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V A Ratner

Publications and source records attributed to V A Ratner.

At least 55 records · Page 3Linked to original sources
PubMed1993

[Comparative hierarchic structure of the genetic language].

The genetical texts and genetic language are built according to hierarchic principle and contain no less than 6 levels of coding sequences, separated by marks of punctuation, separation and indication: codons, cistrons, scriptons, replicons, linkage groups, genomes. Each level has all the attributes of the language. This hierarchic system expresses some general properties and regularities. The rules of genetic language being determined, the variability of genetical texts is generated by block-modular combinatorics on each level. Between levels there are some intermediate sublevels and module types capable of being combined. The genetic language is compared with two different independent linguistic systems: human natural languages and artificial programming languages. Genetic language is a natural one by its origin, but it is a typical technical language of the functioning genetic regulatory system--by its predestination. All three linguistic systems under comparison have evident similarity of the organization principles and hierarchical structures. This argues for similarity of their principles of appearance and evolution.

Genetic Code↗
PubMed1992

Induction of the mobile genetic element Dm-412 transpositions in the Drosophila genome by heat shock treatment.

Males of a Drosophila melanogaster isogenic line with a mutation of the major gene for radius incompletus (ri) were treated by standard light heat shock (37 degrees C for 90 min) and by heavy heat shock (transfer of males from 37 degrees C for 2 hr to 4 degrees C for 1 hr and back; this procedure was repeated three times). In the F1 generation of treated males mated with nontreated females of the same isogenic line, mass transpositions of copia-like mobile genetic element Dm-412 were found. The altered positions of the element seem nonrandom; five "hot spots" of transposition were found. Probabilities of transpositions were estimated after light heat shock and heavy heat shock and in the control sample. These probabilities were, respectively, 3.4 x 10(-2), 8.7 x 10(-2), and less than 4.1 x 10(-4) transpositions per genome per occupied position per generation. Therefore, as a result of heat shock treatment, the probabilities of transpositions were two orders of magnitude greater than those of the control sample in the next generation after induction. Comparison of the results with those after stepwise temperature treatment shows that the induction depends on the intensity of the stress action (temperature treatment) rather than on the type of the stress action.

Animals↗
PubMed1992

[Mobile genetic elements and quantitative characters in Drosophila: facts and hypotheses].

This review is dedicated to the comparison of the facts obtained and the proposed hypotheses, to the critical analysis of the situation arisen, and to the estimation of key propositions of the concept developed. The main point is that mobile genetic elements (MGEs) participate directly in expression, variability, selection and evolution of different quantitative characters. Genetic and selection data are considered, and hypotheses of random fixation, marker effect and direct participation of MGE patterns in expression and selection of quantitative characters are discussed. The consequences of temperature treatment are considered and hypotheses of masked selection and temperature induction of transpositions are discussed. The marker effects are shown to be non-sufficient to explain the properties of quantitative character radius incompletus system. The MGE patterns are important components of genetical system of determination of a quantitative character. MGEs modify, enhance the expression of neighbouring polygenes. Temperature effects could be explained by the influence of stress temperature treatment through the system of heat shock response on the capacity of MGEs to transcribe and transpose. The system of diversed MGE patterns in drosophila chromosomes could be believed to be universal genomic system of "soft" modification of the polygenic control of any limiting quantitative characters.

Animals↗
PubMed1992

[The role of mobile genetic elements (MGE) in microevolution].

The MGEs of Drosophila and other objects contain open reading frames (ORFs) encoding transposition enzymes, and "motifs" similar to functional sites: promoters, enhancers, heat shock regulatory sites, those of reception of different stress external signals and hormones, recombination sites, etc. In other words, MGE play a role of "movable cassettes of regulatory elements" in the genomes. The patterns of genome MGE localization are the important components of polygenic systems of character expression, the subjects of variation and evolution. The summed up density of MGE localization along the genome has probably the upper value corresponding to approx. 1 MGE copy per gene. The transpositional variability of MGE patterns could be random, non-random, self-related and inducible. The MGE patterns are important subjects of microevolution and reconstruction of trees of the pattern similarity is an effective method for its description. The patterns could be changed by selection of limited quantitative characters. The stress induction (temperature, treatment, dysgenic cross, etc.) stimulated the MGE transpositions and excisions, mass in population and multiple in individuals. The temperature induction acts probably through the system of response to heat shock treatment. The totality of MGE patterns make up the genomic system capable of quick reorganizations after stress external and genomic influences. The stress external influences are often correlated with passing of the population through the "bottle-neck" stage. The rate of transpositions has an upper limiting border, so named "boundary of regulation error catastrophe", that corresponds to approx. 1 transposition per genome, per generation. After the stress induction of transpositions this boundary could be exceeded, the state of the population norm becoming disrupted. The changes in MGE patterns are also supposed to accompany the changes of characters of isolation, i.e. to accompany the speciation.

Animals↗
PubMed1991

[Transposition induction of the mobile genetic element Dm412 in the Drosophila genome using heat shock].

