---
_id: '15179'
abstract:
- lang: eng
text: The fungal bioluminescence pathway can be reconstituted in other organisms
allowing luminescence imaging without exogenously supplied substrate. The pathway
starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide
synthase that requires a posttranslational modification for activity. Here, we
report identification of alternative compact hispidin synthases encoded by a phylogenetically
diverse group of plants. A hybrid bioluminescence pathway that combines plant
and fungal genes is more compact, not dependent on availability of machinery for
posttranslational modifications, and confers autonomous bioluminescence in yeast,
mammalian, and plant hosts. The compact size of plant hispidin synthases enables
additional modes of delivery of autoluminescence, such as delivery with viral
vectors.
acknowledgement: "We thank Milaboratory (milaboratory.com) for the access to computing
and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture
line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance
with experiments.\r\nThis study was partially funded by Light Bio and Planta. The
Synthetic biology Group is funded by the MRC London Institute of Medical Sciences
(UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially
supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/.
Plant transformations were funded by RFBR and MOST, project number 21-54-52004.
Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/.
Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional
I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal
de Investigación (cofinanced by the European Regional Development Fund)."
article_number: adk1992
article_processing_charge: Yes
article_type: original
author:
- first_name: Kseniia A.
full_name: Palkina, Kseniia A.
last_name: Palkina
- first_name: Tatiana A.
full_name: Karataeva, Tatiana A.
last_name: Karataeva
- first_name: Maxim M.
full_name: Perfilov, Maxim M.
last_name: Perfilov
- first_name: Liliia I.
full_name: Fakhranurova, Liliia I.
last_name: Fakhranurova
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Elena
full_name: Garcia-Perez, Elena
last_name: Garcia-Perez
- first_name: Marta
full_name: Vazquez-Vilar, Marta
last_name: Vazquez-Vilar
- first_name: Marta
full_name: Rodriguez-Rodriguez, Marta
last_name: Rodriguez-Rodriguez
- first_name: Victor
full_name: Vazquez-Vilriales, Victor
last_name: Vazquez-Vilriales
- first_name: Ekaterina S.
full_name: Shakhova, Ekaterina S.
last_name: Shakhova
- first_name: Tatiana
full_name: Mitiouchkina, Tatiana
last_name: Mitiouchkina
- first_name: Olga A.
full_name: Belozerova, Olga A.
last_name: Belozerova
- first_name: Sergey I.
full_name: Kovalchuk, Sergey I.
last_name: Kovalchuk
- first_name: Anna
full_name: Alekberova, Anna
last_name: Alekberova
- first_name: Alena K.
full_name: Malyshevskaia, Alena K.
last_name: Malyshevskaia
- first_name: Evgenia N.
full_name: Bugaeva, Evgenia N.
last_name: Bugaeva
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Anastasia
full_name: Balakireva, Anastasia
last_name: Balakireva
- first_name: Nikita
full_name: Sytov, Nikita
last_name: Sytov
- first_name: Anastasia
full_name: Bezlikhotnova, Anastasia
last_name: Bezlikhotnova
- first_name: Daria I.
full_name: Boldyreva, Daria I.
last_name: Boldyreva
- first_name: Vladislav V.
full_name: Babenko, Vladislav V.
last_name: Babenko
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir V.
full_name: Choob, Vladimir V.
last_name: Choob
- first_name: Diego
full_name: Orzaez, Diego
last_name: Orzaez
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Karen S.
full_name: Sarkisyan, Karen S.
last_name: Sarkisyan
citation:
ama: Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained
luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992
apa: Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina,
N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for
self-sustained luminescence. Science Advances. American Association for
the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992
chicago: Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I.
Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez,
et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances.
American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992.
ieee: K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,”
Science Advances, vol. 10, no. 10. American Association for the Advancement
of Science, 2024.
ista: Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez
Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales
V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia
AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI,
Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan
KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances.
10(10), adk1992.
mla: Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.”
Science Advances, vol. 10, no. 10, adk1992, American Association for the
Advancement of Science, 2024, doi:10.1126/sciadv.adk1992.
short: K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina,
L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez,
V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk,
A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N.
Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob,
D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024).
date_created: 2024-03-25T08:54:33Z
date_published: 2024-03-01T00:00:00Z
date_updated: 2024-03-25T09:44:53Z
day: '01'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.1126/sciadv.adk1992
file:
- access_level: open_access
checksum: a19c43b260ea0bbaf895a29712e3153c
content_type: application/pdf
creator: dernst
date_created: 2024-03-25T09:42:10Z
date_updated: 2024-03-25T09:42:10Z
file_id: '15185'
file_name: 2024_ScienceAdv_Palkina.pdf
file_size: 1499302
relation: main_file
success: 1
file_date_updated: 2024-03-25T09:42:10Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '10'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: A hybrid pathway for self-sustained luminescence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2024'
...
---
_id: '12758'
abstract:
- lang: eng
text: AlphaFold changed the field of structural biology by achieving three-dimensional
(3D) structure prediction from protein sequence at experimental quality. The astounding
success even led to claims that the protein folding problem is “solved”. However,
protein folding problem is more than just structure prediction from sequence.
Presently, it is unknown if the AlphaFold-triggered revolution could help to solve
other problems related to protein folding. Here we assay the ability of AlphaFold
to predict the impact of single mutations on protein stability (ΔΔG) and function.
To study the question we extracted the pLDDT and metrics from AlphaFold
predictions before and after single mutation in a protein and correlated the predicted
change with the experimentally known ΔΔG values. Additionally, we correlated the
same AlphaFold pLDDT metrics with the impact of a single mutation on structure
using a large scale dataset of single mutations in GFP with the experimentally
assayed levels of fluorescence. We found a very weak or no correlation between
AlphaFold output metrics and change of protein stability or fluorescence. Our
results imply that AlphaFold may not be immediately applied to other problems
or applications in protein folding.
acknowledgement: The authors acknowledge the use of Zhores supercomputer [28] for
obtaining the results presented in this paper.The authors thank Zimin Foundation
and Petrovax for support of the presented study at the School of Molecular and Theoretical
Biology 2021.
article_number: e0282689
article_processing_charge: No
article_type: original
author:
- first_name: Marina A.
full_name: Pak, Marina A.
last_name: Pak
- first_name: Karina A.
full_name: Markhieva, Karina A.
last_name: Markhieva
- first_name: Mariia S.
full_name: Novikova, Mariia S.
last_name: Novikova
- first_name: Dmitry S.
full_name: Petrov, Dmitry S.
last_name: Petrov
- first_name: Ilya S.
full_name: Vorobyev, Ilya S.
last_name: Vorobyev
- first_name: Ekaterina
full_name: Maksimova, Ekaterina
id: 2FBE0DE4-F248-11E8-B48F-1D18A9856A87
last_name: Maksimova
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Dmitry N.
full_name: Ivankov, Dmitry N.
last_name: Ivankov
citation:
ama: Pak MA, Markhieva KA, Novikova MS, et al. Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. 2023;18(3).
doi:10.1371/journal.pone.0282689
apa: Pak, M. A., Markhieva, K. A., Novikova, M. S., Petrov, D. S., Vorobyev, I.
S., Maksimova, E., … Ivankov, D. N. (2023). Using AlphaFold to predict the impact
of single mutations on protein stability and function. PLoS ONE. Public
Library of Science. https://doi.org/10.1371/journal.pone.0282689
chicago: Pak, Marina A., Karina A. Markhieva, Mariia S. Novikova, Dmitry S. Petrov,
Ilya S. Vorobyev, Ekaterina Maksimova, Fyodor Kondrashov, and Dmitry N. Ivankov.
“Using AlphaFold to Predict the Impact of Single Mutations on Protein Stability
and Function.” PLoS ONE. Public Library of Science, 2023. https://doi.org/10.1371/journal.pone.0282689.
ieee: M. A. Pak et al., “Using AlphaFold to predict the impact of single
mutations on protein stability and function,” PLoS ONE, vol. 18, no. 3.
Public Library of Science, 2023.
ista: Pak MA, Markhieva KA, Novikova MS, Petrov DS, Vorobyev IS, Maksimova E, Kondrashov
F, Ivankov DN. 2023. Using AlphaFold to predict the impact of single mutations
on protein stability and function. PLoS ONE. 18(3), e0282689.
mla: Pak, Marina A., et al. “Using AlphaFold to Predict the Impact of Single Mutations
on Protein Stability and Function.” PLoS ONE, vol. 18, no. 3, e0282689,
Public Library of Science, 2023, doi:10.1371/journal.pone.0282689.
short: M.A. Pak, K.A. Markhieva, M.S. Novikova, D.S. Petrov, I.S. Vorobyev, E. Maksimova,
F. Kondrashov, D.N. Ivankov, PLoS ONE 18 (2023).
date_created: 2023-03-26T22:01:07Z
date_published: 2023-03-16T00:00:00Z
date_updated: 2023-08-01T13:47:14Z
day: '16'
ddc:
- '570'
department:
- _id: FyKo
- _id: MaRo
doi: 10.1371/journal.pone.0282689
external_id:
isi:
- '000985134400106'
file:
- access_level: open_access
checksum: 0281bdfccf8d76c4e08dd011c603f6b6
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T07:09:08Z
date_updated: 2023-03-27T07:09:08Z
file_id: '12771'
file_name: 2023_PLoSOne_Pak.pdf
file_size: 856625
relation: main_file
success: 1
file_date_updated: 2023-03-27T07:09:08Z
has_accepted_license: '1'
intvolume: ' 18'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
publication: PLoS ONE
publication_identifier:
eissn:
- 1932-6203
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Using AlphaFold to predict the impact of single mutations on protein stability
and function
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 18
year: '2023'
...
---
_id: '13164'
abstract:
- lang: eng
text: Molecular compatibility between gametes is a prerequisite for successful fertilization.
As long as a sperm and egg can recognize and bind each other via their surface
proteins, gamete fusion may occur even between members of separate species, resulting
in hybrids that can impact speciation. The egg membrane protein Bouncer confers
species specificity to gamete interactions between medaka and zebrafish, preventing
their cross-fertilization. Here, we leverage this specificity to uncover distinct
amino acid residues and N-glycosylation patterns that differentially influence
the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility.
Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer,
seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm,
in line with the pervasive purifying selection that dominates Bouncer’s evolution.
The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary
forces that, for some species, restrict fertilization to closely related fish,
and for others, allow broad gamete compatibility that enables hybridization.
acknowledgement: We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries
and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis;
Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake
Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura
for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana
Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions
about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC
Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported
by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP
Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award
(RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives
institutional funding from Boehringer Ingelheim and the Austrian Research Promotion
Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was
supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was
supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice
Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author
has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM)
version arising from this submission.
article_number: '3506'
article_processing_charge: No
article_type: original
author:
- first_name: Krista R.B.
full_name: Gert, Krista R.B.
last_name: Gert
- first_name: Karin
full_name: Panser, Karin
last_name: Panser
- first_name: Joachim
full_name: Surm, Joachim
last_name: Surm
- first_name: Benjamin S.
full_name: Steinmetz, Benjamin S.
last_name: Steinmetz
- first_name: Alexander
full_name: Schleiffer, Alexander
last_name: Schleiffer
- first_name: Luca
full_name: Jovine, Luca
last_name: Jovine
- first_name: Yehu
full_name: Moran, Yehu
last_name: Moran
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Andrea
full_name: Pauli, Andrea
last_name: Pauli
citation:
ama: Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer
proteins define cross-fertilization boundaries. Nature Communications.
2023;14. doi:10.1038/s41467-023-39317-4
apa: Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine,
L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins
define cross-fertilization boundaries. Nature Communications. Springer
Nature. https://doi.org/10.1038/s41467-023-39317-4
chicago: Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander
Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent
Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.”
Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39317-4.
ieee: K. R. B. Gert et al., “Divergent molecular signatures in fish Bouncer
proteins define cross-fertilization boundaries,” Nature Communications,
vol. 14. Springer Nature, 2023.
ista: Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y,
Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins
define cross-fertilization boundaries. Nature Communications. 14, 3506.
mla: Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer
Proteins Define Cross-Fertilization Boundaries.” Nature Communications,
vol. 14, 3506, Springer Nature, 2023, doi:10.1038/s41467-023-39317-4.
short: K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine,
Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).
date_created: 2023-06-25T22:00:45Z
date_published: 2023-06-14T00:00:00Z
date_updated: 2023-12-13T11:26:34Z
day: '14'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41467-023-39317-4
external_id:
isi:
- '001048208600023'
file:
- access_level: open_access
checksum: d6165f41c7f1c2c04b04256ec9f003fb
content_type: application/pdf
creator: dernst
date_created: 2023-06-26T10:26:04Z
date_updated: 2023-06-26T10:26:04Z
file_id: '13172'
file_name: 2023_NatureComm_Gert.pdf
file_size: 1555006
relation: main_file
success: 1
file_date_updated: 2023-06-26T10:26:04Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergent molecular signatures in fish Bouncer proteins define cross-fertilization
boundaries
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2023'
...
---
_id: '13976'
abstract:
- lang: eng
text: Conflicts and natural disasters affect entire populations of the countries
involved and, in addition to the thousands of lives destroyed, have a substantial
negative impact on the scientific advances these countries provide. The unprovoked
invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria,
and the ongoing conflicts in the Middle East are just a few examples. Millions
of people have been killed or displaced, their futures uncertain. These events
have resulted in extensive infrastructure collapse, with loss of electricity,
transportation, and access to services. Schools, universities, and research centers
have been destroyed along with decades’ worth of data, samples, and findings.
Scholars in disaster areas face short- and long-term problems in terms of what
they can accomplish now for obtaining grants and for employment in the long run.
In our interconnected world, conflicts and disasters are no longer a local problem
but have wide-ranging impacts on the entire world, both now and in the future.
Here, we focus on the current and ongoing impact of war on the scientific community
within Ukraine and from this draw lessons that can be applied to all affected
countries where scientists at risk are facing hardship. We present and classify
examples of effective and feasible mechanisms used to support researchers in countries
facing hardship and discuss how these can be implemented with help from the international
scientific community and what more is desperately needed. Reaching out, providing
accessible training opportunities, and developing collaborations should increase
inclusion and connectivity, support scientific advancements within affected communities,
and expedite postwar and disaster recovery.
acknowledgement: "Our article is dedicated to all freedom-loving people around the
world and to the people of Ukraine who fight for our freedom. Special thanks to
Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful
review, valuable criticism, and useful suggestions while preparing this manuscript,
and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered
their time. No funding supported work on this article."
article_processing_charge: Yes
article_type: original
author:
- first_name: Walter
full_name: Wolfsberger, Walter
last_name: Wolfsberger
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Khrystyna
full_name: Shchubelka, Khrystyna
last_name: Shchubelka
- first_name: Alina
full_name: Frolova, Alina
last_name: Frolova
- first_name: Yuriy
full_name: Salyha, Yuriy
last_name: Salyha
- first_name: Oksana
full_name: Zlenko, Oksana
last_name: Zlenko
- first_name: Mykhailo
full_name: Arych, Mykhailo
last_name: Arych
- first_name: Dmytro
full_name: Dziuba, Dmytro
last_name: Dziuba
- first_name: Andrii
full_name: Parkhomenko, Andrii
last_name: Parkhomenko
- first_name: Volodymyr
full_name: Smolanka, Volodymyr
last_name: Smolanka
- first_name: Zeynep H.
full_name: Gümüş, Zeynep H.
last_name: Gümüş
- first_name: Efe
full_name: Sezgin, Efe
last_name: Sezgin
- first_name: Alondra
full_name: Diaz-Lameiro, Alondra
last_name: Diaz-Lameiro
- first_name: Viktor R.
full_name: Toth, Viktor R.
last_name: Toth
- first_name: Megi
full_name: Maci, Megi
last_name: Maci
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Patricia M.
full_name: Morton, Patricia M.
last_name: Morton
- first_name: Paweł P.
full_name: Łabaj, Paweł P.
last_name: Łabaj
- first_name: Veronika
full_name: Romero, Veronika
last_name: Romero
- first_name: Jakub
full_name: Hlávka, Jakub
last_name: Hlávka
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
- first_name: Taras K.
full_name: Oleksyk, Taras K.
last_name: Oleksyk
citation:
ama: 'Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders:
Lessons from Ukraine. GigaScience. 2023;12. doi:10.1093/gigascience/giad045'
apa: 'Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko,
O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine.
GigaScience. Oxford Academic. https://doi.org/10.1093/gigascience/giad045'
chicago: 'Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova,
Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders:
Lessons from Ukraine.” GigaScience. Oxford Academic, 2023. https://doi.org/10.1093/gigascience/giad045.'
ieee: 'W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,”
GigaScience, vol. 12. Oxford Academic, 2023.'
ista: 'Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych
M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth
VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul
S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience.
12.'
mla: 'Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.”
GigaScience, vol. 12, Oxford Academic, 2023, doi:10.1093/gigascience/giad045.'
short: W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko,
M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro,
V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero,
J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023).
date_created: 2023-08-06T22:01:13Z
date_published: 2023-07-27T00:00:00Z
date_updated: 2023-12-13T12:01:46Z
day: '27'
department:
- _id: FyKo
doi: 10.1093/gigascience/giad045
external_id:
isi:
- '001081086100001'
pmid:
- '37496156'
intvolume: ' 12'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/gigascience/giad045
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: GigaScience
publication_identifier:
eissn:
- 2047-217X
publication_status: epub_ahead
publisher: Oxford Academic
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Scientists without borders: Lessons from Ukraine'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 12
year: '2023'
...
---
_id: '14862'
article_number: ckad160.597
article_processing_charge: No
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Y
full_name: Kulikova, Y
last_name: Kulikova
- first_name: Aygul
full_name: Minnegalieva, Aygul
id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E
last_name: Minnegalieva
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies
prevent the emergence of vaccine resistance. In: European Journal of Public
Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597'
apa: Rella, S., Kulikova, Y., Minnegalieva, A., & Kondrashov, F. (2023). Complex
vaccination strategies prevent the emergence of vaccine resistance. In European
Journal of Public Health (Vol. 33). Oxford University Press. https://doi.org/10.1093/eurpub/ckad160.597
chicago: Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex
Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European
Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597.
ieee: S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination
strategies prevent the emergence of vaccine resistance,” in European Journal
of Public Health, 2023, vol. 33, no. Supplement_2.
ista: Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination
strategies prevent the emergence of vaccine resistance. European Journal of Public
Health. vol. 33, ckad160.597.
mla: Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence
of Vaccine Resistance.” European Journal of Public Health, vol. 33, no.
Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597.
short: S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal
of Public Health, Oxford University Press, 2023.
date_created: 2024-01-22T12:02:28Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-24T11:16:09Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
doi: 10.1093/eurpub/ckad160.597
file:
- access_level: open_access
checksum: 98706755bb4cc5d553818ade7660a7d2
content_type: application/pdf
creator: dernst
date_created: 2024-01-24T11:12:33Z
date_updated: 2024-01-24T11:12:33Z
file_id: '14882'
file_name: 2023_EurJourPublicHealth_Rella.pdf
file_size: 71057
relation: main_file
success: 1
file_date_updated: 2024-01-24T11:12:33Z
has_accepted_license: '1'
intvolume: ' 33'
issue: Supplement_2
keyword:
- Public Health
- Environmental and Occupational Health
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '10'
oa: 1
oa_version: Published Version
publication: European Journal of Public Health
publication_identifier:
eissn:
- 1464-360X
issn:
- 1101-1262
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Complex vaccination strategies prevent the emergence of vaccine resistance
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 33
year: '2023'
...
---
_id: '11187'
abstract:
- lang: eng
text: During the COVID-19 pandemic, genomics and bioinformatics have emerged as
essential public health tools. The genomic data acquired using these methods have
supported the global health response, facilitated the development of testing methods
and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually
unlimited potential for rapid generation and analysis of genomic data is also
coupled with unique technical, scientific and organizational challenges. Here,
we discuss the application of genomic and computational methods for efficient
data-driven COVID-19 response, the advantages of the democratization of viral
sequencing around the world and the challenges associated with viral genome data
collection and processing.
acknowledgement: 'Our paper is dedicated to all freedom-loving people around the world,
and to the people of Ukraine who fight for our freedom. We thank William M. Switzer
and Ellsworth M. Campbell from the Division of HIV/AIDS Prevention, Centers for
Disease Control and Prevention (CDC), Atlanta, GA, USA, for discussions and suggestions.
We thank Jason Ladner from the Pathogen and Microbiome Institute, Northern Arizona
University, Flagstaff, AZ, for providing suggestions and feedback. S.M. was partially
supported by National Science Foundation grants 2041984. T.L. is supported by the
NSFC Excellent Young Scientists Fund (Hong Kong and Macau; 31922087), Research Grants
Council (RGC) Collaborative Research Fund (C7144-20GF), RGC Research Impact Fund
(R7021-20), Innovation and Technology Commission’s InnoHK funding (D24H) and Health
and Medical Research Fund (COVID190223). P.S. was supported by US National Institutes
of Health (NIH) grant 1R01EB025022 and National Science Foundation (NSF) grant 2047828.
M.A. acknowledges King Abdulaziz City for Science and Technology and the Saudi Human
Genome Project for technical and financial support (https://shgp.kacst.edu.sa) N.W.
was supported by US NIH grants R00 AI139445, DP2 AT011966 and R01 AI167910. A.S.
acknowledge funding from NSF grant no. 2029025. A.Z. has been partially supported
by NIH grants 1R01EB025022-01 and 1R21CA241044-01A1. S. Knyazev has been partly
supported by Molecular Basis of Disease at Georgia State University and NIH awards
R01 HG009120, R01 MH115676, R01 AI153827 and U01 HG011715. A.W. has been supported
by the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-061). R.K. was supported
by NSF project 2038509, RAPID: Improving QIIME 2 and UniFrac for Viruses to Respond
to COVID-19, CDC project 30055281 with Scripps led by Kristian Andersen, Genomic
sequencing of SARS-CoV-2 to investigate local and cross-border emergence and spread.
J.O.W. was supported by NIH–National Institute of Allergy and Infectious Diseases
(NIAID) R01 AI135992 and receives funding from the CDC unrelated to this work. T.I.V.
is supported by the Branco Weiss Fellowship. Y.P. was supported by the Ministry
of Science and Higher Education of the Russian Federation within the framework of
state support for the creation and development of World-Class Research Centers “Digital
biodesign and personalized healthcare” N◦075-15-2020-926. E.B. was supported by
a US National Institute of General Medical Sciences IDeA Alaska INBRE (P20GM103395)
and NIAID CEIRR (75N93019R00028). C.E.M. thanks Testing for America (501c3), OpenCovidScreen
Foundation, Igor Tulchinsky and the WorldQuant Foundation, Bill Ackman and Olivia
Flatto and the Pershing Square Foundation, Ken Griffin and Citadel, the US National
Institutes of Health (R01AI125416, R01AI151059, R21AI129851, U01DA053941), and the
Alfred P. Sloan Foundation (G-2015-13964). C.Y.C. is supported by US CDC Epidemiology
and Laboratory Capacity (ELC) for Infectious Diseases grant 6NU50CK000539 to the
California Department of Public Health, the Innovative Genomics Institute (IGI)
at the University of California, Berkeley, and University of California, San Francisco,
NIH grant R33AI12945 and US CDC contract 75D30121C10991. A.K. was partly supported
by RFBR grant 20-515-80017. P.L. acknowledges support from the European Research
Council (ERC) under the European Union’s Horizon 2020 research and innovation program
(grant agreement no. ~725422 - ReservoirDOCS), the Wellcome Trust through project
206298/Z/17/Z (Artic Network) and NIH grants R01 AI153044 and U19 AI135995. K.C.
acknowledges support from the US NSF award EEID-IOS-2109688. F.K.’s work was supported
by an ERC Consolidator grant to F.K. (771209–CharFL).'
article_processing_charge: No
article_type: letter_note
author:
- first_name: Sergey
full_name: Knyazev, Sergey
last_name: Knyazev
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Varuni
full_name: Sarwal, Varuni
last_name: Sarwal
- first_name: Ram
full_name: Ayyala, Ram
last_name: Ayyala
- first_name: Harman
full_name: Singh, Harman
last_name: Singh
- first_name: Smruthi
full_name: Karthikeyan, Smruthi
last_name: Karthikeyan
- first_name: Dhrithi
full_name: Deshpande, Dhrithi
last_name: Deshpande
- first_name: Pelin Icer
full_name: Baykal, Pelin Icer
last_name: Baykal
- first_name: Zoia
full_name: Comarova, Zoia
last_name: Comarova
- first_name: Angela
full_name: Lu, Angela
last_name: Lu
- first_name: Yuri
full_name: Porozov, Yuri
last_name: Porozov
- first_name: Tetyana I.
full_name: Vasylyeva, Tetyana I.
last_name: Vasylyeva
- first_name: Joel O.
full_name: Wertheim, Joel O.
last_name: Wertheim
- first_name: Braden T.
full_name: Tierney, Braden T.
last_name: Tierney
- first_name: Charles Y.
full_name: Chiu, Charles Y.
last_name: Chiu
- first_name: Ren
full_name: Sun, Ren
last_name: Sun
- first_name: Aiping
full_name: Wu, Aiping
last_name: Wu
- first_name: Malak S.
full_name: Abedalthagafi, Malak S.
last_name: Abedalthagafi
- first_name: Victoria M.
full_name: Pak, Victoria M.
last_name: Pak
- first_name: Shivashankar H.
full_name: Nagaraj, Shivashankar H.
last_name: Nagaraj
- first_name: Adam L.
full_name: Smith, Adam L.
last_name: Smith
- first_name: Pavel
full_name: Skums, Pavel
last_name: Skums
- first_name: Bogdan
full_name: Pasaniuc, Bogdan
last_name: Pasaniuc
- first_name: Andrey
full_name: Komissarov, Andrey
last_name: Komissarov
- first_name: Christopher E.
full_name: Mason, Christopher E.
last_name: Mason
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Philippe
full_name: Lemey, Philippe
last_name: Lemey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Niko
full_name: Beerenwinkel, Niko
last_name: Beerenwinkel
- first_name: Tommy Tsan Yuk
full_name: Lam, Tommy Tsan Yuk
last_name: Lam
- first_name: Nicholas C.
full_name: Wu, Nicholas C.
last_name: Wu
- first_name: Alex
full_name: Zelikovsky, Alex
last_name: Zelikovsky
- first_name: Rob
full_name: Knight, Rob
last_name: Knight
- first_name: Keith A.
full_name: Crandall, Keith A.
last_name: Crandall
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
citation:
ama: Knyazev S, Chhugani K, Sarwal V, et al. Unlocking capacities of genomics for
the COVID-19 response and future pandemics. Nature Methods. 2022;19(4):374-380.
doi:10.1038/s41592-022-01444-z
apa: Knyazev, S., Chhugani, K., Sarwal, V., Ayyala, R., Singh, H., Karthikeyan,
S., … Mangul, S. (2022). Unlocking capacities of genomics for the COVID-19 response
and future pandemics. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-022-01444-z
chicago: Knyazev, Sergey, Karishma Chhugani, Varuni Sarwal, Ram Ayyala, Harman Singh,
Smruthi Karthikeyan, Dhrithi Deshpande, et al. “Unlocking Capacities of Genomics
for the COVID-19 Response and Future Pandemics.” Nature Methods. Springer
Nature, 2022. https://doi.org/10.1038/s41592-022-01444-z.
ieee: S. Knyazev et al., “Unlocking capacities of genomics for the COVID-19
response and future pandemics,” Nature Methods, vol. 19, no. 4. Springer
Nature, pp. 374–380, 2022.
ista: Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande
D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney
BT, Chiu CY, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums
P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel
N, Lam TTY, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. 2022. Unlocking
capacities of genomics for the COVID-19 response and future pandemics. Nature
Methods. 19(4), 374–380.
mla: Knyazev, Sergey, et al. “Unlocking Capacities of Genomics for the COVID-19
Response and Future Pandemics.” Nature Methods, vol. 19, no. 4, Springer
Nature, 2022, pp. 374–80, doi:10.1038/s41592-022-01444-z.
short: S. Knyazev, K. Chhugani, V. Sarwal, R. Ayyala, H. Singh, S. Karthikeyan,
D. Deshpande, P.I. Baykal, Z. Comarova, A. Lu, Y. Porozov, T.I. Vasylyeva, J.O.
Wertheim, B.T. Tierney, C.Y. Chiu, R. Sun, A. Wu, M.S. Abedalthagafi, V.M. Pak,
S.H. Nagaraj, A.L. Smith, P. Skums, B. Pasaniuc, A. Komissarov, C.E. Mason, E.
Bortz, P. Lemey, F. Kondrashov, N. Beerenwinkel, T.T.Y. Lam, N.C. Wu, A. Zelikovsky,
R. Knight, K.A. Crandall, S. Mangul, Nature Methods 19 (2022) 374–380.
date_created: 2022-04-17T22:01:48Z
date_published: 2022-04-08T00:00:00Z
date_updated: 2023-08-03T06:46:09Z
day: '08'
department:
- _id: FyKo
doi: 10.1038/s41592-022-01444-z
ec_funded: 1
external_id:
isi:
- '000781199600011'
pmid:
- '35396471'
intvolume: ' 19'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41592-022-01444-z
month: '04'
oa: 1
oa_version: Published Version
page: 374-380
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Methods
publication_identifier:
eissn:
- 1548-7105
issn:
- 1548-7091
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unlocking capacities of genomics for the COVID-19 response and future pandemics
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2022'
...
---
_id: '11344'
abstract:
- lang: eng
text: Until recently, Shigella and enteroinvasive Escherichia coli were thought
to be primate-restricted pathogens. The base of their pathogenicity is the type
3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates
host cell invasion and subsequent proliferation. A large family of T3SS effectors,
E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella
pathogenicity through the modulation of cellular ubiquitination that degrades
host proteins. However, recent genomic studies identified ipaH genes in the genomes
of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted
from fecal samples of bovine calves, suggesting that non-human hosts may also
be infected by these strains, potentially pathogenic to humans. We performed a
comparative genomic study of the functional repertoires in the ipaH gene family
in Shigella and enteroinvasive Escherichia from human and predicted non-human
hosts. We found that fewer than half of Shigella genomes had a complete set of
ipaH genes, with frequent gene losses and duplications that were not consistent
with the species tree and nomenclature. Non-human host IpaH proteins had a diverse
set of substrate-binding domains and, in contrast to the Shigella proteins, two
variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny
and composition of effectors indicate horizontal gene transfer between E. coli
adapted to different hosts. These results provide a framework for understanding
of ipaH-mediated host-pathogens interactions and suggest a need for a genomic
study of fecal samples from diseased animals.
acknowledgement: 'The project was initiated with Aygul Minnegalieva and Yulia Yakovleva
at the Summer School of Molecular and Theoretical Biology (SMTB-2020), supported
by the Zimin Foundation. We thank Inna Shapovalenko, Daria Abuzova, Elizaveta Kaminskaya,
and Dmitriy Zvezdin for their contribution to the project during SMTB-2020. We also
thank Peter Vlasov for fruitful discussions.This study was supported by the Russian
Foundation for Basic Research (RFBR), Grant # 20-54-14005 and Fonds zur Förderung
der wissenschaftlichen Forschung (FWF), Grant # I5127-B. The work of OB is supported
by the European Union’s Horizon 2020 Research and Innovation Programme under the
Marie Skłodowska-Curie Grant Agreement No. 754411. '
article_number: '6868'
article_processing_charge: No
article_type: original
author:
- first_name: NO
full_name: Dranenko, NO
last_name: Dranenko
- first_name: MN
full_name: Tutukina, MN
last_name: Tutukina
- first_name: MS
full_name: Gelfand, MS
last_name: Gelfand
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Olga
full_name: Bochkareva, Olga
id: C4558D3C-6102-11E9-A62E-F418E6697425
last_name: Bochkareva
orcid: 0000-0003-1006-6639
citation:
ama: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
Reports. 2022;12. doi:10.1038/s41598-022-10827-3
apa: Dranenko, N., Tutukina, M., Gelfand, M., Kondrashov, F., & Bochkareva,
O. (2022). Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
Escherichia. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-022-10827-3
chicago: Dranenko, NO, MN Tutukina, MS Gelfand, Fyodor Kondrashov, and Olga Bochkareva.
“Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human Enteroinvasive Escherichia.”
Scientific Reports. Springer Nature, 2022. https://doi.org/10.1038/s41598-022-10827-3.
ieee: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, and O. Bochkareva, “Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia,” Scientific
Reports, vol. 12. Springer Nature, 2022.
ista: Dranenko N, Tutukina M, Gelfand M, Kondrashov F, Bochkareva O. 2022. Chromosome-encoded
IpaH ubiquitin ligases indicate non-human enteroinvasive Escherichia. Scientific
Reports. 12, 6868.
mla: Dranenko, NO, et al. “Chromosome-Encoded IpaH Ubiquitin Ligases Indicate Non-Human
Enteroinvasive Escherichia.” Scientific Reports, vol. 12, 6868, Springer
Nature, 2022, doi:10.1038/s41598-022-10827-3.
short: N. Dranenko, M. Tutukina, M. Gelfand, F. Kondrashov, O. Bochkareva, Scientific
Reports 12 (2022).
date_created: 2022-05-02T07:08:42Z
date_published: 2022-04-27T00:00:00Z
date_updated: 2023-08-03T06:59:49Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-022-10827-3
ec_funded: 1
external_id:
isi:
- '000788639400032'
pmid:
- '35477739'
file:
- access_level: open_access
checksum: 12601b8a5c6b83bb618f92bcb963ecc9
content_type: application/pdf
creator: dernst
date_created: 2022-05-02T09:05:20Z
date_updated: 2022-05-02T09:05:20Z
file_id: '11349'
file_name: 2022_ScientificReports_Dranenko.pdf
file_size: 3564155
relation: main_file
success: 1
file_date_updated: 2022-05-02T09:05:20Z
has_accepted_license: '1'
intvolume: ' 12'
isi: 1
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Scientific Reports
publication_identifier:
issn:
- 2045-2322
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromosome-encoded IpaH ubiquitin ligases indicate non-human enteroinvasive
Escherichia
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 12
year: '2022'
...
---
_id: '11448'
abstract:
- lang: eng
text: Studies of protein fitness landscapes reveal biophysical constraints guiding
protein evolution and empower prediction of functional proteins. However, generalisation
of these findings is limited due to scarceness of systematic data on fitness landscapes
of proteins with a defined evolutionary relationship. We characterized the fitness
peaks of four orthologous fluorescent proteins with a broad range of sequence
divergence. While two of the four studied fitness peaks were sharp, the other
two were considerably flatter, being almost entirely free of epistatic interactions.
Mutationally robust proteins, characterized by a flat fitness peak, were not optimal
templates for machine-learning-driven protein design – instead, predictions were
more accurate for fragile proteins with epistatic landscapes. Our work paves insights
for practical application of fitness landscape heterogeneity in protein engineering.
acknowledged_ssus:
- _id: LifeSc
- _id: Bio
acknowledgement: "We thank Ondřej Draganov, Rodrigo Redondo, Bor Kavčič, Mia Juračić
and Andrea Pauli for discussion and technical advice. We thank Anita Testa Salmazo
for advice on resin protein purification, Dmitry Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure, and Josef Houser and Eva Fujdiarova
for technical assistance and data interpretation. Core facility Biomolecular Interactions
and Crystallization of CEITEC Masaryk University is gratefully acknowledged for
the obtaining of the scientific data presented in this paper. This research was
supported by the Scientific Service Units (SSU) of IST-Austria\r\nthrough resources
provided by the Bioimaging Facility (BIF), and the Life Science Facility (LSF).
MiSeq and HiSeq NGS sequencing was performed by the Next Generation Sequencing Facility
at Vienna BioCenter Core Facilities (VBCF), member of the Vienna BioCenter (VBC),
Austria. FACS was performed at the BioOptics Facility of the Institute of Molecular
Pathology (IMP), Austria. We also thank the Biomolecular Crystallography Facility
in the Vanderbilt University Center for Structural Biology. We are grateful to Joel
M Harp for help with X-ray data collection. This work was supported by the ERC Consolidator
grant to FAK (771209—CharFL). KSS acknowledges support by President’s Grant МК–5405.2021.1.4,
the Imperial College Research Fellowship and the MRC London Institute of Medical
Sciences (UKRI MC-A658-5QEA0).\r\nAF is supported by the Marie Skłodowska-Curie
Fellowship (H2020-MSCA-IF-2019, Grant Agreement No. 898203, Project acronym \"FLINDIP\").
Experiments were partially carried out using equipment provided by the Institute
of Bioorganic Chemistry of the Russian Academy of Sciences Сore Facility (CKP IBCH).
