---
_id: '1897'
abstract:
- lang: eng
text: GNOM is one of the most characterized membrane trafficking regulators in plants,
with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange
factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor)
class to mediate vesicle budding at endomembranes. The crucial role of GNOM in
recycling of PIN auxin transporters and other proteins to the plasma membrane
was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM,
the most prominent regulator of recycling in plants, has been proposed to act
and localize at so far elusive recycling endosomes. Here, we report the GNOM localization
in context of its cellular function in Arabidopsis thaliana. State-of-the-art
imaging, pharmacological interference, and ultrastructure analysis show that GNOM
predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging
microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains
on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus,
whereas prolonged exposures results in GNOM translocation to trans-Golgi network
(TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role
for GNOM in maintaining TGN/EE function. Our results redefine the subcellular
action of GNOM and reevaluate the identity and function of recycling endosomes
in plants.
acknowledgement: This work was supported by the Odysseus Program of the Research Foundation-Flanders
(J.F.).
author:
- first_name: Satoshi
full_name: Naramoto, Satoshi
last_name: Naramoto
- first_name: Marisa
full_name: Otegui, Marisa
last_name: Otegui
- first_name: Natsumaro
full_name: Kutsuna, Natsumaro
last_name: Kutsuna
- first_name: Riet
full_name: De Rycke, Riet
last_name: De Rycke
- first_name: Tomoko
full_name: Dainobu, Tomoko
last_name: Dainobu
- first_name: Michael
full_name: Karampelias, Michael
last_name: Karampelias
- first_name: Masaru
full_name: Fujimoto, Masaru
last_name: Fujimoto
- first_name: Elena
full_name: Feraru, Elena
last_name: Feraru
- first_name: Daisuke
full_name: Miki, Daisuke
last_name: Miki
- first_name: Hiroo
full_name: Fukuda, Hiroo
last_name: Fukuda
- first_name: Akihiko
full_name: Nakano, Akihiko
last_name: Nakano
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and
function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus
in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880
apa: Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias,
M., … Friml, J. (2014). Insights into the localization and function of the membrane
trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant
Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880
chicago: Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko
Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization
and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus
in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014.
https://doi.org/10.1105/tpc.114.125880.
ieee: S. Naramoto et al., “Insights into the localization and function of
the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,”
Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076,
2014.
ista: Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto
M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization
and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus
in Arabidopsis. Plant Cell. 26(7), 3062–3076.
mla: Naramoto, Satoshi, et al. “Insights into the Localization and Function of the
Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.”
Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014,
pp. 3062–76, doi:10.1105/tpc.114.125880.
short: S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias,
M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26
(2014) 3062–3076.
date_created: 2018-12-11T11:54:36Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T06:53:55Z
day: '01'
department:
- _id: JiFr
doi: 10.1105/tpc.114.125880
intvolume: ' 26'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/
month: '07'
oa: 1
oa_version: Submitted Version
page: 3062 - 3076
publication: Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '5199'
scopus_import: 1
status: public
title: Insights into the localization and function of the membrane trafficking regulator
GNOM ARF-GEF at the Golgi apparatus in Arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 26
year: '2014'
...
---
_id: '1898'
abstract:
- lang: eng
text: Fast synaptic transmission is important for rapid information processing.
To explore the maximal rate of neuronal signaling and to analyze the presynaptic
mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally
high action potential (AP) frequencies have been reported invivo. With paired
recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic
granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic
APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels
mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic
efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic
Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore,
a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles
are rapidly recruited to the release site. These data reveal mechanisms of presynaptic
AP generation and transmitter release underlying neuronal kHz signaling.
author:
- first_name: Andreas
full_name: Ritzau Jost, Andreas
last_name: Ritzau Jost
- first_name: Igor
full_name: Delvendahl, Igor
last_name: Delvendahl
- first_name: Annika
full_name: Rings, Annika
last_name: Rings
- first_name: Niklas
full_name: Byczkowicz, Niklas
last_name: Byczkowicz
- first_name: Harumi
full_name: Harada, Harumi
id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87
last_name: Harada
orcid: 0000-0001-7429-7896
- first_name: Ryuichi
full_name: Shigemoto, Ryuichi
id: 499F3ABC-F248-11E8-B48F-1D18A9856A87
last_name: Shigemoto
orcid: 0000-0001-8761-9444
- first_name: Johannes
full_name: Hirrlinger, Johannes
last_name: Hirrlinger
- first_name: Jens
full_name: Eilers, Jens
last_name: Eilers
- first_name: Stefan
full_name: Hallermann, Stefan
last_name: Hallermann
citation:
ama: Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate
kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036
apa: Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto,
R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling
at a central synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036
chicago: Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz,
Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan
Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central
Synapse.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036.
ieee: A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz
signaling at a central synapse,” Neuron, vol. 84, no. 1. Elsevier, pp.
152–163, 2014.
ista: Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R,
Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate
kilohertz signaling at a central synapse. Neuron. 84(1), 152–163.
mla: Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz
Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014,
pp. 152–63, doi:10.1016/j.neuron.2014.08.036.
short: A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto,
J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163.
date_created: 2018-12-11T11:54:36Z
date_published: 2014-10-01T00:00:00Z
date_updated: 2021-01-12T06:53:55Z
day: '01'
department:
- _id: RySh
doi: 10.1016/j.neuron.2014.08.036
intvolume: ' 84'
issue: '1'
language:
- iso: eng
month: '10'
oa_version: None
page: 152 - 163
publication: Neuron
publication_status: published
publisher: Elsevier
publist_id: '5197'
quality_controlled: '1'
scopus_import: 1
status: public
title: Ultrafast action potentials mediate kilohertz signaling at a central synapse
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 84
year: '2014'
...
---
_id: '1899'
abstract:
- lang: eng
text: Asymmetric cell divisions allow stem cells to balance proliferation and differentiation.
During embryogenesis, murine epidermis expands rapidly from a single layer of
unspecified basal layer progenitors to a stratified, differentiated epithelium.
Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation
protein LGN, but little is known about how the apical localization of LGN is regulated.
Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to
explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas
loss of each gene alone leads to randomized division angles, combined loss of
Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of
LGN. These findings lend experimental support for the hitherto untested model
that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular
divisions. Finally, we uncover a developmental switch between delamination-driven
early stratification and spindle-orientation-dependent differentiation that occurs
around E15, revealing a two-step mechanism underlying epidermal maturation.
article_processing_charge: No
article_type: original
author:
- first_name: Scott
full_name: Williams, Scott
last_name: Williams
- first_name: Lyndsay
full_name: Ratliff, Lyndsay
last_name: Ratliff
- first_name: Maria P
full_name: Postiglione, Maria P
id: 2C67902A-F248-11E8-B48F-1D18A9856A87
last_name: Postiglione
- first_name: Juergen
full_name: Knoblich, Juergen
last_name: Knoblich
- first_name: Elaine
full_name: Fuchs, Elaine
last_name: Fuchs
citation:
ama: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and
Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature
Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001
apa: Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E.
(2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions
through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001
chicago: Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich,
and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal
Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group,
2014. https://doi.org/10.1038/ncb3001.
ieee: S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc
and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,”
Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769,
2014.
ista: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc
and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN.
