---
_id: '522'
abstract:
- lang: eng
text: Podoplanin, a mucin-like plasma membrane protein, is expressed by lymphatic
endothelial cells and responsible for separation of blood and lymphatic circulation
through activation of platelets. Here we show that podoplanin is also expressed
by thymic fibroblastic reticular cells (tFRC), a novel thymic medulla stroma cell
type associated with thymic conduits, and involved in development of natural regulatory
T cells (nTreg). Young mice deficient in podoplanin lack nTreg owing to retardation
of CD4+CD25+ thymocytes in the cortex and missing differentiation of Foxp3+ thymocytes
in the medulla. This might be due to CCL21 that delocalizes upon deletion of the
CCL21-binding podoplanin from medullar tFRC to cortex areas. The animals do not
remain devoid of nTreg but generate them delayed within the first month resulting
in Th2-biased hypergammaglobulinemia but not in the death-causing autoimmune phenotype
of Foxp3-deficient Scurfy mice.
author:
- first_name: Elke
full_name: Fuertbauer, Elke
last_name: Fuertbauer
- first_name: Jan
full_name: Zaujec, Jan
last_name: Zaujec
- first_name: Pavel
full_name: Uhrin, Pavel
last_name: Uhrin
- first_name: Ingrid
full_name: Raab, Ingrid
last_name: Raab
- first_name: Michele
full_name: Weber, Michele
id: 3A3FC708-F248-11E8-B48F-1D18A9856A87
last_name: Weber
- first_name: Helga
full_name: Schachner, Helga
last_name: Schachner
- first_name: Miroslav
full_name: Bauer, Miroslav
last_name: Bauer
- first_name: Gerhard
full_name: Schütz, Gerhard
last_name: Schütz
- first_name: Bernd
full_name: Binder, Bernd
last_name: Binder
- 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: Dontscho
full_name: Kerjaschki, Dontscho
last_name: Kerjaschki
- first_name: Hannes
full_name: Stockinger, Hannes
last_name: Stockinger
citation:
ama: Fuertbauer E, Zaujec J, Uhrin P, et al. Thymic medullar conduits-associated
podoplanin promotes natural regulatory T cells. Immunology Letters. 2013;154(1-2):31-41.
doi:10.1016/j.imlet.2013.07.007
apa: Fuertbauer, E., Zaujec, J., Uhrin, P., Raab, I., Weber, M., Schachner, H.,
… Stockinger, H. (2013). Thymic medullar conduits-associated podoplanin promotes
natural regulatory T cells. Immunology Letters. Elsevier. https://doi.org/10.1016/j.imlet.2013.07.007
chicago: Fuertbauer, Elke, Jan Zaujec, Pavel Uhrin, Ingrid Raab, Michele Weber,
Helga Schachner, Miroslav Bauer, et al. “Thymic Medullar Conduits-Associated Podoplanin
Promotes Natural Regulatory T Cells.” Immunology Letters. Elsevier, 2013.
https://doi.org/10.1016/j.imlet.2013.07.007.
ieee: E. Fuertbauer et al., “Thymic medullar conduits-associated podoplanin
promotes natural regulatory T cells,” Immunology Letters, vol. 154, no.
1–2. Elsevier, pp. 31–41, 2013.
ista: Fuertbauer E, Zaujec J, Uhrin P, Raab I, Weber M, Schachner H, Bauer M, Schütz
G, Binder B, Sixt MK, Kerjaschki D, Stockinger H. 2013. Thymic medullar conduits-associated
podoplanin promotes natural regulatory T cells. Immunology Letters. 154(1–2),
31–41.
mla: Fuertbauer, Elke, et al. “Thymic Medullar Conduits-Associated Podoplanin Promotes
Natural Regulatory T Cells.” Immunology Letters, vol. 154, no. 1–2, Elsevier,
2013, pp. 31–41, doi:10.1016/j.imlet.2013.07.007.
short: E. Fuertbauer, J. Zaujec, P. Uhrin, I. Raab, M. Weber, H. Schachner, M. Bauer,
G. Schütz, B. Binder, M.K. Sixt, D. Kerjaschki, H. Stockinger, Immunology Letters
154 (2013) 31–41.
date_created: 2018-12-11T11:46:57Z
date_published: 2013-07-01T00:00:00Z
date_updated: 2021-01-12T08:01:22Z
day: '01'
department:
- _id: MiSi
doi: 10.1016/j.imlet.2013.07.007
intvolume: ' 154'
issue: 1-2
language:
- iso: eng
month: '07'
oa_version: None
page: 31 - 41
publication: Immunology Letters
publication_status: published
publisher: Elsevier
publist_id: '7300'
quality_controlled: '1'
scopus_import: 1
status: public
title: Thymic medullar conduits-associated podoplanin promotes natural regulatory
T cells
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 154
year: '2013'
...
---
_id: '527'
abstract:
- lang: eng
text: The apical-basal axis of the early plant embryo determines the body plan of
the adult organism. To establish a polarized embryonic axis, plants evolved a
unique mechanism that involves directional, cell-to-cell transport of the growth
regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar
subcellular localization determines the flow directionality. PIN-mediated auxin
transport mediates the spatial and temporal activity of the auxin response machinery
[2-7] that contributes to embryo patterning processes, including establishment
of the apical (shoot) and basal (root) embryo poles [8]. However, little is known
of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis
[9]. Here, we developed a model of plant embryogenesis that correctly generates
emergent cell polarities and auxin-mediated sequential initiation of apical-basal
axis of plant embryo. The model relies on two precisely localized auxin sources
and a feedback between auxin and the polar, subcellular PIN transporter localization.
Simulations reproduced PIN polarity and auxin distribution, as well as previously
unknown polarization events during early embryogenesis. The spectrum of validated
model predictions suggests that our model corresponds to a minimal mechanistic
framework for initiation and orientation of the apical-basal axis to guide both
embryonic and postembryonic plant development.
author:
- first_name: Krzysztof T
full_name: Wabnik, Krzysztof T
id: 4DE369A4-F248-11E8-B48F-1D18A9856A87
last_name: Wabnik
orcid: 0000-0001-7263-0560
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Richard
full_name: Smith, Richard
last_name: Smith
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Wabnik KT, Robert H, Smith R, Friml J. Modeling framework for the establishment
of the apical-basal embryonic axis in plants. Current Biology. 2013;23(24):2513-2518.
doi:10.1016/j.cub.2013.10.038
apa: Wabnik, K. T., Robert, H., Smith, R., & Friml, J. (2013). Modeling framework
for the establishment of the apical-basal embryonic axis in plants. Current
Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.10.038
chicago: Wabnik, Krzysztof T, Hélène Robert, Richard Smith, and Jiří Friml. “Modeling
Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.”
Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2013.10.038.
ieee: K. T. Wabnik, H. Robert, R. Smith, and J. Friml, “Modeling framework for the
establishment of the apical-basal embryonic axis in plants,” Current Biology,
vol. 23, no. 24. Cell Press, pp. 2513–2518, 2013.
ista: Wabnik KT, Robert H, Smith R, Friml J. 2013. Modeling framework for the establishment
of the apical-basal embryonic axis in plants. Current Biology. 23(24), 2513–2518.
mla: Wabnik, Krzysztof T., et al. “Modeling Framework for the Establishment of the
Apical-Basal Embryonic Axis in Plants.” Current Biology, vol. 23, no. 24,
Cell Press, 2013, pp. 2513–18, doi:10.1016/j.cub.2013.10.038.
short: K.T. Wabnik, H. Robert, R. Smith, J. Friml, Current Biology 23 (2013) 2513–2518.
date_created: 2018-12-11T11:46:58Z
date_published: 2013-12-16T00:00:00Z
date_updated: 2021-01-12T08:01:24Z
day: '16'
department:
- _id: EvBe
- _id: JiFr
doi: 10.1016/j.cub.2013.10.038
ec_funded: 1
intvolume: ' 23'
issue: '24'
language:
- iso: eng
month: '12'
oa_version: None
page: 2513 - 2518
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7292'
quality_controlled: '1'
scopus_import: 1
status: public
title: Modeling framework for the establishment of the apical-basal embryonic axis
in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '528'
abstract:
- lang: eng
text: Establishment of the embryonic axis foreshadows the main body axis of adults
both in plants and in animals, but underlying mechanisms are considered distinct.
