---
_id: '12203'
abstract:
- lang: eng
text: 'Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis
of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide
biosynthesis. Here we reported for the first time the cloning of a new full-length
cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length
cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained
a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis
showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal,
which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed
that GbGGPPS was a member of polyprenyltransferases with two highly conserved
aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated
that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm
GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.'
acknowledgement: This study was financially supported by China National High-Tech
“863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences,
Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic
tree.
article_processing_charge: No
article_type: original
author:
- first_name: Zhihua
full_name: Liao, Zhihua
last_name: Liao
- first_name: Min
full_name: Chen, Min
last_name: Chen
- first_name: Yifu
full_name: Gong, Yifu
last_name: Gong
- first_name: Liang
full_name: Guo, Liang
last_name: Guo
- first_name: Qiumin
full_name: Tan, Qiumin
last_name: Tan
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xiaofen
full_name: Sun, Xiaofen
last_name: Sun
- first_name: Feng
full_name: Tan, Feng
last_name: Tan
- first_name: Kexuan
full_name: Tang, Kexuan
last_name: Tang
citation:
ama: Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene
from Ginkgo biloba, which intermediates the biosynthesis of the key precursor
for ginkgolides. DNA Sequence. 2004;15(2):153-158. doi:10.1080/10425170410001667348
apa: Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004).
A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides. DNA Sequence. Informa
UK Limited. https://doi.org/10.1080/10425170410001667348
chicago: Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng,
Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase
Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor
for Ginkgolides.” DNA Sequence. Informa UK Limited, 2004. https://doi.org/10.1080/10425170410001667348.
ieee: Z. Liao et al., “A new geranylgeranyl Diphosphate synthase gene from
Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,”
DNA Sequence, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.
ista: Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004.
A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.
mla: Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo
Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.”
DNA Sequence, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:10.1080/10425170410001667348.
short: Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang,
DNA Sequence 15 (2004) 153–158.
date_created: 2023-01-16T09:24:50Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-05-08T10:58:29Z
department:
- _id: XiFe
doi: 10.1080/10425170410001667348
extern: '1'
external_id:
pmid:
- '15352294'
intvolume: ' 15'
issue: '2'
keyword:
- Endocrinology
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
oa_version: None
page: 153-158
pmid: 1
publication: DNA Sequence
publication_identifier:
issn:
- 1042-5179
publication_status: published
publisher: Informa UK Limited
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2004'
...
---
_id: '12658'
abstract:
- lang: eng
text: '[1] During the ablation period 2001 a glaciometeorological experiment was
carried out on Haut Glacier d''Arolla, Switzerland. Five meteorological stations
were installed on the glacier, and one permanent automatic weather station in
the glacier foreland. The altitudes of the stations ranged between 2500 and 3000
m a.s.l., and they were in operation from end of May to beginning of September
2001. The spatial arrangement of the stations and temporal duration of the measurements
generated a unique data set enabling the analysis of the spatial and temporal
variability of the meteorological variables across an alpine glacier. All measurements
were taken at a nominal height of 2 m, and hourly averages were derived for the
analysis. The wind regime was dominated by the glacier wind (mean value 2.8 m
s−1) but due to erosion by the synoptic gradient wind, occasionally the wind would
blow up the valley. A slight decrease in mean 2 m air temperatures with altitude
was found, however the 2 m air temperature gradient varied greatly and frequently
changed its sign. Mean relative humidity was 71% and exhibited limited spatial
variation. Mean incoming shortwave radiation and albedo both generally increased
with elevation. The different components of shortwave radiation are quantified
with a parameterization scheme. Resulting spatial variations are mainly due to
horizon obstruction and reflections from surrounding slopes, i.e., topography.
The effect of clouds accounts for a loss of 30% of the extraterrestrial flux.
Albedos derived from a Landsat TM image of 30 July show remarkably constant values,
in the range 0.49 to 0.50, across snow covered parts of the glacier, while albedo
is highly spatially variable below the zone of continuous snow cover. These results
are verified with ground measurements and compared with parameterized albedo.
Mean longwave radiative fluxes decreased with elevation due to lower air temperatures
and the effect of upper hemisphere slopes. It is shown through parameterization
that this effect would even be more pronounced without the effect of clouds. Results
are discussed with respect to a similar study which has been carried out on Pasterze
Glacier (Austria). The presented algorithms for interpolating, parameterizing
and simulating variables and parameters in alpine regions are integrated in the
software package AMUNDSEN which is freely available to be adapted and further
developed by the community.'
article_number: D03103
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Strasser, Ulrich
last_name: Strasser
- first_name: Javier
full_name: Corripio, Javier
last_name: Corripio
- first_name: Francesca
full_name: Pellicciotti, Francesca
id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70
last_name: Pellicciotti
- first_name: Paolo
full_name: Burlando, Paolo
last_name: Burlando
- first_name: Ben
full_name: Brock, Ben
last_name: Brock
- first_name: Martin
full_name: Funk, Martin
last_name: Funk
citation:
ama: 'Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. Spatial
and temporal variability of meteorological variables at Haut Glacier d’Arolla
(Switzerland) during the ablation season 2001: Measurements and simulations. Journal
of Geophysical Research: Atmospheres. 2004;109(D3). doi:10.1029/2003jd003973'
apa: 'Strasser, U., Corripio, J., Pellicciotti, F., Burlando, P., Brock, B., &
Funk, M. (2004). Spatial and temporal variability of meteorological variables
at Haut Glacier d’Arolla (Switzerland) during the ablation season 2001: Measurements
and simulations. Journal of Geophysical Research: Atmospheres. American
Geophysical Union. https://doi.org/10.1029/2003jd003973'
chicago: 'Strasser, Ulrich, Javier Corripio, Francesca Pellicciotti, Paolo Burlando,
Ben Brock, and Martin Funk. “Spatial and Temporal Variability of Meteorological
Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001:
Measurements and Simulations.” Journal of Geophysical Research: Atmospheres.
American Geophysical Union, 2004. https://doi.org/10.1029/2003jd003973.'
ieee: 'U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, and M.
Funk, “Spatial and temporal variability of meteorological variables at Haut Glacier
d’Arolla (Switzerland) during the ablation season 2001: Measurements and simulations,”
Journal of Geophysical Research: Atmospheres, vol. 109, no. D3. American
Geophysical Union, 2004.'
ista: 'Strasser U, Corripio J, Pellicciotti F, Burlando P, Brock B, Funk M. 2004.
Spatial and temporal variability of meteorological variables at Haut Glacier d’Arolla
(Switzerland) during the ablation season 2001: Measurements and simulations. Journal
of Geophysical Research: Atmospheres. 109(D3), D03103.'
mla: 'Strasser, Ulrich, et al. “Spatial and Temporal Variability of Meteorological
Variables at Haut Glacier d’Arolla (Switzerland) during the Ablation Season 2001:
Measurements and Simulations.” Journal of Geophysical Research: Atmospheres,
vol. 109, no. D3, D03103, American Geophysical Union, 2004, doi:10.1029/2003jd003973.'
short: 'U. Strasser, J. Corripio, F. Pellicciotti, P. Burlando, B. Brock, M. Funk,
Journal of Geophysical Research: Atmospheres 109 (2004).'
date_created: 2023-02-20T08:18:57Z
date_published: 2004-02-16T00:00:00Z
date_updated: 2023-02-20T08:40:21Z
day: '16'
doi: 10.1029/2003jd003973
extern: '1'
intvolume: ' 109'
issue: D3
keyword:
- Paleontology
- Space and Planetary Science
- Earth and Planetary Sciences (miscellaneous)
- Atmospheric Science
- Earth-Surface Processes
- Geochemistry and Petrology
- Soil Science
- Water Science and Technology
- Ecology
- Aquatic Science
- Forestry
- Oceanography
- Geophysics
language:
- iso: eng
month: '02'
oa_version: None
publication: 'Journal of Geophysical Research: Atmospheres'
publication_identifier:
issn:
- 0148-0227
publication_status: published
publisher: American Geophysical Union
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Spatial and temporal variability of meteorological variables at Haut Glacier
d''Arolla (Switzerland) during the ablation season 2001: Measurements and simulations'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 109
year: '2004'
...
---
_id: '8517'
abstract:
- lang: eng
text: We consider the evolution of a connected set on the plane carried by a space
periodic incompressible stochastic flow. While for almost every realization of
the stochastic flow at time t most of the particles are at a distance of order
equation image away from the origin, there is a measure zero set of points that
escape to infinity at the linear rate. We study the set of points visited by the
original set by time t and show that such a set, when scaled down by the factor
of t, has a limiting nonrandom shape.
article_processing_charge: No
article_type: original
author:
- first_name: Dmitry
full_name: Dolgopyat, Dmitry
last_name: Dolgopyat
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Leonid
full_name: Koralov, Leonid
last_name: Koralov
citation:
ama: Dolgopyat D, Kaloshin V, Koralov L. A limit shape theorem for periodic stochastic
dispersion. Communications on Pure and Applied Mathematics. 2004;57(9):1127-1158.
doi:10.1002/cpa.20032
apa: Dolgopyat, D., Kaloshin, V., & Koralov, L. (2004). A limit shape theorem
for periodic stochastic dispersion. Communications on Pure and Applied Mathematics.
