, doi:10.1007/978-3-319-99073-6_6.'
short: E. Androulaki, C. Cachin, A. De Caro, E. Kokoris Kogias, in:, Computer Security,
Springer Nature, 2018, pp. 111–131.
conference:
end_date: 2018-09-07
location: Barcelona, Spain
name: 'ESORICS: European Symposium on Research in Computer Security'
start_date: 2018-09-03
date_created: 2020-08-26T11:47:34Z
date_published: 2018-08-08T00:00:00Z
date_updated: 2021-01-12T08:17:57Z
day: '08'
doi: 10.1007/978-3-319-99073-6_6
extern: '1'
intvolume: ' 11098'
language:
- iso: eng
month: '08'
oa_version: None
page: 111-131
publication: Computer Security
publication_identifier:
eisbn:
- '9783319990736'
isbn:
- '9783319990729'
issn:
- 0302-9743
- 1611-3349
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Channels: Horizontal scaling and confidentiality on permissioned blockchains'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11098
year: '2018'
...
---
_id: '8297'
abstract:
- lang: eng
text: "Designing a secure permissionless distributed ledger (blockchain) that performs
on par with centralized payment\r\nprocessors, such as Visa, is a challenging
task. Most existing distributed ledgers are unable to scale-out, i.e., to grow
their totalprocessing capacity with the number of validators; and those that do,
compromise security or decentralization. We present OmniLedger, a novel scale-out
distributed ledger that preserves longterm security under permissionless operation.
It ensures security and correctness by using a bias-resistant public-randomness
protocol for choosing large, statistically representative shards that process
transactions, and by introducing an efficient crossshard commit protocol that
atomically handles transactions affecting multiple shards. OmniLedger also optimizes
performance via parallel intra-shard transaction processing, ledger pruning via
collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation
for low-value transactions. An evaluation ofour experimental prototype shows that
OmniLedger’s throughput\r\nscales linearly in the number of active validators,
supporting Visa-level workloads and beyond, while confirming typical transactions
in under two seconds."
article_processing_charge: No
author:
- first_name: Eleftherios
full_name: Kokoris Kogias, Eleftherios
id: f5983044-d7ef-11ea-ac6d-fd1430a26d30
last_name: Kokoris Kogias
- first_name: Philipp
full_name: Jovanovic, Philipp
last_name: Jovanovic
- first_name: Linus
full_name: Gasser, Linus
last_name: Gasser
- first_name: Nicolas
full_name: Gailly, Nicolas
last_name: Gailly
- first_name: Ewa
full_name: Syta, Ewa
last_name: Syta
- first_name: Bryan
full_name: Ford, Bryan
last_name: Ford
citation:
ama: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger:
A secure, scale-out, decentralized ledger via sharding. In: 2018 IEEE Symposium
on Security and Privacy. IEEE; 2018:583-598. doi:10.1109/sp.2018.000-5'
apa: 'Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., &
Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding.
In 2018 IEEE Symposium on Security and Privacy (pp. 583–598). San Francisco,
CA, United States: IEEE. https://doi.org/10.1109/sp.2018.000-5'
chicago: 'Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas
Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized
Ledger via Sharding.” In 2018 IEEE Symposium on Security and Privacy, 583–98.
IEEE, 2018. https://doi.org/10.1109/sp.2018.000-5.'
ieee: 'E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford,
“OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in 2018
IEEE Symposium on Security and Privacy, San Francisco, CA, United States,
2018, pp. 583–598.'
ista: 'Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018.
OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE
Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598.'
mla: 'Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized
Ledger via Sharding.” 2018 IEEE Symposium on Security and Privacy, IEEE,
2018, pp. 583–98, doi:10.1109/sp.2018.000-5.'
short: E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford,
in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598.
conference:
end_date: 2018-05-24
location: San Francisco, CA, United States
name: 'SP: Symposium on Security and Privacy'
start_date: 2018-05-20
date_created: 2020-08-26T11:46:35Z
date_published: 2018-07-26T00:00:00Z
date_updated: 2021-01-12T08:17:56Z
day: '26'
doi: 10.1109/sp.2018.000-5
extern: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2017/406
month: '07'
oa: 1
oa_version: Preprint
page: 583-598
publication: 2018 IEEE Symposium on Security and Privacy
publication_identifier:
isbn:
- '9781538643532'
issn:
- 2375-1207
publication_status: published
publisher: IEEE
quality_controlled: '1'
status: public
title: 'OmniLedger: A secure, scale-out, decentralized ledger via sharding'
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '8443'
abstract:
- lang: eng
text: Characterizing the structure of membrane proteins (MPs) generally requires
extraction from their native environment, most commonly with detergents. Yet,
the physicochemical properties of detergent micelles and lipid bilayers differ
markedly and could alter the structural organization of MPs, albeit without general
rules. Dodecylphosphocholine (DPC) is the most widely used detergent for MP structure
determination by NMR, but the physiological relevance of several prominent structures
has been questioned, though indirectly, by other biophysical techniques, e.g.,
functional/thermostability assay (TSA) and molecular dynamics (MD) simulations.
Here, we resolve unambiguously this controversy by probing the functional relevance
of three different mitochondrial carriers (MCs) in DPC at the atomic level, using
an exhaustive set of solution-NMR experiments, complemented by functional/TSA
and MD data. Our results provide atomic-level insight into the structure, substrate
interaction and dynamics of the detergent–membrane protein complexes and demonstrates
cogently that, while high-resolution NMR signals can be obtained for MCs in DPC,
they systematically correspond to nonfunctional states.
article_processing_charge: No
article_type: original
author:
- first_name: Vilius
full_name: Kurauskas, Vilius
last_name: Kurauskas
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Paola
full_name: Lunetti, Paola
last_name: Lunetti
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Lionel
full_name: Imbert, Lionel
last_name: Imbert
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Martin S.
full_name: King, Martin S.
last_name: King
- first_name: Rémy
full_name: Sounier, Rémy
last_name: Sounier
- first_name: Vincenza
full_name: Dolce, Vincenza
last_name: Dolce
- first_name: Edmund R. S.
full_name: Kunji, Edmund R. S.
last_name: Kunji
- first_name: Loredana
full_name: Capobianco, Loredana
last_name: Capobianco
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Kurauskas V, Hessel A, Ma P, et al. How detergent impacts membrane proteins:
Atomic-level views of mitochondrial carriers in dodecylphosphocholine. The
Journal of Physical Chemistry Letters. 2018;9(5):933-938. doi:10.1021/acs.jpclett.8b00269'
apa: 'Kurauskas, V., Hessel, A., Ma, P., Lunetti, P., Weinhäupl, K., Imbert, L.,
… Schanda, P. (2018). How detergent impacts membrane proteins: Atomic-level views
of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical
Chemistry Letters. American Chemical Society. https://doi.org/10.1021/acs.jpclett.8b00269'
chicago: 'Kurauskas, Vilius, Audrey Hessel, Peixiang Ma, Paola Lunetti, Katharina
Weinhäupl, Lionel Imbert, Bernhard Brutscher, et al. “How Detergent Impacts Membrane
Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine.”
The Journal of Physical Chemistry Letters. American Chemical Society, 2018.
https://doi.org/10.1021/acs.jpclett.8b00269.'
ieee: 'V. Kurauskas et al., “How detergent impacts membrane proteins: Atomic-level
views of mitochondrial carriers in dodecylphosphocholine,” The Journal of Physical
Chemistry Letters, vol. 9, no. 5. American Chemical Society, pp. 933–938,
2018.'