Plants utilize directional, cell-to-cell transport of the growth hormone auxin
[1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal
axis [3-6]. The auxin flow directionality depends on the polarized subcellular
localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown
which mechanisms and spatial cues guide cell polarization and axis orientation
in early embryos. Herein, we provide conceptually novel insights into the formation
of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent
auxin biosynthesis [9-12]. Local auxin production at the base of young embryos
and the accompanying PIN7-mediated auxin flow toward the proembryo are required
for the apical auxin response maximum and the specification of apical embryonic
structures. Later in embryogenesis, the precisely timed onset of localized apical
auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and
specification of the root pole. Thus, the tight spatiotemporal control of distinct
local auxin sources provides a necessary, non-cell-autonomous trigger for the
coordinated cell polarization and subsequent apical-basal axis orientation during
embryogenesis and, presumably, also for other polarization events during postembryonic
plant life [13, 14].
author:
- first_name: Hélène
full_name: Robert, Hélène
last_name: Robert
- first_name: Peter
full_name: Grones, Peter
id: 399876EC-F248-11E8-B48F-1D18A9856A87
last_name: Grones
- first_name: Anna
full_name: Stepanova, Anna
last_name: Stepanova
- first_name: Linda
full_name: Robles, Linda
last_name: Robles
- first_name: Annemarie
full_name: Lokerse, Annemarie
last_name: Lokerse
- first_name: Jose
full_name: Alonso, Jose
last_name: Alonso
- first_name: Dolf
full_name: Weijers, Dolf
last_name: Weijers
- first_name: Jirí
full_name: Friml, Jirí
id: 4159519E-F248-11E8-B48F-1D18A9856A87
last_name: Friml
orcid: 0000-0002-8302-7596
citation:
ama: Robert H, Grones P, Stepanova A, et al. Local auxin sources orient the apical
basal axis in arabidopsis embryos. Current Biology. 2013;23(24):2506-2512.
doi:10.1016/j.cub.2013.09.039
apa: Robert, H., Grones, P., Stepanova, A., Robles, L., Lokerse, A., Alonso, J.,
… Friml, J. (2013). Local auxin sources orient the apical basal axis in arabidopsis
embryos. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.09.039
chicago: Robert, Hélène, Peter Grones, Anna Stepanova, Linda Robles, Annemarie Lokerse,
Jose Alonso, Dolf Weijers, and Jiří Friml. “Local Auxin Sources Orient the Apical
Basal Axis in Arabidopsis Embryos.” Current Biology. Cell Press, 2013.
https://doi.org/10.1016/j.cub.2013.09.039.
ieee: H. Robert et al., “Local auxin sources orient the apical basal axis
in arabidopsis embryos,” Current Biology, vol. 23, no. 24. Cell Press,
pp. 2506–2512, 2013.
ista: Robert H, Grones P, Stepanova A, Robles L, Lokerse A, Alonso J, Weijers D,
Friml J. 2013. Local auxin sources orient the apical basal axis in arabidopsis
embryos. Current Biology. 23(24), 2506–2512.
mla: Robert, Hélène, et al. “Local Auxin Sources Orient the Apical Basal Axis in
Arabidopsis Embryos.” Current Biology, vol. 23, no. 24, Cell Press, 2013,
pp. 2506–12, doi:10.1016/j.cub.2013.09.039.
short: H. Robert, P. Grones, A. Stepanova, L. Robles, A. Lokerse, J. Alonso, D.
Weijers, J. Friml, Current Biology 23 (2013) 2506–2512.
date_created: 2018-12-11T11:46:59Z
date_published: 2013-12-16T00:00:00Z
date_updated: 2021-01-12T08:01:25Z
day: '16'
department:
- _id: JiFr
doi: 10.1016/j.cub.2013.09.039
ec_funded: 1
intvolume: ' 23'
issue: '24'
language:
- iso: eng
month: '12'
oa_version: None
page: 2506 - 2512
project:
- _id: 25716A02-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '282300'
name: Polarity and subcellular dynamics in plants
publication: Current Biology
publication_status: published
publisher: Cell Press
publist_id: '7291'
quality_controlled: '1'
scopus_import: 1
status: public
title: Local auxin sources orient the apical basal axis in arabidopsis embryos
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2013'
...
---
_id: '2516'
abstract:
- lang: eng
text: 'We study the problem of object recognition for categories for which we have
no training examples, a task also called zero-data or zero-shot learning. This
situation has hardly been studied in computer vision research, even though it
occurs frequently: the world contains tens of thousands of different object classes
and for only few of them image collections have been formed and suitably annotated.
To tackle the problem we introduce attribute-based classification: objects are
identified based on a high-level description that is phrased in terms of semantic
attributes, such as the object''s color or shape. Because the identification of
each such property transcends the specific learning task at hand, the attribute
classifiers can be pre-learned independently, e.g. from existing image datasets
unrelated to the current task. Afterwards, new classes can be detected based on
their attribute representation, without the need for a new training phase. In
this paper we also introduce a new dataset, Animals with Attributes, of over 30,000
images of 50 animal classes, annotated with 85 semantic attributes. Extensive
experiments on this and two more datasets show that attribute-based classification
indeed is able to categorize images without access to any training images of the
target classes.'
article_processing_charge: No
author:
- first_name: Christoph
full_name: Lampert, Christoph
id: 40C20FD2-F248-11E8-B48F-1D18A9856A87
last_name: Lampert
orcid: 0000-0001-8622-7887
- first_name: Hannes
full_name: Nickisch, Hannes
last_name: Nickisch
- first_name: Stefan
full_name: Harmeling, Stefan
last_name: Harmeling
citation:
ama: Lampert C, Nickisch H, Harmeling S. Attribute-based classification for zero-shot
learning of object categories. IEEE Transactions on Pattern Analysis and Machine
Intelligence. 2013;36(3):453-465. doi:10.1109/TPAMI.2013.140
apa: Lampert, C., Nickisch, H., & Harmeling, S. (2013). Attribute-based classification
for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis
and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2013.140
chicago: Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Attribute-Based
Classification for Zero-Shot Learning of Object Categories.” IEEE Transactions
on Pattern Analysis and Machine Intelligence. IEEE, 2013. https://doi.org/10.1109/TPAMI.2013.140.
ieee: C. Lampert, H. Nickisch, and S. Harmeling, “Attribute-based classification
for zero-shot learning of object categories,” IEEE Transactions on Pattern
Analysis and Machine Intelligence, vol. 36, no. 3. IEEE, pp. 453–465, 2013.
ista: Lampert C, Nickisch H, Harmeling S. 2013. Attribute-based classification for
zero-shot learning of object categories. IEEE Transactions on Pattern Analysis
and Machine Intelligence. 36(3), 453–465.
mla: Lampert, Christoph, et al. “Attribute-Based Classification for Zero-Shot Learning
of Object Categories.” IEEE Transactions on Pattern Analysis and Machine Intelligence,
vol. 36, no. 3, IEEE, 2013, pp. 453–65, doi:10.1109/TPAMI.2013.140.
short: C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis
and Machine Intelligence 36 (2013) 453–465.
das_tickbox: '1'
date_created: 2018-12-11T11:58:08Z
date_published: 2013-07-30T00:00:00Z
date_updated: 2026-06-18T07:51:30Z
day: '30'
ddc:
- '000'
department:
- _id: ChLa
doi: 10.1109/TPAMI.2013.140
intvolume: ' 36'
issue: '3'
language:
- iso: eng
month: '07'
oa_version: None
page: 453 - 465
publication: IEEE Transactions on Pattern Analysis and Machine Intelligence
publication_status: published
publisher: IEEE
publist_id: '4385'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Attribute-based classification for zero-shot learning of object categories
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 36
year: '2013'
...
