---
_id: '10396'
abstract:
- lang: eng
text: Stimfit is a free cross-platform software package for viewing and analyzing
electrophysiological data. It supports most standard file types for cellular neurophysiology
and other biomedical formats. Its analysis algorithms have been used and validated
in several experimental laboratories. Its embedded Python scripting interface
makes Stimfit highly extensible and customizable.
article_number: '000010151520134181'
article_processing_charge: No
article_type: original
author:
- first_name: Alois
full_name: Schlögl, Alois
id: 45BF87EE-F248-11E8-B48F-1D18A9856A87
last_name: Schlögl
orcid: 0000-0002-5621-8100
- first_name: Peter M
full_name: Jonas, Peter M
id: 353C1B58-F248-11E8-B48F-1D18A9856A87
last_name: Jonas
orcid: 0000-0001-5001-4804
- first_name: C.
full_name: Schmidt-Hieber, C.
last_name: Schmidt-Hieber
- first_name: S. J.
full_name: Guzman, S. J.
last_name: Guzman
citation:
ama: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 2013;58(SI-1-Track-G). doi:10.1515/bmt-2013-4181'
apa: 'Schlögl, A., Jonas, P. M., Schmidt-Hieber, C., & Guzman, S. J. (2013).
Stimfit: A fast visualization and analysis environment for cellular neurophysiology.
Biomedical Engineering / Biomedizinische Technik. Graz, Austria: De Gruyter.
https://doi.org/10.1515/bmt-2013-4181'
chicago: 'Schlögl, Alois, Peter M Jonas, C. Schmidt-Hieber, and S. J. Guzman. “Stimfit:
A Fast Visualization and Analysis Environment for Cellular Neurophysiology.” Biomedical
Engineering / Biomedizinische Technik. De Gruyter, 2013. https://doi.org/10.1515/bmt-2013-4181.'
ieee: 'A. Schlögl, P. M. Jonas, C. Schmidt-Hieber, and S. J. Guzman, “Stimfit: A
fast visualization and analysis environment for cellular neurophysiology,” Biomedical
Engineering / Biomedizinische Technik, vol. 58, no. SI-1-Track-G. De Gruyter,
2013.'
ista: 'Schlögl A, Jonas PM, Schmidt-Hieber C, Guzman SJ. 2013. Stimfit: A fast visualization
and analysis environment for cellular neurophysiology. Biomedical Engineering
/ Biomedizinische Technik. 58(SI-1-Track-G), 000010151520134181.'
mla: 'Schlögl, Alois, et al. “Stimfit: A Fast Visualization and Analysis Environment
for Cellular Neurophysiology.” Biomedical Engineering / Biomedizinische Technik,
vol. 58, no. SI-1-Track-G, 000010151520134181, De Gruyter, 2013, doi:10.1515/bmt-2013-4181.'
short: A. Schlögl, P.M. Jonas, C. Schmidt-Hieber, S.J. Guzman, Biomedical Engineering
/ Biomedizinische Technik 58 (2013).
conference:
end_date: 2013-09-21
location: Graz, Austria
name: 'BMT: Biomedizinische Technik '
start_date: 2013-09-19
date_created: 2021-12-01T14:35:35Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-12-02T12:51:12Z
day: '01'
ddc:
- '005'
- '610'
department:
- _id: PeJo
doi: 10.1515/bmt-2013-4181
external_id:
pmid:
- '24042795'
file:
- access_level: open_access
checksum: cdfc5339b530a25d6079f7223f0b1f16
content_type: application/pdf
creator: schloegl
date_created: 2021-12-01T14:38:08Z
date_updated: 2021-12-01T14:38:08Z
file_id: '10397'
file_name: Schloegl_Abstract-BMT2013.pdf
file_size: 149825
relation: main_file
success: 1
file_date_updated: 2021-12-01T14:38:08Z
has_accepted_license: '1'
intvolume: ' 58'
issue: SI-1-Track-G
keyword:
- biomedical engineering
- data analysis
- free software
language:
- iso: eng
month: '08'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Biomedical Engineering / Biomedizinische Technik
publication_identifier:
eissn:
- 1862-278X
issn:
- 0013-5585
publication_status: published
publisher: De Gruyter
quality_controlled: '1'
status: public
title: 'Stimfit: A fast visualization and analysis environment for cellular neurophysiology'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 58
year: '2013'
...
---
_id: '9459'
abstract:
- lang: eng
text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation
of transposable elements, but the reason for this is unknown. How DDM1 interacts
with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM),
which is thought to mediate plant asymmetric methylation through DRM enzymes,
is also unclear. Here, we show that most asymmetric methylation is facilitated
by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find
that heterochromatic sequences preferentially require DDM1 for DNA methylation
and that this preference depends on linker histone H1. RdDM is instead inhibited
by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together,
DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress
transposition and regulate the methylation and expression of genes. Our results
indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin
to allow stable silencing of transposable elements in cooperation with the RdDM
pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Devin
full_name: Coleman-Derr, Devin
last_name: Coleman-Derr
- first_name: Leor
full_name: Eshed-Williams, Leor
last_name: Eshed-Williams
- first_name: Ka
full_name: Thao, Ka
last_name: Thao
- first_name: Stacey L.
full_name: Harmer, Stacey L.
last_name: Harmer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1
allows DNA methyltransferases to access H1-containing heterochromatin. Cell.
2013;153(1):193-205. doi:10.1016/j.cell.2013.02.033
apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L.,
Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin. Cell. Elsevier.
https://doi.org/10.1016/j.cell.2013.02.033
chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor
Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis
Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing
Heterochromatin.” Cell. Elsevier, 2013. https://doi.org/10.1016/j.cell.2013.02.033.
ieee: A. Zemach et al., “The Arabidopsis nucleosome remodeler DDM1 allows
DNA methyltransferases to access H1-containing heterochromatin,” Cell,
vol. 153, no. 1. Elsevier, pp. 193–205, 2013.
ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer
SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases
to access H1-containing heterochromatin. Cell. 153(1), 193–205.
mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA
Methyltransferases to Access H1-Containing Heterochromatin.” Cell, vol.
153, no. 1, Elsevier, 2013, pp. 193–205, doi:10.1016/j.cell.2013.02.033.
short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K.
Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.
date_created: 2021-06-04T12:23:28Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2021-12-14T08:25:35Z
day: '28'
department:
- _id: DaZi
doi: 10.1016/j.cell.2013.02.033
extern: '1'
external_id:
pmid:
- '23540698'
intvolume: ' 153'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2013.02.033
month: '03'
oa: 1
oa_version: Published Version
page: 193-205
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to
access H1-containing heterochromatin
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 153
year: '2013'
...
---
_id: '9481'
abstract:
- lang: eng
text: Arabidopsis thaliana endosperm, a transient tissue that nourishes the embryo,
exhibits extensive localized DNA demethylation on maternally inherited chromosomes.
Demethylation mediates parent-of-origin–specific (imprinted) gene expression but
is apparently unnecessary for the extensive accumulation of maternally biased
small RNA (sRNA) molecules detected in seeds. Endosperm DNA in the distantly related
monocots rice and maize is likewise locally hypomethylated, but whether this hypomethylation
is generally parent-of-origin specific is unknown. Imprinted expression of sRNA
also remains uninvestigated in monocot seeds. Here, we report high-coverage sequencing
of the Kitaake rice cultivar that enabled us to show that localized hypomethylation
in rice endosperm occurs solely on the maternal genome, preferring regions of
high DNA accessibility. Maternally expressed imprinted genes are enriched for
hypomethylation at putative promoter regions and transcriptional termini and paternally
expressed genes at promoters and gene bodies, mirroring our recent results in
A. thaliana. However, unlike in A. thaliana, rice endosperm sRNA populations are
dominated by specific strong sRNA-producing loci, and imprinted 24-nt sRNAs are
expressed from both parental genomes and correlate with hypomethylation. Overlaps
between imprinted sRNA loci and imprinted genes expressed from opposite alleles
suggest that sRNAs may regulate genomic imprinting. Whereas sRNAs in seedling
tissues primarily originate from small class II (cut-and-paste) transposable elements,
those in endosperm are more uniformly derived, including sequences from other
transposon classes, as well as genic and intergenic regions. Our data indicate
that the endosperm exhibits a unique pattern of sRNA expression and suggest that
localized hypomethylation of maternal endosperm DNA is conserved in flowering
plants.
article_processing_charge: No
article_type: original
author:
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Randy
full_name: Ruan, Randy
last_name: Ruan
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Manoj K.
full_name: Sharma, Manoj K.
last_name: Sharma
- first_name: Rita
full_name: Sharma, Rita
last_name: Sharma
- first_name: Pamela C
full_name: Ronald, Pamela C
last_name: Ronald
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Rodrigues JA, Ruan R, Nishimura T, et al. Imprinted expression of genes and
small RNA is associated with localized hypomethylation of the maternal genome
in rice endosperm. Proceedings of the National Academy of Sciences. 2013;110(19):7934-7939.
doi:10.1073/pnas.1306164110
apa: Rodrigues, J. A., Ruan, R., Nishimura, T., Sharma, M. K., Sharma, R., Ronald,
P. C., … Zilberman, D. (2013). Imprinted expression of genes and small RNA is
associated with localized hypomethylation of the maternal genome in rice endosperm.