ista: 'Kurauskas V, Hessel A, Ma P, Lunetti P, Weinhäupl K, Imbert L, Brutscher
B, King MS, Sounier R, Dolce V, Kunji ERS, Capobianco L, Chipot C, Dehez F, Bersch
B, Schanda P. 2018. How detergent impacts membrane proteins: Atomic-level views
of mitochondrial carriers in dodecylphosphocholine. The Journal of Physical Chemistry
Letters. 9(5), 933–938.'
mla: 'Kurauskas, Vilius, et al. “How Detergent Impacts Membrane Proteins: Atomic-Level
Views of Mitochondrial Carriers in Dodecylphosphocholine.” The Journal of Physical
Chemistry Letters, vol. 9, no. 5, American Chemical Society, 2018, pp. 933–38,
doi:10.1021/acs.jpclett.8b00269.'
short: V. Kurauskas, A. Hessel, P. Ma, P. Lunetti, K. Weinhäupl, L. Imbert, B. Brutscher,
M.S. King, R. Sounier, V. Dolce, E.R.S. Kunji, L. Capobianco, C. Chipot, F. Dehez,
B. Bersch, P. Schanda, The Journal of Physical Chemistry Letters 9 (2018) 933–938.
date_created: 2020-09-18T10:05:45Z
date_published: 2018-02-03T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '03'
doi: 10.1021/acs.jpclett.8b00269
extern: '1'
intvolume: ' 9'
issue: '5'
keyword:
- General Materials Science
language:
- iso: eng
month: '02'
oa_version: None
page: 933-938
publication: The Journal of Physical Chemistry Letters
publication_identifier:
issn:
- 1948-7185
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'How detergent impacts membrane proteins: Atomic-level views of mitochondrial
carriers in dodecylphosphocholine'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '8440'
abstract:
- lang: eng
text: Mycobacterium tuberculosis can remain dormant in the host, an ability that
explains the failure of many current tuberculosis treatments. Recently, the natural
products cyclomarin, ecumicin, and lassomycin have been shown to efficiently kill
Mycobacterium tuberculosis persisters. Their target is the N-terminal domain of
the hexameric AAA+ ATPase ClpC1, which recognizes, unfolds, and translocates protein
substrates, such as proteins containing phosphorylated arginine residues, to the
ClpP1P2 protease for degradation. Surprisingly, these antibiotics do not inhibit
ClpC1 ATPase activity, and how they cause cell death is still unclear. Here, using
NMR and small-angle X-ray scattering, we demonstrate that arginine-phosphate binding
to the ClpC1 N-terminal domain induces millisecond dynamics. We show that these
dynamics are caused by conformational changes and do not result from unfolding
or oligomerization of this domain. Cyclomarin binding to this domain specifically
blocked these N-terminal dynamics. On the basis of these results, we propose a
mechanism of action involving cyclomarin-induced restriction of ClpC1 dynamics,
which modulates the chaperone enzymatic activity leading eventually to cell death.
article_processing_charge: No
article_type: original
author:
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Martha
full_name: Brennich, Martha
last_name: Brennich
- first_name: Uli
full_name: Kazmaier, Uli
last_name: Kazmaier
- first_name: Joel
full_name: Lelievre, Joel
last_name: Lelievre
- first_name: Lluis
full_name: Ballell, Lluis
last_name: Ballell
- first_name: Alfred
full_name: Goldberg, Alfred
last_name: Goldberg
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Hugo
full_name: Fraga, Hugo
last_name: Fraga
citation:
ama: Weinhäupl K, Brennich M, Kazmaier U, et al. The antibiotic cyclomarin blocks
arginine-phosphate–induced millisecond dynamics in the N-terminal domain of ClpC1
from Mycobacterium tuberculosis. Journal of Biological Chemistry. 2018;293(22):8379-8393.
doi:10.1074/jbc.ra118.002251
apa: Weinhäupl, K., Brennich, M., Kazmaier, U., Lelievre, J., Ballell, L., Goldberg,
A., … Fraga, H. (2018). The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis.