Males of Drosophila melanogaster isogenic line with oligogene mutation radius incompletus (ri) were exposed to standard heat-shock (SHS: t = 37 degrees C, 90 min) and heavy heat-shock (SHS: three-fold transfer of males from t = 37 degrees C, 2h, t0t = 4 degrees C 1 h, and back). At F1 of the treated males with untreated females of the same isogenic line mass transpositions of MGE Dm412 were found. The new positions of MGE seem to be not random, and 5 "hot sites" of transpositions were detected. The probabilities of transpositions were estimated after SHS and HHS and in control sample. They were, correspondingly, 3.4 x 10(-2), 8.7 x 10(-2) and less than 4.1 x 10(-4) transpositions per genome, per site occupied, per generation. Therefore, as a result of HS treatment, the probabilities of transpositions were two orders of magnitude increased as compared to control, directly at next generation after induction. Comparison of these results with those obtained after step-wise temperature treatment shows that induction is dependent rather of "stressor effect" of temperature treatment than of treatment way used.

Animals↗
PubMed1990

[Expression of the quantitative trait radius incompletus in Drosophila and localization of mobile elements MDG1 and copia].

A series of subpopulations earlier obtained were studied for hybridization of mobile genetic elements (MGE). The subpopulations examined were two "selected" (ris- and ris+), two "temperature" (ri(c113) and ri(c149)) and the control (ric). The method of in situ hybridization with polytene chromosomes of larval salivary glands was used to determine the patterns of MGE localization for all subpopulations. The patterns obtained appeared to be quite different from that of mdg-2. The trees of similarity for subpopulations according to the patterns of every MGE localization were built by conventional clustering methods. These trees were topologically similar to each other and to mdg-2. Distinction spectra of patterns of four daughter subpopulations, in comparison with the control one, were shown for each of these MGE to be independent and individual. However, there are some common regularities among copia-like MGE-mdg-1, copia, mdg-2 and, probably, mdg-3, namely: non-random property of the majority of changes, the similarity of patterns for subpopulations with similar phenotypes etc. So, Drosophila genome can be conceived as a complex system of patterns of different MGE localization, capable of common or independent mass transpositions after external stress action.

Animals↗
PubMed1990

[A concept of limiting genetic factors of expression, organization, and evolution].

Elicitation and analysis of limiting genetic factors represent convenient method for approximate description of complex molecular-genetic systems. In sequential metabolic ways, the limiting is based on the minimum of catalytic activity, in parallel ones--on the maximum activity. In polygenic systems, the expressing polygenes affect always the limiting oligogenes. Limiting genes are only available to selection on the population level, the non-limiting genes being neutrally evolving. This result eliminates the acuteness of the Haldane's dilemma. The complex genetic systems could be quickly evolving by relay-race principle with sequentional change of limiting genes and without violation of Haldane's dilemma. The limiting factors of organization which restrict the possibilities of some special evolutionary directions have the key role in evolution. These limits were historically overcome by acceptance of evolutionary acquirements of wide usage. The sequence of such limits and acquirements was assumed as a basis of "scenario" of Prebiological and Biological Molecular Evolution. The concept is illustrated by some examples and results of theoretical analysis.

Animals↗
PubMed1989

[A phylogenetic analysis of genes of the influenza virus. Phylogenetic trees and fixation rates].

The phylogenetic trees of influenza virus genes of hemagglutinins, neuraminidases, and of NS genes were composed. Considering properties of synonimic replacements to be neutral and their rates constant at each tree, the dates of ancestor branch points were calculated, and the rates of fixation of synonimic (Ks) and non-synonimic (Kns) replacements estimated. The epidemic branches were mostly shown to be "deadlocks", non-epidemic ones being internal or "roots." The ratios of the numbers of synonimic to non-synonimic replacements (vs/vns) were correspondingly 1.32+/-0.42 and 4.78+/-1.28 for all trees, the difference being significant. It was shown that the dated branch points for hemagglutinins are non-randomly clustered around the initial points of the main genetic shifts of the A-type virus, corresponding to the influenza pandemics. It seems that these ancestor forms of virus behave similar to the "train" of these shifts, reproducing together with the pandemic forms under conditions of decreased immune resistance of host population. The rates of fixation of non-synonimic replacements in the epidemic branches of this tree are 4 times increased, as compared to non-epidemic ones.

Genes, Viral↗
PubMed1989

[Phylogenetic analysis of genes of the influenza virus. Relationship between adaptability and neutrality].