Proceedings of the National Academy of Sciences. National Academy of Sciences.
https://doi.org/10.1073/pnas.1306164110
chicago: Rodrigues, Jessica A., Randy Ruan, Toshiro Nishimura, Manoj K. Sharma,
Rita Sharma, Pamela C Ronald, Robert L. Fischer, and Daniel Zilberman. “Imprinted
Expression of Genes and Small RNA Is Associated with Localized Hypomethylation
of the Maternal Genome in Rice Endosperm.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2013. https://doi.org/10.1073/pnas.1306164110.
ieee: J. A. Rodrigues et al., “Imprinted expression of genes and small RNA
is associated with localized hypomethylation of the maternal genome in rice endosperm,”
Proceedings of the National Academy of Sciences, vol. 110, no. 19. National
Academy of Sciences, pp. 7934–7939, 2013.
ista: Rodrigues JA, Ruan R, Nishimura T, Sharma MK, Sharma R, Ronald PC, Fischer
RL, Zilberman D. 2013. Imprinted expression of genes and small RNA is associated
with localized hypomethylation of the maternal genome in rice endosperm. Proceedings
of the National Academy of Sciences. 110(19), 7934–7939.
mla: Rodrigues, Jessica A., et al. “Imprinted Expression of Genes and Small RNA
Is Associated with Localized Hypomethylation of the Maternal Genome in Rice Endosperm.”
Proceedings of the National Academy of Sciences, vol. 110, no. 19, National
Academy of Sciences, 2013, pp. 7934–39, doi:10.1073/pnas.1306164110.
short: J.A. Rodrigues, R. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, P.C. Ronald,
R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 110
(2013) 7934–7939.
date_created: 2021-06-07T07:31:02Z
date_published: 2013-05-07T00:00:00Z
date_updated: 2021-12-14T08:26:44Z
day: '07'
department:
- _id: DaZi
doi: 10.1073/pnas.1306164110
extern: '1'
external_id:
pmid:
- '23613580'
intvolume: ' 110'
issue: '19'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1306164110
month: '05'
oa: 1
oa_version: Published Version
page: 7934-7939
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Imprinted expression of genes and small RNA is associated with localized hypomethylation
of the maternal genome in rice endosperm
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 110
year: '2013'
...
---
_id: '9520'
abstract:
- lang: eng
text: Plants undergo alternation of generation in which reproductive cells develop
in the plant body ("sporophytic generation") and then differentiate into a multicellular
gamete-forming "gametophytic generation." Different populations of helper cells
assist in this transgenerational journey, with somatic tissues supporting early
development and single nurse cells supporting gametogenesis. New data reveal a
two-way relationship between early reproductive cells and their helpers involving
complex epigenetic and signaling networks determining cell number and fate. Later,
the egg cell plays a central role in specifying accessory cells, whereas in both
gametophytes, companion cells contribute non-cell-autonomously to the epigenetic
landscape of the gamete genomes.
article_processing_charge: No
article_type: review
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Hugh
full_name: Dickinson, Hugh
last_name: Dickinson
citation:
ama: 'Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ
cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014'
apa: 'Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across
generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2013.01.014'
chicago: 'Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across
Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier,
2013. https://doi.org/10.1016/j.devcel.2013.01.014.'
ieee: 'X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations:
Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3.
Elsevier, pp. 215–225, 2013.'
ista: 'Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations:
Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.'
mla: 'Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk
in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25,
doi:10.1016/j.devcel.2013.01.014.'
short: X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.
date_created: 2021-06-08T06:14:50Z
date_published: 2013-02-11T00:00:00Z
date_updated: 2023-05-08T11:00:59Z
day: '11'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.devcel.2013.01.014
extern: '1'
external_id:
pmid:
- '23410937'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2013.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 215-225
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A conversation across generations: Soma-germ cell crosstalk in plants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '9749'
abstract:
- lang: eng
text: Cooperative behavior, where one individual incurs a cost to help another,
is a wide spread phenomenon. Here we study direct reciprocity in the context of
the alternating Prisoner's Dilemma. We consider all strategies that can be implemented
by one and two-state automata. We calculate the payoff matrix of all pairwise
encounters in the presence of noise. We explore deterministic selection dynamics
with and without mutation. Using different error rates and payoff values, we observe
convergence to a small number of distinct equilibria. Two of them are uncooperative
strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium
is mixed and represents a cooperative alliance of several strategies, dominated
by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent
has cooperated; it defects once when the opponent has defected, but subsequently
Forgiver attempts to re-establish cooperation even if the opponent has defected
again. Forgiver is not an evolutionarily stable strategy, but the alliance, which
it rules, is asymptotically stable. For a wide range of parameter values the most
commonly observed outcome is convergence to the mixed equilibrium, dominated by
Forgiver. Our results show that although forgiving might incur a short-term loss
it can lead to a long-term gain. Forgiveness facilitates stable cooperation in
the presence of exploitation and noise.
article_processing_charge: No
author:
- first_name: Benjamin
full_name: Zagorsky, Benjamin
last_name: Zagorsky
- first_name: Johannes
full_name: Reiter, Johannes
id: 4A918E98-F248-11E8-B48F-1D18A9856A87
last_name: Reiter
orcid: 0000-0002-0170-7353
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Martin
full_name: Nowak, Martin
last_name: Nowak
citation:
ama: Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating
prisoner’s dilemma . 2013. doi:10.1371/journal.pone.0080814.s001
apa: Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver
triumphs in alternating prisoner’s dilemma . Public Library of Science. https://doi.org/10.1371/journal.pone.0080814.s001
chicago: Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin
Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” Public Library
of Science, 2013. https://doi.org/10.1371/journal.pone.0080814.s001.
ieee: B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in
alternating prisoner’s dilemma .” Public Library of Science, 2013.
ista: Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating
prisoner’s dilemma , Public Library of Science, 10.1371/journal.pone.0080814.s001.
mla: Zagorsky, Benjamin, et al. Forgiver Triumphs in Alternating Prisoner’s Dilemma
. Public Library of Science, 2013, doi:10.1371/journal.pone.0080814.s001.
short: B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, (2013).
date_created: 2021-07-28T15:45:07Z
date_published: 2013-12-12T00:00:00Z
date_updated: 2023-02-23T10:34:39Z
day: '12'
department:
- _id: KrCh
doi: 10.1371/journal.pone.0080814.s001
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '2247'
relation: used_in_publication
status: public
status: public
title: 'Forgiver triumphs in alternating prisoner''s dilemma '
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '9751'
abstract:
- lang: eng
text: High relatedness among interacting individuals has generally been considered
a precondition for the evolution of altruism. However, kin-selection theory also
predicts the evolution of altruism when relatedness is low, as long as the cost
of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence
for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding
to the attack of an obligately lytic phage by committing suicide in order to prevent
parasite transmission to nearby relatives. We found that bacterial suicide provides
large benefits to survivors at marginal costs to committers. The cost of suicide
was low because infected cells are moribund, rapidly dying upon phage infection,
such that no more opportunity for reproduction remains. As a consequence of its
marginal cost, host suicide was selectively favoured even when relatedness between
committers and survivors approached zero. Altogether, our findings demonstrate
that low-cost suicide can evolve with ease, represents an effective host-defence
strategy, and seems to be widespread among microbes. Moreover, low-cost suicide
might also occur in higher organisms as exemplified by infected social insect
workers leaving the colony to die in isolation.
article_processing_charge: No
author:
- first_name: Dominik
full_name: Refardt, Dominik
last_name: Refardt
- first_name: Tobias
full_name: Bergmiller, Tobias
id: 2C471CFA-F248-11E8-B48F-1D18A9856A87
last_name: Bergmiller
orcid: 0000-0001-5396-4346
- first_name: Rolf
full_name: Kümmerli, Rolf
last_name: Kümmerli
citation:
ama: 'Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness
is low: evidence from bacteria committing suicide upon phage infection. 2013.
doi:10.5061/dryad.b1q2n'
apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Data from: Altruism
can evolve when relatedness is low: evidence from bacteria committing suicide
upon phage infection. Dryad. https://doi.org/10.5061/dryad.b1q2n'
chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism
Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide
upon Phage Infection.” Dryad, 2013. https://doi.org/10.5061/dryad.b1q2n.'
ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection.” Dryad, 2013.'
ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve
when relatedness is low: evidence from bacteria committing suicide upon phage
infection, Dryad, 10.5061/dryad.b1q2n.'
mla: 'Refardt, Dominik, et al. Data from: Altruism Can Evolve When Relatedness
Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection. Dryad,
2013, doi:10.5061/dryad.b1q2n.'
short: D. Refardt, T. Bergmiller, R. Kümmerli, (2013).
date_created: 2021-07-30T08:08:09Z
date_published: 2013-03-21T00:00:00Z
date_updated: 2023-10-18T06:43:22Z
day: '21'
department:
- _id: CaGu
doi: 10.5061/dryad.b1q2n
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.b1q2n
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2853'
relation: used_in_publication
status: public
status: public
title: 'Data from: Altruism can evolve when relatedness is low: evidence from bacteria
committing suicide upon phage infection'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '9754'
abstract:
- lang: eng
text: Short-read sequencing technologies have in principle made it feasible to draw
detailed inferences about the recent history of any organism. In practice, however,
this remains challenging due to the difficulty of genome assembly in most organisms
and the lack of statistical methods powerful enough to discriminate among recent,
non-equilibrium histories. We address both the assembly and inference challenges.
We develop a bioinformatic pipeline for generating outgroup-rooted alignments
of orthologous sequence blocks from de novo low-coverage short-read data for a
small number of genomes, and show how such sequence blocks can be used to fit
explicit models of population divergence and admixture in a likelihood framework.
To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding
insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa,
was restricted during Pleistocene ice ages to a longitudinal series of southern
refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled
from a single genome from each of three major glacial refugia reveals support
for an unexpected history dominated by recent admixture. Despite the fact that
80% of the genome is affected by admixture during the last glacial cycle, we are
able to infer the deeper divergence history of these populations. These inferences
are robust to variation in block length, mutation model, and the sampling location
of individual genomes within refugia. This combination of de novo assembly and
numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.
article_processing_charge: No
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
citation:
ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies. 2013.
doi:10.5061/dryad.r3r60'
apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013).
Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60'
chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey
Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low
Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.'
ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from:
Likelihood-based inference of population history from low coverage de novo genome
assemblies.” Dryad, 2013.'
ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies, Dryad,
10.5061/dryad.r3r60.'
mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population
History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.'
short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).
date_created: 2021-07-30T08:31:22Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2023-02-23T10:31:17Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.r3r60
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.r3r60
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2170'
relation: used_in_publication
status: public
status: public
title: 'Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...
---
_id: '2443'
abstract:
- lang: eng
text: The mode of action of auxin is based on its non-uniform distribution within
tissues and organs. Despite the wide use of several auxin analogues in research
and agriculture, little is known about the specificity of different auxin-related
transport and signalling processes towards these compounds. Using seedlings of
Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2),
the physiological activity of several auxin analogues was investigated, together
with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis
and to be transported across the plasma membrane. This study shows that the specificity
criteria for different auxin-related processes vary widely. Notably, the special
behaviour of some synthetic auxin analogues suggests that they might be useful
tools in investigations of the molecular mechanism of auxin action. Thus, due
to their differential stimulatory effects on DR5 expression, indole-3-propionic
(IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of
TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin
signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate
between transcriptional and non-transcriptional pathways of auxin signalling.
The results demonstrate that the major determinants for the auxin-like physiological
potential of a particular compound are very complex and involve its chemical and
metabolic stability, its ability to distribute in tissues in a polar manner and
its activity towards auxin signalling machinery.
acknowledgement: The authors thank Dr Christian Luschnig (University of Natural Resources
and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor
Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds
and, last but not least, to Dr David Morris for critical reading of the manuscript.
We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance.
This work was supported by the Grant Agency of the Czech Republic (P305/11/0797
to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project
CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European
Research Council starting independent research grant ERC-2011-StG-20101109-PSDP
(to J.F.).
article_processing_charge: No
article_type: original
author:
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Martin
full_name: Kubeš, Martin
last_name: Kubeš
- first_name: Pawel
full_name: Baster, Pawel
id: 3028BD74-F248-11E8-B48F-1D18A9856A87
last_name: Baster
- first_name: Stéphanie
full_name: Robert, Stéphanie
last_name: Robert
- first_name: Petre
full_name: Dobrev, Petre
last_name: Dobrev
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Jan
full_name: Petrášek, Jan
last_name: Petrášek
- first_name: Eva
full_name: Zažímalová, Eva
last_name: Zažímalová
citation:
ama: 'Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along
the auxin response chain: A study using auxin analogues. New Phytologist.
2013;200(4):1034-1048. doi:10.1111/nph.12437'
apa: 'Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová,
E. (2013). Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. Wiley. https://doi.org/10.1111/nph.12437'
chicago: 'Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev,
Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes
along the Auxin Response Chain: A Study Using Auxin Analogues.” New Phytologist.
Wiley, 2013. https://doi.org/10.1111/nph.12437.'
ieee: 'S. Simon et al., “Defining the selectivity of processes along the
auxin response chain: A study using auxin analogues,” New Phytologist,
vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.'
ista: 'Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová
E. 2013. Defining the selectivity of processes along the auxin response chain:
A study using auxin analogues. New Phytologist. 200(4), 1034–1048.'
mla: 'Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin
Response Chain: A Study Using Auxin Analogues.” New Phytologist, vol. 200,
no. 4, Wiley, 2013, pp. 1034–48, doi:10.1111/nph.12437.'
short: S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek,
E. Zažímalová, New Phytologist 200 (2013) 1034–1048.
das_tickbox: '1'
date_created: 2018-12-11T11:57:41Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2026-06-18T07:49:41Z
day: '01'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1111/nph.12437
ec_funded: 1
intvolume: ' 200'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/nph.12437
month: '12'
oa: 1
oa_version: Published Version
page: 1034 - 1048
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: New Phytologist
publication_status: published
publisher: Wiley
publist_id: '4460'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Defining the selectivity of processes along the auxin response chain: A study
using auxin analogues'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 200
year: '2013'
...
---
_id: '2444'
abstract:
- lang: eng
text: 'We consider two core algorithmic problems for probabilistic verification:
the maximal end-component decomposition and the almost-sure reachability set computation
for Markov decision processes (MDPs). For MDPs with treewidth k, we present two
improved static algorithms for both the problems that run in time O(n·k 2.38·2k
) and O(m·logn· k), respectively, where n is the number of states and m is the
number of edges, significantly improving the previous known O(n·k·√n· k) bound
for low treewidth. We also present decremental algorithms for both problems for
MDPs with constant treewidth that run in amortized logarithmic time, which is
a huge improvement over the previously known algorithms that require amortized
linear time.'
alternative_title:
- LNCS
article_processing_charge: No
arxiv: 1
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Jakub
full_name: Ła̧Cki, Jakub
last_name: Ła̧Cki
citation:
ama: Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with
low treewidth. 2013;8044:543-558. doi:10.1007/978-3-642-39799-8_36
apa: 'Chatterjee, K., & Ła̧Cki, J. (2013). Faster algorithms for Markov decision
processes with low treewidth. Presented at the CAV: Computer Aided Verification,
St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_36'
chicago: Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov
Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer,
2013. https://doi.org/10.1007/978-3-642-39799-8_36.
ieee: K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes
with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.
ista: Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes
with low treewidth. 8044, 543–558.
mla: Chatterjee, Krishnendu, and Jakub Ła̧Cki. Faster Algorithms for Markov Decision
Processes with Low Treewidth. Vol. 8044, Springer, 2013, pp. 543–58, doi:10.1007/978-3-642-39799-8_36.
short: K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.
conference:
end_date: 2013-07-19
location: St. Petersburg, Russia
name: 'CAV: Computer Aided Verification'
start_date: 2013-07-13
das_tickbox: '1'
date_created: 2018-12-11T11:57:42Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2026-06-18T07:50:03Z
day: '01'
ddc:
- '000'
department:
- _id: KrCh
doi: 10.1007/978-3-642-39799-8_36
ec_funded: 1
external_id:
arxiv:
- '1304.0084'
intvolume: ' 8044'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1304.0084
month: '07'
oa: 1
oa_version: Preprint
page: 543 - 558
project:
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 2587B514-B435-11E9-9278-68D0E5697425
name: Microsoft Research Faculty Fellowship
publication_status: published
publisher: Springer
publist_id: '4459'
quality_controlled: '1'
scopus_import: '1'
series_title: Lecture Notes in Computer Science
status: public
title: Faster algorithms for Markov decision processes with low treewidth
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8044
year: '2013'
...
