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Viral AlkB proteins repair RNA damage by oxidative demethylation

Erwin van den Born, Marina V. Omelchenko, Anders Bekkelund, Vibeke Leihne, Eugene V. Koonin, Valerian V. Dolja, Pål Ø. Falnes
2008 Nucleic Acids Research  
K I GF H A DN E E I FM R G A-P V HT V S MD G N AD F G L Ch V 2 : SY V V L PW A K EL D K LV D C FG ------DF N T AL V Q RY T L GG Y V SW H A DD E P C YS H D D-S I VT I N FN G P AV F S C LB V : VY P H N  ...  RT H C V VE K M RS M T AP Q C I ED I V GV R L HG R T A WF F S KD P T LQ -Y GH H P I B lS c V : P CD A P GA T C L RG -A QA V V CA C G LS M A V SA V P YA E L K----MD F Y PD A L KG R D A AW Y S KE D R E--  ... 
doi:10.1093/nar/gkn519 pmid:18718927 pmcid:PMC2553587 fatcat:6tlfidkdt5ey7f53qd52zdzzgy

Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution

Marina V Omelchenko, Michael Y Galperin, Yuri I Wolf, Eugene V Koonin
2010 Biology Direct  
List Omelchenko et al.  ...  By applying stringent criteria (distinct folds) Omelchenko et al. concluded that at least 1/10 of all enzymes with presently assigned complete EC numbers could have emerged in evolution more than once.  ... 
doi:10.1186/1745-6150-5-31 pmid:20433725 pmcid:PMC2876114 fatcat:v3ru2tm2ubazznvqnfqdc5mine

Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain

Marina V. Omelchenko, Kira S. Makarova, Eugene V. Koonin
2002 FEMS Microbiology Letters  
The lipoyl-binding domain is often present, in one or several copies, in the E2 subunit and, less often, in the E1 and E3 subunits of 2-oxo acid dehydrogenase complexes. Phylogenetic analysis shows evidence of multiple, independent intragenomic recombination events between different versions of the lipoyl-binding domain in various bacteria and eukaryotic mitochondria, leading to homogenization of the sequences of the lipoyl-binding domain within the same enzymatic complex in several bacterial
more » ... neages. This appears to be the first case of sequence homogenization at the level of an individual domain in prokaryotes. ß 2002 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies. : S 0 3 7 8 -1 0 9 7 ( 0 2 ) 0 0 5 1 7 -7
doi:10.1111/j.1574-6968.2002.tb11140.x pmid:12007814 fatcat:ngj4quzphnfilec4tbug5spwoe

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ

Marina V Omelchenko, Kira S Makarova, Yuri I Wolf, Igor B Rogozin, Eugene V Koonin
2003 Genome Biology  
COG0838 COG0649 COG1009 COG1008 COG1007 COG1905 COG1894 COG1034 (a) (b) (c) (d) VNG0648G http://genomebiology.com/2003/4/9/R55 Genome Biology 2003, Volume 4, Issue 9, Article R55 Omelchenko  ... 
doi:10.1186/gb-2003-4-9-r55 pmid:12952534 pmcid:PMC193655 fatcat:f2om3j5ozbfx5flcfmhec3d47e

Evolution of AANAT: expansion of the gene family in the cephalochordate amphioxus

Jiri Pavlicek, Sandrine Sauzet, Laurence Besseau, Steven L Coon, Joan L Weller, Gilles Boeuf, Pascaline Gaildrat, Marina V Omelchenko, Eugene V Koonin, Jack Falcon, David C Klein
2010 BMC Evolutionary Biology  
The 7 genes comprise 4 groups based on sequence simi- V V S K S max m = + ( ) / , larity -group 1: αη group 2: β group 3: γε group 4: δζ.  ...  Calculated values of V max and K m are given in Table 1 .  ... 
doi:10.1186/1471-2148-10-154 pmid:20500864 pmcid:PMC2897805 fatcat:mahmmcm2gbgmndvwcljhvowvfa

Environmental management and the poverty monitoring in the subjects of the Russian Federation

Irina Omelchenko, Oleg Dozortzev, Marina Danilina, Alexander Vas'kov, Olga Selivanova, Tatiana Vartanyanz, V. Breskich
2020 E3S Web of Conferences  
The degradation of the natural world undermines efforts to eradicate poverty, scientists warn and note that the only chance for global prosperity for all countries is to recognize the fight against poverty as an environmental challenge. The most important driver for achieving environmental sustainability is the fight against poverty. It is generally accepted that poverty is a consequence of environmental degradation. On the basis of the materials from 77 constituent entities of the Russian
more » ... ation the authors determined that the provided regional action plans to achieve the national goal of halving the poverty level is not sufficient and propose the additional list of measures to achieve this goal. The authors propose the methods for calculating the target value of the poverty level indicator (the level of the population with incomes below the subsistence level and the distribution of target persons across the constituent entity of the Russian Federation.
doi:10.1051/e3sconf/202021707011 fatcat:5iwhj7zm3bb35aerbjo7lodwam

