---
_id: '12199'
abstract:
- lang: eng
text: The four microsporangia of the flowering plant anther develop from archesporial
cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes
are surrounded by concentric monolayers of tapetal, middle layer and endothecial
cells. How this intricate array of tissues, each containing relatively few cells,
is established in an organ possessing no formal meristems is poorly understood.
We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES
1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually
for plants, tapetal cells are specified very early in development, and are subsequently
stimulated to proliferate by a receptor-like kinase (RLK) complex that includes
EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand
result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly,
these cells continue to develop, isolated at the locular periphery. Mutant and
wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the
periphery of mutant locules becomes occupied by microsporocytes. However, induction
of late expression of EMS1 in the few tapetal initials in ems1 plants results
in their proliferation to generate a functional tapetum, and this proliferation
suppresses microsporocyte number. Our experiments also show that integrity of
the tapetal monolayer is crucial for the maintenance of the polarity of divisions
within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the
context of tissue development in complex plant organs, where constancy in size,
shape and cell number is crucial.
acknowledgement: 'We thank the following for providing mutant lines and reagents:
Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines
and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable
help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing
Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance.
We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the
research was funded by Oxford University through a Clarendon Scholarship to X.F.,
with additional financial support from Magdalen College (Oxford).'
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis
anther. Development. 2010;137(14):2409-2416. doi:10.1242/dev.049320
apa: Feng, X., & Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation
in the Arabidopsis anther. Development. The Company of Biologists. https://doi.org/10.1242/dev.049320
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation
in the Arabidopsis Anther.” Development. The Company of Biologists, 2010.
https://doi.org/10.1242/dev.049320.
ieee: X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation
in the Arabidopsis anther,” Development, vol. 137, no. 14. The Company
of Biologists, pp. 2409–2416, 2010.
ista: Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in
the Arabidopsis anther. Development. 137(14), 2409–2416.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation
in the Arabidopsis Anther.” Development, vol. 137, no. 14, The Company
of Biologists, 2010, pp. 2409–16, doi:10.1242/dev.049320.
short: X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.
date_created: 2023-01-16T09:21:54Z
date_published: 2010-07-15T00:00:00Z
date_updated: 2023-05-08T10:57:11Z
day: '15'
department:
- _id: XiFe
doi: 10.1242/dev.049320
extern: '1'
external_id:
pmid:
- '20570940'
intvolume: ' 137'
issue: '14'
keyword:
- Developmental Biology
- Molecular Biology
- Anther Tapetum
- Arabidopsis
- Cell Fate Establishment
- EMS1
- Reproductive Cell Lineage
language:
- iso: eng
month: '07'
oa_version: None
page: 2409-2416
pmid: 1
publication: Development
publication_identifier:
issn:
- 1477-9129
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tapetal cell fate, lineage and proliferation in the Arabidopsis anther
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2010'
...
---
_id: '12200'
abstract:
- lang: eng
text: Key steps in the evolution of the angiosperm anther include the patterning
of the concentrically organized microsporangium and the incorporation of four
such microsporangia into a leaf-like structure. Mutant studies in the model plant
Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the
cell lineages culminating in the different cell types present in the microsporangium
(the microsporocytes, the tapetum, and the middle and endothecial layers), and
(ii) some of the genes responsible for specifying their fates. However, the processes
that confer polarity on the developing anther and position the microsporangia
within it remain unclear. Certainly, data from a range of experimental strategies
suggest that hormones play a central role in establishing polarity and the patterning
of the anther initial, and may be responsible for locating the microsporangia.
But the fact that microsporangia were originally positioned externally suggests
that their development is likely to be autonomous, perhaps with the reproductive
cells generating signals controlling the growth and division of the investing
anther epidermis. These possibilities are discussed in the context of the expression
of genes which initiate and maintain male and female reproductive development,
and in the perspective of our current views of anther evolution.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Cell–cell interactions during patterning of the Arabidopsis
anther. Biochemical Society Transactions. 2010;38(2):571-576. doi:10.1042/bst0380571
apa: Feng, X., & Dickinson, H. G. (2010). Cell–cell interactions during patterning
of the Arabidopsis anther. Biochemical Society Transactions. Portland
Press Ltd. https://doi.org/10.1042/bst0380571
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning
of the Arabidopsis Anther.” Biochemical Society Transactions. Portland
Press Ltd., 2010. https://doi.org/10.1042/bst0380571.
ieee: X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of
the Arabidopsis anther,” Biochemical Society Transactions, vol.
38, no. 2. Portland Press Ltd., pp. 571–576, 2010.
ista: Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the
Arabidopsis anther. Biochemical Society Transactions. 38(2), 571–576.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning
of the Arabidopsis Anther.” Biochemical Society Transactions, vol.
38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:10.1042/bst0380571.
short: X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.
date_created: 2023-01-16T09:22:18Z
date_published: 2010-03-22T00:00:00Z
date_updated: 2023-05-08T10:57:59Z
day: '22'
department:
- _id: XiFe
doi: 10.1042/bst0380571
extern: '1'
external_id:
pmid:
- '20298223'
intvolume: ' 38'
issue: '2'
keyword:
- Biochemistry
- Anther Development
- Arabidopsis
- Cell Fate
- Microsporangium
- Polarity
- Receptor Kinase
language:
- iso: eng
month: '03'
oa_version: None
page: 571-576
pmid: 1
publication: Biochemical Society Transactions
publication_identifier:
issn:
- 0300-5127
- 1470-8752
publication_status: published
publisher: Portland Press Ltd.
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell–cell interactions during patterning of the Arabidopsis anther
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2010'
...
---
_id: '12653'
abstract:
- lang: eng
text: 'Daily streamflow from stations close to five Swiss glaciers is analyzed for
trends with the Mann-Kendall test. We consider a common period of record (1974–2004)
and longer periods based on data availability. The trend statistical significance
is tested on annual and seasonal bases. We also examine changes in precipitation,
temperature, and snow cover characteristics. Highly glacierized basins show statistically
significant positive trends in annual streamflow caused by increasing streamflow
in spring and summer. Trends are more numerous and stronger at lower and mid than
at the upper quantiles. The basin characterized by lower glacier coverage, conversely,
does not exhibit consistently statistically significant trends. Changes in precipitation
are not sufficient to explain the observed streamflow trends. Air temperature
sees an increase in mean, minimum, and maximum values at all sites. Variations
in the seasonal snow accumulation and ablation process are evident. Solid precipitation
is decreasing at all sites and trends may be due to a shift from snowfall into
rainfall. Mean snow depth is also decreasing, and its duration is getting shorter
because of a decrease in solid precipitation and enhanced melting. Trend magnitude
attenuates with longer time series. Contrasting trends are detected for different
subperiods in the last 70 years: statistically significant negative trends are
observed in the periods 1944–1974 and 1954–1984 for Aletschgletscher, in contrast
with the results for the common period. These trends are explained by different
rates of ice volume changes, and the sign of trends is clearly related to phases
of positive or negative glacier mass balance.'
article_number: W10522
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: A.
full_name: Bauder, A.
last_name: Bauder
- first_name: M.
full_name: Parola, M.
last_name: Parola
citation:
ama: Pellicciotti F, Bauder A, Parola M. Effect of glaciers on streamflow trends
in the Swiss Alps. Water Resources Research. 2010;46(10). doi:10.1029/2009wr009039
apa: Pellicciotti, F., Bauder, A., & Parola, M. (2010). Effect of glaciers on
streamflow trends in the Swiss Alps. Water Resources Research. American
Geophysical Union. https://doi.org/10.1029/2009wr009039
chicago: Pellicciotti, Francesca, A. Bauder, and M. Parola. “Effect of Glaciers
on Streamflow Trends in the Swiss Alps.” Water Resources Research. American
Geophysical Union, 2010. https://doi.org/10.1029/2009wr009039.