Nature Cell Biology. 16(8), 758–769.
mla: Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented
Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no.
8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001.
short: S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature
Cell Biology 16 (2014) 758–769.
date_created: 2018-12-11T11:54:36Z
date_published: 2014-07-13T00:00:00Z
date_updated: 2021-01-12T06:53:55Z
day: '13'
department:
- _id: SiHi
doi: 10.1038/ncb3001
external_id:
pmid:
- '25016959'
intvolume: ' 16'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/
month: '07'
oa: 1
oa_version: Submitted Version
page: 758 - 769
pmid: 1
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5196'
quality_controlled: '1'
scopus_import: 1
status: public
title: Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions
through LGN
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2014'
...
---
_id: '1900'
abstract:
- lang: eng
text: Epithelial cell layers need to be tightly regulated to maintain their integrity
and correct function. Cell integration into epithelial sheets is now shown to
depend on the N-WASP-regulated stabilization of cortical F-actin, which generates
distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell
junctions.
author:
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. Nature
Cell Biology. 2014;16(2):127-129. doi:10.1038/ncb2913
apa: Behrndt, M., & Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead
the way out. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2913
chicago: Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics
Lead the Way Out.” Nature Cell Biology. Nature Publishing Group, 2014.
https://doi.org/10.1038/ncb2913.
ieee: M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way
out,” Nature Cell Biology, vol. 16, no. 2. Nature Publishing Group, pp.
127–129, 2014.
ista: Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out.
Nature Cell Biology. 16(2), 127–129.
mla: Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics
Lead the Way Out.” Nature Cell Biology, vol. 16, no. 2, Nature Publishing
Group, 2014, pp. 127–29, doi:10.1038/ncb2913.
short: M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129.
date_created: 2018-12-11T11:54:37Z
date_published: 2014-01-31T00:00:00Z
date_updated: 2021-01-12T06:53:56Z
day: '31'
department:
- _id: CaHe
doi: 10.1038/ncb2913
intvolume: ' 16'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 127 - 129
publication: Nature Cell Biology
publication_status: published
publisher: Nature Publishing Group
publist_id: '5195'
quality_controlled: '1'
scopus_import: 1
status: public
title: Lateral junction dynamics lead the way out
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2014'
...
---
_id: '1901'
abstract:
- lang: eng
text: In plants, the patterning of stem cell-enriched meristems requires a graded
auxin response maximum that emerges from the concerted action of polar auxin transport,
auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However,
mechanisms underlying this auxin response maximum-mediated root stem cell maintenance
are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED
HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic
genes in the quiescent center (QC) of the root and thus provides a robust mechanism
for the maintenance of auxin response maximum in the root tip. This WOX5 action
is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response
repressor. Our combined genetic, cell biology, and computational modeling studies
revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin
production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback
circuit further assures the maintenance of auxin response maximum in the root
tip and thereby contributes to the maintenance of distal stem cell (DSC) populations.
Our experimental studies and in silico computer simulations both demonstrate that
the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient
in the root tip and the auxin-mediated root DSC differentiation.
acknowledgement: "This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043
and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology)
and the Odysseus program of the Research Foundation-Flanders to J.F\r\n"
author:
- first_name: Huiyu
full_name: Tian, Huiyu
last_name: Tian
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
last_name: Wabnik
- first_name: Tiantian
full_name: Niu, Tiantian
last_name: Niu
- first_name: Hongjiang
full_name: Li, Hongjiang
last_name: Li
- first_name: Qianqian
full_name: Yu, Qianqian
last_name: Yu
- first_name: Stephan
full_name: Pollmann, Stephan
last_name: Pollmann
- first_name: Steffen
full_name: Vanneste, Steffen
last_name: Vanneste
- first_name: Willy
full_name: Govaerts, Willy
last_name: Govaerts
- first_name: Jakub
full_name: Rolčík, Jakub
last_name: Rolčík
- first_name: Markus
full_name: Geisler, Markus
last_name: Geisler
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
- first_name: Zhaojun
full_name: Ding, Zhaojun
last_name: Ding
citation:
ama: Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular
auxin response is crucial for the patterning of root stem cell niches in arabidopsis.
Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118
apa: Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z.
(2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial
for the patterning of root stem cell niches in arabidopsis. Molecular Plant.
Oxford University Press. https://doi.org/10.1093/mp/sst118
chicago: Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu,
Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated
Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches
in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118.
ieee: H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin
response is crucial for the patterning of root stem cell niches in arabidopsis,”
Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014.
ista: Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W,
Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated
cellular auxin response is crucial for the patterning of root stem cell niches
in arabidopsis. Molecular Plant. 7(2), 277–289.
mla: Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response
Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular
Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118.
short: H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W.
Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289.
date_created: 2018-12-11T11:54:37Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:53:57Z
day: '01'
department:
- _id: JiFr
doi: 10.1093/mp/sst118
intvolume: ' 7'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 277 - 289
publication: Molecular Plant
publication_status: published
publisher: Oxford University Press
publist_id: '5194'
scopus_import: 1
status: public
title: WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for
the patterning of root stem cell niches in arabidopsis
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2014'
...
---
_id: '1902'
abstract:
- lang: eng
text: In the 1960s-1980s, determination of bacterial growth rates was an important
tool in microbial genetics, biochemistry, molecular biology, and microbial physiology.
The exciting technical developments of the 1990s and the 2000s eclipsed that tool;
as a result, many investigators today lack experience with growth rate measurements.
Recently, investigators in a number of areas have started to use measurements
of bacterial growth rates for a variety of purposes. Those measurements have been
greatly facilitated by the availability of microwell plate readers that permit
the simultaneous measurements on up to 384 different cultures. Only the exponential
(logarithmic) portions of the resulting growth curves are useful for determining
growth rates, and manual determination of that portion and calculation of growth
rates can be tedious for high-throughput purposes. Here, we introduce the program
GrowthRates that uses plate reader output files to automatically determine the
exponential portion of the curve and to automatically calculate the growth rate,
the maximum culture density, and the duration of the growth lag phase. GrowthRates
is freely available for Macintosh, Windows, and Linux.We discuss the effects of
culture volume, the classical bacterial growth curve, and the differences between
determinations in rich media and minimal (mineral salts) media. This protocol
covers calibration of the plate reader, growth of culture inocula for both rich
and minimal media, and experimental setup. As a guide to reliability, we report
typical day-to-day variation in growth rates and variation within experiments
with respect to position of wells within the plates.
article_processing_charge: No
article_type: original
author:
- first_name: Barry
full_name: Hall, Barry
last_name: Hall
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
- first_name: Anna
full_name: Nandipati, Anna
last_name: Nandipati
- first_name: Miriam
full_name: Barlow, Miriam
last_name: Barlow
citation:
ama: Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular
Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187
apa: Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made
easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187
chicago: Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates
Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014.
https://doi.org/10.1093/molbev/mst187.
ieee: B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular
Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238,
2014.
ista: Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular
Biology and Evolution. 31(1), 232–238.
mla: Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution,
vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187.
short: B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution
31 (2014) 232–238.
date_created: 2018-12-11T11:54:37Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2022-06-07T11:08:13Z
day: '01'
department:
- _id: JoBo
doi: 10.1093/molbev/mst187
external_id:
pmid:
- '24170494'
intvolume: ' 31'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 232 - 238
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
publist_id: '5193'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Growth rates made easy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2014'
...
