---
_id: '532'
abstract:
- lang: eng
text: Ethylene is a gaseous phytohormone that plays vital roles in plant growth
and development. Previous studies uncovered EIN2 as an essential signal transducer
linking ethylene perception on ER to transcriptional regulation in the nucleus
through a “cleave and shuttle” model. In this study, we report another mechanism
of EIN2-mediated ethylene signaling, whereby EIN2 imposes the translational repression
of EBF1 and EBF2 mRNA. We find that the EBF1/2 3′ UTRs mediate EIN2-directed translational
repression and identify multiple poly-uridylates (PolyU) motifs as functional
cis elements of 3′ UTRs. Furthermore, we demonstrate that ethylene induces EIN2
to associate with 3′ UTRs and target EBF1/2 mRNA to cytoplasmic processing-body
(P-body) through interacting with multiple P-body factors, including EIN5 and
PABs. Our study illustrates translational regulation as a key step in ethylene
signaling and presents mRNA 3′ UTR functioning as a “signal transducer” to sense
and relay cellular signaling in plants.
author:
- first_name: Wenyang
full_name: Li, Wenyang
last_name: Li
- first_name: Mengdi
full_name: Ma, Mengdi
last_name: Ma
- first_name: Ying
full_name: Feng, Ying
last_name: Feng
- first_name: Hongjiang
full_name: Li, Hongjiang
id: 33CA54A6-F248-11E8-B48F-1D18A9856A87
last_name: Li
orcid: 0000-0001-5039-9660
- first_name: Yichuan
full_name: Wang, Yichuan
last_name: Wang
- first_name: Yutong
full_name: Ma, Yutong
last_name: Ma
- first_name: Mingzhe
full_name: Li, Mingzhe
last_name: Li
- first_name: Fengying
full_name: An, Fengying
last_name: An
- first_name: Hongwei
full_name: Guo, Hongwei
last_name: Guo
citation:
ama: Li W, Ma M, Feng Y, et al. EIN2-directed translational regulation of ethylene
signaling in arabidopsis. Cell. 2015;163(3):670-683. doi:10.1016/j.cell.2015.09.037
apa: Li, W., Ma, M., Feng, Y., Li, H., Wang, Y., Ma, Y., … Guo, H. (2015). EIN2-directed
translational regulation of ethylene signaling in arabidopsis. Cell. Cell
Press. https://doi.org/10.1016/j.cell.2015.09.037
chicago: Li, Wenyang, Mengdi Ma, Ying Feng, Hongjiang Li, Yichuan Wang, Yutong Ma,
Mingzhe Li, Fengying An, and Hongwei Guo. “EIN2-Directed Translational Regulation
of Ethylene Signaling in Arabidopsis.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.09.037.
ieee: W. Li et al., “EIN2-directed translational regulation of ethylene signaling
in arabidopsis,” Cell, vol. 163, no. 3. Cell Press, pp. 670–683, 2015.
ista: Li W, Ma M, Feng Y, Li H, Wang Y, Ma Y, Li M, An F, Guo H. 2015. EIN2-directed
translational regulation of ethylene signaling in arabidopsis. Cell. 163(3), 670–683.
mla: Li, Wenyang, et al. “EIN2-Directed Translational Regulation of Ethylene Signaling
in Arabidopsis.” Cell, vol. 163, no. 3, Cell Press, 2015, pp. 670–83, doi:10.1016/j.cell.2015.09.037.
short: W. Li, M. Ma, Y. Feng, H. Li, Y. Wang, Y. Ma, M. Li, F. An, H. Guo, Cell
163 (2015) 670–683.
date_created: 2018-12-11T11:47:00Z
date_published: 2015-10-22T00:00:00Z
date_updated: 2021-01-12T08:01:27Z
day: '22'
department:
- _id: JiFr
doi: 10.1016/j.cell.2015.09.037
intvolume: ' 163'
issue: '3'
language:
- iso: eng
month: '10'
oa_version: None
page: 670 - 683
publication: Cell
publication_status: published
publisher: Cell Press
publist_id: '7285'
quality_controlled: '1'
scopus_import: 1
status: public
title: EIN2-directed translational regulation of ethylene signaling in arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 163
year: '2015'
...
---
_id: '12632'
abstract:
- lang: eng
text: We investigate the performance of five glacier melt models over a multi-decadal
period in order to assess their ability to model future glacier response. The
models range from a simple degree-day model, based solely on air temperature,
to more-sophisticated models, including the full shortwave radiation balance.
In addition to the empirical models, the performance of a physically based energy-balance
(EB) model is examined. The melt models are coupled to an accumulation and a surface
evolution model and applied in a distributed manner to Rhonegletscher, Switzerland,
over the period 1929–2012 at hourly resolution. For calibration, seasonal mass-balance
measurements (2006–12) are used. Decadal ice volume changes for six periods in
the years 1929–2012 serve for model validation. Over the period 2006–12, there
are almost no differences in performance between the models, except for EB, which
is less consistent with observations, likely due to lack of meteorological in
situ data. However, simulations over the long term (1929–2012) reveal that models
which include a separate term for shortwave radiation agree best with the observed
ice volume changes, indicating that their melt relationships are robust in time
and thus suitable for long-term modelling, in contrast to more empirical approaches
that are oversensitive to temperature fluctuations.
article_processing_charge: No
article_type: original
author:
- first_name: Jeannette
full_name: Gabbi, Jeannette
last_name: Gabbi
- first_name: Marco
full_name: Carenzo, Marco
last_name: Carenzo
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Andreas
full_name: Bauder, Andreas
last_name: Bauder
- first_name: Martin
full_name: Funk, Martin
last_name: Funk
citation:
ama: Gabbi J, Carenzo M, Pellicciotti F, Bauder A, Funk M. A comparison of empirical
and physically based glacier surface melt models for long-term simulations of
glacier response. Journal of Glaciology. 2014;60(224):1140-1154. doi:10.3189/2014jog14j011
apa: Gabbi, J., Carenzo, M., Pellicciotti, F., Bauder, A., & Funk, M. (2014).
A comparison of empirical and physically based glacier surface melt models for
long-term simulations of glacier response. Journal of Glaciology. International
Glaciological Society. https://doi.org/10.3189/2014jog14j011
chicago: Gabbi, Jeannette, Marco Carenzo, Francesca Pellicciotti, Andreas Bauder,
and Martin Funk. “A Comparison of Empirical and Physically Based Glacier Surface
Melt Models for Long-Term Simulations of Glacier Response.” Journal of Glaciology.