---
_id: '12198'
abstract:
- lang: eng
text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes
DNA demethylation before fertilization, but the targeting preferences, mechanism,
and biological significance of this process remain unclear. Here, we show that
active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for
all of the demethylation in the central cell and preferentially targets small,
AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative
cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation
of similar sequences, and lack of DEMETER in vegetative cells causes reduced small
RNA–directed DNA methylation of transposons in sperm. Our results demonstrate
that demethylation in companion cells reinforces transposon methylation in plant
gametes and likely contributes to stable silencing of transposable elements across
generations.
acknowledgement: We thank S. Harmer for assistance with the analysis of histone modifications,
the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative
cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the
DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415)
to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young
Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian
Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral
Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship
from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas
Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).
article_processing_charge: No
article_type: original
author:
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Adriana
full_name: Machlicova, Adriana
last_name: Machlicova
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Denisse
full_name: Rojas, Denisse
last_name: Rojas
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
- first_name: Daniel
full_name: Zilberman, Daniel
last_name: Zilberman
citation:
ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion
cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364.
doi:10.1126/science.1224839
apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues,
J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1224839
chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie
Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in
Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science.
American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100.
American Association for the Advancement of Science, pp. 1360–1364, 2012.
ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A,
Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman
D. 2012. Active DNA demethylation in plant companion cells reinforces transposon
methylation in gametes. Science. 337(6100), 1360–1364.
mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells
Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100,
American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.
short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues,
A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H.
Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
date_created: 2023-01-16T09:21:24Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2023-10-16T09:27:26Z
day: '14'
department:
- _id: XiFe
doi: 10.1126/science.1224839
external_id:
pmid:
- '22984074'
intvolume: ' 337'
issue: '6100'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/
month: '09'
oa: 1
oa_version: Published Version
page: 1360-1364
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active DNA demethylation in plant companion cells reinforces transposon methylation
in gametes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 337
year: '2012'
...
---
_id: '12644'
abstract:
- lang: eng
text: In the Dry Andes of central Chile, summer water resources originate mostly
from snowmelt and ice melt. We use the physically based, spatially distributed
hydrological model TOPKAPI to study the exchange between glaciers and climate
in the upper Aconcagua River Basin during the summer season and identify the model
parameters that are robust and transferable and those that are more dependent
on calibration. TOPKAPI has recently been adapted to incorporate an enhanced temperature
index approach for snow and ice melting. We suggest a calibration procedure that
allows calibration of parameters in three steps by separating parameters governing
distinct processes. We evaluate the parameters' transferability in time and in
space by applying the model at two spatial scales. TOPKAPI's ability to simulate
the relevant processes is tested against meteorological, ablation, and glacier
runoff data measured on Juncal Norte Glacier during two glacier ablation seasons.
The model was applied successfully to the climatic setting of the Dry Andes once
its parameters were recalibrated. We found a clear distinction between parameters
that are stable in time and those that need recalibration. The parameters of the
melt model are transferable from one season to the other, while the parameters
governing the extrapolation of meteorological input data and the routing of glacier
meltwater need recalibration from one season to the other. Sensitivity analysis
revealed that the model is most sensitive to the temperature lapse rate governing
the extrapolation of air temperature from point measurements to the glacier scale
and to the melt parameter that multiplies the shortwave radiation balance.
article_number: W03509
article_processing_charge: No
article_type: original
author:
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
citation:
ama: 'Ragettli S, Pellicciotti F. Calibration of a physically based, spatially distributed
hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological
processes to constrain model parameters. Water Resources Research. 2012;48(3).
doi:10.1029/2011wr010559'
apa: 'Ragettli, S., & Pellicciotti, F. (2012). Calibration of a physically based,
spatially distributed hydrological model in a glacierized basin: On the use of
knowledge from glaciometeorological processes to constrain model parameters. Water
Resources Research. American Geophysical Union. https://doi.org/10.1029/2011wr010559'
chicago: 'Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically
Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the
Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.”
Water Resources Research. American Geophysical Union, 2012. https://doi.org/10.1029/2011wr010559.'
ieee: 'S. Ragettli and F. Pellicciotti, “Calibration of a physically based, spatially
distributed hydrological model in a glacierized basin: On the use of knowledge
from glaciometeorological processes to constrain model parameters,” Water Resources
Research, vol. 48, no. 3. American Geophysical Union, 2012.'
ista: 'Ragettli S, Pellicciotti F. 2012. Calibration of a physically based, spatially
distributed hydrological model in a glacierized basin: On the use of knowledge
from glaciometeorological processes to constrain model parameters. Water Resources
Research. 48(3), W03509.'
mla: 'Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based,
Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of
Knowledge from Glaciometeorological Processes to Constrain Model Parameters.”
Water Resources Research, vol. 48, no. 3, W03509, American Geophysical
Union, 2012, doi:10.1029/2011wr010559.'
short: S. Ragettli, F. Pellicciotti, Water Resources Research 48 (2012).
date_created: 2023-02-20T08:17:39Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2023-02-21T09:38:36Z
day: '01'
doi: 10.1029/2011wr010559
extern: '1'
intvolume: ' 48'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2011WR010559
month: '03'
oa: 1
oa_version: Published Version
publication: Water Resources Research
publication_identifier:
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Calibration of a physically based, spatially distributed hydrological model
in a glacierized basin: On the use of knowledge from glaciometeorological processes
to constrain model parameters'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 48
year: '2012'
...
---
_id: '12646'
abstract:
- lang: eng
text: Assessment of water resources from remote mountainous catchments plays a crucial
role for the development of rural areas in or in the vicinity of mountain ranges.
The scarcity of data, however, prevents the application of standard approaches
that are based on data-driven models. The Hindu Kush–Karakoram–Himalaya mountain
range is a crucial area in terms of water resources, but our understanding of
the response of its high-elevation catchments to a changing climate is hindered
by lack of hydro-meteorological and cryospheric data. Hydrological modeling is
challenging here because internal inconsistencies—such as an underestimation of
precipitation input that can be compensated for by an overestimation of meltwater—might
be hidden due to the complexity of feedback mechanisms that govern melt and runoff
generation in such basins. Data scarcity adds to this difficulty by preventing
the application of systematic calibration procedures that would allow identification
of the parameter set that could guarantee internal consistency in the simulation
of the single hydrological components. In this work, we use simulations from the
Hunza River Basin in the Karakoram region obtained with the hydrological model
TOPKAPI to quantify the predictive power of discharge and snow-cover data sets,
as well as the combination of both. We also show that short-term measurements
of meteorological variables such as radiative fluxes, wind speed, relative humidity,
and air temperature from glacio-meteorological experiments are crucial for a correct
parameterization of surface melt processes. They enable detailed simulations of
the energy fluxes governing glacier–atmosphere interaction and the resulting ablation
through energy-balance modeling. These simulations are used to derive calibrated
parameters for the simplified snow and glacier routines in TOPKAPI. We demonstrate
that such parameters are stable in space and time in similar climatic regions,
thus reducing the number of parameters requiring calibration.
article_processing_charge: No
article_type: original
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Cyrill
full_name: Buergi, Cyrill
last_name: Buergi
- first_name: Walter Willem
full_name: Immerzeel, Walter Willem
last_name: Immerzeel
- first_name: Markus
full_name: Konz, Markus
last_name: Konz
- first_name: Arun B.
full_name: Shrestha, Arun B.
last_name: Shrestha
citation:
ama: 'Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. Challenges and
uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies. Mountain Research and
Development. 2012;32(1):39-50. doi:10.1659/mrd-journal-d-11-00092.1'
apa: 'Pellicciotti, F., Buergi, C., Immerzeel, W. W., Konz, M., & Shrestha,
A. B. (2012). Challenges and uncertainties in hydrological modeling of remote
Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies.
Mountain Research and Development. International Mountain Society. https://doi.org/10.1659/mrd-journal-d-11-00092.1'
chicago: 'Pellicciotti, Francesca, Cyrill Buergi, Walter Willem Immerzeel, Markus
Konz, and Arun B. Shrestha. “Challenges and Uncertainties in Hydrological Modeling
of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration
Strategies.” Mountain Research and Development. International Mountain
Society, 2012. https://doi.org/10.1659/mrd-journal-d-11-00092.1.'
ieee: 'F. Pellicciotti, C. Buergi, W. W. Immerzeel, M. Konz, and A. B. Shrestha,
“Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies,” Mountain Research and
Development, vol. 32, no. 1. International Mountain Society, pp. 39–50, 2012.'
ista: 'Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. 2012. Challenges
and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies. Mountain Research and Development.
32(1), 39–50.'
mla: 'Pellicciotti, Francesca, et al. “Challenges and Uncertainties in Hydrological
Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for
Calibration Strategies.” Mountain Research and Development, vol. 32, no.