---
_id: '1903'
abstract:
- lang: eng
text: 'We consider two-player zero-sum partial-observation stochastic games on graphs.
Based on the information available to the players these games can be classified
as follows: (a) general partial-observation (both players have partial view of
the game); (b) one-sided partial-observation (one player has partial-observation
and the other player has complete-observation); and (c) perfect-observation (both
players have complete view of the game). The one-sided partial-observation games
subsumes the important special case of one-player partial-observation stochastic
games (or partial-observation Markov decision processes (POMDPs)). Based on the
randomization available for the strategies, (a) the players may not be allowed
to use randomization (pure strategies), or (b) they may choose a probability distribution
over actions but the actual random choice is external and not visible to the player
(actions invisible), or (c) they may use full randomization. We consider all these
classes of games with reachability, and parity objectives that can express all
ω-regular objectives. The analysis problems are classified into the qualitative
analysis that asks for the existence of a strategy that ensures the objective
with probability 1; and the quantitative analysis that asks for the existence
of a strategy that ensures the objective with probability at least λ (0,1). In
this talk we will cover a wide range of results: for perfect-observation games;
for POMDPs; for one-sided partial-observation games; and for general partial-observation
games.'
alternative_title:
- LNCS
author:
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: 'Chatterjee K. Partial-observation stochastic reachability and parity games.
In: Vol 8634. Springer; 2014:1-4. doi:10.1007/978-3-662-44522-8_1'
apa: 'Chatterjee, K. (2014). Partial-observation stochastic reachability and parity
games (Vol. 8634, pp. 1–4). Presented at the MFCS: Mathematical Foundations of
Computer Science, Budapest, Hungary: Springer. https://doi.org/10.1007/978-3-662-44522-8_1'
chicago: Chatterjee, Krishnendu. “Partial-Observation Stochastic Reachability and
Parity Games,” 8634:1–4. Springer, 2014. https://doi.org/10.1007/978-3-662-44522-8_1.
ieee: 'K. Chatterjee, “Partial-observation stochastic reachability and parity games,”
presented at the MFCS: Mathematical Foundations of Computer Science, Budapest,
Hungary, 2014, vol. 8634, no. PART 1, pp. 1–4.'
ista: 'Chatterjee K. 2014. Partial-observation stochastic reachability and parity
games. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 8634, 1–4.'
mla: Chatterjee, Krishnendu. Partial-Observation Stochastic Reachability and
Parity Games. Vol. 8634, no. PART 1, Springer, 2014, pp. 1–4, doi:10.1007/978-3-662-44522-8_1.
short: K. Chatterjee, in:, Springer, 2014, pp. 1–4.
conference:
end_date: 2014-08-29
location: Budapest, Hungary
name: 'MFCS: Mathematical Foundations of Computer Science'
start_date: 2014-08-25
date_created: 2018-12-11T11:54:38Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2023-02-23T12:23:43Z
day: '01'
department:
- _id: KrCh
doi: 10.1007/978-3-662-44522-8_1
ec_funded: 1
intvolume: ' 8634'
issue: PART 1
language:
- iso: eng
month: '01'
oa_version: None
page: 1 - 4
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: '5192'
pubrep_id: '141'
quality_controlled: '1'
related_material:
record:
- id: '2211'
relation: later_version
status: public
- id: '5381'
relation: earlier_version
status: public
scopus_import: 1
status: public
title: Partial-observation stochastic reachability and parity games
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8634
year: '2014'
...
---
_id: '1904'
abstract:
- lang: eng
text: We prove a Strichartz inequality for a system of orthonormal functions, with
an optimal behavior of the constant in the limit of a large number of functions.
The estimate generalizes the usual Strichartz inequality, in the same fashion
as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application,
we consider the Schrödinger equation with a time-dependent potential and we show
the existence of the wave operator in Schatten spaces.
author:
- first_name: Rupert
full_name: Frank, Rupert
last_name: Frank
- first_name: Mathieu
full_name: Lewin, Mathieu
last_name: Lewin
- first_name: Élliott
full_name: Lieb, Élliott
last_name: Lieb
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal
functions. Journal of the European Mathematical Society. 2014;16(7):1507-1526.
doi:10.4171/JEMS/467
apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2014). Strichartz inequality
for orthonormal functions. Journal of the European Mathematical Society.
European Mathematical Society. https://doi.org/10.4171/JEMS/467
chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz
Inequality for Orthonormal Functions.” Journal of the European Mathematical
Society. European Mathematical Society, 2014. https://doi.org/10.4171/JEMS/467.
ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for
orthonormal functions,” Journal of the European Mathematical Society, vol.
16, no. 7. European Mathematical Society, pp. 1507–1526, 2014.
ista: Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal
functions. Journal of the European Mathematical Society. 16(7), 1507–1526.
mla: Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” Journal
of the European Mathematical Society, vol. 16, no. 7, European Mathematical
Society, 2014, pp. 1507–26, doi:10.4171/JEMS/467.
short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical
Society 16 (2014) 1507–1526.
date_created: 2018-12-11T11:54:38Z
date_published: 2014-08-23T00:00:00Z
date_updated: 2021-01-12T06:53:58Z
day: '23'
department:
- _id: RoSe
doi: 10.4171/JEMS/467
intvolume: ' 16'
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1306.1309
month: '08'
oa: 1
oa_version: Submitted Version
page: 1507 - 1526
project:
- _id: 26450934-B435-11E9-9278-68D0E5697425
name: NSERC Postdoctoral fellowship
publication: Journal of the European Mathematical Society
publication_status: published
publisher: European Mathematical Society
publist_id: '5191'
quality_controlled: '1'
scopus_import: 1
status: public
title: Strichartz inequality for orthonormal functions
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2014'
...
---
_id: '1905'
abstract:
- lang: eng
text: The unprecedented polymorphism in the major histocompatibility complex (MHC)
genes is thought to be maintained by balancing selection from parasites. However,
do parasites also drive divergence at MHC loci between host populations, or do
the effects of balancing selection maintain similarities among populations? We
examined MHC variation in populations of the livebearing fish Poecilia mexicana
and characterized their parasite communities. Poecilia mexicana populations in
the Cueva del Azufre system are locally adapted to darkness and the presence of
toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species.
Parasite communities differed significantly across populations, and populations
with higher parasite loads had higher levels of diversity at class II MHC genes.