International Glaciological Society, 2014. https://doi.org/10.3189/2014jog14j011.
ieee: J. Gabbi, M. Carenzo, F. Pellicciotti, A. Bauder, and M. Funk, “A comparison
of empirical and physically based glacier surface melt models for long-term simulations
of glacier response,” Journal of Glaciology, vol. 60, no. 224. International
Glaciological Society, pp. 1140–1154, 2014.
ista: Gabbi J, Carenzo M, Pellicciotti F, Bauder A, Funk M. 2014. A comparison of
empirical and physically based glacier surface melt models for long-term simulations
of glacier response. Journal of Glaciology. 60(224), 1140–1154.
mla: Gabbi, Jeannette, et al. “A Comparison of Empirical and Physically Based Glacier
Surface Melt Models for Long-Term Simulations of Glacier Response.” Journal
of Glaciology, vol. 60, no. 224, International Glaciological Society, 2014,
pp. 1140–54, doi:10.3189/2014jog14j011.
short: J. Gabbi, M. Carenzo, F. Pellicciotti, A. Bauder, M. Funk, Journal of Glaciology
60 (2014) 1140–1154.
date_created: 2023-02-20T08:16:34Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2023-02-24T08:56:35Z
day: '01'
doi: 10.3189/2014jog14j011
extern: '1'
intvolume: ' 60'
issue: '224'
keyword:
- Earth-Surface Processes
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.3189/2014JoG14J011
month: '08'
oa: 1
oa_version: Published Version
page: 1140-1154
publication: Journal of Glaciology
publication_identifier:
eissn:
- 1727-5652
issn:
- 0022-1430
publication_status: published
publisher: International Glaciological Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparison of empirical and physically based glacier surface melt models
for long-term simulations of glacier response
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 60
year: '2014'
...
---
_id: '12634'
abstract:
- lang: eng
text: 'Glaciers in the Andes of Chile seem to be shrinking and possibly loosing
mass, but the number and types of studies conducted, constrained mainly by data
availability, are not sufficient to provide a synopsis of glacier changes for
the past or future or explain in an explicit way causes of the observed changes.
In this paper, we provide a systematic review of changes in glaciers for the entire
country, followed by a discussion of the studies that have provided evidence of
such changes. We identify a missing type of work in distributed, physically-oriented
modelling studies that are needed to bridge the gap between the numerous remote
sensing studies and the specific, point scale works focused on process understanding.
We use an advanced mass balance model applied to one of the best monitored glaciers
in the region to investigate four main research issues that should be addressed
in modelling studies for a sound assessment of glacier changes: 1) the use of
physically-based models of glacier ablation (energy balance models) versus more
empirical models (enhanced temperature index approaches); 2) the importance of
the correct extrapolation of air temperature forcing on glaciers and in high elevation
areas and the large uncertainty in model outputs associated with it; 3) the role
played by snow gravitational redistribution; and 4) the uncertainty associated
with future climate scenarios. We quantify differences in model outputs associated
with each of these choices, and conclude with suggestions for future work directions.'
article_processing_charge: No
article_type: review
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: S.
full_name: Ragettli, S.
last_name: Ragettli
- first_name: M.
full_name: Carenzo, M.
last_name: Carenzo
- first_name: J.
full_name: McPhee, J.
last_name: McPhee
citation:
ama: Pellicciotti F, Ragettli S, Carenzo M, McPhee J. Changes of glaciers in the
Andes of Chile and priorities for future work. Science of The Total Environment.
2014;493:1197-1210. doi:10.1016/j.scitotenv.2013.10.055
apa: Pellicciotti, F., Ragettli, S., Carenzo, M., & McPhee, J. (2014). Changes
of glaciers in the Andes of Chile and priorities for future work. Science of
The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2013.10.055
chicago: Pellicciotti, Francesca, S. Ragettli, M. Carenzo, and J. McPhee. “Changes
of Glaciers in the Andes of Chile and Priorities for Future Work.” Science
of The Total Environment. Elsevier, 2014. https://doi.org/10.1016/j.scitotenv.2013.10.055.
ieee: F. Pellicciotti, S. Ragettli, M. Carenzo, and J. McPhee, “Changes of glaciers
in the Andes of Chile and priorities for future work,” Science of The Total
Environment, vol. 493. Elsevier, pp. 1197–1210, 2014.
ista: Pellicciotti F, Ragettli S, Carenzo M, McPhee J. 2014. Changes of glaciers
in the Andes of Chile and priorities for future work. Science of The Total Environment.
493, 1197–1210.
mla: Pellicciotti, Francesca, et al. “Changes of Glaciers in the Andes of Chile
and Priorities for Future Work.” Science of The Total Environment, vol.
493, Elsevier, 2014, pp. 1197–210, doi:10.1016/j.scitotenv.2013.10.055.
short: F. Pellicciotti, S. Ragettli, M. Carenzo, J. McPhee, Science of The Total
Environment 493 (2014) 1197–1210.
date_created: 2023-02-20T08:16:46Z
date_published: 2014-09-15T00:00:00Z
date_updated: 2023-02-24T08:37:57Z
day: '15'
doi: 10.1016/j.scitotenv.2013.10.055
extern: '1'
intvolume: ' 493'
keyword:
- Pollution
- Waste Management and Disposal
- Environmental Chemistry
- Environmental Engineering
language:
- iso: eng
month: '09'
oa_version: None
page: 1197-1210
publication: Science of The Total Environment
publication_identifier:
issn:
- 0048-9697
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Changes of glaciers in the Andes of Chile and priorities for future work
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 493
year: '2014'
...
---
_id: '12635'
abstract:
- lang: eng
text: 'Switzerland is one of the countries with some of the longest and best glaciological
data sets. Its glaciers and their changes in response to climate have been extensively
investigated, and the number and quality of related studies are notable. However,
a comprehensive review of glacier changes and their impact on the hydrology of
glacierised catchments for Switzerland is missing and we use the opportunity provided
by the EU-FP7 ACQWA project to review the current state of knowledge about past
changes and future projections. We examine the type of models that have been applied
to infer glacier evolution and identify knowledge gaps that should be addressed
in future research in addition to those indicated in previous publications. Common
characteristics in long-term series of projected future glacier runoff are an
initial peak followed by a decline, associated with shifts in seasonality, earlier
melt onset and reduced summer runoff. However, the quantitative predictions are
difficult to compare, as studies differ in terms of model structure, calibration
strategies, input data, temporal and spatial resolution as well as future scenarios
used for impact studies. We identify two sources of uncertainties among those
emerging from recent research, and use simulations over four glaciers to: i) quantify
the importance of the correct extrapolation of air temperature, and ii) point
at the key role played by debris cover in modulating glacier response.'
article_processing_charge: No
article_type: review
author:
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: M.
full_name: Carenzo, M.
last_name: Carenzo
- first_name: R.
full_name: Bordoy, R.
last_name: Bordoy
- first_name: M.
full_name: Stoffel, M.
last_name: Stoffel
citation:
ama: 'Pellicciotti F, Carenzo M, Bordoy R, Stoffel M. Changes in glaciers in the
Swiss Alps and impact on basin hydrology: Current state of the art and future
research. Science of The Total Environment. 2014;493:1152-1170. doi:10.1016/j.scitotenv.2014.04.022'
apa: 'Pellicciotti, F., Carenzo, M., Bordoy, R., & Stoffel, M. (2014). Changes
in glaciers in the Swiss Alps and impact on basin hydrology: Current state of
the art and future research. Science of The Total Environment. Elsevier.