Environmental management and the organization of labor rationing in industrialized countries at the corporate level

Irina Omelchenko, Oleg Dozortzev, Marina Danilina, Alexander Vas'kov, Ekaterina Safonova, Alexander Safonov, V. Breskich
2020 E3S Web of Conferences  
Approaches to solving environmental problems should be developed taking into account the concept of the "triangle of sustainable development". The sides of this triangle are not only "ecology" and "economics" and their interactions, but also "social factors", taking into account direct and reverse relationships. The implementation of active environmental management by companies and an integrated approach to environmental protection require the involvement of personnel at all levels of work to
more » ... dress these issues, motivation of personnel, and the creation of conditions for advanced training in a new area. Under these conditions, the issue of labor rationing is also of particular relevance. Based on content analysis, the authors investigate various systems of developed countries.
doi:10.1051/e3sconf/202021711016 fatcat:m4iwai4vdrdg3brtm2wqchqicy

Bioinformatics and functional analysis define four distinct groups of AlkB DNA-dioxygenases in bacteria

Erwin van den Born, Anders Bekkelund, Marivi N. Moen, Marina V. Omelchenko, Arne Klungland, Pål Ø. Falnes
2009 Nucleic Acids Research  
Tønjum and V. Gonza´lez for providing bacterial genomic DNA. We are grateful to Torbjørn Rognes and Ophe´lie Aussedat for assistance with bioinformatics analysis.  ...  The desired appearance of the tree was obtained in FigTree v. 1.1.2 (http://tree. bio.ed.ac.uk).  ...  Tønjum (Oslo University Hospital, Norway) and Dr V. Gonza´lez (Universidad Nacional Auto´noma de Me´xico, Cuernavaca, Mexico), respectively.  ... 
doi:10.1093/nar/gkp774 pmid:19786499 pmcid:PMC2790896 fatcat:w73a7zqtlfc6xeclewb2lhkkjm

Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance

Marina V Omelchenko, Yuri I Wolf, Elena K Gaidamakova, Vera Y Matrosova, Alexander Vasilenko, Min Zhai, Michael J Daly, Eugene V Koonin, Kira S Makarova
2005 BMC Evolutionary Biology  
Thermus thermophilus and Deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. T. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas D. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. Here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria. By reconstructing the evolution of Thermus and Deinococcus after
more » ... e divergence from their common ancestor, we demonstrate a high level of post-divergence gene flux in both lineages. Various aspects of the adaptation to high temperature in Thermus can be attributed to horizontal gene transfer from archaea and thermophilic bacteria; many of the horizontally transferred genes are located on the single megaplasmid of Thermus. In addition, the Thermus lineage has lost a set of genes that are still present in Deinococcus and many other mesophilic bacteria but are not common among thermophiles. By contrast, Deinococcus seems to have acquired numerous genes related to stress response systems from various bacteria. A comparison of the distribution of orthologous genes among the four partitions of the Deinococcus genome and the two partitions of the Thermus genome reveals homology between the Thermus megaplasmid (pTT27) and Deinococcus megaplasmid (DR177). After the radiation from their common ancestor, the Thermus and Deinococcus lineages have taken divergent paths toward their distinct lifestyles. In addition to extensive gene loss, Thermus seems to have acquired numerous genes from thermophiles, which likely was the decisive contribution to its thermophilic adaptation. By contrast, Deinococcus lost few genes but seems to have acquired many bacterial genes that apparently enhanced its ability to survive different kinds of environmental stresses. Notwithstanding the accumulation of horizontally transferred genes, we also show that the single megaplasmid of Thermus and the DR177 megaplasmid of Deinococcus are homologous and probably were inherited from the common ancestor of these bacteria.
doi:10.1186/1471-2148-5-57 pmid:16242020 pmcid:PMC1274311 fatcat:w4esdeogzfe25b3jvzgddiqnjm

Genome-wide Analysis of Substrate Specificities of theEscherichia coliHaloacid Dehalogenase-like Phosphatase Family

Ekaterina Kuznetsova, Michael Proudfoot, Claudio F. Gonzalez, Greg Brown, Marina V. Omelchenko, Ivan Borozan, Liran Carmel, Yuri I. Wolf, Hirotada Mori, Alexei V. Savchenko, Cheryl H. Arrowsmith, Eugene V. Koonin (+2 others)
2006 Journal of Biological Chemistry  
For K m and V max determination, the phosphatase assays contained substrates at concentrations 0.005-2.0 mM.  ...  (iii) local maximum likelihood optimization of the least squares tree using the ProtML program of the MOLPHY package (30), (iv) quartet puzzling as implemented in the TREE-PUZZLE program (31) , and (v)  ... 
doi:10.1074/jbc.m605449200 pmid:16990279 fatcat:vnudlgaizrh7zjh6unzju7ikpm

