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Polarization of microbial communities between competitive and cooperative metabolism [article]

Daniel Machado, Oleksandr M Maistrenko, Sergej Andrejev, Yongkyu Kim, Peer Bork, Kaustubh R Patil, Kiran R Patil
2020 bioRxiv   pre-print
The latter are most frequent for proline (G. haemolysans, L. hominis, L. inners) and methionine (A. tetradius, M. luteus, R. dentocariosa).  ...  defined as: 1,3 = 1,3 ⋅ @ -1,C ⋅ 3,C C∈E F where SCS (species coupling score), MPS (metabolite production score) and MUS (metabolite uptake score) are calculated as defined in Zelezniak et al 23 , and M  ... 
doi:10.1101/2020.01.28.922583 fatcat:dttqqe7b3zgkpmug736nfet7v4

Effect of Wolbachia Infection on Aging and Longevity-Associated Genes in Drosophila [chapter]

Oleksandr M. Maistrenko, Svitlana V. Serga, Alexander M. Vaiserman, Iryna A. Kozeretska
2015 Life Extension  
Microbiota is known to interact with metabolic and regulatory networks of the host affecting its fitness. The composition of microbiota was shown to change throughout the host aging. Such changes can be likely caused by aging process or, vice versa, changes in microbiota composition can impact the aging process. It is suggested that microbiota plays an important role in life span determination. Several species from the genus Drosophila, especially D. melanogaster, are powerful models to study
more » ... ny biological processes including microbiota functioning and its effects on the host aging. The host fitness can be substantially affected by endosymbiotic bacteria such as Wolbachia that infects up to two-thirds of insects taxa, including Drosophila. Wolbachia was shown to significantly affect Drosophila aging and life span. However, the molecular mechanisms underlying interactions between Wolbachia and Drosophila remain mostly unknown. In this chapter, we summarize data suggesting that Wolbachia-Drosophila molecular cross-talk associated with life span determination and aging can occur through the immune deficiency pathway, stress-induced JNK pathway, insulin/IGF signaling pathway, ecdysteroid biosynthesis and signaling pathway, as well as through the heat shock and autophagy-specific genes/proteins.
doi:10.1007/978-3-319-18326-8_4 fatcat:btbj7co5grfbta6aiapsrf3wvy

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity [article]

Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas SB Schmidt, Simone S. Li, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
2019 bioRxiv   pre-print
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31: 3691-3693. 31. Seemann T.  ... 
doi:10.1101/735696 fatcat:454jtye3nneojd65wccn7dk6fq

Colonization of a temperate-zone region by the fruit fly Drosophila simulans (Diptera: Drosophilidae)

Svitlana V. Serga, Oleksandr M. Maistrenko, Andrii I. Rozhok, Timothy A. Mousseau, Iryna A. Kozeretska
2015 Canadian Journal of Zoology  
Drosophila simulans Sturtevant, 1919 and Drosophila melanogaster Meigen, 1830 are sibling species that occupy similar niches. However, unlike D. simulans, D. melanogaster has spread far beyond tropical and subtropical regions deep into temperate climate zones. A number of invasion events by D. simulans into temperate climate zones have been reported, however its ability to overwinter and establish local populations in these areas is disputed. Here we report the wide dispersal of D. simulans in
more » ... ixed populations with D. melanogaster in Ukraine. D. simulans flies found in Ukraine belong to the siII mtDNA haplogroup and are infected with maternally inherited intracellular symbiotic bacteria of the genus Wolbachia sp. of the strain wRi. These genetic markers indicate a common origin of the Ukrainian D. simulans flies from a subgroup of the species found to invade other temperate climate areas worldwide. Here, we report for the first time detection of D. simulans flies early in the breeding season in a temperate climate area with severe winter conditions. We also report a moderate negative relationship between D. simulans relative abundance and average temperature in the month of sampling reflecting this species' known lower tolerance of high temperatures.
doi:10.1139/cjz-2015-0018 fatcat:qjayknkkgfd5tcmghuxczh74bu