ieee: F. Pellicciotti, A. Bauder, and M. Parola, “Effect of glaciers on streamflow
trends in the Swiss Alps,” Water Resources Research, vol. 46, no. 10. American
Geophysical Union, 2010.
ista: Pellicciotti F, Bauder A, Parola M. 2010. Effect of glaciers on streamflow
trends in the Swiss Alps. Water Resources Research. 46(10), W10522.
mla: Pellicciotti, Francesca, et al. “Effect of Glaciers on Streamflow Trends in
the Swiss Alps.” Water Resources Research, vol. 46, no. 10, W10522, American
Geophysical Union, 2010, doi:10.1029/2009wr009039.
short: F. Pellicciotti, A. Bauder, M. Parola, Water Resources Research 46 (2010).
date_created: 2023-02-20T08:18:27Z
date_published: 2010-10-01T00:00:00Z
date_updated: 2023-02-20T09:39:29Z
day: '01'
doi: 10.1029/2009wr009039
extern: '1'
intvolume: ' 46'
issue: '10'
keyword:
- Water Science and Technology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1029/2009WR009039
month: '10'
oa: 1
oa_version: Published Version
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: Effect of glaciers on streamflow trends in the Swiss Alps
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2010'
...
---
_id: '1300'
abstract:
- lang: eng
text: 'Motion vision is a major function of all visual systems, yet the underlying
neural mechanisms and circuits are still elusive. In the lamina, the first optic
neuropile of Drosophila melanogaster, photoreceptor signals split into five parallel
pathways, L1-L5. Here we examine how these pathways contribute to visual motion
detection by combining genetic block and reconstitution of neural activity in
different lamina cell types with whole-cell recordings from downstream motion-sensitive
neurons. We find reduced responses to moving gratings if L1 or L2 is blocked;
however, reconstitution of photoreceptor input to only L1 or L2 results in wild-type
responses. Thus, the first experiment indicates the necessity of both pathways,
whereas the second indicates sufficiency of each single pathway. This contradiction
can be explained by electrical coupling between L1 and L2, allowing for activation
of both pathways even when only one of them receives photoreceptor input. A fundamental
difference between the L1 pathway and the L2 pathway is uncovered when blocking
L1 or L2 output while presenting moving edges of positive (ON) or negative (OFF)
contrast polarity: blocking L1 eliminates the response to moving ON edges, whereas
blocking L2 eliminates the response to moving OFF edges. Thus, similar to the
segregation of photoreceptor signals in ON and OFF bipolar cell pathways in the
vertebrate retina, photoreceptor signals segregate into ON-L1 and OFF-L2 channels
in the lamina of Drosophila.'
author:
- first_name: Maximilian A
full_name: Maximilian Jösch
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Bettina
full_name: Schnell, Bettina
last_name: Schnell
- first_name: Shamprasad
full_name: Raghu, Shamprasad V
last_name: Raghu
- first_name: Dierk
full_name: Reiff, Dierk F
last_name: Reiff
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
citation:
ama: Jösch MA, Schnell B, Raghu S, Reiff D, Borst A. ON and off pathways in Drosophila
motion vision. Nature. 2010;468(7321):300-304. doi:10.1038/nature09545
apa: Jösch, M. A., Schnell, B., Raghu, S., Reiff, D., & Borst, A. (2010). ON
and off pathways in Drosophila motion vision. Nature. Nature Publishing
Group. https://doi.org/10.1038/nature09545
chicago: Jösch, Maximilian A, Bettina Schnell, Shamprasad Raghu, Dierk Reiff, and
Alexander Borst. “ON and off Pathways in Drosophila Motion Vision.” Nature.
Nature Publishing Group, 2010. https://doi.org/10.1038/nature09545.
ieee: M. A. Jösch, B. Schnell, S. Raghu, D. Reiff, and A. Borst, “ON and off pathways
in Drosophila motion vision,” Nature, vol. 468, no. 7321. Nature Publishing
Group, pp. 300–304, 2010.
ista: Jösch MA, Schnell B, Raghu S, Reiff D, Borst A. 2010. ON and off pathways
in Drosophila motion vision. Nature. 468(7321), 300–304.
mla: Jösch, Maximilian A., et al. “ON and off Pathways in Drosophila Motion Vision.”
Nature, vol. 468, no. 7321, Nature Publishing Group, 2010, pp. 300–04,
doi:10.1038/nature09545.
short: M.A. Jösch, B. Schnell, S. Raghu, D. Reiff, A. Borst, Nature 468 (2010) 300–304.
date_created: 2018-12-11T11:51:14Z
date_published: 2010-11-11T00:00:00Z
date_updated: 2021-01-12T06:49:44Z
day: '11'
doi: 10.1038/nature09545
extern: 1
intvolume: ' 468'
issue: '7321'
month: '11'
page: 300 - 304
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '5970'
quality_controlled: 0
status: public
title: ON and off pathways in Drosophila motion vision
type: journal_article
volume: 468
year: '2010'
...
---
_id: '1301'
abstract:
- lang: eng
text: Motion vision is essential for navigating through the environment. Due to
its genetic amenability, the fruit fly Drosophila has been serving for a lengthy
period as a model organism for studying optomotor behavior as elicited by large-field
horizontal motion. However, the neurons underlying the control of this behavior
have not been studied in Drosophila so far. Here we report the first whole cell
recordings from three cells of the horizontal system (HSN, HSE, and HSS) in the
lobula plate of Drosophila. All three HS cells are tuned to large-field horizontal
motion in a direction-selective way; they become excited by front-to-back motion
and inhibited by back-to-front motion in the ipsilateral field of view. The response
properties of HS cells such as contrast and velocity dependence are in accordance
with the correlation-type model of motion detection. Neurobiotin injection suggests
extensive coupling among ipsilateral HS cells and additional coupling to tangential
cells that have their dendrites in the contralateral hemisphere of the brain.
This connectivity scheme accounts for the complex layout of their receptive fields
and explains their sensitivity both to ipsilateral and to contralateral motion.
Thus the main response properties of Drosophila HS cells are strikingly similar
to the responses of their counterparts in the blowfly Calliphora, although we
found substantial differences with respect to their dendritic structure and connectivity.
This long-awaited functional characterization of HS cells in Drosophila provides
the basis for the future dissection of optomotor behavior and the underlying neural
circuitry by combining genetics, physiology, and behavior.
acknowledgement: This work was supported by the Max-Planck-Society and by a Human
Frontier Science Program grant to K. Ito, A. Borst, and B. Nelson.
article_processing_charge: No
article_type: original
author:
- first_name: Bettina
full_name: Schnell, Bettina
last_name: Schnell
- first_name: Maximilian A
full_name: Jösch, Maximilian A
id: 2BD278E6-F248-11E8-B48F-1D18A9856A87
last_name: Jösch
orcid: 0000-0002-3937-1330
- first_name: Friedrich
full_name: Förstner, Friedrich
last_name: Förstner
- first_name: Shamprasad
full_name: Raghu, Shamprasad
last_name: Raghu
- first_name: Hideo
full_name: Otsuna, Hideo
last_name: Otsuna
- first_name: Kei
full_name: Ito, Kei
last_name: Ito
- first_name: Alexander
full_name: Borst, Alexander
last_name: Borst
- first_name: Dierk
full_name: Reiff, Dierk
last_name: Reiff
citation:
ama: Schnell B, Jösch MA, Förstner F, et al. Processing of horizontal optic flow
in three visual interneurons of the Drosophila brain. Journal of Neurophysiology.
