---
_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'
...