However, despite different parasite communities, marked divergence in adaptive
traits and in neutral genetic markers, we found MHC alleles to be remarkably similar
among host populations. Our findings indicate that balancing selection from parasites
maintains immunogenetic diversity of hosts, but this process does not promote
MHC divergence in this system. On the contrary, we suggest that balancing selection
on immunogenetic loci may outweigh divergent selection causing divergence, thereby
hindering host divergence and speciation. Our findings support the hypothesis
that balancing selection maintains MHC similarities among lineages during and
after speciation (trans-species evolution).
acknowledgement: This study was funded by grants from the National Science Foundation
(NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation
(DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer
Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Tobler, Michael
last_name: Tobler
- first_name: Martin
full_name: Plath, Martin
last_name: Plath
- first_name: Rüdiger
full_name: Riesch, Rüdiger
last_name: Riesch
- first_name: Ingo
full_name: Schlupp, Ingo
last_name: Schlupp
- first_name: Anna V
full_name: Grasse, Anna V
id: 406F989C-F248-11E8-B48F-1D18A9856A87
last_name: Grasse
- first_name: Gopi
full_name: Munimanda, Gopi
last_name: Munimanda
- first_name: C
full_name: Setzer, C
last_name: Setzer
- first_name: Dustin
full_name: Penn, Dustin
last_name: Penn
- first_name: Yoshan
full_name: Moodley, Yoshan
last_name: Moodley
citation:
ama: Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic
diversity but not divergence among locally adapted host populations. Journal
of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370
apa: Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G.,
… Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations. Journal of Evolutionary
Biology. Wiley. https://doi.org/10.1111/jeb.12370
chicago: Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse,
Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites
Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host
Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370.
ieee: M. Tobler et al., “Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations,” Journal of Evolutionary
Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014.
ista: Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C,
Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity
but not divergence among locally adapted host populations. Journal of Evolutionary
Biology. 27(5), 960–974.
mla: Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity
but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary
Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370.
short: M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C.
Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.
date_created: 2018-12-11T11:54:38Z
date_published: 2014-04-12T00:00:00Z
date_updated: 2022-06-07T09:22:20Z
day: '12'
department:
- _id: SyCr
doi: 10.1111/jeb.12370
external_id:
pmid:
- '24725091'
intvolume: ' 27'
issue: '5'
language:
- iso: eng
month: '04'
oa_version: None
page: 960 - 974
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Wiley
publist_id: '5190'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection from parasites favours immunogenetic diversity but not divergence
among locally adapted host populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2014'
...
---
_id: '1906'
abstract:
- lang: eng
text: In this paper, we introduce a novel scene representation for the visualization
of large-scale point clouds accompanied by a set of high-resolution photographs.
Many real-world applications deal with very densely sampled point-cloud data,
which are augmented with photographs that often reveal lighting variations and
inaccuracies in registration. Consequently, the high-quality representation of
the captured data, i.e., both point clouds and photographs together, is a challenging
and time-consuming task. We propose a two-phase approach, in which the first (preprocessing)
phase generates multiple overlapping surface patches and handles the problem of
seamless texture generation locally for each patch. The second phase stitches
these patches at render-time to produce a high-quality visualization of the data.
As a result of the proposed localization of the global texturing problem, our
algorithm is more than an order of magnitude faster than equivalent mesh-based
texturing techniques. Furthermore, since our preprocessing phase requires only
a minor fraction of the whole data set at once, we provide maximum flexibility
when dealing with growing data sets.
acknowledgement: This research was supported by the Austrian Research Promotion Agency
(FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567).
author:
- first_name: Murat
full_name: Arikan, Murat
last_name: Arikan
- first_name: Reinhold
full_name: Preiner, Reinhold
last_name: Preiner
- first_name: Claus
full_name: Scheiblauer, Claus
last_name: Scheiblauer
- first_name: Stefan
full_name: Jeschke, Stefan
id: 44D6411A-F248-11E8-B48F-1D18A9856A87
last_name: Jeschke
- first_name: Michael
full_name: Wimmer, Michael
last_name: Wimmer
citation:
ama: Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud
visualization through localized textured surface reconstruction. IEEE Transactions
on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011
apa: Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014).
Large-scale point-cloud visualization through localized textured surface reconstruction.
IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011
chicago: Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and
Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured
Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics.
IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011.
ieee: M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale
point-cloud visualization through localized textured surface reconstruction,”
IEEE Transactions on Visualization and Computer Graphics, vol. 20, no.
9. IEEE, pp. 1280–1292, 2014.
ista: Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale
point-cloud visualization through localized textured surface reconstruction. IEEE
Transactions on Visualization and Computer Graphics. 20(9), 1280–1292.
mla: Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized
Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer
Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011.
short: M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions
on Visualization and Computer Graphics 20 (2014) 1280–1292.
date_created: 2018-12-11T11:54:39Z
date_published: 2014-09-09T00:00:00Z
date_updated: 2021-01-12T06:53:59Z
day: '09'
ddc:
- '000'
department:
- _id: ChWo
doi: 10.1109/TVCG.2014.2312011
file:
- access_level: open_access
checksum: 5bf58942d2eb20adf03c7f9ea2e68124
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:41Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5297'
file_name: IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf
file_size: 13594598
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 20'
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Submitted Version
page: 1280 - 1292
project:
- _id: 25357BD2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 24352-N23
name: 'Deep Pictures: Creating Visual and Haptic Vector Images'
publication: IEEE Transactions on Visualization and Computer Graphics
publication_status: published
publisher: IEEE
publist_id: '5189'
pubrep_id: '573'
scopus_import: 1
status: public
title: Large-scale point-cloud visualization through localized textured surface reconstruction
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 20
year: '2014'
...
---
_id: '1907'
abstract:
- lang: eng
text: 'Most cryptographic security proofs require showing that two systems are indistinguishable.
A central tool in such proofs is that of a game, where winning the game means
provoking a certain condition, and it is shown that the two systems considered
cannot be distinguished unless this condition is provoked. Upper bounding the
probability of winning such a game, i.e., provoking this condition, for an arbitrary
strategy is usually hard, except in the special case where the best strategy for
winning such a game is known to be non-adaptive. A sufficient criterion for ensuring
the optimality of non-adaptive strategies is that of conditional equivalence to
a system, a notion introduced in [1]. In this paper, we show that this criterion
is not necessary to ensure the optimality of non-adaptive strategies by giving
two results of independent interest: 1) the optimality of non-adaptive strategies
is not preserved under parallel composition; 2) in contrast, conditional equivalence
is preserved under parallel composition.'
article_number: '6875125'
author:
- first_name: Grégory
full_name: Demay, Grégory
last_name: Demay
- first_name: Peter
full_name: Gazi, Peter
id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87
last_name: Gazi
- first_name: Ueli
full_name: Maurer, Ueli
last_name: Maurer
- first_name: Björn
full_name: Tackmann, Björn
last_name: Tackmann
citation:
ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies:
The case of parallel games. In: IEEE International Symposium on Information
Theory. IEEE; 2014. doi:10.1109/ISIT.2014.6875125'
apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2014). Optimality of
non-adaptive strategies: The case of parallel games. In IEEE International
Symposium on Information Theory. Honolulu, USA: IEEE. https://doi.org/10.1109/ISIT.2014.6875125'
chicago: 'Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality
of Non-Adaptive Strategies: The Case of Parallel Games.” In IEEE International
Symposium on Information Theory. IEEE, 2014. https://doi.org/10.1109/ISIT.2014.6875125.'
ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive
strategies: The case of parallel games,” in IEEE International Symposium on
Information Theory, Honolulu, USA, 2014.'
ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies:
The case of parallel games. IEEE International Symposium on Information Theory.
IEEE International Symposium on Information Theory Proceedings, 6875125.'
mla: 'Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of
Parallel Games.” IEEE International Symposium on Information Theory, 6875125,
IEEE, 2014, doi:10.1109/ISIT.2014.6875125.'
short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium
on Information Theory, IEEE, 2014.
conference:
end_date: 2014-07-04
location: Honolulu, USA
name: IEEE International Symposium on Information Theory Proceedings
start_date: 2014-06-29
date_created: 2018-12-11T11:54:39Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:53:59Z
day: '01'
department:
- _id: KrPi
doi: 10.1109/ISIT.2014.6875125
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://eprint.iacr.org/2014/299
month: '01'
oa: 1
oa_version: Submitted Version
publication: IEEE International Symposium on Information Theory
publication_status: published
publisher: IEEE
publist_id: '5188'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Optimality of non-adaptive strategies: The case of parallel games'
type: conference
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
year: '2014'
...
---
_id: '1908'
abstract:
- lang: eng
text: In large populations, multiple beneficial mutations may be simultaneously
spreading. In asexual populations, these mutations must either arise on the same
background or compete against each other. In sexual populations, recombination
can bring together beneficial alleles from different backgrounds, but tightly
linked alleles may still greatly interfere with each other. We show for well-mixed
populations that when this interference is strong, the genome can be seen as consisting
of many effectively asexual stretches linked together. The rate at which beneficial
alleles fix is thus roughly proportional to the rate of recombination and depends
only logarithmically on the mutation supply and the strength of selection. Our
scaling arguments also allow us to predict, with reasonable accuracy, the fitness
distribution of fixed mutations when the mutational effect sizes are broad. We
focus on the regime in which crossovers occur more frequently than beneficial
mutations, as is likely to be the case for many natural populations.
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Oskar
full_name: Hallatschek, Oskar
last_name: Hallatschek
citation:
ama: Weissman D, Hallatschek O. The rate of adaptation in large sexual populations
with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705
apa: Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large
sexual populations with linear chromosomes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.113.160705
chicago: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large
Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society
of America, 2014. https://doi.org/10.1534/genetics.113.160705.
ieee: D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations
with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of
America, pp. 1167–1183, 2014.
ista: Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations
with linear chromosomes. Genetics. 196(4), 1167–1183.
mla: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual
Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics
Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.
short: D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.
date_created: 2018-12-11T11:54:39Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T06:53:59Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.113.160705
ec_funded: 1
intvolume: ' 196'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.0737
month: '04'
oa: 1
oa_version: Submitted Version
page: 1167 - 1183
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5187'
quality_controlled: '1'
scopus_import: 1
status: public
title: The rate of adaptation in large sexual populations with linear chromosomes
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 196
year: '2014'
...
---
_id: '1909'
abstract:
- lang: eng
text: 'Summary: Phenotypes are often environmentally dependent, which requires organisms
to track environmental change. The challenge for organisms is to construct phenotypes
using the most accurate environmental cue. Here, we use a quantitative genetic
model of adaptation by additive genetic variance, within- and transgenerational
plasticity via linear reaction norms and indirect genetic effects respectively.
We show how the relative influence on the eventual phenotype of these components
depends on the predictability of environmental change (fast or slow, sinusoidal
or stochastic) and the developmental lag τ between when the environment is perceived
and when selection acts. We then decompose expected mean fitness into three components
(variance load, adaptation and fluctuation load) to study the fitness costs of
within- and transgenerational plasticity. A strongly negative maternal effect
coefficient m minimizes the variance load, but a strongly positive m minimises
the fluctuation load. The adaptation term is maximized closer to zero, with positive
or negative m preferred under different environmental scenarios. Phenotypic plasticity
is higher when τ is shorter and when the environment changes frequently between
seasonal extremes. Expected mean population fitness is highest away from highest
observed levels of phenotypic plasticity. Within- and transgenerational plasticity
act in concert to deliver well-adapted phenotypes, which emphasizes the need to
study both simultaneously when investigating phenotypic evolution.'
acknowledgement: 'Engineering and Physical Sciences Research Council. Grant Number:
EP/H031928/1'
author:
- first_name: Thomas
full_name: Ezard, Thomas
last_name: Ezard
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Rebecca
full_name: Hoyle, Rebecca
last_name: Hoyle
citation:
ama: Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic
plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701.
doi:10.1111/1365-2435.12207
apa: Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation
via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell.
https://doi.org/10.1111/1365-2435.12207
chicago: Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of
Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology.
Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.
ieee: T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic
plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell,
pp. 693–701, 2014.
ista: Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic
plasticity and maternal effects. Functional Ecology. 28(3), 693–701.
mla: Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity
and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell,
2014, pp. 693–701, doi:10.1111/1365-2435.12207.
short: T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.
date_created: 2018-12-11T11:54:40Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T06:54:00Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1111/1365-2435.12207
file:
- access_level: open_access
checksum: 3cbe8623174709a8ceec2103246f8fe0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:45Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5167'
file_name: IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf
file_size: 536154
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 28'
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 693 - 701
publication: Functional Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5186'
pubrep_id: '419'
scopus_import: 1
status: public
title: The fitness costs of adaptation via phenotypic plasticity and maternal effects
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: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 28
year: '2014'
...
---
_id: '1910'
abstract:
- lang: eng
text: angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express
epithelial adhesion molecules, allowing them to form contacts with epithelial
cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial
adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs
remain immature and sessile within the epidermis or mature and egress to initiate
immune responses. So far, the molecular machinery regulating epithelial adhesion
molecules during LC maturation remains elusive. Here, we generated pure populations
of immature human LCs in vitro to systematically probe for gene-expression changes
during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin,
while they upregulate the mesenchymal marker N-cadherin known to facilitate cell
migration. In addition, N-cadherin is constitutively expressed by monocyte-derived
DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal
DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding
homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce
epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells
undergoing metastasis. Our results provide the first hint that the molecular EMT
machinery might facilitate LC mobilization. Moreover, our study suggests that
N-cadherin plays a role during DC migration.
acknowledgement: 'FWF. Grant Number: P22058-B20'
author:
- first_name: Sabine
full_name: Konradi, Sabine
last_name: Konradi
- first_name: Nighat
full_name: Yasmin, Nighat
last_name: Yasmin
- first_name: Denise
full_name: Haslwanter, Denise
last_name: Haslwanter
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Bernd
full_name: Gesslbauer, Bernd
last_name: Gesslbauer
- first_name: Michael K
full_name: Sixt, Michael K
id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
last_name: Sixt
orcid: 0000-0002-6620-9179
- first_name: Herbert
full_name: Strobl, Herbert
last_name: Strobl
citation:
ama: Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied
by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal
transition ZEB1/2. European Journal of Immunology. 2014;44(2):553-560.
doi:10.1002/eji.201343681
apa: Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M.
