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The evolution of proline synthesis transcriptional regulation in gammaproteobacteria

K. V. Lopatovskaya, K. Yu. Gorbunov, L. Yu. Rusin, A. V. Seliverstov, V. A. Lyubetsky
2010 Moscow University Biological Sciences Bulletin  
We report a conserved motif in the upstream region of the proA and proB genes, which are widely found among γ proteobacteria, particularly in the genera Pseudomonas, Marinobacter, and Shewanella. The conserved protein-DNA binding sites are 8 bp long. Some genes have double sites for cooperative factor binding. The phylogenetic profiles of binding sites and all protein factors were compared. We identify the tetR family protein, an ortholog of the NP_249058 protein from P. aeruginosa PAO1, as a
more » ... anscription factor. Our algorithm was applied to construct the species tree with predicted regulation of the pro genes. The phylogeny of pro genes, transcription factor phylogeny, and a phylogeny of their binding sites were mapped onto the spe cies tree with our algorithm. The obtained scenario displays important HGT and related events.
doi:10.3103/s0096392510040255 fatcat:4tcr4zecg5hmflihrwwnv7qmju

Lichen planus follicularis tumidus

K. O. Chepushtanova, Yu. G. Gorbunov, I. E. Belousova, A. V. Samtsov
2019 Vestnik Dermatologii i Venerologii  
Fig. 1 . 1 Patient K. 65 y.o., brown-purple plaques with multiple cysts on the surface Рис. 2.  ...  Patient K. 65 y.o., scar alopecia focus in the scalp with dimension of 3.0 × 5.0 cm in diameter Fig. 3 . 3 Multiple partially fused infundibular cysts filled with horn masses and surrounded by dense  ... 
doi:10.25208/0042-4609-2019-95-1-46-51 fatcat:7hqlqcyqsfbjhhihhpya6bzbmq

An Almost Exact Linear Complexity Algorithm of the Shortest Transformation of Chain-Cycle Graphs [article]

K. Yu. Gorbunov, V. A. Lyubetsky
2020 arXiv   pre-print
Let us denote the beginning of a gene with name k by k1, and its end, by k2.  ...  [8] and Gorbunov and Lyubetsky [21] . We define five operations over a+b. These are as follows.  ... 
arXiv:2004.14351v1 fatcat:fscogpzas5gsnovovk4yrp3y4m

Reconstructing the evolution of genes along the species tree

K. Yu. Gorbunov, V. A. Lyubetsky
2009 Molecular Biology (Moscow)  
Then two approximate estimates of x are k 1 l 1 and k 2 l 2 , where k 1 = f 11 /f 1 , k 2 = f 12 /f 1 , l 1 = a 1r(v 11 ), l 2 = a 1r(v 12 ).  ...  Designate k = f 2 /f 1 .  ... 
doi:10.1134/s0026893309050197 fatcat:7hyzfzpfp5apravhb2obfssx6q

Reconstruction of ancestral regulatory signals along a transcription factor tree

K. Yu. Gorbunov, V. A. Lyubetsky
2007 Molecular Biology (Moscow)  
A model and an algorithm were developed to reconstruct the ancestral regulatory signals, first and foremost, for DNA-protein interactions, at inner nodes of a transcription factor phylogenetic tree on the basis of the modern signal distribution. The algorithm simultaneously infers the evolutionary scenario as a set of tree edges along which the signal diverged to the greatest extent. The model and algorithm were tested with simulation data and biological findings on the NrdR, MntR, and LacI signals.
doi:10.1134/s0026893307050172 fatcat:ajaibny6t5albe2l7eeue2dq6m


K. Gorbunov, Yu. Selikhov, V. Kotsarenko, H. Ponomarenko, O. Gorbunova
2020 Integrated Technologies and Energy Saving  
Gorbunov K., Selikhov Yu., Kotsarenko V., Ponomarenko H., Gorbunova O. THERMAL ACID INTEGRATION OF SULFURIC ACID VAPORIZATION Currently, Ukraine is an issue of energy conservation.  ... 
doi:10.20998/2078-5364.2020.1.03 fatcat:tskpjud7dnb3pmkmw32ui3idbi

Identification of Ancestral Genes That Introduce Incongruence between Protein- and Species Trees

K. Yu. Gorbunov, V. A. Lyubetsky
2005 Molecular Biology (Moscow)  
In the case of small K'\K, the genes from K' \K = K' \(KK') did not descend from the common ancestral gene K but were transferred to K' or emerged in K' later.  ...  These two sets M = K \K' and M' = K' \K will be referred to as components of clades K and K', respectively.  ... 
doi:10.1007/s11008-005-0089-6 fatcat:axvwdm4kz5dhvgjbaeg3a6637e

The tree nearest on average to a given set of trees

K. Yu. Gorbunov, V. A. Lyubetsky
2011 Problems of Information Transmission  
Hence, in this path there are neighboring vertices k + and k − for which f (k + ) < s < f(k − ), i.e., the edge k + , k − and the vertex s form a loss for f .  ...  By (7) and by the assumption, we have {k | h(k) is a tube} = {k | f (k) is a tube}; ( 8 ) then h(g) is a tube. Consider a vertex s for which h(g) < s < f(g).  ... 
doi:10.1134/s0032946011030069 fatcat:spukmaoisrfcta6geqwtwufwbe