---
_id: '3321'
author:
- first_name: Novi
full_name: Quadrianto, Novi
last_name: Quadrianto
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
citation:
ama: 'Quadrianto N, Lampert C. Kernel based learning. In: Dubitzky W, Wolkenhauer
O, Cho K, Yokota H, eds. Encyclopedia of Systems Biology. Vol 3. Springer;
2013:1069-1069. doi:10.1007/978-1-4419-9863-7_604'
apa: Quadrianto, N., & Lampert, C. (2013). Kernel based learning. In W. Dubitzky,
O. Wolkenhauer, K. Cho, & H. Yokota (Eds.), Encyclopedia of Systems Biology
(Vol. 3, pp. 1069–1069). Springer. https://doi.org/10.1007/978-1-4419-9863-7_604
chicago: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” In Encyclopedia
of Systems Biology, edited by Werner Dubitzky, Olaf Wolkenhauer, Kwang Cho,
and Hiroki Yokota, 3:1069–1069. Springer, 2013. https://doi.org/10.1007/978-1-4419-9863-7_604.
ieee: N. Quadrianto and C. Lampert, “Kernel based learning,” in Encyclopedia
of Systems Biology, vol. 3, W. Dubitzky, O. Wolkenhauer, K. Cho, and H. Yokota,
Eds. Springer, 2013, pp. 1069–1069.
ista: 'Quadrianto N, Lampert C. 2013.Kernel based learning. In: Encyclopedia of
Systems Biology. vol. 3, 1069–1069.'
mla: Quadrianto, Novi, and Christoph Lampert. “Kernel Based Learning.” Encyclopedia
of Systems Biology, edited by Werner Dubitzky et al., vol. 3, Springer, 2013,
pp. 1069–1069, doi:10.1007/978-1-4419-9863-7_604.
short: N. Quadrianto, C. Lampert, in:, W. Dubitzky, O. Wolkenhauer, K. Cho, H. Yokota
(Eds.), Encyclopedia of Systems Biology, Springer, 2013, pp. 1069–1069.
date_created: 2018-12-11T12:02:39Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T07:42:38Z
day: '01'
department:
- _id: ChLa
doi: 10.1007/978-1-4419-9863-7_604
editor:
- first_name: Werner
full_name: Dubitzky, Werner
last_name: Dubitzky
- first_name: Olaf
full_name: Wolkenhauer, Olaf
last_name: Wolkenhauer
- first_name: Kwang
full_name: Cho, Kwang
last_name: Cho
- first_name: Hiroki
full_name: Yokota, Hiroki
last_name: Yokota
intvolume: ' 3'
language:
- iso: eng
month: '01'
oa_version: None
page: 1069 - 1069
publication: Encyclopedia of Systems Biology
publication_status: published
publisher: Springer
publist_id: '3314'
quality_controlled: '1'
status: public
title: Kernel based learning
type: encyclopedia_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2013'
...
---
_id: '450'
abstract:
- lang: eng
text: Understanding the relative importance of heterosis and outbreeding depression
over multiple generations is a key question in evolutionary biology and is essential
for identifying appropriate genetic sources for population and ecosystem restoration.
Here we use 2455 experimental crosses between 12 population pairs of the rare
perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational
(F1, F2, F3) fitness outcomes of inter-population hybridization. We detected no
evidence of outbreeding depression, with inter-population hybrids and backcrosses
showing either similar fitness or significant heterosis for fitness components
across the three generations. Variation in heterosis among population pairs was
best explained by characteristics of the foreign source or home population, and
was greatest when the source population was large, with high genetic diversity
and low inbreeding, and the home population was small and inbred. Our results
indicate that the primary consideration for maximizing progeny fitness following
population augmentation or restoration is the use of seed from large, genetically
diverse populations.
article_number: '2058'
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: David
full_name: Rowell, David
last_name: Rowell
- first_name: Andrew
full_name: Young, Andrew
last_name: Young
citation:
ama: Pickup M, Field D, Rowell D, Young A. Source population characteristics affect
heterosis following genetic rescue of fragmented plant populations. Proceedings
of the Royal Society of London Series B Biological Sciences. 2013;280(1750).
doi:10.1098/rspb.2012.2058
apa: Pickup, M., Field, D., Rowell, D., & Young, A. (2013). Source population
characteristics affect heterosis following genetic rescue of fragmented plant
populations. Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.2058
chicago: Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Source Population
Characteristics Affect Heterosis Following Genetic Rescue of Fragmented Plant
Populations.” Proceedings of the Royal Society of London Series B Biological
Sciences. Royal Society, The, 2013. https://doi.org/10.1098/rspb.2012.2058.
ieee: M. Pickup, D. Field, D. Rowell, and A. Young, “Source population characteristics
affect heterosis following genetic rescue of fragmented plant populations,” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 280, no.
1750. Royal Society, The, 2013.
ista: Pickup M, Field D, Rowell D, Young A. 2013. Source population characteristics
affect heterosis following genetic rescue of fragmented plant populations. Proceedings
of the Royal Society of London Series B Biological Sciences. 280(1750), 2058.
mla: Pickup, Melinda, et al. “Source Population Characteristics Affect Heterosis
Following Genetic Rescue of Fragmented Plant Populations.” Proceedings of the
Royal Society of London Series B Biological Sciences, vol. 280, no. 1750,
2058, Royal Society, The, 2013, doi:10.1098/rspb.2012.2058.
short: M. Pickup, D. Field, D. Rowell, A. Young, Proceedings of the Royal Society
of London Series B Biological Sciences 280 (2013).
date_created: 2018-12-11T11:46:32Z
date_published: 2013-01-07T00:00:00Z
date_updated: 2021-01-12T07:57:25Z
day: '07'
department:
- _id: NiBa
doi: 10.1098/rspb.2012.2058
external_id:
pmid:
- '23173202'
intvolume: ' 280'
issue: '1750'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3574427/
month: '01'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '7372'
quality_controlled: '1'
status: public
title: Source population characteristics affect heterosis following genetic rescue
of fragmented plant populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 280
year: '2013'
...
---
_id: '476'
abstract:
- lang: eng
text: 'Maternal exposure to infection occurring mid-gestation produces a three-fold
increase in the risk of schizophrenia in the offspring. The critical initiating
factor appears to be the maternal immune activation (MIA) that follows infection.
This process can be induced in rodents by exposure of pregnant dams to the viral
mimic Poly I:C, which triggers an immune response that results in structural,
functional, behavioral, and electrophysiological phenotypes in the adult offspring
that model those seen in schizophrenia. We used this model to explore the role
of synchronization in brain neural networks, a process thought to be dysfunctional
in schizophrenia and previously associated with positive, negative, and cognitive
symptoms of schizophrenia. Exposure of pregnant dams to Poly I:C on GD15 produced
an impairment in long-range neural synchrony in adult offspring between two regions
implicated in schizophrenia pathology; the hippocampus and the medial prefrontal
cortex (mPFC). This reduction in synchrony was ameliorated by acute doses of the
antipsychotic clozapine. MIA animals have previously been shown to have impaired
pre-pulse inhibition (PPI), a gold-standard measure of schizophrenia-like deficits
in animal models. Our data showed that deficits in synchrony were positively correlated
with the impairments in PPI. Subsequent analysis of LFP activity during the PPI
response also showed that reduced coupling between the mPFC and the hippocampus
following processing of the pre-pulse was associated with reduced PPI. The ability
of the MIA intervention to model neurodevelopmental aspects of schizophrenia pathology
provides a useful platform from which to investigate the ontogeny of aberrant
synchronous processes. Further, the way in which the model expresses translatable
deficits such as aberrant synchrony and reduced PPI will allow researchers to
explore novel intervention strategies targeted to these changes. '
author:
- first_name: Desiree
full_name: Dickerson, Desiree
id: 444EB89E-F248-11E8-B48F-1D18A9856A87
last_name: Dickerson
- first_name: David
full_name: Bilkey, David
last_name: Bilkey
citation:
ama: 'Dickerson D, Bilkey D. Aberrant neural synchrony in the maternal immune activation
model: Using translatable measures to explore targeted interventions. Frontiers
in Behavioral Neuroscience. 2013;7(DEC). doi:10.3389/fnbeh.2013.00217'
apa: 'Dickerson, D., & Bilkey, D. (2013). Aberrant neural synchrony in the maternal
immune activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fnbeh.2013.00217'
chicago: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the
Maternal Immune Activation Model: Using Translatable Measures to Explore Targeted
Interventions.” Frontiers in Behavioral Neuroscience. Frontiers Research
Foundation, 2013. https://doi.org/10.3389/fnbeh.2013.00217.'
ieee: 'D. Dickerson and D. Bilkey, “Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions,”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC. Frontiers Research
Foundation, 2013.'
ista: 'Dickerson D, Bilkey D. 2013. Aberrant neural synchrony in the maternal immune
activation model: Using translatable measures to explore targeted interventions.
Frontiers in Behavioral Neuroscience. 7(DEC).'
mla: 'Dickerson, Desiree, and David Bilkey. “Aberrant Neural Synchrony in the Maternal
Immune Activation Model: Using Translatable Measures to Explore Targeted Interventions.”