K., & Strobl, H. (2014). Langerhans cell maturation is accompanied by induction
of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition
ZEB1/2. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201343681
chicago: Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd
Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is
Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal
Transition ZEB1/2.” European Journal of Immunology. Wiley-Blackwell, 2014.
https://doi.org/10.1002/eji.201343681.
ieee: S. Konradi et al., “Langerhans cell maturation is accompanied by induction
of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition
ZEB1/2,” European Journal of Immunology, vol. 44, no. 2. Wiley-Blackwell,
pp. 553–560, 2014.
ista: Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl
H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin
and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2.
European Journal of Immunology. 44(2), 553–560.
mla: Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction
of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition
ZEB1/2.” European Journal of Immunology, vol. 44, no. 2, Wiley-Blackwell,
2014, pp. 553–60, doi:10.1002/eji.201343681.
short: S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt,
H. Strobl, European Journal of Immunology 44 (2014) 553–560.
date_created: 2018-12-11T11:54:40Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2021-01-12T06:54:01Z
day: '01'
department:
- _id: MiSi
doi: 10.1002/eji.201343681
intvolume: ' 44'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 553 - 560
publication: European Journal of Immunology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5185'
scopus_import: 1
status: public
title: Langerhans cell maturation is accompanied by induction of N-cadherin and the
transcriptional regulators of epithelial-mesenchymal transition ZEB1/2
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 44
year: '2014'
...
---
_id: '1911'
abstract:
- lang: eng
text: The topological Tverberg theorem has been generalized in several directions
by setting extra restrictions on the Tverberg partitions. Restricted Tverberg
partitions, defined by the idea that certain points cannot be in the same part,
are encoded with graphs. When two points are adjacent in the graph, they are not
in the same part. If the restrictions are too harsh, then the topological Tverberg
theorem fails. The colored Tverberg theorem corresponds to graphs constructed
as disjoint unions of small complete graphs. Hell studied the case of paths and
cycles. In graph theory these partitions are usually viewed as graph colorings.
As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections
between several notions of graph colorings and topological combinatorics. For
ordinary graph colorings it is enough to require that the number of colors q satisfy
q>Δ, where Δ is the maximal degree of the graph. It was proven by the first
author using equivariant topology that if q>Δ 2 then the topological Tverberg
theorem still works. It is conjectured that q>KΔ is also enough for some constant
K, and in this paper we prove a fixed-parameter version of that conjecture. The
required topological connectivity results are proven with shellability, which
also strengthens some previous partial results where the topological connectivity
was proven with the nerve lemma.
acknowledgement: Patrik Norén gratefully acknowledges support from the Wallenberg
foundation
author:
- first_name: Alexander
full_name: Engström, Alexander
last_name: Engström
- first_name: Patrik
full_name: Noren, Patrik
id: 46870C74-F248-11E8-B48F-1D18A9856A87
last_name: Noren
citation:
ama: Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. Discrete &
Computational Geometry. 2014;51(1):207-220. doi:10.1007/s00454-013-9556-3
apa: Engström, A., & Noren, P. (2014). Tverberg’s Theorem and Graph Coloring.
Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9556-3
chicago: Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.”
Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-013-9556-3.
ieee: A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” Discrete
& Computational Geometry, vol. 51, no. 1. Springer, pp. 207–220, 2014.
ista: Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete
& Computational Geometry. 51(1), 207–220.
mla: Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.”
Discrete & Computational Geometry, vol. 51, no. 1, Springer, 2014,
pp. 207–20, doi:10.1007/s00454-013-9556-3.
short: A. Engström, P. Noren, Discrete & Computational Geometry 51 (2014) 207–220.
date_created: 2018-12-11T11:54:40Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:54:01Z
day: '01'
department:
- _id: CaUh
doi: 10.1007/s00454-013-9556-3
intvolume: ' 51'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 207 - 220
publication: Discrete & Computational Geometry
publication_status: published
publisher: Springer
publist_id: '5183'
scopus_import: 1
status: public
title: Tverberg's Theorem and Graph Coloring
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 51
year: '2014'
...
---
_id: '1912'
abstract:
- lang: eng
text: Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the
embryo along its left-right (LR) axis. Regional differences in cell shape within
the lumen-lining KV epithelium are essential for its LR patterning function. However,
the processes by which KV cells acquire their characteristic shapes are largely
unknown. Here, we show that the notochord induces regional differences in cell
shape within KV by triggering extracellular matrix (ECM) accumulation adjacent
to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts
apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen
growth. Our study provides mechanistic insight into the processes by which KV
translates global embryonic patterning into regional cell shape differences required
for its LR symmetry-breaking function.
acknowledgement: We are grateful to members of the C.-P.H. lab, M. Concha, D. Siekhaus,
and J. Vermot for comments on the manuscript and to M. Furutani-Seiki for sharing
reagents. This work was supported by the Institute of Science and Technology Austria
and an Alexander von Humboldt Foundation fellowship to J.C.
article_processing_charge: No
author:
- first_name: Julien
full_name: Compagnon, Julien
id: 2E3E0988-F248-11E8-B48F-1D18A9856A87
last_name: Compagnon
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Srivarsha
full_name: Rajshekar, Srivarsha
last_name: Rajshekar
- first_name: Rita
full_name: Kottmeier, Rita
last_name: Kottmeier
- first_name: Kornelija
full_name: Pranjic-Ferscha, Kornelija
id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
last_name: Pranjic-Ferscha
- first_name: Martin
full_name: Behrndt, Martin
id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87
last_name: Behrndt
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Compagnon J, Barone V, Rajshekar S, et al. The notochord breaks bilateral symmetry
by controlling cell shapes in the Zebrafish laterality organ. Developmental
Cell. 2014;31(6):774-783. doi:10.1016/j.devcel.2014.11.003
apa: Compagnon, J., Barone, V., Rajshekar, S., Kottmeier, R., Pranjic-Ferscha, K.,
Behrndt, M., & Heisenberg, C.-P. J. (2014). The notochord breaks bilateral
symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental
Cell. Cell Press. https://doi.org/10.1016/j.devcel.2014.11.003
chicago: Compagnon, Julien, Vanessa Barone, Srivarsha Rajshekar, Rita Kottmeier,
Kornelija Pranjic-Ferscha, Martin Behrndt, and Carl-Philipp J Heisenberg. “The
Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish
Laterality Organ.” Developmental Cell. Cell Press, 2014. https://doi.org/10.1016/j.devcel.2014.11.003.
ieee: J. Compagnon et al., “The notochord breaks bilateral symmetry by controlling
cell shapes in the Zebrafish laterality organ,” Developmental Cell, vol.
31, no. 6. Cell Press, pp. 774–783, 2014.
ista: Compagnon J, Barone V, Rajshekar S, Kottmeier R, Pranjic-Ferscha K, Behrndt
M, Heisenberg C-PJ. 2014. The notochord breaks bilateral symmetry by controlling
cell shapes in the Zebrafish laterality organ. Developmental Cell. 31(6), 774–783.
mla: Compagnon, Julien, et al. “The Notochord Breaks Bilateral Symmetry by Controlling
Cell Shapes in the Zebrafish Laterality Organ.” Developmental Cell, vol.