Encapsulated in silica: genome, proteome and physiology of the thermophilic bacterium Anoxybacillus flavithermus WK1

Jimmy H Saw, Bruce W Mountain, Lu Feng, Marina V Omelchenko, Shaobin Hou, Jennifer A Saito, Matthew B Stott, Dan Li, Guang Zhao, Junli Wu, Michael Y Galperin, Eugene V Koonin (+6 others)
2008 Genome Biology  
For SDS-PAGE, proteins were denatured at 100°C for 5 minutes in the presence of 0.1% SDS and 1% 2-mercaptoethanol, loaded in a 5% (w/v) stacking gel and separated in a 10% (w/v) separation gel.  ...  For protein identification, spots were excised from the gels, washed with 25 mM NH 4 HCO 3 in 50% (v/v) acetonitrile for 3 × 15 minutes at room temperature, dried in a vacuum centrifuge, and incubated  ... 
doi:10.1186/gb-2008-9-11-r161 pmid:19014707 pmcid:PMC2614493 fatcat:qagbn45hqvf6hci5dcadptk7bq

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Kira S. Makarova, Marina V. Omelchenko, Elena K. Gaidamakova, Vera Y. Matrosova, Alexander Vasilenko, Min Zhai, Alla Lapidus, Alex Copeland, Edwin Kim, Miriam Land, Konstantinos Mavromatis, Samuel Pitluck (+15 others)
2007 PLoS ONE  
Citation: Makarova KS, Omelchenko MV, Gaidamakova EK, Matrosova VY, Vasilenko A, et al (2007) Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks. PLoS ONE 2(9): e955.  ...  Individual white recombinant colonies were selected and picked into 384-well microtiter plates containing LB/glycerol (7.5% v/v) media containing 50 mg/mL of ampicillin or 20 mg/ mL of chloramphenicol  ...  The end-repaired DNA was run on a 1% TBE low melting point agarose gel for 13 hours using the following conditions (Temperature: 14uC, Voltage: 4.5 V/cm, Pulse initial: 1.0-final: 7.0 sec, Angle: 120u)  ... 
doi:10.1371/journal.pone.0000955 pmid:17895995 pmcid:PMC1978522 fatcat:gm7m7raozvfwjadece52cdbcnm

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

Shaobin Hou, Kira S Makarova, Jimmy HW Saw, Pavel Senin, Benjamin V Ly, Zhemin Zhou, Yan Ren, Jianmei Wang, Michael Y Galperin, Marina V Omelchenko, Yuri I Wolf, Natalya Yutin (+9 others)
2008 Biology Direct  
v) methane as sole source of energy.  ...  The organism grows optimally at pH between 2.0 to 2.5 and temperature of 60°C when supplemented with 25% (v/v) methane as the sole source of energy.  ...  My updating of the RpoB sequences indicates that the 3 aa insert in this protein is uniquely found in all of the Chlamydiae, Verrucomicrobia (V. spinosum DSM 4136, Opitutus terrae PB90-1, Opitutaceae bacterium  ... 
doi:10.1186/1745-6150-3-26 pmid:18593465 pmcid:PMC2474590 fatcat:64ouz7eahnajfb56ee5kvyjizi

Table of Contents

2020 2020 Cognitive Sciences, Genomics and Bioinformatics (CSGB)  
Dubrovina, Marina V. Ovsyukova, Natalya P. Bgatova, Chih-Li Lin, Alexander B. Pupyshev, Evgeniy L. Zavjalov, Elena V.  ...  Fazullina, Maksim V.  ... 
doi:10.1109/csgb51356.2020.9214704 fatcat:6h5ku653bbelhoqvnajj7qfucq

Membedah Keterlibatan Negara dan Masyarakat Rusia dalam Persoalan Gender, Seks, dan Famili pada Masa dan Pasca Uni Soviet

Mina Elfira
2007 Wacana: Journal of the Humanities of Indonesia  
Meshcherkina, Elena Omelchenko, dan Irina Tartakovskaya.  ...  Ungkapan di atas diutarakan oleh V. I. Lenin dalam bukunya On the Emancipation of Women (1977) , pemimpin partai Bolshevik dan pendiri Negara Uni Soviet.  ... 
doi:10.17510/wjhi.v9i1.228 fatcat:enqdwtzz35eijnmdoyw3rjhrwy
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