This work was supported by a Russian Science Foundation grant 19-74-10102.This project
has received funding from the European Union’s Horizon 2020 research and innovation
programme under the Marie Skłodowska-Curie Grant Agreement No. 665,385."
article_number: '75842'
article_processing_charge: No
article_type: original
author:
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Aubin
full_name: Fleiss, Aubin
last_name: Fleiss
- first_name: Alexander S
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: Nina G
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Anna A
full_name: Igolkina, Anna A
last_name: Igolkina
- first_name: Jens
full_name: Meiler, Jens
last_name: Meiler
- first_name: Maria-Elisenda
full_name: Alaball Pujol, Maria-Elisenda
last_name: Alaball Pujol
- first_name: Ekaterina V
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Karen S
full_name: Sarkisyan, Karen S
last_name: Sarkisyan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Gonzalez Somermeyer L, Fleiss A, Mishin AS, et al. Heterogeneity of the GFP
fitness landscape and data-driven protein design. eLife. 2022;11. doi:10.7554/elife.75842
apa: Gonzalez Somermeyer, L., Fleiss, A., Mishin, A. S., Bozhanova, N. G., Igolkina,
A. A., Meiler, J., … Kondrashov, F. (2022). Heterogeneity of the GFP fitness landscape
and data-driven protein design. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.75842
chicago: Gonzalez Somermeyer, Louisa, Aubin Fleiss, Alexander S Mishin, Nina G Bozhanova,
Anna A Igolkina, Jens Meiler, Maria-Elisenda Alaball Pujol, Ekaterina V Putintseva,
Karen S Sarkisyan, and Fyodor Kondrashov. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife. eLife Sciences Publications, 2022.
https://doi.org/10.7554/elife.75842.
ieee: L. Gonzalez Somermeyer et al., “Heterogeneity of the GFP fitness landscape
and data-driven protein design,” eLife, vol. 11. eLife Sciences Publications,
2022.
ista: Gonzalez Somermeyer L, Fleiss A, Mishin AS, Bozhanova NG, Igolkina AA, Meiler
J, Alaball Pujol M-E, Putintseva EV, Sarkisyan KS, Kondrashov F. 2022. Heterogeneity
of the GFP fitness landscape and data-driven protein design. eLife. 11, 75842.
mla: Gonzalez Somermeyer, Louisa, et al. “Heterogeneity of the GFP Fitness Landscape
and Data-Driven Protein Design.” ELife, vol. 11, 75842, eLife Sciences
Publications, 2022, doi:10.7554/elife.75842.
short: L. Gonzalez Somermeyer, A. Fleiss, A.S. Mishin, N.G. Bozhanova, A.A. Igolkina,
J. Meiler, M.-E. Alaball Pujol, E.V. Putintseva, K.S. Sarkisyan, F. Kondrashov,
ELife 11 (2022).
date_created: 2022-06-18T09:06:59Z
date_published: 2022-05-05T00:00:00Z
date_updated: 2023-08-03T07:20:15Z
day: '05'
ddc:
- '570'
department:
- _id: GradSch
- _id: FyKo
doi: 10.7554/elife.75842
ec_funded: 1
external_id:
isi:
- '000799197200001'
file:
- access_level: open_access
checksum: 7573c28f44028ab0cc81faef30039e44
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:44:19Z
date_updated: 2022-06-20T07:44:19Z
file_id: '11454'
file_name: 2022_eLife_Somermeyer.pdf
file_size: 5297213
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:44:19Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Heterogeneity of the GFP fitness landscape and data-driven protein design
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '11447'
abstract:
- lang: eng
text: Empirical essays of fitness landscapes suggest that they may be rugged, that
is having multiple fitness peaks. Such fitness landscapes, those that have multiple
peaks, necessarily have special local structures, called reciprocal sign epistasis
(Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the
quantitative relationship between the number of fitness peaks and the number of
reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk
et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis
is a necessary but not sufficient condition for the existence of multiple peaks.
Applying discrete Morse theory, which to our knowledge has never been used in
this context, we extend this result by giving the minimal number of reciprocal
sign epistatic interactions required to create a given number of peaks.
acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful
discussions. Open access funding provided by Austrian Science Fund (FWF). Partially
supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund
(I5127-B) grants to FAK.
article_number: '74'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number
of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z
apa: Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation
between the number of peaks and the number of reciprocal sign epistatic interactions.
Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z
chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova.
“Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic
Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022.
https://doi.org/10.1007/s11538-022-01029-z.
ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between
the number of peaks and the number of reciprocal sign epistatic interactions,”
Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the
number of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 84(8), 74.
mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and
the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical
Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical
Biology 84 (2022).
date_created: 2022-06-17T16:16:15Z
date_published: 2022-06-17T00:00:00Z
date_updated: 2023-08-03T07:20:53Z
day: '17'
ddc:
- '510'
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.1007/s11538-022-01029-z
ec_funded: 1
external_id:
isi:
- '000812509800001'
file:
- access_level: open_access
checksum: 05a1fe7d10914a00c2bca9b447993a65
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:51:32Z
date_updated: 2022-06-20T07:51:32Z
file_id: '11455'
file_name: 2022_BulletinMathBiology_Saona.pdf
file_size: 463025
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:51:32Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '8'
keyword:
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- Pharmacology
- General Environmental Science
- General Biochemistry
- Genetics and Molecular Biology
- General Mathematics
- Immunology
- General Neuroscience
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: Bulletin of Mathematical Biology
publication_identifier:
eissn:
- 1522-9602
issn:
- 0092-8240
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11538-022-01118-z
scopus_import: '1'
status: public
title: Relation between the number of peaks and the number of reciprocal sign epistatic
interactions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 84
year: '2022'
...
---
_id: '12116'
abstract:
- lang: eng
text: Russia’s unprovoked attack on Ukraine has destroyed civilian infrastructure,
including universities, research centers, and other academic infrastructure (1).
Many Ukrainian scholars and researchers remain in Ukraine, and their work has
suffered from major setbacks (2–4). We call on international scientists and institutions
to support them.
article_processing_charge: No
article_type: letter_note
author:
- first_name: Karishma
full_name: Chhugani, Karishma
last_name: Chhugani
- first_name: Alina
full_name: Frolova, Alina
last_name: Frolova
- first_name: Yuriy
full_name: Salyha, Yuriy
last_name: Salyha
- first_name: Andrada
full_name: Fiscutean, Andrada
last_name: Fiscutean
- first_name: Oksana
full_name: Zlenko, Oksana
last_name: Zlenko
- first_name: Sanita
full_name: Reinsone, Sanita
last_name: Reinsone
- first_name: Walter W.
full_name: Wolfsberger, Walter W.
last_name: Wolfsberger
- first_name: Oleksandra V.
full_name: Ivashchenko, Oleksandra V.
last_name: Ivashchenko
- first_name: Megi
full_name: Maci, Megi
last_name: Maci
- first_name: Dmytro
full_name: Dziuba, Dmytro
last_name: Dziuba
- first_name: Andrii
full_name: Parkhomenko, Andrii
last_name: Parkhomenko
- first_name: Eric
full_name: Bortz, Eric
last_name: Bortz
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Paweł P.
full_name: Łabaj, Paweł P.
last_name: Łabaj
- first_name: Veronika
full_name: Romero, Veronika
last_name: Romero
- first_name: Jakub
full_name: Hlávka, Jakub
last_name: Hlávka
- first_name: Taras K.
full_name: Oleksyk, Taras K.
last_name: Oleksyk
- first_name: Serghei
full_name: Mangul, Serghei
last_name: Mangul
citation:
ama: Chhugani K, Frolova A, Salyha Y, et al. Remote opportunities for scholars in
Ukraine. Science. 2022;378(6626):1285-1286. doi:10.1126/science.adg0797
apa: Chhugani, K., Frolova, A., Salyha, Y., Fiscutean, A., Zlenko, O., Reinsone,
S., … Mangul, S. (2022). Remote opportunities for scholars in Ukraine. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.adg0797
chicago: Chhugani, Karishma, Alina Frolova, Yuriy Salyha, Andrada Fiscutean, Oksana
Zlenko, Sanita Reinsone, Walter W. Wolfsberger, et al. “Remote Opportunities for
Scholars in Ukraine.” Science. American Association for the Advancement
of Science, 2022. https://doi.org/10.1126/science.adg0797.
ieee: K. Chhugani et al., “Remote opportunities for scholars in Ukraine,”
Science, vol. 378, no. 6626. American Association for the Advancement of
Science, pp. 1285–1286, 2022.
ista: Chhugani K, Frolova A, Salyha Y, Fiscutean A, Zlenko O, Reinsone S, Wolfsberger
WW, Ivashchenko OV, Maci M, Dziuba D, Parkhomenko A, Bortz E, Kondrashov F, Łabaj
PP, Romero V, Hlávka J, Oleksyk TK, Mangul S. 2022. Remote opportunities for scholars
in Ukraine. Science. 378(6626), 1285–1286.
mla: Chhugani, Karishma, et al. “Remote Opportunities for Scholars in Ukraine.”
Science, vol. 378, no. 6626, American Association for the Advancement of
Science, 2022, pp. 1285–86, doi:10.1126/science.adg0797.
short: K. Chhugani, A. Frolova, Y. Salyha, A. Fiscutean, O. Zlenko, S. Reinsone,
W.W. Wolfsberger, O.V. Ivashchenko, M. Maci, D. Dziuba, A. Parkhomenko, E. Bortz,
F. Kondrashov, P.P. Łabaj, V. Romero, J. Hlávka, T.K. Oleksyk, S. Mangul, Science
378 (2022) 1285–1286.
date_created: 2023-01-12T11:56:30Z
date_published: 2022-12-22T00:00:00Z
date_updated: 2023-10-03T11:01:06Z
day: '22'
department:
- _id: FyKo
doi: 10.1126/science.adg0797
external_id:
isi:
- '000963463700023'
intvolume: ' 378'
isi: 1
issue: '6626'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1126/science.adg0797
month: '12'
oa: 1
oa_version: Published Version
page: 1285-1286
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: Remote opportunities for scholars in Ukraine
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 378
year: '2022'
...
---
_id: '9910'
abstract:
- lang: eng
text: Adult height inspired the first biometrical and quantitative genetic studies
and is a test-case trait for understanding heritability. The studies of height
led to formulation of the classical polygenic model, that has a profound influence
on the way we view and analyse complex traits. An essential part of the classical
model is an assumption of additivity of effects and normality of the distribution
of the residuals. However, it may be expected that the normal approximation will
become insufficient in bigger studies. Here, we demonstrate that when the height
of hundreds of thousands of individuals is analysed, the model complexity needs
to be increased to include non-additive interactions between sex, environment
and genes. Alternatively, the use of log-normal approximation allowed us to still
use the additive effects model. These findings are important for future genetic
and methodologic studies that make use of adult height as an exemplar trait.
acknowledgement: "We are grateful to Marianna Bevova and Pavel Borodin for fruitful
discussion and help with conceptualising our findings and to Lennart C. Karssen
for help with handling the UK Biobank data.\r\n\r\nFunding\r\nThis research has
been conducted using the UK Biobank Resource (project # 41601, “Non-additive effects
in control of complex human traits”). The work of SAS, IAK, and TIS were supported
by Russian Ministry of Science and Education under the 5–100 Excellence Programme.
The work of YSA and TIA was supported by the Ministry of Education and Science of
the RF via the Institute of Cytology and Genetics SB RAS (project number 0324-2019-0040-C-01/AAAA-A17-117092070032-4).
FAK is supported by the ERC Consolidator Grant (ChrFL: 771209)."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Sergei A.
full_name: Slavskii, Sergei A.
last_name: Slavskii
- first_name: Ivan A.
full_name: Kuznetsov, Ivan A.
last_name: Kuznetsov
- first_name: Tatiana I.
full_name: Shashkova, Tatiana I.
last_name: Shashkova
- first_name: Georgii A.
full_name: Bazykin, Georgii A.
last_name: Bazykin
- first_name: Tatiana I.
full_name: Axenovich, Tatiana I.
last_name: Axenovich
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yurii S.
full_name: Aulchenko, Yurii S.
last_name: Aulchenko
citation:
ama: Slavskii SA, Kuznetsov IA, Shashkova TI, et al. The limits of normal approximation
for adult height. European Journal of Human Genetics. 2021;29(7):1082-1091.
doi:10.1038/s41431-021-00836-7
apa: Slavskii, S. A., Kuznetsov, I. A., Shashkova, T. I., Bazykin, G. A., Axenovich,
T. I., Kondrashov, F., & Aulchenko, Y. S. (2021). The limits of normal approximation
for adult height. European Journal of Human Genetics. Springer Nature.
https://doi.org/10.1038/s41431-021-00836-7
chicago: Slavskii, Sergei A., Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A.
Bazykin, Tatiana I. Axenovich, Fyodor Kondrashov, and Yurii S. Aulchenko. “The
Limits of Normal Approximation for Adult Height.” European Journal of Human
Genetics. Springer Nature, 2021. https://doi.org/10.1038/s41431-021-00836-7.
ieee: S. A. Slavskii et al., “The limits of normal approximation for adult
height,” European Journal of Human Genetics, vol. 29, no. 7. Springer Nature,
pp. 1082–1091, 2021.
ista: Slavskii SA, Kuznetsov IA, Shashkova TI, Bazykin GA, Axenovich TI, Kondrashov
F, Aulchenko YS. 2021. The limits of normal approximation for adult height. European
Journal of Human Genetics. 29(7), 1082–1091.
mla: Slavskii, Sergei A., et al. “The Limits of Normal Approximation for Adult Height.”
European Journal of Human Genetics, vol. 29, no. 7, Springer Nature, 2021,
pp. 1082–91, doi:10.1038/s41431-021-00836-7.
short: S.A. Slavskii, I.A. Kuznetsov, T.I. Shashkova, G.A. Bazykin, T.I. Axenovich,
F. Kondrashov, Y.S. Aulchenko, European Journal of Human Genetics 29 (2021) 1082–1091.
date_created: 2021-08-15T22:01:28Z
date_published: 2021-07-01T00:00:00Z
date_updated: 2023-08-11T10:33:42Z
day: '01'
ddc:
- '576'
department:
- _id: FyKo
doi: 10.1038/s41431-021-00836-7
ec_funded: 1
external_id:
isi:
- '000625853200001'
pmid:
- '33664501'
file:
- access_level: open_access
checksum: a676d76f91b0dbe0504c63e469129c2a
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T09:14:36Z
date_updated: 2021-08-16T09:14:36Z
file_id: '9921'
file_name: 2021_EuropeanJournalOfHumanGenetics_Slavskii.pdf
file_size: 1079395
relation: main_file
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file_date_updated: 2021-08-16T09:14:36Z
has_accepted_license: '1'
intvolume: ' 29'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1082-1091
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: European Journal of Human Genetics
publication_identifier:
eissn:
- '14765438'
issn:
- '10184813'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: The limits of normal approximation for adult height
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 29
year: '2021'
...
---
_id: '9905'
abstract:
- lang: eng
text: Vaccines are thought to be the best available solution for controlling the
ongoing SARS-CoV-2 pandemic. However, the emergence of vaccine-resistant strains
may come too rapidly for current vaccine developments to alleviate the health,
economic and social consequences of the pandemic. To quantify and characterize
the risk of such a scenario, we created a SIR-derived model with initial stochastic
dynamics of the vaccine-resistant strain to study the probability of its emergence
and establishment. Using parameters realistically resembling SARS-CoV-2 transmission,
we model a wave-like pattern of the pandemic and consider the impact of the rate
of vaccination and the strength of non-pharmaceutical intervention measures on
the probability of emergence of a resistant strain. As expected, we found that
a fast rate of vaccination decreases the probability of emergence of a resistant
strain. Counterintuitively, when a relaxation of non-pharmaceutical interventions
happened at a time when most individuals of the population have already been vaccinated
the probability of emergence of a resistant strain was greatly increased. Consequently,
we show that a period of transmission reduction close to the end of the vaccination
campaign can substantially reduce the probability of resistant strain establishment.
Our results suggest that policymakers and individuals should consider maintaining
non-pharmaceutical interventions and transmission-reducing behaviours throughout
the entire vaccination period.
acknowledgement: We thank Alexey Kondrashov, Nick Machnik, Raimundo Julian Saona Urmeneta,
Gasper Tkacik and Nick Barton for fruitful discussions. We also thank participants
of EvoLunch seminar at IST Austria and the internal seminar at the Banco de España
for useful comments. The opinions expressed in this document are exclusively of
the authors and, therefore, do not necessarily coincide with those of the Banco
de España or the Eurosystem. ETD is supported by the Swiss National Science and
Louis Jeantet Foundation. The work of FAK was in part supported by the ERC Consolidator
Grant (771209-CharFL).
article_number: '15729'
article_processing_charge: Yes
article_type: original
author:
- first_name: Simon
full_name: Rella, Simon
id: B4765ACA-AA38-11E9-AC9A-0930E6697425
last_name: Rella
- first_name: Yuliya A.
full_name: Kulikova, Yuliya A.
last_name: Kulikova
- first_name: Emmanouil T.
full_name: Dermitzakis, Emmanouil T.
last_name: Dermitzakis
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. Rates of SARS-CoV-2 transmission
and vaccination impact the fate of vaccine-resistant strains. Scientific Reports.
2021;11(1). doi:10.1038/s41598-021-95025-3
apa: Rella, S., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. (2021).
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-021-95025-3
chicago: Rella, Simon, Yuliya A. Kulikova, Emmanouil T. Dermitzakis, and Fyodor
Kondrashov. “Rates of SARS-CoV-2 Transmission and Vaccination Impact the Fate
of Vaccine-Resistant Strains.” Scientific Reports. Springer Nature, 2021.
https://doi.org/10.1038/s41598-021-95025-3.
ieee: S. Rella, Y. A. Kulikova, E. T. Dermitzakis, and F. Kondrashov, “Rates of
SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains,”
Scientific Reports, vol. 11, no. 1. Springer Nature, 2021.
ista: Rella S, Kulikova YA, Dermitzakis ET, Kondrashov F. 2021. Rates of SARS-CoV-2
transmission and vaccination impact the fate of vaccine-resistant strains. Scientific
Reports. 11(1), 15729.
mla: Rella, Simon, et al. “Rates of SARS-CoV-2 Transmission and Vaccination Impact
the Fate of Vaccine-Resistant Strains.” Scientific Reports, vol. 11, no.
1, 15729, Springer Nature, 2021, doi:10.1038/s41598-021-95025-3.
short: S. Rella, Y.A. Kulikova, E.T. Dermitzakis, F. Kondrashov, Scientific Reports
11 (2021).
date_created: 2021-08-15T22:01:26Z
date_published: 2021-07-30T00:00:00Z
date_updated: 2023-08-11T10:42:58Z
day: '30'
ddc:
- '570'
- '610'
department:
- _id: FyKo
doi: 10.1038/s41598-021-95025-3
ec_funded: 1
external_id:
isi:
- '000683329100001'
pmid:
- '34330988'
file:
- access_level: open_access
checksum: ac86892ed17e6724c7251844da5cef5c
content_type: application/pdf
creator: asandaue
date_created: 2021-08-16T11:36:49Z
date_updated: 2021-08-16T11:36:49Z
file_id: '9927'
file_name: 2021_ScientificReports_Rella.pdf
file_size: 3432001
relation: main_file
success: 1
file_date_updated: 2021-08-16T11:36:49Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- description: News on IST Website
relation: press_release
url: https://ist.ac.at/en/news/counterintuitive-dynamics-threaten-the-end-of-the-pandemic/
scopus_import: '1'
status: public
title: Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant
strains
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2021'
...
---
_id: '8151'
abstract:
- lang: eng
text: The main idea behind the Core Project is to teach first year students at IST
scientific communication skills and let them practice by presenting their research
within an interdisciplinary environment. Over the course of the first semester,
students participated in seminars, where they shared their results with the colleagues
from other fields and took part in discussions on relevant subjects. The main
focus during this sessions was on delivering the information in a simplified and
comprehensible way, going into the very basics of a subject if necessary. At the
end, the students were asked to present their research in the written form to
exercise their writing skills. The reports were gathered in this document. All
of them were reviewed by the teaching assistants and write-ups illustrating unique
stylistic features and, in general, an outstanding level of writing skills, were
honorably mentioned in the section "Selected Reports".
article_processing_charge: No
author:
- first_name: Mikhail
full_name: Maslov, Mikhail
id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87
last_name: Maslov
orcid: 0000-0003-4074-2570
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Christina
full_name: Artner, Christina
id: 45DF286A-F248-11E8-B48F-1D18A9856A87
last_name: Artner
- first_name: Mike
full_name: Hennessey-Wesen, Mike
id: 3F338C72-F248-11E8-B48F-1D18A9856A87
last_name: Hennessey-Wesen
- first_name: Bor
full_name: Kavcic, Bor
id: 350F91D2-F248-11E8-B48F-1D18A9856A87
last_name: Kavcic
orcid: 0000-0001-6041-254X
- first_name: Nick N
full_name: Machnik, Nick N
id: 3591A0AA-F248-11E8-B48F-1D18A9856A87
last_name: Machnik
- first_name: Roshan K
full_name: Satapathy, Roshan K
id: 46046B7A-F248-11E8-B48F-1D18A9856A87
last_name: Satapathy
- first_name: Isabella
full_name: Tomanek, Isabella
id: 3981F020-F248-11E8-B48F-1D18A9856A87
last_name: Tomanek
orcid: 0000-0001-6197-363X
citation:
ama: Maslov M, Kondrashov F, Artner C, et al. Core Project Proceedings. IST
Austria; 2020.
apa: Maslov, M., Kondrashov, F., Artner, C., Hennessey-Wesen, M., Kavcic, B., Machnik,
N. N., … Tomanek, I. (2020). Core Project Proceedings. IST Austria.
chicago: Maslov, Mikhail, Fyodor Kondrashov, Christina Artner, Mike Hennessey-Wesen,
Bor Kavcic, Nick N Machnik, Roshan K Satapathy, and Isabella Tomanek. Core
Project Proceedings. IST Austria, 2020.
ieee: M. Maslov et al., Core Project Proceedings. IST Austria, 2020.
ista: Maslov M, Kondrashov F, Artner C, Hennessey-Wesen M, Kavcic B, Machnik NN,
Satapathy RK, Tomanek I. 2020. Core Project Proceedings, IST Austria, 425p.
mla: Maslov, Mikhail, et al. Core Project Proceedings. IST Austria, 2020.
short: M. Maslov, F. Kondrashov, C. Artner, M. Hennessey-Wesen, B. Kavcic, N.N.
Machnik, R.K. Satapathy, I. Tomanek, Core Project Proceedings, IST Austria, 2020.
date_created: 2020-07-22T14:48:14Z
date_published: 2020-06-01T00:00:00Z
date_updated: 2023-02-23T13:26:00Z
day: '01'
ddc:
- '510'
- '530'
- '570'
extern: '1'
file:
- access_level: local
content_type: application/pdf
creator: dernst
date_created: 2020-07-22T14:45:07Z
date_updated: 2020-07-22T14:45:07Z
file_id: '8152'
file_name: Core_Project_Proceedings_mod.pdf
file_size: 169620437
relation: main_file
file_date_updated: 2020-07-22T14:45:07Z
has_accepted_license: '1'
language:
- iso: eng
month: '06'
oa_version: None
page: '425'
publication_status: published
publisher: IST Austria
status: public
title: Core Project Proceedings
type: report
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2020'
...
---
_id: '7931'
abstract:
- lang: eng
text: In the course of sample preparation for Next Generation Sequencing (NGS),
DNA is fragmented by various methods. Fragmentation shows a persistent bias with
regard to the cleavage rates of various dinucleotides. With the exception of CpG
dinucleotides the previously described biases were consistent with results of
the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides
including the methylated CpG and unmethylated CpG dinucleotides using data of
the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that
the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides.
Using this information, we developed a classifier for distinguishing cancer and
healthy tissues based on their CpG islands statuses of the fragmentation. A simple
Support Vector Machine classifier based on this algorithm shows an accuracy of
84%. The proposed method allows the detection of epigenetic markers purely based
on mechanochemical DNA fragmentation, which can be detected by a simple analysis
of the NGS sequencing data.
article_number: '8635'
article_processing_charge: No
article_type: original
author:
- first_name: Leonid A.
full_name: Uroshlev, Leonid A.
last_name: Uroshlev
- first_name: Eldar T.
full_name: Abdullaev, Eldar T.
last_name: Abdullaev
- first_name: Iren R.
full_name: Umarova, Iren R.
last_name: Umarova
- first_name: Irina A.
full_name: Il’Icheva, Irina A.
last_name: Il’Icheva
- first_name: Larisa A.
full_name: Panchenko, Larisa A.
last_name: Panchenko
- first_name: Robert V.
full_name: Polozov, Robert V.
last_name: Polozov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Yury D.
full_name: Nechipurenko, Yury D.
last_name: Nechipurenko
- first_name: Sergei L.
full_name: Grokhovsky, Sergei L.
last_name: Grokhovsky
citation:
ama: Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of
the methylation level of CpG islands from NGS data. Scientific Reports.
2020;10. doi:10.1038/s41598-020-65406-1
apa: Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko,
L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports.
Springer Nature. https://doi.org/10.1038/s41598-020-65406-1
chicago: Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva,
Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko,
and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level
of CpG Islands from NGS Data.” Scientific Reports. Springer Nature, 2020.
https://doi.org/10.1038/s41598-020-65406-1.
ieee: L. A. Uroshlev et al., “A method for identification of the methylation
level of CpG islands from NGS data,” Scientific Reports, vol. 10. Springer
Nature, 2020.
ista: Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov
RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification
of the methylation level of CpG islands from NGS data. Scientific Reports. 10,
8635.
mla: Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation
Level of CpG Islands from NGS Data.” Scientific Reports, vol. 10, 8635,
Springer Nature, 2020, doi:10.1038/s41598-020-65406-1.
short: L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko,
R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports
10 (2020).
date_created: 2020-06-07T22:00:51Z
date_published: 2020-05-25T00:00:00Z
date_updated: 2023-08-21T07:00:17Z
day: '25'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41598-020-65406-1
external_id:
isi:
- '000560774200007'
file:
- access_level: open_access
checksum: 099e51611a5b7ca04244d03b2faddf33
content_type: application/pdf
creator: dernst
date_created: 2020-06-08T06:27:32Z
date_updated: 2020-07-14T12:48:05Z
file_id: '7947'
file_name: 2020_ScientificReports_Uroshlev.pdf
file_size: 1001724
relation: main_file
file_date_updated: 2020-07-14T12:48:05Z
has_accepted_license: '1'
intvolume: ' 10'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_identifier:
eissn:
- '20452322'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: A method for identification of the methylation level of CpG islands from NGS
data
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 10
year: '2020'
...
---
_id: '8645'
abstract:
- lang: eng
text: 'Epistasis, the context-dependence of the contribution of an amino acid substitution
to fitness, is common in evolution. To detect epistasis, fitness must be measured
for at least four genotypes: the reference genotype, two different single mutants
and a double mutant with both of the single mutations. For higher-order epistasis
of the order n, fitness has to be measured for all 2n genotypes of an n-dimensional
hypercube in genotype space forming a ‘combinatorially complete dataset’. So far,
only a handful of such datasets have been produced by manual curation. Concurrently,
random mutagenesis experiments have produced measurements of fitness and other
phenotypes in a high-throughput manner, potentially containing a number of combinatorially
complete datasets. We present an effective recursive algorithm for finding all
hypercube structures in random mutagenesis experimental data. To test the algorithm,
we applied it to the data from a recent HIS3 protein dataset and found all 199
847 053 unique combinatorially complete genotype combinations of dimensionality
ranging from 2 to 12. The algorithm may be useful for researchers looking for
higher-order epistasis in their high-throughput experimental data.'
acknowledgement: 'This work was supported by the European Research Council under the
European Union’s Seventh Framework Programme (FP7/2007-2013, ERC grant agreement
335980_EinME) and Startup package to the Ivankov laboratory at Skolkovo Institute
of Science and Technology. The work was started at the School of Molecular and Theoretical
Biology 2017 supported by the Zimin Foundation. N.S.B. was supported by the Woman
Scientists Support Grant in Centre for Genomic Regulation (CRG). '
article_processing_charge: No
article_type: original
author:
- first_name: Laura A
full_name: Esteban, Laura A
last_name: Esteban
- first_name: Lyubov R
full_name: Lonishin, Lyubov R
last_name: Lonishin
- first_name: Daniil M
full_name: Bobrovskiy, Daniil M
last_name: Bobrovskiy
- first_name: Gregory
full_name: Leleytner, Gregory
last_name: Leleytner
- first_name: Natalya S
full_name: Bogatyreva, Natalya S
last_name: Bogatyreva
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: 'Dmitry N '
full_name: 'Ivankov, Dmitry N '
last_name: Ivankov
citation:
ama: 'Esteban LA, Lonishin LR, Bobrovskiy DM, et al. HypercubeME: Two hundred million
combinatorially complete datasets from a single experiment. Bioinformatics.
2020;36(6):1960-1962. doi:10.1093/bioinformatics/btz841'
apa: 'Esteban, L. A., Lonishin, L. R., Bobrovskiy, D. M., Leleytner, G., Bogatyreva,
N. S., Kondrashov, F., & Ivankov, D. N. (2020). HypercubeME: Two hundred million
combinatorially complete datasets from a single experiment. Bioinformatics.
Oxford Academic. https://doi.org/10.1093/bioinformatics/btz841'
chicago: 'Esteban, Laura A, Lyubov R Lonishin, Daniil M Bobrovskiy, Gregory Leleytner,
Natalya S Bogatyreva, Fyodor Kondrashov, and Dmitry N Ivankov. “HypercubeME:
Two Hundred Million Combinatorially Complete Datasets from a Single Experiment.”
Bioinformatics. Oxford Academic, 2020. https://doi.org/10.1093/bioinformatics/btz841.'
ieee: 'L. A. Esteban et al., “HypercubeME: Two hundred million combinatorially
complete datasets from a single experiment,” Bioinformatics, vol. 36, no.
6. Oxford Academic, pp. 1960–1962, 2020.'
ista: 'Esteban LA, Lonishin LR, Bobrovskiy DM, Leleytner G, Bogatyreva NS, Kondrashov
F, Ivankov DN. 2020. HypercubeME: Two hundred million combinatorially complete
datasets from a single experiment. Bioinformatics. 36(6), 1960–1962.'
mla: 'Esteban, Laura A., et al. “HypercubeME: Two Hundred Million Combinatorially
Complete Datasets from a Single Experiment.” Bioinformatics, vol. 36, no.
6, Oxford Academic, 2020, pp. 1960–62, doi:10.1093/bioinformatics/btz841.'
short: L.A. Esteban, L.R. Lonishin, D.M. Bobrovskiy, G. Leleytner, N.S. Bogatyreva,
F. Kondrashov, D.N. Ivankov, Bioinformatics 36 (2020) 1960–1962.
date_created: 2020-10-11T22:01:14Z
date_published: 2020-03-15T00:00:00Z
date_updated: 2023-08-22T09:57:29Z
day: '15'
ddc:
- '000'
- '570'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/btz841
ec_funded: 1
external_id:
isi:
- '000538696800054'
pmid:
- '31742320'
file:
- access_level: open_access
checksum: 21d6f71839deb3b83e4a356193f72767
content_type: application/pdf
creator: dernst
date_created: 2020-10-12T12:02:09Z
date_updated: 2020-10-12T12:02:09Z
file_id: '8649'
file_name: 2020_Bioinformatics_Esteban.pdf
file_size: 308341
relation: main_file
success: 1
file_date_updated: 2020-10-12T12:02:09Z
has_accepted_license: '1'
intvolume: ' 36'
isi: 1
issue: '6'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 1960-1962
pmid: 1
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Bioinformatics
publication_identifier:
eissn:
- 1460-2059
issn:
- 1367-4803
publication_status: published
publisher: Oxford Academic
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'HypercubeME: Two hundred million combinatorially complete datasets from a
single experiment'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2020'
...
---
_id: '7889'
abstract:
- lang: eng
text: Autoluminescent plants engineered to express a bacterial bioluminescence gene
cluster in plastids have not been widely adopted because of low light output.
We engineered tobacco plants with a fungal bioluminescence system that converts
caffeic acid (present in all plants) into luciferin and report self-sustained
luminescence that is visible to the naked eye. Our findings could underpin development
of a suite of imaging tools for plants.
acknowledgement: "This study was designed, performed and funded by Planta LLC. We
thank K. Wood for assisting in manuscript development. Planta acknowledges support
from the Skolkovo Innovation Centre. We thank D. Bolotin and the Milaboratory (milaboratory.com)
for access to computing and storage infrastructure. We thank S. Shakhov for providing\r\nphotography
equipment. The Synthetic Biology Group is funded by the MRC London Institute of
Medical Sciences (UKRI MC-A658-5QEA0, K.S.S.). K.S.S. is supported by an Imperial
College Research Fellowship. Experiments were partially carried out using equipment
provided by the Institute of Bioorganic Chemistry of the Russian Academy\r\nof Sciences
Сore Facility (CKP IBCH; supported by the Russian Ministry of Education and Science
Grant RFMEFI62117X0018). The F.A.K. lab is supported by ERC grant agreement 771209—CharFL.
This project received funding from the European Union’s Horizon 2020 Research and
Innovation Programme under Marie Skłodowska-Curie\r\nGrant Agreement 665385. K.S.S.
acknowledges support by President’s Grant 075-15-2019-411. Design and assembly of
some of the plasmids was supported by Russian Science Foundation grant 19-74-10102.
Imaging experiments were partially supported by Russian Science Foundation grant
17-14-01169p. LC-MS/MS analyses of extracts were\r\nsupported by Russian Science
Foundation grant 16-14-00052p. Design and assembly of plasmids was partially supported
by grant 075-15-2019-1789 from the Ministry of Science and Higher Education of the
Russian Federation allocated to the Center for Precision Genome Editing and Genetic
Technologies for Biomedicine. The authors\r\nwould like to acknowledge the work
of Genomics Core Facility of the Skolkovo Institute of Science and Technology, which
performed the sequencing and bioinformatic analysis."
article_processing_charge: No
article_type: original
author:
- first_name: Tatiana
full_name: Mitiouchkina, Tatiana
last_name: Mitiouchkina
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Tatiana V.
full_name: Chepurnyh, Tatiana V.
last_name: Chepurnyh
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Tatiana A.
full_name: Karataeva, Tatiana A.
last_name: Karataeva
- first_name: Kseniia A.
full_name: Palkina, Kseniia A.
last_name: Palkina
- first_name: Ekaterina S.
full_name: Shakhova, Ekaterina S.
last_name: Shakhova
- first_name: Liliia I.
full_name: Fakhranurova, Liliia I.
last_name: Fakhranurova
- first_name: Sofia V.
full_name: Chekova, Sofia V.
last_name: Chekova
- first_name: Aleksandra S.
full_name: Tsarkova, Aleksandra S.
last_name: Tsarkova
- first_name: Yaroslav V.
full_name: Golubev, Yaroslav V.
last_name: Golubev
- first_name: Vadim V.
full_name: Negrebetsky, Vadim V.
last_name: Negrebetsky
- first_name: Sergey A.
full_name: Dolgushin, Sergey A.
last_name: Dolgushin
- first_name: Pavel V.
full_name: Shalaev, Pavel V.
last_name: Shalaev
- first_name: Dmitry
full_name: Shlykov, Dmitry
last_name: Shlykov
- first_name: Olesya A.
full_name: Melnik, Olesya A.
last_name: Melnik
- first_name: Victoria O.
full_name: Shipunova, Victoria O.
last_name: Shipunova
- first_name: Sergey M.
full_name: Deyev, Sergey M.
last_name: Deyev
- first_name: Andrey I.
full_name: Bubyrev, Andrey I.
last_name: Bubyrev
- first_name: Alexander S.
full_name: Pushin, Alexander S.
last_name: Pushin
- first_name: Vladimir V.
full_name: Choob, Vladimir V.
last_name: Choob
- first_name: Sergey V.
full_name: Dolgov, Sergey V.
last_name: Dolgov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
- first_name: Karen S.
full_name: Sarkisyan, Karen S.
last_name: Sarkisyan
citation:
ama: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, et al. Plants with genetically
encoded autoluminescence. Nature Biotechnology. 2020;38:944-946. doi:10.1038/s41587-020-0500-9
apa: Mitiouchkina, T., Mishin, A. S., Gonzalez Somermeyer, L., Markina, N. M., Chepurnyh,
T. V., Guglya, E. B., … Sarkisyan, K. S. (2020). Plants with genetically encoded
autoluminescence. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-020-0500-9
chicago: Mitiouchkina, Tatiana, Alexander S. Mishin, Louisa Gonzalez Somermeyer,
Nadezhda M. Markina, Tatiana V. Chepurnyh, Elena B. Guglya, Tatiana A. Karataeva,
et al. “Plants with Genetically Encoded Autoluminescence.” Nature Biotechnology.
Springer Nature, 2020. https://doi.org/10.1038/s41587-020-0500-9.
ieee: T. Mitiouchkina et al., “Plants with genetically encoded autoluminescence,”
Nature Biotechnology, vol. 38. Springer Nature, pp. 944–946, 2020.
ista: Mitiouchkina T, Mishin AS, Gonzalez Somermeyer L, Markina NM, Chepurnyh TV,
Guglya EB, Karataeva TA, Palkina KA, Shakhova ES, Fakhranurova LI, Chekova SV,
Tsarkova AS, Golubev YV, Negrebetsky VV, Dolgushin SA, Shalaev PV, Shlykov D,
Melnik OA, Shipunova VO, Deyev SM, Bubyrev AI, Pushin AS, Choob VV, Dolgov SV,
Kondrashov F, Yampolsky IV, Sarkisyan KS. 2020. Plants with genetically encoded
autoluminescence. Nature Biotechnology. 38, 944–946.
mla: Mitiouchkina, Tatiana, et al. “Plants with Genetically Encoded Autoluminescence.”
Nature Biotechnology, vol. 38, Springer Nature, 2020, pp. 944–46, doi:10.1038/s41587-020-0500-9.
short: T. Mitiouchkina, A.S. Mishin, L. Gonzalez Somermeyer, N.M. Markina, T.V.
Chepurnyh, E.B. Guglya, T.A. Karataeva, K.A. Palkina, E.S. Shakhova, L.I. Fakhranurova,
S.V. Chekova, A.S. Tsarkova, Y.V. Golubev, V.V. Negrebetsky, S.A. Dolgushin, P.V.
Shalaev, D. Shlykov, O.A. Melnik, V.O. Shipunova, S.M. Deyev, A.I. Bubyrev, A.S.