2010;103(3):1646-1657. doi:10.1152/jn.00950.2009
apa: Schnell, B., Jösch, M. A., Förstner, F., Raghu, S., Otsuna, H., Ito, K., …
Reiff, D. (2010). Processing of horizontal optic flow in three visual interneurons
of the Drosophila brain. Journal of Neurophysiology. American Physiological
Society. https://doi.org/10.1152/jn.00950.2009
chicago: Schnell, Bettina, Maximilian A Jösch, Friedrich Förstner, Shamprasad Raghu,
Hideo Otsuna, Kei Ito, Alexander Borst, and Dierk Reiff. “Processing of Horizontal
Optic Flow in Three Visual Interneurons of the Drosophila Brain.” Journal of
Neurophysiology. American Physiological Society, 2010. https://doi.org/10.1152/jn.00950.2009.
ieee: B. Schnell et al., “Processing of horizontal optic flow in three visual
interneurons of the Drosophila brain,” Journal of Neurophysiology, vol.
103, no. 3. American Physiological Society, pp. 1646–1657, 2010.
ista: Schnell B, Jösch MA, Förstner F, Raghu S, Otsuna H, Ito K, Borst A, Reiff
D. 2010. Processing of horizontal optic flow in three visual interneurons of the
Drosophila brain. Journal of Neurophysiology. 103(3), 1646–1657.
mla: Schnell, Bettina, et al. “Processing of Horizontal Optic Flow in Three Visual
Interneurons of the Drosophila Brain.” Journal of Neurophysiology, vol.
103, no. 3, American Physiological Society, 2010, pp. 1646–57, doi:10.1152/jn.00950.2009.
short: B. Schnell, M.A. Jösch, F. Förstner, S. Raghu, H. Otsuna, K. Ito, A. Borst,
D. Reiff, Journal of Neurophysiology 103 (2010) 1646–1657.
date_created: 2018-12-11T11:51:14Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2021-01-12T06:49:44Z
day: '01'
doi: 10.1152/jn.00950.2009
extern: '1'
external_id:
pmid:
- '20089816'
intvolume: ' 103'
issue: '3'
language:
- iso: eng
month: '03'
oa_version: None
page: 1646 - 1657
pmid: 1
publication: Journal of Neurophysiology
publication_identifier:
eissn:
- 1522-1598
issn:
- ' 0022-3077'
publication_status: published
publisher: American Physiological Society
publist_id: '5971'
quality_controlled: '1'
status: public
title: Processing of horizontal optic flow in three visual interneurons of the Drosophila
brain
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 103
year: '2010'
...
---
_id: '8472'
abstract:
- lang: eng
text: Characterization of protein dynamics by solid-state NMR spectroscopy requires
robust and accurate measurement protocols, which are not yet fully developed.
In this study, we investigate the backbone dynamics of microcrystalline ubiquitin
using different approaches. A rotational-echo double-resonance type (REDOR-type)
methodology allows one to accurately measure 1H−15N order parameters in highly
deuterated samples. We show that the systematic errors in the REDOR experiment
are as low as 1% or even less, giving access to accurate data for the amplitudes
of backbone mobility. Combining such dipolar-coupling-derived order parameters
with autocorrelated and cross-correlated 15N relaxation rates, we are able to
quantitate amplitudes and correlation times of backbone dynamics on picosecond
and nanosecond time scales in a residue-resolved manner. While the mobility on
picosecond time scales appears to have rather uniform amplitude throughout the
protein, we unambiguously identify and quantitate nanosecond mobility with order
parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics
has also been revealed in solution state. The methodology used here, a combination
of accurate dipolar-coupling measurements and different relaxation parameters,
yields details about dynamics on different time scales and can be applied to solid
protein samples such as amyloid fibrils or membrane proteins.
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: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
citation:
ama: Schanda P, Meier BH, Ernst M. Quantitative analysis of protein backbone dynamics
in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal of the
American Chemical Society. 2010;132(45):15957-15967. doi:10.1021/ja100726a
apa: Schanda, P., Meier, B. H., & Ernst, M. (2010). Quantitative analysis of
protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy.
Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/ja100726a
chicago: Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Quantitative Analysis
of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR
Spectroscopy.” Journal of the American Chemical Society. American Chemical
Society, 2010. https://doi.org/10.1021/ja100726a.
ieee: P. Schanda, B. H. Meier, and M. Ernst, “Quantitative analysis of protein backbone
dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy,” Journal
of the American Chemical Society, vol. 132, no. 45. American Chemical Society,
pp. 15957–15967, 2010.
ista: Schanda P, Meier BH, Ernst M. 2010. Quantitative analysis of protein backbone
dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal
of the American Chemical Society. 132(45), 15957–15967.
mla: Schanda, Paul, et al. “Quantitative Analysis of Protein Backbone Dynamics in
Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” Journal of the
American Chemical Society, vol. 132, no. 45, American Chemical Society, 2010,
pp. 15957–67, doi:10.1021/ja100726a.
short: P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society
132 (2010) 15957–15967.
date_created: 2020-09-18T10:11:13Z
date_published: 2010-10-26T00:00:00Z
date_updated: 2021-01-12T08:19:30Z
day: '26'
doi: 10.1021/ja100726a
extern: '1'
intvolume: ' 132'
issue: '45'
language:
- iso: eng
month: '10'
oa_version: None
page: 15957-15967
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: Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin
by solid-state NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 132
year: '2010'
...
---
_id: '8473'
abstract:
- lang: eng
text: β2-microglobulin (β2m), the light chain of class I major histocompatibility
complex, is responsible for the dialysis-related amyloidosis and, in patients
undergoing long term dialysis, the full-length and chemically unmodified β2m converts
into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily,
in common to other members of this family, experiences during its folding a long-lived
intermediate associated to the trans-to-cis isomerization of Pro-32 that has been
addressed as the precursor of the amyloid fibril formation. In this respect, previous
studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril
formation in mild aggregating condition, prompted us to reinvestigate the refolding
kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The
analysis, conducted at ambient temperature by the band selective flip angle short
transient real-time two-dimensional NMR techniques and probing the β2m states
every 15 s, revealed a more complex folding energy landscape than previously reported
for wild type β2m, involving more than a single intermediate species, and shedding
new light into the fibrillogenic pathway. Moreover, a significant difference in
the kinetic scheme previously characterized by optical spectroscopic methods was
discovered for the W60G β2m mutant.
article_processing_charge: No
article_type: original
author:
- first_name: Alessandra
full_name: Corazza, Alessandra
last_name: Corazza
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Maria Chiara
full_name: Mimmi, Maria Chiara
last_name: Mimmi
- first_name: Thomas
full_name: Cutuil, Thomas
last_name: Cutuil
- first_name: Sara
full_name: Raimondi, Sara
last_name: Raimondi
- first_name: Sofia
full_name: Giorgetti, Sofia
last_name: Giorgetti
- first_name: Federico
full_name: Fogolari, Federico
last_name: Fogolari
- first_name: Paolo
full_name: Viglino, Paolo
last_name: Viglino
- first_name: Lucio
full_name: Frydman, Lucio
last_name: Frydman
- first_name: Maayan
full_name: Gal, Maayan
last_name: Gal
- first_name: Vittorio
full_name: Bellotti, Vittorio
last_name: Bellotti
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
- first_name: Gennaro
full_name: Esposito, Gennaro
last_name: Esposito
citation:
ama: Corazza A, Rennella E, Schanda P, et al. Native-unlike long-lived intermediates
along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed
by real-time two-dimensional NMR. Journal of Biological Chemistry. 2010;285(8):5827-5835.
doi:10.1074/jbc.m109.061168
apa: Corazza, A., Rennella, E., Schanda, P., Mimmi, M. C., Cutuil, T., Raimondi,
S., … Esposito, G. (2010). Native-unlike long-lived intermediates along the folding
pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional
NMR. Journal of Biological Chemistry. American Society for Biochemistry
& Molecular Biology. https://doi.org/10.1074/jbc.m109.061168
chicago: Corazza, Alessandra, Enrico Rennella, Paul Schanda, Maria Chiara Mimmi,
Thomas Cutuil, Sara Raimondi, Sofia Giorgetti, et al. “Native-Unlike Long-Lived
Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin
Revealed by Real-Time Two-Dimensional NMR.” Journal of Biological Chemistry.