https://doi.org/10.1016/j.scitotenv.2014.04.022'
chicago: 'Pellicciotti, Francesca, M. Carenzo, R. Bordoy, and M. Stoffel. “Changes
in Glaciers in the Swiss Alps and Impact on Basin Hydrology: Current State of
the Art and Future Research.” Science of The Total Environment. Elsevier,
2014. https://doi.org/10.1016/j.scitotenv.2014.04.022.'
ieee: 'F. Pellicciotti, M. Carenzo, R. Bordoy, and M. Stoffel, “Changes in glaciers
in the Swiss Alps and impact on basin hydrology: Current state of the art and
future research,” Science of The Total Environment, vol. 493. Elsevier,
pp. 1152–1170, 2014.'
ista: 'Pellicciotti F, Carenzo M, Bordoy R, Stoffel M. 2014. Changes in glaciers
in the Swiss Alps and impact on basin hydrology: Current state of the art and
future research. Science of The Total Environment. 493, 1152–1170.'
mla: 'Pellicciotti, Francesca, et al. “Changes in Glaciers in the Swiss Alps and
Impact on Basin Hydrology: Current State of the Art and Future Research.” Science
of The Total Environment, vol. 493, Elsevier, 2014, pp. 1152–70, doi:10.1016/j.scitotenv.2014.04.022.'
short: F. Pellicciotti, M. Carenzo, R. Bordoy, M. Stoffel, Science of The Total
Environment 493 (2014) 1152–1170.
date_created: 2023-02-20T08:16:51Z
date_published: 2014-09-15T00:00:00Z
date_updated: 2023-02-24T08:36:04Z
day: '15'
doi: 10.1016/j.scitotenv.2014.04.022
extern: '1'
intvolume: ' 493'
keyword:
- Pollution
- Waste Management and Disposal
- Environmental Chemistry
- Environmental Engineering
language:
- iso: eng
month: '09'
oa_version: None
page: 1152-1170
publication: Science of The Total Environment
publication_identifier:
issn:
- 0048-9697
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Changes in glaciers in the Swiss Alps and impact on basin hydrology: Current
state of the art and future research'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 493
year: '2014'
...
---
_id: '12636'
abstract:
- lang: eng
text: Himalayan glacier tongues are commonly debris covered and they are an important
source of melt water. However, they remain relatively unstudied because of the
inaccessibility of the terrain and the difficulties in field work caused by the
thick debris mantles. Observations of debris-covered glaciers are therefore scarce
and airborne remote sensing may bridge the gap between scarce field observations
and coarse resolution space-borne remote sensing. In this study we deploy an Unmanned
Aerial Vehicle (UAV) before and after the melt and monsoon season (May and October
2013) over the debris-covered tongue of the Lirung Glacier in Nepal. Based on
stereo-imaging and the structure for motion algorithm we derive highly detailed
ortho-mosaics and digital elevation models (DEMs), which we geometrically correct
using differential GPS observations collected in the field. Based on DEM differencing
and manual feature tracking we derive the mass loss and the surface velocity of
the glacier at a high spatial accuracy. On average, mass loss is limited and the
surface velocity is very small. However, the spatial variability of melt rates
is very high, and ice cliffs and supra-glacial ponds show mass losses that can
be an order of magnitude higher than the average. We suggest that future research
should focus on the interaction between supra-glacial ponds, ice cliffs and englacial
hydrology to further understand the dynamics of debris-covered glaciers. Finally,
we conclude that UAV deployment has large potential in glaciology and it may revolutionize
methods currently applied in studying glacier surface features.
article_processing_charge: No
article_type: original
author:
- first_name: W.W.
full_name: Immerzeel, W.W.
last_name: Immerzeel
- first_name: P.D.A.
full_name: Kraaijenbrink, P.D.A.
last_name: Kraaijenbrink
- first_name: J.M.
full_name: Shea, J.M.
last_name: Shea
- first_name: A.B.
full_name: Shrestha, A.B.
last_name: Shrestha
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: M.F.P.
full_name: Bierkens, M.F.P.
last_name: Bierkens
- first_name: S.M.
full_name: de Jong, S.M.
last_name: de Jong
citation:
ama: Immerzeel WW, Kraaijenbrink PDA, Shea JM, et al. High-resolution monitoring
of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing
of Environment. 2014;150(7):93-103. doi:10.1016/j.rse.2014.04.025
apa: Immerzeel, W. W., Kraaijenbrink, P. D. A., Shea, J. M., Shrestha, A. B., Pellicciotti,
F., Bierkens, M. F. P., & de Jong, S. M. (2014). High-resolution monitoring
of Himalayan glacier dynamics using unmanned aerial vehicles. Remote Sensing
of Environment. Elsevier. https://doi.org/10.1016/j.rse.2014.04.025
chicago: Immerzeel, W.W., P.D.A. Kraaijenbrink, J.M. Shea, A.B. Shrestha, Francesca
Pellicciotti, M.F.P. Bierkens, and S.M. de Jong. “High-Resolution Monitoring of
Himalayan Glacier Dynamics Using Unmanned Aerial Vehicles.” Remote Sensing
of Environment. Elsevier, 2014. https://doi.org/10.1016/j.rse.2014.04.025.
ieee: W. W. Immerzeel et al., “High-resolution monitoring of Himalayan glacier
dynamics using unmanned aerial vehicles,” Remote Sensing of Environment,
vol. 150, no. 7. Elsevier, pp. 93–103, 2014.
ista: Immerzeel WW, Kraaijenbrink PDA, Shea JM, Shrestha AB, Pellicciotti F, Bierkens
MFP, de Jong SM. 2014. High-resolution monitoring of Himalayan glacier dynamics
using unmanned aerial vehicles. Remote Sensing of Environment. 150(7), 93–103.
mla: Immerzeel, W. W., et al. “High-Resolution Monitoring of Himalayan Glacier Dynamics
Using Unmanned Aerial Vehicles.” Remote Sensing of Environment, vol. 150,
no. 7, Elsevier, 2014, pp. 93–103, doi:10.1016/j.rse.2014.04.025.
short: W.W. Immerzeel, P.D.A. Kraaijenbrink, J.M. Shea, A.B. Shrestha, F. Pellicciotti,
M.F.P. Bierkens, S.M. de Jong, Remote Sensing of Environment 150 (2014) 93–103.
date_created: 2023-02-20T08:16:56Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2023-02-24T08:32:39Z
day: '01'
doi: 10.1016/j.rse.2014.04.025
extern: '1'
intvolume: ' 150'
issue: '7'
keyword:
- Computers in Earth Sciences
- Geology
- Soil Science
language:
- iso: eng
month: '07'
oa_version: None
page: 93-103
publication: Remote Sensing of Environment
publication_identifier:
issn:
- 0034-4257
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: High-resolution monitoring of Himalayan glacier dynamics using unmanned aerial
vehicles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 150
year: '2014'
...
---
_id: '12637'
abstract:
- lang: eng
text: The performance of glaciohydrological models which simulate catchment response
to climate variability depends to a large degree on the data used to force the
models. The forcing data become increasingly important in high-elevation, glacierized
catchments where the interplay between extreme topography, climate, and the cryosphere
is complex. It is challenging to generate a reliable forcing data set that captures
this spatial heterogeneity. In this paper, we analyze the results of a 1 year
field campaign focusing on air temperature and precipitation observations in the
Langtang valley in the Nepalese Himalayas. We use the observed time series to
characterize both temperature lapse rates (LRs) and precipitation gradients (PGs).