1, International Mountain Society, 2012, pp. 39–50, doi:10.1659/mrd-journal-d-11-00092.1.'
short: F. Pellicciotti, C. Buergi, W.W. Immerzeel, M. Konz, A.B. Shrestha, Mountain
Research and Development 32 (2012) 39–50.
date_created: 2023-02-20T08:17:47Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2023-02-21T09:31:54Z
day: '01'
doi: 10.1659/mrd-journal-d-11-00092.1
extern: '1'
intvolume: ' 32'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1659/MRD-JOURNAL-D-11-00092.1
month: '02'
oa: 1
oa_version: Published Version
page: 39-50
publication: Mountain Research and Development
publication_identifier:
eissn:
- 1994-7151
issn:
- 0276-4741
publication_status: published
publisher: International Mountain Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan
(HKH) basins: Suggestions for calibration strategies'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...
---
_id: '12647'
abstract:
- lang: eng
text: Accurate quantification of the spatial distribution of precipitation in mountain
regions is crucial for assessments of water resources and for the understanding
of high-altitude hydrology, yet it is one of the largest unknowns due to the lack
of high-altitude observations. The Hunza basin in Pakistan contains very large
glacier systems, which, given the melt, cannot persist unless precipitation (snow
input) is much higher than what is observed at the meteorological stations, mostly
located in mountain valleys. Several studies, therefore, suggest strong positive
vertical precipitation lapse rates; in the present study, we quantify this lapse
rate by using glaciers as a proxy. We assume a neutral mass balance for the glaciers
for the period from 2001 to 2003, and we inversely model the precipitation lapse
by balancing the total accumulation in the catchment area and the ablation over
the glacier area for the 50 largest glacier systems in the Hunza basin in the
Karakoram. Our results reveal a vertical precipitation lapse rate that equals
0.21 ± 0.12% m−1, with a maximum precipitation at an elevation of 5500 masl. We
showed that the total annual basin precipitation (828 mm) is 260% higher than
what is estimated based on interpolated observations (319 mm); this has major
consequences for hydrological modeling and water resource assessments in general.
Our results were validated by using previously published studies on individual
glaciers as well as the water balance of the Hunza basin. The approach is more
widely applicable in mountain ranges where precipitation measurements at high
altitude are lacking.
article_processing_charge: No
article_type: original
author:
- first_name: Walter Willem
full_name: Immerzeel, Walter Willem
last_name: Immerzeel
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Arun B.
full_name: Shrestha, Arun B.
last_name: Shrestha
citation:
ama: Immerzeel WW, Pellicciotti F, Shrestha AB. Glaciers as a proxy to quantify
the spatial distribution of precipitation in the Hunza basin. Mountain Research
and Development. 2012;32(1):30-38. doi:10.1659/mrd-journal-d-11-00097.1
apa: Immerzeel, W. W., Pellicciotti, F., & Shrestha, A. B. (2012). Glaciers
as a proxy to quantify the spatial distribution of precipitation in the Hunza
basin. Mountain Research and Development. International Mountain Society.
https://doi.org/10.1659/mrd-journal-d-11-00097.1
chicago: Immerzeel, Walter Willem, Francesca Pellicciotti, and Arun B. Shrestha.
“Glaciers as a Proxy to Quantify the Spatial Distribution of Precipitation in
the Hunza Basin.” Mountain Research and Development. International Mountain
Society, 2012. https://doi.org/10.1659/mrd-journal-d-11-00097.1.
ieee: W. W. Immerzeel, F. Pellicciotti, and A. B. Shrestha, “Glaciers as a proxy
to quantify the spatial distribution of precipitation in the Hunza basin,” Mountain
Research and Development, vol. 32, no. 1. International Mountain Society,
pp. 30–38, 2012.
ista: Immerzeel WW, Pellicciotti F, Shrestha AB. 2012. Glaciers as a proxy to quantify
the spatial distribution of precipitation in the Hunza basin. Mountain Research
and Development. 32(1), 30–38.
mla: Immerzeel, Walter Willem, et al. “Glaciers as a Proxy to Quantify the Spatial
Distribution of Precipitation in the Hunza Basin.” Mountain Research and Development,
vol. 32, no. 1, International Mountain Society, 2012, pp. 30–38, doi:10.1659/mrd-journal-d-11-00097.1.
short: W.W. Immerzeel, F. Pellicciotti, A.B. Shrestha, Mountain Research and Development
32 (2012) 30–38.
date_created: 2023-02-20T08:17:52Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2023-02-21T08:56:29Z
day: '01'
doi: 10.1659/mrd-journal-d-11-00097.1
extern: '1'
intvolume: ' 32'
issue: '1'
keyword:
- General Environmental Science
- Development
- Environmental Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1659/MRD-JOURNAL-D-11-00097.1
month: '02'
oa: 1
oa_version: Published Version
page: 30-38
publication: Mountain Research and Development
publication_identifier:
eissn:
- 1994-7151
issn:
- 0276-4741
publication_status: published
publisher: International Mountain Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Glaciers as a proxy to quantify the spatial distribution of precipitation in
the Hunza basin
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...
---
_id: '12648'
abstract:
- lang: eng
text: Distributed glacier melt models generally assume that the glacier surface
consists of bare exposed ice and snow. In reality, many glaciers are wholly or
partially covered in layers of debris that tend to suppress ablation rates. In
this paper, an existing physically based point model for the ablation of debris-covered
ice is incorporated in a distributed melt model and applied to Haut Glacier d'Arolla,
Switzerland, which has three large patches of debris cover on its surface. The
model is based on a 10 m resolution digital elevation model (DEM) of the area;
each glacier pixel in the DEM is defined as either bare or debris-covered ice,
and may be covered in snow that must be melted off before ice ablation is assumed
to occur. Each debris-covered pixel is assigned a debris thickness value using
probability distributions based on over 1000 manual thickness measurements. Locally
observed meteorological data are used to run energy balance calculations in every
pixel, using an approach suitable for snow, bare ice or debris-covered ice as
appropriate. The use of the debris model significantly reduces the total ablation
in the debris-covered areas, however the precise reduction is sensitive to the
temperature extrapolation used in the model distribution because air near the
debris surface tends to be slightly warmer than over bare ice. Overall results
suggest that the debris patches, which cover 10% of the glacierized area, reduce
total runoff from the glacierized part of the basin by up to 7%.
article_number: D18105
article_processing_charge: No
article_type: original
author:
- first_name: T. D.
full_name: Reid, T. D.
last_name: Reid
- first_name: M.
full_name: Carenzo, M.
last_name: Carenzo
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: B. W.
full_name: Brock, B. W.
last_name: Brock
citation:
ama: 'Reid TD, Carenzo M, Pellicciotti F, Brock BW. Including debris cover effects
in a distributed model of glacier ablation. Journal of Geophysical Research:
Atmospheres. 2012;117(D18). doi:10.1029/2012jd017795'
apa: 'Reid, T. D., Carenzo, M., Pellicciotti, F., & Brock, B. W. (2012). Including
debris cover effects in a distributed model of glacier ablation. Journal of
Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1029/2012jd017795'
chicago: 'Reid, T. D., M. Carenzo, Francesca Pellicciotti, and B. W. Brock. “Including
Debris Cover Effects in a Distributed Model of Glacier Ablation.” Journal of
Geophysical Research: Atmospheres. American Geophysical Union, 2012. https://doi.org/10.1029/2012jd017795.'
ieee: 'T. D. Reid, M. Carenzo, F. Pellicciotti, and B. W. Brock, “Including debris
cover effects in a distributed model of glacier ablation,” Journal of Geophysical
Research: Atmospheres, vol. 117, no. D18. American Geophysical Union, 2012.'
ista: 'Reid TD, Carenzo M, Pellicciotti F, Brock BW. 2012. Including debris cover
effects in a distributed model of glacier ablation. Journal of Geophysical Research:
Atmospheres. 117(D18), D18105.'
mla: 'Reid, T. D., et al. “Including Debris Cover Effects in a Distributed Model
of Glacier Ablation.” Journal of Geophysical Research: Atmospheres, vol.