Pushin, V.V. Choob, S.V. Dolgov, F. Kondrashov, I.V. Yampolsky, K.S. Sarkisyan,
Nature Biotechnology 38 (2020) 944–946.
date_created: 2020-05-25T15:02:00Z
date_published: 2020-04-27T00:00:00Z
date_updated: 2023-09-05T15:30:34Z
day: '27'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1038/s41587-020-0500-9
ec_funded: 1
external_id:
isi:
- '000529298800003'
pmid:
- '32341562'
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oa_version: Submitted Version
page: 944-946
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call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Biotechnology
publication_identifier:
eissn:
- 1546-1696
issn:
- 1087-0156
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
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url: https://doi.org/10.1038/s41587-020-0578-0
scopus_import: '1'
status: public
title: Plants with genetically encoded autoluminescence
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 38
year: '2020'
...
---
_id: '6419'
abstract:
- lang: eng
text: Characterizing the fitness landscape, a representation of fitness for a large
set of genotypes, is key to understanding how genetic information is interpreted
to create functional organisms. Here we determined the evolutionarily-relevant
segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine
synthesis pathway, focusing on combinations of amino acid states found at orthologous
sites of extant species. Just 15% of amino acids found in yeast His3 orthologues
were always neutral while the impact on fitness of the remaining 85% depended
on the genetic background. Furthermore, at 67% of sites, amino acid replacements
were under sign epistasis, having both strongly positive and negative effect in
different genetic backgrounds. 46% of sites were under reciprocal sign epistasis.
The fitness impact of amino acid replacements was influenced by only a few genetic
backgrounds but involved interaction of multiple sites, shaping a rugged fitness
landscape in which many of the shortest paths between highly fit genotypes are
inaccessible.
article_number: e1008079
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author:
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full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the
interactions of amino acids from orthologous sequences shaping a complex fitness
landscape. PLoS Genetics. 2019;15(4). doi:10.1371/journal.pgen.1008079
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions
of amino acids from orthologous sequences shaping a complex fitness landscape.
PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An
Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences
Shaping a Complex Fitness Landscape.” PLoS Genetics. Public Library of
Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.
ieee: V. Pokusaeva et al., “An experimental assay of the interactions of
amino acids from orthologous sequences shaping a complex fitness landscape,” PLoS
Genetics, vol. 15, no. 4. Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino
acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics.
15(4), e1008079.
mla: Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino
Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” PLoS
Genetics, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).
date_created: 2019-05-13T07:58:38Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:37Z
day: '10'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079
ec_funded: 1
external_id:
isi:
- '000466866000029'
file:
- access_level: open_access
checksum: cf3889c8a8a16053dacf9c3776cbe217
content_type: application/pdf
creator: dernst
date_created: 2019-05-14T08:26:08Z
date_updated: 2020-07-14T12:47:30Z
file_id: '6445'
file_name: 2019_PLOSGenetics_Pokusaeva.pdf
file_size: 3726017
relation: main_file
file_date_updated: 2020-07-14T12:47:30Z
has_accepted_license: '1'
intvolume: ' 15'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: PLoS Genetics
publication_identifier:
eissn:
- '15537404'
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
related_material:
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relation: research_data
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relation: research_data
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relation: research_data
status: public
scopus_import: '1'
status: public
title: An experimental assay of the interactions of amino acids from orthologous sequences
shaping a complex fitness landscape
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
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orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.
ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and
sequencing results.” Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. A statistical summary of segment libraries and sequencing
results, Public Library of Science, 10.1371/journal.pgen.1008079.s011.
mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and
Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:50:15Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
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relation: used_in_publication
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status: public
title: A statistical summary of segment libraries and sequencing results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
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---
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author:
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id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. A statistical summary of segment
libraries and sequencing results. 2019. doi:10.1371/journal.pgen.1008079.s011
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). A statistical summary of segment libraries
and sequencing results. Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s011
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “A
Statistical Summary of Segment Libraries and Sequencing Results.” Public Library
of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s011.
ieee: V. Pokusaeva et al., “A statistical summary of segment libraries and
sequencing results.” Public Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov
F. 2019. A statistical summary of segment libraries and sequencing results, Public
Library of Science, 10.1371/journal.pgen.1008079.s011.
mla: Pokusaeva, Victoria, et al. A Statistical Summary of Segment Libraries and
Sequencing Results. Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s011.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, I.S. Povolotskaya, G.J. Filion,
L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T11:08:20Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s011
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
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relation: used_in_publication
status: public
status: public
title: A statistical summary of segment libraries and sequencing results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
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- first_name: Victoria
full_name: Pokusaeva, Victoria
id: 3184041C-F248-11E8-B48F-1D18A9856A87
last_name: Pokusaeva
orcid: 0000-0001-7660-444X
- first_name: Dinara R.
full_name: Usmanova, Dinara R.
last_name: Usmanova
- first_name: Ekaterina V.
full_name: Putintseva, Ekaterina V.
last_name: Putintseva
- first_name: Lorena
full_name: Espinar, Lorena
last_name: Espinar
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Natalya S.
full_name: Bogatyreva, Natalya S.
last_name: Bogatyreva
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
- first_name: Arseniy
full_name: Akopyan, Arseniy
id: 430D2C90-F248-11E8-B48F-1D18A9856A87
last_name: Akopyan
orcid: 0000-0002-2548-617X
- first_name: Sergey
full_name: Avvakumov, Sergey
id: 3827DAC8-F248-11E8-B48F-1D18A9856A87
last_name: Avvakumov
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Guillaume J.
full_name: Filion, Guillaume J.
last_name: Filion
- first_name: Lucas B.
full_name: Carey, Lucas B.
last_name: Carey
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Pokusaeva V, Usmanova DR, Putintseva EV, et al. Multiple alignment of His3
orthologues. 2019. doi:10.1371/journal.pgen.1008079.s010
apa: Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan,
K., Mishin, A. S., … Kondrashov, F. (2019). Multiple alignment of His3 orthologues.
Public Library of Science. https://doi.org/10.1371/journal.pgen.1008079.s010
chicago: Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena
Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “Multiple
Alignment of His3 Orthologues.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pgen.1008079.s010.
ieee: V. Pokusaeva et al., “Multiple alignment of His3 orthologues.” Public
Library of Science, 2019.
ista: Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS,
Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ,
Carey LB, Kondrashov F. 2019. Multiple alignment of His3 orthologues, Public Library
of Science, 10.1371/journal.pgen.1008079.s010.
mla: Pokusaeva, Victoria, et al. Multiple Alignment of His3 Orthologues.
Public Library of Science, 2019, doi:10.1371/journal.pgen.1008079.s010.
short: V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S.
Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya,
G.J. Filion, L.B. Carey, F. Kondrashov, (2019).
date_created: 2021-08-06T08:38:50Z
date_published: 2019-04-10T00:00:00Z
date_updated: 2023-08-25T10:30:36Z
day: '10'
department:
- _id: FyKo
doi: 10.1371/journal.pgen.1008079.s010
month: '04'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '6419'
relation: used_in_publication
status: public
status: public
title: Multiple alignment of His3 orthologues
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '7181'
abstract:
- lang: eng
text: Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary
predictions1,2, but the complexity of aligning large datasets requires the use
of approximate solutions3, including the progressive algorithm4. Progressive MSA
methods start by aligning the most similar sequences and subsequently incorporate
the remaining sequences, from leaf-to-root, based on a guide-tree. Their accuracy
declines substantially as the number of sequences is scaled up5. We introduce
a regressive algorithm that enables MSA of up to 1.4 million sequences on a standard
workstation and substantially improves accuracy on datasets larger than 10,000
sequences. Our regressive algorithm works the other way around to the progressive
algorithm and begins by aligning the most dissimilar sequences. It uses an efficient
divide-and-conquer strategy to run third-party alignment methods in linear time,
regardless of their original complexity. Our approach will enable analyses of
extremely large genomic datasets such as the recently announced Earth BioGenome
Project, which comprises 1.5 million eukaryotic genomes6.
article_processing_charge: No
article_type: original
author:
- first_name: Edgar
full_name: Garriga, Edgar
last_name: Garriga
- first_name: Paolo
full_name: Di Tommaso, Paolo
last_name: Di Tommaso
- first_name: Cedrik
full_name: Magis, Cedrik
last_name: Magis
- first_name: Ionas
full_name: Erb, Ionas
last_name: Erb
- first_name: Leila
full_name: Mansouri, Leila
last_name: Mansouri
- first_name: Athanasios
full_name: Baltzis, Athanasios
last_name: Baltzis
- first_name: Hafid
full_name: Laayouni, Hafid
last_name: Laayouni
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Evan
full_name: Floden, Evan
last_name: Floden
- first_name: Cedric
full_name: Notredame, Cedric
last_name: Notredame
citation:
ama: Garriga E, Di Tommaso P, Magis C, et al. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 2019;37(12):1466-1470.
doi:10.1038/s41587-019-0333-6
apa: Garriga, E., Di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,
… Notredame, C. (2019). Large multiple sequence alignments with a root-to-leaf
regressive method. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-019-0333-6
chicago: Garriga, Edgar, Paolo Di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri,
Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric
Notredame. “Large Multiple Sequence Alignments with a Root-to-Leaf Regressive
Method.” Nature Biotechnology. Springer Nature, 2019. https://doi.org/10.1038/s41587-019-0333-6.
ieee: E. Garriga et al., “Large multiple sequence alignments with a root-to-leaf
regressive method,” Nature Biotechnology, vol. 37, no. 12. Springer Nature,
pp. 1466–1470, 2019.
ista: Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H,
Kondrashov F, Floden E, Notredame C. 2019. Large multiple sequence alignments
with a root-to-leaf regressive method. Nature Biotechnology. 37(12), 1466–1470.
mla: Garriga, Edgar, et al. “Large Multiple Sequence Alignments with a Root-to-Leaf
Regressive Method.” Nature Biotechnology, vol. 37, no. 12, Springer Nature,
2019, pp. 1466–70, doi:10.1038/s41587-019-0333-6.
short: E. Garriga, P. Di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H.
Laayouni, F. Kondrashov, E. Floden, C. Notredame, Nature Biotechnology 37 (2019)
1466–1470.
date_created: 2019-12-15T23:00:43Z
date_published: 2019-12-01T00:00:00Z
date_updated: 2023-09-06T14:32:52Z
day: '01'
department:
- _id: FyKo
doi: 10.1038/s41587-019-0333-6
ec_funded: 1
external_id:
isi:
- '000500748900021'
pmid:
- '31792410'
intvolume: ' 37'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943/
month: '12'
oa: 1
oa_version: Submitted Version
page: 1466-1470
pmid: 1
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
publication: Nature Biotechnology
publication_identifier:
eissn:
- '15461696'
issn:
- '10870156'
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
record:
- id: '13059'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Large multiple sequence alignments with a root-to-leaf regressive method
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 37
year: '2019'
...
---
_id: '13059'
abstract:
- lang: eng
text: "This dataset contains a GitHub repository containing all the data, analysis,
Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast
and accurate large multiple sequence alignments with a root-to-leaf regressive
method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated
and well as the main figures and tables from the manuscript.\r\nThe repository
is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor
details on how to use the regressive alignment algorithm, see the T-Coffee software
suite (https://github.com/cbcrg/tcoffee)."
article_processing_charge: No
author:
- first_name: Edgar
full_name: Garriga, Edgar
last_name: Garriga
- first_name: Paolo
full_name: di Tommaso, Paolo
last_name: di Tommaso
- first_name: Cedrik
full_name: Magis, Cedrik
last_name: Magis
- first_name: Ionas
full_name: Erb, Ionas
last_name: Erb
- first_name: Leila
full_name: Mansouri, Leila
last_name: Mansouri
- first_name: Athanasios
full_name: Baltzis, Athanasios
last_name: Baltzis
- first_name: Hafid
full_name: Laayouni, Hafid
last_name: Laayouni
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Evan
full_name: Floden, Evan
last_name: Floden
- first_name: Cedric
full_name: Notredame, Cedric
last_name: Notredame
citation:
ama: Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence
alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846
apa: Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A.,
… Notredame, C. (2018). Fast and accurate large multiple sequence alignments with
a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846
chicago: Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri,
Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric
Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf
Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846.
ieee: E. Garriga et al., “Fast and accurate large multiple sequence alignments
with a root-to-leaf regressive method.” Zenodo, 2018.
ista: Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H,
Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence
alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.
mla: Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments
with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.
short: E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H.
Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).
date_created: 2023-05-23T16:08:20Z
date_published: 2018-12-07T00:00:00Z
date_updated: 2023-09-06T14:32:51Z
day: '07'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.5281/ZENODO.2025846
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.3271452
month: '12'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '7181'
relation: used_in_publication
status: public
status: public
title: Fast and accurate large multiple sequence alignments with a root-to-leaf regressive
method
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '5780'
abstract:
- lang: eng
text: Bioluminescence is found across the entire tree of life, conferring a spectacular
set of visually oriented functions from attracting mates to scaring off predators.
Half a dozen different luciferins, molecules that emit light when enzymatically
oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis
has been described in full, which is found only in bacteria. Here, we report identification
of the fungal luciferase and three other key enzymes that together form the biosynthetic
cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite.
Introduction of the identified genes into the genome of the yeast Pichia pastoris
along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent
in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis
cycle and found that fungal bioluminescence emerged through a series of events
that included two independent gene duplications. The retention of the duplicated
enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication
was followed by functional sequence divergence of enzymes of at least one gene
in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence
proceeded through several closely related stepping stone nonluminescent biochemical
reactions with adaptive roles. The availability of a complete eukaryotic luciferin
biosynthesis pathway provides several applications in biomedicine and bioengineering.
article_processing_charge: No
author:
- first_name: Alexey A.
full_name: Kotlobay, Alexey A.
last_name: Kotlobay
- first_name: Karen
full_name: Sarkisyan, Karen
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Yuliana A.
full_name: Mokrushina, Yuliana A.
last_name: Mokrushina
- first_name: Marina
full_name: Marcet-Houben, Marina
last_name: Marcet-Houben
- first_name: Ekaterina O.
full_name: Serebrovskaya, Ekaterina O.
last_name: Serebrovskaya
- first_name: Nadezhda M.
full_name: Markina, Nadezhda M.
last_name: Markina
- first_name: Louisa
full_name: Gonzalez Somermeyer, Louisa
id: 4720D23C-F248-11E8-B48F-1D18A9856A87
last_name: Gonzalez Somermeyer
orcid: 0000-0001-9139-5383
- first_name: Andrey Y.
full_name: Gorokhovatsky, Andrey Y.
last_name: Gorokhovatsky
- first_name: Andrey
full_name: Vvedensky, Andrey
last_name: Vvedensky
- first_name: Konstantin V.
full_name: Purtov, Konstantin V.
last_name: Purtov
- first_name: Valentin N.
full_name: Petushkov, Valentin N.
last_name: Petushkov
- first_name: Natalja S.
full_name: Rodionova, Natalja S.
last_name: Rodionova
- first_name: Tatiana V.
full_name: Chepurnyh, Tatiana V.
last_name: Chepurnyh
- first_name: Liliia
full_name: Fakhranurova, Liliia
last_name: Fakhranurova
- first_name: Elena B.
full_name: Guglya, Elena B.
last_name: Guglya
- first_name: Rustam
full_name: Ziganshin, Rustam
last_name: Ziganshin
- first_name: Aleksandra S.
full_name: Tsarkova, Aleksandra S.
last_name: Tsarkova
- first_name: Zinaida M.
full_name: Kaskova, Zinaida M.
last_name: Kaskova
- first_name: Victoria
full_name: Shender, Victoria
last_name: Shender
- first_name: Maxim
full_name: Abakumov, Maxim
last_name: Abakumov
- first_name: Tatiana O.
full_name: Abakumova, Tatiana O.
last_name: Abakumova
- first_name: Inna S.
full_name: Povolotskaya, Inna S.
last_name: Povolotskaya
- first_name: Fedor M.
full_name: Eroshkin, Fedor M.
last_name: Eroshkin
- first_name: Andrey G.
full_name: Zaraisky, Andrey G.
last_name: Zaraisky
- first_name: Alexander S.
full_name: Mishin, Alexander S.
last_name: Mishin
- first_name: Sergey V.
full_name: Dolgov, Sergey V.
last_name: Dolgov
- first_name: Tatiana Y.
full_name: Mitiouchkina, Tatiana Y.
last_name: Mitiouchkina
- first_name: Eugene P.
full_name: Kopantzev, Eugene P.
last_name: Kopantzev
- first_name: Hans E.
full_name: Waldenmaier, Hans E.
last_name: Waldenmaier
- first_name: Anderson G.
full_name: Oliveira, Anderson G.
last_name: Oliveira
- first_name: Yuichi
full_name: Oba, Yuichi
last_name: Oba
- first_name: Ekaterina
full_name: Barsova, Ekaterina
last_name: Barsova
- first_name: Ekaterina A.
full_name: Bogdanova, Ekaterina A.
last_name: Bogdanova
- first_name: Toni
full_name: Gabaldón, Toni
last_name: Gabaldón
- first_name: Cassius V.
full_name: Stevani, Cassius V.
last_name: Stevani
- first_name: Sergey
full_name: Lukyanov, Sergey
last_name: Lukyanov
- first_name: Ivan V.
full_name: Smirnov, Ivan V.
last_name: Smirnov
- first_name: Josef I.
full_name: Gitelson, Josef I.
last_name: Gitelson
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ilia V.
full_name: Yampolsky, Ilia V.
last_name: Yampolsky
citation:
ama: Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115
apa: Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya,
E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent
system from fungi. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115
chicago: Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben,
Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et
al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of
the National Academy of Sciences of the United States of America. National
Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.
ieee: A. A. Kotlobay et al., “Genetically encodable bioluminescent system
from fungi,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732,
2018.
ista: Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO,
Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov
VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova
AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin
FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier
HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov
S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable
bioluminescent system from fungi. Proceedings of the National Academy of Sciences
of the United States of America. 115(50), 12728–12732.
mla: Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from
Fungi.” Proceedings of the National Academy of Sciences of the United States
of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32,
doi:10.1073/pnas.1803615115.
short: A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya,
N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov,
V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya,
R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova,
I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y.
Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova,
E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson,
F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences
of the United States of America 115 (2018) 12728–12732.
date_created: 2018-12-23T22:59:18Z
date_published: 2018-12-11T00:00:00Z
date_updated: 2023-09-11T14:04:05Z
day: '11'
ddc:
- '580'
department:
- _id: FyKo
doi: 10.1073/pnas.1803615115
external_id:
isi:
- '000452866000068'
file:
- access_level: open_access
checksum: 46b2c12185eb2ddb598f4c7b4bd267bf
content_type: application/pdf
creator: dernst
date_created: 2019-02-05T15:21:40Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5926'
file_name: 2018_PNAS_Kotlobay.pdf
file_size: 1271988
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
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language:
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month: '12'
oa: 1
oa_version: Published Version
page: 12728-12732
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetically encodable bioluminescent system from fungi
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '279'
abstract:
- lang: eng
text: 'Background: Natural selection shapes cancer genomes. Previous studies used
signatures of positive selection to identify genes driving malignant transformation.
However, the contribution of negative selection against somatic mutations that
affect essential tumor functions or specific domains remains a controversial topic.
Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA
data to explore the portion of the cancer exome under negative selection. Although
we find most of the genes neutrally evolving in a pan-cancer framework, we identify
essential cancer genes and immune-exposed protein regions under significant negative
selection. Moreover, our simulations suggest that the amount of negative selection
is underestimated. We therefore choose an empirical approach to identify genes,
functions, and protein regions under negative selection. We find that expression
and mutation status of negatively selected genes is indicative of patient survival.
Processes that are most strongly conserved are those that play fundamental cellular
roles such as protein synthesis, glucose metabolism, and molecular transport.
Intriguingly, we observe strong signals of selection in the immunopeptidome and
proteins controlling peptide exposition, highlighting the importance of immune
surveillance evasion. Additionally, tumor type-specific immune activity correlates
with the strength of negative selection on human epitopes. Conclusions: In summary,
our results show that negative selection is a hallmark of cell essentiality and
immune response in cancer. The functional domains identified could be exploited
therapeutically, ultimately allowing for the development of novel cancer treatments.'
article_number: '67'
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative
selection in tumor genome evolution acts on essential cellular functions and the
immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0
apa: Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0
chicago: Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential
Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central,
2018. https://doi.org/10.1186/s13059-018-1434-0.
ieee: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Negative selection in tumor genome evolution acts on essential cellular functions
and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018.
ista: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative
selection in tumor genome evolution acts on essential cellular functions and the
immunopeptidome. Genome Biology. 19, 67.
mla: Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on
Essential Cellular Functions and the Immunopeptidome.” Genome Biology,
vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0.
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
Genome Biology 19 (2018).
date_created: 2018-12-11T11:45:35Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:32Z
day: '31'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1186/s13059-018-1434-0
ec_funded: 1
external_id:
isi:
- '000433986200001'
file:
- access_level: open_access
checksum: f3e4922486bd9bf1483271bdbed394a7
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T14:05:01Z
date_updated: 2020-07-14T12:45:47Z
file_id: '5708'
file_name: 2018_GenomeBiology_Zapata.pdf
file_size: 1414722
relation: main_file
file_date_updated: 2020-07-14T12:45:47Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Genome Biology
publication_status: published
publisher: BioMed Central
publist_id: '7620'
quality_controlled: '1'
related_material:
record:
- id: '9811'
relation: research_data
status: public
- id: '9812'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Negative selection in tumor genome evolution acts on essential cellular functions
and the immunopeptidome
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 19
year: '2018'
...
---
_id: '9812'
abstract:
- lang: eng
text: This document contains the full list of genes with their respective significance
and dN/dS values. (TXT 4499Â kb)
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
file 2: Of negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1'
apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 2: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401414.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.'
ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
Additional file 2: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.'
mla: 'Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor
Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.
Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
date_created: 2021-08-06T12:58:25Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:31Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401414.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.6401414.v1
month: '05'
oa: 1
oa_version: Published Version
publisher: Springer Nature
related_material:
record:
- id: '279'
relation: used_in_publication
status: public
status: public
title: 'Additional file 2: Of negative selection in tumor genome evolution acts on
essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '9811'
abstract:
- lang: eng
text: This document contains additional supporting evidence presented as supplemental
tables. (XLSX 50Â kb)
article_processing_charge: No
author:
- first_name: Luis
full_name: Zapata, Luis
last_name: Zapata
- first_name: Oriol
full_name: Pich, Oriol
last_name: Pich
- first_name: Luis
full_name: Serrano, Luis
last_name: Serrano
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Stephan
full_name: Ossowski, Stephan
last_name: Ossowski
- first_name: Martin
full_name: Schaefer, Martin
last_name: Schaefer
citation:
ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional
file 1: Of negative selection in tumor genome evolution acts on essential cellular
functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1'
apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer,
M. (2018). Additional file 1: Of negative selection in tumor genome evolution
acts on essential cellular functions and the immunopeptidome. Springer Nature.
https://doi.org/10.6084/m9.figshare.6401390.v1'
chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski,
and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome
Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer
Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.'
ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer,
“Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome.” Springer Nature, 2018.'
ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018.
Additional file 1: Of negative selection in tumor genome evolution acts on essential
cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.'
mla: 'Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor
Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.
Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.'
short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer,
(2018).
date_created: 2021-08-06T12:53:49Z
date_published: 2018-05-31T00:00:00Z
date_updated: 2023-09-13T09:01:31Z
day: '31'
department:
- _id: FyKo
doi: 10.6084/m9.figshare.6401390.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.6401390.v1
month: '05'
oa: 1
oa_version: Preprint
publisher: Springer Nature
related_material:
record:
- id: '279'
relation: used_in_publication
status: public
status: public
title: 'Additional file 1: Of negative selection in tumor genome evolution acts on
essential cellular functions and the immunopeptidome'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '5995'
abstract:
- lang: eng
text: "Motivation\r\nComputational prediction of the effect of mutations on protein
stability is used by researchers in many fields. The utility of the prediction
methods is affected by their accuracy and bias. Bias, a systematic shift of the
predicted change of stability, has been noted as an issue for several methods,
but has not been investigated systematically. Presence of the bias may lead to
misleading results especially when exploring the effects of combination of different
mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function
of the number of introduced mutations. It is based on a self-consistency test
of the reciprocity the effect of a mutation. An advantage of the used approach
is that it relies solely on crystal structures without experimentally measured
stability values. We applied the protocol to four popular algorithms predicting
change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant,
and found an inherent bias. For one program, FoldX, we manage to substantially
reduce the bias using additional relaxation by Modeller. Authors using algorithms
for predicting effects of mutations should be aware of the bias described here."
article_processing_charge: No
author:
- first_name: Dinara R
full_name: Usmanova, Dinara R
last_name: Usmanova
- first_name: Natalya S
full_name: Bogatyreva, Natalya S
last_name: Bogatyreva
- first_name: Joan
full_name: Ariño Bernad, Joan
last_name: Ariño Bernad
- first_name: Aleksandra A
full_name: Eremina, Aleksandra A
last_name: Eremina
- first_name: Anastasiya A
full_name: Gorshkova, Anastasiya A
last_name: Gorshkova
- first_name: German M
full_name: Kanevskiy, German M
last_name: Kanevskiy
- first_name: Lyubov R
full_name: Lonishin, Lyubov R
last_name: Lonishin
- first_name: Alexander V
full_name: Meister, Alexander V
last_name: Meister
- first_name: Alisa G
full_name: Yakupova, Alisa G
last_name: Yakupova
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Dmitry
full_name: Ivankov, Dmitry
id: 49FF1036-F248-11E8-B48F-1D18A9856A87
last_name: Ivankov
citation:
ama: Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals
systematic bias in programs for prediction change of stability upon mutation.
Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340
apa: Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova,
A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic
bias in programs for prediction change of stability upon mutation. Bioinformatics.
Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340
chicago: Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra
A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al.
“Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change
of Stability upon Mutation.” Bioinformatics. Oxford University Press ,
2018. https://doi.org/10.1093/bioinformatics/bty340.
ieee: D. R. Usmanova et al., “Self-consistency test reveals systematic bias
in programs for prediction change of stability upon mutation,” Bioinformatics,
vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.
ista: Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy
GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency
test reveals systematic bias in programs for prediction change of stability upon
mutation. Bioinformatics. 34(21), 3653–3658.
mla: Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias
in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics,
vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.
short: D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova,
G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D.
Ivankov, Bioinformatics 34 (2018) 3653–3658.
date_created: 2019-02-14T12:48:00Z
date_published: 2018-11-01T00:00:00Z
date_updated: 2023-09-19T14:31:13Z
day: '01'
ddc:
- '570'
department:
- _id: FyKo
doi: 10.1093/bioinformatics/bty340
ec_funded: 1
external_id:
isi:
- '000450038900008'
pmid:
- '29722803'
file:
- access_level: open_access
checksum: 7e0495153f44211479674601d7f6ee03
content_type: application/pdf
creator: kschuh
date_created: 2019-02-14T13:00:55Z
date_updated: 2020-07-14T12:47:15Z
file_id: '5997'
file_name: 2018_Oxford_Usmanova.pdf
file_size: 291969
relation: main_file
file_date_updated: 2020-07-14T12:47:15Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '21'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 3653-3658
pmid: 1
project:
- _id: 26120F5C-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '335980'
name: Systematic investigation of epistasis in molecular evolution
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: 'Oxford University Press '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-consistency test reveals systematic bias in programs for prediction change
of stability upon mutation
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 34
year: '2018'
...
---
_id: '850'
abstract:
- lang: eng
text: Fitness landscapes depict how genotypes manifest at the phenotypic level and
form the basis of our understanding of many areas of biology, yet their properties
remain elusive. Previous studies have analysed specific genes, often using their
function as a proxy for fitness, experimentally assessing the effect on function
of single mutations and their combinations in a specific sequence or in different
sequences. However, systematic high-throughput studies of the local fitness landscape
of an entire protein have not yet been reported. Here we visualize an extensive
region of the local fitness landscape of the green fluorescent protein from Aequorea
Victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands
of derivative genotypes of avGFP. We show that the fitness landscape of avGFP
is narrow, with 3/4 of the derivatives with a single mutation showing reduced
fluorescence and half of the derivatives with four mutations being completely
non-fluorescent. The narrowness is enhanced by epistasis, which was detected in
up to 30% of genotypes with multiple mutations and mostly occurred through the
cumulative effect of slightly deleterious mutations causing a threshold-like decrease
in protein stability and a concomitant loss of fluorescence. A model of orthologous
sequence divergence spanning hundreds of millions of years predicted the extent
of epistasis in our data, indicating congruence between the fitness landscape
properties at the local and global scales. The characterization of the local fitness
landscape of avGFP has important implications for several fields including molecular
evolution, population genetics and protein design.
acknowledgement: We thank Y. Kulikova and G. Filion for discussion on statistical
analysis and I. Osterman, R. Moretti and J. Meiler for technical assistance and
M. Friesen for a critical reading of the manuscript. We thank H. Himmelbauer, CRG
Genomic Unit and the Russian Science Foundation project (14-50-00150) for sequencing.
Experiments were partially carried out using the equipment provided by the IBCH
core facility (CKP IBCH). The work was supported by HHMI International Early Career
Scientist Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329),
Spanish Ministry of Economy and Competitiveness Centro de Excelencia Severo Ochoa
2013-2017 grant (SEV-2012-0208), Secretaria d'Universitats i Recerca del Departament
d'Economia i Coneixement de la Generalitat's AGAUR program (2014 SGR 0974), Russian
Science Foundation (14-25-00129) and the European Research Council under the European
Union's Seventh Framework Programme (FP7/2007-2013, ERC grant agreement, 335980-EinME).
author:
- first_name: Karen
full_name: Karen Sarkisyan
id: 39A7BF80-F248-11E8-B48F-1D18A9856A87
last_name: Sarkisyan
orcid: 0000-0002-5375-6341
- first_name: Dmitry
full_name: Bolotin, Dmitry A
last_name: Bolotin
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Dinara
full_name: Usmanova, Dinara R
last_name: Usmanova
- first_name: Alexander
full_name: Mishin, Alexander S
last_name: Mishin
- first_name: George
full_name: Sharonov, George V
last_name: Sharonov
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Nina
full_name: Bozhanova, Nina G
last_name: Bozhanova
- first_name: Mikhail
full_name: Baranov, Mikhail S
last_name: Baranov
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Natalya
full_name: Bogatyreva, Natalya S
last_name: Bogatyreva
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Evgeny
full_name: Egorov, Evgeny S
last_name: Egorov
- first_name: Maria
full_name: Logacheva, Maria D
last_name: Logacheva
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Dmitriy
full_name: Chudakov, Dmitriy M
last_name: Chudakov
- first_name: Ekaterina
full_name: Putintseva, Ekaterina V
last_name: Putintseva
- first_name: Ilgar
full_name: Mamedov, Ilgar Z
last_name: Mamedov
- first_name: Dan
full_name: Tawfik, Dan S
last_name: Tawfik
- first_name: Konstantin
full_name: Lukyanov, Konstantin A
last_name: Lukyanov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Sarkisyan K, Bolotin D, Meer M, et al. Local fitness landscape of the green
fluorescent protein. Nature. 2016;533:397-401. doi:10.1038/nature17995
apa: Sarkisyan, K., Bolotin, D., Meer, M., Usmanova, D., Mishin, A., Sharonov, G.,
… Kondrashov, F. (2016). Local fitness landscape of the green fluorescent protein.
Nature. Nature Publishing Group. https://doi.org/10.1038/nature17995
chicago: Sarkisyan, Karen, Dmitry Bolotin, Margarita Meer, Dinara Usmanova, Alexander
Mishin, George Sharonov, Dmitry Ivankov, et al. “Local Fitness Landscape of the
Green Fluorescent Protein.” Nature. Nature Publishing Group, 2016. https://doi.org/10.1038/nature17995.
ieee: K. Sarkisyan et al., “Local fitness landscape of the green fluorescent
protein,” Nature, vol. 533. Nature Publishing Group, pp. 397–401, 2016.
ista: Sarkisyan K, Bolotin D, Meer M, Usmanova D, Mishin A, Sharonov G, Ivankov
D, Bozhanova N, Baranov M, Soylemez O, Bogatyreva N, Vlasov P, Egorov E, Logacheva
M, Kondrashov A, Chudakov D, Putintseva E, Mamedov I, Tawfik D, Lukyanov K, Kondrashov
F. 2016. Local fitness landscape of the green fluorescent protein. Nature. 533,
397–401.
mla: Sarkisyan, Karen, et al. “Local Fitness Landscape of the Green Fluorescent
Protein.” Nature, vol. 533, Nature Publishing Group, 2016, pp. 397–401,
doi:10.1038/nature17995.
short: K. Sarkisyan, D. Bolotin, M. Meer, D. Usmanova, A. Mishin, G. Sharonov, D.
Ivankov, N. Bozhanova, M. Baranov, O. Soylemez, N. Bogatyreva, P. Vlasov, E. Egorov,
M. Logacheva, A. Kondrashov, D. Chudakov, E. Putintseva, I. Mamedov, D. Tawfik,
K. Lukyanov, F. Kondrashov, Nature 533 (2016) 397–401.
date_created: 2018-12-11T11:48:50Z
date_published: 2016-05-11T00:00:00Z
date_updated: 2021-01-12T08:19:42Z
day: '11'
doi: 10.1038/nature17995
extern: 1
intvolume: ' 533'
month: '05'
page: 397 - 401
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6799'
quality_controlled: 0
status: public
title: Local fitness landscape of the green fluorescent protein
type: journal_article
volume: 533
year: '2016'
...
---
_id: '896'
abstract:
- lang: eng
text: Multicellular eukaryotes have evolved a range of mechanisms for immune recognition.
A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing
(NLR) proteins.Mammals have small numbers of NLR proteins, whereas in some species,
mostly those without adaptive immune systems, NLRs have expanded into very large
families.We describe a family of nearly 400NLR proteins encoded in the zebrafish
genome. The proteins share a defining overall structure, which arose in fishes
after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided
into four groups based on their NACHT domains. Gene conversion acting differentially
on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence
of positive selection in the B30.2 domain indicates that this domain rather than
the leucine-rich repeats acts as the pathogen recognition module. In an unusual
chromosomal organization, the majority of the genes are located on one chromosome
arm, interspersed with other large multigene families, including a new family
encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with
diversity in the specific recognition module that is present in fishes in spite
of the parallel existence of an adaptive immune system.
acknowledgement: Financial support was provided by EMBO and the DFG SFB 670 'Zellautonome
Immunität' to M.L., DFG SFB 680 'Molecular basis of evolutionary innovation' to
T.W., DFG SPP1819 to M.L. and T.W., the HHMI International Early Career Scientist
Programme (55007424), MINECO (Sev-2012-0208), AGAUR programme (2014 SGR 0974), and
an ERC Starting Grant (335980-EinME) to F.K., the European Molecular Biology Laboratory
to J.M., the Wellcome Trust to K.H. (zebrafish genome sequencing project) and the
National Human Genome Research Institute (NHGRI) grant HG002659 to G.K.L. (gene
annotation), and a grant from the Volkswagen Foundation to P.H.S. We thank the CHEOPS
support team and the Bundesland Nordrhein Westfalen for making HPC applications
freely available at the University of Cologne.
author:
- first_name: Kerstin
full_name: Howe, Kerstin L
last_name: Howe
- first_name: Philipp
full_name: Schiffer, Philipp H
last_name: Schiffer
- first_name: Julia
full_name: Zielinski, Julia G
last_name: Zielinski
- first_name: Thomas
full_name: Wiehe, Thomas H
last_name: Wiehe
- first_name: Gavin
full_name: Laird, Gavin K
last_name: Laird
- first_name: John
full_name: Marioni, John C
last_name: Marioni
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Maria
full_name: Leptin, Maria
last_name: Leptin
citation:
ama: Howe K, Schiffer P, Zielinski J, et al. Structure and evolutionary history
of a large family of NLR proteins in the zebrafish. Open Biology. 2016;6(4).
doi:10.1098/rsob.160009
apa: Howe, K., Schiffer, P., Zielinski, J., Wiehe, T., Laird, G., Marioni, J., …
Leptin, M. (2016). Structure and evolutionary history of a large family of NLR
proteins in the zebrafish. Open Biology. Royal Society, The. https://doi.org/10.1098/rsob.160009
chicago: Howe, Kerstin, Philipp Schiffer, Julia Zielinski, Thomas Wiehe, Gavin Laird,
John Marioni, Onuralp Soylemez, Fyodor Kondrashov, and Maria Leptin. “Structure
and Evolutionary History of a Large Family of NLR Proteins in the Zebrafish.”
Open Biology. Royal Society, The, 2016. https://doi.org/10.1098/rsob.160009.
ieee: K. Howe et al., “Structure and evolutionary history of a large family
of NLR proteins in the zebrafish,” Open Biology, vol. 6, no. 4. Royal Society,
The, 2016.
ista: Howe K, Schiffer P, Zielinski J, Wiehe T, Laird G, Marioni J, Soylemez O,
Kondrashov F, Leptin M. 2016. Structure and evolutionary history of a large family
of NLR proteins in the zebrafish. Open Biology. 6(4).
mla: Howe, Kerstin, et al. “Structure and Evolutionary History of a Large Family
of NLR Proteins in the Zebrafish.” Open Biology, vol. 6, no. 4, Royal Society,
The, 2016, doi:10.1098/rsob.160009.
short: K. Howe, P. Schiffer, J. Zielinski, T. Wiehe, G. Laird, J. Marioni, O. Soylemez,
F. Kondrashov, M. Leptin, Open Biology 6 (2016).
date_created: 2018-12-11T11:49:04Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:32Z
day: '01'
doi: 10.1098/rsob.160009
extern: 1
intvolume: ' 6'
issue: '4'
month: '01'
publication: Open Biology
publication_status: published
publisher: Royal Society, The
publist_id: '6754'
quality_controlled: 0
status: public
title: Structure and evolutionary history of a large family of NLR proteins in the
zebrafish
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 6
year: '2016'
...