We study their spatial and temporal variability, and we attempt to identify possible
controlling factors. We show that very clear LRs exist in the valley and that
there are strong seasonal differences related to the water vapor content in the
atmosphere. Results also show that the LRs are generally shallower than the commonly
used environmental lapse rates. The analysis of the precipitation observations
reveals that there is great variability in precipitation over short horizontal
distances. A uniform valley wide PG cannot be established, and several scale-dependent
mechanisms may explain our observations. We complete our analysis by showing the
impact of the observed LRs and PGs on the outputs of the TOPKAPI-ETH glaciohydrological
model. We conclude that LRs and PGs have a very large impact on the water balance
composition and that short-term monitoring campaigns have the potential to improve
model quality considerably.
article_processing_charge: No
article_type: original
author:
- first_name: W. W.
full_name: Immerzeel, W. W.
last_name: Immerzeel
- first_name: L.
full_name: Petersen, L.
last_name: Petersen
- 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: Immerzeel WW, Petersen L, Ragettli S, Pellicciotti F. The importance of observed
gradients of air temperature and precipitation for modeling runoff from a glacierized
watershed in the Nepalese Himalayas. Water Resources Research. 2014;50(3):2212-2226.
doi:10.1002/2013wr014506
apa: Immerzeel, W. W., Petersen, L., Ragettli, S., & Pellicciotti, F. (2014).
The importance of observed gradients of air temperature and precipitation for
modeling runoff from a glacierized watershed in the Nepalese Himalayas. Water
Resources Research. American Geophysical Union. https://doi.org/10.1002/2013wr014506
chicago: Immerzeel, W. W., L. Petersen, S. Ragettli, and Francesca Pellicciotti.
“The Importance of Observed Gradients of Air Temperature and Precipitation for
Modeling Runoff from a Glacierized Watershed in the Nepalese Himalayas.” Water
Resources Research. American Geophysical Union, 2014. https://doi.org/10.1002/2013wr014506.
ieee: W. W. Immerzeel, L. Petersen, S. Ragettli, and F. Pellicciotti, “The importance
of observed gradients of air temperature and precipitation for modeling runoff
from a glacierized watershed in the Nepalese Himalayas,” Water Resources Research,
vol. 50, no. 3. American Geophysical Union, pp. 2212–2226, 2014.
ista: Immerzeel WW, Petersen L, Ragettli S, Pellicciotti F. 2014. The importance
of observed gradients of air temperature and precipitation for modeling runoff
from a glacierized watershed in the Nepalese Himalayas. Water Resources Research.
50(3), 2212–2226.
mla: Immerzeel, W. W., et al. “The Importance of Observed Gradients of Air Temperature
and Precipitation for Modeling Runoff from a Glacierized Watershed in the Nepalese
Himalayas.” Water Resources Research, vol. 50, no. 3, American Geophysical
Union, 2014, pp. 2212–26, doi:10.1002/2013wr014506.
short: W.W. Immerzeel, L. Petersen, S. Ragettli, F. Pellicciotti, Water Resources
Research 50 (2014) 2212–2226.
date_created: 2023-02-20T08:17:01Z
date_published: 2014-03-01T00:00:00Z
date_updated: 2023-02-24T08:28:23Z
day: '01'
doi: 10.1002/2013wr014506
extern: '1'
intvolume: ' 50'
issue: '3'
keyword:
- Water Science and Technology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1002/2013WR014506
month: '03'
oa: 1
oa_version: Published Version
page: 2212-2226
publication: Water Resources Research
publication_identifier:
eissn:
- 1944-7973
issn:
- 0043-1397
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: The importance of observed gradients of air temperature and precipitation for
modeling runoff from a glacierized watershed in the Nepalese Himalayas
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2014'
...
---
_id: '1309'
abstract:
- lang: eng
text: We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation
display infinite speed of support propagation. We apply our method to the case
of the quantum drift-diffusion equation which augments the DLSS equation with
a drift term and possibly a second-order diffusion term. The proof is accomplished
using weighted entropy estimates, Hardy's inequality and a family of singular
weight functions to derive a differential inequality; the differential inequality
shows exponential growth of the weighted entropy, with the growth constant blowing
up very fast as the singularity of the weight becomes sharper. To the best of
our knowledge, this is the first example of a nonnegativity-preserving higher-order
parabolic equation displaying infinite speed of support propagation.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0
apa: Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0
chicago: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn
Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations
and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0.
ieee: J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models,” Nonlinear Differential Equations
and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014.
ista: Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models. Nonlinear Differential Equations
and Applications. 21(1), 27–50.
mla: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn
Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations
and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0.
short: J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014)
27–50.
date_created: 2018-12-11T11:51:17Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:47Z
day: '01'
doi: 10.1007/s00030-013-0235-0
extern: 1
intvolume: ' 21'
issue: '1'
month: '01'
page: 27 - 50
publication: Nonlinear Differential Equations and Applications
publication_status: published
publisher: Birkhäuser
publist_id: '5960'
quality_controlled: 0
status: public
title: Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn
equation and quantum drift-diffusion models
type: journal_article
volume: 21
year: '2014'
...
---
_id: '1312'
abstract:
- lang: eng
text: We derive upper bounds on the waiting time of solutions to the thin-film equation
in the regime of weak slippage n ∈ [2, 32\11). In particular, we give sufficient
conditions on the initial data for instantaneous forward motion of the free boundary.
For n ∈ (2, 32\11), our estimates are sharp, for n = 2, they are sharp up to a
logarithmic correction term. Note that the case n = 2 corresponds-with a grain
of salt-to the assumption of the Navier slip condition at the fluid-solid interface.
We also obtain results in the regime of strong slippage n ∈ (1,2); however, in
this regime we expect them not to be optimal. Our method is based on weighted
backward entropy estimates, Hardy's inequality and singular weight functions;
we deduce a differential inequality which would enforce blowup of the weighted
entropy if the contact line were to remain stationary for too long.
author:
- first_name: Julian L
full_name: Julian Fischer
id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87
last_name: Fischer
orcid: 0000-0002-0479-558X
citation:
ama: 'Fischer JL. Upper bounds on waiting times for the Thin-film equation: The
case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818.
doi:10.1007/s00205-013-0690-0'
apa: 'Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage. Archive for Rational Mechanics and Analysis.
Springer. https://doi.org/10.1007/s00205-013-0690-0'
chicago: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation:
The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis.