117, no. D18, D18105, American Geophysical Union, 2012, doi:10.1029/2012jd017795.'
short: 'T.D. Reid, M. Carenzo, F. Pellicciotti, B.W. Brock, Journal of Geophysical
Research: Atmospheres 117 (2012).'
date_created: 2023-02-20T08:17:57Z
date_published: 2012-09-27T00:00:00Z
date_updated: 2023-02-20T10:57:31Z
day: '27'
doi: 10.1029/2012jd017795
extern: '1'
intvolume: ' 117'
issue: D18
keyword:
- Paleontology
- Space and Planetary Science
- Earth and Planetary Sciences (miscellaneous)
- Atmospheric Science
- Earth-Surface Processes
- Geochemistry and Petrology
- Soil Science
- Water Science and Technology
- Ecology
- Aquatic Science
- Forestry
- Oceanography
- Geophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2012JD017795
month: '09'
oa: 1
oa_version: Published Version
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
issn:
- 0148-0227
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: Including debris cover effects in a distributed model of glacier ablation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2012'
...
---
_id: '13075'
abstract:
- lang: eng
text: Little is known about the stability of trophic relationships in complex natural
communities over evolutionary timescales. Here, we use sequence data from 18 nuclear
loci to reconstruct and compare the intraspecific histories of major Pleistocene
refugial populations in the Middle East, the Balkans and Iberia in a guild of
four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota
and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood
method to numerically estimate models of divergence between three populations
from multilocus data. We investigate the power of this framework on simulated
data, and - using triplet alignments of intronic loci - quantify the support for
all possible divergence relationships between refugial populations in the four
parasitoids. Although an East to West order of population divergence has highest
support in all but one species, we cannot rule out alternative population tree
topologies. Comparing the estimated times of population splits between species,
we find that one species, M. amaenus, has a significantly older history than the
rest of the guild and must have arrived in central Europe at least one glacial
cycle prior to other guild members. This suggests that although all four species
may share a common origin in the East, they expanded westwards into Europe at
different times.
article_processing_charge: No
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- 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: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: George
full_name: Melika, George
last_name: Melika
citation:
ama: 'Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison
of population histories in a parasitoid guild. 2012. doi:10.5061/DRYAD.0G0FS'
apa: 'Lohse, K., Barton, N. H., Stone, G., & Melika, G. (2012). Data from: A
likelihood-based comparison of population histories in a parasitoid guild. Dryad.
https://doi.org/10.5061/DRYAD.0G0FS'
chicago: 'Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data
from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.”
Dryad, 2012. https://doi.org/10.5061/DRYAD.0G0FS.'
ieee: 'K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based
comparison of population histories in a parasitoid guild.” Dryad, 2012.'
ista: 'Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based
comparison of population histories in a parasitoid guild, Dryad, 10.5061/DRYAD.0G0FS.'
mla: 'Lohse, Konrad, et al. Data from: A Likelihood-Based Comparison of Population
Histories in a Parasitoid Guild. Dryad, 2012, doi:10.5061/DRYAD.0G0FS.'
short: K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).
date_created: 2023-05-23T17:01:02Z
date_published: 2012-06-08T00:00:00Z
date_updated: 2025-05-28T11:56:58Z
day: '08'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.0G0FS
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.0g0fs
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2968'
relation: used_in_publication
status: public
status: public
title: 'Data from: A likelihood-based comparison of population histories in a parasitoid
guild'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2012'
...
---
_id: '8246'
abstract:
- lang: eng
text: The Staphylococcus aureus cell wall stress stimulon (CWSS) is activated by
cell envelope-targeting antibiotics or depletion of essential cell wall biosynthesis
enzymes. The functionally uncharacterized S. aureus LytR-CpsA-Psr (LCP) proteins,
MsrR, SA0908 and SA2103, all belong to the CWSS. Although not essential, deletion
of all three LCP proteins severely impairs cell division. We show here that VraSR-dependent
CWSS expression was up to 250-fold higher in single, double and triple LCP mutants
than in wild type S. aureus in the absence of external stress. The LCP triple
mutant was virtually depleted of wall teichoic acids (WTA), which could be restored
to different degrees by any of the single LCP proteins. Subinhibitory concentrations
of tunicamycin, which inhibits the first WTA synthesis enzyme TarO (TagO), could
partially complement the severe growth defect of the LCP triple mutant. Both of
the latter findings support a role for S. aureus LCP proteins in late WTA synthesis,
as in Bacillus subtilis where LCP proteins were recently proposed to transfer
WTA from lipid carriers to the cell wall peptidoglycan. Intrinsic activation of
the CWSS upon LCP deletion and the fact that LCP proteins were essential for WTA-loading
of the cell wall, highlight their important role(s) in S. aureus cell envelope
biogenesis.
article_processing_charge: No
article_type: original
author:
- first_name: Vanina
full_name: Dengler, Vanina
last_name: Dengler
- first_name: Patricia Stutzmann
full_name: Meier, Patricia Stutzmann
last_name: Meier
- first_name: Ronald
full_name: Heusser, Ronald
last_name: Heusser
- first_name: Peter
full_name: Kupferschmied, Peter
last_name: Kupferschmied
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: Sarah
full_name: Friebe, Sarah
last_name: Friebe
- first_name: Sibylle Burger
full_name: Staufer, Sibylle Burger
last_name: Staufer
- first_name: Paul A.
full_name: Majcherczyk, Paul A.
last_name: Majcherczyk
- first_name: Philippe
full_name: Moreillon, Philippe
last_name: Moreillon
- first_name: Brigitte
full_name: Berger-Bächi, Brigitte
last_name: Berger-Bächi
- first_name: Nadine
full_name: McCallum, Nadine
last_name: McCallum
citation:
ama: Dengler V, Meier PS, Heusser R, et al. Deletion of hypothetical wall teichoic
acid ligases in Staphylococcus aureus activates the cell wall stress response.
FEMS Microbiology Letters. 2012;333(2):109-120. doi:10.1111/j.1574-6968.2012.02603.x
apa: Dengler, V., Meier, P. S., Heusser, R., Kupferschmied, P., Singer, J., Friebe,
S., … McCallum, N. (2012). Deletion of hypothetical wall teichoic acid ligases
in Staphylococcus aureus activates the cell wall stress response. FEMS Microbiology
Letters. Oxford University Press. https://doi.org/10.1111/j.1574-6968.2012.02603.x
chicago: Dengler, Vanina, Patricia Stutzmann Meier, Ronald Heusser, Peter Kupferschmied,
Judit Singer, Sarah Friebe, Sibylle Burger Staufer, et al. “Deletion of Hypothetical
Wall Teichoic Acid Ligases in Staphylococcus Aureus Activates the Cell Wall Stress
Response.” FEMS Microbiology Letters. Oxford University Press, 2012. https://doi.org/10.1111/j.1574-6968.2012.02603.x.
ieee: V. Dengler et al., “Deletion of hypothetical wall teichoic acid ligases
in Staphylococcus aureus activates the cell wall stress response,” FEMS Microbiology
Letters, vol. 333, no. 2. Oxford University Press, pp. 109–120, 2012.
ista: Dengler V, Meier PS, Heusser R, Kupferschmied P, Singer J, Friebe S, Staufer
SB, Majcherczyk PA, Moreillon P, Berger-Bächi B, McCallum N. 2012. Deletion of
hypothetical wall teichoic acid ligases in Staphylococcus aureus activates the
cell wall stress response. FEMS Microbiology Letters. 333(2), 109–120.
mla: Dengler, Vanina, et al. “Deletion of Hypothetical Wall Teichoic Acid Ligases
in Staphylococcus Aureus Activates the Cell Wall Stress Response.” FEMS Microbiology
Letters, vol. 333, no. 2, Oxford University Press, 2012, pp. 109–20, doi:10.1111/j.1574-6968.2012.02603.x.
short: V. Dengler, P.S. Meier, R. Heusser, P. Kupferschmied, J. Singer, S. Friebe,
S.B. Staufer, P.A. Majcherczyk, P. Moreillon, B. Berger-Bächi, N. McCallum, FEMS
Microbiology Letters 333 (2012) 109–120.
date_created: 2020-08-10T11:54:47Z
date_published: 2012-08-01T00:00:00Z
date_updated: 2021-01-12T08:17:43Z
day: '01'
doi: 10.1111/j.1574-6968.2012.02603.x
extern: '1'
external_id:
pmid:
- '22640011'
intvolume: ' 333'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
page: 109-120
pmid: 1
publication: FEMS Microbiology Letters
publication_identifier:
issn:
- 0378-1097
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Deletion of hypothetical wall teichoic acid ligases in Staphylococcus aureus
activates the cell wall stress response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 333
year: '2012'
...