---
_id: '849'
abstract:
- lang: eng
text: Understanding the principles that led to the current complexity of the genetic
code is a central question in evolution. Expansion of the genetic code required
the selection of new transfer RNAs (tRNAs) with specific recognition signals that
allowed them to be matured, modified, aminoacylated, and processed by the ribosome
without compromising the fidelity or efficiency of protein synthesis. We show
that saturation of recognition signals blocks the emergence of new tRNA identities
and that the rate of nucleotide substitutions in tRNAs is higher in species with
fewer tRNA genes. We propose that the growth of the genetic code stalled because
a limit was reached in the number of identity elements that can be effectively
used in the tRNA structure.
acknowledgement: |-
We thank D. Söll, H. Grosjean, and L. Filonava for comments and suggestions.
M.O. and P.D.D. thank the Barcelona Supercomputing Center for CPU/GPU time on MareNostrum/
MinoTauro. P.D.D. is a PEDECIBA (Programa de Desarrollo de las Ciencias Básicas) and an SNI
(Sistema Nacional de Investigadores) (ANII, Uruguay) researcher. Funding: This work was
supported in part by the Spanish Ministry of Economy and Competitiveness (grants
BIO2012-32200, Sev-2012-0208, and BIO2012-32868 to L.R.d.P., F.A.K., and M.O., respectively)
and by the Catalan Government (grants 2014-SGR-0771, 2014-SGR-0974, and 2014-SGR-0134 to
L.R.d.P., F.A.K., and M.O., respectively). This work was also supported by the Howard Hughes
Medical Institute International Early Career Scientist Program (55007424), by a European Research
Council (ERC) Starting Grant (335980_EinME to F.K.), and by a grant from the ERC (ERC_SimDNA to
M.O). A.G.T. and C.B. are funded by the Spanish Ministry of Economy and Competitiveness
(FPDI-2013-17742 and BES-2013-064004, respectively).
author:
- first_name: Adélaïde
full_name: Saint-Léger, Adélaïde
last_name: Saint Léger
- first_name: Carla
full_name: Bello, Carla
last_name: Bello
- first_name: Pablo
full_name: Dans, Pablo D
last_name: Dans
- first_name: Adrian
full_name: Torres, Adrian G
last_name: Torres
- first_name: Eva
full_name: Novoa, Eva M
last_name: Novoa
- first_name: Noelia
full_name: Camacho, Noelia
last_name: Camacho
- first_name: Modesto
full_name: Orozco, Modesto
last_name: Orozco
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Lluís
full_name: Ribas De Pouplana, Lluís
last_name: Ribas De Pouplana
citation:
ama: Saint Léger A, Bello C, Dans P, et al. Saturation of recognition elements blocks
evolution of new tRNA identities. Science advances. 2016;2(4):e1501860-e1501860.
doi:10.1126/sciadv.1501860
apa: Saint Léger, A., Bello, C., Dans, P., Torres, A., Novoa, E., Camacho, N., …
Ribas De Pouplana, L. (2016). Saturation of recognition elements blocks evolution
of new tRNA identities. Science Advances. American Association for the
Advancement of Science. https://doi.org/10.1126/sciadv.1501860
chicago: Saint Léger, Adélaïde, Carla Bello, Pablo Dans, Adrian Torres, Eva Novoa,
Noelia Camacho, Modesto Orozco, Fyodor Kondrashov, and Lluís Ribas De Pouplana.
“Saturation of Recognition Elements Blocks Evolution of New TRNA Identities.”
Science Advances. American Association for the Advancement of Science,
2016. https://doi.org/10.1126/sciadv.1501860.
ieee: A. Saint Léger et al., “Saturation of recognition elements blocks evolution
of new tRNA identities,” Science advances, vol. 2, no. 4. American Association
for the Advancement of Science, pp. e1501860–e1501860, 2016.
ista: Saint Léger A, Bello C, Dans P, Torres A, Novoa E, Camacho N, Orozco M, Kondrashov
F, Ribas De Pouplana L. 2016. Saturation of recognition elements blocks evolution
of new tRNA identities. Science advances. 2(4), e1501860–e1501860.
mla: Saint Léger, Adélaïde, et al. “Saturation of Recognition Elements Blocks Evolution
of New TRNA Identities.” Science Advances, vol. 2, no. 4, American Association
for the Advancement of Science, 2016, pp. e1501860–e1501860, doi:10.1126/sciadv.1501860.
short: A. Saint Léger, C. Bello, P. Dans, A. Torres, E. Novoa, N. Camacho, M. Orozco,
F. Kondrashov, L. Ribas De Pouplana, Science Advances 2 (2016) e1501860–e1501860.
date_created: 2018-12-11T11:48:50Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:38Z
day: '01'
doi: 10.1126/sciadv.1501860
extern: 1
intvolume: ' 2'
issue: '4'
month: '04'
page: e1501860 - e1501860
publication: Science advances
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '6798'
quality_controlled: 0
status: public
title: Saturation of recognition elements blocks evolution of new tRNA identities
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
volume: 2
year: '2016'
...
---
_id: '853'
abstract:
- lang: eng
text: A comparative analysis of the metagenomes from two 30 000-year-old permafrost
samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex
sediments, revealed significant differences within microbial communities. The
late Pleistocene Ice Complex sediments (which have been characterized by the absence
of methane with lower values of redox potential and Fe2+ content) showed a low
abundance of methanogenic archaea and enzymes from both the carbon and nitrogen
cycles, but a higher abundance of enzymes associated with the sulfur cycle. The
metagenomic and geochemical analyses described in the paper provide evidence that
the formation of the sampled late Pleistocene Ice Complex sediments likely took
place under much more aerobic conditions than lake-alluvial sediments.
acknowledgement: This work was supported by grants from the Russian Scientific Fund
(14-14-01115) to Elizaveta Rivkina; from the National Science Foundation (DEB-1442262)
to Tatiana Vish- nivetskaya; and from the HHMI International Early Career Scientist
Program (55007424), the EMBO Young Investigator Programme, MINECO (BFU2012-31329
and Sev-2012-0208), and the AGAUR program (2014 SGR 0974) to Fyodor Kondrashov.
Support from the Russian Scientific Fund (14-14-01115) was allocated for sample
collection, gDNA isolation, and analysis of metagenomic data.
author:
- first_name: Elizaveta
full_name: Rivkina, Elizaveta
last_name: Rivkina
- first_name: Lada
full_name: Petrovskaya, Lada E
last_name: Petrovskaya
- first_name: Tatiana
full_name: Vishnivetskaya, Tatiana A
last_name: Vishnivetskaya
- first_name: Kirill
full_name: Krivushin, Kirill V
last_name: Krivushin
- first_name: Lyubov
full_name: Shmakova, Lyubov A
last_name: Shmakova
- first_name: Maria
full_name: Tutukina, Maria
last_name: Tutukina
- first_name: Arthur
full_name: Meyers, Arthur J
last_name: Meyers
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rivkina E, Petrovskaya L, Vishnivetskaya T, et al. Metagenomic analyses of
the late Pleistocene permafrost - Additional tools for reconstruction of environmental
conditions. Biogeosciences. 2016;13(7):2207-2219. doi:10.5194/bg-13-2207-2016
apa: Rivkina, E., Petrovskaya, L., Vishnivetskaya, T., Krivushin, K., Shmakova,
L., Tutukina, M., … Kondrashov, F. (2016). Metagenomic analyses of the late Pleistocene
permafrost - Additional tools for reconstruction of environmental conditions.
Biogeosciences. European Geosciences Union. https://doi.org/10.5194/bg-13-2207-2016
chicago: Rivkina, Elizaveta, Lada Petrovskaya, Tatiana Vishnivetskaya, Kirill Krivushin,
Lyubov Shmakova, Maria Tutukina, Arthur Meyers, and Fyodor Kondrashov. “Metagenomic
Analyses of the Late Pleistocene Permafrost - Additional Tools for Reconstruction
of Environmental Conditions.” Biogeosciences. European Geosciences Union,
2016. https://doi.org/10.5194/bg-13-2207-2016.
ieee: E. Rivkina et al., “Metagenomic analyses of the late Pleistocene permafrost
- Additional tools for reconstruction of environmental conditions,” Biogeosciences,
vol. 13, no. 7. European Geosciences Union, pp. 2207–2219, 2016.
ista: Rivkina E, Petrovskaya L, Vishnivetskaya T, Krivushin K, Shmakova L, Tutukina
M, Meyers A, Kondrashov F. 2016. Metagenomic analyses of the late Pleistocene
permafrost - Additional tools for reconstruction of environmental conditions.
Biogeosciences. 13(7), 2207–2219.
mla: Rivkina, Elizaveta, et al. “Metagenomic Analyses of the Late Pleistocene Permafrost
- Additional Tools for Reconstruction of Environmental Conditions.” Biogeosciences,
vol. 13, no. 7, European Geosciences Union, 2016, pp. 2207–19, doi:10.5194/bg-13-2207-2016.
short: E. Rivkina, L. Petrovskaya, T. Vishnivetskaya, K. Krivushin, L. Shmakova,
M. Tutukina, A. Meyers, F. Kondrashov, Biogeosciences 13 (2016) 2207–2219.
date_created: 2018-12-11T11:48:51Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:54Z
day: '01'
doi: 10.5194/bg-13-2207-2016
extern: 1
intvolume: ' 13'
issue: '7'
month: '04'
page: 2207 - 2219
publication: Biogeosciences
publication_status: published
publisher: European Geosciences Union
publist_id: '6793'
quality_controlled: 0
status: public
title: Metagenomic analyses of the late Pleistocene permafrost - Additional tools
for reconstruction of environmental conditions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 13
year: '2016'
...
---
_id: '848'
abstract:
- lang: eng
text: The nature of factors governing the tempo and mode of protein evolution is
a fundamental issue in evolutionary biology. Specifically, whether or not interactions
between different sites, or epistasis, are important in directing the course of
evolution became one of the central questions. Several recent reports have scrutinized
patterns of long-term protein evolution claiming them to be compatible only with
an epistatic fitness landscape. However, these claims have not yet been substantiated
with a formal model of protein evolution. Here, we formulate a simple covarion-like
model of protein evolution focusing on the rate at which the fitness impact of
amino acids at a site changes with time. We then apply the model to the data on
convergent and divergent protein evolution to test whether or not the incorporation
of epistatic interactions is necessary to explain the data. We find that convergent
evolution cannot be explained without the incorporation of epistasis and the rate
at which an amino acid state switches from being acceptable at a site to being
deleterious is faster than the rate of amino acid substitution. Specifically,
for proteins that have persisted in modern prokaryotic organisms since the last
universal common ancestor for one amino acid substitution approximately ten amino
acid states switch from being accessible to being deleterious, or vice versa.
Thus, molecular evolution can only be perceived in the context of rapid turnover
of which amino acids are available for evolution.
author:
- first_name: Dinara
full_name: Usmanova, Dinara
last_name: Usmanova
- first_name: Luca
full_name: Ferretti, Luca
last_name: Ferretti
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Peter
full_name: Vlasov, Peter
last_name: Vlasov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. A model of
substitution trajectories in sequence space and long-term protein evolution. Molecular
Biology and Evolution. 2015;32(2):542-554. doi:10.1093/molbev/msu318
apa: Usmanova, D., Ferretti, L., Povolotskaya, I., Vlasov, P., & Kondrashov,
F. (2015). A model of substitution trajectories in sequence space and long-term
protein evolution. Molecular Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/molbev/msu318
chicago: Usmanova, Dinara, Luca Ferretti, Inna Povolotskaya, Peter Vlasov, and Fyodor
Kondrashov. “A Model of Substitution Trajectories in Sequence Space and Long-Term
Protein Evolution.” Molecular Biology and Evolution. Oxford University
Press, 2015. https://doi.org/10.1093/molbev/msu318.
ieee: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, and F. Kondrashov, “A
model of substitution trajectories in sequence space and long-term protein evolution,”
Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press,
pp. 542–554, 2015.
ista: Usmanova D, Ferretti L, Povolotskaya I, Vlasov P, Kondrashov F. 2015. A model
of substitution trajectories in sequence space and long-term protein evolution.
Molecular Biology and Evolution. 32(2), 542–554.
mla: Usmanova, Dinara, et al. “A Model of Substitution Trajectories in Sequence
Space and Long-Term Protein Evolution.” Molecular Biology and Evolution,
vol. 32, no. 2, Oxford University Press, 2015, pp. 542–54, doi:10.1093/molbev/msu318.
short: D. Usmanova, L. Ferretti, I. Povolotskaya, P. Vlasov, F. Kondrashov, Molecular
Biology and Evolution 32 (2015) 542–554.
date_created: 2018-12-11T11:48:49Z
date_published: 2015-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:33Z
day: '01'
doi: 10.1093/molbev/msu318
extern: '1'
intvolume: ' 32'
issue: '2'
language:
- iso: eng
month: '02'
oa_version: None
page: 542 - 554
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6804'
quality_controlled: '1'
status: public
title: A model of substitution trajectories in sequence space and long-term protein
evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2015'
...
---
_id: '906'
abstract:
- lang: eng
text: The origin and evolution of novel biochemical functions remains one of the
key questions in molecular evolution. We study recently emerged methacrylate reductase
function that is thought to have emerged in the last century and reported in Geobacter
sulfurreducens strain AM-1. We report the sequence and study the evolution of
the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme
cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal
peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex
mechanism of biogenesis for chromoproteids of the methacrylate redox system. The
homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres
are also organized into an operon and their phylogenetic distribution suggested
that these two genes tend to be horizontally transferred together. Specifically,
the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any
of the homologs found in other Geobacter genomes. The acquisition of methacrylate
reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene
transfer event. However, the new function of the products of mrd and mcc may have
evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.
acknowledgement: 'Funding: The work has been supported by a grant of the HHMI International
Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness
(EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish
Ministry of Economy and Competitiveness, "Centro de Excelencia Severo Ochoa 2013–2017
(Sev-2012-0208)" and (BFU2012-31329), the European Union and the European Research
Council under grant agreement 335980_EinME. The funders had no role in study design,
data collection and analysis, decision to publish, or preparation of the manuscript.Our
author Dr., Prof. Akimenko Vasilii K. (1942–2013) passed away during work on the
article. Prof. Akimenko was a leading biochemist in IBPM RAS and active researcher
until last days. A number of his work remains unfinished. We mourn premature care
of Prof. Akimenko Vasilii. We thank Heinz Himmelbauer and the CRG Genomic Unit for
the sequencing.'
author:
- first_name: Oksana
full_name: Arkhipova, Oksana V
last_name: Arkhipova
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Galina
full_name: Mikoulinskaia, Galina V
last_name: Mikoulinskaia
- first_name: Marina
full_name: Zakharova, Marina V
last_name: Zakharova
- first_name: Alexander
full_name: Galushko, Alexander S
last_name: Galushko
- first_name: Vasilii
full_name: Akimenko, Vasilii K
last_name: Akimenko
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Arkhipova O, Meer M, Mikoulinskaia G, et al. Recent origin of the methacrylate
redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer.
PLoS One. 2015;10(5). doi:10.1371/journal.pone.0125888
apa: Arkhipova, O., Meer, M., Mikoulinskaia, G., Zakharova, M., Galushko, A., Akimenko,
V., & Kondrashov, F. (2015). Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer. PLoS One.
Public Library of Science. https://doi.org/10.1371/journal.pone.0125888
chicago: Arkhipova, Oksana, Margarita Meer, Galina Mikoulinskaia, Marina Zakharova,
Alexander Galushko, Vasilii Akimenko, and Fyodor Kondrashov. “Recent Origin of
the Methacrylate Redox System in Geobacter Sulfurreducens AM-1 through Horizontal
Gene Transfer.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0125888.
ieee: O. Arkhipova et al., “Recent origin of the methacrylate redox system
in Geobacter sulfurreducens AM-1 through horizontal gene transfer,” PLoS One,
vol. 10, no. 5. Public Library of Science, 2015.
ista: Arkhipova O, Meer M, Mikoulinskaia G, Zakharova M, Galushko A, Akimenko V,
Kondrashov F. 2015. Recent origin of the methacrylate redox system in Geobacter
sulfurreducens AM-1 through horizontal gene transfer. PLoS One. 10(5).
mla: Arkhipova, Oksana, et al. “Recent Origin of the Methacrylate Redox System in
Geobacter Sulfurreducens AM-1 through Horizontal Gene Transfer.” PLoS One,
vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0125888.
short: O. Arkhipova, M. Meer, G. Mikoulinskaia, M. Zakharova, A. Galushko, V. Akimenko,
F. Kondrashov, PLoS One 10 (2015).
date_created: 2018-12-11T11:49:08Z
date_published: 2015-05-11T00:00:00Z
date_updated: 2021-01-12T08:21:48Z
day: '11'
doi: 10.1371/journal.pone.0125888
extern: 1
intvolume: ' 10'
issue: '5'
month: '05'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6742'
quality_controlled: 0
status: public
title: Recent origin of the methacrylate redox system in Geobacter sulfurreducens
AM-1 through horizontal gene transfer
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 10
year: '2015'
...
---
_id: '866'
abstract:
- lang: eng
text: Proteases play important roles in many biologic processes and are key mediators
of cancer, inflammation, and thrombosis. However, comprehensive and quantitative
techniques to define the substrate specificity profile of proteases are lacking.
The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand
factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage
display library based on a 73-amino acid fragment of VWF was constructed, and
the ADAMTS13-dependent change in library complexity was evaluated over reaction
time points, using high-throughput sequencing. Reaction rate constants (kcat/KM)
were calculated for nearly every possible single amino acid substitution within
this fragment. This massively parallel enzyme kinetics analysis detailed the specificity
of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues
while defining exosite binding domains. These data provided empirical evidence
for the propensity for epistasis within VWF and showed strong correlation to conservation
across orthologs, highlighting evolutionary selective pressures for VWF.
acknowledgement: |
We thank Isabel Wang and Vivian Cheung from the Life Sciences Institute, University of Michigan, for assistance with high- throughput sequencing experiments and valuable discussions. We also thank J. Evan Sadler (Washington University) and Sriram Krishnaswamy (Children’s Hospital of Philadelphia) for helpful discussions. We thank Jeff Weitz (McMaster University), Jim Fredenburgh (McMaster University), and Steve Weiss (University of Michigan) for critical review of the manuscript. C.A.K. was awarded the Judith Graham Pool Fellowship from National Hemophilia Foundation. This work was supported by the National Institutes of Health (R01 HL039693), the National Heart, Lung, and Blood Institute (P01- HL057346), Ministerio de Economía y Competitividad Grants BFU2012- 31329 and Sev-2012-0208, and European Research Council Starting Grant 335980_EinME. D.G. is an investigator of the Howard Hughes Medical In- stitute, and F.A.K. is a Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Colin
full_name: Kretz, Colin A
last_name: Kretz
- first_name: Manhong
full_name: Dai, Manhong
last_name: Dai
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Andrew
full_name: Yee, Andrew
last_name: Yee
- first_name: Karl
full_name: Desch, Karl C
last_name: Desch
- first_name: David
full_name: Siemieniak, David R
last_name: Siemieniak
- first_name: Kärt
full_name: Tomberg, Kärt
last_name: Tomberg
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Fan
full_name: Meng, Fan
last_name: Meng
- first_name: David
full_name: Ginsburg, David B
last_name: Ginsburg
citation:
ama: Kretz C, Dai M, Soylemez O, et al. Massively parallel enzyme kinetics reveals
the substrate recognition landscape of the metalloprotease ADAMTS13. PNAS.
2015;112(30):9328-9333. doi:10.1073/pnas.1511328112
apa: Kretz, C., Dai, M., Soylemez, O., Yee, A., Desch, K., Siemieniak, D., … Ginsburg,
D. (2015). Massively parallel enzyme kinetics reveals the substrate recognition
landscape of the metalloprotease ADAMTS13. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1511328112
chicago: Kretz, Colin, Manhong Dai, Onuralp Soylemez, Andrew Yee, Karl Desch, David
Siemieniak, Kärt Tomberg, Fyodor Kondrashov, Fan Meng, and David Ginsburg. “Massively
Parallel Enzyme Kinetics Reveals the Substrate Recognition Landscape of the Metalloprotease
ADAMTS13.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1511328112.
ieee: C. Kretz et al., “Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13,” PNAS, vol. 112,
no. 30. National Academy of Sciences, pp. 9328–9333, 2015.
ista: Kretz C, Dai M, Soylemez O, Yee A, Desch K, Siemieniak D, Tomberg K, Kondrashov
F, Meng F, Ginsburg D. 2015. Massively parallel enzyme kinetics reveals the substrate
recognition landscape of the metalloprotease ADAMTS13. PNAS. 112(30), 9328–9333.
mla: Kretz, Colin, et al. “Massively Parallel Enzyme Kinetics Reveals the Substrate
Recognition Landscape of the Metalloprotease ADAMTS13.” PNAS, vol. 112,
no. 30, National Academy of Sciences, 2015, pp. 9328–33, doi:10.1073/pnas.1511328112.
short: C. Kretz, M. Dai, O. Soylemez, A. Yee, K. Desch, D. Siemieniak, K. Tomberg,
F. Kondrashov, F. Meng, D. Ginsburg, PNAS 112 (2015) 9328–9333.
date_created: 2018-12-11T11:48:55Z
date_published: 2015-07-28T00:00:00Z
date_updated: 2021-01-12T08:20:26Z
day: '28'
doi: 10.1073/pnas.1511328112
extern: 1
intvolume: ' 112'
issue: '30'
month: '07'
page: 9328 - 9333
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '6783'
quality_controlled: 0
status: public
title: Massively parallel enzyme kinetics reveals the substrate recognition landscape
of the metalloprotease ADAMTS13
type: journal_article
volume: 112
year: '2015'
...
---
_id: '886'
abstract:
- lang: eng
text: The factors that determine the tempo and mode of protein evolution continue
to be a central question in molecular evolution. Traditionally, studies of protein
evolution focused on the rates of amino acid substitutions. More recently, with
the availability of sequence data and advanced experimental techniques, the focus
of attention has shifted toward the study of evolutionary trajectories and the
overall layout of protein fitness landscapes. In this review we describe the effect
of epistasis on the topology of evolutionary pathways that are likely to be found
in fitness landscapes and develop a simple theory to connect the number of maladapted
genotypes to the topology of fitness landscapes with epistatic interactions. Finally,
we review recent studies that have probed the extent of epistatic interactions
and have begun to chart the fitness landscapes in protein sequence space.
acknowledgement: 'This work has been supported by a grant from the HHMI International
Early Career Scientist Program (#55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP program, two grants
from the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo
Ochoa 2013–2017 (#Sev-2012-0208) and BES-2013-064004 funded by the European Regional
Development Fund (ERDF), the European Union, and the European Research Council under
grant agreement no 335980_EinME.'
author:
- first_name: Dmitry
full_name: Kondrashov, Dmitry A
last_name: Kondrashov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov D, Kondrashov F. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 2015;31(1):24-33. doi:10.1016/j.tig.2014.09.009
apa: Kondrashov, D., & Kondrashov, F. (2015). Topological features of rugged
fitness landscapes in sequence space. Trends in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2014.09.009
chicago: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics. Elsevier, 2015.
https://doi.org/10.1016/j.tig.2014.09.009.
ieee: D. Kondrashov and F. Kondrashov, “Topological features of rugged fitness landscapes
in sequence space,” Trends in Genetics, vol. 31, no. 1. Elsevier, pp. 24–33,
2015.
ista: Kondrashov D, Kondrashov F. 2015. Topological features of rugged fitness landscapes
in sequence space. Trends in Genetics. 31(1), 24–33.
mla: Kondrashov, Dmitry, and Fyodor Kondrashov. “Topological Features of Rugged
Fitness Landscapes in Sequence Space.” Trends in Genetics, vol. 31, no.
1, Elsevier, 2015, pp. 24–33, doi:10.1016/j.tig.2014.09.009.
short: D. Kondrashov, F. Kondrashov, Trends in Genetics 31 (2015) 24–33.
date_created: 2018-12-11T11:49:01Z
date_published: 2015-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:16Z
day: '01'
doi: 10.1016/j.tig.2014.09.009
extern: 1
intvolume: ' 31'
issue: '1'
month: '01'
page: 24 - 33
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6764'
quality_controlled: 0
status: public
title: Topological features of rugged fitness landscapes in sequence space
type: journal_article
volume: 31
year: '2015'
...
---
_id: '852'
abstract:
- lang: eng
text: 'Rapid divergence of gene copies after duplication is thought to determine
the fate of the copies and evolution of novel protein functions. However, data
on howlong the gene copies continue to experience an elevated rate of evolution
remain scarce. Standard theory of gene duplications based on some level of genetic
redundancy of gene copies predicts that the period of accelerated evolutionmust
end relatively quickly. Using a maximum-likelihood approach we estimate preduplication,
initial postduplication, and recent postduplication rates of evolution that occurred
in themammalian lineage.Wefind that both gene copies experience a similar in magnitude
acceleration in their rate of evolution. The copy located in the original genomic
position typically returns to the preduplication rates of evolution in a short
period of time. The burst of faster evolution of the copy that is located in a
new genomic position typically lasts longer. Furthermore, the fast-evolving copies
on average continue to evolve faster than the preduplication rates far longer
than predicted by standard theory of gene duplications.We hypothesize that the
prolonged elevated rates of evolution are determined by functional properties
that were acquired during, or soon after, the gene duplication event. '
author:
- first_name: Oriol
full_name: Rosello, Oriol P
last_name: Rosello
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Rosello O, Kondrashov F. Long-Term asymmetrical acceleration of protein evolution
after gene duplication. Genome Biology and Evolution. 2014;6(8):1949-1955.
doi:10.1093/gbe/evu159
apa: Rosello, O., & Kondrashov, F. (2014). Long-Term asymmetrical acceleration
of protein evolution after gene duplication. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evu159
chicago: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/gbe/evu159.
ieee: O. Rosello and F. Kondrashov, “Long-Term asymmetrical acceleration of protein
evolution after gene duplication,” Genome Biology and Evolution, vol. 6,
no. 8. Oxford University Press, pp. 1949–1955, 2014.
ista: Rosello O, Kondrashov F. 2014. Long-Term asymmetrical acceleration of protein
evolution after gene duplication. Genome Biology and Evolution. 6(8), 1949–1955.
mla: Rosello, Oriol, and Fyodor Kondrashov. “Long-Term Asymmetrical Acceleration
of Protein Evolution after Gene Duplication.” Genome Biology and Evolution,
vol. 6, no. 8, Oxford University Press, 2014, pp. 1949–55, doi:10.1093/gbe/evu159.
short: O. Rosello, F. Kondrashov, Genome Biology and Evolution 6 (2014) 1949–1955.
date_created: 2018-12-11T11:48:51Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:51Z
day: '01'
doi: 10.1093/gbe/evu159
extern: 1
intvolume: ' 6'
issue: '8'
month: '08'
page: 1949 - 1955
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6797'
quality_controlled: 0
status: public
title: Long-Term asymmetrical acceleration of protein evolution after gene duplication
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 6
year: '2014'
...
---
_id: '856'
abstract:
- lang: eng
text: The emergence of new genes throughout evolution requires rewiring and extension
of regulatory networks. However, the molecular details of how the transcriptional
regulation of new gene copies evolves remain largely unexplored. Here we show
how duplication of a transcription factor gene allowed the emergence of two independent
regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous
and could bind different motifs in its target promoters. After duplication, one
paralogue evolved increased binding specificity so that it only binds one type
of motif, whereas the other copy evolved a decreased activity so that it only
activates promoters that contain multiple binding sites. Interestingly, only a
few mutations in both the DNA-binding domains and in the promoter binding sites
were required to gradually disentangle the two networks. These results reveal
how duplication of a promiscuous transcription factor followed by concerted cis
and trans mutations allows expansion of a regulatory network.
acknowledgement: 'K.P. acknowledges financial support from TRIPLE I and a Belspo mobility
grant from the Belgian Federal Science Policy Office co-funded by the Marie Curie
Actions from the European Commission. Research in the lab of K.J.V. is supported
by ERC Starting Grant 241426, HFSP programme grant RGP0050/2013, VIB, EMBO YIP programme,
KU Leuven Programme Financing, FWO, and IWT. A.V. acknowledges RIKEN for the FPR
grant. The work of F.A.K. was supported by a grant of the HHMI International Early
Career Scientist Programme (grant #55007424), the Spanish Ministry of Economy and
Competitiveness (grant #BFU2012-31329) as part of the EMBO YIP programme, two grants
from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia
Severo Ochoa 2013–2017 (grant #Sev-2012-0208)’ and (grant #BES-2013-064004) funded
by the European Regional Development Fund (ERDF), the European Union and the European
Research Council (grant #335980_EinME). K.V. is supported by an FWO postdoctoral
fellowship. Funders had no role in study design, data collection and analysis, decision
to publish or preparation of the manuscript.'
author:
- first_name: Ksenia
full_name: Pougach, Ksenia S
last_name: Pougach
- first_name: Arnout
full_name: Voet, Arnout R
last_name: Voet
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Karin
full_name: Voordeckers, Karin
last_name: Voordeckers
- first_name: Joaquin
full_name: Christiaens, Joaquin F
last_name: Christiaens
- first_name: Bianka
full_name: Baying, Bianka
last_name: Baying
- first_name: Vladimı́R
full_name: Bénès, Vladimı́r
last_name: Bénès
- first_name: Ryo
full_name: Sakai, Ryo
last_name: Sakai
- first_name: Jan
full_name: Aerts, Jan A
last_name: Aerts
- first_name: Bo
full_name: Zhu, Bo
last_name: Zhu
- first_name: Patrick
full_name: Van Dijck, Patrick
last_name: Van Dijck
- first_name: Kevin
full_name: Verstrepen, Kevin J
last_name: Verstrepen
citation:
ama: Pougach K, Voet A, Kondrashov F, et al. Duplication of a promiscuous transcription
factor drives the emergence of a new regulatory network. Nature Communications.
2014;5. doi:10.1038/ncomms5868
apa: Pougach, K., Voet, A., Kondrashov, F., Voordeckers, K., Christiaens, J., Baying,
B., … Verstrepen, K. (2014). Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms5868
chicago: Pougach, Ksenia, Arnout Voet, Fyodor Kondrashov, Karin Voordeckers, Joaquin
Christiaens, Bianka Baying, Vladimı́R Bénès, et al. “Duplication of a Promiscuous
Transcription Factor Drives the Emergence of a New Regulatory Network.” Nature
Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms5868.
ieee: K. Pougach et al., “Duplication of a promiscuous transcription factor
drives the emergence of a new regulatory network,” Nature Communications,
vol. 5. Nature Publishing Group, 2014.
ista: Pougach K, Voet A, Kondrashov F, Voordeckers K, Christiaens J, Baying B, Bénès
V, Sakai R, Aerts J, Zhu B, Van Dijck P, Verstrepen K. 2014. Duplication of a
promiscuous transcription factor drives the emergence of a new regulatory network.
Nature Communications. 5.
mla: Pougach, Ksenia, et al. “Duplication of a Promiscuous Transcription Factor
Drives the Emergence of a New Regulatory Network.” Nature Communications,
vol. 5, Nature Publishing Group, 2014, doi:10.1038/ncomms5868.
short: K. Pougach, A. Voet, F. Kondrashov, K. Voordeckers, J. Christiaens, B. Baying,
V. Bénès, R. Sakai, J. Aerts, B. Zhu, P. Van Dijck, K. Verstrepen, Nature Communications
5 (2014).
date_created: 2018-12-11T11:48:52Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:01Z
day: '01'
doi: 10.1038/ncomms5868
extern: 1
intvolume: ' 5'
month: '01'
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '6790'
quality_controlled: 0
status: public
title: Duplication of a promiscuous transcription factor drives the emergence of a
new regulatory network
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 5
year: '2014'
...
---
_id: '863'
abstract:
- lang: eng
text: The origins of neural systems remain unresolved. In contrast to other basal
metazoans, ctenophores (comb jellies) have both complex nervous and mesoderm-derived
muscular systems. These holoplanktonic predators also have sophisticated ciliated
locomotion, behaviour and distinct development. Here we present the draft genome
of Pleurobrachia bachei, Pacific sea gooseberry, together with ten other ctenophore
transcriptomes, and show that they are remarkably distinct from other animal genomes
in their content of neurogenic, immune and developmental genes. Our integrative
analyses place Ctenophora as the earliest lineage within Metazoa. This hypothesis
is supported by comparative analysis of multiple gene families, including the
apparent absence of HOX genes, canonical microRNA machinery, and reduced immune
complement in ctenophores. Although two distinct nervous systems are well recognized
in ctenophores, many bilaterian neuron-specific genes and genes of 'classical'
neurotransmitter pathways either are absent or, if present, are not expressed
in neurons. Our metabolomic and physiological data are consistent with the hypothesis
that ctenophore neural systems, and possibly muscle specification, evolved independently
from those in other animals.
acknowledgement: We thank Friday Harbor Laboratories for facilities during animal
collection and Marine Genomics apprenticeships (L.L.M., B.J.S.); E. Dabe, G. Winters,
J. Netherton, N. Churches and C. Bostwick for help with animal, tissue, in situ,
RNA and DNA assays; and X.-X. Tan, F. Lu and T. Tyazelova for sequencing. We thank
F. Nivens for videos and P. L. Williams for database support. This work was supported
by NSF (NSF-0744649 and NSF CNS-0821622 to L.L.M.; NSF CHE-1111705 to J.V.S.), NIH
(1R01GM097502, R01MH097062, R21RR025699 and 5R21DA030118 to L.L.M.; P30 DA018310
to J.V.S.; R01 AG029360 and 1S10RR027052 to E.I.R.), NASA NNX13AJ31G (to K.M.H.,
L.L.M. and K.M.K.), NSERC 458115 and 211598 (J.P.R.), University of Florida Opportunity
Funds/McKnight Brain Research and Florida Biodiversity Institute (L.L.M.), Rostock
Inc./A.V. Chikunov (E.I.R.), grant from Russian Federation Government 14.B25.31.0033
(Resolution No.220) (E.I.R.). F.A.K., I.S.P. and R.D. were supported by HHMI (55007424),
EMBO and MINECO (BFU2012-31329 and Sev-2012-0208). Contributions of AU Marine Biology
Program 117 and Molette laboratory 22.
author:
- first_name: Leonid
full_name: Moroz, Leonid L
last_name: Moroz
- first_name: Kevin
full_name: Kocot, Kevin M
last_name: Kocot
- first_name: Mathew
full_name: Citarella, Mathew R
last_name: Citarella
- first_name: Sohn
full_name: Dosung, Sohn
last_name: Dosung
- first_name: Tigran
full_name: Norekian, Tigran P
last_name: Norekian
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Christopher
full_name: Dailey, Christopher A
last_name: Dailey
- first_name: Eugene
full_name: Berezikov, Eugene
last_name: Berezikov
- first_name: Katherine
full_name: Buckley, Katherine M
last_name: Buckley
- first_name: Andrey
full_name: Ptitsyn, Andrey A
last_name: Ptitsyn
- first_name: Denis
full_name: Reshetov, Denis A
last_name: Reshetov
- first_name: Krishanu
full_name: Mukherjee, Krishanu
last_name: Mukherjee
- first_name: Tatiana
full_name: Moroz, Tatiana P
last_name: Moroz
- first_name: Yelena
full_name: Bobkova, Yelena V
last_name: Bobkova
- first_name: Fahong
full_name: Yu, Fahong
last_name: Yu
- first_name: Vladimir
full_name: Kapitonov, Vladimir V
last_name: Kapitonov
- first_name: Jerzy
full_name: Jurka, Jerzy W
last_name: Jurka
- first_name: Yuriy
full_name: Bobkov, Yuriy V
last_name: Bobkov
- first_name: Joshua
full_name: Swore, Joshua J
last_name: Swore
- first_name: David
full_name: Girardo, David O
last_name: Girardo
- first_name: Alexander
full_name: Fodor, Alexander
last_name: Fodor
- first_name: Fedor
full_name: Gusev, Fedor E
last_name: Gusev
- first_name: Rachel
full_name: Sanford, Rachel S
last_name: Sanford
- first_name: Rebecca
full_name: Bruders, Rebecca
last_name: Bruders
- first_name: Ellen
full_name: Kittler, Ellen L
last_name: Kittler
- first_name: Claudia
full_name: Mills, Claudia E
last_name: Mills
- first_name: Jonathan
full_name: Rast, Jonathan P
last_name: Rast
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Victor
full_name: Solovyev, Victor
last_name: Solovyev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Billie
full_name: Swalla, Billie J
last_name: Swalla
- first_name: Jonathan
full_name: Sweedler, Jonathan V
last_name: Sweedler
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Kenneth
full_name: Halanych, Kenneth M
last_name: Halanych
- first_name: Andrea
full_name: Kohn, Andrea B
last_name: Kohn
citation:
ama: Moroz L, Kocot K, Citarella M, et al. The ctenophore genome and the evolutionary
origins of neural systems. Nature. 2014;510(7503):109-114. doi:10.1038/nature13400
apa: Moroz, L., Kocot, K., Citarella, M., Dosung, S., Norekian, T., Povolotskaya,
I., … Kohn, A. (2014). The ctenophore genome and the evolutionary origins of neural
systems. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13400
chicago: Moroz, Leonid, Kevin Kocot, Mathew Citarella, Sohn Dosung, Tigran Norekian,
Inna Povolotskaya, Anastasia Grigorenko, et al. “The Ctenophore Genome and the
Evolutionary Origins of Neural Systems.” Nature. Nature Publishing Group,
2014. https://doi.org/10.1038/nature13400.
ieee: L. Moroz et al., “The ctenophore genome and the evolutionary origins
of neural systems,” Nature, vol. 510, no. 7503. Nature Publishing Group,
pp. 109–114, 2014.
ista: Moroz L, Kocot K, Citarella M, Dosung S, Norekian T, Povolotskaya I, Grigorenko
A, Dailey C, Berezikov E, Buckley K, Ptitsyn A, Reshetov D, Mukherjee K, Moroz
T, Bobkova Y, Yu F, Kapitonov V, Jurka J, Bobkov Y, Swore J, Girardo D, Fodor
A, Gusev F, Sanford R, Bruders R, Kittler E, Mills C, Rast J, Derelle R, Solovyev
V, Kondrashov F, Swalla B, Sweedler J, Rogaev E, Halanych K, Kohn A. 2014. The
ctenophore genome and the evolutionary origins of neural systems. Nature. 510(7503),
109–114.
mla: Moroz, Leonid, et al. “The Ctenophore Genome and the Evolutionary Origins of
Neural Systems.” Nature, vol. 510, no. 7503, Nature Publishing Group, 2014,
pp. 109–14, doi:10.1038/nature13400.
short: L. Moroz, K. Kocot, M. Citarella, S. Dosung, T. Norekian, I. Povolotskaya,
A. Grigorenko, C. Dailey, E. Berezikov, K. Buckley, A. Ptitsyn, D. Reshetov, K.
Mukherjee, T. Moroz, Y. Bobkova, F. Yu, V. Kapitonov, J. Jurka, Y. Bobkov, J.