Wiley. https://doi.org/10.1002/cpa.20032
chicago: Dolgopyat, Dmitry, Vadim Kaloshin, and Leonid Koralov. “A Limit Shape Theorem
for Periodic Stochastic Dispersion.” Communications on Pure and Applied Mathematics.
Wiley, 2004. https://doi.org/10.1002/cpa.20032.
ieee: D. Dolgopyat, V. Kaloshin, and L. Koralov, “A limit shape theorem for periodic
stochastic dispersion,” Communications on Pure and Applied Mathematics,
vol. 57, no. 9. Wiley, pp. 1127–1158, 2004.
ista: Dolgopyat D, Kaloshin V, Koralov L. 2004. A limit shape theorem for periodic
stochastic dispersion. Communications on Pure and Applied Mathematics. 57(9),
1127–1158.
mla: Dolgopyat, Dmitry, et al. “A Limit Shape Theorem for Periodic Stochastic Dispersion.”
Communications on Pure and Applied Mathematics, vol. 57, no. 9, Wiley,
2004, pp. 1127–58, doi:10.1002/cpa.20032.
short: D. Dolgopyat, V. Kaloshin, L. Koralov, Communications on Pure and Applied
Mathematics 57 (2004) 1127–1158.
date_created: 2020-09-18T10:49:12Z
date_published: 2004-09-01T00:00:00Z
date_updated: 2021-01-12T08:19:50Z
day: '01'
doi: 10.1002/cpa.20032
extern: '1'
intvolume: ' 57'
issue: '9'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '09'
oa_version: None
page: 1127-1158
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- 0010-3640
- 1097-0312
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: A limit shape theorem for periodic stochastic dispersion
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 57
year: '2004'
...
---
_id: '8518'
article_processing_charge: No
article_type: original
author:
- first_name: Leonid
full_name: Koralov, Leonid
last_name: Koralov
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Dmitry
full_name: Dolgopyat, Dmitry
last_name: Dolgopyat
citation:
ama: Koralov L, Kaloshin V, Dolgopyat D. Sample path properties of the stochastic
flows. The Annals of Probability. 2004;32(1A):1-27. doi:10.1214/aop/1078415827
apa: Koralov, L., Kaloshin, V., & Dolgopyat, D. (2004). Sample path properties
of the stochastic flows. The Annals of Probability. Institute of Mathematical
Statistics. https://doi.org/10.1214/aop/1078415827
chicago: Koralov, Leonid, Vadim Kaloshin, and Dmitry Dolgopyat. “Sample Path Properties
of the Stochastic Flows.” The Annals of Probability. Institute of Mathematical
Statistics, 2004. https://doi.org/10.1214/aop/1078415827.
ieee: L. Koralov, V. Kaloshin, and D. Dolgopyat, “Sample path properties of the
stochastic flows,” The Annals of Probability, vol. 32, no. 1A. Institute
of Mathematical Statistics, pp. 1–27, 2004.
ista: Koralov L, Kaloshin V, Dolgopyat D. 2004. Sample path properties of the stochastic
flows. The Annals of Probability. 32(1A), 1–27.
mla: Koralov, Leonid, et al. “Sample Path Properties of the Stochastic Flows.” The
Annals of Probability, vol. 32, no. 1A, Institute of Mathematical Statistics,
2004, pp. 1–27, doi:10.1214/aop/1078415827.
short: L. Koralov, V. Kaloshin, D. Dolgopyat, The Annals of Probability 32 (2004)
1–27.
date_created: 2020-09-18T10:49:19Z
date_published: 2004-03-04T00:00:00Z
date_updated: 2021-01-12T08:19:50Z
day: '04'
doi: 10.1214/aop/1078415827
extern: '1'
intvolume: ' 32'
issue: 1A
language:
- iso: eng
month: '03'
oa_version: None
page: 1-27
publication: The Annals of Probability
publication_identifier:
issn:
- 0091-1798
publication_status: published
publisher: Institute of Mathematical Statistics
quality_controlled: '1'
status: public
title: Sample path properties of the stochastic flows
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2004'
...
---
_id: '864'
abstract:
- lang: eng
text: 'We present a method for prediction of functional sites in a set of aligned
protein sequences. The method selects sites which are both well conserved and
clustered together in space, as inferred from the 3D structures of proteins included
in the alignment. We tested the method using 86 alignments from the NCBI CDD database,
where the sites of experimentally determined ligand and/or macromolecular interactions
are annotated. In agreement with earlier investigations, we found that functional
site predictions are most successful when overall background sequence conservation
is low, such that sites under evolutionary constraint become apparent. In addition,
we found that averaging of conservation values across spatially clustered sites
improves predictions under certain conditions: that is, when overall conservation
is relatively high and when the site in question involves a large macromolecular
binding interface. Under these conditions it is better to look for clusters of
conserved sites than to look for particular conserved sites.'
acknowledgement: We thank John Spouge, Ben Shoemaker, and Michael Galperin forhelpful
suggestions, and the NIH Intramural Research Program forsupport.
author:
- first_name: Anna
full_name: Panchenko, Anna R
last_name: Panchenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephen
full_name: Bryant, Stephen H
last_name: Bryant
citation:
ama: Panchenko A, Kondrashov F, Bryant S. Prediction of functional sites by analysis
of sequence and structure conservation. Protein Science. 2004;13(4):884-892.
doi:10.1110/ps.03465504
apa: Panchenko, A., Kondrashov, F., & Bryant, S. (2004). Prediction of functional
sites by analysis of sequence and structure conservation. Protein Science.
Wiley-Blackwell. https://doi.org/10.1110/ps.03465504
chicago: Panchenko, Anna, Fyodor Kondrashov, and Stephen Bryant. “Prediction of
Functional Sites by Analysis of Sequence and Structure Conservation.” Protein
Science. Wiley-Blackwell, 2004. https://doi.org/10.1110/ps.03465504.
ieee: A. Panchenko, F. Kondrashov, and S. Bryant, “Prediction of functional sites
by analysis of sequence and structure conservation,” Protein Science, vol.
13, no. 4. Wiley-Blackwell, pp. 884–892, 2004.
ista: Panchenko A, Kondrashov F, Bryant S. 2004. Prediction of functional sites
by analysis of sequence and structure conservation. Protein Science. 13(4), 884–892.
mla: Panchenko, Anna, et al. “Prediction of Functional Sites by Analysis of Sequence
and Structure Conservation.” Protein Science, vol. 13, no. 4, Wiley-Blackwell,
2004, pp. 884–92, doi:10.1110/ps.03465504.
short: A. Panchenko, F. Kondrashov, S. Bryant, Protein Science 13 (2004) 884–892.
date_created: 2018-12-11T11:48:55Z
date_published: 2004-04-01T00:00:00Z
date_updated: 2021-01-12T08:20:22Z
day: '01'
doi: 10.1110/ps.03465504
extern: 1
intvolume: ' 13'
issue: '4'
month: '04'
page: 884 - 892
publication: Protein Science
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6786'
quality_controlled: 0
status: public
title: Prediction of functional sites by analysis of sequence and structure conservation
type: journal_article
volume: 13
year: '2004'
...
---
_id: '870'
abstract:
- lang: eng
text: Only a fraction of eukaryotic genes affect the phenotype drastically. We compared
18 parameters in 1273 human morbid genes, known to cause diseases, and in the
remaining 16 580 unambiguous human genes. Morbid genes evolve more slowly, have
wider phylogenetic distributions, are more similar to essential genes of Drosophila
melanogaster, code for longer proteins containing more alanine and glycine and
less histidine, lysine and methionine, possess larger numbers of longer introns
with more accurate splicing signals and have higher and broader expressions. These
differences make it possible to classify as non-morbid 34% of human genes with
unknown morbidity, when only 5% of known morbid genes are incorrectly classified
as non-morbid. This classification can help to identify disease-causing genes
among multiple candidates.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey Yu
last_name: Ogurtsov
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Ogurtsov A, Kondrashov A. Bioinformatical assay of human gene
morbidity. Nucleic Acids Research. 2004;32(5):1731-1737. doi:10.1093/nar/gkh330
apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2004). Bioinformatical
assay of human gene morbidity. Nucleic Acids Research. Oxford University
Press. https://doi.org/10.1093/nar/gkh330
chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Bioinformatical
Assay of Human Gene Morbidity.” Nucleic Acids Research. Oxford University
Press, 2004. https://doi.org/10.1093/nar/gkh330.
ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Bioinformatical assay of human
gene morbidity,” Nucleic Acids Research, vol. 32, no. 5. Oxford University
Press, pp. 1731–1737, 2004.
ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2004. Bioinformatical assay of human
gene morbidity. Nucleic Acids Research. 32(5), 1731–1737.
mla: Kondrashov, Fyodor, et al. “Bioinformatical Assay of Human Gene Morbidity.”
Nucleic Acids Research, vol. 32, no. 5, Oxford University Press, 2004,
pp. 1731–37, doi:10.1093/nar/gkh330.
short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Nucleic Acids Research 32 (2004)
1731–1737.
date_created: 2018-12-11T11:48:56Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:37Z
day: '01'
doi: 10.1093/nar/gkh330
extern: 1
intvolume: ' 32'
issue: '5'
month: '01'
page: 1731 - 1737
publication: Nucleic Acids Research
publication_status: published
publisher: Oxford University Press
publist_id: '6780'
quality_controlled: 0
status: public
title: Bioinformatical assay of human gene morbidity
type: journal_article
volume: 32
year: '2004'
...
---
_id: '875'
abstract:
- lang: eng
text: The dominance of wild-type alleles and the concomitant recessivity of deleterious
mutant alleles might have evolved by natural selection or could be a by-product
of the molecular and physiological mechanisms of gene action. We compared the
properties of human haplosufficient genes, whose wild-type alleles are dominant
over loss-of-function alleles, with haploinsufficient (recessive wild-type) genes,
which produce an abnormal phenotype when heterozygous for a loss-of-function allele.
The fraction of haplosufficient genes is the highest among the genes that encode
enzymes, which is best compatible with the physiological theory. Haploinsufficient
genes, on average, have more paralogs than haplosufficient genes, supporting the
idea that gene dosage could be important for the initial fixation of duplications.
Thus, haplo(in)sufficiency of a gene and its propensity for duplication might
have a common evolutionary basis.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
citation:
ama: Kondrashov F, Koonin E. A common framework for understanding the origin of
genetic dominance and evolutionary fates of gene duplications. Trends in Genetics.
2004;20(7):287-291. doi:10.1016/j.tig.2004.05.001
apa: Kondrashov, F., & Koonin, E. (2004). A common framework for understanding
the origin of genetic dominance and evolutionary fates of gene duplications. Trends
in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2004.05.001
chicago: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding
the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.”
Trends in Genetics. Elsevier, 2004. https://doi.org/10.1016/j.tig.2004.05.001.
ieee: F. Kondrashov and E. Koonin, “A common framework for understanding the origin
of genetic dominance and evolutionary fates of gene duplications,” Trends in
Genetics, vol. 20, no. 7. Elsevier, pp. 287–291, 2004.
ista: Kondrashov F, Koonin E. 2004. A common framework for understanding the origin
of genetic dominance and evolutionary fates of gene duplications. Trends in Genetics.
20(7), 287–291.
mla: Kondrashov, Fyodor, and Eugene Koonin. “A Common Framework for Understanding
the Origin of Genetic Dominance and Evolutionary Fates of Gene Duplications.”
Trends in Genetics, vol. 20, no. 7, Elsevier, 2004, pp. 287–91, doi:10.1016/j.tig.2004.05.001.
short: F. Kondrashov, E. Koonin, Trends in Genetics 20 (2004) 287–291.
date_created: 2018-12-11T11:48:58Z
date_published: 2004-07-01T00:00:00Z
date_updated: 2021-01-12T08:20:54Z
day: '01'
doi: 10.1016/j.tig.2004.05.001
extern: 1
intvolume: ' 20'
issue: '7'
month: '07'
page: 287 - 291
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6775'
quality_controlled: 0
status: public
title: A common framework for understanding the origin of genetic dominance and evolutionary
fates of gene duplications
type: journal_article
volume: 20
year: '2004'
...
---
_id: '889'
abstract:
- lang: eng
text: 'The function of protein and RNA molecules depends on complex epistatic interactions
between sites. Therefore, the deleterious effect of a mutation can be suppressed
by a compensatory second-site substitution. In relating a list of 86 pathogenic
mutations in human IRNAs encoded by mitochondrial genes to the sequences of their
mammalian orthologs, we noted that 52 pathogenic mutations were present in normal
tRNAs of one or several nonhuman mammals. We found at least five mechanisms of
compensation for 32 pathogenic mutations that destroyed a Watson-Crick pair in
one of the four tRNA stems: restoration of the affected Watson-Crick interaction
(25 cases), strengthening of another pair (4 cases), creation of a new pair (8
cases), changes of multiple interactions in the affected stem (11 cases) and changes
involving the interaction between the loop and stem structures (3 cases). A pathogenic
mutation and its compensating substitution are fixed in a lineage in rapid succession,
and often a compensatory interaction evolves convergently in different clades.
At least 10%, and perhaps as many as 50%, of all nucleotide substitutions in evolving
mammalian (RNAs participate in such interactions, indicating that the evolution
of tRNAs proceeds along highly epistatic fitness ridges.'
acknowledgement: We thank J. Gillespie, M. Hahn, L. Horth, A. Kondrashov, A. Kopp,
S. Nuzhdin, M. Turelli and D. Weinreich for their contributions. The authors were
supported by a grant from the US National Institutes of Health to S. Nuzhdin, and
A.D.K. is a Howard Hughes
author:
- first_name: Andrew
full_name: Kern, Andrew D
last_name: Kern
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kern A, Kondrashov F. Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs. Nature Genetics. 2004;36(11):1207-1212.
doi:10.1038/ng1451
apa: Kern, A., & Kondrashov, F. (2004). Mechanisms and convergence of compensatory
evolution in mammalian mitochondrial tRNAs. Nature Genetics. Nature Publishing
Group. https://doi.org/10.1038/ng1451
chicago: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory
Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics. Nature Publishing
Group, 2004. https://doi.org/10.1038/ng1451.
ieee: A. Kern and F. Kondrashov, “Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs,” Nature Genetics, vol. 36, no. 11. Nature
Publishing Group, pp. 1207–1212, 2004.
ista: Kern A, Kondrashov F. 2004. Mechanisms and convergence of compensatory evolution
in mammalian mitochondrial tRNAs. Nature Genetics. 36(11), 1207–1212.
mla: Kern, Andrew, and Fyodor Kondrashov. “Mechanisms and Convergence of Compensatory
Evolution in Mammalian Mitochondrial TRNAs.” Nature Genetics, vol. 36,
no. 11, Nature Publishing Group, 2004, pp. 1207–12, doi:10.1038/ng1451.
short: A. Kern, F. Kondrashov, Nature Genetics 36 (2004) 1207–1212.
date_created: 2018-12-11T11:49:02Z
date_published: 2004-11-01T00:00:00Z
date_updated: 2021-01-12T08:21:17Z
day: '01'
doi: 10.1038/ng1451
extern: 1
intvolume: ' 36'
issue: '11'
month: '11'
page: 1207 - 1212
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6759'
quality_controlled: 0
status: public
title: Mechanisms and convergence of compensatory evolution in mammalian mitochondrial
tRNAs
type: journal_article
volume: 36
year: '2004'
...
---
_id: '898'
abstract:
- lang: eng
text: New alleles become fixed owing to random drift of nearly neutral mutations
or to positive selection of substantially advantageous mutations. After decades
of debate, the fraction of fixations driven by selection remains uncertain. Within
9,390 genes, we analysed 28,196 codons at which rat and mouse differ from each
other at two nucleotide sites and 1,982 codons with three differences. At codons
where rat-mouse divergence involved two non-synonymous substitutions, both of
them occurred in the same lineage, either rat or mouse, in 64% of cases; however,
independent substitutions would occur in the same lineage with a probability of
only 50%. All three non-synonymous substitutions occurred in the same lineage
for 46% of codons, instead of the 25% expected. Furthermore, comparison of 12
pairs of prokaryotic genomes also shows clumping of multiple non-synonymous substitutions
in the same lineage. This pattern cannot be explained by correlated mutation or
episodes of relaxed negative selection, but instead indicates that positive selection
acts at many sites of rapid, successive amino acid replacement.
acknowledgement: We thank N. Bierne for a number of suggestions. G.A.B. was supported
by a BWF graduate fellowship. S.S. was supported by Genome Canada Foundation.
author:
- first_name: Georgii
full_name: Bazykin, Georgii A
last_name: Bazykin
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Aleksey
full_name: Ogurtsov, Aleksey Yu
last_name: Ogurtsov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. Positive selection
at sites of multiple amino acid replacements since rat-mouse divergence. Nature.
2004;429(6991):558-562. doi:10.1038/nature02601
apa: Bazykin, G., Kondrashov, F., Ogurtsov, A., Sunyaev, S., & Kondrashov, A.