American Society for Biochemistry & Molecular Biology, 2010. https://doi.org/10.1074/jbc.m109.061168.
ieee: A. Corazza et al., “Native-unlike long-lived intermediates along the
folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time
two-dimensional NMR,” Journal of Biological Chemistry, vol. 285, no. 8.
American Society for Biochemistry & Molecular Biology, pp. 5827–5835, 2010.
ista: Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti
S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito
G. 2010. Native-unlike long-lived intermediates along the folding pathway of the
amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR.
Journal of Biological Chemistry. 285(8), 5827–5835.
mla: Corazza, Alessandra, et al. “Native-Unlike Long-Lived Intermediates along the
Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time
Two-Dimensional NMR.” Journal of Biological Chemistry, vol. 285, no. 8,
American Society for Biochemistry & Molecular Biology, 2010, pp. 5827–35,
doi:10.1074/jbc.m109.061168.
short: A. Corazza, E. Rennella, P. Schanda, M.C. Mimmi, T. Cutuil, S. Raimondi,
S. Giorgetti, F. Fogolari, P. Viglino, L. Frydman, M. Gal, V. Bellotti, B. Brutscher,
G. Esposito, Journal of Biological Chemistry 285 (2010) 5827–5835.
date_created: 2020-09-18T10:11:23Z
date_published: 2010-02-19T00:00:00Z
date_updated: 2021-01-12T08:19:31Z
day: '19'
doi: 10.1074/jbc.m109.061168
extern: '1'
intvolume: ' 285'
issue: '8'
keyword:
- Cell Biology
- Biochemistry
- Molecular Biology
language:
- iso: eng
month: '02'
oa_version: None
page: 5827-5835
publication: Journal of Biological Chemistry
publication_identifier:
issn:
- 0021-9258
- 1083-351X
publication_status: published
publisher: American Society for Biochemistry & Molecular Biology
quality_controlled: '1'
status: public
title: Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic
protein β2-Microglobulin revealed by real-time two-dimensional NMR
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 285
year: '2010'
...
---
_id: '8506'
article_processing_charge: No
author:
- first_name: Brian R.
full_name: Hunt, Brian R.
last_name: Hunt
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: 'Hunt BR, Kaloshin V. Prevalence. In: Handbook of Dynamical Systems.
Vol 3. Elsevier; 2010:43-87. doi:10.1016/s1874-575x(10)00310-3'
apa: Hunt, B. R., & Kaloshin, V. (2010). Prevalence. In Handbook of Dynamical
Systems (Vol. 3, pp. 43–87). Elsevier. https://doi.org/10.1016/s1874-575x(10)00310-3
chicago: Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” In Handbook of Dynamical
Systems, 3:43–87. Elsevier, 2010. https://doi.org/10.1016/s1874-575x(10)00310-3.
ieee: B. R. Hunt and V. Kaloshin, “Prevalence,” in Handbook of Dynamical Systems,
vol. 3, Elsevier, 2010, pp. 43–87.
ista: 'Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems.
vol. 3, 43–87.'
mla: Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” Handbook of Dynamical
Systems, vol. 3, Elsevier, 2010, pp. 43–87, doi:10.1016/s1874-575x(10)00310-3.
short: B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, Elsevier, 2010,
pp. 43–87.
date_created: 2020-09-18T10:47:48Z
date_published: 2010-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:45Z
day: '01'
doi: 10.1016/s1874-575x(10)00310-3
extern: '1'
intvolume: ' 3'
language:
- iso: eng
month: '01'
oa_version: None
page: 43-87
publication: Handbook of Dynamical Systems
publication_identifier:
isbn:
- '9780444531414'
issn:
- 1874-575X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Prevalence
type: book_chapter
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2010'
...
---
_id: '8507'
abstract:
- lang: eng
text: "We study a Cr nearly integrable Hamiltonian system defined on \U0001D54B3
× ℝ3. Let and µΣ1 be the restriction of Lebesgue measure on \U0001D54B3 × ℝ3
to ∑. We prove there is a perturbation , and an orbit (q(t), p(t)): ℝ → \U0001D54B3
× ℝ3 of the Hamiltonian equation such that ."
article_processing_charge: No
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: KE
full_name: ZHANG, KE
last_name: ZHANG
- first_name: YONG
full_name: ZHENG, YONG
last_name: ZHENG
citation:
ama: 'Kaloshin V, ZHANG K, ZHENG Y. Almost dense orbit on energy surface. In: XVIth
International Congress on Mathematical Physics. World Scientific; 2010:314-322.
doi:10.1142/9789814304634_0017'
apa: 'Kaloshin, V., ZHANG, K., & ZHENG, Y. (2010). Almost dense orbit on energy
surface. In XVIth International Congress on Mathematical Physics (pp. 314–322).
Prague, Czech Republic: World Scientific. https://doi.org/10.1142/9789814304634_0017'
chicago: Kaloshin, Vadim, KE ZHANG, and YONG ZHENG. “Almost Dense Orbit on Energy
Surface.” In XVIth International Congress on Mathematical Physics, 314–22.
World Scientific, 2010. https://doi.org/10.1142/9789814304634_0017.
ieee: V. Kaloshin, K. ZHANG, and Y. ZHENG, “Almost dense orbit on energy surface,”
in XVIth International Congress on Mathematical Physics, Prague, Czech
Republic, 2010, pp. 314–322.
ista: Kaloshin V, ZHANG K, ZHENG Y. 2010. Almost dense orbit on energy surface.
XVIth International Congress on Mathematical Physics. International Congress on
Mathematical Physics, 314–322.
mla: Kaloshin, Vadim, et al. “Almost Dense Orbit on Energy Surface.” XVIth International
Congress on Mathematical Physics, World Scientific, 2010, pp. 314–22, doi:10.1142/9789814304634_0017.
short: V. Kaloshin, K. ZHANG, Y. ZHENG, in:, XVIth International Congress on Mathematical
Physics, World Scientific, 2010, pp. 314–322.
conference:
end_date: 2009-08-08
location: Prague, Czech Republic
name: International Congress on Mathematical Physics
start_date: 2009-08-03
date_created: 2020-09-18T10:47:56Z
date_published: 2010-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:46Z
day: '01'
doi: 10.1142/9789814304634_0017
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
page: 314-322
publication: XVIth International Congress on Mathematical Physics
publication_identifier:
isbn:
- '9789814304627'
- '9789814304634'
publication_status: published
publisher: World Scientific
quality_controlled: '1'
status: public
title: Almost dense orbit on energy surface
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2010'
...
---
_id: '857'
abstract:
- lang: eng
text: 'The need to maintain the structural and functional integrity of an evolving
protein severely restricts the repertoire of acceptable amino-acid substitutions.
However, it is not known whether these restrictions impose a global limit on how
far homologous protein sequences can diverge from each other. Here we explore
the limits of protein evolution using sequence divergence data. We formulate a
computational approach to study the rate of divergence of distant protein sequences
and measure this rate for ancient proteins, those that were present in the last
universal common ancestor. We show that ancient proteins are still diverging from
each other, indicating an ongoing expansion of the protein sequence universe.