---
_id: '826'
abstract:
- lang: eng
text: Plants exhibit a unique developmental flexibility to ever-changing environmental
conditions. To achieve their profound adaptability, plants are able to maintain
permanent stem cell populations and form new organs during the entire plant life
cycle. Signaling substances, called plant hormones, such as auxin, cytokinin,
abscisic acid, brassinosteroid, ethylene, gibberellin, jasmonic acid, and strigolactone,
govern and coordinate these developmental processes. Physiological and genetic
studies have dissected the molecular components of signal perception and transduction
of the individual hormonal pathways. However, over recent years it has become
evident that hormones do not act only in a linear pathway. Hormonal pathways are
interconnected by a complex network of interactions and feedback circuits that
determines the final outcome of the individual hormone actions. This raises questions
about the molecular mechanisms underlying hormonal cross talk and about how these
hormonal networks are established, maintained, and modulated throughout plant
development.
acknowledgement: We would like to thank Annick Bleys for help in preparing the manuscript.
This work was supported by the European Research Council with a Starting Independent
Research grant (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043
(to the Central European Institute of Technology, CEITEC) to E.B. M.V. is a postdoctoral
fellow of the Research Foundation Flanders. We apologize that, because of space
restrictions, the scientific contributions of only a limited number of original
articles could be cited and discussed.
author:
- first_name: Marleen
full_name: Vanstraelen, Marleen
last_name: Vanstraelen
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Vanstraelen M, Benková E. Hormonal interactions in the regulation of plant
development. Annual Review of Cell and Developmental Biology. 2012;28:463-487.
doi:10.1146/annurev-cellbio-101011-155741
apa: Vanstraelen, M., & Benková, E. (2012). Hormonal interactions in the regulation
of plant development. Annual Review of Cell and Developmental Biology.
Annual Reviews. https://doi.org/10.1146/annurev-cellbio-101011-155741
chicago: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation
of Plant Development.” Annual Review of Cell and Developmental Biology.
Annual Reviews, 2012. https://doi.org/10.1146/annurev-cellbio-101011-155741.
ieee: M. Vanstraelen and E. Benková, “Hormonal interactions in the regulation of
plant development,” Annual Review of Cell and Developmental Biology, vol.
28. Annual Reviews, pp. 463–487, 2012.
ista: Vanstraelen M, Benková E. 2012. Hormonal interactions in the regulation of
plant development. Annual Review of Cell and Developmental Biology. 28, 463–487.
mla: Vanstraelen, Marleen, and Eva Benková. “Hormonal Interactions in the Regulation
of Plant Development.” Annual Review of Cell and Developmental Biology,
vol. 28, Annual Reviews, 2012, pp. 463–87, doi:10.1146/annurev-cellbio-101011-155741.
short: M. Vanstraelen, E. Benková, Annual Review of Cell and Developmental Biology
28 (2012) 463–487.
date_created: 2018-12-11T11:48:43Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T08:17:46Z
day: '01'
doi: 10.1146/annurev-cellbio-101011-155741
extern: 1
intvolume: ' 28'
month: '11'
page: 463 - 487
publication: Annual Review of Cell and Developmental Biology
publication_status: published
publisher: Annual Reviews
publist_id: '6822'
quality_controlled: 0
status: public
title: Hormonal interactions in the regulation of plant development
type: journal_article
volume: 28
year: '2012'
...
---
_id: '829'
abstract:
- lang: eng
text: The architecture of a plant's root system, established postembryonically,
results from both coordinated root growth and lateral root branching. The plant
hormones auxin and cytokinin are central endogenous signaling molecules that regulate
lateral root organogenesis positively and negatively, respectively. Tight control
and mutual balance of their antagonistic activities are particularly important
during the early phases of lateral root organogenesis to ensure continuous lateral
root initiation (LRI) and proper development of lateral root primordia (LRP).
Here, we show that the early phases of lateral root organogenesis, including priming
and initiation, take place in root zones with a repressed cytokinin response.
Accordingly, ectopic overproduction of cytokinin in the root basal meristem most
efficiently inhibits LRI. Enhanced cytokinin responses in pericycle cells between
existing LRP might restrict LRI near existing LRP and, when compromised, ectopic
LRI occurs. Furthermore, our results demonstrate that young LRP are more sensitive
to perturbations in the cytokinin activity than are developmentally more advanced
primordia. We hypothesize that the effect of cytokinin on the development of primordia
possibly depends on the robustness and stability of the auxin gradient.
acknowledgement: We thank Jen Sheen, Dolf Weijers, Tatsuo Kakimoto, Stephen Depuydt,
and Laurent Laplaze for sharing published material, Jiri Friml for discussions,
and Martine De Cock and Annick Bleys for help in preparing the manuscript. This
work was supported by a Starting Independent Research grant from the European Research
Council (ERC-2007-Stg-207362-HCPO) and the project CZ.1.07/2.3.00/20.0043 to the
Central European Institute of Technology to E.B. and grants from the Ministry of
Education, Youth, and Sports of the Czech Republic (MSM 6198959216) and the Centre
of the Region Haná for Biotechnological and Agricultural Research (ED0007/01/01)
to P.T.
author:
- first_name: Agnieszka
full_name: Bielach, Agnieszka
last_name: Bielach
- first_name: Katerina
full_name: Podlesakova, Katerina
last_name: Podlesakova
- first_name: Peter
full_name: Peter Marhavy
id: 3F45B078-F248-11E8-B48F-1D18A9856A87
last_name: Marhavy
orcid: 0000-0001-5227-5741
- first_name: Jérôme
full_name: Duclercq, Jérôme
last_name: Duclercq
- first_name: Candela
full_name: Candela Cuesta
id: 33A3C818-F248-11E8-B48F-1D18A9856A87
last_name: Cuesta
orcid: 0000-0003-1923-2410
- first_name: Bruno
full_name: Muller, Bruno
last_name: Muller
- first_name: Wim
full_name: Grunewald, Wim
last_name: Grunewald
- first_name: Petr
full_name: Tarkowski, Petr
last_name: Tarkowski
- first_name: Eva
full_name: Eva Benková
id: 38F4F166-F248-11E8-B48F-1D18A9856A87
last_name: Benková
orcid: 0000-0002-8510-9739
citation:
ama: Bielach A, Podlesakova K, Marhavý P, et al. Spatiotemporal regulation of lateral
root organogenesis in Arabidopsis by cytokinin. The Plant Cell. 2012;24(10):3967-3981.
doi:10.1105/tpc.112.103044
apa: Bielach, A., Podlesakova, K., Marhavý, P., Duclercq, J., Cuesta, C., Muller,
B., … Benková, E. (2012). Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin. The Plant Cell. American Society of Plant
Biologists. https://doi.org/10.1105/tpc.112.103044
chicago: Bielach, Agnieszka, Katerina Podlesakova, Peter Marhavý, Jérôme Duclercq,
Candela Cuesta, Bruno Muller, Wim Grunewald, Petr Tarkowski, and Eva Benková.
“Spatiotemporal Regulation of Lateral Root Organogenesis in Arabidopsis by Cytokinin.”
The Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.103044.
ieee: A. Bielach et al., “Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin,” The Plant Cell, vol. 24, no. 10. American
Society of Plant Biologists, pp. 3967–3981, 2012.
ista: Bielach A, Podlesakova K, Marhavý P, Duclercq J, Cuesta C, Muller B, Grunewald
W, Tarkowski P, Benková E. 2012. Spatiotemporal regulation of lateral root organogenesis
in Arabidopsis by cytokinin. The Plant Cell. 24(10), 3967–3981.
mla: Bielach, Agnieszka, et al. “Spatiotemporal Regulation of Lateral Root Organogenesis
in Arabidopsis by Cytokinin.” The Plant Cell, vol. 24, no. 10, American
Society of Plant Biologists, 2012, pp. 3967–81, doi:10.1105/tpc.112.103044.
short: A. Bielach, K. Podlesakova, P. Marhavý, J. Duclercq, C. Cuesta, B. Muller,
W. Grunewald, P. Tarkowski, E. Benková, The Plant Cell 24 (2012) 3967–3981.
date_created: 2018-12-11T11:48:43Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2021-01-12T08:17:55Z
day: '01'
doi: 10.1105/tpc.112.103044
extern: 1
intvolume: ' 24'
issue: '10'
month: '10'
page: 3967 - 3981
publication: The Plant Cell
publication_status: published
publisher: American Society of Plant Biologists
publist_id: '6819'
quality_controlled: 0
status: public
title: Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin
type: journal_article
volume: 24
year: '2012'
...