(2004). Positive selection at sites of multiple amino acid replacements since
rat-mouse divergence. Nature. Nature Publishing Group. https://doi.org/10.1038/nature02601
chicago: Bazykin, Georgii, Fyodor Kondrashov, Aleksey Ogurtsov, Shamil Sunyaev,
and Alexey Kondrashov. “Positive Selection at Sites of Multiple Amino Acid Replacements
since Rat-Mouse Divergence.” Nature. Nature Publishing Group, 2004. https://doi.org/10.1038/nature02601.
ieee: G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, and A. Kondrashov, “Positive
selection at sites of multiple amino acid replacements since rat-mouse divergence,”
Nature, vol. 429, no. 6991. Nature Publishing Group, pp. 558–562, 2004.
ista: Bazykin G, Kondrashov F, Ogurtsov A, Sunyaev S, Kondrashov A. 2004. Positive
selection at sites of multiple amino acid replacements since rat-mouse divergence.
Nature. 429(6991), 558–562.
mla: Bazykin, Georgii, et al. “Positive Selection at Sites of Multiple Amino Acid
Replacements since Rat-Mouse Divergence.” Nature, vol. 429, no. 6991, Nature
Publishing Group, 2004, pp. 558–62, doi:10.1038/nature02601.
short: G. Bazykin, F. Kondrashov, A. Ogurtsov, S. Sunyaev, A. Kondrashov, Nature
429 (2004) 558–562.
date_created: 2018-12-11T11:49:05Z
date_published: 2004-06-03T00:00:00Z
date_updated: 2021-01-12T08:21:37Z
day: '03'
doi: 10.1038/nature02601
extern: 1
intvolume: ' 429'
issue: '6991'
month: '06'
page: 558 - 562
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6746'
quality_controlled: 0
status: public
title: Positive selection at sites of multiple amino acid replacements since rat-mouse
divergence
type: journal_article
volume: 429
year: '2004'
...
---
_id: '902'
abstract:
- lang: eng
text: 'We compare the functional spectrum of protein evolution in two separate animal
lineages with respect to two hypotheses: (1) rates of divergence are distributed
similarly among functional classes within both lineages, indicating that selective
pressure on the proteome is largely independent of organismic-level biological
requirements; and (2) rates of divergence are distributed differently among functional
classes within each lineage, indicating species-specific selective regimes impact
genome-wide substitutional patterns. Integrating comparative genome sequence with
data from tissue-specific expressed-sequence-tag (EST) libraries and detailed
database annotations, we find a functional genomic signature of rapid evolution
and selective constraint shared between mammalian and nematode lineages despite
their extensive morphological and ecological differences and distant common ancestry.
In both phyla, we find evidence of accelerated evolution among components of molecular
systems involved in coevolutionary change. In mammals, lineage-specific fast evolving
genes include those involved in reproduction, immunity, and possibly, maternal-fetal
conflict. Likelihood ratio tests provide evidence for positive selection in these
rapidly evolving functional categories in mammals. In contrast, slowly evolving
genes, in terms of amino acid or insertion/deletion (indel) change, in both phyla
are involved in core molecular processes such as transcription, translation, and
protein transport. Thus, strong purifying selection appears to act on the same
core cellular processes in both mammalian and nematode lineages, whereas positive
and/or relaxed selection acts on different biological processes in each lineage.'
acknowledgement: |-
We thank all members of the Hartl lab for their friendly support and Guillaume Achaz for valuable comments. We also thank the Sanger Institute and the Genome Sequencing Center at Wash- ington University, St. Louis and Lincoln Stein for providing un- finished C. briggsae sequence. Special thanks to the Bauer Center for Genomics Research at Harvard University and Gordon Kindl- mann at the University of Utah Scientific Computing and Imag- ing Institute for computational resources. R.J.K. is financially supported by a postdoctoral fellowship from the Natural Sciences and Engineering Research Council of Canada.
The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 USC section 1734 solely to indicate this fact.
author:
- first_name: Cristian
full_name: Castillo-Davis, Cristian I
last_name: Castillo Davis
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Daniel
full_name: Hartl, Daniel L
last_name: Hartl
- first_name: Rob
full_name: Kulathinal, Rob J
last_name: Kulathinal
citation:
ama: 'Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. The functional genomic
distribution of protein divergence in two animal phyla: Coevolution, genomic conflict,
and constraint. Genome Research. 2004;14(5):802-811. doi:10.1101/gr.2195604'
apa: 'Castillo Davis, C., Kondrashov, F., Hartl, D., & Kulathinal, R. (2004).
The functional genomic distribution of protein divergence in two animal phyla:
Coevolution, genomic conflict, and constraint. Genome Research. Cold Spring
Harbor Laboratory Press. https://doi.org/10.1101/gr.2195604'
chicago: 'Castillo Davis, Cristian, Fyodor Kondrashov, Daniel Hartl, and Rob Kulathinal.
“The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla:
Coevolution, Genomic Conflict, and Constraint.” Genome Research. Cold Spring
Harbor Laboratory Press, 2004. https://doi.org/10.1101/gr.2195604.'
ieee: 'C. Castillo Davis, F. Kondrashov, D. Hartl, and R. Kulathinal, “The functional
genomic distribution of protein divergence in two animal phyla: Coevolution, genomic
conflict, and constraint,” Genome Research, vol. 14, no. 5. Cold Spring
Harbor Laboratory Press, pp. 802–811, 2004.'
ista: 'Castillo Davis C, Kondrashov F, Hartl D, Kulathinal R. 2004. The functional
genomic distribution of protein divergence in two animal phyla: Coevolution, genomic
conflict, and constraint. Genome Research. 14(5), 802–811.'
mla: 'Castillo Davis, Cristian, et al. “The Functional Genomic Distribution of Protein
Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint.”
Genome Research, vol. 14, no. 5, Cold Spring Harbor Laboratory Press, 2004,
pp. 802–11, doi:10.1101/gr.2195604.'
short: C. Castillo Davis, F. Kondrashov, D. Hartl, R. Kulathinal, Genome Research
14 (2004) 802–811.
date_created: 2018-12-11T11:49:06Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:47Z
day: '01'
doi: 10.1101/gr.2195604
extern: 1
intvolume: ' 14'
issue: '5'
month: '05'
page: 802 - 811
publication: Genome Research
publication_status: published
publisher: Cold Spring Harbor Laboratory Press
publist_id: '6750'
quality_controlled: 0
status: public
title: 'The functional genomic distribution of protein divergence in two animal phyla:
Coevolution, genomic conflict, and constraint'
type: journal_article
volume: 14
year: '2004'
...
---
_id: '7333'
abstract:
- lang: eng
text: The analysis of the complete H2/air polymer electrolyte fuel cell system shows
that process air humidification is one of the biggest obstacles for a high performance
portable system in the kW range. Therefore, a new concept, with passive process
air humidification integrated into the stack, has been developed. Humidification
in each cell makes the process independent from the number of cells and the operation
mode, thus making the concept fully scalable. Without external humidification
the system is simpler, smaller, and cheaper. The humidification of the process
air is achieved by transfer of product water from the exhaust air, through part
of the membrane, to the dry intake air. Tests have shown that cells using the
concept of internal humidification and operated with dry air at 70 ° have almost
the same performance as when operated with external humidification. A 42‐cell
stack with this internal humidification concept was built and integrated into
a portable 1 kW power generator system.
article_processing_charge: No
article_type: original
author:
- first_name: M.
full_name: Santis, M.
last_name: Santis
- first_name: D.
full_name: Schmid, D.
last_name: Schmid
- first_name: M.
full_name: Ruge, M.
last_name: Ruge
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: F.N.
full_name: Büchi, F.N.
last_name: Büchi
citation:
ama: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. Modular stack-internal
air humidification concept-verification in a 1 kW stack. Fuel Cells. 2004;4(3):214-218.
doi:10.1002/fuce.200400028
apa: Santis, M., Schmid, D., Ruge, M., Freunberger, S. A., & Büchi, F. N. (2004).
Modular stack-internal air humidification concept-verification in a 1 kW stack.
Fuel Cells. Wiley. https://doi.org/10.1002/fuce.200400028
chicago: Santis, M., D. Schmid, M. Ruge, Stefan Alexander Freunberger, and F.N.