Journal of Biological Chemistry. American Society for Biochemistry &
Molecular Biology. https://doi.org/10.1074/jbc.ra118.002251
chicago: Weinhäupl, Katharina, Martha Brennich, Uli Kazmaier, Joel Lelievre, Lluis
Ballell, Alfred Goldberg, Paul Schanda, and Hugo Fraga. “The Antibiotic Cyclomarin
Blocks Arginine-Phosphate–Induced Millisecond Dynamics in the N-Terminal Domain
of ClpC1 from Mycobacterium Tuberculosis.” Journal of Biological Chemistry.
American Society for Biochemistry & Molecular Biology, 2018. https://doi.org/10.1074/jbc.ra118.002251.
ieee: K. Weinhäupl et al., “The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis,”
Journal of Biological Chemistry, vol. 293, no. 22. American Society for
Biochemistry & Molecular Biology, pp. 8379–8393, 2018.
ista: Weinhäupl K, Brennich M, Kazmaier U, Lelievre J, Ballell L, Goldberg A, Schanda
P, Fraga H. 2018. The antibiotic cyclomarin blocks arginine-phosphate–induced
millisecond dynamics in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis.
Journal of Biological Chemistry. 293(22), 8379–8393.
mla: Weinhäupl, Katharina, et al. “The Antibiotic Cyclomarin Blocks Arginine-Phosphate–Induced
Millisecond Dynamics in the N-Terminal Domain of ClpC1 from Mycobacterium Tuberculosis.”
Journal of Biological Chemistry, vol. 293, no. 22, American Society for
Biochemistry & Molecular Biology, 2018, pp. 8379–93, doi:10.1074/jbc.ra118.002251.
short: K. Weinhäupl, M. Brennich, U. Kazmaier, J. Lelievre, L. Ballell, A. Goldberg,
P. Schanda, H. Fraga, Journal of Biological Chemistry 293 (2018) 8379–8393.
date_created: 2020-09-18T10:05:18Z
date_published: 2018-06-01T00:00:00Z
date_updated: 2021-01-12T08:19:17Z
day: '01'
doi: 10.1074/jbc.ra118.002251
extern: '1'
intvolume: ' 293'
issue: '22'
keyword:
- Cell Biology
- Biochemistry
- Molecular Biology
language:
- iso: eng
month: '06'
oa_version: None
page: 8379-8393
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
- 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: The antibiotic cyclomarin blocks arginine-phosphate–induced millisecond dynamics
in the N-terminal domain of ClpC1 from Mycobacterium tuberculosis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 293
year: '2018'
...
---
_id: '8442'
abstract:
- lang: eng
text: Membrane proteins perform a host of vital cellular functions. Deciphering
the molecular mechanisms whereby they fulfill these functions requires detailed
biophysical and structural investigations. Detergents have proven pivotal to extract
the protein from its native surroundings. Yet, they provide a milieu that departs
significantly from that of the biological membrane, to the extent that the structure,
the dynamics, and the interactions of membrane proteins in detergents may considerably
vary, as compared to the native environment. Understanding the impact of detergents
on membrane proteins is, therefore, crucial to assess the biological relevance
of results obtained in detergents. Here, we review the strengths and weaknesses
of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR
studies of membrane proteins. While this class of detergents is often successful
for membrane protein solubilization, a growing list of examples points to destabilizing
and denaturing properties, in particular for α-helical membrane proteins. Our
comprehensive analysis stresses the importance of stringent controls when working
with this class of detergents and when analyzing the structure and dynamics of
membrane proteins in alkyl phosphocholine detergents.
article_processing_charge: No
article_type: original
author:
- first_name: Christophe
full_name: Chipot, Christophe
last_name: Chipot
- first_name: François
full_name: Dehez, François
last_name: Dehez
- first_name: Jason R.
full_name: Schnell, Jason R.