The slow rate of this divergence is imposed by the sparseness of functional protein
sequences in sequence space and the ruggedness of the protein fitness landscape:
98 per cent of sites cannot accept an amino-acid substitution at any given moment
but a vast majority of all sites may eventually be permitted to evolve when other,
compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach
the limit of divergent evolution of proteins, and for most proteins the limit
of sequence similarity imposed by common function may not exceed that of random
sequences.'
acknowledgement: |
We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space.
author:
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Povolotskaya I, Kondrashov F. Sequence space and the ongoing expansion of the
protein universe. Nature. 2010;465(7300):922-926. doi:10.1038/nature09105
apa: Povolotskaya, I., & Kondrashov, F. (2010). Sequence space and the ongoing
expansion of the protein universe. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09105
chicago: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing
Expansion of the Protein Universe.” Nature. Nature Publishing Group, 2010.
https://doi.org/10.1038/nature09105.
ieee: I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion
of the protein universe,” Nature, vol. 465, no. 7300. Nature Publishing
Group, pp. 922–926, 2010.
ista: Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion
of the protein universe. Nature. 465(7300), 922–926.
mla: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing
Expansion of the Protein Universe.” Nature, vol. 465, no. 7300, Nature
Publishing Group, 2010, pp. 922–26, doi:10.1038/nature09105.
short: I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.
date_created: 2018-12-11T11:48:52Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2021-01-12T08:20:05Z
day: '17'
doi: 10.1038/nature09105
extern: 1
intvolume: ' 465'
issue: '7300'
month: '06'
page: 922 - 926
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6791'
quality_controlled: 0
status: public
title: Sequence space and the ongoing expansion of the protein universe
type: journal_article
volume: 465
year: '2010'
...
---
_id: '862'
abstract:
- lang: eng
text: A long-standing controversy in evolutionary biology is whether or not evolving
lineages can cross valleys on the fitness landscape that correspond to low-fitness
genotypes, which can eventually enable them to reach isolated fitness peaks1-9.
Here we study the fitness landscapes traversed by switches between different AU
and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer
RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches
occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles
corresponding to GU and AC non-Watson-Crick intermediate states segregate within
human populations at low frequencies, similar to those of non-synonymous alleles.
Substitutions leading to a Watson-Crick switch are strongly correlated, especially
in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial
genome. Using these data we estimate that a typical Watson-Crick switch involves
crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC
intermediates being slightly more deleterious than GU intermediates. This compensatory
evolution must proceed through rare intermediate variants that never reach fixation.
The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs
and other molecules implies that simultaneous fixation of two alleles that are
individually deleterious may be a common phenomenon at the molecular level.
acknowledgement: We thank H. Innan, M. Laessig, R. Guigo, I. Povolotskaya, D. Ivankov
and M. Breen for thoughtful discussions and critical reading of the manuscript.
author:
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Yael
full_name: Artzy-Randrup, Yael
last_name: Artzy Randrup
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. Compensatory evolution
in mitochondrial tRNAs navigates valleys of low fitness. Nature. 2010;464(7286):279-282.
doi:10.1038/nature08691
apa: Meer, M., Kondrashov, A., Artzy Randrup, Y., & Kondrashov, F. (2010). Compensatory
evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature.
Nature Publishing Group. https://doi.org/10.1038/nature08691
chicago: Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov.
“Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.”
Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature08691.
ieee: M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory
evolution in mitochondrial tRNAs navigates valleys of low fitness,” Nature,
vol. 464, no. 7286. Nature Publishing Group, pp. 279–282, 2010.
ista: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution
in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.
mla: Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates
Valleys of Low Fitness.” Nature, vol. 464, no. 7286, Nature Publishing
Group, 2010, pp. 279–82, doi:10.1038/nature08691.
short: M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010)
279–282.
date_created: 2018-12-11T11:48:54Z
date_published: 2010-03-11T00:00:00Z
date_updated: 2021-01-12T08:20:20Z
day: '11'
doi: 10.1038/nature08691
extern: 1
intvolume: ' 464'
issue: '7286'
month: '03'
page: 279 - 282
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6784'
quality_controlled: 0
status: public
title: Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
type: journal_article
volume: 464
year: '2010'
...
---
_id: '872'
abstract:
- lang: eng
text: The rate of spontaneous mutation in natural populations is a fundamental parameter
for many evolutionary phenomena. Because the rate of mutation is generally low,
most of what is currently known about mutation has been obtained through indirect,
complex and imprecise methodological approaches. However, in the past few years
genome-wide sequencing of closely related individuals has made it possible to
estimate the rates of mutation directly at the level of the DNA, avoiding most
of the problems associated with using indirect methods. Here, we review the methods
used in the past with an emphasis on next generation sequencing, which may soon
make the accurate measurement of spontaneous mutation rates a matter of routine.
author:
- 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
citation:
ama: Kondrashov F, Kondrashov A. Measurements of spontaneous rates of mutations
in the recent past and the near future. Philosophical Transactions of the Royal
Society of London Series B, Biological Sciences. 2010;365(1544):1169-1176.
doi:10.1098/rstb.2009.0286
apa: Kondrashov, F., & Kondrashov, A. (2010). Measurements of spontaneous rates
of mutations in the recent past and the near future. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rstb.2009.0286
chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous
Rates of Mutations in the Recent Past and the near Future.” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The, 2010. https://doi.org/10.1098/rstb.2009.0286.
ieee: F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations
in the recent past and the near future,” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544.
Royal Society, The, pp. 1169–1176, 2010.
ista: Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations
in the recent past and the near future. Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences. 365(1544), 1169–1176.
mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates
of Mutations in the Recent Past and the near Future.” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences, vol. 365, no.
1544, Royal Society, The, 2010, pp. 1169–76, doi:10.1098/rstb.2009.0286.
short: F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society
of London. Series B, Biological Sciences 365 (2010) 1169–1176.
date_created: 2018-12-11T11:48:57Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2021-01-12T08:20:43Z
day: '27'
doi: 10.1098/rstb.2009.0286
extern: 1
intvolume: ' 365'
issue: '1544'
month: '04'
page: 1169 - 1176
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6772'
quality_controlled: 0
status: public
title: Measurements of spontaneous rates of mutations in the recent past and the near
future
type: journal_article
volume: 365
year: '2010'
...
---
_id: '884'
abstract:
- lang: eng
text: 'Background: Divergence of two independently evolving sequences that originated
from a common ancestor can be described by two parameters, the asymptotic level
of divergence E and the rate r at which this level of divergence is approached.
Constant negative selection impedes allele replacements and, therefore, is routinely
assumed to decelerate sequence divergence. However, its impact on E and on r has
not been formally investigated.Results: Strong selection that favors only one
allele can make E arbitrarily small and r arbitrarily large. In contrast, in the
case of 4 possible alleles and equal mutation rates, the lowest value of r, attained
when two alleles confer equal fitnesses and the other two are strongly deleterious,
is only two times lower than its value under selective neutrality.Conclusions:
Constant selection can strongly constrain the level of sequence divergence, but
cannot reduce substantially the rate at which this level is approached. In particular,
under any constant selection the divergence of sequences that accumulated one
substitution per neutral site since their origin from the common ancestor must
already constitute at least one half of the asymptotic divergence at sites under
such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei
Maslov, and Nick Grishin.'
author:
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. Rate of sequence divergence
under constant selection. Biology Direct. 2010;5. doi:10.1186/1745-6150-5-5
apa: Kondrashov, A., Povolotskaya, I., Ivankov, D., & Kondrashov, F. (2010).
Rate of sequence divergence under constant selection. Biology Direct. BioMed
Central. https://doi.org/10.1186/1745-6150-5-5
chicago: Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov.
“Rate of Sequence Divergence under Constant Selection.” Biology Direct.
BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-5.
ieee: A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence
divergence under constant selection,” Biology Direct, vol. 5. BioMed Central,
2010.
ista: Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence
divergence under constant selection. Biology Direct. 5.
mla: Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.”
Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-5.
short: A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct
5 (2010).
date_created: 2018-12-11T11:49:00Z
date_published: 2010-01-21T00:00:00Z
date_updated: 2021-01-12T08:21:15Z
day: '21'
doi: 10.1186/1745-6150-5-5
extern: 1
intvolume: ' 5'
month: '01'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6762'
quality_controlled: 0
status: public
title: Rate of sequence divergence under constant selection
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: '2010'
...
---
_id: '89'
abstract:
- lang: eng
text: We demonstrate the operation of a device that can produce chitosan nanoparticles
in a tunable size range from 50-300 nm with small size dispersion. A piezoelectric
oscillator operated at megahertz frequencies is used to aerosolize a solution
containing dissolved chitosan. The solvent is then evaporated from the aerosolized
droplets in a heat pipe, leaving monodisperse nanoparticles to be collected. The
nanoparticle size is controlled both by the concentration of the dissolved polymer
and by the size of the aerosol droplets that are created. Our device can be used
with any polymer or polymer/therapeutic combination that can be prepared in a
homogeneous solution and vaporized.
acknowledgement: This work was supported by the National Science Foundation under
Grants PHY-0456898 and PHY-0757989, and acknowledgment is made to the Donors of
the Petroleum Research Fund administered by the American Chemical Society for partial
support of this research.
author:
- first_name: Ian
full_name: Wright, Ian
last_name: Wright
- first_name: Andrew P
full_name: Higginbotham, Andrew P
id: 4AD6785A-F248-11E8-B48F-1D18A9856A87
last_name: Higginbotham
orcid: 0000-0003-2607-2363
- first_name: Shenda
full_name: Baker, Shenda
last_name: Baker
- first_name: Tom
full_name: Donnelly, Tom
last_name: Donnelly
citation:
ama: Wright I, Higginbotham AP, Baker S, Donnelly T. Generation of nanoparticles
of controlled size using ultrasonic piezoelectric oscillators in solution. ACS
Applied Materials and Interfaces. 2010;2(8):2360-2364. doi:10.1021/am100375w
apa: Wright, I., Higginbotham, A. P., Baker, S., & Donnelly, T. (2010). Generation
of nanoparticles of controlled size using ultrasonic piezoelectric oscillators
in solution. ACS Applied Materials and Interfaces. American Chemical Society.
https://doi.org/10.1021/am100375w
chicago: Wright, Ian, Andrew P Higginbotham, Shenda Baker, and Tom Donnelly. “Generation
of Nanoparticles of Controlled Size Using Ultrasonic Piezoelectric Oscillators
in Solution.” ACS Applied Materials and Interfaces. American Chemical Society,
2010. https://doi.org/10.1021/am100375w.
ieee: I. Wright, A. P. Higginbotham, S. Baker, and T. Donnelly, “Generation of nanoparticles
of controlled size using ultrasonic piezoelectric oscillators in solution,” ACS
Applied Materials and Interfaces, vol. 2, no. 8. American Chemical Society,
pp. 2360–2364, 2010.
ista: Wright I, Higginbotham AP, Baker S, Donnelly T. 2010. Generation of nanoparticles
of controlled size using ultrasonic piezoelectric oscillators in solution. ACS
Applied Materials and Interfaces. 2(8), 2360–2364.
mla: Wright, Ian, et al. “Generation of Nanoparticles of Controlled Size Using Ultrasonic
Piezoelectric Oscillators in Solution.” ACS Applied Materials and Interfaces,
vol. 2, no. 8, American Chemical Society, 2010, pp. 2360–64, doi:10.1021/am100375w.
short: I. Wright, A.P. Higginbotham, S. Baker, T. Donnelly, ACS Applied Materials
and Interfaces 2 (2010) 2360–2364.
date_created: 2018-12-11T11:44:34Z
date_published: 2010-07-20T00:00:00Z
date_updated: 2021-01-12T08:21:17Z
day: '20'
doi: 10.1021/am100375w
extern: '1'
external_id:
pmid:
- ' 20735108'
intvolume: ' 2'
issue: '8'
language:
- iso: eng
month: '07'
oa_version: None
page: 2360 - 2364
pmid: 1
publication: ACS Applied Materials and Interfaces
publication_status: published
publisher: American Chemical Society
publist_id: '7965'
quality_controlled: '1'
status: public
title: Generation of nanoparticles of controlled size using ultrasonic piezoelectric
oscillators in solution
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 2
year: '2010'
...
---
_id: '891'
abstract:
- lang: eng
text: Gene duplications and their subsequent divergence play an important part in
the evolution of novel gene functions. Several models for the emergence, maintenance
and evolution of gene copies have been proposed. However, a clear consensus on
how gene duplications are fixed and maintained in genomes is lacking. Here, we
present a comprehensive classification of the models that are relevant to all
stages of the evolution of gene duplications. Each model predicts a unique combination
of evolutionary dynamics and functional properties. Setting out these predictions
is an important step towards identifying the main mechanisms that are involved
in the evolution of gene duplications.
acknowledgement: |
We thank M. Lynch for insightful comments on the manuscript.
author:
- first_name: Hideki
full_name: Innan, Hideki
last_name: Innan
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Innan H, Kondrashov F. The evolution of gene duplications: Classifying and
distinguishing between models. Nature Reviews Genetics. 2010;11(2):97-108.
doi:10.1038/nrg2689'
apa: 'Innan, H., & Kondrashov, F. (2010). The evolution of gene duplications:
Classifying and distinguishing between models. Nature Reviews Genetics.
Nature Publishing Group. https://doi.org/10.1038/nrg2689'
chicago: 'Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications:
Classifying and Distinguishing between Models.” Nature Reviews Genetics.
Nature Publishing Group, 2010. https://doi.org/10.1038/nrg2689.'
ieee: 'H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying
and distinguishing between models,” Nature Reviews Genetics, vol. 11, no.
2. Nature Publishing Group, pp. 97–108, 2010.'
ista: 'Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying
and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.'
mla: 'Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications:
Classifying and Distinguishing between Models.” Nature Reviews Genetics,
vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:10.1038/nrg2689.'
short: H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.
date_created: 2018-12-11T11:49:03Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2021-01-12T08:21:19Z
day: '01'
doi: 10.1038/nrg2689
extern: 1
intvolume: ' 11'
issue: '2'
month: '02'
page: 97 - 108
publication: Nature Reviews Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6755'
quality_controlled: 0
status: public
title: 'The evolution of gene duplications: Classifying and distinguishing between
models'
type: journal_article
volume: 11
year: '2010'
...
---
_id: '901'
abstract:
- lang: eng
text: 'Background: Surveying deleterious variation in human populations is crucial
for our understanding, diagnosis and potential treatment of human genetic pathologies.
A number of recent genome-wide analyses focused on the prevalence of segregating
deleterious alleles in the nuclear genome. However, such studies have not been
conducted for the mitochondrial genome.Results: We present a systematic survey
of polymorphisms in the human mitochondrial genome, including those predicted
to be deleterious and those that correspond to known pathogenic mutations. Analyzing
4458 completely sequenced mitochondrial genomes we characterize the genetic diversity
of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes)
and non-African (M and N haplotypes) populations. We find that the overall level
of polymorphism is higher in the mitochondrial compared to the nuclear genome,
although the mitochondrial genome appears to be under stronger selection as indicated
by proportionally fewer nonsynonymous than synonymous substitutions. The African
mitochondrial genomes show higher heterozygosity, a greater number of polymorphic
sites and higher frequencies of polymorphisms for synonymous, benign and damaging
polymorphism than non-African genomes. However, African genomes carry significantly
fewer SNPs that have been previously characterized as pathogenic compared to non-African
genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category
of polymorphisms that are more abundant in non-African genomes is best explained
by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms
segregating in non-African populations. This further suggests that, contrary to
the common disease-common variant hypothesis, pathogenic mutations are largely
population-specific and different SNPs may be associated with the same disease
in different populations. Therefore, to obtain a comprehensive picture of the
deleterious variability in the human population, as well as to improve the diagnostics
of individuals carrying African mitochondrial haplotypes, it is necessary to survey
different populations independently.Reviewers: This article was reviewed by Dr
Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David
Rand (nominated by Dr Laurence Hurst).'
acknowledgement: We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance
with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science
and Innovation, Plan Nacional Program grant BFU2009-09271 for funding.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific.