Büchi. “Modular Stack-Internal Air Humidification Concept-Verification in a 1 KW
Stack.” Fuel Cells. Wiley, 2004. https://doi.org/10.1002/fuce.200400028.
ieee: M. Santis, D. Schmid, M. Ruge, S. A. Freunberger, and F. N. Büchi, “Modular
stack-internal air humidification concept-verification in a 1 kW stack,” Fuel
Cells, vol. 4, no. 3. Wiley, pp. 214–218, 2004.
ista: Santis M, Schmid D, Ruge M, Freunberger SA, Büchi FN. 2004. Modular stack-internal
air humidification concept-verification in a 1 kW stack. Fuel Cells. 4(3), 214–218.
mla: Santis, M., et al. “Modular Stack-Internal Air Humidification Concept-Verification
in a 1 KW Stack.” Fuel Cells, vol. 4, no. 3, Wiley, 2004, pp. 214–18, doi:10.1002/fuce.200400028.
short: M. Santis, D. Schmid, M. Ruge, S.A. Freunberger, F.N. Büchi, Fuel Cells 4
(2004) 214–218.
date_created: 2020-01-15T12:24:14Z
date_published: 2004-08-01T00:00:00Z
date_updated: 2021-01-12T08:13:08Z
day: '01'
doi: 10.1002/fuce.200400028
extern: '1'
intvolume: ' 4'
issue: '3'
language:
- iso: eng
month: '08'
oa_version: None
page: 214-218
publication: Fuel Cells
publication_identifier:
issn:
- 1615-6846
- 1615-6854
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Modular stack-internal air humidification concept-verification in a 1 kW stack
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 4
year: '2004'
...
---
_id: '7334'
abstract:
- lang: eng
text: 'Fundamental and phenomenological models for cells, stacks, and complete systems
of PEFC and SOFC are reviewed and their predictive power is assessed by comparing
model simulations against experiments. Computationally efficient models suited
for engineering design include the (1+1) dimensionality approach, which decouples
the membrane in-plane and through-plane processes, and the volume-averaged-method
(VAM) that considers only the lumped effect of pre-selected system components.
The former model was shown to capture the measured lateral current density inhomogeneities
in a PEFC and the latter was used for the optimization of commercial SOFC systems.
State Space Modeling (SSM) was used to identify the main reaction pathways in
SOFC and, in conjunction with the implementation of geometrically well-defined
electrodes, has opened a new direction for the understanding of electrochemical
reactions. Furthermore, SSM has advanced the understanding of the COpoisoning-induced
anode impedance in PEFC. Detailed numerical models such as the Lattice Boltzmann
(LB) method for transport in porous media and the full 3-D Computational Fluid
Dynamics (CFD) Navier-Stokes simulations are addressed. These models contain all
components of the relevant physics and they can improve the understanding of the
related phenomena, a necessary condition for the development of both appropriate
simplified models as well as reliable technologies. Within the LB framework, a
technique for the characterization and computer-reconstruction of the porous electrode
structure was developed using advanced pattern recognition algorithms. In CFD
modeling, 3-D simulations were used to investigate SOFC with internal methane
steam reforming and have exemplified the significance of porous and novel fractal
channel distributors for the fuel and oxidant delivery, as well as for the cooling
of PEFC. As importantly, the novel concept has been put forth of functionally
designed, fractal-shaped fuel cells, showing promise of significant performance
improvements over the conventional rectangular shaped units. Thermo-economic modeling
for the optimization of PEFC is finally addressed. '
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Mantzaras, John
last_name: Mantzaras
- first_name: Stefan Alexander
full_name: Freunberger, Stefan Alexander
id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425
last_name: Freunberger
orcid: 0000-0003-2902-5319
- first_name: Felix N.
full_name: Büchi, Felix N.
last_name: Büchi
- first_name: Markus
full_name: Roos, Markus
last_name: Roos
- first_name: Wilhelm
full_name: Brandstätter, Wilhelm
last_name: Brandstätter
- first_name: Michel
full_name: Prestat, Michel
last_name: Prestat
- first_name: Ludwig J.
full_name: Gauckler, Ludwig J.
last_name: Gauckler
- first_name: Bernhard
full_name: Andreaus, Bernhard
last_name: Andreaus
- first_name: Faegheh
full_name: Hajbolouri, Faegheh
last_name: Hajbolouri
- first_name: Stephan M.
full_name: Senn, Stephan M.
last_name: Senn
- first_name: Dimos
full_name: Poulikakos, Dimos
last_name: Poulikakos
- first_name: Andreas K.
full_name: Chaniotis, Andreas K.
last_name: Chaniotis
- first_name: Diego
full_name: Larrain, Diego
last_name: Larrain
- first_name: Nordahl
full_name: Autissier, Nordahl
last_name: Autissier
- first_name: François
full_name: Maréchal, François
last_name: Maréchal
citation:
ama: Mantzaras J, Freunberger SA, Büchi FN, et al. Fuel cell modeling and simulations.
CHIMIA International Journal for Chemistry. 2004;58(12):857-868. doi:10.2533/000942904777677029
apa: Mantzaras, J., Freunberger, S. A., Büchi, F. N., Roos, M., Brandstätter, W.,
Prestat, M., … Maréchal, F. (2004). Fuel cell modeling and simulations. CHIMIA
International Journal for Chemistry. Swiss Chemical Society. https://doi.org/10.2533/000942904777677029
chicago: Mantzaras, John, Stefan Alexander Freunberger, Felix N. Büchi, Markus Roos,
Wilhelm Brandstätter, Michel Prestat, Ludwig J. Gauckler, et al. “Fuel Cell Modeling
and Simulations.” CHIMIA International Journal for Chemistry. Swiss Chemical
Society, 2004. https://doi.org/10.2533/000942904777677029.
ieee: J. Mantzaras et al., “Fuel cell modeling and simulations,” CHIMIA
International Journal for Chemistry, vol. 58, no. 12. Swiss Chemical Society,
pp. 857–868, 2004.
ista: Mantzaras J, Freunberger SA, Büchi FN, Roos M, Brandstätter W, Prestat M,
Gauckler LJ, Andreaus B, Hajbolouri F, Senn SM, Poulikakos D, Chaniotis AK, Larrain
D, Autissier N, Maréchal F. 2004. Fuel cell modeling and simulations. CHIMIA International
Journal for Chemistry. 58(12), 857–868.
mla: Mantzaras, John, et al. “Fuel Cell Modeling and Simulations.” CHIMIA International
Journal for Chemistry, vol. 58, no. 12, Swiss Chemical Society, 2004, pp.
857–68, doi:10.2533/000942904777677029.
short: J. Mantzaras, S.A. Freunberger, F.N. Büchi, M. Roos, W. Brandstätter, M.
Prestat, L.J. Gauckler, B. Andreaus, F. Hajbolouri, S.M. Senn, D. Poulikakos,
A.K. Chaniotis, D. Larrain, N. Autissier, F. Maréchal, CHIMIA International Journal
for Chemistry 58 (2004) 857–868.
date_created: 2020-01-15T12:24:23Z
date_published: 2004-12-01T00:00:00Z
date_updated: 2021-01-12T08:13:09Z
day: '01'
doi: 10.2533/000942904777677029
extern: '1'
intvolume: ' 58'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
page: 857-868
publication: CHIMIA International Journal for Chemistry
publication_identifier:
issn:
- 0009-4293
publication_status: published
publisher: Swiss Chemical Society
quality_controlled: '1'
status: public
title: Fuel cell modeling and simulations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 58
year: '2004'
...
---
_id: '7706'
abstract:
- lang: eng
text: 'The Sir2 deacetylase modulates organismal life-span in various species. However,
the molecular mechanisms by which Sir2 increases longevity are largely unknown.
We show that in mammalian cells, the Sir2 homolog SIRT1 appears to control the
cellular response to stress by regulating the FOXO family of Forkhead transcription
factors, a family of proteins that function as sensors of the insulin signaling
pathway and as regulators of organismal longevity. SIRT1 and the FOXO transcription
factor FOXO3 formed a complex in cells in response to oxidative stress, and SIRT1
deacetylated FOXO3 in vitro and within cells. SIRT1 had a dual effect on FOXO3
function: SIRT1 increased FOXO3''s ability to induce cell cycle arrest and resistance
to oxidative stress but inhibited FOXO3''s ability to induce cell death. Thus,
one way in which members of the Sir2 family of proteins may increase organismal
longevity is by tipping FOXO-dependent responses away from apoptosis and toward
stress resistance.'
article_processing_charge: No
article_type: original
author:
- first_name: Anne
full_name: Brunet, Anne
last_name: Brunet
- first_name: Lora Beatrice Jaeger
full_name: Sweeney, Lora Beatrice Jaeger
id: 56BE8254-C4F0-11E9-8E45-0B23E6697425
last_name: Sweeney
orcid: 0000-0001-9242-5601
- first_name: 'J Fitzhugh '
full_name: 'Sturgill, J Fitzhugh '
last_name: Sturgill
- first_name: Katrin
full_name: Chua, Katrin
last_name: Chua
- first_name: Paul
full_name: Greer, Paul
last_name: Greer
- first_name: Yingxi
full_name: Lin, Yingxi
last_name: Lin
- first_name: Hien
full_name: Tran, Hien
last_name: Tran
- first_name: Sarah
full_name: Ross, Sarah
last_name: Ross
- first_name: Raul
full_name: Mostoslavsky, Raul
last_name: Mostoslavsky
- first_name: Haim
full_name: Cohen, Haim
last_name: Cohen
- first_name: Linda
full_name: Hu, Linda
last_name: Hu
- first_name: Hwei-Ling
full_name: Chen, Hwei-Ling
last_name: Chen
- first_name: Mark
full_name: Jedrychowski, Mark
last_name: Jedrychowski
- first_name: Steven
full_name: Gygi, Steven
last_name: Gygi
- first_name: David
full_name: Sinclair, David
last_name: Sinclair
- first_name: Frederick
full_name: Alt, Frederick
last_name: Alt
- first_name: Michael
full_name: Greenberg, Michael
last_name: Greenberg
citation:
ama: Brunet A, Sweeney LB, Sturgill JF, et al. Stress-dependent regulation of FOXO
transcription factors by the SIRT1 deacetylase. Science. 2004;303(5666):2011-2015.
