---
_id: '888'
abstract:
- lang: eng
text: 'BACKGROUND: Detection of changes in a protein''s evolutionary rate may reveal
cases of change in that protein''s function. We developed and implemented a simple
relative rates test in an attempt to assess the rate constancy of protein evolution
and to detect cases of functional diversification between orthologous proteins.
The test was performed on clusters of orthologous protein sequences from complete
bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae),
complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and
partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid
sequence evolution rates are significantly correlated on different branches of
phylogenetic trees representing the great majority of analyzed orthologous protein
sets from all three domains of life. However, approximately 1% of the proteins
from each group of species deviates from this pattern and instead shows variation
that is consistent with an acceleration of the rate of amino-acid substitution,
which may be due to functional diversification. Most of the putative functionally
diversified proteins from all three species groups are predicted to function at
the periphery of the cells and mediate their interaction with the environment.
CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the
three species groups analyzed here. Deviations from this rate constancy are probably
due to changes in selective constraints associated with diversification between
orthologs. Functional diversification between orthologs is thought to be a relatively
rare event. However, the resolution afforded by the test designed specifically
for genomic-scale datasets allowed us to identify numerous cases of possible functional
diversification between orthologous proteins.'
acknowledgement: We thank Alexey Kondrashov for many helpful discussions and constructive
criticisms, Charles DeLisi, David Landsman, Detlef Leipe, Wojciech Makalowski and
Itai Yanai for critical reading of the manuscript and constructive comments and
L. Aravind for advice on protein function prediction. The release of the unpublished
P. furiosus genome sequence by the Utah Genome Center at the University of Utah
is acknowledged and appreciated.
article_number: research0053.1
article_processing_charge: No
article_type: original
author:
- first_name: Ingo
full_name: Jordan, Ingo
last_name: Jordan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Roman
full_name: Tatusov, Roman
last_name: Tatusov
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. Constant relative
rate of protein evolution and detection of functional diversification among bacterial,
archaeal and eukaryotic proteins . Genome Biology. 2001;2(12). doi:10.1186/gb-2001-2-12-research0053
apa: Jordan, I., Kondrashov, F., Rogozin, I., Tatusov, R., Wolf, Y., & Koonin,
E. (2001). Constant relative rate of protein evolution and detection of functional
diversification among bacterial, archaeal and eukaryotic proteins . Genome
Biology. BioMed Central. https://doi.org/10.1186/gb-2001-2-12-research0053
chicago: Jordan, Ingo, Fyodor Kondrashov, Igor Rogozin, Roman Tatusov, Yuri Wolf,
and Eugene Koonin. “Constant Relative Rate of Protein Evolution and Detection
of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins
.” Genome Biology. BioMed Central, 2001. https://doi.org/10.1186/gb-2001-2-12-research0053.
ieee: I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin,
“Constant relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol.
2, no. 12. BioMed Central, 2001.
ista: Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. 2001. Constant
relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2(12), research0053.1.
mla: Jordan, Ingo, et al. “Constant Relative Rate of Protein Evolution and Detection
of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins
.” Genome Biology, vol. 2, no. 12, research0053.1, BioMed Central, 2001,
doi:10.1186/gb-2001-2-12-research0053.
short: I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, E. Koonin, Genome
Biology 2 (2001).
date_created: 2018-12-11T11:49:02Z
date_published: 2001-01-01T00:00:00Z
date_updated: 2023-05-31T12:15:37Z
day: '01'
doi: 10.1186/gb-2001-2-12-research0053
extern: '1'
external_id:
pmid:
- '11790256'
intvolume: ' 2'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC64838/
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1465-6906
publication_status: published
publisher: BioMed Central
publist_id: '6758'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Constant relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins '
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2
year: '2001'
...
---
_id: '1453'
abstract:
- lang: eng
text: In this Letter we exhibit a one-parameter family of new Taub-NUT instantons
parameterized by a half-line. The endpoint of the half-line will be the reducible
Yang-Mills instanton corresponding to the Eguchi-Hanson-Gibbons L2 harmonic 2-form,
while at an inner point we recover the Pope-Yuille instanton constructed as a
projection of the Levi-Civitá connection onto the positive su(2)+ ⊂ so(4) subalgebra.