---
_id: '846'
abstract:
- lang: eng
text: Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this
question has not been comprehensively addressed at the molecular level. Here,
we use data from 221 human genes with known pathogenic mutations to estimate the
rate of irreversibility in protein evolution. For these genes, we reconstruct
ancestral amino acid sequences along the mammalian phylogeny and identify ancestral
amino acid states that match known pathogenic mutations. Such cases represent
inherent evolutionary irreversibility because, at the present moment, reversals
to these ancestral amino acid states are impossible for the human lineage. We
estimate that approximately 10% of all amino acid substitutions along the mammalian
phylogeny are irreversible, such that a return to the ancestral amino acid state
would lead to a pathogenic phenotype. For a subset of 51 genes with high rates
of irreversibility, as much as 40% of all amino acid evolution was estimated to
be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes,
the molecular nature of the high rate of irreversibility in proteins is best explained
by evolution with a high prevalence of compensatory, epistatic interactions between
amino acid sites. Under such mode of protein evolution, once an amino acid substitution
is fixed, the probability of its reversal declines as the protein sequence accumulates
changes that affect the phenotypic manifestation of the ancestral state. The prevalence
of epistasis in evolution indicates that the observed high rate of irreversibility
in protein evolution is an inherent property of protein structure and function.
acknowledgement: This work was supported by Plan Nacional grant BFU2009-09271 from
the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado
Universitario) program grant AP2008-01888 from the Spanish Ministry of Education
to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and
Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein
evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096
apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility
in protein evolution. Genome Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/gbe/evs096
chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution. Oxford University
Press, 2012. https://doi.org/10.1093/gbe/evs096.
ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in
protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford
University Press, pp. 1213–1222, 2012.
ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in
protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.
mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford
University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096.
short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222.
date_created: 2018-12-11T11:48:49Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/gbe/evs096
extern: 1
intvolume: ' 4'
issue: '12'
month: '01'
page: 1213 - 1222
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6802'
quality_controlled: 0
status: public
title: Estimating the rate of irreversibility in protein evolution
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
volume: 4
year: '2012'
...
---
_id: '8463'
abstract:
- lang: eng
text: The 1H dipolar network, which is the major obstacle for applying proton detection
in the solid-state, can be reduced by deuteration, employing the RAP (Reduced
Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable
sites. We present here a systematic study on the optimal degree of random sidechain
protonation in RAP samples as a function of the MAS (magic angle spinning) frequency.
In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein,
the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in
the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external
field of 19.96 T (850 MHz), we find that using a proton concentration between
15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity
and resolution, with an achievable average 1H linewidth on the order of 40–50
Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in
sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C
correlation experiments. In total, we find that spectra recorded with a 1.3 mm
rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully
packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The
improved sensitivity is attributed to 1H line narrowing due to fast MAS and to
the increased efficiency of the 1.3 mm coil.
article_processing_charge: No
article_type: original
author:
- first_name: Sam
full_name: Asami, Sam
last_name: Asami
- first_name: Kathrin
full_name: Szekely, Kathrin
last_name: Szekely
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Bernd
full_name: Reif, Bernd
last_name: Reif
citation:
ama: Asami S, Szekely K, Schanda P, Meier BH, Reif B. Optimal degree of protonation
for 1H detection of aliphatic sites in randomly deuterated proteins as a function
of the MAS frequency. Journal of Biomolecular NMR. 2012;54(2):155-168.
doi:10.1007/s10858-012-9659-9
apa: Asami, S., Szekely, K., Schanda, P., Meier, B. H., & Reif, B. (2012). Optimal
degree of protonation for 1H detection of aliphatic sites in randomly deuterated
proteins as a function of the MAS frequency. Journal of Biomolecular NMR.
Springer Nature. https://doi.org/10.1007/s10858-012-9659-9
chicago: Asami, Sam, Kathrin Szekely, Paul Schanda, Beat H. Meier, and Bernd Reif.
“Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly
Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular
NMR. Springer Nature, 2012. https://doi.org/10.1007/s10858-012-9659-9.
ieee: S. Asami, K. Szekely, P. Schanda, B. H. Meier, and B. Reif, “Optimal degree
of protonation for 1H detection of aliphatic sites in randomly deuterated proteins
as a function of the MAS frequency,” Journal of Biomolecular NMR, vol.
54, no. 2. Springer Nature, pp. 155–168, 2012.
ista: Asami S, Szekely K, Schanda P, Meier BH, Reif B. 2012. Optimal degree of protonation
for 1H detection of aliphatic sites in randomly deuterated proteins as a function
of the MAS frequency. Journal of Biomolecular NMR. 54(2), 155–168.
mla: Asami, Sam, et al. “Optimal Degree of Protonation for 1H Detection of Aliphatic
Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal
of Biomolecular NMR, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:10.1007/s10858-012-9659-9.
short: S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular
NMR 54 (2012) 155–168.
date_created: 2020-09-18T10:09:18Z
date_published: 2012-08-23T00:00:00Z
date_updated: 2021-01-12T08:19:27Z
day: '23'
doi: 10.1007/s10858-012-9659-9
extern: '1'
intvolume: ' 54'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
page: 155-168
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Optimal degree of protonation for 1H detection of aliphatic sites in randomly
deuterated proteins as a function of the MAS frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2012'
...
---
_id: '8465'
abstract:
- lang: eng
text: We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond
time scales can be detected and quantified by solid-state NMR spectroscopy. We
show two independent approaches that measure the effect of conformational exchange
on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion
experiments and measurement of differential multiple-quantum coherence decay.
Long coherence lifetimes, as required for these experiments, are achieved by the
use of highly deuterated samples and fast magic-angle spinning. The usefulness
of the approaches is demonstrated by application to microcrystalline ubiquitin.
We detect a conformational exchange process in a region of the protein for which
dynamics have also been observed in solution. Interestingly, quantitative analysis
of the data reveals that the exchange process is more than 1 order of magnitude
slower than in solution, and this points to the impact of the crystalline environment
on free energy barriers.
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. Site-resolved measurement
of microsecond-to-millisecond conformational-exchange processes in proteins by
solid-state NMR spectroscopy. Journal of the American Chemical Society.
2012;134(36):14800-14807. doi:10.1021/ja303591y
apa: Tollinger, M., Sivertsen, A. C., Meier, B. H., Ernst, M., & Schanda, P.
(2012). Site-resolved measurement of microsecond-to-millisecond conformational-exchange
processes in proteins by solid-state NMR spectroscopy. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja303591y
chicago: Tollinger, Martin, Astrid C. Sivertsen, Beat H. Meier, Matthias Ernst,
and Paul Schanda. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange
Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American
Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja303591y.
ieee: M. Tollinger, A. C. Sivertsen, B. H. Meier, M. Ernst, and P. Schanda, “Site-resolved
measurement of microsecond-to-millisecond conformational-exchange processes in
proteins by solid-state NMR spectroscopy,” Journal of the American Chemical
Society, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012.
ista: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. 2012. Site-resolved
measurement of microsecond-to-millisecond conformational-exchange processes in
proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society.
134(36), 14800–14807.
mla: Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond
Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.”
Journal of the American Chemical Society, vol. 134, no. 36, American Chemical
Society, 2012, pp. 14800–07, doi:10.1021/ja303591y.
short: M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of
the American Chemical Society 134 (2012) 14800–14807.
date_created: 2020-09-18T10:10:20Z
date_published: 2012-08-21T00:00:00Z
date_updated: 2021-01-12T08:19:27Z
day: '21'
doi: 10.1021/ja303591y
extern: '1'
intvolume: ' 134'
issue: '36'
language:
- iso: eng
month: '08'
oa_version: None
page: 14800-14807
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Site-resolved measurement of microsecond-to-millisecond conformational-exchange
processes in proteins by solid-state NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...