doi:10.1126/science.1094637
apa: Brunet, A., Sweeney, L. B., Sturgill, J. F., Chua, K., Greer, P., Lin, Y.,
… Greenberg, M. (2004). Stress-dependent regulation of FOXO transcription factors
by the SIRT1 deacetylase. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1094637
chicago: Brunet, Anne, Lora B. Sweeney, J Fitzhugh Sturgill, Katrin Chua, Paul
Greer, Yingxi Lin, Hien Tran, et al. “Stress-Dependent Regulation of FOXO Transcription
Factors by the SIRT1 Deacetylase.” Science. American Association for the
Advancement of Science, 2004. https://doi.org/10.1126/science.1094637.
ieee: A. Brunet et al., “Stress-dependent regulation of FOXO transcription
factors by the SIRT1 deacetylase,” Science, vol. 303, no. 5666. American
Association for the Advancement of Science, pp. 2011–2015, 2004.
ista: Brunet A, Sweeney LB, Sturgill JF, Chua K, Greer P, Lin Y, Tran H, Ross S,
Mostoslavsky R, Cohen H, Hu L, Chen H-L, Jedrychowski M, Gygi S, Sinclair D, Alt
F, Greenberg M. 2004. Stress-dependent regulation of FOXO transcription factors
by the SIRT1 deacetylase. Science. 303(5666), 2011–2015.
mla: Brunet, Anne, et al. “Stress-Dependent Regulation of FOXO Transcription Factors
by the SIRT1 Deacetylase.” Science, vol. 303, no. 5666, American Association
for the Advancement of Science, 2004, pp. 2011–15, doi:10.1126/science.1094637.
short: A. Brunet, L.B. Sweeney, J.F. Sturgill, K. Chua, P. Greer, Y. Lin, H. Tran,
S. Ross, R. Mostoslavsky, H. Cohen, L. Hu, H.-L. Chen, M. Jedrychowski, S. Gygi,
D. Sinclair, F. Alt, M. Greenberg, Science 303 (2004) 2011–2015.
date_created: 2020-04-30T10:37:41Z
date_published: 2004-03-26T00:00:00Z
date_updated: 2024-01-31T10:14:17Z
day: '26'
doi: 10.1126/science.1094637
extern: '1'
intvolume: ' 303'
issue: '5666'
language:
- iso: eng
month: '03'
oa_version: None
page: 2011-2015
publication: Science
publication_identifier:
issn:
- 0036-8075
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
status: public
title: Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 303
year: '2004'
...
---
_id: '1963'
abstract:
- lang: eng
text: The mechanism coupling electron transfer and proton pumping in respiratory
complex I (NADH-ubiquinone oxidoreductase) has not been established, but it has
been suggested that it involves conformational changes. Here, the influence of
substrates on the conformation of purified complex I from Escherichia coli was
studied by cross-linking and electron microscopy. When a zero-length cross-linking
reagent was used, the presence of NAD(P)H, in contrast to that of NAD+, prevented
the formation of cross-links between the hydrophilic subunits of the complex,
including NuoB, NuoI, and NuoCD. Comparisons using different cross-linkers suggested
that NuoB, which is likely to coordinate the key iron-sulfur cluster N2, is the
most mobile subunit. The presence of NAD(P)H led also to enhanced proteolysis
of subunit NuoG. These data indicate that upon NAD(P)H binding, the peripheral
arm of the complex adopts a more open conformation, with increased distances between
subunits. Single particle analysis showed the nature of this conformational change.
The enzyme retains its L-shape in the presence of NADH, but exhibits a significantly
more open or expanded structure both in the peripheral arm and, unexpectedly,
in the membrane domain also.
acknowledgement: This work was supported by the Medical Research Council and by a
Royal Society/North Atlantic Treaty Organization postdoctoral fellowship (to A.
A. M.)
author:
- first_name: Aygun
full_name: Mamedova, Aygun A
last_name: Mamedova
- first_name: Peter
full_name: Holt, Peter J
last_name: Holt
- first_name: Joe
full_name: Carroll, Joe D
last_name: Carroll
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Mamedova A, Holt P, Carroll J, Sazanov LA. Substrate-induced conformational
change in bacterial complex I. Journal of Biological Chemistry. 2004;279(22):23830-23836.
doi:10.1074/jbc.M401539200
apa: Mamedova, A., Holt, P., Carroll, J., & Sazanov, L. A. (2004). Substrate-induced
conformational change in bacterial complex I. Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology. https://doi.org/10.1074/jbc.M401539200
chicago: Mamedova, Aygun, Peter Holt, Joe Carroll, and Leonid A Sazanov. “Substrate-Induced
Conformational Change in Bacterial Complex I.” Journal of Biological Chemistry.
American Society for Biochemistry and Molecular Biology, 2004. https://doi.org/10.1074/jbc.M401539200.
ieee: A. Mamedova, P. Holt, J. Carroll, and L. A. Sazanov, “Substrate-induced conformational
change in bacterial complex I,” Journal of Biological Chemistry, vol. 279,
no. 22. American Society for Biochemistry and Molecular Biology, pp. 23830–23836,
2004.
ista: Mamedova A, Holt P, Carroll J, Sazanov LA. 2004. Substrate-induced conformational
change in bacterial complex I. Journal of Biological Chemistry. 279(22), 23830–23836.
mla: Mamedova, Aygun, et al. “Substrate-Induced Conformational Change in Bacterial
Complex I.” Journal of Biological Chemistry, vol. 279, no. 22, American
Society for Biochemistry and Molecular Biology, 2004, pp. 23830–36, doi:10.1074/jbc.M401539200.
short: A. Mamedova, P. Holt, J. Carroll, L.A. Sazanov, Journal of Biological Chemistry
279 (2004) 23830–23836.
date_created: 2018-12-11T11:54:56Z
date_published: 2004-05-28T00:00:00Z
date_updated: 2021-01-12T06:54:22Z
day: '28'
doi: 10.1074/jbc.M401539200
extern: 1
intvolume: ' 279'
issue: '22'
month: '05'
page: 23830 - 23836
publication: Journal of Biological Chemistry
publication_status: published
publisher: American Society for Biochemistry and Molecular Biology
publist_id: '5123'
quality_controlled: 0
status: public
title: Substrate-induced conformational change in bacterial complex I
type: journal_article
volume: 279
year: '2004'
...
---
_id: '13434'
abstract:
- lang: eng
text: Thin films of ionically doped gelatin have been color-patterned with submicrometer
precision using the wet-stamping technique. Inorganic salts are delivered onto
the gelatin surface from an agarose stamp, and diffuse into the gelatine layer,
producting deeply colored precipitates. Reaction fronts originating from different
features of the stamp cease within < 1 μm of each other, leaving sharp, transparent
regions in between.
article_processing_charge: No
article_type: original
author:
- first_name: C. J.
full_name: Campbell, C. J.
last_name: Campbell
- first_name: M.
full_name: Fialkowski, M.
last_name: Fialkowski
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: I. T.
full_name: Bensemann, I. T.
last_name: Bensemann
- first_name: B. A.
full_name: Grzybowski, B. A.
last_name: Grzybowski
citation:
ama: Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. Color micro-
and nanopatterning with counter-propagating reaction-diffusion fronts. Advanced
Materials. 2004;16(21):1912-1917. doi:10.1002/adma.200400383
apa: Campbell, C. J., Fialkowski, M., Klajn, R., Bensemann, I. T., & Grzybowski,
B. A. (2004). Color micro- and nanopatterning with counter-propagating reaction-diffusion
fronts. Advanced Materials. Wiley. https://doi.org/10.1002/adma.200400383
chicago: Campbell, C. J., M. Fialkowski, Rafal Klajn, I. T. Bensemann, and B. A.
Grzybowski. “Color Micro- and Nanopatterning with Counter-Propagating Reaction-Diffusion
Fronts.” Advanced Materials. Wiley, 2004. https://doi.org/10.1002/adma.200400383.
ieee: C. J. Campbell, M. Fialkowski, R. Klajn, I. T. Bensemann, and B. A. Grzybowski,
“Color micro- and nanopatterning with counter-propagating reaction-diffusion fronts,”
Advanced Materials, vol. 16, no. 21. Wiley, pp. 1912–1917, 2004.
ista: Campbell CJ, Fialkowski M, Klajn R, Bensemann IT, Grzybowski BA. 2004. Color
micro- and nanopatterning with counter-propagating reaction-diffusion fronts.