Springer, 2014. https://doi.org/10.1007/s00205-013-0690-0.'
ieee: 'J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage,” Archive for Rational Mechanics and Analysis,
vol. 211, no. 3. Springer, pp. 771–818, 2014.'
ista: 'Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation:
The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3),
771–818.'
mla: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation:
The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis,
vol. 211, no. 3, Springer, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0.'
short: J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818.
date_created: 2018-12-11T11:51:18Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:48Z
day: '01'
doi: 10.1007/s00205-013-0690-0
extern: 1
intvolume: ' 211'
issue: '3'
month: '01'
page: 771 - 818
publication: Archive for Rational Mechanics and Analysis
publication_status: published
publisher: Springer
publist_id: '5959'
quality_controlled: 0
status: public
title: 'Upper bounds on waiting times for the Thin-film equation: The case of weak
slippage'
type: journal_article
volume: 211
year: '2014'
...
---
_id: '8244'
abstract:
- lang: eng
text: Passive immunotherapy with monoclonal antibodies represents a cornerstone
of human anticancer therapies, but has not been established in veterinary medicine
yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between
humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab
in human clinical oncology, we present here a “caninized” version of this antibody,
can225IgG, for comparative oncology studies. Variable region genes of 225, the
murine precursor of cetuximab, were fused with canine constant heavy gamma and
kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO)
DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected
according to productivity and highest specificity in EGFR-coated ELISA. Upon purification
with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity,
correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing
cells was assessed by flow cytometry and immunofluorescence; moreover, binding
to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability
and proliferation assays, incubation with can225IgG led to significant tumor cell
growth inhibition. Moreover, this antibody mediated significant tumor cell killing
via phagocytosis in vitro. We thus present here, for the first time, the generation
of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like
binding site, on the one hand, and the expression of a 91% homologous EGFR molecule
in canine cancer, on the other hand, this antibody may be a promising research
compound to establish passive immunotherapy in dog patients with cancer.
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Singer, J.
last_name: Singer
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: W.
full_name: Wang, W.
last_name: Wang
- first_name: M.
full_name: Weichselbaumer, M.
last_name: Weichselbaumer
- first_name: M.
full_name: Matz, M.
last_name: Matz
- first_name: A.
full_name: Mader, A.
last_name: Mader
- first_name: W.
full_name: Steinfellner, W.
last_name: Steinfellner
- first_name: S.
full_name: Meitz, S.
last_name: Meitz
- first_name: D.
full_name: Mechtcheriakova, D.
last_name: Mechtcheriakova
- first_name: Y.
full_name: Sobanov, Y.
last_name: Sobanov
- first_name: M.
full_name: Willmann, M.
last_name: Willmann
- first_name: T.
full_name: Stockner, T.
last_name: Stockner
- first_name: E.
full_name: Spillner, E.
last_name: Spillner
- first_name: R.
full_name: Kunert, R.
last_name: Kunert
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
citation:
ama: Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1)
antibody for passive immunotherapy in dog cancer patients. Molecular Cancer
Therapeutics. 2014;13(7):1777-1790. doi:10.1158/1535-7163.mct-13-0288
apa: Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A.,
… Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
American Association for Cancer Research. https://doi.org/10.1158/1535-7163.mct-13-0288
chicago: Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader,
W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics.
American Association for Cancer Research, 2014. https://doi.org/10.1158/1535-7163.mct-13-0288.
ieee: J. Singer et al., “Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients,” Molecular Cancer Therapeutics,
vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014.
ista: Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner
W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E,
Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
13(7), 1777–1790.
mla: Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics,
vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:10.1158/1535-7163.mct-13-0288.
short: J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner,
S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner,
R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790.
date_created: 2020-08-10T11:54:29Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T08:17:42Z
day: '01'
doi: 10.1158/1535-7163.mct-13-0288
extern: '1'
intvolume: ' 13'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 1777-1790
publication: Molecular Cancer Therapeutics
publication_identifier:
issn:
- 1535-7163
- 1538-8514
publication_status: published
publisher: American Association for Cancer Research
quality_controlled: '1'
status: public
title: Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy
in dog cancer patients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2014'
...
---
_id: '845'
abstract:
- lang: eng
text: Recombination between double-stranded DNA molecules is a key genetic process
which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs
during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population
nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable
and it is unclear how CO can occur between genotypes with less than 90% sequence
identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan
basidiomycete mushroom, a frequently encountered decayer of woody substrates.
We crossed two haploid individuals, from the United States and from Russia, and
obtained genome sequences for their 17 offspring. The average genetic distance
between the parents was 14%, making it possible to study CO at very high resolution.
We found reduced levels of linkage disequilibrium between loci flanking the CO
sites indicating that they are mostly confined to hotspots of recombination. Furthermore,
CO events preferentially occurred in regions under stronger negative selection,
in particular within exons that showed reduced levels of nucleotide diversity.
Apparently, in hypervariable species CO must avoid regions of higher divergence
between the recombining genomes due to limitations imposed by the mismatch repair
system, with regions under strong negative selection providing the opportunity
for recombination. These patterns are opposite to those observed in a number of
less variable species indicating that population genomics of hypervariable species
may reveal novel biological phenomena.
acknowledgement: The authors are grateful to Georgii Bazykin for valuable discussion
and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology
for Sanger sequencing. This study was supported by the Russian government grant
No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute
International Early Career Scientist Award and EMBO Young Investigator Program,
and core funds provided by the University of Michigan.
author:
- first_name: Vladimir
full_name: Seplyarskiy, Vladimir B
last_name: Seplyarskiy
- first_name: Maria
full_name: Logacheva, Maria D
last_name: Logacheva
- first_name: Aleksey
full_name: Penin, Aleksey A
last_name: Penin
- first_name: Maria
full_name: Baranová, Maria A
last_name: Baranová
- first_name: Evgeny
full_name: Leushkin, Evgeny V
last_name: Leushkin
- first_name: Natalia
full_name: Demidenko, Natalia V
last_name: Demidenko
- first_name: Anna
full_name: Klepikova, Anna V
last_name: Klepikova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Timothy
full_name: James, Timothy Y
last_name: James
citation:
ama: Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable
species preferentially occurs in regions of high local similarity. Molecular
Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242
apa: Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko,
N., … James, T. (2014). Crossing-over in a hypervariable species preferentially
occurs in regions of high local similarity. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msu242
chicago: Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová,
Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey
Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially
Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu242.
ieee: V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially
occurs in regions of high local similarity,” Molecular Biology and Evolution,
vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014.
ista: Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N,
Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable
species preferentially occurs in regions of high local similarity. Molecular Biology
and Evolution. 31(11), 3016–3025.
mla: Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially
Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution,
vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242.
short: V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko,
A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution
31 (2014) 3016–3025.
date_created: 2018-12-11T11:48:48Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:21Z
day: '01'
doi: 10.1093/molbev/msu242
extern: 1
intvolume: ' 31'
issue: '11'
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
page: 3016 - 3025
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6801'
quality_controlled: 0
status: public
title: Crossing-over in a hypervariable species preferentially occurs in regions of
high local similarity
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
volume: 31
year: '2014'
...