Swore, D. Girardo, A. Fodor, F. Gusev, R. Sanford, R. Bruders, E. Kittler, C.
Mills, J. Rast, R. Derelle, V. Solovyev, F. Kondrashov, B. Swalla, J. Sweedler,
E. Rogaev, K. Halanych, A. Kohn, Nature 510 (2014) 109–114.
date_created: 2018-12-11T11:48:54Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:21Z
day: '01'
doi: 10.1038/nature13400
extern: 1
intvolume: ' 510'
issue: '7503'
month: '01'
page: 109 - 114
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6785'
quality_controlled: 0
status: public
title: The ctenophore genome and the evolutionary origins of neural systems
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
BY-NC-SA 4.0)
short: CC BY-NC-SA (4.0)
type: journal_article
volume: 510
year: '2014'
...
---
_id: '865'
abstract:
- lang: eng
text: Research on existing drugs often discovers novel mechanisms of their action
and leads to the expansion of their therapeutic scope and subsequent remarketing.
The Wnt signaling pathway is of the immediate therapeutic relevance, as it plays
critical roles in cancer development and progression. However, drugs which disrupt
this pathway are unavailable despite the high demand. Here we report an attempt
to identify antagonists of the Wnt-FZD interaction among the library of the FDA-approved
drugs. We performed an in silico screening which brought up several potential
antagonists of the ligand-receptor interaction. 14 of these substances were tested
using the TopFlash luciferase reporter assay and four of them identified as active
and specific inhibitors of the Wnt3a-induced signaling. However, further analysis
through GTP-binding and β-catenin stabilization assays showed that the compounds
do not target the Wnt-FZD pair, but inhibit the signaling at downstream levels.
We further describe the previously unknown inhibitory activity of an anti-leprosy
drug clofazimine in the Wnt pathway and provide data demonstrating its efficiency
in suppressing growth of Wnt-dependent triple-negative breast cancer cells. These
data provide a basis for further investigations of the efficiency of clofazimine
in treatment of Wnt-dependent cancers.
author:
- first_name: Alexey
full_name: Koval, Alexey V
last_name: Koval
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Polina
full_name: Shichkova, Polina
last_name: Shichkova
- first_name: S
full_name: Khunderyakova, S
last_name: Khunderyakova
- first_name: Yury
full_name: Markov, Yury
last_name: Markov
- first_name: J
full_name: Panchenko, J
last_name: Panchenko
- first_name: A
full_name: Volodina, A
last_name: Volodina
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Katanaev, Vladimir L
last_name: Katanaev
citation:
ama: Koval A, Vlasov P, Shichkova P, et al. Anti leprosy drug clofazimine inhibits
growth of triple-negative breast cancer cells via inhibition of canonical Wnt
signaling. Biochemical Pharmacology. 2014;87(4):571-578. doi:10.1016/j.bcp.2013.12.007
apa: Koval, A., Vlasov, P., Shichkova, P., Khunderyakova, S., Markov, Y., Panchenko,
J., … Katanaev, V. (2014). Anti leprosy drug clofazimine inhibits growth of triple-negative
breast cancer cells via inhibition of canonical Wnt signaling. Biochemical
Pharmacology. Elsevier. https://doi.org/10.1016/j.bcp.2013.12.007
chicago: Koval, Alexey, Peter Vlasov, Polina Shichkova, S Khunderyakova, Yury Markov,
J Panchenko, A Volodina, Fyodor Kondrashov, and Vladimir Katanaev. “Anti Leprosy
Drug Clofazimine Inhibits Growth of Triple-Negative Breast Cancer Cells via Inhibition
of Canonical Wnt Signaling.” Biochemical Pharmacology. Elsevier, 2014.
https://doi.org/10.1016/j.bcp.2013.12.007.
ieee: A. Koval et al., “Anti leprosy drug clofazimine inhibits growth of
triple-negative breast cancer cells via inhibition of canonical Wnt signaling,”
Biochemical Pharmacology, vol. 87, no. 4. Elsevier, pp. 571–578, 2014.
ista: Koval A, Vlasov P, Shichkova P, Khunderyakova S, Markov Y, Panchenko J, Volodina
A, Kondrashov F, Katanaev V. 2014. Anti leprosy drug clofazimine inhibits growth
of triple-negative breast cancer cells via inhibition of canonical Wnt signaling.
Biochemical Pharmacology. 87(4), 571–578.
mla: Koval, Alexey, et al. “Anti Leprosy Drug Clofazimine Inhibits Growth of Triple-Negative
Breast Cancer Cells via Inhibition of Canonical Wnt Signaling.” Biochemical
Pharmacology, vol. 87, no. 4, Elsevier, 2014, pp. 571–78, doi:10.1016/j.bcp.2013.12.007.
short: A. Koval, P. Vlasov, P. Shichkova, S. Khunderyakova, Y. Markov, J. Panchenko,
A. Volodina, F. Kondrashov, V. Katanaev, Biochemical Pharmacology 87 (2014) 571–578.
date_created: 2018-12-11T11:48:55Z
date_published: 2014-02-15T00:00:00Z
date_updated: 2021-01-12T08:20:24Z
day: '15'
doi: 10.1016/j.bcp.2013.12.007
extern: 1
intvolume: ' 87'
issue: '4'
month: '02'
page: 571 - 578
publication: Biochemical Pharmacology
publication_status: published
publisher: Elsevier
publist_id: '6782'
quality_controlled: 0
status: public
title: Anti leprosy drug clofazimine inhibits growth of triple-negative breast cancer
cells via inhibition of canonical Wnt signaling
type: journal_article
volume: 87
year: '2014'
...
---
_id: '845'
abstract:
- lang: eng
text: Recombination between double-stranded DNA molecules is a key genetic process
which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs
during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population
nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable
and it is unclear how CO can occur between genotypes with less than 90% sequence
identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan
basidiomycete mushroom, a frequently encountered decayer of woody substrates.
We crossed two haploid individuals, from the United States and from Russia, and
obtained genome sequences for their 17 offspring. The average genetic distance
between the parents was 14%, making it possible to study CO at very high resolution.
We found reduced levels of linkage disequilibrium between loci flanking the CO
sites indicating that they are mostly confined to hotspots of recombination. Furthermore,
CO events preferentially occurred in regions under stronger negative selection,
in particular within exons that showed reduced levels of nucleotide diversity.
Apparently, in hypervariable species CO must avoid regions of higher divergence
between the recombining genomes due to limitations imposed by the mismatch repair
system, with regions under strong negative selection providing the opportunity
for recombination. These patterns are opposite to those observed in a number of
less variable species indicating that population genomics of hypervariable species
may reveal novel biological phenomena.
acknowledgement: The authors are grateful to Georgii Bazykin for valuable discussion
and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology
for Sanger sequencing. This study was supported by the Russian government grant
No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute
International Early Career Scientist Award and EMBO Young Investigator Program,
and core funds provided by the University of Michigan.
author:
- first_name: Vladimir
full_name: Seplyarskiy, Vladimir B
last_name: Seplyarskiy
- first_name: Maria
full_name: Logacheva, Maria D
last_name: Logacheva
- first_name: Aleksey
full_name: Penin, Aleksey A
last_name: Penin
- first_name: Maria
full_name: Baranová, Maria A
last_name: Baranová
- first_name: Evgeny
full_name: Leushkin, Evgeny V
last_name: Leushkin
- first_name: Natalia
full_name: Demidenko, Natalia V
last_name: Demidenko
- first_name: Anna
full_name: Klepikova, Anna V
last_name: Klepikova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Timothy
full_name: James, Timothy Y
last_name: James
citation:
ama: Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable
species preferentially occurs in regions of high local similarity. Molecular
Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242
apa: Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko,
N., … James, T. (2014). Crossing-over in a hypervariable species preferentially
occurs in regions of high local similarity. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msu242
chicago: Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová,
Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey
Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially
Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution.
Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu242.
ieee: V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially
occurs in regions of high local similarity,” Molecular Biology and Evolution,
vol. 31, no. 11. Oxford University Press, pp. 3016–3025, 2014.
ista: Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N,
Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable
species preferentially occurs in regions of high local similarity. Molecular Biology
and Evolution. 31(11), 3016–3025.
mla: Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially
Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution,
vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242.
short: V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko,
A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution
31 (2014) 3016–3025.
date_created: 2018-12-11T11:48:48Z
date_published: 2014-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:21Z
day: '01'
doi: 10.1093/molbev/msu242
extern: 1
intvolume: ' 31'
issue: '11'
month: '11'
page: 3016 - 3025
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6801'
quality_controlled: 0
status: public
title: Crossing-over in a hypervariable species preferentially occurs in regions of
high local similarity
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 31
year: '2014'
...
---
_id: '892'
abstract:
- lang: eng
text: The study of molecular evolution is important because it reveals how protein
functions emerge and evolve. Recently, several types of studies indicated that
substitutions in molecular evolution occur in a compensatory manner, whereby the
occurrence of a substitution depends on the amino acid residues at other sites.
However, a molecular or structural basis behind the compensation often remains
obscure. Here, we review studies on the interface of structural biology and molecular
evolution that revealed novel aspects of compensatory evolution. In many cases
structural studies benefit from evolutionary data while structural data often
add a functional dimension to the study of molecular evolution.
acknowledgement: |
The work has been supported by a grant of the HHMI International Early Career Scientist Program (55007424), the Spanish Ministry of Economy and Competitiveness (EUI-EURYIP-2011-4320) as part of the EMBO YIP program, two grants from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017 (Sev-2012-0208)’ and (BFU2012-31329), the European Union and the European Research Council grant (335980_EinME), RFBR (13-04-00253a), MCB RAS (01201358029) and MES RK Grants.
author:
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Alexei
full_name: Finkelstein, Alexei V
last_name: Finkelstein
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Ivankov D, Finkelstein A, Kondrashov F. A structural perspective of compensatory
evolution. Current Opinion in Structural Biology. 2014;26(1):104-112. doi:10.1016/j.sbi.2014.05.004
apa: Ivankov, D., Finkelstein, A., & Kondrashov, F. (2014). A structural perspective
of compensatory evolution. Current Opinion in Structural Biology. Elsevier.
https://doi.org/10.1016/j.sbi.2014.05.004
chicago: Ivankov, Dmitry, Alexei Finkelstein, and Fyodor Kondrashov. “A Structural
Perspective of Compensatory Evolution.” Current Opinion in Structural Biology.
Elsevier, 2014. https://doi.org/10.1016/j.sbi.2014.05.004.
ieee: D. Ivankov, A. Finkelstein, and F. Kondrashov, “A structural perspective of
compensatory evolution,” Current Opinion in Structural Biology, vol. 26,
no. 1. Elsevier, pp. 104–112, 2014.
ista: Ivankov D, Finkelstein A, Kondrashov F. 2014. A structural perspective of
compensatory evolution. Current Opinion in Structural Biology. 26(1), 104–112.
mla: Ivankov, Dmitry, et al. “A Structural Perspective of Compensatory Evolution.”
Current Opinion in Structural Biology, vol. 26, no. 1, Elsevier, 2014,
pp. 104–12, doi:10.1016/j.sbi.2014.05.004.
short: D. Ivankov, A. Finkelstein, F. Kondrashov, Current Opinion in Structural
Biology 26 (2014) 104–112.
date_created: 2018-12-11T11:49:03Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2021-01-12T08:21:21Z
day: '01'
doi: 10.1016/j.sbi.2014.05.004
extern: 1
intvolume: ' 26'
issue: '1'
month: '06'
page: 104 - 112
publication: Current Opinion in Structural Biology
publication_status: published
publisher: Elsevier
publist_id: '6756'
quality_controlled: 0
status: public
title: A structural perspective of compensatory evolution
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
volume: 26
year: '2014'
...
---
_id: '899'
abstract:
- lang: eng
text: Understanding fitness landscapes, a conceptual depiction of the genotype-to-phenotype
relationship, is crucial to many areas of biology. Two aspects of fitness landscapes
are the focus of contemporary studies of molecular evolution. First, the local
shape of the fitness landscape defined by the contribution of individual alleles
to fitness that is independent of all genetic interactions. Second, the global,
multidimensional fitness landscape shape determined by how interactions between
alleles at different loci change each other’s fitness impact, or epistasis. In
explaining the high amino-acid usage (u), we focused on the global shape of the
fitness landscape, ignoring the perturbations at individual sites.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Cédric
full_name: Notredame, Cédric
last_name: Notredame
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Breen et al. reply.
Nature. 2013;497(7451):E2-E3. doi:10.1038/nature12220
apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2013).
Breen et al. reply. Nature. Nature Publishing Group. https://doi.org/10.1038/nature12220
chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor
Kondrashov. “Breen et Al. Reply.” Nature. Nature Publishing Group, 2013.
https://doi.org/10.1038/nature12220.
ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Breen et
al. reply,” Nature, vol. 497, no. 7451. Nature Publishing Group, pp. E2–E3,
2013.
ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2013. Breen et al.
reply. Nature. 497(7451), E2–E3.
mla: Breen, Michael, et al. “Breen et Al. Reply.” Nature, vol. 497, no. 7451,
Nature Publishing Group, 2013, pp. E2–3, doi:10.1038/nature12220.
short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 497 (2013)
E2–E3.
date_created: 2018-12-11T11:49:05Z
date_published: 2013-05-30T00:00:00Z
date_updated: 2021-01-12T08:21:40Z
day: '30'
doi: 10.1038/nature12220
extern: 1
intvolume: ' 497'
issue: '7451'
month: '05'
page: E2 - E3
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6747'
quality_controlled: 0
status: public
title: Breen et al. reply
type: journal_article
volume: 497
year: '2013'
...
---
_id: '894'
abstract:
- lang: eng
text: 'Background: Genetic variation at the melanocortin-1 receptor (MC1R) gene
is correlated with melanin color variation in many birds. Feral pigeons (Columba
livia) show two major melanin-based colorations: a red coloration due to pheomelanic
pigment and a black coloration due to eumelanic pigment. Furthermore, within each
color type, feral pigeons display continuous variation in the amount of melanin
pigment present in the feathers, with individuals varying from pure white to a
full dark melanic color. Coloration is highly heritable and it has been suggested
that it is under natural or sexual selection, or both. Our objective was to investigate
whether MC1R allelic variants are associated with plumage color in feral pigeons.
Findings. We sequenced 888 bp of the coding sequence of MC1R among pigeons varying
both in the type, eumelanin or pheomelanin, and the amount of melanin in their
feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution
but none of them were associated with a plumage type. It remains possible that
non-synonymous substitutions that influence coloration are present in the short
MC1R fragment that we did not sequence but this seems unlikely because we analyzed
the entire functionally important region of the gene. Conclusions: Our results
show that color differences among feral pigeons are probably not attributable
to amino acid variation at the MC1R locus. Therefore, variation in regulatory
regions of MC1R or variation in other genes may be responsible for the color polymorphism
of feral pigeons.'
acknowledgement: Romain Derelle was supported by grant from Plan Nacional 004302 BFU2012-31329.
Fyodor A Kondrashov was supported by grants HHMI (Howard Hughes Medical Institute)
003803 and EMBO 003691 EUI-EURYIP-2011-4320.
author:
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Arkhipov, Vladimir
last_name: Arkhipov
- first_name: Hélène
full_name: Corbel, Hélène
last_name: Corbel
- first_name: Adrien
full_name: Frantz, Adrien
last_name: Frantz
- first_name: Julien
full_name: Gasparini, Julien
last_name: Gasparini
- first_name: Lisa
full_name: Jacquin, Lisa
last_name: Jacquin
- first_name: Gwenaël
full_name: Jacob, Gwenaël
last_name: Jacob
- first_name: Sophie
full_name: Thibault, Sophie
last_name: Thibault
- first_name: Emmanuelle
full_name: Baudry, Emmanuelle
last_name: Baudry
citation:
ama: Derelle R, Kondrashov F, Arkhipov V, et al. Color differences among feral pigeons
(Columba livia) are not attributable to sequence variation in the coding region
of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 2013;6(1).
doi:10.1186/1756-0500-6-310
apa: Derelle, R., Kondrashov, F., Arkhipov, V., Corbel, H., Frantz, A., Gasparini,
J., … Baudry, E. (2013). Color differences among feral pigeons (Columba livia)
are not attributable to sequence variation in the coding region of the melanocortin-1
receptor gene MC1R. BMC Research Notes. BioMed Central. https://doi.org/10.1186/1756-0500-6-310
chicago: Derelle, Romain, Fyodor Kondrashov, Vladimir Arkhipov, Hélène Corbel, Adrien
Frantz, Julien Gasparini, Lisa Jacquin, Gwenaël Jacob, Sophie Thibault, and Emmanuelle
Baudry. “Color Differences among Feral Pigeons (Columba Livia) Are Not Attributable
to Sequence Variation in the Coding Region of the Melanocortin-1 Receptor Gene
MC1R.” BMC Research Notes. BioMed Central, 2013. https://doi.org/10.1186/1756-0500-6-310.
ieee: R. Derelle et al., “Color differences among feral pigeons (Columba
livia) are not attributable to sequence variation in the coding region of the
melanocortin-1 receptor gene MC1R,” BMC Research Notes, vol. 6, no. 1.
BioMed Central, 2013.
ista: Derelle R, Kondrashov F, Arkhipov V, Corbel H, Frantz A, Gasparini J, Jacquin
L, Jacob G, Thibault S, Baudry E. 2013. Color differences among feral pigeons
(Columba livia) are not attributable to sequence variation in the coding region
of the melanocortin-1 receptor gene MC1R. BMC Research Notes. 6(1).
mla: Derelle, Romain, et al. “Color Differences among Feral Pigeons (Columba Livia)
Are Not Attributable to Sequence Variation in the Coding Region of the Melanocortin-1
Receptor Gene MC1R.” BMC Research Notes, vol. 6, no. 1, BioMed Central,
2013, doi:10.1186/1756-0500-6-310.
short: R. Derelle, F. Kondrashov, V. Arkhipov, H. Corbel, A. Frantz, J. Gasparini,
L. Jacquin, G. Jacob, S. Thibault, E. Baudry, BMC Research Notes 6 (2013).
date_created: 2018-12-11T11:49:04Z
date_published: 2013-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:25Z
day: '01'
doi: 10.1186/1756-0500-6-310
extern: '1'
intvolume: ' 6'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: BMC Research Notes
publication_status: published
publisher: BioMed Central
publist_id: '6752'
status: public
title: Color differences among feral pigeons (Columba livia) are not attributable
to sequence variation in the coding region of the melanocortin-1 receptor gene MC1R
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2013'
...
---
_id: '905'
abstract:
- lang: eng
text: A survey of avifauna was carried out in the Mys Shmidta area, north Chukotka,
Russia from 8 June to 12 July 2011. A total of 90 species was recorded in the
area, which together with literature data made a final list of 104 species. For
several species this area is beyond the northern, north-eastern or north-western
limits of their known distribution. We collected new data for 19 globally or locally
threatened species. Tundra Swan Cygnus columbianus, Emperor Goose Anser canagica,
American Golden Plover Pluvialis dominica, Western Sandpiper Calidris mauri, Semipalmated
Sandpiper C. pusilla, Northern House Martin Delichon urbica and Barn Swallow Hirundo
rustica were all confirmed to be breeding. Breeding of Brent Goose Branta bernicla
nigricans, Spectacled Eider Somateria fischeri and Steller's Eider Polysticta
stelleri was judged to be 'very likely'. There was no evidence for breeding of
Ross's Gull Rhodostethia rosea despite several records. Two Eurasian Dotterels
Eudromias morinellus were recorded displaying for the first time in the area,
but the status of the species is unclear. The area is important for Snowy Owl
Nyctea scandiaca, and as moulting grounds for Emperor Goose. Canada Goose Branta
canadensis, Baikal Teal Anas formosa, Bar-tailed Godwit Limosa lapponica, Slaty-backed
Gull Larus schistisagus, Thayer's Gull L. thayeri, Black-headed Gull L. ridibundus,
White-tailed Eagle Haliaeetus albicilla, Steller's Sea Eagle H. pelagicus, Osprey
Pandion haliaetus, Arctic Warbler Phylloscopus borealis and House Sparrow Passer
domesticus are more likely to be rare vagrants or migrants. An observation of
a Pine Siskin Carduelis pinus is the first record for Eurasia.
acknowledgement: We thank Natalya Kveten and Oksana Makarova, heads of administrations
of Mys Shmidta and Ryrkaypiy for hospitality and for help with organising our excursions.
Warm thanks too to Pavel Tomkovich for useful comments on local birds and ornithological
literature. We are very grateful to The David and Lucile Packard Foundation for
the support to Birds Russia’s Spoon-billed Sandpiper conservation programme in 2011
and to Evgeny Syroechkovsky Jr, the leader of the Spoon-billed Sandpiper conservation
team in Russia.
author:
- first_name: Vladimir
full_name: Arkhipov, Vladimir Y
last_name: Arkhipov
- first_name: T
full_name: Noah T
last_name: Noah
- first_name: Steffen
full_name: Koschkar, Steffen
last_name: Koschkar
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Arkhipov V, Noah T, Koschkar S, Kondrashov F. Birds of Mys Shmidta, north Chukotka,
Russia. Forktail. 2013;(29):25-30.
apa: Arkhipov, V., Noah, T., Koschkar, S., & Kondrashov, F. (2013). Birds of
Mys Shmidta, north Chukotka, Russia. Forktail. Oriental Bird Club.
chicago: Arkhipov, Vladimir, T Noah, Steffen Koschkar, and Fyodor Kondrashov. “Birds
of Mys Shmidta, North Chukotka, Russia.” Forktail. Oriental Bird Club,
2013.
ieee: V. Arkhipov, T. Noah, S. Koschkar, and F. Kondrashov, “Birds of Mys Shmidta,
north Chukotka, Russia,” Forktail, no. 29. Oriental Bird Club, pp. 25–30,
2013.
ista: Arkhipov V, Noah T, Koschkar S, Kondrashov F. 2013. Birds of Mys Shmidta,
north Chukotka, Russia. Forktail. (29), 25–30.
mla: Arkhipov, Vladimir, et al. “Birds of Mys Shmidta, North Chukotka, Russia.”
Forktail, no. 29, Oriental Bird Club, 2013, pp. 25–30.
short: V. Arkhipov, T. Noah, S. Koschkar, F. Kondrashov, Forktail (2013) 25–30.
date_created: 2018-12-11T11:49:07Z
date_published: 2013-09-01T00:00:00Z
date_updated: 2021-01-12T08:21:48Z
day: '01'
extern: 1
issue: '29'
main_file_link:
- open_access: '1'
url: http://orientalbirdclub.org/forktail29/
month: '09'
oa: 1
page: 25 - 30
publication: Forktail
publication_status: published
publisher: Oriental Bird Club
publist_id: '6741'
quality_controlled: 0
status: public
title: Birds of Mys Shmidta, north Chukotka, Russia
type: journal_article
year: '2013'
...
---
_id: '846'
abstract:
- lang: eng
text: Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this
question has not been comprehensively addressed at the molecular level. Here,
we use data from 221 human genes with known pathogenic mutations to estimate the
rate of irreversibility in protein evolution. For these genes, we reconstruct
ancestral amino acid sequences along the mammalian phylogeny and identify ancestral
amino acid states that match known pathogenic mutations. Such cases represent
inherent evolutionary irreversibility because, at the present moment, reversals
to these ancestral amino acid states are impossible for the human lineage. We
estimate that approximately 10% of all amino acid substitutions along the mammalian
phylogeny are irreversible, such that a return to the ancestral amino acid state
would lead to a pathogenic phenotype. For a subset of 51 genes with high rates
of irreversibility, as much as 40% of all amino acid evolution was estimated to
be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes,
the molecular nature of the high rate of irreversibility in proteins is best explained
by evolution with a high prevalence of compensatory, epistatic interactions between
amino acid sites. Under such mode of protein evolution, once an amino acid substitution
is fixed, the probability of its reversal declines as the protein sequence accumulates
changes that affect the phenotypic manifestation of the ancestral state. The prevalence
of epistasis in evolution indicates that the observed high rate of irreversibility
in protein evolution is an inherent property of protein structure and function.
acknowledgement: This work was supported by Plan Nacional grant BFU2009-09271 from
the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado
Universitario) program grant AP2008-01888 from the Spanish Ministry of Education
to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and
Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein
evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096
apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility
in protein evolution. Genome Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/gbe/evs096
chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution. Oxford University
Press, 2012. https://doi.org/10.1093/gbe/evs096.
ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in
protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford
University Press, pp. 1213–1222, 2012.
ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in
protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.
mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford
University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096.
short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222.
date_created: 2018-12-11T11:48:49Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/gbe/evs096
extern: 1
intvolume: ' 4'
issue: '12'
month: '01'
page: 1213 - 1222
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6802'
quality_controlled: 0
status: public
title: Estimating the rate of irreversibility in protein evolution
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
volume: 4
year: '2012'
...
---
_id: '858'
abstract:
- lang: eng
text: 'ackground: The evolution and genomic stop codon frequencies have not been
rigorously studied with the exception of coding of non-canonical amino acids.
Here we study the rate of evolution and frequency distribution of stop codons
in bacterial genomes.Results: We show that in bacteria stop codons evolve slower
than synonymous sites, suggesting the action of weak negative selection. However,
the frequency of stop codons relative to genomic nucleotide content indicated
that this selection regime is not straightforward. The frequency of TAA and TGA
stop codons is GC-content dependent, with TAA decreasing and TGA increasing with
GC-content, while TAG frequency is independent of GC-content. Applying a formal,
analytical model to these data we found that the relationship between stop codon
frequencies and nucleotide content cannot be explained by mutational biases or
selection on nucleotide content. However, with weak nucleotide content-dependent
selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates
the relationship between TAG and nucleotide content. For biologically plausible
rates of mutations we show that, in bacteria, TAG stop codon is universally associated
with lower fitness, with TAA being the optimal for G-content < 16% while for G-content
> 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG
codon is universally suboptimal in the bacterial lineage, such that TAA is likely
to be the preferred stop codon for low GC content while the TGA is the preferred
stop codon for high GC content. The optimization of stop codon usage may therefore
be useful in genome engineering or gene expression optimization applications.Reviewers:
This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev.
For the full reviews, please go to the Reviewers'' Comments section.'
acknowledgement: |
We thank Elena Alkalaeva and Peter Kolosov for insightful discussion and Brian Charlesworth for a critical reading of our manuscript. The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards.
author:
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alice
full_name: Ledda, Alice
last_name: Ledda
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
citation:
ama: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are
not selectively equivalent. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-30
apa: Povolotskaya, I., Kondrashov, F., Ledda, A., & Vlasov, P. (2012). Stop
codons in bacteria are not selectively equivalent. Biology Direct. BioMed
Central. https://doi.org/10.1186/1745-6150-7-30
chicago: Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop
Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct. BioMed
Central, 2012. https://doi.org/10.1186/1745-6150-7-30.
ieee: I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria
are not selectively equivalent,” Biology Direct, vol. 7. BioMed Central,
2012.
ista: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria
are not selectively equivalent. Biology Direct. 7.
mla: Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.”
Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30.
short: I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012).
date_created: 2018-12-11T11:48:52Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2021-01-12T08:20:08Z
day: '01'
doi: 10.1186/1745-6150-7-30
extern: 1
intvolume: ' 7'
month: '09'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6792'
quality_controlled: 0
status: public
title: Stop codons in bacteria are not selectively equivalent
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 7
year: '2012'
...
---
_id: '900'
abstract:
- lang: eng
text: 'The main forces directing long-term molecular evolution remain obscure. A
sizable fraction of amino-acid substitutions seem to be fixed by positive selection,
but it is unclear to what degree long-term protein evolution is constrained by
epistasis, that is, instances when substitutions that are accepted in one genotype
are deleterious in another. Here we obtain a quantitative estimate of the prevalence
of epistasis in long-term protein evolution by relating data on amino-acid usage
in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term
evolution. We studied multiple alignments of at least 1,000 orthologues for each
of these 16 proteins from species from a diverse phylogenetic background and found
that an average site contained approximately eight different amino acids. Thus,
without epistasis an average site should accept two-fifths of all possible amino
acids, and the average rate of amino-acid substitutions should therefore be about
three-fifths lower than the rate of neutral evolution. However, we found that
the measured rate of amino-acid substitution in recent evolution is 20 times lower
than the rate of neutral evolution and an order of magnitude lower than that expected
in the absence of epistasis. These data indicate that epistasis is pervasive throughout
protein evolution: about 90 per cent of all amino-acid substitutions have a neutral
or beneficial impact only in the genetic backgrounds in which they occur, and
must therefore be deleterious in a different background of other species. Our
findings show that most amino-acid substitutions have different fitness effects
in different species and that epistasis provides the primary conceptual framework
to describe the tempo and mode of long-term protein evolution.'
acknowledgement: |
The work was supported by Plan Nacional grants from the Spanish Ministry of Science and Innovation, to F.A.K. and C.N. C.K. was supported by the European Union FP7 project Quantomics (KBBE2A222664). F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. We thank B. Lehner and T. Warnecke for input and a critical reading of the manuscript.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Cédric
full_name: Notredame, Cédric
last_name: Notredame
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Epistasis as the primary
factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510
apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2012).
Epistasis as the primary factor in molecular evolution. Nature. Nature
Publishing Group. https://doi.org/10.1038/nature11510
chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor
Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature.
Nature Publishing Group, 2012. https://doi.org/10.1038/nature11510.
ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis
as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421.
Nature Publishing Group, pp. 535–538, 2012.
ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as
the primary factor in molecular evolution. Nature. 490(7421), 535–538.
mla: Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.”
Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38,
doi:10.1038/nature11510.
short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012)
535–538.
date_created: 2018-12-11T11:49:06Z
date_published: 2012-10-25T00:00:00Z
date_updated: 2021-01-12T08:21:45Z
day: '25'
doi: 10.1038/nature11510
extern: 1
intvolume: ' 490'
issue: '7421'
month: '10'
page: 535 - 538
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6748'
quality_controlled: 0
status: public
title: Epistasis as the primary factor in molecular evolution
type: journal_article
volume: 490
year: '2012'
...
---
_id: '887'
abstract:
- lang: eng
text: A subject of extensive study in evolutionary theory has been the issue of
how neutral, redundant copies can be maintained in the genome for long periods
of time. Concurrently, examples of adaptive gene duplications to various environmental
conditions in different species have been described. At this point, it is too
early to tell whether or not a substantial fraction of gene copies have initially
achieved fixation by positive selection for increased dosage. Nevertheless, enough
examples have accumulated in the literature that such a possibility should be
considered. Here, I review the recent examples of adaptive gene duplications and
make an attempt to draw generalizations on what types of genes may be particularly
prone to be selected for under certain environmental conditions. The identification
of copy-number variation in ecological field studies of species adapting to stressful
or novel environmental conditions may improve our understanding of gene duplications
as a mechanism of adaptation and its relevance to the long-term persistence of
gene duplications.
acknowledgement: The work was supported by a Plan Nacional grant no. BFU2009-09271
from the Spanish Ministry of Science and Innovation. The author is a European Molecular
Biology Organization Young Investigator and Howard Hughes Medical Institute International
Early Career Scientist.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. Gene duplication as a mechanism of genomic adaptation to a changing
environment. Proceedings of the Royal Society of London Series B Biological
Sciences. 2012;279(1749):5048-5057. doi:10.1098/rspb.2012.1108
apa: Kondrashov, F. (2012). Gene duplication as a mechanism of genomic adaptation
to a changing environment. Proceedings of the Royal Society of London Series
B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.1108
chicago: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation
to a Changing Environment.” Proceedings of the Royal Society of London Series
B Biological Sciences. Royal Society, The, 2012. https://doi.org/10.1098/rspb.2012.1108.
ieee: F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a
changing environment,” Proceedings of the Royal Society of London Series B
Biological Sciences, vol. 279, no. 1749. Royal Society, The, pp. 5048–5057,
2012.
ista: Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation
to a changing environment. Proceedings of the Royal Society of London Series B
Biological Sciences. 279(1749), 5048–5057.
mla: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation
to a Changing Environment.” Proceedings of the Royal Society of London Series
B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57,
doi:10.1098/rspb.2012.1108.
short: F. Kondrashov, Proceedings of the Royal Society of London Series B Biological
Sciences 279 (2012) 5048–5057.
date_created: 2018-12-11T11:49:01Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:16Z
day: '01'
doi: 10.1098/rspb.2012.1108
extern: 1
intvolume: ' 279'
issue: '1749'
month: '01'
page: 5048 - 5057
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6765'
quality_controlled: 0
status: public
title: Gene duplication as a mechanism of genomic adaptation to a changing environment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 279
year: '2012'
...
---
_id: '890'
abstract:
- lang: eng
text: Recent discovery of the Large-billed Reed Warbler (Acrocephalus orinus) in
museums and in the wild significantly expanded our knowledge of its morphological
traits and genetic variability, and revealed new data on geographical distribution
of the breeding grounds, migration routes and wintering locations of this species.
It is now certain that A. orinus is breeding in Central Asia; however, the precise
area of distribution remains unclear. The difficulty in the further study of this
species lies in the small number of known specimens, with only 13 currently available
in museums, and in the relative uncertainty of the breeding area and habitat of
this species. Following morphological and genetic analyses from Svensson, et al,
we describe 14 new A. orinus specimens from collections of Zoological Museums
of the former USSR from the territory of Central Asian states. All of these specimens
were erroneously labeled as Blyth's Reed Warbler (A. dumetorum), which is thought
to be a breeding species in these areas. The 14 new A. orinus specimens were collected
during breeding season while most of the 85 A. dumetorum specimens from the same
area were collected during the migration period. Our data indicate that the Central
Asian territory previously attributed as breeding grounds of A. dumetorum is likely
to constitute the breeding territory of A. orinus. This rare case of a re-description
of the breeding territory of a lost species emphasizes the importance of maintenance
of museum collections around the world. If the present data on the breeding grounds
of A. orinus are confirmed with field observations and collections, the literature
on the biology of A. dumetorum from the southern part of its range may have to
be reconsidered.
acknowledgement: |
The work was supported by the Plan Nacional grant number BFU2009-09271 from the Spanish Ministry of Science and Innovation.
We extend our thanks to A.M. Peklo and I.V. Fadeev for granting us access to ornithological collections, to V.S. Shishkin, M.V. Kalyakin, R.D. Kashkarov, O.V. Belyalov and V.M. Loskot for valuable insights and to L. Svensson for extensive feedback on the manuscript. We thank E.I. Rogaev for access to ancient DNA facility.
author:
- first_name: Evgeniy
full_name: Koblik, Evgeniy A
last_name: Koblik
- first_name: Yaroslav
full_name: Red'Kin, Yaroslav A
last_name: Red'Kin
- first_name: Margarita
full_name: Meer, Margarita S
last_name: Meer
- first_name: Romain
full_name: Derelle, Romain
last_name: Derelle
- first_name: Sofia
full_name: Golenkina, Sofia A
last_name: Golenkina
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Vladimir
full_name: Arkhipov, Vladimir Y
last_name: Arkhipov
citation:
ama: 'Koblik E, Red’Kin Y, Meer M, et al. Acrocephalus orinus: A case of Mistaken
identity. PLoS One. 2011;6(4). doi:10.1371/journal.pone.0017716'
apa: 'Koblik, E., Red’Kin, Y., Meer, M., Derelle, R., Golenkina, S., Kondrashov,
F., & Arkhipov, V. (2011). Acrocephalus orinus: A case of Mistaken identity.
PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0017716'
chicago: 'Koblik, Evgeniy, Yaroslav Red’Kin, Margarita Meer, Romain Derelle, Sofia
Golenkina, Fyodor Kondrashov, and Vladimir Arkhipov. “Acrocephalus Orinus: A Case
of Mistaken Identity.” PLoS One. Public Library of Science, 2011. https://doi.org/10.1371/journal.pone.0017716.'
ieee: 'E. Koblik et al., “Acrocephalus orinus: A case of Mistaken identity,”
PLoS One, vol. 6, no. 4. Public Library of Science, 2011.'
ista: 'Koblik E, Red’Kin Y, Meer M, Derelle R, Golenkina S, Kondrashov F, Arkhipov
V. 2011. Acrocephalus orinus: A case of Mistaken identity. PLoS One. 6(4).'
mla: 'Koblik, Evgeniy, et al. “Acrocephalus Orinus: A Case of Mistaken Identity.”
PLoS One, vol. 6, no. 4, Public Library of Science, 2011, doi:10.1371/journal.pone.0017716.'
short: E. Koblik, Y. Red’Kin, M. Meer, R. Derelle, S. Golenkina, F. Kondrashov,
V. Arkhipov, PLoS One 6 (2011).
date_created: 2018-12-11T11:49:02Z
date_published: 2011-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:18Z
day: '01'
doi: 10.1371/journal.pone.0017716
extern: 1
intvolume: ' 6'
issue: '4'
month: '01'
publication: PLoS One
publication_status: published
publisher: Public Library of Science
publist_id: '6760'
quality_controlled: 0
status: public
title: 'Acrocephalus orinus: A case of Mistaken identity'
type: journal_article
volume: 6
year: '2011'
...