Advanced Materials. 16(21), 1912–1917.
mla: Campbell, C. J., et al. “Color Micro- and Nanopatterning with Counter-Propagating
Reaction-Diffusion Fronts.” Advanced Materials, vol. 16, no. 21, Wiley,
2004, pp. 1912–17, doi:10.1002/adma.200400383.
short: C.J. Campbell, M. Fialkowski, R. Klajn, I.T. Bensemann, B.A. Grzybowski,
Advanced Materials 16 (2004) 1912–1917.
date_created: 2023-08-01T10:39:09Z
date_published: 2004-11-14T00:00:00Z
date_updated: 2023-08-08T12:41:23Z
day: '14'
doi: 10.1002/adma.200400383
extern: '1'
intvolume: ' 16'
issue: '21'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- General Materials Science
language:
- iso: eng
month: '11'
oa_version: None
page: 1912-1917
publication: Advanced Materials
publication_identifier:
eissn:
- 1521-4095
issn:
- 0935-9648
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Color micro- and nanopatterning with counter-propagating reaction-diffusion
fronts
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2004'
...
---
_id: '13435'
abstract:
- lang: eng
text: Micropatterning of surfaces with several chemicals at different spatial locations
usually requires multiple stamping and registration steps. Here, we describe an
experimental method based on reaction–diffusion phenomena that allows for simultaneous
micropatterning of a substrate with several coloured chemicals. In this method,
called wet stamping (WETS), aqueous solutions of two or more inorganic salts are
delivered onto a film of dry, ionically doped gelatin from an agarose stamp patterned
in bas relief. Once in conformal contact, these salts diffuse into the gelatin,
where they react to give deeply coloured precipitates. Separation of colours in
the plane of the surface is the consequence of the differences in the diffusion
coefficients, the solubility products, and the amounts of different salts delivered
from the stamp, and is faithfully reproduced by a theoretical model based on a
system of reaction–diffusion partial differential equations. The multicolour micropatterns
are useful as non-binary optical elements, and could potentially form the basis
of new applications in microseparations and in controlled delivery.
article_processing_charge: No
article_type: original
author:
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
- first_name: Marcin
full_name: Fialkowski, Marcin
last_name: Fialkowski
- first_name: Igor T.
full_name: Bensemann, Igor T.
last_name: Bensemann
- first_name: Agnieszka
full_name: Bitner, Agnieszka
last_name: Bitner
- first_name: C. J.
full_name: Campbell, C. J.
last_name: Campbell
- first_name: Kyle
full_name: Bishop, Kyle
last_name: Bishop
- first_name: Stoyan
full_name: Smoukov, Stoyan
last_name: Smoukov
- first_name: Bartosz A.
full_name: Grzybowski, Bartosz A.
last_name: Grzybowski
citation:
ama: Klajn R, Fialkowski M, Bensemann IT, et al. Multicolour micropatterning of
thin films of dry gels. Nature Materials. 2004;3:729-735. doi:10.1038/nmat1231
apa: Klajn, R., Fialkowski, M., Bensemann, I. T., Bitner, A., Campbell, C. J., Bishop,
K., … Grzybowski, B. A. (2004). Multicolour micropatterning of thin films of dry
gels. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat1231
chicago: Klajn, Rafal, Marcin Fialkowski, Igor T. Bensemann, Agnieszka Bitner, C.
J. Campbell, Kyle Bishop, Stoyan Smoukov, and Bartosz A. Grzybowski. “Multicolour
Micropatterning of Thin Films of Dry Gels.” Nature Materials. Springer
Nature, 2004. https://doi.org/10.1038/nmat1231.
ieee: R. Klajn et al., “Multicolour micropatterning of thin films of dry
gels,” Nature Materials, vol. 3. Springer Nature, pp. 729–735, 2004.
ista: Klajn R, Fialkowski M, Bensemann IT, Bitner A, Campbell CJ, Bishop K, Smoukov
S, Grzybowski BA. 2004. Multicolour micropatterning of thin films of dry gels.
Nature Materials. 3, 729–735.
mla: Klajn, Rafal, et al. “Multicolour Micropatterning of Thin Films of Dry Gels.”
Nature Materials, vol. 3, Springer Nature, 2004, pp. 729–35, doi:10.1038/nmat1231.
short: R. Klajn, M. Fialkowski, I.T. Bensemann, A. Bitner, C.J. Campbell, K. Bishop,
S. Smoukov, B.A. Grzybowski, Nature Materials 3 (2004) 729–735.
date_created: 2023-08-01T10:39:23Z
date_published: 2004-09-19T00:00:00Z
date_updated: 2023-08-08T12:42:51Z
day: '19'
doi: 10.1038/nmat1231
extern: '1'
external_id:
pmid:
- '15378052'
intvolume: ' 3'
keyword:
- Mechanical Engineering
- Mechanics of Materials
- Condensed Matter Physics
- General Materials Science
- General Chemistry
language:
- iso: eng
month: '09'
oa_version: None
page: 729-735
pmid: 1
publication: Nature Materials
publication_identifier:
eissn:
- 1476-4660
issn:
- 1476-1122
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multicolour micropatterning of thin films of dry gels
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2004'
...
---
_id: '1456'
abstract:
- lang: eng
text: We study the space of L2 harmonic forms on complete manifolds with metrics
of fibred boundary or fibred cusp type. These metrics generalize the geometric
structures at infinity of several different well-known classes of metrics, including
asymptotically locally Euclidean manifolds, the (known types of) gravitational
instantons, and also Poincaré metrics on ℚ-rank 1 ends of locally symmetric spaces
and on the complements of smooth divisors in Kähler manifolds. The answer in all
cases is given in terms of intersection cohomology of a stratified compactification
of the manifold. The L2 signature formula implied by our result is closely related
to the one proved by Dai and more generally by Vaillant and identifies Dai's τ-invariant
directly in terms of intersection cohomology of differing perversities. This work
is also closely related to a recent paper of Carron and the forthcoming paper
of Cheeger and Dai. We apply our results to a number of examples, gravitational
instantons among them, arising in predictions about L2 harmonic forms in duality
theories in string theory.
acknowledgement: |-
Hausel’s work supported by a Miller Research Fellowship at the University of California, Berkeley.
Hunsicker’s work partially supported by Stanford University.
Mazzeo’s work supported by National Science Foundation grant numbers DMS-991975 and DMS-0204730 and
by the Mathematical Sciences Research Institute.
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Eugénie
full_name: Hunsicker, Eugénie
last_name: Hunsicker
- first_name: Rafe
full_name: Mazzeo, Rafe R
last_name: Mazzeo
citation:
ama: Hausel T, Hunsicker E, Mazzeo R. Hodge cohomology of gravitational instantons.
Duke Mathematical Journal. 2004;122(3):485-548. doi:10.1215/S0012-7094-04-12233-X
apa: Hausel, T., Hunsicker, E., & Mazzeo, R. (2004). Hodge cohomology of gravitational
instantons. Duke Mathematical Journal. Duke University Press. https://doi.org/10.1215/S0012-7094-04-12233-X
chicago: Hausel, Tamás, Eugénie Hunsicker, and Rafe Mazzeo. “Hodge Cohomology of
Gravitational Instantons.” Duke Mathematical Journal. Duke University Press,
2004. https://doi.org/10.1215/S0012-7094-04-12233-X.
ieee: T. Hausel, E. Hunsicker, and R. Mazzeo, “Hodge cohomology of gravitational
instantons,” Duke Mathematical Journal, vol. 122, no. 3. Duke University
Press, pp. 485–548, 2004.
ista: Hausel T, Hunsicker E, Mazzeo R. 2004. Hodge cohomology of gravitational instantons.
Duke Mathematical Journal. 122(3), 485–548.
mla: Hausel, Tamás, et al. “Hodge Cohomology of Gravitational Instantons.” Duke
Mathematical Journal, vol. 122, no. 3, Duke University Press, 2004, pp. 485–548,
doi:10.1215/S0012-7094-04-12233-X.
short: T. Hausel, E. Hunsicker, R. Mazzeo, Duke Mathematical Journal 122 (2004)
485–548.
date_created: 2018-12-11T11:52:08Z
date_published: 2004-04-15T00:00:00Z
date_updated: 2021-01-12T06:50:52Z
day: '15'
doi: 10.1215/S0012-7094-04-12233-X
extern: 1
intvolume: ' 122'
issue: '3'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0207169
month: '04'
oa: 1
page: 485 - 548
publication: Duke Mathematical Journal
publication_status: published
publisher: Duke University Press
publist_id: '5737'
quality_controlled: 0
status: public
title: Hodge cohomology of gravitational instantons
type: journal_article
volume: 122
year: '2004'
...