Frontiers in Behavioral Neuroscience, vol. 7, no. DEC, Frontiers Research
Foundation, 2013, doi:10.3389/fnbeh.2013.00217.'
short: D. Dickerson, D. Bilkey, Frontiers in Behavioral Neuroscience 7 (2013).
date_created: 2018-12-11T11:46:41Z
date_published: 2013-12-27T00:00:00Z
date_updated: 2021-01-12T08:00:53Z
day: '27'
ddc:
- '571'
department:
- _id: JoCs
doi: 10.3389/fnbeh.2013.00217
file:
- access_level: open_access
checksum: cd7183121e56251176100ccac165c95c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:10Z
date_updated: 2020-07-14T12:46:35Z
file_id: '5128'
file_name: IST-2018-953-v1+1_2013_Dickerson_Aberrant_neural.pdf
file_size: 530134
relation: main_file
file_date_updated: 2020-07-14T12:46:35Z
has_accepted_license: '1'
intvolume: ' 7'
issue: DEC
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Frontiers in Behavioral Neuroscience
publication_status: published
publisher: Frontiers Research Foundation
publist_id: '7346'
pubrep_id: '953'
quality_controlled: '1'
status: public
title: 'Aberrant neural synchrony in the maternal immune activation model: Using translatable
measures to explore targeted interventions'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2013'
...
---
_id: '499'
abstract:
- lang: eng
text: Exposure of an isogenic bacterial population to a cidal antibiotic typically
fails to eliminate a small fraction of refractory cells. Historically, fractional
killing has been attributed to infrequently dividing or nondividing "persisters."
Using microfluidic cultures and time-lapse microscopy, we found that Mycobacterium
smegmatis persists by dividing in the presence of the drug isoniazid (INH). Although
persistence in these studies was characterized by stable numbers of cells, this
apparent stability was actually a dynamic state of balanced division and death.
Single cells expressed catalase-peroxidase (KatG), which activates INH, in stochastic
pulses that were negatively correlated with cell survival. These behaviors may
reflect epigenetic effects, because KatG pulsing and death were correlated between
sibling cells. Selection of lineages characterized by infrequent KatG pulsing
could allow nonresponsive adaptation during prolonged drug exposure.
author:
- first_name: Yurichi
full_name: Wakamoto, Yurichi
last_name: Wakamoto
- first_name: Neraaj
full_name: Dhar, Neraaj
last_name: Dhar
- first_name: Remy P
full_name: Chait, Remy P
id: 3464AE84-F248-11E8-B48F-1D18A9856A87
last_name: Chait
orcid: 0000-0003-0876-3187
- first_name: Katrin
full_name: Schneider, Katrin
last_name: Schneider
- first_name: François
full_name: Signorino Gelo, François
last_name: Signorino Gelo
- first_name: Stanislas
full_name: Leibler, Stanislas
last_name: Leibler
- first_name: John
full_name: Mckinney, John
last_name: Mckinney
citation:
ama: Wakamoto Y, Dhar N, Chait RP, et al. Dynamic persistence of antibiotic-stressed
mycobacteria. Science. 2013;339(6115):91-95. doi:10.1126/science.1229858
apa: Wakamoto, Y., Dhar, N., Chait, R. P., Schneider, K., Signorino Gelo, F., Leibler,
S., & Mckinney, J. (2013). Dynamic persistence of antibiotic-stressed mycobacteria.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1229858
chicago: Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François
Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of
Antibiotic-Stressed Mycobacteria.” Science. American Association for the
Advancement of Science, 2013. https://doi.org/10.1126/science.1229858.
ieee: Y. Wakamoto et al., “Dynamic persistence of antibiotic-stressed mycobacteria,”
Science, vol. 339, no. 6115. American Association for the Advancement of
Science, pp. 91–95, 2013.
ista: Wakamoto Y, Dhar N, Chait RP, Schneider K, Signorino Gelo F, Leibler S, Mckinney
J. 2013. Dynamic persistence of antibiotic-stressed mycobacteria. Science. 339(6115),
91–95.
mla: Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”
Science, vol. 339, no. 6115, American Association for the Advancement of
Science, 2013, pp. 91–95, doi:10.1126/science.1229858.
short: Y. Wakamoto, N. Dhar, R.P. Chait, K. Schneider, F. Signorino Gelo, S. Leibler,
J. Mckinney, Science 339 (2013) 91–95.
date_created: 2018-12-11T11:46:48Z
date_published: 2013-01-04T00:00:00Z
date_updated: 2021-01-12T08:01:06Z
day: '04'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1126/science.1229858
intvolume: ' 339'
issue: '6115'
language:
- iso: eng
month: '01'
oa_version: None
page: 91 - 95
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7321'
quality_controlled: '1'
scopus_import: 1
status: public
title: Dynamic persistence of antibiotic-stressed mycobacteria
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 339
year: '2013'
...
---
_id: '500'
abstract:
- lang: eng
text: 'Background: Reassortment between the RNA segments encoding haemagglutinin
(HA) and neuraminidase (NA), the major antigenic influenza proteins, produces
viruses with novel HA and NA subtype combinations and has preceded the emergence
of pandemic strains. It has been suggested that productive viral infection requires
a balance in the level of functional activity of HA and NA, arising from their
closely interacting roles in the viral life cycle, and that this functional balance
could be mediated by genetic changes in the HA and NA. Here, we investigate how
the selective pressure varies for H7 avian influenza HA on different NA subtype
backgrounds. Results: By extending Bayesian stochastic mutational mapping methods
to calculate the ratio of the rate of non-synonymous change to the rate of synonymous
change (d N/d S), we found the average d N/d S across the avian influenza H7 HA1
region to be significantly greater on an N2 NA subtype background than on an N1,
N3 or N7 background. Observed differences in evolutionary rates of H7 HA on different
NA subtype backgrounds could not be attributed to underlying differences between
avian host species or virus pathogenicity. Examination of d N/d S values for each
subtype on a site-by-site basis indicated that the elevated d N/d S on the N2
NA background was a result of increased selection, rather than a relaxation of
selective constraint. Conclusions: Our results are consistent with the hypothesis
that reassortment exposes influenza HA to significant changes in selective pressure
through genetic interactions with NA. Such epistatic effects might be explicitly
accounted for in future models of influenza evolution.'
acknowledgement: "This work was supported by the Biotechnology and Biological Sciences
Research Council, the Government of the Republic of Panama, the Interdisciplinary
Centre for Human and Avian Influenza Research (www.ichair-flu.org) funded by the
Scottish Funding Council, and the Institute for Science and Technology Austria.\r\nCC
BY 2.0\r\n"
article_number: '222'
author:
- first_name: Melissa
full_name: Ward, Melissa
last_name: Ward
- first_name: Samantha
full_name: Lycett, Samantha
last_name: Lycett
- first_name: Dorita
full_name: Avila, Dorita
last_name: Avila
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Andrew
full_name: Leigh Brown, Andrew
last_name: Leigh Brown
citation:
ama: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. Evolutionary interactions
between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary
Biology. 2013;13(1). doi:10.1186/1471-2148-13-222
apa: Ward, M., Lycett, S., Avila, D., Bollback, J. P., & Leigh Brown, A. (2013).
Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza.
BMC Evolutionary Biology. BioMed Central. https://doi.org/10.1186/1471-2148-13-222
chicago: Ward, Melissa, Samantha Lycett, Dorita Avila, Jonathan P Bollback, and
Andrew Leigh Brown. “Evolutionary Interactions between Haemagglutinin and Neuraminidase
in Avian Influenza.” BMC Evolutionary Biology. BioMed Central, 2013. https://doi.org/10.1186/1471-2148-13-222.
ieee: M. Ward, S. Lycett, D. Avila, J. P. Bollback, and A. Leigh Brown, “Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza,” BMC
Evolutionary Biology, vol. 13, no. 1. BioMed Central, 2013.
ista: Ward M, Lycett S, Avila D, Bollback JP, Leigh Brown A. 2013. Evolutionary
interactions between haemagglutinin and neuraminidase in avian influenza. BMC
Evolutionary Biology. 13(1), 222.
mla: Ward, Melissa, et al. “Evolutionary Interactions between Haemagglutinin and
Neuraminidase in Avian Influenza.” BMC Evolutionary Biology, vol. 13, no.
1, 222, BioMed Central, 2013, doi:10.1186/1471-2148-13-222.
short: M. Ward, S. Lycett, D. Avila, J.P. Bollback, A. Leigh Brown, BMC Evolutionary
Biology 13 (2013).
date_created: 2018-12-11T11:46:49Z
date_published: 2013-10-09T00:00:00Z
date_updated: 2021-01-12T08:01:08Z
day: '09'
ddc:
- '576'
department:
- _id: JoBo
doi: 10.1186/1471-2148-13-222
file:
- access_level: open_access
checksum: 52cf48a7c1794676ae8b0029573a84a9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4722'
file_name: IST-2018-941-v1+1_2013_Bollback_Evolutionary_interactionspdf.pdf
file_size: 1150052
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '7320'
pubrep_id: '941'
quality_controlled: '1'
scopus_import: 1
status: public
title: Evolutionary interactions between haemagglutinin and neuraminidase in avian
influenza
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2013'
...