last_name: Schnell
- first_name: Nicole
full_name: Zitzmann, Nicole
last_name: Zitzmann
- first_name: Eva
full_name: Pebay-Peyroula, Eva
last_name: Pebay-Peyroula
- first_name: Laurent J.
full_name: Catoire, Laurent J.
last_name: Catoire
- first_name: Bruno
full_name: Miroux, Bruno
last_name: Miroux
- first_name: Edmund R. S.
full_name: Kunji, Edmund R. S.
last_name: Kunji
- first_name: Gianluigi
full_name: Veglia, Gianluigi
last_name: Veglia
- first_name: Timothy A.
full_name: Cross, Timothy A.
last_name: Cross
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: 'Chipot C, Dehez F, Schnell JR, et al. Perturbations of native membrane protein
structure in alkyl phosphocholine detergents: A critical assessment of NMR and
biophysical studies. Chemical Reviews. 2018;118(7):3559-3607. doi:10.1021/acs.chemrev.7b00570'
apa: 'Chipot, C., Dehez, F., Schnell, J. R., Zitzmann, N., Pebay-Peyroula, E., Catoire,
L. J., … Schanda, P. (2018). Perturbations of native membrane protein structure
in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical
studies. Chemical Reviews. American Chemical Society. https://doi.org/10.1021/acs.chemrev.7b00570'
chicago: 'Chipot, Christophe, François Dehez, Jason R. Schnell, Nicole Zitzmann,
Eva Pebay-Peyroula, Laurent J. Catoire, Bruno Miroux, et al. “Perturbations of
Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical
Assessment of NMR and Biophysical Studies.” Chemical Reviews. American
Chemical Society, 2018. https://doi.org/10.1021/acs.chemrev.7b00570.'
ieee: 'C. Chipot et al., “Perturbations of native membrane protein structure
in alkyl phosphocholine detergents: A critical assessment of NMR and biophysical
studies,” Chemical Reviews, vol. 118, no. 7. American Chemical Society,
pp. 3559–3607, 2018.'
ista: 'Chipot C, Dehez F, Schnell JR, Zitzmann N, Pebay-Peyroula E, Catoire LJ,
Miroux B, Kunji ERS, Veglia G, Cross TA, Schanda P. 2018. Perturbations of native
membrane protein structure in alkyl phosphocholine detergents: A critical assessment
of NMR and biophysical studies. Chemical Reviews. 118(7), 3559–3607.'
mla: 'Chipot, Christophe, et al. “Perturbations of Native Membrane Protein Structure
in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical
Studies.” Chemical Reviews, vol. 118, no. 7, American Chemical Society,
2018, pp. 3559–607, doi:10.1021/acs.chemrev.7b00570.'
short: C. Chipot, F. Dehez, J.R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L.J. Catoire,
B. Miroux, E.R.S. Kunji, G. Veglia, T.A. Cross, P. Schanda, Chemical Reviews 118
(2018) 3559–3607.
date_created: 2020-09-18T10:05:35Z
date_published: 2018-02-28T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '28'
doi: 10.1021/acs.chemrev.7b00570
extern: '1'
intvolume: ' 118'
issue: '7'
keyword:
- General Chemistry
language:
- iso: eng
month: '02'
oa_version: None
page: 3559-3607
publication: Chemical Reviews
publication_identifier:
issn:
- 0009-2665
- 1520-6890
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: 'Perturbations of native membrane protein structure in alkyl phosphocholine
detergents: A critical assessment of NMR and biophysical studies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2018'
...