---
_id: '881'
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Kondrashov F. Gene Dosage and Duplication. In: Evolution after Gene Duplication.
Wiley-Blackwell; 2011:57-76. doi:10.1002/9780470619902.ch4'
apa: Kondrashov, F. (2011). Gene Dosage and Duplication. In Evolution after Gene
Duplication (pp. 57–76). Wiley-Blackwell. https://doi.org/10.1002/9780470619902.ch4
chicago: Kondrashov, Fyodor. “Gene Dosage and Duplication.” In Evolution after
Gene Duplication, 57–76. Wiley-Blackwell, 2011. https://doi.org/10.1002/9780470619902.ch4.
ieee: F. Kondrashov, “Gene Dosage and Duplication,” in Evolution after Gene Duplication,
Wiley-Blackwell, 2011, pp. 57–76.
ista: 'Kondrashov F. 2011.Gene Dosage and Duplication. In: Evolution after Gene
Duplication. , 57–76.'
mla: Kondrashov, Fyodor. “Gene Dosage and Duplication.” Evolution after Gene
Duplication, Wiley-Blackwell, 2011, pp. 57–76, doi:10.1002/9780470619902.ch4.
short: F. Kondrashov, in:, Evolution after Gene Duplication, Wiley-Blackwell, 2011,
pp. 57–76.
date_created: 2018-12-11T11:49:00Z
date_published: 2011-03-14T00:00:00Z
date_updated: 2021-01-12T08:21:08Z
day: '14'
doi: 10.1002/9780470619902.ch4
extern: 1
month: '03'
page: 57 - 76
publication: Evolution after Gene Duplication
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6766'
quality_controlled: 0
status: public
title: Gene Dosage and Duplication
type: book_chapter
year: '2011'
...
---
_id: '891'
abstract:
- lang: eng
text: Gene duplications and their subsequent divergence play an important part in
the evolution of novel gene functions. Several models for the emergence, maintenance
and evolution of gene copies have been proposed. However, a clear consensus on
how gene duplications are fixed and maintained in genomes is lacking. Here, we
present a comprehensive classification of the models that are relevant to all
stages of the evolution of gene duplications. Each model predicts a unique combination
of evolutionary dynamics and functional properties. Setting out these predictions
is an important step towards identifying the main mechanisms that are involved
in the evolution of gene duplications.
acknowledgement: |
We thank M. Lynch for insightful comments on the manuscript.
author:
- first_name: Hideki
full_name: Innan, Hideki
last_name: Innan
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: 'Innan H, Kondrashov F. The evolution of gene duplications: Classifying and
distinguishing between models. Nature Reviews Genetics. 2010;11(2):97-108.
doi:10.1038/nrg2689'
apa: 'Innan, H., & Kondrashov, F. (2010). The evolution of gene duplications:
Classifying and distinguishing between models. Nature Reviews Genetics.
Nature Publishing Group. https://doi.org/10.1038/nrg2689'
chicago: 'Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications:
Classifying and Distinguishing between Models.” Nature Reviews Genetics.
Nature Publishing Group, 2010. https://doi.org/10.1038/nrg2689.'
ieee: 'H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying
and distinguishing between models,” Nature Reviews Genetics, vol. 11, no.
2. Nature Publishing Group, pp. 97–108, 2010.'
ista: 'Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying
and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.'
mla: 'Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications:
Classifying and Distinguishing between Models.” Nature Reviews Genetics,
vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:10.1038/nrg2689.'
short: H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108.
date_created: 2018-12-11T11:49:03Z
date_published: 2010-02-01T00:00:00Z
date_updated: 2021-01-12T08:21:19Z
day: '01'
doi: 10.1038/nrg2689
extern: 1
intvolume: ' 11'
issue: '2'
month: '02'
page: 97 - 108
publication: Nature Reviews Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6755'
quality_controlled: 0
status: public
title: 'The evolution of gene duplications: Classifying and distinguishing between
models'
type: journal_article
volume: 11
year: '2010'
...
---
_id: '901'
abstract:
- lang: eng
text: 'Background: Surveying deleterious variation in human populations is crucial
for our understanding, diagnosis and potential treatment of human genetic pathologies.
A number of recent genome-wide analyses focused on the prevalence of segregating
deleterious alleles in the nuclear genome. However, such studies have not been
conducted for the mitochondrial genome.Results: We present a systematic survey
of polymorphisms in the human mitochondrial genome, including those predicted
to be deleterious and those that correspond to known pathogenic mutations. Analyzing
4458 completely sequenced mitochondrial genomes we characterize the genetic diversity
of different types of single nucleotide polymorphisms (SNPs) in African (L haplotypes)
and non-African (M and N haplotypes) populations. We find that the overall level
of polymorphism is higher in the mitochondrial compared to the nuclear genome,
although the mitochondrial genome appears to be under stronger selection as indicated
by proportionally fewer nonsynonymous than synonymous substitutions. The African
mitochondrial genomes show higher heterozygosity, a greater number of polymorphic
sites and higher frequencies of polymorphisms for synonymous, benign and damaging
polymorphism than non-African genomes. However, African genomes carry significantly
fewer SNPs that have been previously characterized as pathogenic compared to non-African
genomes.Conclusions: Finding SNPs classified as pathogenic to be the only category
of polymorphisms that are more abundant in non-African genomes is best explained
by a systematic ascertainment bias that favours the discovery of pathogenic polymorphisms
segregating in non-African populations. This further suggests that, contrary to
the common disease-common variant hypothesis, pathogenic mutations are largely
population-specific and different SNPs may be associated with the same disease
in different populations. Therefore, to obtain a comprehensive picture of the
deleterious variability in the human population, as well as to improve the diagnostics
of individuals carrying African mitochondrial haplotypes, it is necessary to survey
different populations independently.Reviewers: This article was reviewed by Dr
Mikhail Gelfand, Dr Vasily Ramensky (nominated by Dr Eugene Koonin) and Dr David
Rand (nominated by Dr Laurence Hurst).'
acknowledgement: We thank Ivan Adzhubei and Shamil Sunyaev for extensive assistance
with PolyPhen 2 and insightful discussion. We thank the Spanish Ministry of Science
and Innovation, Plan Nacional Program grant BFU2009-09271 for funding.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kondrashov F. Mitochondrial pathogenic mutations are population-specific.
Biology Direct. 2010;5. doi:10.1186/1745-6150-5-68
apa: Breen, M., & Kondrashov, F. (2010). Mitochondrial pathogenic mutations
are population-specific. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-5-68
chicago: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations
Are Population-Specific.” Biology Direct. BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-68.
ieee: M. Breen and F. Kondrashov, “Mitochondrial pathogenic mutations are population-specific,”
Biology Direct, vol. 5. BioMed Central, 2010.
ista: Breen M, Kondrashov F. 2010. Mitochondrial pathogenic mutations are population-specific.
Biology Direct. 5.
mla: Breen, Michael, and Fyodor Kondrashov. “Mitochondrial Pathogenic Mutations
Are Population-Specific.” Biology Direct, vol. 5, BioMed Central, 2010,
doi:10.1186/1745-6150-5-68.
short: M. Breen, F. Kondrashov, Biology Direct 5 (2010).
date_created: 2018-12-11T11:49:06Z
date_published: 2010-12-31T00:00:00Z
date_updated: 2021-01-12T08:21:46Z
day: '31'
doi: 10.1186/1745-6150-5-68
extern: 1
intvolume: ' 5'
month: '12'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6749'
quality_controlled: 0
status: public
title: Mitochondrial pathogenic mutations are population-specific
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 5
year: '2010'
...
---
_id: '857'
abstract:
- lang: eng
text: 'The need to maintain the structural and functional integrity of an evolving
protein severely restricts the repertoire of acceptable amino-acid substitutions.
However, it is not known whether these restrictions impose a global limit on how
far homologous protein sequences can diverge from each other. Here we explore
the limits of protein evolution using sequence divergence data. We formulate a
computational approach to study the rate of divergence of distant protein sequences
and measure this rate for ancient proteins, those that were present in the last
universal common ancestor. We show that ancient proteins are still diverging from
each other, indicating an ongoing expansion of the protein sequence universe.
The slow rate of this divergence is imposed by the sparseness of functional protein
sequences in sequence space and the ruggedness of the protein fitness landscape:
98 per cent of sites cannot accept an amino-acid substitution at any given moment
but a vast majority of all sites may eventually be permitted to evolve when other,
compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach
the limit of divergent evolution of proteins, and for most proteins the limit
of sequence similarity imposed by common function may not exceed that of random
sequences.'
acknowledgement: |
We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space.
author:
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Povolotskaya I, Kondrashov F. Sequence space and the ongoing expansion of the
protein universe. Nature. 2010;465(7300):922-926. doi:10.1038/nature09105
apa: Povolotskaya, I., & Kondrashov, F. (2010). Sequence space and the ongoing
expansion of the protein universe. Nature. Nature Publishing Group. https://doi.org/10.1038/nature09105
chicago: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing
Expansion of the Protein Universe.” Nature. Nature Publishing Group, 2010.
https://doi.org/10.1038/nature09105.
ieee: I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion
of the protein universe,” Nature, vol. 465, no. 7300. Nature Publishing
Group, pp. 922–926, 2010.
ista: Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion
of the protein universe. Nature. 465(7300), 922–926.
mla: Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing
Expansion of the Protein Universe.” Nature, vol. 465, no. 7300, Nature
Publishing Group, 2010, pp. 922–26, doi:10.1038/nature09105.
short: I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.
date_created: 2018-12-11T11:48:52Z
date_published: 2010-06-17T00:00:00Z
date_updated: 2021-01-12T08:20:05Z
day: '17'
doi: 10.1038/nature09105
extern: 1
intvolume: ' 465'
issue: '7300'
month: '06'
page: 922 - 926
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6791'
quality_controlled: 0
status: public
title: Sequence space and the ongoing expansion of the protein universe
type: journal_article
volume: 465
year: '2010'
...
---
_id: '862'
abstract:
- lang: eng
text: A long-standing controversy in evolutionary biology is whether or not evolving
lineages can cross valleys on the fitness landscape that correspond to low-fitness
genotypes, which can eventually enable them to reach isolated fitness peaks1-9.
Here we study the fitness landscapes traversed by switches between different AU
and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer
RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches
occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles
corresponding to GU and AC non-Watson-Crick intermediate states segregate within
human populations at low frequencies, similar to those of non-synonymous alleles.
Substitutions leading to a Watson-Crick switch are strongly correlated, especially
in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial
genome. Using these data we estimate that a typical Watson-Crick switch involves
crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC
intermediates being slightly more deleterious than GU intermediates. This compensatory
evolution must proceed through rare intermediate variants that never reach fixation.
The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs
and other molecules implies that simultaneous fixation of two alleles that are
individually deleterious may be a common phenomenon at the molecular level.
acknowledgement: We thank H. Innan, M. Laessig, R. Guigo, I. Povolotskaya, D. Ivankov
and M. Breen for thoughtful discussions and critical reading of the manuscript.
author:
- first_name: Margarita
full_name: Meer, Margarita V
last_name: Meer
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Yael
full_name: Artzy-Randrup, Yael
last_name: Artzy Randrup
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. Compensatory evolution
in mitochondrial tRNAs navigates valleys of low fitness. Nature. 2010;464(7286):279-282.
doi:10.1038/nature08691
apa: Meer, M., Kondrashov, A., Artzy Randrup, Y., & Kondrashov, F. (2010). Compensatory
evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature.
Nature Publishing Group. https://doi.org/10.1038/nature08691
chicago: Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov.
“Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.”
Nature. Nature Publishing Group, 2010. https://doi.org/10.1038/nature08691.
ieee: M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory
evolution in mitochondrial tRNAs navigates valleys of low fitness,” Nature,
vol. 464, no. 7286. Nature Publishing Group, pp. 279–282, 2010.
ista: Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution
in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.
mla: Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates
Valleys of Low Fitness.” Nature, vol. 464, no. 7286, Nature Publishing
Group, 2010, pp. 279–82, doi:10.1038/nature08691.
short: M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010)
279–282.
date_created: 2018-12-11T11:48:54Z
date_published: 2010-03-11T00:00:00Z
date_updated: 2021-01-12T08:20:20Z
day: '11'
doi: 10.1038/nature08691
extern: 1
intvolume: ' 464'
issue: '7286'
month: '03'
page: 279 - 282
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6784'
quality_controlled: 0
status: public
title: Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness
type: journal_article
volume: 464
year: '2010'
...
---
_id: '872'
abstract:
- lang: eng
text: The rate of spontaneous mutation in natural populations is a fundamental parameter
for many evolutionary phenomena. Because the rate of mutation is generally low,
most of what is currently known about mutation has been obtained through indirect,
complex and imprecise methodological approaches. However, in the past few years
genome-wide sequencing of closely related individuals has made it possible to
estimate the rates of mutation directly at the level of the DNA, avoiding most
of the problems associated with using indirect methods. Here, we review the methods
used in the past with an emphasis on next generation sequencing, which may soon
make the accurate measurement of spontaneous mutation rates a matter of routine.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Kondrashov A. Measurements of spontaneous rates of mutations
in the recent past and the near future. Philosophical Transactions of the Royal
Society of London Series B, Biological Sciences. 2010;365(1544):1169-1176.
doi:10.1098/rstb.2009.0286
apa: Kondrashov, F., & Kondrashov, A. (2010). Measurements of spontaneous rates
of mutations in the recent past and the near future. Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The. https://doi.org/10.1098/rstb.2009.0286
chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous
Rates of Mutations in the Recent Past and the near Future.” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences. Royal Society,
The, 2010. https://doi.org/10.1098/rstb.2009.0286.
ieee: F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations
in the recent past and the near future,” Philosophical Transactions of the
Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1544.
Royal Society, The, pp. 1169–1176, 2010.
ista: Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations
in the recent past and the near future. Philosophical Transactions of the Royal
Society of London. Series B, Biological Sciences. 365(1544), 1169–1176.
mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates
of Mutations in the Recent Past and the near Future.” Philosophical Transactions
of the Royal Society of London. Series B, Biological Sciences, vol. 365, no.
1544, Royal Society, The, 2010, pp. 1169–76, doi:10.1098/rstb.2009.0286.
short: F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society
of London. Series B, Biological Sciences 365 (2010) 1169–1176.
date_created: 2018-12-11T11:48:57Z
date_published: 2010-04-27T00:00:00Z
date_updated: 2021-01-12T08:20:43Z
day: '27'
doi: 10.1098/rstb.2009.0286
extern: 1
intvolume: ' 365'
issue: '1544'
month: '04'
page: 1169 - 1176
publication: Philosophical Transactions of the Royal Society of London. Series B,
Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6772'
quality_controlled: 0
status: public
title: Measurements of spontaneous rates of mutations in the recent past and the near
future
type: journal_article
volume: 365
year: '2010'
...
---
_id: '884'
abstract:
- lang: eng
text: 'Background: Divergence of two independently evolving sequences that originated
from a common ancestor can be described by two parameters, the asymptotic level
of divergence E and the rate r at which this level of divergence is approached.
Constant negative selection impedes allele replacements and, therefore, is routinely
assumed to decelerate sequence divergence. However, its impact on E and on r has
not been formally investigated.Results: Strong selection that favors only one
allele can make E arbitrarily small and r arbitrarily large. In contrast, in the
case of 4 possible alleles and equal mutation rates, the lowest value of r, attained
when two alleles confer equal fitnesses and the other two are strongly deleterious,
is only two times lower than its value under selective neutrality.Conclusions:
Constant selection can strongly constrain the level of sequence divergence, but
cannot reduce substantially the rate at which this level is approached. In particular,
under any constant selection the divergence of sequences that accumulated one
substitution per neutral site since their origin from the common ancestor must
already constitute at least one half of the asymptotic divergence at sites under
such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei
Maslov, and Nick Grishin.'
author:
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Dmitry
full_name: Ivankov, Dmitry N
last_name: Ivankov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. Rate of sequence divergence
under constant selection. Biology Direct. 2010;5. doi:10.1186/1745-6150-5-5
apa: Kondrashov, A., Povolotskaya, I., Ivankov, D., & Kondrashov, F. (2010).
Rate of sequence divergence under constant selection. Biology Direct. BioMed
Central. https://doi.org/10.1186/1745-6150-5-5
chicago: Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov.
“Rate of Sequence Divergence under Constant Selection.” Biology Direct.
BioMed Central, 2010. https://doi.org/10.1186/1745-6150-5-5.
ieee: A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence
divergence under constant selection,” Biology Direct, vol. 5. BioMed Central,
2010.
ista: Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence
divergence under constant selection. Biology Direct. 5.
mla: Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.”
Biology Direct, vol. 5, BioMed Central, 2010, doi:10.1186/1745-6150-5-5.
short: A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct
5 (2010).
date_created: 2018-12-11T11:49:00Z
date_published: 2010-01-21T00:00:00Z
date_updated: 2021-01-12T08:21:15Z
day: '21'
doi: 10.1186/1745-6150-5-5
extern: 1
intvolume: ' 5'
month: '01'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6762'
quality_controlled: 0
status: public
title: Rate of sequence divergence under constant selection
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 5
year: '2010'
...
---
_id: '908'
abstract:
- lang: eng
text: Although some data link archaeal and eukaryotic translation, the overall mechanism
of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1)
and eukaryotic (eRF1) single release factors recognize all three stop codons.
The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses
the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis
of the last stage of archaeal translation in pyrrolysine-utilizing species. We
demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses
activity and recognizes all three stop codons. The second aRF1 homolog may have
another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae
is discussed.
acknowledgement: We are grateful to Andrey Poltaraus and his colleagues for sequencing
a/eRF1 genes. We thank Tatyana Pestova and Chris Hellen for the gift of plasmids
encoding initiation factors eIF1, eIF1A, eIF4A, eIF4B, eIF4G, eIF5, eIF5B, and Anna
Yaremchuk and Michael Tukalo for M. jannaschii aRF1. This work was supported by
grants from the Presidium of the (Program Molecular and Cell Biology), the Russian
Foundation for Basic Research (08-04-01091-а to E.A. and 08-04-00375a to L.F.),
the National Institute for General Medical Sciences (to D.S.), the National Science
Foundation (to D.S.) and the Office of Basic Energy Sciences, DOE (to D.S.).
author:
- first_name: Elena
full_name: Alkalaeva, Elena Z
last_name: Alkalaeva
- first_name: Boris
full_name: Eliseev, Boris D
last_name: Eliseev
- first_name: Alexandre
full_name: Ambrogelly, Alexandre
last_name: Ambrogelly
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Sarath
full_name: Gundllapalli, Sarath B
last_name: Gundllapalli
- first_name: Ludmila
full_name: Frolova, Ludmila Y
last_name: Frolova
- first_name: Dieter
full_name: Söll, Dieter G
last_name: Söll
- first_name: Lev
full_name: Kisselev, Lev L
last_name: Kisselev
citation:
ama: Alkalaeva E, Eliseev B, Ambrogelly A, et al. Translation termination in pyrrolysine-utilizing
archaea. FEBS Letters. 2009;583(21):3455-3460. doi:10.1016/j.febslet.2009.09.044
apa: Alkalaeva, E., Eliseev, B., Ambrogelly, A., Vlasov, P., Kondrashov, F., Gundllapalli,
S., … Kisselev, L. (2009). Translation termination in pyrrolysine-utilizing archaea.
FEBS Letters. Elsevier. https://doi.org/10.1016/j.febslet.2009.09.044
chicago: Alkalaeva, Elena, Boris Eliseev, Alexandre Ambrogelly, Peter Vlasov, Fyodor
Kondrashov, Sarath Gundllapalli, Ludmila Frolova, Dieter Söll, and Lev Kisselev.
“Translation Termination in Pyrrolysine-Utilizing Archaea.” FEBS Letters.
Elsevier, 2009. https://doi.org/10.1016/j.febslet.2009.09.044.
ieee: E. Alkalaeva et al., “Translation termination in pyrrolysine-utilizing
archaea,” FEBS Letters, vol. 583, no. 21. Elsevier, pp. 3455–3460, 2009.
ista: Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov F, Gundllapalli
S, Frolova L, Söll D, Kisselev L. 2009. Translation termination in pyrrolysine-utilizing
archaea. FEBS Letters. 583(21), 3455–3460.
mla: Alkalaeva, Elena, et al. “Translation Termination in Pyrrolysine-Utilizing
Archaea.” FEBS Letters, vol. 583, no. 21, Elsevier, 2009, pp. 3455–60,
doi:10.1016/j.febslet.2009.09.044.
short: E. Alkalaeva, B. Eliseev, A. Ambrogelly, P. Vlasov, F. Kondrashov, S. Gundllapalli,
L. Frolova, D. Söll, L. Kisselev, FEBS Letters 583 (2009) 3455–3460.
date_created: 2018-12-11T11:49:08Z
date_published: 2009-11-03T00:00:00Z
date_updated: 2021-01-12T08:21:49Z
day: '03'
doi: 10.1016/j.febslet.2009.09.044
extern: 1
intvolume: ' 583'
issue: '21'
month: '11'
page: 3455 - 3460
publication: FEBS Letters
publication_status: published
publisher: Elsevier
publist_id: '6740'
quality_controlled: 0
status: public
title: Translation termination in pyrrolysine-utilizing archaea
type: journal_article
volume: 583
year: '2009'
...
---
_id: '844'
abstract:
- lang: eng
text: Mutation rate varies greatly between nucleotide sites of the human genome
and depends both on the global genomic location and the local sequence context
of a site. In particular, CpG context elevates the mutation rate by an order of
magnitude. Mutations also vary widely in their effect on the molecular function,
phenotype, and fitness. Independence of the probability of occurrence of a new
mutation's effect has been a fundamental premise in genetics. However, highly
mutable contexts may be preserved by negative selection at important sites but
destroyed by mutation at sites under no selection. Thus, there may be a positive
correlation between the rate of mutations at a nucleotide site and the magnitude
of their effect on fitness. We studied the impact of CpG context on the rate of
human-chimpanzee divergence and on intrahuman nucleotide diversity at non-synonymous
coding sites. We compared nucleotides that occupy identical positions within codons
of identical amino acids and only differ by being within versus outside CpG context.
Nucleotides within CpG context are under a stronger negative selection, as revealed
by their lower, proportionally to the mutation rate, rate of evolution and nucleotide
diversity. In particular, the probability of fixation of a non-synonymous transition
at a CpG site is two times lower than at a CpG site. Thus, sites with different
mutation rates are not necessarily selectively equivalent. This suggests that
the mutation rate may complement sequence conservation as a characteristic predictive
of functional importance of nucleotide sites.
acknowledgement: This work was supported in part by NIH grants R01 GM078598 and U54
LM008748.
author:
- first_name: Steffen
full_name: Schmidt, Steffen
last_name: Schmidt
- first_name: Anna
full_name: Gerasimova, Anna
last_name: Gerasimova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ivan
full_name: Adzuhbei, Ivan A
last_name: Adzuhbei
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
citation:
ama: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S.
Hypermutable non-synonymous sites are under stronger negative selection. PLoS
Genetics. 2008;4(11). doi:10.1371/journal.pgen.1000281
apa: Schmidt, S., Gerasimova, A., Kondrashov, F., Adzuhbei, I., Kondrashov, A.,
& Sunyaev, S. (2008). Hypermutable non-synonymous sites are under stronger
negative selection. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000281
chicago: Schmidt, Steffen, Anna Gerasimova, Fyodor Kondrashov, Ivan Adzuhbei, Alexey
Kondrashov, and Shamil Sunyaev. “Hypermutable Non-Synonymous Sites Are under Stronger
Negative Selection.” PLoS Genetics. Public Library of Science, 2008. https://doi.org/10.1371/journal.pgen.1000281.
ieee: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, and
S. Sunyaev, “Hypermutable non-synonymous sites are under stronger negative selection,”
PLoS Genetics, vol. 4, no. 11. Public Library of Science, 2008.
ista: Schmidt S, Gerasimova A, Kondrashov F, Adzuhbei I, Kondrashov A, Sunyaev S.
2008. Hypermutable non-synonymous sites are under stronger negative selection.
PLoS Genetics. 4(11).
mla: Schmidt, Steffen, et al. “Hypermutable Non-Synonymous Sites Are under Stronger
Negative Selection.” PLoS Genetics, vol. 4, no. 11, Public Library of Science,
2008, doi:10.1371/journal.pgen.1000281.
short: S. Schmidt, A. Gerasimova, F. Kondrashov, I. Adzuhbei, A. Kondrashov, S.
Sunyaev, PLoS Genetics 4 (2008).
date_created: 2018-12-11T11:48:48Z
date_published: 2008-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:16Z
day: '01'
doi: 10.1371/journal.pgen.1000281
extern: 1
intvolume: ' 4'
issue: '11'
month: '11'
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '6800'
quality_controlled: 0
status: public
title: Hypermutable non-synonymous sites are under stronger negative selection
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 4
year: '2008'
...
---
_id: '895'
abstract:
- lang: eng
text: Background. The arginine vasopressin V1a receptor (V1aR) modulates social
cognition and behavior in a wide variety of species. Variation in a repetitive
microsatellite element in the 5′ flanking region of the V1aR gene (AVPR1A) in
rodents has been associated with variation in brain V1aR expression and in social
behavior. In humans, the 5′ flanking region of AVPR1A contains a tandem duplication
of two ∼350 bp, microsatellite-containing elements located approximately 3.5 kb
upstream of the transcription start site. The first block, referred to as DupA,
contains a polymorphic (GT) 25microsatellite; the second block, DupB, has a complex
(CT) 4-(TT)-(CT)8-(GT)24polymorphic motif, known as RS3. Polymorphisms in RS3
have been associated with variation in sociobehavioral traits in humans, including
autism spectrum disorders. Thus, evolution of these regions may have contributed
to variation in social behavior in primates. We examined the structure of these
regions in six ape, six monkey, and one prosimian species. Results. Both tandem
repeat blocks are present upstream of the AVPR1A coding region in five of the
ape species we investigated, while monkeys have only one copy of this region.
As in humans, the microsatellites within DupA and DupB are polymorphic in many
primate species. Furthermore, both single (lacking DupB) and duplicated alleles
(containing both DupA and DupB) are present in chimpanzee (Pan troglodytes) populations
with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles,
respectively, based on the analysis of 47 wild-caught individuals. Finally, a
phylogenetic reconstruction suggests two alternate evolutionary histories for
this locus. Conclusion. There is no obvious relationship between the presence
of the RS3 duplication and social organization in primates. However, polymorphisms
identified in some species may be useful in future genetic association studies.
In particular, the presence of both single and duplicated alleles in chimpanzees
provides a unique opportunity to assess the functional role of this duplication
in contributing to variation in social behavior in primates. While our initial
studies show no signs of directional selection on this locus in chimps, pharmacological
and genetic association studies support a potential role for this region in influencing
V1aR expression and social behavior.
acknowledgement: |
We thank the caretakers at Zoo Atlanta and Yerkes National Primate Center for help with procuring specimens. Additional DNA samples were supplied by Bill Hopkins, Emory University (chimpanzee), Allyson Bennet, Wake Forest University (chimpanzee, rhesus macaque, bonnet macaque), Mar Sanchez, Emory University (rhesus macaque), and Anne Yoder, Duke University (galago). Susan Lambeth, M.D. Anderson Cancer Center, and Katie Chace, Yerkes National Primate Center, helped provide records regarding the origins of wild born chimps at these centers. We would like to thank Dr Lisa McGraw and two anonymous reviewers for their com- ments on this manuscript. This work was supported by NSF IBN-9876754, NIH RR00165, NIMH56897 (LJY), MH64692 (LJY) and a Howard Hughes Predoctoral Fellowship (ZRD).
author:
- first_name: Zoe
full_name: Donaldson, Zoe R
last_name: Donaldson
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Andrea
full_name: Putnam, Andrea S
last_name: Putnam
- first_name: Yaohui
full_name: Bai, Yaohui
last_name: Bai
- first_name: Tara
full_name: Stoinski, Tara S
last_name: Stoinski
- first_name: Elizabeth
full_name: Hammock, Elizabeth A
last_name: Hammock
- first_name: Larry
full_name: Young, Larry
last_name: Young
citation:
ama: Donaldson Z, Kondrashov F, Putnam A, et al. Evolution of a behavior-linked
microsatellite-containing element in the 5′ flanking region of the primate AVPR1A
gene. BMC Evolutionary Biology. 2008;8(1). doi:10.1186/1471-2148-8-180
apa: Donaldson, Z., Kondrashov, F., Putnam, A., Bai, Y., Stoinski, T., Hammock,
E., & Young, L. (2008). Evolution of a behavior-linked microsatellite-containing
element in the 5′ flanking region of the primate AVPR1A gene. BMC Evolutionary
Biology. BioMed Central. https://doi.org/10.1186/1471-2148-8-180
chicago: Donaldson, Zoe, Fyodor Kondrashov, Andrea Putnam, Yaohui Bai, Tara Stoinski,
Elizabeth Hammock, and Larry Young. “Evolution of a Behavior-Linked Microsatellite-Containing
Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary
Biology. BioMed Central, 2008. https://doi.org/10.1186/1471-2148-8-180.
ieee: Z. Donaldson et al., “Evolution of a behavior-linked microsatellite-containing
element in the 5′ flanking region of the primate AVPR1A gene,” BMC Evolutionary
Biology, vol. 8, no. 1. BioMed Central, 2008.
ista: Donaldson Z, Kondrashov F, Putnam A, Bai Y, Stoinski T, Hammock E, Young L.
2008. Evolution of a behavior-linked microsatellite-containing element in the
5′ flanking region of the primate AVPR1A gene. BMC Evolutionary Biology. 8(1).
mla: Donaldson, Zoe, et al. “Evolution of a Behavior-Linked Microsatellite-Containing
Element in the 5′ Flanking Region of the Primate AVPR1A Gene.” BMC Evolutionary
Biology, vol. 8, no. 1, BioMed Central, 2008, doi:10.1186/1471-2148-8-180.
short: Z. Donaldson, F. Kondrashov, A. Putnam, Y. Bai, T. Stoinski, E. Hammock,
L. Young, BMC Evolutionary Biology 8 (2008).
date_created: 2018-12-11T11:49:04Z
date_published: 2008-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:29Z
day: '01'
doi: 10.1186/1471-2148-8-180
extern: 1
intvolume: ' 8'
issue: '1'
month: '01'
publication: BMC Evolutionary Biology
publication_status: published
publisher: BioMed Central
publist_id: '6753'
quality_controlled: 0
status: public
title: Evolution of a behavior-linked microsatellite-containing element in the 5′
flanking region of the primate AVPR1A gene
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 8
year: '2008'
...
---
_id: '907'
abstract:
- lang: eng
text: The most common form of protein-coding gene overlap in eukaryotes is a simple
nested structure, whereby one gene is embedded in an intron of another. Analysis
of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed
substantially higher rates of evolutionary gains than losses. The accumulation
of nested gene structures could not be attributed to any obvious functional relationships
between the genes involved and represents an increase of the organizational complexity
of animal genomes via a neutral process.
author:
- first_name: Raquel
full_name: Assis, Raquel
last_name: Assis
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Assis R, Kondrashov A, Koonin E, Kondrashov F. Nested genes and increasing
organizational complexity of metazoan genomes. Trends in Genetics. 2008;24(10):475-478.
doi:10.1016/j.tig.2008.08.003
apa: Assis, R., Kondrashov, A., Koonin, E., & Kondrashov, F. (2008). Nested
genes and increasing organizational complexity of metazoan genomes. Trends
in Genetics. Elsevier. https://doi.org/10.1016/j.tig.2008.08.003
chicago: Assis, Raquel, Alexey Kondrashov, Eugene Koonin, and Fyodor Kondrashov.
“Nested Genes and Increasing Organizational Complexity of Metazoan Genomes.” Trends
in Genetics. Elsevier, 2008. https://doi.org/10.1016/j.tig.2008.08.003.
ieee: R. Assis, A. Kondrashov, E. Koonin, and F. Kondrashov, “Nested genes and increasing
organizational complexity of metazoan genomes,” Trends in Genetics, vol.
24, no. 10. Elsevier, pp. 475–478, 2008.
ista: Assis R, Kondrashov A, Koonin E, Kondrashov F. 2008. Nested genes and increasing
organizational complexity of metazoan genomes. Trends in Genetics. 24(10), 475–478.
mla: Assis, Raquel, et al. “Nested Genes and Increasing Organizational Complexity
of Metazoan Genomes.” Trends in Genetics, vol. 24, no. 10, Elsevier, 2008,
pp. 475–78, doi:10.1016/j.tig.2008.08.003.
short: R. Assis, A. Kondrashov, E. Koonin, F. Kondrashov, Trends in Genetics 24
(2008) 475–478.
date_created: 2018-12-11T11:49:08Z
date_published: 2008-10-01T00:00:00Z
date_updated: 2021-01-12T08:21:49Z
day: '01'
doi: 10.1016/j.tig.2008.08.003
extern: 1
intvolume: ' 24'
issue: '10'
month: '10'
page: 475 - 478
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6743'
quality_controlled: 0
status: public
title: Nested genes and increasing organizational complexity of metazoan genomes
type: journal_article
volume: 24
year: '2008'
...
---
_id: '860'
abstract:
- lang: eng
text: We identified a mutation in the CRYGD gene (P23S) of the γ-crystallin gene
cluster that is associated with a polymorphic congenital cataract that occurs
with frequency of ∼0.3% in a human population. To gain insight into the molecular
mechanism of the pathogenesis of γ-crystallin isoforms, we undertook an evolutionary
analysis of the available mammalian and newly obtained primate sequences of the
γ-crystallin genes. The cataract-associated serine at site 23 corresponds to the
ancestral state, since it was found in CRYGD of a lower primate and all the surveyed
nonprimate mammals. Crystallin proteins include two structurally similar domains,
and substitutions in mammalian CRYGD protein at site 23 of the first domain were
always associated with substitutions in the structurally reciprocal sites 109
and 136 of the second domain. These data suggest that the cataractogenic effect
of serine at site 23 in the N-terminal domain of CRYGD may be compensated indirectly
by amino acid changes in a distal domain. We also found that gene conversion was
a factor in the evolution of the γ-crystallin gene cluster throughout different
mammalian clades. The high rate of gene conversion observed between the functional
CRYGD gene and two primate γ-crystallin pseudogenes (CRYGEP1 and CRYGFP1) coupled
with a surprising finding of apparent negative selection in primate pseudogenes
suggest a deleterious impact of recently derived pseudogenes involved in gene
conversion in the γ-crystallin gene cluster.
acknowledgement: This study was supported by the Biodiversity and Dynamics of Gene
Pools program of the Presidium of the Russian Academy of Sciences (support to E.I.R.).
E.I.R. is also supported in part by the National Institute of Diabetes and Digestive
and Kidney Diseases and National Institute of Neurological Disorders and Stroke
(National Institutes of Health), and F.A.K. is supported by a National Science Foundation
graduate research fellowship.
author:
- first_name: Olga
full_name: Plotnikova, Olga V
last_name: Plotnikova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
- first_name: Evgeny
full_name: Ginter, Evgeny K
last_name: Ginter
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
citation:
ama: Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. Conversion
and compensatory evolution of the γ-crystallin genes and identification of a cataractogenic
mutation that reverses the sequence of the human CRYGD gene to an ancestral state.
American Journal of Human Genetics. 2007;81(1):32-43. doi:10.1086/518616
apa: Plotnikova, O., Kondrashov, F., Vlasov, P., Grigorenko, A., Ginter, E., &
Rogaev, E. (2007). Conversion and compensatory evolution of the γ-crystallin genes
and identification of a cataractogenic mutation that reverses the sequence of
the human CRYGD gene to an ancestral state. American Journal of Human Genetics.
Cell Press. https://doi.org/10.1086/518616
chicago: Plotnikova, Olga, Fyodor Kondrashov, Peter Vlasov, Anastasia Grigorenko,
Evgeny Ginter, and Evgeny Rogaev. “Conversion and Compensatory Evolution of the
γ-Crystallin Genes and Identification of a Cataractogenic Mutation That Reverses
the Sequence of the Human CRYGD Gene to an Ancestral State.” American Journal
of Human Genetics. Cell Press, 2007. https://doi.org/10.1086/518616.
ieee: O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, and E.
Rogaev, “Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state,” American Journal of Human Genetics, vol. 81, no.
1. Cell Press, pp. 32–43, 2007.
ista: Plotnikova O, Kondrashov F, Vlasov P, Grigorenko A, Ginter E, Rogaev E. 2007.
Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state. American Journal of Human Genetics. 81(1), 32–43.
mla: Plotnikova, Olga, et al. “Conversion and Compensatory Evolution of the γ-Crystallin
Genes and Identification of a Cataractogenic Mutation That Reverses the Sequence
of the Human CRYGD Gene to an Ancestral State.” American Journal of Human Genetics,
vol. 81, no. 1, Cell Press, 2007, pp. 32–43, doi:10.1086/518616.
short: O. Plotnikova, F. Kondrashov, P. Vlasov, A. Grigorenko, E. Ginter, E. Rogaev,
American Journal of Human Genetics 81 (2007) 32–43.
date_created: 2018-12-11T11:48:53Z
date_published: 2007-07-01T00:00:00Z
date_updated: 2021-01-12T08:20:14Z
day: '01'
doi: 10.1086/518616
extern: 1
intvolume: ' 81'
issue: '1'
month: '07'
page: 32 - 43
publication: American Journal of Human Genetics
publication_status: published
publisher: Cell Press
publist_id: '6788'
quality_controlled: 0
status: public
title: Conversion and compensatory evolution of the γ-crystallin genes and identification
of a cataractogenic mutation that reverses the sequence of the human CRYGD gene
to an ancestral state
type: journal_article
volume: 81
year: '2007'
...