---
_id: '1464'
abstract:
- lang: eng
text: "The moduli space of stable vector bundles on a Riemann surface is smooth
when the rank and degree are coprime, and is diffeomorphic to the space of unitary
connections of central constant curvature. A classic result of Newstead and Atiyah
and Bott asserts that its rational cohomology ring is generated by the universal
classes, that is, by the Kunneth components of the Chern classes of the universal
bundle.\n\nThis paper studies the larger, non-compact moduli space of Higgs bundles,
as introduced by Hitchin and Simpson, with values in the canonical bundle K. This
is diffeomorphic to the space of all connections of central constant curvature,
whether unitary or not. The main result of the paper is that, in the rank 2 case,
the rational cohomology ring of this space is again generated by universal classes.\n\nThe
spaces of Higgs bundles with values in K(n) for n > 0 turn out to be essential
to the story. Indeed, we show that their direct limit has the homotopy type of
the classifying space of the gauge group, and hence has cohomology generated by
universal classes. 2000 Mathematics Subject Classification 14H60 (primary), 14D20,
14H81, 32Q55, 58D27 (secondary). "
author:
- first_name: Tamas
full_name: Tamas Hausel
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Michael
full_name: Thaddeus, Michael
last_name: Thaddeus
citation:
ama: Hausel T, Thaddeus M. Generators for the cohomology ring of the moduli space
of rank 2 higgs bundles. Proceedings of the London Mathematical Society.
2004;88(3):632-658. doi:10.1112/S0024611503014618
apa: Hausel, T., & Thaddeus, M. (2004). Generators for the cohomology ring of
the moduli space of rank 2 higgs bundles. Proceedings of the London Mathematical
Society. Oxford University Press. https://doi.org/10.1112/S0024611503014618
chicago: Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring
of the Moduli Space of Rank 2 Higgs Bundles.” Proceedings of the London Mathematical
Society. Oxford University Press, 2004. https://doi.org/10.1112/S0024611503014618.
ieee: T. Hausel and M. Thaddeus, “Generators for the cohomology ring of the moduli
space of rank 2 higgs bundles,” Proceedings of the London Mathematical Society,
vol. 88, no. 3. Oxford University Press, pp. 632–658, 2004.
ista: Hausel T, Thaddeus M. 2004. Generators for the cohomology ring of the moduli
space of rank 2 higgs bundles. Proceedings of the London Mathematical Society.
88(3), 632–658.
mla: Hausel, Tamás, and Michael Thaddeus. “Generators for the Cohomology Ring of
the Moduli Space of Rank 2 Higgs Bundles.” Proceedings of the London Mathematical
Society, vol. 88, no. 3, Oxford University Press, 2004, pp. 632–58, doi:10.1112/S0024611503014618.
short: T. Hausel, M. Thaddeus, Proceedings of the London Mathematical Society 88
(2004) 632–658.
date_created: 2018-12-11T11:52:10Z
date_published: 2004-05-01T00:00:00Z
date_updated: 2021-01-12T06:50:55Z
day: '01'
doi: 10.1112/S0024611503014618
extern: 1
intvolume: ' 88'
issue: '3'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0003093
month: '05'
oa: 1
page: 632 - 658
publication: Proceedings of the London Mathematical Society
publication_status: published
publisher: Oxford University Press
publist_id: '5736'
quality_controlled: 0
status: public
title: Generators for the cohomology ring of the moduli space of rank 2 higgs bundles
type: journal_article
volume: 88
year: '2004'
...
---
_id: '6155'
abstract:
- lang: eng
text: 'The genome of the nematode Caenorhabditis elegans encodes seven soluble guanylate
cyclases (sGCs) [1]. In mammals, sGCs function as α/β heterodimers activated by
gaseous ligands binding to a haem prosthetic group 2, 3. The principal activator
is nitric oxide, which acts through sGCs to regulate diverse cellular events.
In C. elegans the function of sGCs is mysterious: the worm genome does not appear
to encode nitric oxide synthase, and all C. elegans sGC subunits are more closely
related to mammalian β than α subunits [1]. Here, we show that two of the seven
C. elegans sGCs, GCY-35 and GCY-36, promote aggregation behavior. gcy-35 and gcy-36
are expressed in a small number of neurons. These include the body cavity neurons
AQR, PQR, and URX, which are directly exposed to the blood equivalent of C. elegans
and regulate aggregation behavior [4]. We show that GCY-35 and GCY-36 act as α-like
and β-like sGC subunits and that their function in the URX sensory neurons is
sufficient for strong nematode aggregation. Neither GCY-35 nor GCY-36 is absolutely
required for C. elegans to aggregate. Instead, these molecules may transduce one
of several pathways that induce C. elegans to aggregate or may modulate aggregation
by responding to cues in C. elegans body fluid.'
author:
- first_name: Benny H.H
full_name: Cheung, Benny H.H
last_name: Cheung
- first_name: Fausto
full_name: Arellano-Carbajal, Fausto
last_name: Arellano-Carbajal
- first_name: Irene
full_name: Rybicki, Irene
last_name: Rybicki
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
citation:
ama: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. Soluble guanylate cyclases
act in neurons exposed to the body fluid to promote C. elegans aggregation behavior.
Current Biology. 2004;14(12):1105-1111. doi:10.1016/j.cub.2004.06.027
apa: Cheung, B. H. ., Arellano-Carbajal, F., Rybicki, I., & de Bono, M. (2004).
Soluble guanylate cyclases act in neurons exposed to the body fluid to promote
C. elegans aggregation behavior. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.027
chicago: Cheung, Benny H.H, Fausto Arellano-Carbajal, Irene Rybicki, and Mario de
Bono. “Soluble Guanylate Cyclases Act in Neurons Exposed to the Body Fluid to
Promote C. Elegans Aggregation Behavior.” Current Biology. Elsevier, 2004.
https://doi.org/10.1016/j.cub.2004.06.027.
ieee: B. H. . Cheung, F. Arellano-Carbajal, I. Rybicki, and M. de Bono, “Soluble
guanylate cyclases act in neurons exposed to the body fluid to promote C. elegans
aggregation behavior,” Current Biology, vol. 14, no. 12. Elsevier, pp.
1105–1111, 2004.
ista: Cheung BH., Arellano-Carbajal F, Rybicki I, de Bono M. 2004. Soluble guanylate
cyclases act in neurons exposed to the body fluid to promote C. elegans aggregation
behavior. Current Biology. 14(12), 1105–1111.
mla: Cheung, Benny H. .., et al. “Soluble Guanylate Cyclases Act in Neurons Exposed
to the Body Fluid to Promote C. Elegans Aggregation Behavior.” Current Biology,
vol. 14, no. 12, Elsevier, 2004, pp. 1105–11, doi:10.1016/j.cub.2004.06.027.
short: B.H.. Cheung, F. Arellano-Carbajal, I. Rybicki, M. de Bono, Current Biology
14 (2004) 1105–1111.
date_created: 2019-03-21T09:42:01Z
date_published: 2004-06-22T00:00:00Z
date_updated: 2021-01-12T08:06:25Z
day: '22'
doi: 10.1016/j.cub.2004.06.027
extern: '1'
external_id:
pmid:
- '15203005'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '06'
oa_version: None
page: 1105-1111
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Soluble guanylate cyclases act in neurons exposed to the body fluid to promote
C. elegans aggregation behavior
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2004'
...
---
_id: '9454'
article_processing_charge: No
article_type: original
author:
- first_name: Simon W.-L.
full_name: Chan, Simon W.-L.
last_name: Chan
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: ' Zhixin'
full_name: Xie, Zhixin
last_name: Xie
- first_name: ' Lisa K.'
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen
SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303(5662):1336.
doi:10.1126/science.1095989
apa: Chan, S. W.-L., Zilberman, D., Xie, Zhixin, Johansen, Lisa K., Carrington,
J. C., & Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1095989
chicago: Chan, Simon W.-L., Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James
C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA
Methylation.” Science. American Association for the Advancement of Science,
2004. https://doi.org/10.1126/science.1095989.
ieee: S. W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J. C. Carrington,
and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” Science,
vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336,
2004.
ista: Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen
SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662),
1336.
mla: Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.”
Science, vol. 303, no. 5662, American Association for the Advancement of
Science, 2004, p. 1336, doi:10.1126/science.1095989.
short: S.W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J.C. Carrington,
S.E. Jacobsen, Science 303 (2004) 1336.
date_created: 2021-06-04T11:12:35Z
date_published: 2004-02-27T00:00:00Z
date_updated: 2021-12-14T09:13:53Z
day: '27'
department:
- _id: DaZi
doi: 10.1126/science.1095989
extern: '1'
external_id:
pmid:
- '14988555'
intvolume: ' 303'
issue: '5662'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa_version: None
page: '1336'
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: RNA silencing genes control de novo DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 303
year: '2004'
...