---
_id: '8441'
abstract:
- lang: eng
text: Solid-state near-rotary-resonance measurements of the spin–lattice relaxation
rate in the rotating frame (R1ρ) is a powerful NMR technique for studying molecular
dynamics in the microsecond time scale. The small difference between the spin-lock
(SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions,
at the same time it brings up some methodological challenges. In this work, several
issues affecting correct measurements and analysis of 15N R1ρ data are considered
in detail. Among them are signal amplitude as a function of the difference between
SL and MAS frequencies, “dead time” in the initial part of the relaxation decay
caused by transient spin-dynamic oscillations, measurements under HORROR condition
and proper treatment of the multi-exponential relaxation decays. The multiple
15N R1ρ measurements at different SL fields and temperatures have been conducted
in 1D mode (i.e. without site-specific resolution) for a set of four different
microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin)
to study the overall protein rocking in a crystal. While the amplitude of this
motion varies very significantly, its correlation time for all four sample is
practically the same, 30–50 μs. The amplitude of the rocking motion correlates
with the packing density of a protein crystal. It has been suggested that the
rocking motion is not diffusive but likely a jump-like dynamic process.
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
full_name: Krushelnitsky, Alexey
last_name: Krushelnitsky
- first_name: Diego
full_name: Gauto, Diego
last_name: Gauto
- first_name: Diana C.
full_name: Rodriguez Camargo, Diana C.
last_name: Rodriguez Camargo
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Kay
full_name: Saalwächter, Kay
last_name: Saalwächter
citation:
ama: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K.
Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals. Journal of Biomolecular
NMR. 2018;71(1):53-67. doi:10.1007/s10858-018-0191-4'
apa: 'Krushelnitsky, A., Gauto, D., Rodriguez Camargo, D. C., Schanda, P., &
Saalwächter, K. (2018). Microsecond motions probed by near-rotary-resonance R1ρ
15N MAS NMR experiments: The model case of protein overall-rocking in crystals.
Journal of Biomolecular NMR. Springer Nature. https://doi.org/10.1007/s10858-018-0191-4'
chicago: 'Krushelnitsky, Alexey, Diego Gauto, Diana C. Rodriguez Camargo, Paul Schanda,
and Kay Saalwächter. “Microsecond Motions Probed by Near-Rotary-Resonance R1ρ
15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.”
Journal of Biomolecular NMR. Springer Nature, 2018. https://doi.org/10.1007/s10858-018-0191-4.'
ieee: 'A. Krushelnitsky, D. Gauto, D. C. Rodriguez Camargo, P. Schanda, and K. Saalwächter,
“Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals,” Journal of Biomolecular
NMR, vol. 71, no. 1. Springer Nature, pp. 53–67, 2018.'
ista: 'Krushelnitsky A, Gauto D, Rodriguez Camargo DC, Schanda P, Saalwächter K.
2018. Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals. Journal of Biomolecular
NMR. 71(1), 53–67.'
mla: 'Krushelnitsky, Alexey, et al. “Microsecond Motions Probed by Near-Rotary-Resonance
R1ρ 15N MAS NMR Experiments: The Model Case of Protein Overall-Rocking in Crystals.”
Journal of Biomolecular NMR, vol. 71, no. 1, Springer Nature, 2018, pp.
53–67, doi:10.1007/s10858-018-0191-4.'
short: A. Krushelnitsky, D. Gauto, D.C. Rodriguez Camargo, P. Schanda, K. Saalwächter,
Journal of Biomolecular NMR 71 (2018) 53–67.
date_created: 2020-09-18T10:05:28Z
date_published: 2018-05-30T00:00:00Z
date_updated: 2021-01-12T08:19:17Z
day: '30'
doi: 10.1007/s10858-018-0191-4
extern: '1'
intvolume: ' 71'
issue: '1'
language:
- iso: eng
month: '05'
oa_version: Published Version
page: 53-67
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: 'Microsecond motions probed by near-rotary-resonance R1ρ 15N MAS NMR experiments:
The model case of protein overall-rocking in crystals'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 71
year: '2018'
...
---
_id: '8439'
abstract:
- lang: eng
text: Lipopolysaccharides (LPS) are complex glycolipids forming the outside layer
of Gram-negative bacteria. Their hydrophobic and heterogeneous nature greatly
hampers their structural study in an environment similar to the bacterial surface.