---
_id: '879'
abstract:
- lang: eng
text: Having an extra copy of a gene is thought to provide some functional redundancy,
which results in a higher rate of evolution in duplicated genes. In this article,
we estimate the impact of gene duplication on the selection of tuf paralogs, and
we find that in the absence of gene conversion, tuf paralogs have evolved significantly
slower than when gene conversion has been a factor in their evolution. Thus, tuf
gene copies evolve under a selective pressure that ensures their functional uniformity,
and gene conversion reduces selection against amino acid substitutions that affect
the function of the encoded protein, EF-Tu.
acknowledgement: We thank Peter Andolfatto, Doris Bachtrog, Robert Cutler, Hideki
Innan, Eugene Koonin, Alexey Kondrashov and Martin Lercher for comments on the manuscript
and for discussions on the interplay between gene conversion and selection. This
work was supported by a National Science Foundation Graduate Research Fellowship
(F.A.K.) and a Molecular and Cellular Biology RAS (Program No 10) grant (P.K.V.).
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Tatiana
full_name: Gurbich, Tatiana A
last_name: Gurbich
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
citation:
ama: Kondrashov F, Gurbich T, Vlasov P. Selection for functional uniformity of tuf
duplicates in γ-proteobacteria. Trends in Genetics. 2007;23(5):215-218.
doi:10.1016/j.tig.2007.03.002
apa: Kondrashov, F., Gurbich, T., & Vlasov, P. (2007). Selection for functional
uniformity of tuf duplicates in γ-proteobacteria. Trends in Genetics. Elsevier.
https://doi.org/10.1016/j.tig.2007.03.002
chicago: Kondrashov, Fyodor, Tatiana Gurbich, and Peter Vlasov. “Selection for Functional
Uniformity of Tuf Duplicates in γ-Proteobacteria.” Trends in Genetics.
Elsevier, 2007. https://doi.org/10.1016/j.tig.2007.03.002.
ieee: F. Kondrashov, T. Gurbich, and P. Vlasov, “Selection for functional uniformity
of tuf duplicates in γ-proteobacteria,” Trends in Genetics, vol. 23, no.
5. Elsevier, pp. 215–218, 2007.
ista: Kondrashov F, Gurbich T, Vlasov P. 2007. Selection for functional uniformity
of tuf duplicates in γ-proteobacteria. Trends in Genetics. 23(5), 215–218.
mla: Kondrashov, Fyodor, et al. “Selection for Functional Uniformity of Tuf Duplicates
in γ-Proteobacteria.” Trends in Genetics, vol. 23, no. 5, Elsevier, 2007,
pp. 215–18, doi:10.1016/j.tig.2007.03.002.
short: F. Kondrashov, T. Gurbich, P. Vlasov, Trends in Genetics 23 (2007) 215–218.
date_created: 2018-12-11T11:48:59Z
date_published: 2007-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:04Z
day: '01'
doi: 10.1016/j.tig.2007.03.002
extern: 1
intvolume: ' 23'
issue: '5'
month: '05'
page: 215 - 218
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6771'
quality_controlled: 0
status: public
title: Selection for functional uniformity of tuf duplicates in γ-proteobacteria
type: journal_article
volume: 23
year: '2007'
...
---
_id: '904'
abstract:
- lang: eng
text: 'Background: Independently evolving lineages mostly accumulate different changes,
which leads to their gradual divergence. However, parallel accumulation of identical
changes is also common, especially in traits with only a small number of possible
states. Results: We characterize parallelism in evolution of coding sequences
in three four-species sets of genomes of mammals, Drosophila, and yeasts. Each
such set contains two independent evolutionary paths, which we call paths I and
II. An amino acid replacement which occurred along path I also occurs along path
II with the probability 50-8211;80% of that expected under selective neutrality.
Thus, the per site rate of parallel evolution of proteins is several times higher
than their average rate of evolution, but still lower than the rate of evolution
of neutral sequences. This deficit may be caused by changes in the fitness landscape,
leading to a replacement being possible along path I but not along path II. However,
constant, weak selection assumed by the nearly neutral model of evolution appears
to be a more likely explanation. Then, the average coefficient of selection associated
with an amino acid replacement, in the units of the effective population size,
must exceed ∼0.4, and the fraction of effectively neutral replacements must be
below ∼30%. At a majority of evolvable amino acid sites, only a relatively small
number of different amino acids is permitted. Conclusion: High, but below-neutral,
rates of parallel amino acid replacements suggest that a majority of amino acid
replacements that occur in evolution are subject to weak, but non-trivial, selection,
as predicted by Ohta''s nearly-neutral theory.'
acknowledgement: G.A.B. gratefully acknowledges fellowships from the Pew Charitable
Trusts award 2000-002558 and the Burroughs Wellcome Fund award 1001782, both to
Princeton University. F.A.K. is a National Science Foundation Graduate Fellow. M.B.'s
work is partially supported by the NSERC Discovery grant. I.D. and A.P. were partially
supported by grant HL066681 (L.A.P., I.D. and S.M.), Berkeley-PGA, under the Programs
for Genomic Applications, funded by National Heart, Lung, & Blood Institute and
Department of Energy Contract DE-AC02-05CH11231, University of California. This
work was partially supported through the Molecular and Cellular Biology Program
of the Russian Academy of Sciences.
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: Michael
full_name: Brudno, Michael
last_name: Brudno
- first_name: Alexander
full_name: Poliakov, Alexander V
last_name: Poliakov
- first_name: Inna
full_name: Dubchak, Inna L
last_name: Dubchak
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. Extensive
parallelism in protein evolution. Biology Direct. 2007;2. doi:10.1186/1745-6150-2-20
apa: Bazykin, G., Kondrashov, F., Brudno, M., Poliakov, A., Dubchak, I., & Kondrashov,
A. (2007). Extensive parallelism in protein evolution. Biology Direct.
BioMed Central. https://doi.org/10.1186/1745-6150-2-20
chicago: Bazykin, Georgii, Fyodor Kondrashov, Michael Brudno, Alexander Poliakov,
Inna Dubchak, and Alexey Kondrashov. “Extensive Parallelism in Protein Evolution.”
Biology Direct. BioMed Central, 2007. https://doi.org/10.1186/1745-6150-2-20.
ieee: G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, and A. Kondrashov,
“Extensive parallelism in protein evolution,” Biology Direct, vol. 2. BioMed
Central, 2007.
ista: Bazykin G, Kondrashov F, Brudno M, Poliakov A, Dubchak I, Kondrashov A. 2007.
Extensive parallelism in protein evolution. Biology Direct. 2.
mla: Bazykin, Georgii, et al. “Extensive Parallelism in Protein Evolution.” Biology
Direct, vol. 2, BioMed Central, 2007, doi:10.1186/1745-6150-2-20.
short: G. Bazykin, F. Kondrashov, M. Brudno, A. Poliakov, I. Dubchak, A. Kondrashov,
Biology Direct 2 (2007).
date_created: 2018-12-11T11:49:07Z
date_published: 2007-08-16T00:00:00Z
date_updated: 2021-01-12T08:21:47Z
day: '16'
doi: 10.1186/1745-6150-2-20
extern: 1
intvolume: ' 2'
month: '08'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6745'
quality_controlled: 0
status: public
title: Extensive parallelism in protein evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 2
year: '2007'
...
---
_id: '861'
abstract:
- lang: eng
text: 'Background: Mitochondrial tRNAs have been the subject of study for structural
biologists interested in their secondary structure characteristics, evolutionary
biologists have researched patterns of compensatory and structural evolution and
medical studies have been directed towards understanding the basis of human disease.
However, an up to date, manually curated database of mitochondrially encoded tRNAs
from higher animals is currently not available. Description: We obtained the complete
mitochondrial sequence for 277 tetrapod species from GenBank and re-annotated
all of the tRNAs based on a multiple alignment of each tRNA gene and secondary
structure prediction made independently for each tRNA. The mitochondrial (mt)
tRNA sequences and the secondary structure based multiple alignments are freely
available as Supplemental Information online. Conclusion: We compiled a manually
curated database of mitochondrially encoded tRNAs from tetrapods with completely
sequenced genomes. In the course of our work, we reannotated more than 10% of
all tetrapod mt-tRNAs and subsequently predicted the secondary structures of 6060
mitochondrial tRNAs. This carefully constructed database can be utilized to enhance
our knowledge in several different fields including the evolution of mt-tRNA secondary
structure and prediction of pathogenic mt-tRNA mutations. In addition, researchers
reporting novel mitochondrial genome sequences should check their tRNA gene annotations
against our database to ensure a higher level of fidelity of their annotation.'
acknowledgement: KYuP and LAM were supported by the Molecular and Cellular Biology
Program of the Russian Academy of Science. KYuP was supported by the Russian Fund
of Basic Research (grant 04-04-49623). LAM was partially supported by grants from
the Howard Hughes Medical Institute (55005610), INTAS (05-1000008-8028). FAK is
a National Science Foundation Graduate Research Fellow.
author:
- first_name: Konstantin
full_name: Popadin, Konstantin Yu
last_name: Popadin
- first_name: Leila
full_name: Mamirova, Leila A
last_name: Mamirova
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Popadin K, Mamirova L, Kondrashov F. A manually curated database of tetrapod
mitochondrially encoded tRNA sequences and secondary structures. BMC Bioinformatics.
2007;8. doi:10.1186/1471-2105-8-441
apa: Popadin, K., Mamirova, L., & Kondrashov, F. (2007). A manually curated
database of tetrapod mitochondrially encoded tRNA sequences and secondary structures.
BMC Bioinformatics. BioMed Central. https://doi.org/10.1186/1471-2105-8-441
chicago: Popadin, Konstantin, Leila Mamirova, and Fyodor Kondrashov. “A Manually
Curated Database of Tetrapod Mitochondrially Encoded TRNA Sequences and Secondary
Structures.” BMC Bioinformatics. BioMed Central, 2007. https://doi.org/10.1186/1471-2105-8-441.
ieee: K. Popadin, L. Mamirova, and F. Kondrashov, “A manually curated database of
tetrapod mitochondrially encoded tRNA sequences and secondary structures,” BMC
Bioinformatics, vol. 8. BioMed Central, 2007.
ista: Popadin K, Mamirova L, Kondrashov F. 2007. A manually curated database of
tetrapod mitochondrially encoded tRNA sequences and secondary structures. BMC
Bioinformatics. 8.
mla: Popadin, Konstantin, et al. “A Manually Curated Database of Tetrapod Mitochondrially
Encoded TRNA Sequences and Secondary Structures.” BMC Bioinformatics, vol.
8, BioMed Central, 2007, doi:10.1186/1471-2105-8-441.
short: K. Popadin, L. Mamirova, F. Kondrashov, BMC Bioinformatics 8 (2007).
date_created: 2018-12-11T11:48:54Z
date_published: 2007-11-14T00:00:00Z
date_updated: 2021-01-12T08:20:18Z
day: '14'
doi: 10.1186/1471-2105-8-441
extern: 1
intvolume: ' 8'
month: '11'
publication: BMC Bioinformatics
publication_status: published
publisher: BioMed Central
publist_id: '6789'
quality_controlled: 0
status: public
title: A manually curated database of tetrapod mitochondrially encoded tRNA sequences
and secondary structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 8
year: '2007'
...
---
_id: '854'
abstract:
- lang: eng
text: Phylogenetic relationships between the extinct woolly mammoth (Mammuthus primigenius),
and the Asian (Elephas maximus) and African savanna (Loxodonta africana) elephants
remain unresolved. Here, we report the sequence of the complete mitochondrial
genome (16,842 base pairs) of a woolly mammoth extracted from permafrost-preserved
remains from the Pleistocene epoch - the oldest mitochondrial genome sequence
determined to date. We demonstrate that well-preserved mitochondrial genome fragments,
as long as ∼1,600-1700 base pairs, can be retrieved from pre-Holocene remains
of an extinct species. Phylogenetic reconstruction of the Elephantinae clade suggests
that M. primigenius and E. maximus are sister species that diverged soon after
their common ancestor split from the L. africana lineage. Low nucleotide diversity
found between independently determined mitochondrial genomic sequences of woolly
mammoths separated geographically and in time suggests that north-eastern Siberia
was occupied by a relatively homogeneous population of M. primigenius throughout
the late Pleistocene.
acknowledgement: |-
FAK is supported by the NSF Graduate Research Fellowship.
We thank the Natural History Museum, North-Eastern Research Center, Far Eastern Branch of the Russian Academy of Sciences for photographic material ofM. primigenius leg, V. A. Nikishina for artwork and technical support, Y.B. Yurov, G. Dvoryanchikov, N. Riazanskaya and T. Kolesnikova for technical support, K. Mehren and C. Gray for elephant specimens, and V. Y. Solovyev for help with artwork of animal images.
author:
- first_name: Evgeny
full_name: Rogaev, Evgeny I
last_name: Rogaev
- first_name: Yuri
full_name: Moliaka, Yuri K
last_name: Moliaka
- first_name: Boris
full_name: Malyarchuk, Boris A
last_name: Malyarchuk
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Miroslava
full_name: Derenko, Miroslava V
last_name: Derenko
- first_name: Ilya
full_name: Chumakov, Ilya M
last_name: Chumakov
- first_name: Anastasia
full_name: Grigorenko, Anastasia P
last_name: Grigorenko
citation:
ama: Rogaev E, Moliaka Y, Malyarchuk B, et al. Complete mitochondrial genome and
phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biology. 2006;4(3):0403-0410.
doi:10.1371/journal.pbio.0040073
apa: Rogaev, E., Moliaka, Y., Malyarchuk, B., Kondrashov, F., Derenko, M., Chumakov,
I., & Grigorenko, A. (2006). Complete mitochondrial genome and phylogeny of
pleistocene mammoth Mammuthus primigenius. PLoS Biology. Public Library
of Science. https://doi.org/10.1371/journal.pbio.0040073
chicago: Rogaev, Evgeny, Yuri Moliaka, Boris Malyarchuk, Fyodor Kondrashov, Miroslava
Derenko, Ilya Chumakov, and Anastasia Grigorenko. “Complete Mitochondrial Genome
and Phylogeny of Pleistocene Mammoth Mammuthus Primigenius.” PLoS Biology.
Public Library of Science, 2006. https://doi.org/10.1371/journal.pbio.0040073.
ieee: E. Rogaev et al., “Complete mitochondrial genome and phylogeny of pleistocene
mammoth Mammuthus primigenius,” PLoS Biology, vol. 4, no. 3. Public Library
of Science, pp. 0403–0410, 2006.
ista: Rogaev E, Moliaka Y, Malyarchuk B, Kondrashov F, Derenko M, Chumakov I, Grigorenko
A. 2006. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus
primigenius. PLoS Biology. 4(3), 0403–0410.
mla: Rogaev, Evgeny, et al. “Complete Mitochondrial Genome and Phylogeny of Pleistocene
Mammoth Mammuthus Primigenius.” PLoS Biology, vol. 4, no. 3, Public Library
of Science, 2006, pp. 0403–10, doi:10.1371/journal.pbio.0040073.
short: E. Rogaev, Y. Moliaka, B. Malyarchuk, F. Kondrashov, M. Derenko, I. Chumakov,
A. Grigorenko, PLoS Biology 4 (2006) 0403–0410.
date_created: 2018-12-11T11:48:51Z
date_published: 2006-03-01T00:00:00Z
date_updated: 2021-01-12T08:19:58Z
day: '01'
doi: 10.1371/journal.pbio.0040073
extern: 1
intvolume: ' 4'
issue: '3'
month: '03'
page: 0403 - 0410
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6794'
quality_controlled: 0
status: public
title: Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus
primigenius
type: journal_article
volume: 4
year: '2006'
...
---
_id: '868'
abstract:
- lang: eng
text: 'Background: The glyoxylate cycle is thought to be present in bacteria, protists,
plants, fungi, and nematodes, but not in other Metazoa. However, activity of the
glyoxylate cycle enzymes, malate synthase (MS) and isocitrate lyase (ICL), in
animal tissues has been reported. In order to clarify the status of the MS and
ICL genes in animals and get an insight into their evolution, we undertook a comparative-genomic
study. Results: Using sequence similarity searches, we identified MS genes in
arthropods, echinoderms, and vertebrates, including platypus and opossum, but
not in the numerous sequenced genomes of placental mammals. The regions of the
placental mammals'' genomes expected to code for malate synthase, as determined
by comparison of the gene orders in vertebrate genomes, show clear similarity
to the opossum MS sequence but contain stop codons, indicating that the MS gene
became a pseudogene in placental mammals. By contrast, the ICL gene is undetectable
in animals other than the nematodes that possess a bifunctional, fused ICL-MS
gene. Examination of phylogenetic trees of MS and ICL suggests multiple horizontal
gene transfer events that probably went in both directions between several bacterial
and eukaryotic lineages. The strongest evidence was obtained for the acquisition
of the bifunctional ICL-MS gene from an as yet unknown bacterial source with the
corresponding operonic organization by the common ancestor of the nematodes. Conclusion:
The distribution of the MS and ICL genes in animals suggests that either they
encode alternative enzymes of the glyoxylate cycle that are not orthologous to
the known MS and ICL or the animal MS acquired a new function that remains to
be characterized. Regardless of the ultimate solution to this conundrum, the genes
for the glyoxylate cycle enzymes present a remarkable variety of evolutionary
events including unusual horizontal gene transfer from bacteria to animals.'
acknowledgement: The authors thank Alexey Kondrashov for suggesting the possibility
of non- orthologous gene displacement in glyoxylate cycle specific enzymes and for
critical reading of this manuscript. FAK is a National Science Foundation Graduate
Fellow.
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
- first_name: Igor
full_name: Morgunov, Igor G
last_name: Morgunov
- first_name: Tatiana
full_name: Finogenova, Tatiana V
last_name: Finogenova
- first_name: Marie
full_name: Kondrashova, Marie N
last_name: Kondrashova
citation:
ama: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. Evolution
of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer
events and pseudogene formation. Biology Direct. 2006;1. doi:10.1186/1745-6150-1-31
apa: Kondrashov, F., Koonin, E., Morgunov, I., Finogenova, T., & Kondrashova,
M. (2006). Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple
horizontal transfer events and pseudogene formation. Biology Direct. BioMed
Central. https://doi.org/10.1186/1745-6150-1-31
chicago: Kondrashov, Fyodor, Eugene Koonin, Igor Morgunov, Tatiana Finogenova, and
Marie Kondrashova. “Evolution of Glyoxylate Cycle Enzymes in Metazoa Evidence
of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology Direct.
BioMed Central, 2006. https://doi.org/10.1186/1745-6150-1-31.
ieee: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, and M. Kondrashova,
“Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal
transfer events and pseudogene formation,” Biology Direct, vol. 1. BioMed
Central, 2006.
ista: Kondrashov F, Koonin E, Morgunov I, Finogenova T, Kondrashova M. 2006. Evolution
of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal transfer
events and pseudogene formation. Biology Direct. 1.
mla: Kondrashov, Fyodor, et al. “Evolution of Glyoxylate Cycle Enzymes in Metazoa
Evidence of Multiple Horizontal Transfer Events and Pseudogene Formation.” Biology
Direct, vol. 1, BioMed Central, 2006, doi:10.1186/1745-6150-1-31.
short: F. Kondrashov, E. Koonin, I. Morgunov, T. Finogenova, M. Kondrashova, Biology
Direct 1 (2006).
date_created: 2018-12-11T11:48:56Z
date_published: 2006-10-23T00:00:00Z
date_updated: 2021-01-12T08:20:31Z
day: '23'
doi: 10.1186/1745-6150-1-31
extern: 1
intvolume: ' 1'
month: '10'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6778'
quality_controlled: 0
status: public
title: Evolution of glyoxylate cycle enzymes in Metazoa Evidence of multiple horizontal
transfer events and pseudogene formation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 1
year: '2006'
...
---
_id: '873'
abstract:
- lang: eng
text: New genes commonly appear through complete or partial duplications of pre-existing
genes. Duplications of long DNA segments are constantly produced by rare mutations,
may become fixed in a population by selection or random drift, and are subject
to divergent evolution of the paralogous sequences after fixation, although gene
conversion can impede this process. New data shed some light on each of these
processes. Mutations which involve duplications can occur through at least two
different mechanisms, backward strand slippage during DNA replication and unequal
crossing-over. The background rate of duplication of a complete gene in humans
is 10-9-10-10 per generation, although many genes located within hot-spots of
large-scale mutation are duplicated much more often. Many gene duplications affect
fitness strongly, and are responsible, through gene dosage effects, for a number
of genetic diseases. However, high levels of intrapopulation polymorphism caused
by presence or absence of long, gene-containing DNA segments imply that some duplications
are not under strong selection. The polymorphism to fixation ratios appear to
be approximately the same for gene duplications and for presumably selectively
neutral nucleotide substitutions, which, according to the McDonald-Kreitman test,
is consistent with selective neutrality of duplications. However, this pattern
can also be due to negative selection against most of segregating duplications
and positive selection for at least some duplications which become fixed. Patterns
in post-fixation evolution of duplicated genes do not easily reveal the causes
of fixations. Many gene duplications which became fixed recently in a variety
of organisms were positively selected because the increased expression of the
corresponding genes was beneficial. The effects of gene dosage provide a unified
framework for studying all phases of the life history of a gene duplication. Application
of well-known methods of evolutionary genetics to accumulating data on new, polymorphic,
and fixed duplication will enhance our understanding of the role of natural selection
in the evolution by gene duplication.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Kondrashov F, Kondrashov A. Role of selection in fixation of gene duplications.
Journal of Theoretical Biology. 2006;239(2):141-151. doi:10.1016/j.jtbi.2005.08.033
apa: Kondrashov, F., & Kondrashov, A. (2006). Role of selection in fixation
of gene duplications. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.08.033
chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation
of Gene Duplications.” Journal of Theoretical Biology. Elsevier, 2006.
https://doi.org/10.1016/j.jtbi.2005.08.033.
ieee: F. Kondrashov and A. Kondrashov, “Role of selection in fixation of gene duplications,”
Journal of Theoretical Biology, vol. 239, no. 2. Elsevier, pp. 141–151,
2006.
ista: Kondrashov F, Kondrashov A. 2006. Role of selection in fixation of gene duplications.
Journal of Theoretical Biology. 239(2), 141–151.
mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Role of Selection in Fixation of
Gene Duplications.” Journal of Theoretical Biology, vol. 239, no. 2, Elsevier,
2006, pp. 141–51, doi:10.1016/j.jtbi.2005.08.033.
short: F. Kondrashov, A. Kondrashov, Journal of Theoretical Biology 239 (2006) 141–151.
date_created: 2018-12-11T11:48:57Z
date_published: 2006-03-21T00:00:00Z
date_updated: 2021-01-12T08:20:47Z
day: '21'
doi: 10.1016/j.jtbi.2005.08.033
extern: 1
intvolume: ' 239'
issue: '2'
month: '03'
page: 141 - 151
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '6773'
quality_controlled: 0
status: public
title: Role of selection in fixation of gene duplications
type: journal_article
volume: 239
year: '2006'
...
---
_id: '869'
abstract:
- lang: eng
text: The impact of synonymous nucleotide substitutions on fitness in mammals remains
controversial. Despite some indications of selective constraint, synonymous sites
are often assumed to be neutral, and the rate of their evolution is used as a
proxy for mutation rate. We subdivide all sites into four classes in terms of
the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold
synonymous sites and intron sites residing outside transposable elements. The
distribution of the rate of evolution across all synonymous sites is trimodal.
Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed
by G, is ∼10% below that at such intron sites. In contrast, rate of evolution
at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally,
synonymous and intron postC and preG sites evolve at similar rates. The relationship
between the levels of polymorphism at the corresponding synonymous and intron
sites is very similar to that between their rates of evolution. Within every class,
synonymous sites are occupied by G or C much more often than intron sites, whose
nucleotide composition is consistent with neutral mutation-drift equilibrium.
These patterns suggest that synonymous sites are under weak selection in favor
of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective
population size. Such selection decelerates evolution and reduces variability
at sites with symmetric mutation, but has the opposite effects at sites where
the favored nucleotides are more mutable. The amino-acid composition of proteins
dictates that many synonymous sites are CpGprone, which causes them, on average,
to evolve faster and to be more polymorphic than intron sites. An average genotype
carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic
epistasis in selection against them.
acknowledgement: This research was supported in part by the Intramural Research Program
of the NIH, National Library of Medicine.
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. Selection in favor of nucleotides G
and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites. Journal of Theoretical Biology. 2006;240(4):616-626. doi:10.1016/j.jtbi.2005.10.020
apa: Kondrashov, F., Ogurtsov, A., & Kondrashov, A. (2006). Selection in favor
of nucleotides G and C diversifies evolution rates and levels of polymorphism
at mammalian synonymous sites. Journal of Theoretical Biology. Elsevier.
https://doi.org/10.1016/j.jtbi.2005.10.020
chicago: Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection
in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism
at Mammalian Synonymous Sites.” Journal of Theoretical Biology. Elsevier,
2006. https://doi.org/10.1016/j.jtbi.2005.10.020.
ieee: F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides
G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites,” Journal of Theoretical Biology, vol. 240, no. 4. Elsevier, pp.
616–626, 2006.
ista: Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides
G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous
sites. Journal of Theoretical Biology. 240(4), 616–626.
mla: Kondrashov, Fyodor, et al. “Selection in Favor of Nucleotides G and C Diversifies
Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” Journal
of Theoretical Biology, vol. 240, no. 4, Elsevier, 2006, pp. 616–26, doi:10.1016/j.jtbi.2005.10.020.
short: F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology
240 (2006) 616–626.
date_created: 2018-12-11T11:48:56Z
date_published: 2006-06-21T00:00:00Z
date_updated: 2021-01-12T08:20:33Z
day: '21'
doi: 10.1016/j.jtbi.2005.10.020
extern: 1
intvolume: ' 240'
issue: '4'
month: '06'
page: 616 - 626
publication: Journal of Theoretical Biology
publication_status: published
publisher: Elsevier
publist_id: '6779'
quality_controlled: 0
status: public
title: Selection in favor of nucleotides G and C diversifies evolution rates and levels
of polymorphism at mammalian synonymous sites
type: journal_article
volume: 240
year: '2006'
...
---
_id: '903'
abstract:
- lang: eng
text: 'Background: Carcinogenesis typically involves multiple somatic mutations
in caretaker (DNA repair) and gatekeeper (tumor suppressors and oncogenes) genes.
Analysis of mutation spectra of the tumor suppressor that is most commonly mutated
in human cancers, p53, unexpectedly suggested that somatic evolution of the p53
gene during tumorigenesis is dominated by positive selection for gain of function.
This conclusion is supported by accumulating experimental evidence of evolution
of new functions of p53 in tumors. These findings prompted a genome-wide analysis
of possible positive selection during tumor evolution. Methods: A comprehensive
analysis of probable somatic mutations in the sequences of Expressed Sequence
Tags (ESTs) from malignant tumors and normal tissues was performed in order to
access the prevalence of positive selection in cancer evolution. For each EST,
the numbers of synonymous and non-synonymous substitutions were calculated. In
order to identify genes with a signature of positive selection in cancers, these
numbers were compared to: i) expected numbers and ii) the numbers for the respective
genes in the ESTs from normal tissues. Results: We identified 112 genes with a
signature of positive selection in cancers, i.e., a significantly elevated ratio
of non-synonymous to synonymous substitutions, in tumors as compared to 37 such
genes in an approximately equal-sized EST collection from normal tissues. A substantial
fraction of the tumor-specific positive-selection candidates have experimentally
demonstrated or strongly predicted links to cancer. Conclusion: The results of
EST analysis should be interpreted with extreme caution given the noise introduced
by sequencing errors and undetected polymorphisms. Furthermore, an inherent limitation
of EST analysis is that multiple mutations amenable to statistical analysis can
be detected only in relatively highly expressed genes. Nevertheless, the present
results suggest that positive selection might affect a substantial number of genes
during tumorigenic somatic evolution.'
acknowledgement: This work was supported by the Intramural Research Program of the
National Library of Medicine at the National Institutes of Health/DHHS. FAK is an
NSF Graduate Fellow. We thank Yuri Pavlov for helpful discussions.
author:
- first_name: Vladimir
full_name: Babenko, Vladimir N
last_name: Babenko
- first_name: Malay
full_name: Basu, Malay K
last_name: Basu
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Igor
full_name: Rogozin, Igor B
last_name: Rogozin
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
citation:
ama: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. Signs of positive selection
of somatic mutations in human cancers detected by EST sequence analysis. BMC
Cancer. 2006;6. doi:10.1186/1471-2407-6-36
apa: Babenko, V., Basu, M., Kondrashov, F., Rogozin, I., & Koonin, E. (2006).
Signs of positive selection of somatic mutations in human cancers detected by
EST sequence analysis. BMC Cancer. BioMed Central. https://doi.org/10.1186/1471-2407-6-36
chicago: Babenko, Vladimir, Malay Basu, Fyodor Kondrashov, Igor Rogozin, and Eugene
Koonin. “Signs of Positive Selection of Somatic Mutations in Human Cancers Detected
by EST Sequence Analysis.” BMC Cancer. BioMed Central, 2006. https://doi.org/10.1186/1471-2407-6-36.
ieee: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, and E. Koonin, “Signs of positive
selection of somatic mutations in human cancers detected by EST sequence analysis,”
BMC Cancer, vol. 6. BioMed Central, 2006.
ista: Babenko V, Basu M, Kondrashov F, Rogozin I, Koonin E. 2006. Signs of positive
selection of somatic mutations in human cancers detected by EST sequence analysis.
BMC Cancer. 6.
mla: Babenko, Vladimir, et al. “Signs of Positive Selection of Somatic Mutations
in Human Cancers Detected by EST Sequence Analysis.” BMC Cancer, vol. 6,
BioMed Central, 2006, doi:10.1186/1471-2407-6-36.
short: V. Babenko, M. Basu, F. Kondrashov, I. Rogozin, E. Koonin, BMC Cancer 6 (2006).
date_created: 2018-12-11T11:49:07Z
date_published: 2006-02-09T00:00:00Z
date_updated: 2021-01-12T08:21:47Z
day: '09'
doi: 10.1186/1471-2407-6-36
extern: 1
intvolume: ' 6'
month: '02'
publication: BMC Cancer
publication_status: published
publisher: BioMed Central
publist_id: '6744'
quality_controlled: 0
status: public
title: Signs of positive selection of somatic mutations in human cancers detected
by EST sequence analysis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 6
year: '2006'
...
---
_id: '843'
abstract:
- lang: eng
text: The impact of an amino acid replacement on the organism's fitness can vary
from lethal to selectively neutral and even, in rare cases, beneficial. Substantial
data are available on either pathogenic or acceptable replacements. However, the
whole distribution of coefficients of selection against individual replacements
is not known for any organism. To ascertain this distribution for human proteins,
we combined data on pathogenic missense mutations, on human non-synonymous SNPs
and on human-chimpanzee divergence of orthologous proteins. Fractions of amino
acid replacements which reduce fitness by >10-2, 10-2-10-4, 10-4-10-5 and <10-5
are 25, 49, 14 and 12%, respectively. On average, the strength of selection against
a replacement is substantially higher when chemically dissimilar amino acids are
involved, and the Grantham's index of a replacement explains 35% of variance in
the average logarithm of selection coefficients associated with different replacements.
Still, the impact of a replacement depends on its context within the protein more
than on its own nature. Reciprocal replacements are often associated with rather
different selection coefficients, in particular, replacements of non-polar amino
acids with polar ones are typically much more deleterious than replacements in
the opposite direction. However, differences between evolutionary fluxes of reciprocal
replacements are only weakly correlated with the differences between the corresponding
selection coefficients.
author:
- first_name: Lev
full_name: Yampolsky, Lev Y
last_name: Yampolsky
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
citation:
ama: Yampolsky L, Kondrashov F, Kondrashov A. Distribution of the strength of selection
against amino acid replacements in human proteins. Human Molecular Genetics.
2005;14(21):3191-3201. doi:10.1093/hmg/ddi350
apa: Yampolsky, L., Kondrashov, F., & Kondrashov, A. (2005). Distribution of
the strength of selection against amino acid replacements in human proteins. Human
Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddi350
chicago: Yampolsky, Lev, Fyodor Kondrashov, and Alexey Kondrashov. “Distribution
of the Strength of Selection against Amino Acid Replacements in Human Proteins.”
Human Molecular Genetics. Oxford University Press, 2005. https://doi.org/10.1093/hmg/ddi350.
ieee: L. Yampolsky, F. Kondrashov, and A. Kondrashov, “Distribution of the strength
of selection against amino acid replacements in human proteins,” Human Molecular
Genetics, vol. 14, no. 21. Oxford University Press, pp. 3191–3201, 2005.
ista: Yampolsky L, Kondrashov F, Kondrashov A. 2005. Distribution of the strength
of selection against amino acid replacements in human proteins. Human Molecular
Genetics. 14(21), 3191–3201.
mla: Yampolsky, Lev, et al. “Distribution of the Strength of Selection against Amino
Acid Replacements in Human Proteins.” Human Molecular Genetics, vol. 14,
no. 21, Oxford University Press, 2005, pp. 3191–201, doi:10.1093/hmg/ddi350.
short: L. Yampolsky, F. Kondrashov, A. Kondrashov, Human Molecular Genetics 14 (2005)
3191–3201.
date_created: 2018-12-11T11:48:48Z
date_published: 2005-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:13Z
day: '01'
doi: 10.1093/hmg/ddi350
extern: 1
intvolume: ' 14'
issue: '21'
month: '11'
page: 3191 - 3201
publication: Human Molecular Genetics
publication_status: published
publisher: Oxford University Press
publist_id: '6807'
quality_controlled: 0
status: public
title: Distribution of the strength of selection against amino acid replacements in
human proteins
type: journal_article
volume: 14
year: '2005'
...
---
_id: '877'
abstract:
- lang: eng
text: "Sequence analysis of protein and mitochondrially encoded tRNA genes shows
that substitutions\r\nproducing pathogenic effects in humans are often found in
normal, healthy individuals from other species.\r\nAnalysis of stability of protein
and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations
can be neutralized by other, compensatory substitutions that restore the structural
stability of the\r\nmolecule. Further study of such substitutions will, hopefully,
lead to new methods for curing genetic dis-\r\neases that may be based on the
correction of molecule stability as a whole instead of reversing an individual\r\npathogenic
mutation."
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
citation:
ama: Kondrashov F. The analysis of monomer sequences in protein and tRNA and the
manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. 2005;50(3):389-395.
apa: Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA
and the manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. Pleiades Publishing.
chicago: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA
and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.”
Biofizika. Pleiades Publishing, 2005.
ieee: F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and
the manifestation of the compensation of pathogenic deviations in their evolution,”
Biofizika, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005.
ista: Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA
and the manifestation of the compensation of pathogenic deviations in their evolution.
Biofizika. 50(3), 389–395.
mla: Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA
and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.”
Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95.
short: F. Kondrashov, Biofizika 50 (2005) 389–395.
date_created: 2018-12-11T11:48:58Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:01Z
day: '01'
extern: '1'
external_id:
pmid:
- '15977826'
intvolume: ' 50'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf
month: '05'
oa_version: None
page: 389 - 395
pmid: 1
publication: Biofizika
publication_status: published
publisher: Pleiades Publishing
publist_id: '6769'
quality_controlled: '1'
status: public
title: The analysis of monomer sequences in protein and tRNA and the manifestation
of the compensation of pathogenic deviations in their evolution
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2005'
...
---
_id: '878'
abstract:
- lang: eng
text: |
Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. In search of the limits of evolution. Nature Genetics.
2005;37(1):9-10. doi:10.1038/ng0105-9
apa: Kondrashov, F. (2005). In search of the limits of evolution. Nature Genetics.
Nature Publishing Group. https://doi.org/10.1038/ng0105-9
chicago: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics.
Nature Publishing Group, 2005. https://doi.org/10.1038/ng0105-9.
ieee: F. Kondrashov, “In search of the limits of evolution,” Nature Genetics,
vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005.
ista: Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics.
37(1), 9–10.
mla: Kondrashov, Fyodor. “In Search of the Limits of Evolution.” Nature Genetics,
vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:10.1038/ng0105-9.
short: F. Kondrashov, Nature Genetics 37 (2005) 9–10.
date_created: 2018-12-11T11:48:59Z
date_published: 2005-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:02Z
day: '01'
doi: 10.1038/ng0105-9
extern: 1
intvolume: ' 37'
issue: '1'
month: '01'
page: 9 - 10
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6770'
quality_controlled: 0
status: public
title: In search of the limits of evolution
type: journal_article
volume: 37
year: '2005'
...
---
_id: '882'
abstract:
- lang: eng
text: Some mutations in human mitochondrial tRNAs are severely pathogenic. The available
computational methods have a poor record of predicting the impact of a tRNA mutation
on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor
pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms
were compared. Mutations that are pathogenic to humans occupy more conservative
sites, are only rarely fixed in closely related species, and, when located in
stem structures, often disrupt Watson-Crick pairing and display signs of compensatory
evolution. These observations make it possible to classify ∼90% of all known pathogenic
mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms
segregate at frequencies that are more than two times lower than frequencies of
polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms
in mitochondrial tRNAs affect fitness negatively.
acknowledgement: |
The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded
human tRNAs. Human Molecular Genetics. 2005;14(16):2415-2419. doi:10.1093/hmg/ddi243
apa: Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially
encoded human tRNAs. Human Molecular Genetics. Oxford University Press.
https://doi.org/10.1093/hmg/ddi243
chicago: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially
Encoded Human TRNAs.” Human Molecular Genetics. Oxford University Press,
2005. https://doi.org/10.1093/hmg/ddi243.
ieee: F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded
human tRNAs,” Human Molecular Genetics, vol. 14, no. 16. Oxford University
Press, pp. 2415–2419, 2005.
ista: Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially
encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.
mla: Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially
Encoded Human TRNAs.” Human Molecular Genetics, vol. 14, no. 16, Oxford
University Press, 2005, pp. 2415–19, doi:10.1093/hmg/ddi243.
short: F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.
date_created: 2018-12-11T11:49:00Z
date_published: 2005-08-15T00:00:00Z
date_updated: 2021-01-12T08:21:10Z
day: '15'
doi: 10.1093/hmg/ddi243
extern: 1
intvolume: ' 14'
issue: '16'
month: '08'
page: 2415 - 2419
publication: Human Molecular Genetics
publication_status: published
publisher: Oxford University Press
publist_id: '6767'
quality_controlled: 0
status: public
title: Prediction of pathogenic mutations in mitochondrially encoded human tRNAs
type: journal_article
volume: 14
year: '2005'
...