Biology Direct. 2010;5. doi:10.1186/1745-6150-5-68
apa: Breen, M., & Kondrashov, F. (2010). Mitochondrial pathogenic mutations
are population-specific. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-5-68
chicago: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations
Are Population-Specific.” Biology Direct. BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-68.
ieee: M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,”
Biology Direct, vol. 5. BioMed Central, 2010.
ista: Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific.
Biology Direct. 5.
mla: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations
Are Population-Specific.” Biology Direct, vol. 5, BioMed Central, 2010,
doi:10.1186/1745-6150-5-68.
short: M. Breen, F. Kondrashov, Biology Direct 5 (2010).
date_created: 2018-12-11T11:49:06Z
date_published: 2010-12-31T00:00:00Z
date_updated: 2021-01-12T08:21:46Z
day: '31'
doi: 10.1186/1745-6150-5-68
extern: 1
intvolume: ' 5'
month: '12'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6749'
quality_controlled: 0
status: public
title: Mitochondrial pathogenic mutations are population-specific
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: '2010'
...
---
_id: '9012'
abstract:
- lang: eng
text: In this Letter, we characterize experimentally the diffusiophoretic motion
of colloids and λ-DNA toward higher concentration of solutes, using microfluidic
technology to build spatially and temporally controlled concentration gradients.
We then demonstrate that segregation and spatial patterning of the particles can
be achieved from temporal variations of the solute concentration profile. This
segregation takes the form of a strong trapping potential, stemming from an osmotically
induced rectification mechanism of the solute time-dependent variations. Depending
on the spatial and temporal symmetry of the solute signal, localization patterns
with various shapes can be achieved. These results highlight the role of solute
contrasts in out-of-equilibrium processes occurring in soft matter.
article_number: '138302'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Benjamin
full_name: Abécassis, Benjamin
last_name: Abécassis
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: Christophe
full_name: Ybert, Christophe
last_name: Ybert
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
citation:
ama: Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility
and pattern formation under rectified diffusiophoresis. Physical Review Letters.
2010;104(13). doi:10.1103/physrevlett.104.138302
apa: Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., & Bocquet,
L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.104.138302
chicago: Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe
Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified
Diffusiophoresis.” Physical Review Letters. American Physical Society,
2010. https://doi.org/10.1103/physrevlett.104.138302.
ieee: J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet,
“Colloidal motility and pattern formation under rectified diffusiophoresis,” Physical
Review Letters, vol. 104, no. 13. American Physical Society, 2010.
ista: Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal
motility and pattern formation under rectified diffusiophoresis. Physical Review
Letters. 104(13), 138302.
mla: Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under
Rectified Diffusiophoresis.” Physical Review Letters, vol. 104, no. 13,
138302, American Physical Society, 2010, doi:10.1103/physrevlett.104.138302.
short: J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical
Review Letters 104 (2010).
date_created: 2021-01-19T10:25:04Z
date_published: 2010-04-02T00:00:00Z
date_updated: 2023-02-23T13:46:40Z
day: '02'
doi: 10.1103/physrevlett.104.138302
extern: '1'
external_id:
arxiv:
- '1004.1256 '
pmid:
- '20481918'
intvolume: ' 104'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.1256
month: '04'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Colloidal motility and pattern formation under rectified diffusiophoresis
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 104
year: '2010'
...
---
_id: '9013'
abstract:
- lang: eng
text: In this Letter, we investigate experimentally the nonequilibrium steady state
of an active colloidal suspension under gravity field. The active particles are
made of chemically powered colloids, showing self propulsion in the presence of
an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated
microfluidic device, made of permeable gel microstructures. Both the microdynamics
of individual colloids and the global stationary state of the suspension under
gravity are measured with optical microscopy. This yields a direct measurement
of the effective temperature of the active system as a function of the particle
activity, on the basis of the fluctuation-dissipation relationship. Our work is
a first step in the experimental exploration of the out-of-equilibrium properties
of active colloidal systems.
article_number: '088304'
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Cécile
full_name: Cottin-Bizonne, Cécile
last_name: Cottin-Bizonne
- first_name: Christophe
full_name: Ybert, Christophe
last_name: Ybert
- first_name: Lydéric
full_name: Bocquet, Lydéric
last_name: Bocquet
citation:
ama: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Sedimentation and effective
temperature of active colloidal suspensions. Physical Review Letters. 2010;105(8).
doi:10.1103/physrevlett.105.088304
apa: Palacci, J. A., Cottin-Bizonne, C., Ybert, C., & Bocquet, L. (2010). Sedimentation
and effective temperature of active colloidal suspensions. Physical Review
Letters. American Physical Society . https://doi.org/10.1103/physrevlett.105.088304
chicago: Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric
Bocquet. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.”
Physical Review Letters. American Physical Society , 2010. https://doi.org/10.1103/physrevlett.105.088304.
ieee: J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Sedimentation
and effective temperature of active colloidal suspensions,” Physical Review
Letters, vol. 105, no. 8. American Physical Society , 2010.
ista: Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Sedimentation and
effective temperature of active colloidal suspensions. Physical Review Letters.
105(8), 088304.
mla: Palacci, Jérémie A., et al. “Sedimentation and Effective Temperature of Active
Colloidal Suspensions.” Physical Review Letters, vol. 105, no. 8, 088304,
American Physical Society , 2010, doi:10.1103/physrevlett.105.088304.
short: J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters
105 (2010).
date_created: 2021-01-19T10:26:33Z
date_published: 2010-08-20T00:00:00Z
date_updated: 2023-02-23T13:46:42Z
day: '20'
doi: 10.1103/physrevlett.105.088304
extern: '1'
external_id:
arxiv:
- '1004.4340'
pmid:
- '20868136'
intvolume: ' 105'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1004.4340
month: '08'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- '10797114'
issn:
- '00319007'
publication_status: published
publisher: 'American Physical Society '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sedimentation and effective temperature of active colloidal suspensions
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 105
year: '2010'
...
---
_id: '9145'
abstract:
- lang: eng
text: "We have found a new way to express the solutions of the RSM (Reynolds Stress
Model) equations that allows us to present the turbulent diffusivities for heat,
salt and momentum in a way that is considerably simpler and thus easier to implement
than in previous work. The RSM provides the dimensionless mixing efficiencies
Γα (α stands for heat, salt and momentum). However, to compute the diffusivities,
one needs additional information, specifically, the dissipation ε. Since a dynamic
equation for the latter that includes the physical processes relevant to the ocean
is still not available, one must resort to different sources of information outside
the RSM to obtain a complete Mixing Scheme usable in OGCMs.\r\nAs for the RSM
results, we show that the Γα’s are functions of both Ri and Rρ (Richardson number
and density ratio representing double diffusion, DD); the Γα are different for
heat, salt and momentum; in the case of heat, the traditional value Γh = 0.2 is
valid only in the presence of strong shear (when DD is inoperative) while when
shear subsides, NATRE data show that Γh can be three times as large, a result
that we reproduce. The salt Γs is given in terms of Γh. The momentum Γm has thus
far been guessed with different prescriptions while the RSM provides a well defined
expression for Γm(Ri, Rρ). Having tested Γh, we then test the momentum Γm by showing
that the turbulent Prandtl number Γm/Γh vs. Ri reproduces the available data quite
well.\r\n\r\nAs for the dissipation ε, we use different representations, one for
the mixed layer (ML), one for the thermocline and one for the ocean’s bottom.