Our method imitates the Jackiw-Nohl-Rebbi construction originally designed for
flat R4. That is we find a one-parameter family of harmonic functions on the Taub-NUT
space with a point singularity, rescale the metric and project the obtained Levi-Civitá
connection onto the other negative su(2)- ⊂ so(4) part. Our solutions will possess
the full U(2) symmetry, and thus provide more solutions to the recently proposed
U(2) symmetric ansatz of Kim and Yoon.
acknowledgement: We would like to acknowledge the financial support provided by the
Miller Institute of Basic Research in Science, the Japan Society for the Promotion
of Science, grant No. P99736 and the partial support by OTKA grant No. T032478.
article_processing_charge: No
article_type: original
author:
- first_name: Gábor
full_name: Etesi, Gábor
last_name: Etesi
- first_name: Tamas
full_name: Hausel, Tamas
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: 'Etesi G, Hausel T. Geometric construction of new Yang-Mills instantons over
Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle and
High-Energy Physics. 2001;514(1-2):189-199. doi:10.1016/S0370-2693(01)00821-8'
apa: 'Etesi, G., & Hausel, T. (2001). Geometric construction of new Yang-Mills
instantons over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary
Particle and High-Energy Physics. Elsevier. https://doi.org/10.1016/S0370-2693(01)00821-8'
chicago: 'Etesi, Gábor, and Tamás Hausel. “Geometric Construction of New Yang-Mills
Instantons over Taub-NUT Space.” Physics Letters, Section B: Nuclear, Elementary
Particle and High-Energy Physics. Elsevier, 2001. https://doi.org/10.1016/S0370-2693(01)00821-8.'
ieee: 'G. Etesi and T. Hausel, “Geometric construction of new Yang-Mills instantons
over Taub-NUT space,” Physics Letters, Section B: Nuclear, Elementary Particle
and High-Energy Physics, vol. 514, no. 1–2. Elsevier, pp. 189–199, 2001.'
ista: 'Etesi G, Hausel T. 2001. Geometric construction of new Yang-Mills instantons
over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle
and High-Energy Physics. 514(1–2), 189–199.'
mla: 'Etesi, Gábor, and Tamás Hausel. “Geometric Construction of New Yang-Mills
Instantons over Taub-NUT Space.” Physics Letters, Section B: Nuclear, Elementary
Particle and High-Energy Physics, vol. 514, no. 1–2, Elsevier, 2001, pp. 189–99,
doi:10.1016/S0370-2693(01)00821-8.'
short: 'G. Etesi, T. Hausel, Physics Letters, Section B: Nuclear, Elementary Particle
and High-Energy Physics 514 (2001) 189–199.'
date_created: 2018-12-11T11:52:07Z
date_published: 2001-08-09T00:00:00Z
date_updated: 2023-05-31T11:51:37Z
day: '09'
doi: 10.1016/S0370-2693(01)00821-8
extern: '1'
external_id:
arxiv:
- hep-th/0105118
intvolume: ' 514'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/hep-th/0105118
month: '08'
oa: 1
oa_version: Preprint
page: 189 - 199
publication: 'Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy
Physics'
publication_identifier:
issn:
- 0370-2693
publication_status: published
publisher: Elsevier
publist_id: '5743'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometric construction of new Yang-Mills instantons over Taub-NUT space
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 514
year: '2001'
...
---
_id: '1454'
abstract:
- lang: eng
text: We address the problem of finding Abelian instantons of finite energy on the
Euclidean Schwarzschild manifold. This amounts to construct self-dual L2 harmonic
2-forms on the space. Gibbons found a non-topological L2 harmonic form in the
Taub-NUT metric, leading to Abelian instantons with continuous energy. We imitate
his construction in the case of the Euclidean Schwarzschild manifold and find
a non-topological self-dual L2 harmonic 2-form on it. We show how this gives rise
to Abelian instantons and identify them with SU(2)-instantons of Pontryagin number
2n2 found by Charap and Duff in 1977. Using results of Dodziuk and Hitchin we
also calculate the full L2 harmonic space for the Euclidean Schwarzschild manifold.
acknowledgement: The work in this paper was done when Tamás Hausel visited the Yukawa
Institute of Kyoto University in February 2000. We are grateful for Prof. G.W. Gibbons
for insightful discussions and Prof. H. Kodama and the Yukawa Institute for the
invitation and hospitality.