---
_id: '880'
abstract:
- lang: eng
text: Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA
in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY).
Such evolution sheds light on the relationship between structure and function
of tRNA molecules and its impact on the patterns of molecular evolution.
article_processing_charge: No
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. The convergent evolution of the secondary structure of mitochondrial
cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika.
2005;50(3):396-403.
apa: Kondrashov, F. (2005). The convergent evolution of the secondary structure
of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus.
Biofizika. Pleiades Publishing.
chicago: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure
of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.”
Biofizika. Pleiades Publishing, 2005.
ieee: F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial
cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” Biofizika,
vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005.
ista: Kondrashov F. 2005. The convergent evolution of the secondary structure of
mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus.
Biofizika. 50(3), 396–403.
mla: Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of
Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.”
Biofizika, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403.
short: F. Kondrashov, Biofizika 50 (2005) 396–403.
date_created: 2018-12-11T11:48:59Z
date_published: 2005-05-01T00:00:00Z
date_updated: 2021-01-12T08:21:07Z
day: '01'
extern: '1'
external_id:
pmid:
- '15977827'
intvolume: ' 50'
issue: '3'
language:
- iso: eng
main_file_link:
- url: http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf
month: '05'
oa_version: None
page: 396 - 403
pmid: 1
publication: Biofizika
publication_status: published
publisher: Pleiades Publishing
publist_id: '6768'
quality_controlled: '1'
status: public
title: The convergent evolution of the secondary structure of mitochondrial cysteine
tRNA in the nine-banded armadillo Dasypus novemcinctus
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2005'
...
---
_id: '893'
abstract:
- lang: eng
text: Amino acid composition of proteins varies substantially between taxa and,
thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich)
genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However,
no universal trends in ongoing changes of amino acid frequencies have been reported.
We compared sets of orthologous proteins encoded by triplets of closely related
genomes from 15 taxa representing all three domains of life (Bacteria, Archaea
and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys,
Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly
are consistently lost. The same nine amino acids are currently accrued or lost
in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms.
All amino acids with declining frequencies are thought to be among the first incorporated
into the genetic code; conversely, all amino acids with increasing frequencies,
except Ser, were probably recruited late. Thus, expansion of initially under-represented
amino acids, which began over 3,400 million years ago, apparently continues to
this day.
acknowledgement: S.S. and I.A.A. were supported by the Genome Canada Foundation.
author:
- first_name: Ingo
full_name: Jordan, Ingo K
last_name: Jordan
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Ivan
full_name: Adzhubeǐ, Ivan A
last_name: Adzhubeǐ
- first_name: Yuri
full_name: Wolf, Yuri I
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene V
last_name: Koonin
- first_name: Alexey
full_name: Kondrashov, Alexey S
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
citation:
ama: Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid
gain and loss in protein evolution. Nature. 2005;433(7026):633-638. doi:10.1038/nature03306
apa: Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov,
A., & Sunyaev, S. (2005). A universal trend of amino acid gain and loss in
protein evolution. Nature. Nature Publishing Group. https://doi.org/10.1038/nature03306
chicago: Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin,
Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and
Loss in Protein Evolution.” Nature. Nature Publishing Group, 2005. https://doi.org/10.1038/nature03306.
ieee: I. Jordan et al., “A universal trend of amino acid gain and loss in
protein evolution,” Nature, vol. 433, no. 7026. Nature Publishing Group,
pp. 633–638, 2005.
ista: Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev
S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature.
433(7026), 633–638.
mla: Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein
Evolution.” Nature, vol. 433, no. 7026, Nature Publishing Group, 2005,
pp. 633–38, doi:10.1038/nature03306.
short: I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov,
S. Sunyaev, Nature 433 (2005) 633–638.
date_created: 2018-12-11T11:49:03Z
date_published: 2005-02-10T00:00:00Z
date_updated: 2021-01-12T08:21:23Z
day: '10'
doi: 10.1038/nature03306
extern: 1
intvolume: ' 433'
issue: '7026'
month: '02'
page: 633 - 638
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6757'
quality_controlled: 0
status: public
title: A universal trend of amino acid gain and loss in protein evolution
type: journal_article
volume: 433
year: '2005'
...
---
_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: '847'
abstract:
- lang: eng
text: The accumulation of genome-wide information on single nucleotide polymorphisms
in humans provides an unprecedented opportunity to detect the evolutionary forces
responsible for heterogeneity of the level of genetic variability across loci.
Previous studies have shown that history of recombination events has produced
long haplotype blocks in the human genome, which contribute to this heterogeneity.
Other factors, however, such as natural selection or the heterogeneity of mutation
rates across loci, may also lead to heterogeneity of genetic variability. We compared
synonymous and non-synonymous variability within human genes with their divergence
from murine orthologs. We separately analyzed the non-synonymous variants predicted
to damage protein structure or function and the variants predicted to be functionally
benign. The predictions were based on comparative sequence analysis and, in some
cases, on the analysis of protein structure. A strong correlation between non-synonymous,
benign variability and non-synonymous human-mouse divergence suggests that selection
played an important role in shaping the pattern of variability in coding regions
of human genes. However, the lack of correlation between deleterious variability
and evolutionary divergence shows that a substantial proportion of the observed
non-synonymous single-nucleotide polymorphisms reduces fitness and never reaches
fixation. Evolutionary and medical implications of the impact of selection on
human polymorphisms are discussed.
acknowledgement: We are grateful to Alexey Kondrashov and Alison Wellman for the careful
reading of the manuscript and providing us with their valuable comments.
author:
- first_name: Shamil
full_name: Sunyaev, Shamil R
last_name: Sunyaev
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Peer
full_name: Bork, Peer
last_name: Bork
- first_name: Vasily
full_name: Ramensky, Vasily
last_name: Ramensky
citation:
ama: Sunyaev S, Kondrashov F, Bork P, Ramensky V. Impact of selection, mutation
rate and genetic drift on human genetic variation. Human Molecular Genetics.
2003;12(24):3325-3330. doi:10.1093/hmg/ddg359
apa: Sunyaev, S., Kondrashov, F., Bork, P., & Ramensky, V. (2003). Impact of
selection, mutation rate and genetic drift on human genetic variation. Human
Molecular Genetics. Oxford University Press. https://doi.org/10.1093/hmg/ddg359
chicago: Sunyaev, Shamil, Fyodor Kondrashov, Peer Bork, and Vasily Ramensky. “Impact
of Selection, Mutation Rate and Genetic Drift on Human Genetic Variation.” Human
Molecular Genetics. Oxford University Press, 2003. https://doi.org/10.1093/hmg/ddg359.
ieee: S. Sunyaev, F. Kondrashov, P. Bork, and V. Ramensky, “Impact of selection,
mutation rate and genetic drift on human genetic variation,” Human Molecular
Genetics, vol. 12, no. 24. Oxford University Press, pp. 3325–3330, 2003.
ista: Sunyaev S, Kondrashov F, Bork P, Ramensky V. 2003. Impact of selection, mutation
rate and genetic drift on human genetic variation. Human Molecular Genetics. 12(24),
3325–3330.
mla: Sunyaev, Shamil, et al. “Impact of Selection, Mutation Rate and Genetic Drift
on Human Genetic Variation.” Human Molecular Genetics, vol. 12, no. 24,
Oxford University Press, 2003, pp. 3325–30, doi:10.1093/hmg/ddg359.
short: S. Sunyaev, F. Kondrashov, P. Bork, V. Ramensky, Human Molecular Genetics
12 (2003) 3325–3330.
date_created: 2018-12-11T11:48:49Z
date_published: 2003-12-15T00:00:00Z
date_updated: 2021-01-12T08:19:29Z
day: '15'
doi: 10.1093/hmg/ddg359
extern: 1
intvolume: ' 12'
issue: '24'
month: '12'
page: 3325 - 3330
publication: Human Molecular Genetics
publication_status: published
publisher: Oxford University Press
publist_id: '6803'
quality_controlled: 0
status: public
title: Impact of selection, mutation rate and genetic drift on human genetic variation
type: journal_article
volume: 12
year: '2003'
...
---
_id: '876'
abstract:
- lang: eng
text: Alternative splicing is thought to be a major source of functional diversity
in animal proteins. We analyzed the evolutionary conservation of proteins encoded
by alternatively spliced genes and predicted the ancestral state for 73 cases
of alternative splicing (25 insertions and 48 deletions). The amino acid sequences
of most of the inserts in proteins produced by alternative splicing are as conserved
as the surrounding sequences. Thus, alternative splicing often creates novel isoforms
by the insertion of new, functional protein sequences that probably originated
from noncoding sequences of introns.
acknowledgement: We thank Peer Bork, Mikhail Gelfand, Alexey Kondrashov, David Lipman
and Shamil Sunyaev for critical reading of the manuscript and useful suggestions
and the Koonin group members for helpful discussions.
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. Evolution of alternative splicing: Deletions, insertions
and origin of functional parts of proteins from intron sequences. Trends in
Genetics. 2003;19(3):115-119. doi:10.1016/S0168-9525(02)00029-X'
apa: 'Kondrashov, F., & Koonin, E. (2003). Evolution of alternative splicing:
Deletions, insertions and origin of functional parts of proteins from intron sequences.
Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(02)00029-X'
chicago: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing:
Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.”
Trends in Genetics. Elsevier, 2003. https://doi.org/10.1016/S0168-9525(02)00029-X.'
ieee: 'F. Kondrashov and E. Koonin, “Evolution of alternative splicing: Deletions,
insertions and origin of functional parts of proteins from intron sequences,”
Trends in Genetics, vol. 19, no. 3. Elsevier, pp. 115–119, 2003.'
ista: 'Kondrashov F, Koonin E. 2003. Evolution of alternative splicing: Deletions,
insertions and origin of functional parts of proteins from intron sequences. Trends
in Genetics. 19(3), 115–119.'
mla: 'Kondrashov, Fyodor, and Eugene Koonin. “Evolution of Alternative Splicing:
Deletions, Insertions and Origin of Functional Parts of Proteins from Intron Sequences.”
Trends in Genetics, vol. 19, no. 3, Elsevier, 2003, pp. 115–19, doi:10.1016/S0168-9525(02)00029-X.'
short: F. Kondrashov, E. Koonin, Trends in Genetics 19 (2003) 115–119.
date_created: 2018-12-11T11:48:58Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2021-01-12T08:20:58Z
day: '01'
doi: 10.1016/S0168-9525(02)00029-X
extern: 1
intvolume: ' 19'
issue: '3'
month: '01'
page: 115 - 119
publication: Trends in Genetics
publication_status: published
publisher: Elsevier
publist_id: '6776'
quality_controlled: 0
status: public
title: 'Evolution of alternative splicing: Deletions, insertions and origin of functional
parts of proteins from intron sequences'
type: journal_article
volume: 19
year: '2003'
...
---
_id: '885'
abstract:
- lang: eng
text: We study fitness landscape in the space of protein sequences by relating sets
of human pathogenic missense mutations in 32 proteins to amino acid substitutions
that occurred in the course of evolution of these proteins. On average, ≈10% of
deviations of a nonhuman protein from its human ortholog are compensated pathogenic
deviations (CPDs), i.e., are caused by an amino acid substitution that, at this
site, would be pathogenic to humans. Normal functioning of a CPD-containing protein
must be caused by other, compensatory deviations of the nonhuman species from
humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky-Muller
incompatibility that can be visualized as the corner on a fitness ridge. Thus,
proteins evolve along fitness ridges which contain only ≈10 steps between sucessive
corners. The fraction of CPDs among all deviations of a protein from its human
ortholog does not increase with the evolutionary distance between the proteins,
indicating that subtitutions that carry evolving proteins around these corners
occur in rapid succession, driven by positive selection. Data on fitness of interspecies
hybrids suggest that the compensatory change that makes a CPD fit usually occurs
within the same protein. Data on protein structures and on cooccurrence of amino
acids at different sites of multiple orthologous proteins often make it possible
to provisionally identify the substitution that compensates a partiCUlar CPD.
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
full_name: Kondrashov, Alexey
last_name: Kondrashov
- first_name: Shamil
full_name: Sunyaev, Shamil
last_name: Sunyaev
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov A, Sunyaev S, Kondrashov F. Dobzhansky-Muller incompatibilities
in protein evolution. PNAS. 2002;99(23):14878-14883. doi:10.1073/pnas.232565499
apa: Kondrashov, A., Sunyaev, S., & Kondrashov, F. (2002). Dobzhansky-Muller
incompatibilities in protein evolution. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.232565499
chicago: Kondrashov, Alexey, Shamil Sunyaev, and Fyodor Kondrashov. “Dobzhansky-Muller
Incompatibilities in Protein Evolution.” PNAS. National Academy of Sciences,
2002. https://doi.org/10.1073/pnas.232565499.
ieee: A. Kondrashov, S. Sunyaev, and F. Kondrashov, “Dobzhansky-Muller incompatibilities
in protein evolution,” PNAS, vol. 99, no. 23. National Academy of Sciences,
pp. 14878–14883, 2002.
ista: Kondrashov A, Sunyaev S, Kondrashov F. 2002. Dobzhansky-Muller incompatibilities
in protein evolution. PNAS. 99(23), 14878–14883.
mla: Kondrashov, Alexey, et al. “Dobzhansky-Muller Incompatibilities in Protein
Evolution.” PNAS, vol. 99, no. 23, National Academy of Sciences, 2002,
pp. 14878–83, doi:10.1073/pnas.232565499.
short: A. Kondrashov, S. Sunyaev, F. Kondrashov, PNAS 99 (2002) 14878–14883.
date_created: 2018-12-11T11:49:01Z
date_published: 2002-11-12T00:00:00Z
date_updated: 2023-07-26T09:48:37Z
day: '12'
doi: 10.1073/pnas.232565499
extern: '1'
external_id:
pmid:
- '12403824'
intvolume: ' 99'
issue: '23'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC137512/
month: '11'
oa: 1
oa_version: Published Version
page: 14878 - 14883
pmid: 1
publication: PNAS
publication_identifier:
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '6763'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dobzhansky-Muller incompatibilities in protein evolution
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 99
year: '2002'
...
---
_id: '897'
abstract:
- lang: eng
text: "Transcription is a slow and expensive process: in eukaryotes, approximately
20 nucleotides can be transcribed per second at the expense of at least two ATP
molecules per nucleotide. Thus, at least for highly expressed genes, transcription
of long introns, which are particularly common in mammals, is costly. Using data
on the expression of genes that encode proteins in Caenorhabditis elegans and
Homo sapiens, we show that introns in highly expressed genes are substantially
shorter than those in genes that are expressed at low levels. This difference
is greater in humans, such that introns are, on average, 14 times shorter in highly
expressed genes than in genes with low expression, whereas in C. Elegans the difference
in intron length is only twofold. In contrast, the density of introns in a gene
does not strongly depend on the level of gene expression. Thus, natural selection
appears to favor short introns in highly expressed genes to minimize the cost
of transcription and other molecular processes, such as splicing.\r\n"
acknowledgement: We are grateful to A. Kondrashov, I. Rogozin and A. Feldman for reading
the manuscript and P. Bouman, J. Cherry, J. Blumensteil and T. Kim for discussion.
article_processing_charge: No
article_type: original
author:
- first_name: Cristian
full_name: Castillo Davis, Cristian
last_name: Castillo Davis
- first_name: Sergei
full_name: Mekhedov, Sergei
last_name: Mekhedov
- first_name: Daniel
full_name: Hartl, Daniel
last_name: Hartl
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Castillo Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F. Selection for
short introns in highly expressed genes. Nature Genetics. 2002;31(4):415-418.
doi:10.1038/ng940
apa: Castillo Davis, C., Mekhedov, S., Hartl, D., Koonin, E., & Kondrashov,
F. (2002). Selection for short introns in highly expressed genes. Nature Genetics.
Nature Publishing Group. https://doi.org/10.1038/ng940
chicago: Castillo Davis, Cristian, Sergei Mekhedov, Daniel Hartl, Eugene Koonin,
and Fyodor Kondrashov. “Selection for Short Introns in Highly Expressed Genes.”
Nature Genetics. Nature Publishing Group, 2002. https://doi.org/10.1038/ng940.
ieee: C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, and F. Kondrashov, “Selection
for short introns in highly expressed genes,” Nature Genetics, vol. 31,
no. 4. Nature Publishing Group, pp. 415–418, 2002.
ista: Castillo Davis C, Mekhedov S, Hartl D, Koonin E, Kondrashov F. 2002. Selection
for short introns in highly expressed genes. Nature Genetics. 31(4), 415–418.
mla: Castillo Davis, Cristian, et al. “Selection for Short Introns in Highly Expressed
Genes.” Nature Genetics, vol. 31, no. 4, Nature Publishing Group, 2002,
pp. 415–18, doi:10.1038/ng940.
short: C. Castillo Davis, S. Mekhedov, D. Hartl, E. Koonin, F. Kondrashov, Nature
Genetics 31 (2002) 415–418.
date_created: 2018-12-11T11:49:05Z
date_published: 2002-08-01T00:00:00Z
date_updated: 2023-07-26T09:45:30Z
day: '01'
doi: 10.1038/ng940
extern: '1'
external_id:
pmid:
- '12134150'
intvolume: ' 31'
issue: '4'
language:
- iso: eng
month: '08'
oa_version: None
page: 415 - 418
pmid: 1
publication: Nature Genetics
publication_status: published
publisher: Nature Publishing Group
publist_id: '6751'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection for short introns in highly expressed genes
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 31
year: '2002'
...
---
_id: '871'
abstract:
- lang: eng
text: 'BACKGROUND: Gene duplications have a major role in the evolution of new biological
functions. Theoretical studies often assume that a duplication per se is selectively
neutral and that, following a duplication, one of the gene copies is freed from
purifying (stabilizing) selection, which creates the potential for evolution of
a new function. RESULTS: In search of systematic evidence of accelerated evolution
after duplication, we used data from 26 bacterial, six archaeal, and seven eukaryotic
genomes to compare the mode and strength of selection acting on recently duplicated
genes (paralogs) and on similarly diverged, unduplicated orthologous genes in
different species. We find that the ratio of nonsynonymous to synonymous substitutions
(Kn/Ks) in most paralogous pairs is <<1 and that paralogs typically evolve
at similar rates, without significant asymmetry, indicating that both paralogs
produced by a duplication are subject to purifying selection. This selection is,
however, substantially weaker than the purifying selection affecting unduplicated
orthologs that have diverged to the same extent as the analyzed paralogs. Most
of the recently duplicated genes appear to be involved in various forms of environmental
response; in particular, many of them encode membrane and secreted proteins. CONCLUSIONS:
The results of this analysis indicate that recently duplicated paralogs evolve
faster than orthologs with the same level of divergence and similar functions,
but apparently do not experience a phase of neutral evolution. We hypothesize
that gene duplications that persist in an evolving lineage are beneficial from
the time of their origin, due primarily to a protein dosage effect in response
to variable environmental conditions; duplications are likely to give rise to
new functions at a later phase of their evolution once a higher level of divergence
is reached.'
acknowledgement: We are grateful to A.S. Kondrashov for numerous helpful suggestions,
to I. King Jordan, M.A. Roytberg, J.L. Spouge and D.A. Kondrashov for useful discussions
and to A.S. Kondrashov, I. King Jordan and D.J. Lipman for critical reading of the
manuscript.
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: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: Kondrashov F, Rogozin I, Wolf Y, Koonin E. Selection in the evolution of gene
duplications . Genome Biology. 2002;3(2). doi:10.1186/gb-2002-3-2-research0008
apa: Kondrashov, F., Rogozin, I., Wolf, Y., & Koonin, E. (2002). Selection in
the evolution of gene duplications . Genome Biology. BioMed Central. https://doi.org/10.1186/gb-2002-3-2-research0008
chicago: Kondrashov, Fyodor, Igor Rogozin, Yuri Wolf, and Eugene Koonin. “Selection
in the Evolution of Gene Duplications .” Genome Biology. BioMed Central,
2002. https://doi.org/10.1186/gb-2002-3-2-research0008.
ieee: F. Kondrashov, I. Rogozin, Y. Wolf, and E. Koonin, “Selection in the evolution
of gene duplications ,” Genome Biology, vol. 3, no. 2. BioMed Central,
2002.
ista: Kondrashov F, Rogozin I, Wolf Y, Koonin E. 2002. Selection in the evolution
of gene duplications . Genome Biology. 3(2).
mla: Kondrashov, Fyodor, et al. “Selection in the Evolution of Gene Duplications
.” Genome Biology, vol. 3, no. 2, BioMed Central, 2002, doi:10.1186/gb-2002-3-2-research0008.
short: F. Kondrashov, I. Rogozin, Y. Wolf, E. Koonin, Genome Biology 3 (2002).
date_created: 2018-12-11T11:48:57Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-07-26T11:48:27Z
day: '01'
doi: 10.1186/gb-2002-3-2-research0008
extern: '1'
external_id:
pmid:
- '11864370'
intvolume: ' 3'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC65685/
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: '6781'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Selection in the evolution of gene duplications '
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 3
year: '2002'
...
---
_id: '859'
abstract:
- lang: eng
text: The polymeric ubiquitin (poly-u) genes are composed of tandem 228-bp repeats
with no spacer sequences between individual monomer units. Ubiquitin is one of
the most conserved proteins known to date, and the individual units within a number
of poly-u genes are significantly more similar to each other than would be expected
if each unit evolved independently. It has been proposed that the rather striking
similarity among poly-u monomers in some lineages is caused by a series of homogenization
events. Here we report the sequences of the polyubiquitin-C (Ubc) genes in two
mouse strains. Analysis of these sequences, as well as those of the previously
reported Chinese hamster and rat poly-u genes, supports the assertion that the
homogenization of the ubiquitin-C gene in rodents is due to unequal crossing-over
events. The sequence divergence of noncoding DNA was used to estimate the frequency
of unequal crossing-over events (6.3 x 10-5 events per generation) in the Ubc
gene, as well as to provide evidence of apparent selection in the poly-u gene.
acknowledgement: We are thankful to J.A. Southerland and P.L. Jiang for technical
assistance in DNA sequencing, as well as to Y.I. Pavlov for helpful discussions.
This work was supported by public Health Service Research Grant AI45135 from the
Institute of Allergy and Infectious Diseases, National Institutes of Health.
article_processing_charge: No
article_type: original
author:
- first_name: Andrey
full_name: Perelygin, Andrey
last_name: Perelygin
- 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: Margo
full_name: Brinton, Margo
last_name: Brinton
citation:
ama: Perelygin A, Kondrashov F, Rogozin I, Brinton M. Evolution of the mouse polyubiquitin
C gene. Journal of Molecular Evolution. 2002;55(2):202-210. doi:10.1007/s00239-002-2318-0
apa: Perelygin, A., Kondrashov, F., Rogozin, I., & Brinton, M. (2002). Evolution
of the mouse polyubiquitin C gene. Journal of Molecular Evolution. Springer.
https://doi.org/10.1007/s00239-002-2318-0
chicago: Perelygin, Andrey, Fyodor Kondrashov, Igor Rogozin, and Margo Brinton.
“Evolution of the Mouse Polyubiquitin C Gene.” Journal of Molecular Evolution.
Springer, 2002. https://doi.org/10.1007/s00239-002-2318-0.
ieee: A. Perelygin, F. Kondrashov, I. Rogozin, and M. Brinton, “Evolution of the
mouse polyubiquitin C gene,” Journal of Molecular Evolution, vol. 55, no.
2. Springer, pp. 202–210, 2002.
ista: Perelygin A, Kondrashov F, Rogozin I, Brinton M. 2002. Evolution of the mouse
polyubiquitin C gene. Journal of Molecular Evolution. 55(2), 202–210.
mla: Perelygin, Andrey, et al. “Evolution of the Mouse Polyubiquitin C Gene.” Journal
of Molecular Evolution, vol. 55, no. 2, Springer, 2002, pp. 202–10, doi:10.1007/s00239-002-2318-0.
short: A. Perelygin, F. Kondrashov, I. Rogozin, M. Brinton, Journal of Molecular
Evolution 55 (2002) 202–210.
date_created: 2018-12-11T11:48:53Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-07-26T12:01:34Z
day: '01'
doi: 10.1007/s00239-002-2318-0
extern: '1'
external_id:
pmid:
- '12107596'
intvolume: ' 55'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 202 - 210
pmid: 1
publication: Journal of Molecular Evolution
publication_identifier:
issn:
- 0022-2844
publication_status: published
publisher: Springer
publist_id: '6787'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of the mouse polyubiquitin C gene
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 55
year: '2002'
...
---
_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: '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'
...
---
_id: '867'
abstract:
- lang: eng
text: Genes with new functions often evolve by gene duplication. Alternative splicing
is another means of evolutionary innovation in eukaryotes, which allows a single
gene to encode functionally diverse proteins. We investigate a connection between
these two evolutionary phenomena. For ∼10% of the described cases of substitution
alternative splicing, such that either one or another amino acid sequence is included
into the protein, evidence of origin by tandem exon duplication was found. This
is a conservative estimate because alternative exons are typically short and,
on many occasions, duplicates may have diverged beyond recognition. Dating exon
duplications through a combination of the available experimental data on alternative
splicing in orthologous genes from different species and computational analysis
indicates that most of the duplications antedate at least the radiation of mammalian
orders or even the radiation of vertebrate classes. At present, tandem exon duplication
is the only mechanism of evolution of substitution alternative splicing that can
be specifically demonstrated. Along with gene duplication, this could be a major
route for generating functional diversity during evolution of multicellular eukaryotes.
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: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: Kondrashov F, Koonin E. Origin of alternative splicing by tandem exon duplication.
Human Molecular Genetics. 2001;10(23):2661-2669. doi:10.1093/hmg/10.23.2661
apa: Kondrashov, F., & Koonin, E. (2001). Origin of alternative splicing by
tandem exon duplication. Human Molecular Genetics. Oxford University Press.
https://doi.org/10.1093/hmg/10.23.2661
chicago: Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing
by Tandem Exon Duplication.” Human Molecular Genetics. Oxford University
Press, 2001. https://doi.org/10.1093/hmg/10.23.2661.
ieee: F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon
duplication,” Human Molecular Genetics, vol. 10, no. 23. Oxford University
Press, pp. 2661–2669, 2001.
ista: Kondrashov F, Koonin E. 2001. Origin of alternative splicing by tandem exon
duplication. Human Molecular Genetics. 10(23), 2661–2669.
mla: Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem
Exon Duplication.” Human Molecular Genetics, vol. 10, no. 23, Oxford University
Press, 2001, pp. 2661–69, doi:10.1093/hmg/10.23.2661.
short: F. Kondrashov, E. Koonin, Human Molecular Genetics 10 (2001) 2661–2669.
date_created: 2018-12-11T11:48:55Z
date_published: 2001-11-01T00:00:00Z
date_updated: 2023-06-02T08:39:47Z
day: '01'
doi: 10.1093/hmg/10.23.2661
extern: '1'
external_id:
pmid:
- '11726553'
intvolume: ' 10'
issue: '23'
language:
- iso: eng
month: '11'
oa_version: Published Version
page: 2661 - 2669
pmid: 1
publication: Human Molecular Genetics
publication_identifier:
issn:
- 0964-6906
publication_status: published
publisher: Oxford University Press
publist_id: '6777'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Origin of alternative splicing by tandem exon duplication
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 10
year: '2001'
...
---
_id: '851'
abstract:
- lang: eng
text: 'The study and comparison of mutation(al) spectra is an important problem
in molecular biology, because these spectra often reflect on important features
of mutations and their fixation. Such features include the interaction of DNA
with various mutagens, the function of repair/replication enzymes, and properties
of target proteins. It is known that mutability varies significantly along nucleotide
sequences, such that mutations often concentrate at certain positions, called
"hotspots," in a sequence. In this paper, we discuss in detail two approaches
for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL
program, (FTP: sunsite.unc.edu/pub/academic/ biology/dna-mutations/hyperg) and
hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation;
ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for
mutational spectra analysis, such as the analysis of a target protein structure,
hotspot context revealing, multiple spectra comparisons, as well as a number of
mutation databases are briefly described. Mutation spectra in the lacI gene of
E. coli and the human p53 gene are used for illustration of various difficulties
of such analysis.'
acknowledgement: 'Russian Fund of Fundamental Research. Grant Number: 99-04-49535.
NIH. Grant Number: GM 20293. NASA. Grant Number: NCC2-1057'
article_processing_charge: No
article_type: original
author:
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Galina
full_name: Glazko, Galina
last_name: Glazko
citation:
ama: Rogozin I, Kondrashov F, Glazko G. Use of mutation spectra analysis software.
Human Mutation. 2001;17(2):83-102. doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E
apa: Rogozin, I., Kondrashov, F., & Glazko, G. (2001). Use of mutation spectra
analysis software. Human Mutation. Wiley-Blackwell. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E
chicago: Rogozin, Igor, Fyodor Kondrashov, and Galina Glazko. “Use of Mutation Spectra
Analysis Software.” Human Mutation. Wiley-Blackwell, 2001. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.
ieee: I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis
software,” Human Mutation, vol. 17, no. 2. Wiley-Blackwell, pp. 83–102,
2001.
ista: Rogozin I, Kondrashov F, Glazko G. 2001. Use of mutation spectra analysis
software. Human Mutation. 17(2), 83–102.
mla: Rogozin, Igor, et al. “Use of Mutation Spectra Analysis Software.” Human
Mutation, vol. 17, no. 2, Wiley-Blackwell, 2001, pp. 83–102, doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.
short: I. Rogozin, F. Kondrashov, G. Glazko, Human Mutation 17 (2001) 83–102.
date_created: 2018-12-11T11:48:50Z
date_published: 2001-01-01T00:00:00Z
date_updated: 2023-06-02T09:22:17Z
day: '01'
doi: 10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E
extern: '1'
external_id:
pmid:
- '11180592'
intvolume: ' 17'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 83 - 102
pmid: 1
publication: Human Mutation
publication_identifier:
issn:
- 1059-7794
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6796'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Use of mutation spectra analysis software
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 17
year: '2001'
...
---
_id: '841'
article_processing_charge: No
article_type: original
author:
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- 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
citation:
ama: 'Wolf Y, Kondrashov F, Koonin E. Footprints of primordial introns on the eukaryotic
genome: still no clear traces . Trends in Genetics. 2001;17(9):499-501.
doi:10.1016/S0168-9525(01)02376-9'
apa: 'Wolf, Y., Kondrashov, F., & Koonin, E. (2001). Footprints of primordial
introns on the eukaryotic genome: still no clear traces . Trends in Genetics.
Elsevier. https://doi.org/10.1016/S0168-9525(01)02376-9'
chicago: 'Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “Footprints of Primordial
Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics.
Elsevier, 2001. https://doi.org/10.1016/S0168-9525(01)02376-9.'
ieee: 'Y. Wolf, F. Kondrashov, and E. Koonin, “Footprints of primordial introns
on the eukaryotic genome: still no clear traces ,” Trends in Genetics,
vol. 17, no. 9. Elsevier, pp. 499–501, 2001.'
ista: 'Wolf Y, Kondrashov F, Koonin E. 2001. Footprints of primordial introns on
the eukaryotic genome: still no clear traces . Trends in Genetics. 17(9), 499–501.'
mla: 'Wolf, Yuri, et al. “Footprints of Primordial Introns on the Eukaryotic Genome:
Still No Clear Traces .” Trends in Genetics, vol. 17, no. 9, Elsevier,
2001, pp. 499–501, doi:10.1016/S0168-9525(01)02376-9.'
short: Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 17 (2001) 499–501.
date_created: 2018-12-11T11:48:47Z
date_published: 2001-09-01T00:00:00Z
date_updated: 2023-06-02T09:38:37Z
day: '01'
doi: 10.1016/S0168-9525(01)02376-9
extern: '1'
external_id:
pmid:
- '11721681'
intvolume: ' 17'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 499 - 501
pmid: 1
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9479
publication_status: published
publisher: Elsevier
publist_id: '6805'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Footprints of primordial introns on the eukaryotic genome: still no clear
traces '
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 17
year: '2001'
...
---
_id: '842'
article_processing_charge: No
article_type: original
author:
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- 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
citation:
ama: Wolf Y, Kondrashov F, Koonin E. No footprints of primordial introns in a eukaryotic
genome. Trends in Genetics. 2000;16(8):333-334. doi:10.1016/S0168-9525(00)02059-X
apa: Wolf, Y., Kondrashov, F., & Koonin, E. (2000). No footprints of primordial
introns in a eukaryotic genome. Trends in Genetics. Elsevier. https://doi.org/10.1016/S0168-9525(00)02059-X
chicago: Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “No Footprints of Primordial
Introns in a Eukaryotic Genome.” Trends in Genetics. Elsevier, 2000. https://doi.org/10.1016/S0168-9525(00)02059-X.
ieee: Y. Wolf, F. Kondrashov, and E. Koonin, “No footprints of primordial introns
in a eukaryotic genome,” Trends in Genetics, vol. 16, no. 8. Elsevier,
pp. 333–334, 2000.
ista: Wolf Y, Kondrashov F, Koonin E. 2000. No footprints of primordial introns
in a eukaryotic genome. Trends in Genetics. 16(8), 333–334.
mla: Wolf, Yuri, et al. “No Footprints of Primordial Introns in a Eukaryotic Genome.”
Trends in Genetics, vol. 16, no. 8, Elsevier, 2000, pp. 333–34, doi:10.1016/S0168-9525(00)02059-X.
short: Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 16 (2000) 333–334.
date_created: 2018-12-11T11:48:48Z
date_published: 2000-08-01T00:00:00Z
date_updated: 2023-05-08T09:22:03Z
day: '01'
doi: 10.1016/S0168-9525(00)02059-X
extern: '1'
external_id:
pmid:
- '10904260 '
intvolume: ' 16'
issue: '8'
language:
- iso: eng
month: '08'
oa_version: None
page: 333 - 334
pmid: 1
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9479
publication_status: published
publisher: Elsevier
publist_id: '6806'
quality_controlled: '1'
scopus_import: '1'
status: public
title: No footprints of primordial introns in a eukaryotic genome
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 16
year: '2000'
...
---
_id: '883'
abstract:
- lang: eng
text: Sympatric speciation, the origin of two or more species from a single local
population, has almost certainly been involved in formation of several species
flocks, and may be fairly common in nature. The most straightforward scenario
for sympatric speciation requires disruptive selection favouring two substantially
different phenotypes, and consists of the evolution of reproductive isolation
between them followed by the elimination of all intermediate phenotypes. Here
we use the hypergeometric phenotypic model to show that sympatric speciation is
possible even when fitness and mate choice depend on different quantitative traits,
so that speciation must involve formation of covariance between these traits.
The increase in the number of variable loci affecting fitness facilitates sympatric
speciation, whereas the increase in the number of variable loci affecting mate
choice has the opposite effect. These predictions may enable more cases of sympatric
speciation to be identified.
acknowledgement: This study was supported by a grant from the NSF.
article_processing_charge: No
article_type: original
author:
- first_name: Alexey
full_name: Kondrashov, Alexey
last_name: Kondrashov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov A, Kondrashov F. Interactions among quantitative traits in the course
of sympatric speciation. Nature. 1999;400(6742):351-354. doi:10.1038/22514
apa: Kondrashov, A., & Kondrashov, F. (1999). Interactions among quantitative
traits in the course of sympatric speciation. Nature. Nature Publishing
Group. https://doi.org/10.1038/22514
chicago: Kondrashov, Alexey, and Fyodor Kondrashov. “Interactions among Quantitative
Traits in the Course of Sympatric Speciation.” Nature. Nature Publishing
Group, 1999. https://doi.org/10.1038/22514.
ieee: A. Kondrashov and F. Kondrashov, “Interactions among quantitative traits in
the course of sympatric speciation,” Nature, vol. 400, no. 6742. Nature
Publishing Group, pp. 351–354, 1999.
ista: Kondrashov A, Kondrashov F. 1999. Interactions among quantitative traits in
the course of sympatric speciation. Nature. 400(6742), 351–354.
mla: Kondrashov, Alexey, and Fyodor Kondrashov. “Interactions among Quantitative
Traits in the Course of Sympatric Speciation.” Nature, vol. 400, no. 6742,
Nature Publishing Group, 1999, pp. 351–54, doi:10.1038/22514.
short: A. Kondrashov, F. Kondrashov, Nature 400 (1999) 351–354.
date_created: 2018-12-11T11:49:00Z
date_published: 1999-07-01T00:00:00Z
date_updated: 2023-04-13T10:33:44Z
day: '01'
doi: 10.1038/22514
extern: '1'
external_id:
pmid:
- '10432111'
intvolume: ' 400'
issue: '6742'
language:
- iso: eng
month: '07'
oa_version: None
page: 351 - 354
pmid: 1
publication: Nature
publication_identifier:
issn:
- 0028-0836
publication_status: published
publisher: Nature Publishing Group
publist_id: '6761'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interactions among quantitative traits in the course of sympatric speciation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 400
year: '1999'
...