We have studied LPS purified from E. coli and pathogenic P. aeruginosa with long
O-antigen polysaccharides assembled in solution as vesicles or elongated micelles.
Solid-state NMR with magic-angle spinning permitted the identification of NMR
signals arising from regions with different flexibilities in the LPS, from the
lipid components to the O-antigen polysaccharides. Atomic scale data on the LPS
enabled the study of the interaction of gentamicin antibiotic bound to P. aeruginosa
LPS, for which we could confirm that a specific oligosaccharide is involved in
the antibiotic binding. The possibility to study LPS alone and bound to a ligand
when it is assembled in membrane-like structures opens great prospects for the
investigation of proteins and antibiotics that specifically target such an important
molecule at the surface of Gram-negative bacteria.
article_processing_charge: No
article_type: original
author:
- first_name: Cedric
full_name: Laguri, Cedric
last_name: Laguri
- first_name: Alba
full_name: Silipo, Alba
last_name: Silipo
- first_name: Alessandra M.
full_name: Martorana, Alessandra M.
last_name: Martorana
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Roberta
full_name: Marchetti, Roberta
last_name: Marchetti
- first_name: Alessandra
full_name: Polissi, Alessandra
last_name: Polissi
- first_name: Antonio
full_name: Molinaro, Antonio
last_name: Molinaro
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Laguri C, Silipo A, Martorana AM, et al. Solid state NMR studies of intact
lipopolysaccharide endotoxin. ACS Chemical Biology. 2018;13(8):2106-2113.
doi:10.1021/acschembio.8b00271
apa: Laguri, C., Silipo, A., Martorana, A. M., Schanda, P., Marchetti, R., Polissi,
A., … Simorre, J.-P. (2018). Solid state NMR studies of intact lipopolysaccharide
endotoxin. ACS Chemical Biology. American Chemical Society. https://doi.org/10.1021/acschembio.8b00271
chicago: Laguri, Cedric, Alba Silipo, Alessandra M. Martorana, Paul Schanda, Roberta
Marchetti, Alessandra Polissi, Antonio Molinaro, and Jean-Pierre Simorre. “Solid
State NMR Studies of Intact Lipopolysaccharide Endotoxin.” ACS Chemical Biology.
American Chemical Society, 2018. https://doi.org/10.1021/acschembio.8b00271.
ieee: C. Laguri et al., “Solid state NMR studies of intact lipopolysaccharide
endotoxin,” ACS Chemical Biology, vol. 13, no. 8. American Chemical Society,
pp. 2106–2113, 2018.
ista: Laguri C, Silipo A, Martorana AM, Schanda P, Marchetti R, Polissi A, Molinaro
A, Simorre J-P. 2018. Solid state NMR studies of intact lipopolysaccharide endotoxin.
ACS Chemical Biology. 13(8), 2106–2113.
mla: Laguri, Cedric, et al. “Solid State NMR Studies of Intact Lipopolysaccharide
Endotoxin.” ACS Chemical Biology, vol. 13, no. 8, American Chemical Society,
2018, pp. 2106–13, doi:10.1021/acschembio.8b00271.
short: C. Laguri, A. Silipo, A.M. Martorana, P. Schanda, R. Marchetti, A. Polissi,
A. Molinaro, J.-P. Simorre, ACS Chemical Biology 13 (2018) 2106–2113.
date_created: 2020-09-18T10:05:09Z
date_published: 2018-07-02T00:00:00Z
date_updated: 2021-01-12T08:19:16Z
day: '02'
doi: 10.1021/acschembio.8b00271
extern: '1'
intvolume: ' 13'
issue: '8'
keyword:
- Molecular Medicine
- Biochemistry
- General Medicine
language:
- iso: eng
month: '07'
oa_version: None
page: 2106-2113
publication: ACS Chemical Biology
publication_identifier:
issn:
- 1554-8929
- 1554-8937
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Solid state NMR studies of intact lipopolysaccharide endotoxin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2018'
...