---
_id: '501'
abstract:
- lang: eng
text: 'All known species of extant tapirs are allopatric: 1 in southeastern Asia
and 3 in Central and South America. The fossil record for tapirs, however, is
much wider in geographical range, including Europe, Asia, and North and South
America, going back to the late Oligocene, making the present distribution a relict
of the original one. We here describe a new species of living Tapirus from the
Amazon rain forest, the 1st since T. bairdii Gill, 1865, and the 1st new Perissodactyla
in more than 100 years, from both morphological and molecular characters. It is
shorter in stature than T. terrestris (Linnaeus, 1758) and has distinctive skull
morphology, and it is basal to the clade formed by T. terrestris and T. pinchaque
(Roulin, 1829). This highlights the unrecognized biodiversity in western Amazonia,
where the biota faces increasing threats. Local peoples have long recognized our
new species, suggesting a key role for traditional knowledge in understanding
the biodiversity of the region.'
author:
- first_name: Mario
full_name: Cozzuol, Mario
last_name: Cozzuol
- first_name: Camila
full_name: Clozato, Camila
last_name: Clozato
- first_name: Elizete
full_name: Holanda, Elizete
last_name: Holanda
- first_name: Flávio
full_name: Rodrigues, Flávio
last_name: Rodrigues
- first_name: Samuel
full_name: Nienow, Samuel
last_name: Nienow
- first_name: Benoit
full_name: De Thoisy, Benoit
last_name: De Thoisy
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Fabrício
full_name: Santos, Fabrício
last_name: Santos
citation:
ama: Cozzuol M, Clozato C, Holanda E, et al. A new species of tapir from the Amazon.
Journal of Mammalogy. 2013;94(6):1331-1345. doi:10.1644/12-MAMM-A-169.1
apa: Cozzuol, M., Clozato, C., Holanda, E., Rodrigues, F., Nienow, S., De Thoisy,
B., … Santos, F. (2013). A new species of tapir from the Amazon. Journal of
Mammalogy. Oxford University Press. https://doi.org/10.1644/12-MAMM-A-169.1
chicago: Cozzuol, Mario, Camila Clozato, Elizete Holanda, Flávio Rodrigues, Samuel
Nienow, Benoit De Thoisy, Rodrigo A Fernandes Redondo, and Fabrício Santos. “A
New Species of Tapir from the Amazon.” Journal of Mammalogy. Oxford University
Press, 2013. https://doi.org/10.1644/12-MAMM-A-169.1.
ieee: M. Cozzuol et al., “A new species of tapir from the Amazon,” Journal
of Mammalogy, vol. 94, no. 6. Oxford University Press, pp. 1331–1345, 2013.
ista: Cozzuol M, Clozato C, Holanda E, Rodrigues F, Nienow S, De Thoisy B, Fernandes
Redondo RA, Santos F. 2013. A new species of tapir from the Amazon. Journal of
Mammalogy. 94(6), 1331–1345.
mla: Cozzuol, Mario, et al. “A New Species of Tapir from the Amazon.” Journal
of Mammalogy, vol. 94, no. 6, Oxford University Press, 2013, pp. 1331–45,
doi:10.1644/12-MAMM-A-169.1.
short: M. Cozzuol, C. Clozato, E. Holanda, F. Rodrigues, S. Nienow, B. De Thoisy,
R.A. Fernandes Redondo, F. Santos, Journal of Mammalogy 94 (2013) 1331–1345.
date_created: 2018-12-11T11:46:49Z
date_published: 2013-12-01T00:00:00Z
date_updated: 2021-01-12T08:01:09Z
day: '01'
ddc:
- '570'
department:
- _id: JoBo
doi: 10.1644/12-MAMM-A-169.1
file:
- access_level: open_access
checksum: 8007815078dccac21ecd1cf73a269dc6
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:59Z
date_updated: 2020-07-14T12:46:36Z
file_id: '4980'
file_name: IST-2018-940-v1+1_2013_Redondo_A_new.pdf
file_size: 1040765
relation: main_file
file_date_updated: 2020-07-14T12:46:36Z
has_accepted_license: '1'
intvolume: ' 94'
issue: '6'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '12'
oa: 1
oa_version: Published Version
page: 1331 - 1345
publication: Journal of Mammalogy
publication_status: published
publisher: Oxford University Press
publist_id: '7319'
pubrep_id: '940'
quality_controlled: '1'
scopus_import: 1
status: public
title: A new species of tapir from the Amazon
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: 94
year: '2013'
...
---
_id: '502'
abstract:
- lang: eng
text: 'Blind signatures allow users to obtain signatures on messages hidden from
the signer; moreover, the signer cannot link the resulting message/signature pair
to the signing session. This paper presents blind signature schemes, in which
the number of interactions between the user and the signer is minimal and whose
blind signatures are short. Our schemes are defined over bilinear groups and are
proved secure in the common-reference-string model without random oracles and
under standard assumptions: CDH and the decision-linear assumption. (We also give
variants over asymmetric groups based on similar assumptions.) The blind signatures
are Waters signatures, which consist of 2 group elements. Moreover, we instantiate
partially blind signatures, where the message consists of a part hidden from the
signer and a commonly known public part, and schemes achieving perfect blindness.
We propose new variants of blind signatures, such as signer-friendly partially
blind signatures, where the public part can be chosen by the signer without prior
agreement, 3-party blind signatures, as well as blind signatures on multiple aggregated
messages provided by independent sources. We also extend Waters signatures to
non-binary alphabets by proving a new result on the underlying hash function. '
author:
- first_name: Olivier
full_name: Blazy, Olivier
last_name: Blazy
- first_name: Georg
full_name: Fuchsbauer, Georg
id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87
last_name: Fuchsbauer
- first_name: David
full_name: Pointcheval, David
last_name: Pointcheval
- first_name: Damien
full_name: Vergnaud, Damien
last_name: Vergnaud
citation:
ama: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. Short blind signatures. Journal
of Computer Security. 2013;21(5):627-661. doi:10.3233/JCS-130477
apa: Blazy, O., Fuchsbauer, G., Pointcheval, D., & Vergnaud, D. (2013). Short
blind signatures. Journal of Computer Security. IOS Press. https://doi.org/10.3233/JCS-130477
chicago: Blazy, Olivier, Georg Fuchsbauer, David Pointcheval, and Damien Vergnaud.
“Short Blind Signatures.” Journal of Computer Security. IOS Press, 2013.
https://doi.org/10.3233/JCS-130477.
ieee: O. Blazy, G. Fuchsbauer, D. Pointcheval, and D. Vergnaud, “Short blind signatures,”
Journal of Computer Security, vol. 21, no. 5. IOS Press, pp. 627–661, 2013.
ista: Blazy O, Fuchsbauer G, Pointcheval D, Vergnaud D. 2013. Short blind signatures.
Journal of Computer Security. 21(5), 627–661.
mla: Blazy, Olivier, et al. “Short Blind Signatures.” Journal of Computer Security,
vol. 21, no. 5, IOS Press, 2013, pp. 627–61, doi:10.3233/JCS-130477.
short: O. Blazy, G. Fuchsbauer, D. Pointcheval, D. Vergnaud, Journal of Computer
Security 21 (2013) 627–661.
date_created: 2018-12-11T11:46:50Z
date_published: 2013-11-22T00:00:00Z
date_updated: 2021-01-12T08:01:09Z
day: '22'
department:
- _id: KrPi
doi: 10.3233/JCS-130477
intvolume: ' 21'
issue: '5'
language:
- iso: eng
month: '11'
oa_version: None
page: 627 - 661
publication: Journal of Computer Security
publication_status: published
publisher: IOS Press
publist_id: '7318'
quality_controlled: '1'
scopus_import: 1
status: public
title: Short blind signatures
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 21
year: '2013'
...
---
_id: '505'
abstract:
- lang: eng
text: Alkyd resins are polyesters containing unsaturated fatty acids that are used
as binding agents in paints and coatings. Chemical drying of these polyesters
is based on heavy metal catalyzed cross-linking of the unsaturated fatty acid
moieties. Among the heavy-metal catalysts, cobalt complexes are the most effective,
yet they have been proven to be carcinogenic. Therefore, strategies to replace
the cobalt-based catalyst by environmentally friendlier and less toxic alternatives
are under development. Here, we demonstrate for the first time that a laccase-mediator
system can effectively replace the heavy-metal catalyst and cross-link alkyd resins.