C. difficile is overdiagnosed in adults and a commensal in infants [article]

Pamela Ferretti, Jakob Wirbel, Oleksandr M Maistrenko, Thea Van Rossum, Renato Alves, Anthony Fullam, Wasiu Akanni, Christian Schudoma, Anna Schwarz, Roman Thielemann, Leonie Thomas, Michael Kuhn (+3 others)
2022 bioRxiv   pre-print
Following command was used to build phylogenetic tree: iqtree -s <input snp file> -m GTR+ASC -B 1000.  ... 
doi:10.1101/2022.02.16.480740 fatcat:7sjzyz2dfrhsdj73lifdbkbuqu

Extensive Transmission of Microbes along the Gastrointestinal Tract [article]

Thomas SB Schmidt, Matthew R Hayward, Luis P Coelho, Simone S Li, Paul I Costea, Anita Y Voigt, Jakob Wirbel, Oleksandr M Maistrenko, Renato J Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani (+5 others)
2018 biorxiv/medrxiv   pre-print
(M = 21.52, s.d. = 1.81). Participants had normal or corrected to normal vision and gave their written consent to participate.  ...  (M = 23.15, s.d. = 2.52). Participants had normal or corrected to normal vision and gave their written consent to participate. Participants received 30 euros for their participation.  ... 
doi:10.1101/507194 fatcat:oupqksmwobdcdapyeaxeqdazta

Extensive transmission of microbes along the gastrointestinal tract

Thomas Sebastian Benedikt Schmidt, Matthew Robert Hayward, Luis Pedro Coelho, Simone S Li, Paul Igor Costea, Anita Yvonne Voigt, Jakob Wirbel, Oleksandr M Maistrenko, Renato JC Alves, Emma Bergsten, Carine de Beaufort, Iradj Sobhani (+5 others)
2019 eLife  
Acknowledgements The authors would like to thank Sina Klai of the University of Zü rich, Switzerland, Johanna M Schmidt and Gereon Rieke of the University of Bonn, Germany, for helpful comments and discussions  ...  We thank Anna M Glazek and Yan Ping Yuan for bioinformatics support, Stefanie Kandels-Lewis of the EMBL for support on sample logistics and administration, Rajna Hercog, Jan Provaznik and Vladimir Benes  ...  M Maistrenko, Resources, Investigation, Writing-review and editing; Renato JC Alves, Data curation, Investigation; Emma Bergsten, Investigation, Writing-review and editing; Carine de Beaufort, Iradj Sobhani  ... 
doi:10.7554/elife.42693 pmid:30747106 pmcid:PMC6424576 fatcat:tfl3gmfjizhdhlhvvylf7pkqfm

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

Oleksandr M. Maistrenko, Daniel R. Mende, Mechthild Luetge, Falk Hildebrand, Thomas S. B. Schmidt, Simone S. Li, João F. Matias Rodrigues, Christian von Mering, Luis Pedro Coelho, Jaime Huerta-Cepas, Shinichi Sunagawa, Peer Bork
2020 The ISME Journal  
Affiliations Oleksandr M. Maistrenko 1 • Daniel R. Mende  ... 
doi:10.1038/s41396-020-0600-z pmid:32047279 pmcid:PMC7174425 fatcat:vkxd73n52jdnzkq3fdve6mntay

Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

Martin Kapun, Joaquin C B Nunez, María Bogaerts-Márquez, Jesús Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P García Guerreiro, Sònia Casillas, Dorcas J Orengo (+59 others)
2021 Molecular biology and evolution  
The MPILEUP files were processed using npstat v.1 (Ferretti et al. 2013) with 323 parameters -maxcov 10000 and -nolowfreq m=0 in order to include all filtered positions for 324 analysis.  ...  Here, the two populations were sampled for n/2 individuals and 361 genotyped at m=33,000 markers. Furthermore, we included SNPs as a function of the percent 362 variance explained by each PC.  ... 
doi:10.1093/molbev/msab259 pmid:34469576 pmcid:PMC8662648 fatcat:c76teiscf5hrdozrqaaia6inj4