---
_id: '8458'
abstract:
- lang: eng
text: The maintenance of bacterial cell shape and integrity is largely attributed
to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform
this cross-linking are important targets for antibiotics. Despite this biomedical
importance, to date no structure of a protein in complex with an intact bacterial
peptidoglycan has been resolved, primarily due to the large size and flexibility
of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for
the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis
bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly,
the model obtained from protein chemical shift perturbation data shows that both
domains—the catalytic domain as well as the proposed peptidoglycan recognition
domain—are important for the interaction and reveals a novel binding motif that
involves residues outside of the classical enzymatic pocket. Experiments on mutants
and truncated protein constructs independently confirm the binding site and the
implication of both domains. Through measurements of dipolar-coupling derived
order parameters of bond motion we show that protein binding reduces the flexibility
of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan
complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases.
The strategy developed here can be extended to the study of a large variety of
enzymes involved in peptidoglycan morphogenesis.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Sébastien
full_name: Triboulet, Sébastien
last_name: Triboulet
- first_name: Cédric
full_name: Laguri, Cédric
last_name: Laguri
- first_name: Catherine M.
full_name: Bougault, Catherine M.
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Morgane
full_name: Callon, Morgane
last_name: Callon
- first_name: Michel
full_name: Arthur, Michel
last_name: Arthur
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking
enzyme in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987
apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon,
M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987
chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault,
Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic
Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial
Peptidoglycan.” Journal of the American Chemical Society. American Chemical
Society, 2014. https://doi.org/10.1021/ja5105987.
ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan,” Journal of the American
Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860,
2014.
ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M,
Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex
with an intact bacterial peptidoglycan. Journal of the American Chemical Society.
136(51), 17852–17860.
mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in
Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical
Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60,
doi:10.1021/ja5105987.
short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon,
M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014)
17852–17860.
date_created: 2020-09-18T10:07:52Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '27'
doi: 10.1021/ja5105987
extern: '1'
intvolume: ' 136'
issue: '51'
language:
- iso: eng
month: '11'
oa_version: None
page: 17852-17860
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: Atomic model of a cell-wall cross-linking enzyme in complex with an intact
bacterial peptidoglycan
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '8459'
abstract:
- lang: eng
text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion
of biomolecules at the atomic level. One technique, the analysis of relaxation
dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics
of biological processes. Built on top of the relax computational environment for
NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate
and easy-to-use. The software supports more models, both numeric and analytic,
than current solutions. An automated protocol, available for scripting and driving
the graphical user interface (GUI), is designed to simplify the analysis of dispersion
data for NMR spectroscopists. Decreases in optimization time are granted by parallelization
for running on computer clusters and by skipping an initial grid search by using
parameters from one solution as the starting point for another —using analytic
model results for the numeric models, taking advantage of model nesting, and using
averaged non-clustered results for the clustered analysis.
article_processing_charge: No
article_type: original
author:
- first_name: Sébastien
full_name: Morin, Sébastien
last_name: Morin
- first_name: Troels E
full_name: Linnet, Troels E
last_name: Linnet
- first_name: Mathilde
full_name: Lescanne, Mathilde
last_name: Lescanne
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gary S
full_name: Thompson, Gary S
last_name: Thompson
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Kaare
full_name: Teilum, Kaare
last_name: Teilum
- first_name: Stéphane
full_name: Gagné, Stéphane
last_name: Gagné
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Christian
full_name: Griesinger, Christian
last_name: Griesinger
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Edward J
full_name: d’Auvergne, Edward J
last_name: d’Auvergne
citation:
ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular
kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics.
2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166'
apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger,
M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford
University Press. https://doi.org/10.1093/bioinformatics/btu166'
chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary
S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular
Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics.
Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.'
ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol.
30, no. 15. Oxford University Press, pp. 2219–2220, 2014.'
ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum
K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax:
The analysis of biomolecular kinetics and thermodynamics using NMR relaxation
dispersion data. Bioinformatics. 30(15), 2219–2220.'
mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and
Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol.
30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.'
short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger,
K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne,
Bioinformatics 30 (2014) 2219–2220.
date_created: 2020-09-18T10:08:07Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/bioinformatics/btu166
extern: '1'
intvolume: ' 30'
issue: '15'
keyword:
- Statistics and Probability
- Computational Theory and Mathematics
- Biochemistry
- Molecular Biology
- Computational Mathematics
- Computer Science Applications
language:
- iso: eng
month: '08'
oa_version: None
page: 2219-2220
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/bioinformatics/btz397
status: public
title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR
relaxation dispersion data'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '8460'
abstract:
- lang: eng
text: The function of proteins depends on their ability to sample a variety of states
differing in structure and free energy. Deciphering how the various thermally
accessible conformations are connected, and understanding their structures and
relative energies is crucial in rationalizing protein function. Many biomolecular
reactions take place within microseconds to milliseconds, and this timescale is
therefore of central functional importance. Here we show that R1ρ relaxation dispersion
experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible
to investigate the thermodynamics and kinetics of such exchange process, and gain
insight into structural features of short‐lived states.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Jérémy
full_name: Zajakala, Jérémy
last_name: Zajakala
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states
of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte
Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275
apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold,
D., … Schanda, P. (2014). Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/anie.201311275
chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen,
Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational
States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.”
Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275.
ieee: P. Ma et al., “Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie
International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.
ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier
J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state
R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition.
53(17), 4312–4317.
mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by
Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie
International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275.
short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J.
Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.
date_created: 2020-09-18T10:08:53Z
date_published: 2014-03-18T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '18'
doi: 10.1002/anie.201311275
extern: '1'
intvolume: ' 53'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 4312-4317
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '8500'
abstract:
- lang: eng
text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor
coupling. If the coupling is weak, then the system is near‐integrable and KAM
tori fill most of the phase space. For all KAM trajectories the energy of each
pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily
weak coupling of a certain localized type, the neighboring pendula can exchange
energy. In fact, the energy can be transferred between the pendula in any prescribed
way.
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: Mark
full_name: Levi, Mark
last_name: Levi
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications
on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509
apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a
pendulum lattice. Communications on Pure and Applied Mathematics. Wiley.
https://doi.org/10.1002/cpa.21509
chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in
a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley,
2014. https://doi.org/10.1002/cpa.21509.
ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,”
Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley,
pp. 748–775, 2014.
ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice.
Communications on Pure and Applied Mathematics. 67(5), 748–775.
mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications
on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75,
doi:10.1002/cpa.21509.
short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics
67 (2014) 748–775.
date_created: 2020-09-18T10:47:01Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2022-08-25T13:58:13Z
day: '01'
doi: 10.1002/cpa.21509
extern: '1'
intvolume: ' 67'
issue: '5'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '05'
oa_version: None
page: 748-775
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Arnol′d diffusion in a pendulum lattice
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2014'
...
---
_id: '8501'
abstract:
- lang: eng
text: In this paper, we study small perturbations of a class of non-convex integrable
Hamiltonians with two degrees of freedom, and we prove a result of diffusion for
an open and dense set of perturbations, with an optimal time of diffusion which
grows linearly with respect to the inverse of the size of the perturbation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal.
2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203
apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class
of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical
Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203
chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class
of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical
Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203.
ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal,
vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.
ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2),
181–203.
mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of
Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal,
vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203.
short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.
date_created: 2020-09-18T10:47:09Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:43Z
day: '01'
doi: 10.17323/1609-4514-2014-14-2-181-203
extern: '1'
external_id:
arxiv:
- '1304.3050'
intvolume: ' 14'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa_version: Preprint
page: 181-203
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- 1609-3321
- 1609-4514
publication_status: published
publisher: Independent University of Moscow
quality_controlled: '1'
status: public
title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees
of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '852'
abstract:
- lang: eng
text: 'Rapid divergence of gene copies after duplication is thought to determine
the fate of the copies and evolution of novel protein functions. However, data
on howlong the gene copies continue to experience an elevated rate of evolution
remain scarce. Standard theory of gene duplications based on some level of genetic
redundancy of gene copies predicts that the period of accelerated evolutionmust
end relatively quickly. Using a maximum-likelihood approach we estimate preduplication,
initial postduplication, and recent postduplication rates of evolution that occurred
in themammalian lineage.Wefind that both gene copies experience a similar in magnitude
acceleration in their rate of evolution. The copy located in the original genomic
position typically returns to the preduplication rates of evolution in a short
period of time. The burst of faster evolution of the copy that is located in a
new genomic position typically lasts longer. Furthermore, the fast-evolving copies
on average continue to evolve faster than the preduplication rates far longer
than predicted by standard theory of gene duplications.We hypothesize that the
prolonged elevated rates of evolution are determined by functional properties
that were acquired during, or soon after, the gene duplication event. '
author:
- first_name: Oriol
full_name: Rosello, Oriol P
last_name: Rosello
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution
after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955.
doi:10.1093/gbe/evu159
apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration
of protein evolution after gene duplication. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evu159
chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159.
ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein
evolution after gene duplication,” Genome Biology and Evolution, vol. 6,
no. 8. Oxford University Press, pp. 1949–1955, 2014.
ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein
evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.
mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution,
vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159.
short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.
date_created: 2018-12-11T11:48:51Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:51Z
day: '01'
doi: 10.1093/gbe/evu159
extern: 1
intvolume: ' 6'
issue: '8'
month: '08'
page: 1949 - 1955
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6797'
quality_controlled: 0
status: public
title: Long-Term asymmetrical acceleration of protein evolution after gene duplication
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
volume: 6
year: '2014'
...
---
_id: '856'
abstract:
- lang: eng
text: The emergence of new genes throughout evolution requires rewiring and extension
of regulatory networks. However, the molecular details of how the transcriptional
regulation of new gene copies evolves remain largely unexplored. Here we show
how duplication of a transcription factor gene allowed the emergence of two independent
regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous
and could bind different motifs in its target promoters. After duplication, one
paralogue evolved increased binding specificity so that it only binds one type
of motif, whereas the other copy evolved a decreased activity so that it only
activates promoters that contain multiple binding sites. Interestingly, only a
few mutations in both the DNA-binding domains and in the promoter binding sites
were required to gradually disentangle the two networks. These results reveal
how duplication of a promiscuous transcription factor followed by concerted cis
and trans mutations allows expansion of a regulatory network.
acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility
grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie
Actions from the European Commission. Research in the lab of K.J.V. is supported
by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme,
KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR
grant. The work of F.A.K. was supported by a grant of the HHMI International Early
Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants
from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia
Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded
by the European Regional Development Fund (ERDF), the European Union and the European
Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral
fellowship. Funders had no role in study design, data collection and analysis, decision
to publish or preparation of the manuscript.'
author:
- first_name: Ksenia
full_name: Pougach, Ksenia S
last_name: Pougach
- first_name: Arnout
full_name: Voet, Arnout R
last_name: Voet
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Karin
full_name: Voordeckers, Karin
last_name: Voordeckers
- first_name: Joaquin
full_name: Christiaens, Joaquin F
last_name: Christiaens
- first_name: Bianka
full_name: Baying, Bianka
last_name: Baying
- first_name: Vladimı́R
full_name: Bénès, Vladimı́r
last_name: Bénès
- first_name: Ryo
full_name: Sakai, Ryo
last_name: Sakai
- first_name: Jan
full_name: Aerts, Jan A
last_name: Aerts
- first_name: Bo
full_name: Zhu, Bo
last_name: Zhu
- first_name: Patrick
full_name: Van Dijck, Patrick
last_name: Van Dijck
- first_name: Kevin
full_name: Verstrepen, Kevin J
last_name: Verstrepen
citation:
ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription
factor drives the emergence of a new regulatory network. Nature Communications.
2014;5. doi:10.1038/ncomms5868
apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying,
B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms5868
chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin
Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous
Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature
Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868.
ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network,” Nature Communications,
vol. 5. Nature Publishing Group, 2014.
ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès
V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a
promiscuous transcription factor drives the emergence of a new regulatory network.
Nature Communications. 5.
mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor
Drives the Emergence of a New Regulatory Network.” Nature Communications,
vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868.
short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying,
V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications
5 (2014).
date_created: 2018-12-11T11:48:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:01Z
day: '01'
doi: 10.1038/ncomms5868
extern: 1
intvolume: ' 5'
month: '01'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '6790'
quality_controlled: 0
status: public
title: Duplication of a promiscuous transcription factor drives the emergence of a
new regulatory network
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
volume: 5
year: '2014'
...
---
_id: '863'
abstract:
- lang: eng
text: The origins of neural systems remain unresolved. In contrast to other basal
metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived
muscular systems. These holoplanktonic predators also have sophisticated ciliated
locomotion, behaviour and distinct development. Here we present the draft genome
of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore
transcriptomes, and show that they are remarkably distinct from other animal genomes
in their content of neurogenic, immune and developmental genes. Our integrative
analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis
is supported by comparative analysis of multiple gene families, including the
apparent absence of HOX genes, canonical microRNA machinery, and reduced immune
complement in ctenophores. Although two distinct nervous systems are well recognized
in ctenophores, many bilaterian neuron-specific genes and genes of 'classical'
neurotransmitter pathways either are absent or, if present, are not expressed
in neurons. Our metabolomic and physiological data are consistent with the hypothesis
that ctenophore neural systems, and possibly muscle specification, evolved independently
from those in other animals.
acknowledgement: We thank Friday Harbor Laboratories for facilities during animal
collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters,
J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ,
RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank
F. Nivens for videos and P. L. Williams for database support. This work was supported
by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH
(1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310
to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H.,
L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity
Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock
Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033
(Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424),
EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology
Program 117 and Molette laboratory 22.