Interestingly, the biocatalytic reaction does not only work in aqueous media,
but also in a solid film, where enzyme diffusion is limited. Within the catalytic
cycle, the mediator oxidizes the alkyd resin and is regenerated by the laccase,
which is uniformly distributed within the drying film as evidenced by confocal
laser scanning microscopy. During gradual build-up of molecular weight, there
is a concomitant decrease of the oxygen content in the film. A new optical sensor
to follow oxygen consumption during the cross-linking reaction was developed and
validated with state of the art techniques. A remarkable feature is the low sample
amount required, which allows faster screening of new catalysts.
acknowledgement: "This study was performed within the Austrian Centre of Indus-\r\ntrial
Biotechnology ACIB and the COST Action 868. This work\r\nhas been supported by the
Federal Ministry of Economy,\r\nFamily and Youth (BMWFJ), the Federal Ministry of
Tra\r\nffi\r\nc,\r\nInnovation and Technology (bmvit), the Styrian Business\r\nPromotion
Agency SFG, the Standortagentur Tirol and ZIT\r\n–\r\nTechnology Agency of the
\ City of Vienna through the\r\nCOMET-Funding Program managed by the Austrian
Research\r\nPromotion Agency FFG. Dr Massimiliano Cardinale (Institute of\r\nEnvironmental
Biotechnology, TU Graz) is gratefully acknowl-\r\nedged for technical support with
the CLSM measurements."
author:
- first_name: Katrin
full_name: Greimel, Katrin
last_name: Greimel
- first_name: Veronika
full_name: Perz, Veronika
last_name: Perz
- first_name: Klaus
full_name: Koren, Klaus
id: 382FBD6A-F248-11E8-B48F-1D18A9856A87
last_name: Koren
- first_name: Roland
full_name: Feola, Roland
last_name: Feola
- first_name: Armin
full_name: Temel, Armin
last_name: Temel
- first_name: Christian
full_name: Sohar, Christian
last_name: Sohar
- first_name: Enrique
full_name: Herrero Acero, Enrique
last_name: Herrero Acero
- first_name: Ingo
full_name: Klimant, Ingo
last_name: Klimant
- first_name: Georg
full_name: Guebitz, Georg
last_name: Guebitz
citation:
ama: 'Greimel K, Perz V, Koren K, et al. Banning toxic heavy-metal catalysts from
paints: Enzymatic cross-linking of alkyd resins. Green Chemistry. 2013;15(2):381-388.
doi:10.1039/c2gc36666e'
apa: 'Greimel, K., Perz, V., Koren, K., Feola, R., Temel, A., Sohar, C., … Guebitz,
G. (2013). Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking
of alkyd resins. Green Chemistry. Royal Society of Chemistry. https://doi.org/10.1039/c2gc36666e'
chicago: 'Greimel, Katrin, Veronika Perz, Klaus Koren, Roland Feola, Armin Temel,
Christian Sohar, Enrique Herrero Acero, Ingo Klimant, and Georg Guebitz. “Banning
Toxic Heavy-Metal Catalysts from Paints: Enzymatic Cross-Linking of Alkyd Resins.”
Green Chemistry. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c2gc36666e.'
ieee: 'K. Greimel et al., “Banning toxic heavy-metal catalysts from paints:
Enzymatic cross-linking of alkyd resins,” Green Chemistry, vol. 15, no.
2. Royal Society of Chemistry, pp. 381–388, 2013.'
ista: 'Greimel K, Perz V, Koren K, Feola R, Temel A, Sohar C, Herrero Acero E, Klimant
I, Guebitz G. 2013. Banning toxic heavy-metal catalysts from paints: Enzymatic
cross-linking of alkyd resins. Green Chemistry. 15(2), 381–388.'
mla: 'Greimel, Katrin, et al. “Banning Toxic Heavy-Metal Catalysts from Paints:
Enzymatic Cross-Linking of Alkyd Resins.” Green Chemistry, vol. 15, no.
2, Royal Society of Chemistry, 2013, pp. 381–88, doi:10.1039/c2gc36666e.'
short: K. Greimel, V. Perz, K. Koren, R. Feola, A. Temel, C. Sohar, E. Herrero Acero,
I. Klimant, G. Guebitz, Green Chemistry 15 (2013) 381–388.
date_created: 2018-12-11T11:46:51Z
date_published: 2013-02-01T00:00:00Z
date_updated: 2021-01-12T08:01:11Z
day: '01'
department:
- _id: HaJa
doi: 10.1039/c2gc36666e
intvolume: ' 15'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 381 - 388
publication: Green Chemistry
publication_status: published
publisher: Royal Society of Chemistry
publist_id: '7313'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Banning toxic heavy-metal catalysts from paints: Enzymatic cross-linking of
alkyd resins'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2013'
...
---
_id: '507'
abstract:
- lang: eng
text: Fertilization in flowering plants requires the temporal and spatial coordination
of many developmental processes, including pollen production, anther dehiscence,
ovule production, and pollen tube elongation. However, it remains elusive as to
how this coordination occurs during reproduction. Here, we present evidence that
endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays
a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays
multiple defects in pollen production and viability, as well as elongation of
staminal filaments and pollen tubes, all of which are pivotal processes needed
for fertilization. Of these abnormalities, the defects in elongation of staminal
filaments and pollen tubes were partially rescued by exogenous auxin. Moreover,
DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments
and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed
defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl)
pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar
localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments.
Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an
inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent
endocytosis plays a crucial role in coordinating the multiple developmental aspects
of male reproductive organs by modulating cellular auxin level through the regulation
of the amount and polarity of PINs.
author:
- first_name: Soo
full_name: Kim, Soo
last_name: Kim
- first_name: Zheng
full_name: Xu, Zheng
last_name: Xu
- first_name: Kyungyoung
full_name: Song, Kyungyoung
last_name: Song
- first_name: Dae
full_name: Kim, Dae
last_name: Kim
- first_name: Hyangju
full_name: Kang, Hyangju
last_name: Kang
- first_name: Ilka
full_name: Reichardt, Ilka
last_name: Reichardt
- first_name: Eun
full_name: Sohn, Eun
last_name: Sohn
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Gerd
full_name: Juergens, Gerd
last_name: Juergens
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
citation:
ama: Kim S, Xu Z, Song K, et al. Adaptor protein complex 2-mediated endocytosis
is crucial for male reproductive organ development in arabidopsis. Plant Cell.
2013;25(8):2970-2985. doi:10.1105/tpc.113.114264
apa: Kim, S., Xu, Z., Song, K., Kim, D., Kang, H., Reichardt, I., … Hwang, I. (2013).
Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive
organ development in arabidopsis. Plant Cell. American Society of Plant
Biologists. https://doi.org/10.1105/tpc.113.114264
chicago: Kim, Soo, Zheng Xu, Kyungyoung Song, Dae Kim, Hyangju Kang, Ilka Reichardt,
Eun Sohn, Jiří Friml, Gerd Juergens, and Inhwan Hwang. “Adaptor Protein Complex
2-Mediated Endocytosis Is Crucial for Male Reproductive Organ Development in Arabidopsis.”
Plant Cell. American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114264.
ieee: S. Kim et al., “Adaptor protein complex 2-mediated endocytosis is crucial
for male reproductive organ development in arabidopsis,” Plant Cell, vol.
25, no. 8. American Society of Plant Biologists, pp. 2970–2985, 2013.
ista: Kim S, Xu Z, Song K, Kim D, Kang H, Reichardt I, Sohn E, Friml J, Juergens
G, Hwang I. 2013. Adaptor protein complex 2-mediated endocytosis is crucial for
male reproductive organ development in arabidopsis. Plant Cell. 25(8), 2970–2985.
mla: Kim, Soo, et al. “Adaptor Protein Complex 2-Mediated Endocytosis Is Crucial
for Male Reproductive Organ Development in Arabidopsis.” Plant Cell, vol.
25, no. 8, American Society of Plant Biologists, 2013, pp. 2970–85, doi:10.1105/tpc.113.114264.
short: S. Kim, Z. Xu, K. Song, D. Kim, H. Kang, I. Reichardt, E. Sohn, J. Friml,
G. Juergens, I. Hwang, Plant Cell 25 (2013) 2970–2985.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:01:12Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114264
external_id:
pmid:
- '23975898'
intvolume: ' 25'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784592/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2970 - 2985
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7312'
quality_controlled: '1'
scopus_import: 1
status: public
title: Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive
organ development in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...
---
_id: '508'
abstract:
- lang: eng
text: The phagocyte NADPH oxidase catalyzes the reduction of O2 to reactive oxygen
species with microbicidal activity. It is composed of two membrane-spanning subunits,
gp91-phox and p22-phox (encoded by CYBB and CYBA, respectively), and three cytoplasmic
subunits, p40-phox, p47-phox, and p67-phox (encoded by NCF4, NCF1, and NCF2, respectively).