article_processing_charge: No
article_type: original
author:
- first_name: Gábor
full_name: Etesi, Gábor
last_name: Etesi
- first_name: Tamas
full_name: Hausel, Tamas
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: Etesi G, Hausel T. Geometric interpretation of Schwarzschild instantons. Journal
of Geometry and Physics. 2001;37(1-2):126-136. doi:10.1016/S0393-0440(00)00040-1
apa: Etesi, G., & Hausel, T. (2001). Geometric interpretation of Schwarzschild
instantons. Journal of Geometry and Physics. Elsevier. https://doi.org/10.1016/S0393-0440(00)00040-1
chicago: Etesi, Gábor, and Tamás Hausel. “Geometric Interpretation of Schwarzschild
Instantons.” Journal of Geometry and Physics. Elsevier, 2001. https://doi.org/10.1016/S0393-0440(00)00040-1.
ieee: G. Etesi and T. Hausel, “Geometric interpretation of Schwarzschild instantons,”
Journal of Geometry and Physics, vol. 37, no. 1–2. Elsevier, pp. 126–136,
2001.
ista: Etesi G, Hausel T. 2001. Geometric interpretation of Schwarzschild instantons.
Journal of Geometry and Physics. 37(1–2), 126–136.
mla: Etesi, Gábor, and Tamás Hausel. “Geometric Interpretation of Schwarzschild
Instantons.” Journal of Geometry and Physics, vol. 37, no. 1–2, Elsevier,
2001, pp. 126–36, doi:10.1016/S0393-0440(00)00040-1.
short: G. Etesi, T. Hausel, Journal of Geometry and Physics 37 (2001) 126–136.
date_created: 2018-12-11T11:52:07Z
date_published: 2001-01-01T00:00:00Z
date_updated: 2023-05-31T12:08:45Z
day: '01'
doi: 10.1016/S0393-0440(00)00040-1
extern: '1'
external_id:
arxiv:
- hep-th/0003239
intvolume: ' 37'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/hep-th/0003239
month: '01'
oa: 1
oa_version: Preprint
page: 126 - 136
publication: Journal of Geometry and Physics
publication_identifier:
issn:
- 0393-0440
publication_status: published
publisher: Elsevier
publist_id: '5744'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometric interpretation of Schwarzschild instantons
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 37
year: '2001'
...
---
_id: '855'
abstract:
- lang: eng
text: 'Motivation: The context of the start codon (typically, AUG) and the features
of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation
regulation in eukaryotic mRNAs and for accurate prediction of the coding region
in genomic and cDNA sequences. The presence of AUG triplets in 5′ UTRs (upstream
AUGs) might effect the initiation rate and, in the context of gene prediction,
could reduce the accuracy of the identification of the authentic start. To reveal
potential connections between the presence of upstream AUGs and other features
of 5′ UTRs, such as their length and the start codon context, we undertook a systematic
analysis of the available eukaryotic 5′ UTR sequences. Results: We show that a
large fraction of 5′ UTRs in the available cDNA sequences, 15-53% depending on
the organism, contain upstream ATGs. A negative correlation was observed between
the information content of the translation start signal and the length of the
5′ UTR. Similarly, a negative correlation exists between the ''strength'' of the
start context and the number of upstream ATGs. Typically, cDNAs containing long
5′ UTRs with multiple upstream ATGs have a ''weak'' start context, and in contrast,
cDNAs containing short 5′ UTRs without ATGs have ''strong'' starts. These counter-intuitive
results may be interpreted in terms of upstream AUGs having an important role
in the regulation of translation efficiency by ensuring low basal translation
level via double negative control and creating the potential for additional regulatory
mechanisms. One of such mechanisms, supported by experimental studies of some
mRNAs, includes removal of the AUG-containing portion of the 5′ UTR by alternative
splicing.'
acknowledgement: This work has been partially supported by EU 'TRADAT' project and
by CNR Genetic Engineering (Italy), the RFBR grant for support of scientific schools
(00-15-97968) and SD RAS grant for young scientists (AVK). The authors wish to thank
J.Lyons-Weiler for helpful comments and A. Sorokin for help with the ATG_EVALUATOR
program.
article_processing_charge: No
article_type: original
author:
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Alex
full_name: Kochetov, Alex
last_name: Kochetov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
- first_name: Luciano
full_name: Milanesi, Luciano
last_name: Milanesi
citation:
ama: Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. Presence of ATG
triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context
of the start codon. Bioinformatics. 2001;17(10):890-900. doi:10.1093/bioinformatics/17.10.890
apa: Rogozin, I., Kochetov, A., Kondrashov, F., Koonin, E., & Milanesi, L. (2001).
Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates
with a ’weak’context of the start codon. Bioinformatics. Oxford University
Press. https://doi.org/10.1093/bioinformatics/17.10.890
chicago: Rogozin, Igor, Alex Kochetov, Fyodor Kondrashov, Eugene Koonin, and Luciano
Milanesi. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs
Correlates with a ’weak’context of the Start Codon.” Bioinformatics. Oxford
University Press, 2001. https://doi.org/10.1093/bioinformatics/17.10.890.
ieee: I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, and L. Milanesi, “Presence
of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with
a ’weak’context of the start codon,” Bioinformatics, vol. 17, no. 10. Oxford
University Press, pp. 890–900, 2001.
ista: Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. 2001. Presence
of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with
a ’weak’context of the start codon. Bioinformatics. 17(10), 890–900.
mla: Rogozin, Igor, et al. “Presence of ATG Triplets in 5′ Untranslated Regions
of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics,
vol. 17, no. 10, Oxford University Press, 2001, pp. 890–900, doi:10.1093/bioinformatics/17.10.890.
short: I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, L. Milanesi, Bioinformatics
17 (2001) 890–900.
date_created: 2018-12-11T11:48:52Z
date_published: 2001-10-01T00:00:00Z
date_updated: 2023-06-02T09:08:25Z
day: '01'
doi: 10.1093/bioinformatics/17.10.890
extern: '1'
external_id:
pmid:
- '11673233'
intvolume: ' 17'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 890 - 900
pmid: 1
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
publication_status: published
publisher: Oxford University Press
publist_id: '6795'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates
with a 'weak'context of the start codon
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 17
year: '2001'
...
---
_id: '874'
abstract:
- lang: eng
text: Sex is thought to facilitate accumulation of initially rare beneficial mutations
by allowing simultaneous allele replacements at many loci. However, this advantage
of sex depends on a restrictive assumption that the fitness of a genotype is determined
by fitness potential, a single intermediate variable to which all loci contribute
additively, so that new alleles can accumulate in any order. Individual-based
simulations of sexual and asexual populations reveal that under generic selection,
sex often retards adaptive evolution. When new alleles are beneficial only if
they accumulate in a prescribed order, a sexual population may evolve two or more
times slower than an asexual population because only asexual reproduction allows
some overlap of successive allele replacements. Many other fitness surfaces lead
to an even greater disadvantage of sex. Thus, either sex exists in spite of its
impact on the rate of adaptive allele replacements, or natural fitness surfaces
have rather specific properties, at least at the scale of intrapopulation genetic
variability.
article_processing_charge: No
article_type: original
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey
last_name: Kondrashov
citation:
ama: Kondrashov F, Kondrashov A. Multidimensional epistasis and the disadvantage
of sex. PNAS. 2001;98(21):12089-12092. doi:10.1073/pnas.211214298
apa: Kondrashov, F., & Kondrashov, A. (2001). Multidimensional epistasis and
the disadvantage of sex. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.211214298
chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis
and the Disadvantage of Sex.” PNAS. National Academy of Sciences, 2001.
https://doi.org/10.1073/pnas.211214298.
ieee: F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage
of sex,” PNAS, vol. 98, no. 21. National Academy of Sciences, pp. 12089–12092,
2001.
ista: Kondrashov F, Kondrashov A. 2001. Multidimensional epistasis and the disadvantage
of sex. PNAS. 98(21), 12089–12092.
mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and
the Disadvantage of Sex.” PNAS, vol. 98, no. 21, National Academy of Sciences,
2001, pp. 12089–92, doi:10.1073/pnas.211214298.
short: F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092.
date_created: 2018-12-11T11:48:58Z
date_published: 2001-10-09T00:00:00Z
date_updated: 2023-06-02T08:18:22Z
day: '09'
doi: 10.1073/pnas.211214298
extern: '1'
external_id:
pmid:
- '11593020'
intvolume: ' 98'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59772/
month: '10'
oa: 1
oa_version: Published Version
page: 12089 - 12092
pmid: 1
publication: PNAS
publication_identifier:
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '6774'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multidimensional epistasis and the disadvantage of sex
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 98
year: '2001'
...