31, no. 6, Cell Press, 2014, pp. 774–83, doi:10.1016/j.devcel.2014.11.003.
short: J. Compagnon, V. Barone, S. Rajshekar, R. Kottmeier, K. Pranjic-Ferscha,
M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 31 (2014) 774–783.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-12-22T00:00:00Z
date_updated: 2023-09-07T12:05:08Z
day: '22'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2014.11.003
external_id:
pmid:
- '25535919'
intvolume: ' 31'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/25535919
month: '12'
oa: 1
oa_version: Published Version
page: 774 - 783
pmid: 1
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '5182'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish
laterality organ
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 31
year: '2014'
...
---
_id: '1913'
abstract:
- lang: eng
text: 'Deposits of phosphorylated tau protein and convergence of pathology in the
hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed
to evaluate whether regional and cellular vulnerability patterns in the hippocampus
distinguish tauopathies or are influenced by their concomitant presence. Methods:
We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal
subregions/layers in individuals with Alzheimer''s disease (AD)-related neurofibrillary
degeneration (n = 40), Pick''s disease (n = 8), progressive supranuclear palsy
(n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n
= 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly
(n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis.
Results: Our study reveals disease-specific hot spots and regional selective vulnerability
for these disorders. The pattern of hippocampal AD-related tau pathology is strongly
influenced by concomitant AGD. Mathematical analysis reveals that hippocampal
involvement in primary tauopathies is distinguishable from early-stage AD-related
neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific
AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies,
which primarily do not affect the hippocampus. These hot spots can be shifted
to other regions by the co-occurrence of tauopathies like AGD. Our observations
support the notion that globular glial tauopathies and tau-astrogliopathy of the
elderly are distinct entities.'
acknowledgement: This study was supported by the European Commission’s 7th Framework
Programme under GA No. 278486, ‘DEVELAGE’.
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Milenković, Ivan
last_name: Milenković
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
- first_name: Gábor
full_name: Kovács, Gábor
last_name: Kovács
citation:
ama: Milenković I, Petrov T, Kovács G. Patterns of hippocampal tau pathology differentiate
neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders.
2014;38(5-6):375-388. doi:10.1159/000365548
apa: Milenković, I., Petrov, T., & Kovács, G. (2014). Patterns of hippocampal
tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric
Cognitive Disorders. Karger Publishers. https://doi.org/10.1159/000365548
chicago: Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal
Tau Pathology Differentiate Neurodegenerative Dementias.” Dementia and Geriatric
Cognitive Disorders. Karger Publishers, 2014. https://doi.org/10.1159/000365548.
ieee: I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology
differentiate neurodegenerative dementias,” Dementia and Geriatric Cognitive
Disorders, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014.
ista: Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology
differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders.
38(5–6), 375–388.
mla: Milenković, Ivan, et al. “Patterns of Hippocampal Tau Pathology Differentiate
Neurodegenerative Dementias.” Dementia and Geriatric Cognitive Disorders,
vol. 38, no. 5–6, Karger Publishers, 2014, pp. 375–88, doi:10.1159/000365548.
short: I. Milenković, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders
38 (2014) 375–388.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-11-07T00:00:00Z
date_updated: 2023-10-17T10:21:17Z
day: '07'
department:
- _id: CaGu
doi: 10.1159/000365548
external_id:
pmid:
- '25195847'
intvolume: ' 38'
issue: 5-6
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf
month: '11'
oa: 1
oa_version: Published Version
page: 375 - 388
pmid: 1
publication: Dementia and Geriatric Cognitive Disorders
publication_identifier:
issn:
- 1420-8008
publication_status: published
publisher: Karger Publishers
publist_id: '5181'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Patterns of hippocampal tau pathology differentiate neurodegenerative dementias
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2014'
...
---
_id: '1914'
abstract:
- lang: eng
text: Targeting membrane proteins for degradation requires the sequential action
of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally
conserved among kingdoms, plants lack the essential ESCRT-0 components. A new
report closes this gap by identifying a novel protein family that substitutes
for ESCRT-0 function in plants.
author:
- first_name: Michael
full_name: Sauer, Michael
last_name: Sauer
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: 'Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition.
Current Biology. 2014;24(1):R27-R29. doi:10.1016/j.cub.2013.11.019'
apa: 'Sauer, M., & Friml, J. (2014). Plant biology: Gatekeepers of the road
to protein perdition. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.11.019'
chicago: 'Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road
to Protein Perdition.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2013.11.019.'
ieee: 'M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein
perdition,” Current Biology, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.'
ista: 'Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein
perdition. Current Biology. 24(1), R27–R29.'
mla: 'Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to
Protein Perdition.” Current Biology, vol. 24, no. 1, Cell Press, 2014,
pp. R27–29, doi:10.1016/j.cub.2013.11.019.'
short: M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-01-06T00:00:00Z
date_updated: 2021-01-12T06:54:02Z
day: '06'
department:
- _id: JiFr
doi: 10.1016/j.cub.2013.11.019
intvolume: ' 24'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: R27 - R29
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '5180'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'Plant biology: Gatekeepers of the road to protein perdition'
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2014'
...
---
_id: '1915'
abstract:
- lang: eng
text: ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small
GTPases that function as essential molecular switches to control diverse cellular
processes including cytoskeleton organization, cell polarization, cytokinesis,
cell differentiation and vesicle trafficking. Although the machineries of vesicle
trafficking and cell polarity in plants have been individually well addressed,
how ROPs co-ordinate those processes is still largely unclear. Recent progress
has been made towards an understanding of the coordination of ROP signalling and
trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both
root and leaf pavement cells. PIN transporters constantly shuttle between the
endosomal compartments and the polar plasma membrane domains, therefore the modulation
of PIN-dependent auxin transport between cells is a main developmental output
of ROP-regulated vesicle trafficking. The present review focuses on these cellular
mechanisms, especially the integration of ROP-based vesicle trafficking and plant
cell polarity.
acknowledgement: This work was supported by the European Research Council [project
ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant
number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043]
and the Czec
article_processing_charge: No
article_type: original
author:
- first_name: Xu
full_name: Chen, Xu
id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87
last_name: Chen
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity.
Biochemical Society Transactions. 2014;42(1):212-218. doi:10.1042/BST20130269
apa: Chen, X., & Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking
in plant cell polarity. Biochemical Society Transactions. Portland Press.
https://doi.org/10.1042/BST20130269
chicago: Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in
Plant Cell Polarity.” Biochemical Society Transactions. Portland Press,
2014. https://doi.org/10.1042/BST20130269.
ieee: X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell
polarity,” Biochemical Society Transactions, vol. 42, no. 1. Portland Press,
pp. 212–218, 2014.
ista: Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell
polarity. Biochemical Society Transactions. 42(1), 212–218.
mla: Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant
Cell Polarity.” Biochemical Society Transactions, vol. 42, no. 1, Portland
Press, 2014, pp. 212–18, doi:10.1042/BST20130269.
short: X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218.
date_created: 2018-12-11T11:54:41Z
date_published: 2014-02-01T00:00:00Z
date_updated: 2025-05-07T11:12:31Z
day: '01'
department:
- _id: JiFr
doi: 10.1042/BST20130269
ec_funded: 1
external_id:
pmid:
- '24450654'
intvolume: ' 42'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 212 - 218
pmid: 1
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Biochemical Society Transactions
publication_identifier:
eissn:
- 1470-8752
issn:
- 0300-5127
publication_status: published
publisher: Portland Press
publist_id: '5179'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Rho-GTPase-regulated vesicle trafficking in plant cell polarity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2014'
...