Mutations in any of these genes can result in chronic granulomatous disease, a
primary immunodeficiency characterized by recurrent infections. Using evolutionary
mapping, we determined that episodes of adaptive natural selection have shaped
the extracellular portion of gp91-phox during the evolution of mammals, which
suggests that this region may have a function in host-pathogen interactions. On
the basis of a resequencing analysis of approximately 35 kb of CYBB, CYBA, NCF2,
and NCF4 in 102 ethnically diverse individuals (24 of African ancestry, 31 of
European ancestry, 24 of Asian/Oceanians, and 23 US Hispanics), we show that the
pattern of CYBA diversity is compatible with balancing natural selection, perhaps
mediated by catalase-positive pathogens. NCF2 in Asian populations shows a pattern
of diversity characterized by a differentiated haplotype structure. Our study
provides insight into the role of pathogen-driven natural selection in an innate
immune pathway and sheds light on the role of CYBA in endothelial, nonphagocytic
NADPH oxidases, which are relevant in the pathogenesis of cardiovascular and other
complex diseases.
author:
- first_name: Eduardo
full_name: Tarazona Santos, Eduardo
last_name: Tarazona Santos
- first_name: Moara
full_name: Machado, Moara
last_name: Machado
- first_name: Wagner
full_name: Magalhães, Wagner
last_name: Magalhães
- first_name: Renee
full_name: Chen, Renee
last_name: Chen
- first_name: Fernanda
full_name: Lyon, Fernanda
last_name: Lyon
- first_name: Laurie
full_name: Burdett, Laurie
last_name: Burdett
- first_name: Andrew
full_name: Crenshaw, Andrew
last_name: Crenshaw
- first_name: Cristina
full_name: Fabbri, Cristina
last_name: Fabbri
- first_name: Latife
full_name: Pereira, Latife
last_name: Pereira
- first_name: Laelia
full_name: Pinto, Laelia
last_name: Pinto
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Ben
full_name: Sestanovich, Ben
last_name: Sestanovich
- first_name: Meredith
full_name: Yeager, Meredith
last_name: Yeager
- first_name: Stephen
full_name: Chanock, Stephen
last_name: Chanock
citation:
ama: 'Tarazona Santos E, Machado M, Magalhães W, et al. Evolutionary dynamics of
the human NADPH oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications.
Molecular Biology and Evolution. 2013;30(9):2157-2167. doi:10.1093/molbev/mst119'
apa: 'Tarazona Santos, E., Machado, M., Magalhães, W., Chen, R., Lyon, F., Burdett,
L., … Chanock, S. (2013). Evolutionary dynamics of the human NADPH oxidase genes
CYBB, CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst119'
chicago: 'Tarazona Santos, Eduardo, Moara Machado, Wagner Magalhães, Renee Chen,
Fernanda Lyon, Laurie Burdett, Andrew Crenshaw, et al. “Evolutionary Dynamics
of the Human NADPH Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.”
Molecular Biology and Evolution. Oxford University Press, 2013. https://doi.org/10.1093/molbev/mst119.'
ieee: 'E. Tarazona Santos et al., “Evolutionary dynamics of the human NADPH
oxidase genes CYBB, CYBA, NCF2, and NCF4: Functional implications,” Molecular
Biology and Evolution, vol. 30, no. 9. Oxford University Press, pp. 2157–2167,
2013.'
ista: 'Tarazona Santos E, Machado M, Magalhães W, Chen R, Lyon F, Burdett L, Crenshaw
A, Fabbri C, Pereira L, Pinto L, Fernandes Redondo RA, Sestanovich B, Yeager M,
Chanock S. 2013. Evolutionary dynamics of the human NADPH oxidase genes CYBB,
CYBA, NCF2, and NCF4: Functional implications. Molecular Biology and Evolution.
30(9), 2157–2167.'
mla: 'Tarazona Santos, Eduardo, et al. “Evolutionary Dynamics of the Human NADPH
Oxidase Genes CYBB, CYBA, NCF2, and NCF4: Functional Implications.” Molecular
Biology and Evolution, vol. 30, no. 9, Oxford University Press, 2013, pp.
2157–67, doi:10.1093/molbev/mst119.'
short: E. Tarazona Santos, M. Machado, W. Magalhães, R. Chen, F. Lyon, L. Burdett,
A. Crenshaw, C. Fabbri, L. Pereira, L. Pinto, R.A. Fernandes Redondo, B. Sestanovich,
M. Yeager, S. Chanock, Molecular Biology and Evolution 30 (2013) 2157–2167.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:01:12Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/molbev/mst119
external_id:
pmid:
- '23821607'
intvolume: ' 30'
issue: '9'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3748357/
month: '09'
oa: 1
oa_version: Submitted Version
page: 2157 - 2167
pmid: 1
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '7310'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Evolutionary dynamics of the human NADPH oxidase genes CYBB, CYBA, NCF2, and
NCF4: Functional implications'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2013'
...
---
_id: '509'
abstract:
- lang: eng
text: 'Clathrin-mediated endocytosis (CME) regulates many aspects of plant development,
including hormone signaling and responses to environmental stresses. Despite the
importance of this process, the machinery that regulates CME in plants is largely
unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is
required for the formation of clathrin-coated vesicles at the plasma membrane
(PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana,
the biochemistry and functionality of the complex is still uncharacterized. Here,
we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification
and found that one of the large AP-2 subunits, AP2A1, localized at the PM and
interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat
receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2.
Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative
version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced
the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis
is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. '
author:
- first_name: Simone
full_name: Di Rubbo, Simone
last_name: Di Rubbo
- first_name: Niloufer
full_name: Irani, Niloufer
last_name: Irani
- first_name: Soo
full_name: Kim, Soo
last_name: Kim
- first_name: Zheng
full_name: Xu, Zheng
last_name: Xu
- first_name: Astrid
full_name: Gadeyne, Astrid
last_name: Gadeyne
- first_name: Wim
full_name: Dejonghe, Wim
last_name: Dejonghe
- first_name: Isabelle
full_name: Vanhoutte, Isabelle
last_name: Vanhoutte
- first_name: Geert
full_name: Persiau, Geert
last_name: Persiau
- first_name: Dominique
full_name: Eeckhout, Dominique
last_name: Eeckhout
- first_name: Sibu
full_name: Simon, Sibu
id: 4542EF9A-F248-11E8-B48F-1D18A9856A87
last_name: Simon
orcid: 0000-0002-1998-6741
- first_name: Kyungyoung
full_name: Song, Kyungyoung
last_name: Song
- first_name: Jürgen
full_name: Kleine Vehn, Jürgen
last_name: Kleine Vehn
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Geert
full_name: De Jaeger, Geert
last_name: De Jaeger
- first_name: Daniël
full_name: Van Damme, Daniël
last_name: Van Damme
- first_name: Inhwan
full_name: Hwang, Inhwan
last_name: Hwang
- first_name: Eugenia
full_name: Russinova, Eugenia
last_name: Russinova
citation:
ama: Di Rubbo S, Irani N, Kim S, et al. The clathrin adaptor complex AP-2 mediates
endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell.
2013;25(8):2986-2997. doi:10.1105/tpc.113.114058
apa: Di Rubbo, S., Irani, N., Kim, S., Xu, Z., Gadeyne, A., Dejonghe, W., … Russinova,
E. (2013). The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid
INSENSITIVE1 in arabidopsis. Plant Cell. American Society of Plant Biologists.
https://doi.org/10.1105/tpc.113.114058
chicago: Di Rubbo, Simone, Niloufer Irani, Soo Kim, Zheng Xu, Astrid Gadeyne, Wim
Dejonghe, Isabelle Vanhoutte, et al. “The Clathrin Adaptor Complex AP-2 Mediates
Endocytosis of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell.
American Society of Plant Biologists, 2013. https://doi.org/10.1105/tpc.113.114058.
ieee: S. Di Rubbo et al., “The clathrin adaptor complex AP-2 mediates endocytosis
of brassinosteroid INSENSITIVE1 in arabidopsis,” Plant Cell, vol. 25, no.
8. American Society of Plant Biologists, pp. 2986–2997, 2013.
ista: Di Rubbo S, Irani N, Kim S, Xu Z, Gadeyne A, Dejonghe W, Vanhoutte I, Persiau
G, Eeckhout D, Simon S, Song K, Kleine Vehn J, Friml J, De Jaeger G, Van Damme
D, Hwang I, Russinova E. 2013. The clathrin adaptor complex AP-2 mediates endocytosis
of brassinosteroid INSENSITIVE1 in arabidopsis. Plant Cell. 25(8), 2986–2997.
mla: Di Rubbo, Simone, et al. “The Clathrin Adaptor Complex AP-2 Mediates Endocytosis
of Brassinosteroid INSENSITIVE1 in Arabidopsis.” Plant Cell, vol. 25, no.
8, American Society of Plant Biologists, 2013, pp. 2986–97, doi:10.1105/tpc.113.114058.
short: S. Di Rubbo, N. Irani, S. Kim, Z. Xu, A. Gadeyne, W. Dejonghe, I. Vanhoutte,
G. Persiau, D. Eeckhout, S. Simon, K. Song, J. Kleine Vehn, J. Friml, G. De Jaeger,
D. Van Damme, I. Hwang, E. Russinova, Plant Cell 25 (2013) 2986–2997.
date_created: 2018-12-11T11:46:52Z
date_published: 2013-08-01T00:00:00Z
date_updated: 2021-01-12T08:01:13Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.113.114058
external_id:
pmid:
- '23975899'
intvolume: ' 25'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784593/
month: '08'
oa: 1
oa_version: Submitted Version
page: 2986 - 2997
pmid: 1
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '7311'
quality_controlled: '1'
scopus_import: 1
status: public
title: The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1
in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2013'
...