Yu. Selikhov, V. Kotsarenko, K. Gorbunov, V. Rossikhin
2020 Integrated Technologies and Energy Saving  
., Gorbunov K.A., Rossikhin V.V.  ... 
doi:10.20998/2078-5364.2020.1.07 fatcat:oprlvdl5cbg77a7z44y7b6ohfu

Modeling evolution of the bacterial regulatory signals involving secondary structure

K. Yu. Gorbunov, E. V. Lyubetskaya, E. A. Asarin, V. A. Lyubetsky
2009 Molecular Biology (Moscow)  
This functional H ( σ ) = H 1 ( σ ) + H 2 ( σ ) comprises two conditions (constraints) for the desired configuration σ : (1) for each sequence σ ( k ) (i.e., for the value of σ in the k th tree node) and  ...  GORBUNOV et al. serv.html, where the available software for constructing phylogenetic trees and the reconstruction of ancestral sequences are listed).  ... 
doi:10.1134/s0026893309030170 fatcat:kmijzw3ytjbjfazl6isce2yyuy

The method of normal splines for linear DAEs on the number semi-axis

Vladimir K. Gorbunov, Vyacheslav Yu. Sviridov
2009 Applied Numerical Mathematics  
The method of normal spline-collocation for ordinary linear integral, differential and integro-differential equations, including implicit equations, has been created by Gorbunov in the eighties.  ...  functional (LCF) l ik (x) = n j =1 a ij (t k )ẍ j (t k ) + b ij (t k )ẋ j (t k ) + c ij (t k )x j (t k ) . (13) The boundary/initial conditions also define composite functionals.  ...  t k ) + C(t k )x(t k ) = f (t k ), k = 1, . . . , m. (12) The required z-normal solution x z satisfies this finite system, consisting of the n * m scalar equations, and the corresponding 2n conditions  ... 
doi:10.1016/j.apnum.2008.03.009 fatcat:fq5dfq4wkvhppaikckduxamihu

An Estimate of the Tree-Width of a Planar Graph Which Has Not a Given Planar Grid as a Minor [chapter]

K. Yu. Gorbunov
1998 Lecture Notes in Computer Science  
Then we suppose that K can be partitioned into two (unknown) parts K 1 and K 2 being n-divisible by ≤ m dividing.  ...  Let K = K \(O 1 O 2 ). We call a path clear if all its vertices except, maybe, ends lie in K \ (P 1 P 2 ). For each vertex a in K consider two the following conditions. 1.  ... 
doi:10.1007/10692760_30 fatcat:2qcisq7r45dthlps4hxaicgiv4

Cardiac tumors: analysis of surgical treatment

V. A. Sakovich, D. B. Drobot, A. A. Chernova, D. N. Gorbunov, D. I. Buyankov, Yu. V. Gross, M. K. Verkhoturov, M. A. Stavtseva
2021 Russian Journal of Cardiology  
ORCID: 0000-0003-2977-1792, Gorbunov D. N. ORCID: 0000-0003-1424-683Х, Buyankov D. I. ORCID: 0000-0001-9774-7888, Gross Yu. V. ORCID: 0000-0003-2657-8049, Verkhoturov M. K.  ...  A., Gorbunov D. N., Buya nkov D. I., Gross Yu. V., Verkhoturov M. K., Stavtseva M. A. Cardiac tumors: analysis of surgical treatment. Russian Journal of Cardiology. 2021;26(8):4598. (In Russ.)  ... 
doi:10.15829/1560-4071-2021-4598 fatcat:bkiaexaxgvhxlewalehqtccp2a

An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers [chapter]

Jean-Philippe Doyon, Celine Scornavacca, K. Yu. Gorbunov, Gergely J. Szöllősi, Vincent Ranwez, Vincent Berry
2010 Lecture Notes in Computer Science  
Given a subset of leaves K ⊆ L(T ), the homeomorphic tree of T connecting K, denoted T K , is the smallest binary tree induced from T such that L( T K )=K.  ...  G is the homeomorphic tree G o K , where K = L C (G o ). from one of its descendant leaves (which leaf does not matter as they are all at the same distance from x).  ... 
doi:10.1007/978-3-642-16181-0_9 fatcat:uy2tgtu5xbhjfmrmr4u5copjlq

Transverse muon polarization in $K^+\to\mu^+\nu_\mu\gamma$ : scanning over the Dalitz plot

F. L. Bezrukov, D. S. Gorbunov, Yu G. Kudenko
2003 European Physical Journal C: Particles and Fields  
We study the potential of the measurement of the transverse muon polarization P_T in the K->mu nu gamma decay with the sensitivity of δ P_T 10^-4.  ...  (R) , (5) where N Kµ2γ (R) is the number of K µ2γ events in the region R.  ...  In this paper, we study the T -odd muon polarization in the decay K + → µ + ν µ γ (K µ2γ ).  ... 
doi:10.1140/epjc/s2003-01297-x fatcat:bvg5hgv5prbozcd6jqt4hobrwy
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