author:
- first_name: Leonid
full_name: Moroz, Leonid L
last_name: Moroz
- first_name: Kevin
full_name: Kocot, Kevin M
last_name: Kocot
- first_name: Mathew
full_name: Citarella, Mathew R
last_name: Citarella
- first_name: Sohn
full_name: Dosung, Sohn
last_name: Dosung
- first_name: Tigran
full_name: Norekian, Tigran P
last_name: Norekian
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Christopher
full_name: Dailey, Christopher A
last_name: Dailey
- first_name: Eugene
full_name: Berezikov, Eugene
last_name: Berezikov
- first_name: Katherine
full_name: Buckley, Katherine M
last_name: Buckley
- first_name: Andrey
full_name: Ptitsyn, Andrey A
last_name: Ptitsyn
- first_name: Denis
full_name: Reshetov, Denis A
last_name: Reshetov
- first_name: Krishanu
full_name: Mukherjee, Krishanu
last_name: Mukherjee
- first_name: Tatiana
full_name: Moroz, Tatiana P
last_name: Moroz
- first_name: Yelena
full_name: Bobkova, Yelena V
last_name: Bobkova
- first_name: Fahong
full_name: Yu, Fahong
last_name: Yu
- first_name: Vladimir
full_name: Kapitonov, Vladimir V
last_name: Kapitonov
- first_name: Jerzy
full_name: Jurka, Jerzy W
last_name: Jurka
- first_name: Yuriy
full_name: Bobkov, Yuriy V
last_name: Bobkov
- first_name: Joshua
full_name: Swore, Joshua J
last_name: Swore
- first_name: David
full_name: Girardo, David O
last_name: Girardo
- first_name: Alexander
full_name: Fodor, Alexander
last_name: Fodor
- first_name: Fedor
full_name: Gusev, Fedor E
last_name: Gusev
- first_name: Rachel
full_name: Sanford, Rachel S
last_name: Sanford
- first_name: Rebecca
full_name: Bruders, Rebecca
last_name: Bruders
- first_name: Ellen
full_name: Kittler, Ellen L
last_name: Kittler
- first_name: Claudia
full_name: Mills, Claudia E
last_name: Mills
- first_name: Jonathan
full_name: Rast, Jonathan P
last_name: Rast
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Victor
full_name: Solovyev, Victor
last_name: Solovyev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Billie
full_name: Swalla, Billie J
last_name: Swalla
- first_name: Jonathan
full_name: Sweedler, Jonathan V
last_name: Sweedler
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Kenneth
full_name: Halanych, Kenneth M
last_name: Halanych
- first_name: Andrea
full_name: Kohn, Andrea B
last_name: Kohn
citation:
ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary
origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400
apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya,
I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural
systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400
chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian,
Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the
Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group,
2014. https://doi.org/10.1038/nature13400.
ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins
of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group,
pp. 109–114, 2014.
ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko
A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz
T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor
A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev
V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The
ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503),
109–114.
mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of
Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014,
pp. 109–14, doi:10.1038/nature13400.
short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya,
A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K.
Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J.
Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C.
Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler,
E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.
date_created: 2018-12-11T11:48:54Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:21Z
day: '01'
doi: 10.1038/nature13400
extern: 1
intvolume: ' 510'
issue: '7503'
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '01'
page: 109 - 114
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6785'
quality_controlled: 0
status: public
title: The ctenophore genome and the evolutionary origins of neural systems
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
volume: 510
year: '2014'
...
---
_id: '865'
abstract:
- lang: eng
text: Research on existing drugs often discovers novel mechanisms of their action
and leads to the expansion of their therapeutic scope and subsequent remarketing.
The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays
critical roles in cancer development and progression. However, drugs which disrupt
this pathway are unavailable despite the high demand. Here we report an attempt
to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved
drugs. We performed an in silico screening which brought up several potential
antagonists of the ligand-receptor interaction. 14 of these substances were tested
using the TopFlash luciferase reporter assay and four of them identified as active
and specific inhibitors of the Wnt3a-induced signaling. However, further analysis
through GTP-binding and β-catenin stabilization assays showed that the compounds
do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels.
We further describe the previously unknown inhibitory activity of an anti-leprosy
drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency
in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These
data provide a basis for further investigations of the efficiency of clofazimine
in treatment of Wnt-dependent cancers.
author:
- first_name: Alexey
full_name: Koval, Alexey V
last_name: Koval
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Polina
full_name: Shichkova, Polina
last_name: Shichkova
- first_name: S
full_name: Khunderyakova, S
last_name: Khunderyakova
- first_name: Yury
full_name: Markov, Yury
last_name: Markov
- first_name: J
full_name: Panchenko, J
last_name: Panchenko
- first_name: A
full_name: Volodina, A
last_name: Volodina
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Katanaev, Vladimir L
last_name: Katanaev
citation:
ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits
growth of triple-negative breast cancer cells via inhibition of canonical Wnt
signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007
apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko,
J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative
breast cancer cells via inhibition of canonical Wnt signaling. Biochemical
Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007
chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov,
J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy
Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition
of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014.
https://doi.org/10.1016/j.bcp.2013.12.007.
ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of
triple-negative breast cancer cells via inhibition of canonical Wnt signaling,”
Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014.
ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina
A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth
of triple-negative breast cancer cells via inhibition of canonical Wnt signaling.
Biochemical Pharmacology. 87(4), 571–578.
mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative
Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical
Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007.
short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko,
A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.
date_created: 2018-12-11T11:48:55Z
date_published: 2014-02-15T00:00:00Z
date_updated: 2021-01-12T08:20:24Z
day: '15'
doi: 10.1016/j.bcp.2013.12.007
extern: 1
intvolume: ' 87'
issue: '4'
month: '02'
page: 571 - 578
publication: Biochemical Pharmacology
publication_status: published
publisher: Elsevier
publist_id: '6782'
quality_controlled: 0
status: public
title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer
cells via inhibition of canonical Wnt signaling
type: journal_article
volume: 87
year: '2014'
...
---
_id: '892'
abstract:
- lang: eng
text: The study of molecular evolution is important because it reveals how protein
functions emerge and evolve. Recently, several types of studies indicated that
substitutions in molecular evolution occur in a compensatory manner, whereby the
occurrence of a substitution depends on the amino acid residues at other sites.
However, a molecular or structural basis behind the compensation often remains
obscure. Here, we review studies on the interface of structural biology and molecular
evolution that revealed novel aspects of compensatory evolution. In many cases
structural studies benefit from evolutionary data while structural data often
add a functional dimension to the study of molecular evolution.
acknowledgement: |
The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.
author:
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Alexei
full_name: Finkelstein, Alexei V
last_name: Finkelstein
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory
evolution. Current Opinion in Structural Biology. 2014;26(1):104-112. doi:10.1016/j.sbi.2014.05.004
apa: Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective
of compensatory evolution. Current Opinion in Structural Biology. Elsevier.
https://doi.org/10.1016/j.sbi.2014.05.004
chicago: Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural
Perspective of Compensatory Evolution.” Current Opinion in Structural Biology.
Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004.
ieee: D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of
compensatory evolution,” Current Opinion in Structural Biology, vol. 26,
no. 1. Elsevier, pp. 104–112, 2014.
ista: Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of
compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.
mla: Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.”
Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014,
pp. 104–12, doi:10.1016/j.sbi.2014.05.004.
short: D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural
Biology 26 (2014) 104–112.
date_created: 2018-12-11T11:49:03Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T08:21:21Z
day: '01'
doi: 10.1016/j.sbi.2014.05.004
extern: 1
intvolume: ' 26'
issue: '1'
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '06'
page: 104 - 112
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '6756'
quality_controlled: 0
status: public
title: A structural perspective of compensatory evolution
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 26
year: '2014'
...