---
_id: '1916'
abstract:
- lang: eng
text: Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases
characterized by progressive age-dependent loss of corticospinal motor tract function.
Although the genetic basis is partly understood, only a fraction of cases can
receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome
sequencing in combination with network analysis, we identified 18 previously unknown
putative HSP genes and validated nearly all of these genes functionally or genetically.
The pathways highlighted by these mutations link HSP to cellular transport, nucleotide
metabolism, and synapse and axon development. Network analysis revealed a host
of further candidate genes, of which three were mutated in our cohort. Our analysis
links HSP to other neurodegenerative disorders and can facilitate gene discovery
and mechanistic understanding of disease.
acknowledgement: Supported by the Deutsche Forschungsgemeinschaft (G.N.)
article_processing_charge: No
article_type: original
author:
- first_name: Gaia
full_name: Novarino, Gaia
id: 3E57A680-F248-11E8-B48F-1D18A9856A87
last_name: Novarino
orcid: 0000-0002-7673-7178
- first_name: Ali
full_name: Fenstermaker, Ali
last_name: Fenstermaker
- first_name: Maha
full_name: Zaki, Maha
last_name: Zaki
- first_name: Matan
full_name: Hofree, Matan
last_name: Hofree
- first_name: Jennifer
full_name: Silhavy, Jennifer
last_name: Silhavy
- first_name: Andrew
full_name: Heiberg, Andrew
last_name: Heiberg
- first_name: Mostafa
full_name: Abdellateef, Mostafa
last_name: Abdellateef
- first_name: Başak
full_name: Rosti, Başak
last_name: Rosti
- first_name: Eric
full_name: Scott, Eric
last_name: Scott
- first_name: Lobna
full_name: Mansour, Lobna
last_name: Mansour
- first_name: Amira
full_name: Masri, Amira
last_name: Masri
- first_name: Hülya
full_name: Kayserili, Hülya
last_name: Kayserili
- first_name: Jumana
full_name: Al Aama, Jumana
last_name: Al Aama
- first_name: Ghada
full_name: Abdel Salam, Ghada
last_name: Abdel Salam
- first_name: Ariana
full_name: Karminejad, Ariana
last_name: Karminejad
- first_name: Majdi
full_name: Kara, Majdi
last_name: Kara
- first_name: Bülent
full_name: Kara, Bülent
last_name: Kara
- first_name: Bita
full_name: Bozorgmehri, Bita
last_name: Bozorgmehri
- first_name: Tawfeg
full_name: Ben Omran, Tawfeg
last_name: Ben Omran
- first_name: Faezeh
full_name: Mojahedi, Faezeh
last_name: Mojahedi
- first_name: Iman
full_name: Mahmoud, Iman
last_name: Mahmoud
- first_name: Naïma
full_name: Bouslam, Naïma
last_name: Bouslam
- first_name: Ahmed
full_name: Bouhouche, Ahmed
last_name: Bouhouche
- first_name: Ali
full_name: Benomar, Ali
last_name: Benomar
- first_name: Sylvain
full_name: Hanein, Sylvain
last_name: Hanein
- first_name: Laure
full_name: Raymond, Laure
last_name: Raymond
- first_name: Sylvie
full_name: Forlani, Sylvie
last_name: Forlani
- first_name: Massimo
full_name: Mascaro, Massimo
last_name: Mascaro
- first_name: Laila
full_name: Selim, Laila
last_name: Selim
- first_name: Nabil
full_name: Shehata, Nabil
last_name: Shehata
- first_name: Nasir
full_name: Al Allawi, Nasir
last_name: Al Allawi
- first_name: Parayil
full_name: Bindu, Parayil
last_name: Bindu
- first_name: Matloob
full_name: Azam, Matloob
last_name: Azam
- first_name: Murat
full_name: Günel, Murat
last_name: Günel
- first_name: Ahmet
full_name: Caglayan, Ahmet
last_name: Caglayan
- first_name: Kaya
full_name: Bilgüvar, Kaya
last_name: Bilgüvar
- first_name: Aslihan
full_name: Tolun, Aslihan
last_name: Tolun
- first_name: Mahmoud
full_name: Issa, Mahmoud
last_name: Issa
- first_name: Jana
full_name: Schroth, Jana
last_name: Schroth
- first_name: Emily
full_name: Spencer, Emily
last_name: Spencer
- first_name: Rasim
full_name: Rosti, Rasim
last_name: Rosti
- first_name: Naiara
full_name: Akizu, Naiara
last_name: Akizu
- first_name: Keith
full_name: Vaux, Keith
last_name: Vaux
- first_name: Anide
full_name: Johansen, Anide
last_name: Johansen
- first_name: Alice
full_name: Koh, Alice
last_name: Koh
- first_name: Hisham
full_name: Megahed, Hisham
last_name: Megahed
- first_name: Alexandra
full_name: Dürr, Alexandra
last_name: Dürr
- first_name: Alexis
full_name: Brice, Alexis
last_name: Brice
- first_name: Giovanni
full_name: Stévanin, Giovanni
last_name: Stévanin
- first_name: Stacy
full_name: Gabriel, Stacy
last_name: Gabriel
- first_name: Trey
full_name: Ideker, Trey
last_name: Ideker
- first_name: Joseph
full_name: Gleeson, Joseph
last_name: Gleeson
citation:
ama: Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal
motor neuron disease to common neurodegenerative disorders. Science. 2014;343(6170):506-511.
doi:10.1126/science.1247363
apa: Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg,
A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease
to common neurodegenerative disorders. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.1247363
chicago: Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy,
Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal
Motor Neuron Disease to Common Neurodegenerative Disorders.” Science. American
Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1247363.
ieee: G. Novarino et al., “Exome sequencing links corticospinal motor neuron
disease to common neurodegenerative disorders,” Science, vol. 343, no.
6170. American Association for the Advancement of Science, pp. 506–511, 2014.
ista: Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef
M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G,
Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud
I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro
M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar
K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A,
Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J.
2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative
disorders. Science. 343(6170), 506–511.
mla: Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease
to Common Neurodegenerative Disorders.” Science, vol. 343, no. 6170, American
Association for the Advancement of Science, 2014, pp. 506–11, doi:10.1126/science.1247363.
short: G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg,
M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al
Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben
Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein,
L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu,
M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E.
Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr,
A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511.
date_created: 2018-12-11T11:54:42Z
date_published: 2014-01-31T00:00:00Z
date_updated: 2021-01-12T06:54:03Z
day: '31'
department:
- _id: GaNo
doi: 10.1126/science.1247363
external_id:
pmid:
- '24482476'
intvolume: ' 343'
issue: '6170'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/
month: '01'
oa: 1
oa_version: Submitted Version
page: 506 - 511
pmid: 1
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5178'
quality_controlled: '1'
scopus_import: 1
status: public
title: Exome sequencing links corticospinal motor neuron disease to common neurodegenerative
disorders
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 343
year: '2014'
...