---
_id: '8466'
abstract:
- lang: eng
text: Recent advances in NMR spectroscopy and the availability of high magnetic
field strengths now offer the possibility to record real-time 3D NMR spectra of
short-lived protein states, e.g., states that become transiently populated during
protein folding. Here we present a strategy for obtaining sequential NMR assignments
as well as atom-resolved information on structural and dynamic features within
a folding intermediate of the amyloidogenic protein β2-microglobulin that has
a half-lifetime of only 20 min.
article_processing_charge: No
article_type: original
author:
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Thomas
full_name: Cutuil, Thomas
last_name: Cutuil
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Vincent
full_name: Forge, Vincent
last_name: Forge
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. Real-time NMR
characterization of structure and dynamics in a transiently populated protein
folding intermediate. Journal of the American Chemical Society. 2012;134(19):8066-8069.
doi:10.1021/ja302598j
apa: Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Forge, V., & Brutscher,
B. (2012). Real-time NMR characterization of structure and dynamics in a transiently
populated protein folding intermediate. Journal of the American Chemical Society.
American Chemical Society. https://doi.org/10.1021/ja302598j
chicago: Rennella, Enrico, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge,
and Bernhard Brutscher. “Real-Time NMR Characterization of Structure and Dynamics
in a Transiently Populated Protein Folding Intermediate.” Journal of the American
Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja302598j.
ieee: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, and B. Brutscher,
“Real-time NMR characterization of structure and dynamics in a transiently populated
protein folding intermediate,” Journal of the American Chemical Society,
vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012.
ista: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. 2012. Real-time
NMR characterization of structure and dynamics in a transiently populated protein
folding intermediate. Journal of the American Chemical Society. 134(19), 8066–8069.
mla: Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics
in a Transiently Populated Protein Folding Intermediate.” Journal of the American
Chemical Society, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69,
doi:10.1021/ja302598j.
short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal
of the American Chemical Society 134 (2012) 8066–8069.
date_created: 2020-09-18T10:10:28Z
date_published: 2012-05-03T00:00:00Z
date_updated: 2021-01-12T08:19:28Z
day: '03'
doi: 10.1021/ja302598j
extern: '1'
intvolume: ' 134'
issue: '19'
language:
- iso: eng
month: '05'
oa_version: None
page: 8066-8069
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Real-time NMR characterization of structure and dynamics in a transiently populated
protein folding intermediate
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...
---
_id: '8467'
abstract:
- lang: eng
text: Partial deuteration is a powerful tool to increase coherence life times and
spectral resolution in proton solid-state NMR. The J coupling to deuterium needs,
however, to be decoupled to maintain the good resolution in the (usually indirect)
13C dimension(s). We present a simple and reversible way to expand a commercial
1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling
of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator
and requires no significant modifications to the probe. The performance and the
realizable gains in sensitivity and resolution are demonstrated using perdeuterated
ubiquitin, with selectively CHD2-labeled methyl groups.
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Huber, Matthias
last_name: Huber
- first_name: Oliver
full_name: With, Oliver
last_name: With
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: René
full_name: Verel, René
last_name: Verel
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
citation:
ama: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil
for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance.
2012;214:76-80. doi:10.1016/j.jmr.2011.10.010
apa: Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., & Meier, B. H.
(2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes.
Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.10.010
chicago: Huber, Matthias, Oliver With, Paul Schanda, René Verel, Matthias Ernst,
and Beat H. Meier. “A Supplementary Coil for 2H Decoupling with Commercial HCN
MAS Probes.” Journal of Magnetic Resonance. Elsevier, 2012. https://doi.org/10.1016/j.jmr.2011.10.010.
ieee: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, and B. H. Meier, “A supplementary
coil for 2H decoupling with commercial HCN MAS probes,” Journal of Magnetic
Resonance, vol. 214. Elsevier, pp. 76–80, 2012.
ista: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. 2012. A supplementary
coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance.
214, 76–80.
mla: Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial
HCN MAS Probes.” Journal of Magnetic Resonance, vol. 214, Elsevier, 2012,
pp. 76–80, doi:10.1016/j.jmr.2011.10.010.
short: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of
Magnetic Resonance 214 (2012) 76–80.
date_created: 2020-09-18T10:10:36Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:28Z
day: '01'
doi: 10.1016/j.jmr.2011.10.010
extern: '1'
intvolume: ' 214'
language:
- iso: eng
month: '01'
oa_version: None
page: 76-80
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A supplementary coil for 2H decoupling with commercial HCN MAS probes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 214
year: '2012'
...
---
_id: '8502'
abstract:
- lang: eng
text: 'The famous ergodic hypothesis suggests that for a typical Hamiltonian on
a typical energy surface nearly all trajectories are dense. KAM theory disproves
it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics.
Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers.
Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis
claiming that a typical Hamiltonian on a typical energy surface has a dense orbit.
This question is wide open. Herman (Proceedings of the International Congress
of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin:
Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian
near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper
we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set
of maximal Hausdorff dimension equal to 5 on the unit energy surface.'
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system
with a trajectory dense in a set of maximal Hausdorff dimension. Communications
in Mathematical Physics. 2012;315(3):643-697. doi:10.1007/s00220-012-1532-x
apa: Kaloshin, V., & Saprykina, M. (2012). An example of a nearly integrable
Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension.
Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-012-1532-x
chicago: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable
Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.”
Communications in Mathematical Physics. Springer Nature, 2012. https://doi.org/10.1007/s00220-012-1532-x.
ieee: V. Kaloshin and M. Saprykina, “An example of a nearly integrable Hamiltonian
system with a trajectory dense in a set of maximal Hausdorff dimension,” Communications
in Mathematical Physics, vol. 315, no. 3. Springer Nature, pp. 643–697, 2012.
ista: Kaloshin V, Saprykina M. 2012. An example of a nearly integrable Hamiltonian
system with a trajectory dense in a set of maximal Hausdorff dimension. Communications
in Mathematical Physics. 315(3), 643–697.
mla: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian
System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications
in Mathematical Physics, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97,
doi:10.1007/s00220-012-1532-x.
short: V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012)
643–697.
date_created: 2020-09-18T10:47:16Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:44Z
day: '01'
doi: 10.1007/s00220-012-1532-x
extern: '1'
intvolume: ' 315'
issue: '3'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '11'
oa_version: None
page: 643-697
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- 0010-3616
- 1432-0916
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: An example of a nearly integrable Hamiltonian system with a trajectory dense
in a set of maximal Hausdorff dimension
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 315
year: '2012'
...
---
_id: '8503'
abstract:
- lang: eng
text: We prove there are finitely many isometry classes of planar central configurations
(also called relative equilibria) in the Newtonian 5-body problem, except perhaps
if the 5-tuple of positive masses belongs to a given codimension 2 subvariety
of the mass space.
article_processing_charge: No
article_type: original
author:
- first_name: Alain
full_name: Albouy, Alain
last_name: Albouy
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Albouy A, Kaloshin V. Finiteness of central configurations of five bodies in
the plane. Annals of Mathematics. 2012;176(1):535-588. doi:10.4007/annals.2012.176.1.10
apa: Albouy, A., & Kaloshin, V. (2012). Finiteness of central configurations
of five bodies in the plane. Annals of Mathematics. Princeton University
Press. https://doi.org/10.4007/annals.2012.176.1.10
chicago: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations
of Five Bodies in the Plane.” Annals of Mathematics. Princeton University
Press, 2012. https://doi.org/10.4007/annals.2012.176.1.10.
ieee: A. Albouy and V. Kaloshin, “Finiteness of central configurations of five bodies
in the plane,” Annals of Mathematics, vol. 176, no. 1. Princeton University
Press, pp. 535–588, 2012.
ista: Albouy A, Kaloshin V. 2012. Finiteness of central configurations of five bodies
in the plane. Annals of Mathematics. 176(1), 535–588.
mla: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of
Five Bodies in the Plane.” Annals of Mathematics, vol. 176, no. 1, Princeton
University Press, 2012, pp. 535–88, doi:10.4007/annals.2012.176.1.10.
short: A. Albouy, V. Kaloshin, Annals of Mathematics 176 (2012) 535–588.
date_created: 2020-09-18T10:47:24Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:44Z
day: '01'
doi: 10.4007/annals.2012.176.1.10
extern: '1'
intvolume: ' 176'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 535-588
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Princeton University Press
quality_controlled: '1'
status: public
title: Finiteness of central configurations of five bodies in the plane
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 176
year: '2012'
...