Oleksandr V. Majstrenko, Roman V. Bubenshсhykov, Ruslan V. Bondar, Oleksandr V. Poplinskyi
2018 Sučasnì Informacìjnì Tehnologìï u Sferì Bezpeki ta Oboroni  
Maistrenko O.V.  ...  Mauder J. (1981) Investigation of Operations: monograph. [ Yssledovanye operacyj], M, Mir, 678 p. 16.  ... 
doaj:4a803ed71c1a49f8a0fbe965512e0ff8 fatcat:z3dtce627bdhtmozix3xl3p6dm

A faecal microbiota signature with high specificity for pancreatic cancer

Ece Kartal, Thomas S B Schmidt, Esther Molina-Montes, Sandra Rodríguez-Perales, Jakob Wirbel, Oleksandr M Maistrenko, Wasiu A Akanni, Bilal Alashkar Alhamwe, Renato J Alves, Alfredo Carrato, Hans-Peter Erasmus, Lidia Estudillo (+24 others)
M Maistrenko Wasiu A Akanni Bilal Alashkar Alhamwe Renato J Alves  ... Esther Molina-Montes Sandra Rodríguez-Perales Jakob Wirbel Oleksandr  ...  Hybridisation was done in 20 µL of hybridisation buffer (20 nM Tris, pH 8.0. 0.9 M NaCl, 0.02% sodium dodecyl sulfate, 30% formamide) added to 100 ng of the probe.  ... 
doi:10.1136/gutjnl-2021-324755 pmid:35260444 fatcat:egidus6rfvfavayug47nrffq2e


2005 International Journal of Bifurcation and Chaos in Applied Sciences and Engineering  
For more details on Eq. (14) and the threedimensional Kuramoto model (13) see [Maistrenko et al., 2004; Maistrenko et al., 2005] .  ...  With the transformation ψ i → ψ i + C, the dynamics is reduced from M C to M = M 0 of the form (6).  ... 
doi:10.1142/s0218127405014155 fatcat:lqrfp7qc7vcsvdek3tuuviqmxe

Digitization of natural collections – the way to immortality

Novikov Andriy
2019 Zenodo  
Biodiversity Data Journal 4: e10293. Shiyan, Natalia M. 2011. Herbaria of Ukraine. Index Herbariorum Ucrainicum. Kyiv: Altpress.  ...  ZooKeys 618: 145-158. Thiers, Barbara M. 2019. "The World's Herbaria 2018: A Summary Report Based on Data from Index Herbariorum."  ... 
doi:10.5281/zenodo.3594473 fatcat:zwwltjpzlfbnddziscofrjq4aq

Weak chimeras in minimal networks of coupled phase oscillators

Peter Ashwin, Oleksandr Burylko
2015 Chaos  
Acknowledgments We thank the following for stimulating discussions in relation to this work: Danny Abrams, Ana Dias, Christian Kuehn, Carlo Laing, Yuri Maistrenko, Erik Martens, Mark Panaggio and Jan Sieber  ...  We particularly thank the reviewers for making a number of comments that allowed us to improve the exposition in the paper, and we thank Yuri Maistrenko for suggesting the phrase "weak chimera".  ...  The network decouples in the case ǫ = 0 into m uncoupled but identical modules (networks) of k phase oscillators.  ... 
doi:10.1063/1.4905197 pmid:25637917 fatcat:uvb7q7yftrgudcjzg23gjze46u

STDP in oscillatory recurrent networks: theoretical conditions for desynchronization and applications to deep brain stimulation

2010 Frontiers in Computational Neuroscience  
First, Eq. 20 assumes the limit of large networks, i.e., N, M whereas in the numerical simulations, we used N = M = 100.  ...  Maistrenko et al. (2007) describe as well neurons as phase oscillators, but they allow potentiation and depression time constants to be different.  ...  If we insert this expression back into Eq. 36, we get: ACKNOWLEDGMENTS We thank Oleksandr Popovych for fruitful discussions. Jean-Pascal Pfister has been supported by the Wellcome Trust.  ... 
doi:10.3389/fncom.2010.00022 pmid:20802859 pmcid:PMC2928668 fatcat:7jxu5gzaj5grhlaf7v4zknykgm
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