For the ML, we adopt a procedure analogous to the one successfully used in PB
(planetary boundary layer) studies; for the thermocline, we employ an expression
for the variable εN−2 from studies of the internal gravity waves spectra which
includes a latitude dependence; for the ocean bottom, we adopt the enhanced bottom
diffusivity expression used by previous authors but with a state of the art internal
tidal energy formulation and replace the fixed Γα = 0.2 with the RSM result that
brings into the problem the Ri, Rρ dependence of the Γα; the unresolved bottom
drag, which has thus far been either ignored or modeled with heuristic relations,
is modeled using a formalism we previously developed and tested in PBL studies.\r\nWe
carried out several tests without an OGCM. Prandtl and flux Richardson numbers
vs. Ri. The RSM model reproduces both types of data satisfactorily. DD and Mixing
efficiency Γh(Ri, Rρ). The RSM model reproduces well the NATRE data. Bimodal ε-distribution.
NATRE data show that ε(Ri < 1) ≈ 10ε(Ri > 1), which our model reproduces. Heat
to salt flux ratio. In the Ri ≫ 1 regime, the RSM predictions reproduce the data
satisfactorily. NATRE mass diffusivity. The z-profile of the mass diffusivity
reproduces well the measurements at NATRE. The local form of the mixing scheme
is algebraic with one cubic equation to solve."
article_processing_charge: No
article_type: original
author:
- first_name: V.M.
full_name: Canuto, V.M.
last_name: Canuto
- first_name: A.M.
full_name: Howard, A.M.
last_name: Howard
- first_name: Y.
full_name: Cheng, Y.
last_name: Cheng
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
- first_name: A.
full_name: Leboissetier, A.
last_name: Leboissetier
- first_name: S.R.
full_name: Jayne, S.R.
last_name: Jayne
citation:
ama: 'Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. Ocean
turbulence, III: New GISS vertical mixing scheme. Ocean Modelling. 2010;34(3-4):70-91.
doi:10.1016/j.ocemod.2010.04.006'
apa: 'Canuto, V. M., Howard, A. M., Cheng, Y., Muller, C. J., Leboissetier, A.,
& Jayne, S. R. (2010). Ocean turbulence, III: New GISS vertical mixing scheme.
Ocean Modelling. Elsevier. https://doi.org/10.1016/j.ocemod.2010.04.006'
chicago: 'Canuto, V.M., A.M. Howard, Y. Cheng, Caroline J Muller, A. Leboissetier,
and S.R. Jayne. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.” Ocean
Modelling. Elsevier, 2010. https://doi.org/10.1016/j.ocemod.2010.04.006.'
ieee: 'V. M. Canuto, A. M. Howard, Y. Cheng, C. J. Muller, A. Leboissetier, and
S. R. Jayne, “Ocean turbulence, III: New GISS vertical mixing scheme,” Ocean
Modelling, vol. 34, no. 3–4. Elsevier, pp. 70–91, 2010.'
ista: 'Canuto VM, Howard AM, Cheng Y, Muller CJ, Leboissetier A, Jayne SR. 2010.
Ocean turbulence, III: New GISS vertical mixing scheme. Ocean Modelling. 34(3–4),
70–91.'
mla: 'Canuto, V. M., et al. “Ocean Turbulence, III: New GISS Vertical Mixing Scheme.”
Ocean Modelling, vol. 34, no. 3–4, Elsevier, 2010, pp. 70–91, doi:10.1016/j.ocemod.2010.04.006.'
short: V.M. Canuto, A.M. Howard, Y. Cheng, C.J. Muller, A. Leboissetier, S.R. Jayne,
Ocean Modelling 34 (2010) 70–91.
date_created: 2021-02-15T14:40:19Z
date_published: 2010-05-12T00:00:00Z
date_updated: 2022-01-24T13:51:35Z
day: '12'
doi: 10.1016/j.ocemod.2010.04.006
extern: '1'
intvolume: ' 34'
issue: 3-4
keyword:
- Computer Science (miscellaneous)
- Geotechnical Engineering and Engineering Geology
- Atmospheric Science
- Oceanography
language:
- iso: eng
month: '05'
oa_version: None
page: 70-91
publication: Ocean Modelling
publication_identifier:
issn:
- 1463-5003
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: 'Ocean turbulence, III: New GISS vertical mixing scheme'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 34
year: '2010'
...
---
_id: '9146'
abstract:
- lang: eng
text: "The factors governing the rate of change in the amount of atmospheric water
vapor are analyzed in simulations of climate change. The global-mean amount of
water vapor is estimated to increase at a differential rate of 7.3% K − 1 with
respect to global-mean surface air temperature in the multi-model mean. Larger
rates of change result if the fractional change is evaluated over a finite change
in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean
column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron
scaling is directly evaluated using an invariant distribution of monthly-mean
relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There
are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor
in the tropics and mid-latitudes, but they largely cancel in the global mean.
A purely thermodynamic scaling based on a saturated troposphere gives a higher
global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of
5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface
specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there
are widespread decreases in surface relative humidity over land (by more than
1% K − 1 in many regions), and it is argued that decreases of this magnitude could
result from the land/ocean contrast in surface warming."
article_number: '025207'
article_processing_charge: No
article_type: original
author:
- first_name: P A
full_name: O’Gorman, P A
last_name: O’Gorman
- first_name: Caroline J
full_name: Muller, Caroline J
id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b
last_name: Muller
orcid: 0000-0001-5836-5350
citation:
ama: O’Gorman PA, Muller CJ. How closely do changes in surface and column water
vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental
Research Letters. 2010;5(2). doi:10.1088/1748-9326/5/2/025207
apa: O’Gorman, P. A., & Muller, C. J. (2010). How closely do changes in surface
and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?
Environmental Research Letters. IOP Publishing. https://doi.org/10.1088/1748-9326/5/2/025207
chicago: O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface
and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?”
Environmental Research Letters. IOP Publishing, 2010. https://doi.org/10.1088/1748-9326/5/2/025207.
ieee: P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column
water vapor follow Clausius–Clapeyron scaling in climate change simulations?,”
Environmental Research Letters, vol. 5, no. 2. IOP Publishing, 2010.
ista: O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column
water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental
Research Letters. 5(2), 025207.
mla: O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface
and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?”
Environmental Research Letters, vol. 5, no. 2, 025207, IOP Publishing,
2010, doi:10.1088/1748-9326/5/2/025207.
short: P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).
date_created: 2021-02-15T14:40:46Z
date_published: 2010-04-09T00:00:00Z
date_updated: 2022-01-24T13:51:02Z
day: '09'
doi: 10.1088/1748-9326/5/2/025207
extern: '1'
intvolume: ' 5'
issue: '2'
keyword:
- Renewable Energy
- Sustainability and the Environment
- Public Health
- Environmental and Occupational Health
- General Environmental Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1088/1748-9326/5/2/025207
month: '04'
oa: 1
oa_version: Published Version
publication: Environmental Research Letters
publication_identifier:
issn:
- 1748-9326
publication_status: published
publisher: IOP Publishing
quality_controlled: '1'
status: public
title: How closely do changes in surface and column water vapor follow Clausius–Clapeyron
scaling in climate change simulations?
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2010'
...