Detailed phylogenetic analysis of the gene family of hemagglutinin H3 of influenza A-type virus was fulfilled, taking into account the domain structure of protein and positions of antigen determinants. The densities of distribution of fixed synonimic replacements between domains HA1 and HA2 were shown to be actually equal (rho (HA1) = rho (HA2], and those of nonsynonimic ones to be unequal: their ratios were rho (HA1): rho (HA2) = 2.8 for nonepidemic branches, and rho (HA1): rho (HA2) = 7.7 for epidemic ones. For the positions of antigen determinants (agd) these densities differ still stronger from HA2: rho (agd): rho (HA2) = 10 for nonepidemic branches, and rho (agd): rho (HA2) = 36 for epidemic ones. In total, the rate of fixation of nonsynonimic replacements per position of antigen determinants for epidemic branches is 32 times higher than for nonepidemic ones. The absolute value of this estimation is K(ns)d = (9.1 +/- 0.7).10(-3) of nonsynonimic replacements per nonsynonimic position per year and seems to be twice as much as the maximum rate of neutral fixations Ks = (4.28 +/- 0.68).10(-3). Therefore, the epidemic reproduction of influenza virus is highly adaptive, exactly being focused on positions of antigen determinants. The evolution of influenza virus is stochastic process, both with the neutral and adaptive fixations.

Genes, Viral↗
PubMed1987

[Expression of the quantitative trait radius incompletus, temperature effects and localization of mobile elements in Drosophila. I. Properties of test subpopulations].

From the control sub-population, ric, with interrupted radial vein (L2) of the fly wing, two sub-populations were developed by selection: ris-, with distal and proximal fragments of L2 almost totally eliminated, as a result of minus-selection; ris+, with totally restored radial vein, resulting from plus-selection. Two sub-populations, ric113 and ric149, were also developed from the same original ric by changing gradually the cultivation temperature (29 degrees----18 degrees C) at the age of 113 +/- 5 h and 149 +/- 5 h, respectively. The former contained 2 times less and the latter 1.5 times more L2 than ric. These phenotypes were stably inherited in over 140 generations, expressing the "epigenic" properties. The genetic system of expression of ri oligogene was shown by genetic analysis to be corresponding to the polygene model of Mather. The main properties of 5 sub-populations used further for hybridization with mobile genetic elements, are described. Possible genetic mechanisms of the temperature effects are discussed.

Animals↗
PubMed1987

[Expression of the quantitative trait radius incompletus, temperature effects and localization of mobile genetic elements in Drosophila. II. Mobile genetic elements Dm-412].

Two "selection" sub-populations (ris- and ris+), as well as two "temperature" ones (ric113 and ric149) were earlier developed from the control ric sub-population with interrupted vein of the fly wing. All five sub-populations were investigated for hybridization of MGE Dm-412 with drosophila polytene chromosomes in situ. The tree of similarity of MGE Dm-412 hybridization patterns was built by the methods of matrix clusterization. The sub-populations with the most resembling expressions of characters (ris- and ric113, ris+ and ric149) were found to be also most similar in patterns of MGE localization and their changes. Nonrandomness of these changes was shown, the similarity of patterns being demonstrated to be mainly the result of the changes. There is evidence that such effects cannot be accounted for by genetic drift and independent stochastic changes in MGE localization.

Animals↗
PubMed1987

[Adaptive significance of the limited gene expression of the immune system].

Evolutionary development of immunity multigene systems seems to involve host-parasite molecular coevolution, as evidenced by comparison of metasoans and unicellular organisms in fixation rates of neutral and adaptive point mutations per one pair of corresponding genes. The estimations we attempted revealed that organisms with maximal restriction of Ig-like gene repertoire expression by an individual immune cell are more adaptive in formation of competent antigen-induced immune response, provided that the magnitude of potential repertoire of functional Ig-like receptors exceeds lymphoid cell population size. In contrast, when phage and bacteria populations are in coevolution, there is no need to limit the repertoire of expressive genes encoding bacteria surface receptor proteins which are recognized by a phage adsorption system. Other hypotheses of evolutionary premises and stimulus of immune genes expression limitation (allelic, isotypic etc.) are critically discussed.

Adaptation, Physiological↗
PubMed1986

[Enhancer-like structures in moderately repetitive sequences of eukaryotic genomes].

The results of contextual analysis of 25 different middle repetitive DNA sequences are presented. It was shown that each of these repetitive DNA sequences contains at least one enhancer-like structure homologous to real enhancers, as well as to their consensus. The enhancer-like structures have been also revealed in the replication origin of some prokaryote genomes. The results are discussed in the light of a possible role of middle repetitive DNA sequences in the modulation of gene expression. Some aspects of genomes' evolution, in relation to enhancers, are also considered.

Animals↗
PubMed1984

The template RNAs of RNA polymerases can have compact secondary structure, formed by long double helices with partial violations of the complementarity.

A new method of contextual analysis was used to search the long non-random inverted repeats and the complementary palindromes in the genes of E. coli and T7 RNA polymerases. These genes were found to contain from 25% to 50% of all the nucleotides involved in such helices. The 5' -and 3' -ends of mRNA can be protected by neighbouring double helices from the nuclease attack. Some double helices are competing and very similar to the attenuator of E. coli trp-operon.

Base Composition↗
PubMed1980

[Expanded model of lambda phage ontogeny].

An enlarged threshold model of regulatory system of development of lambda phage (RSDP lambda-2) is built. It includes 15 synthetic blocks of proteins and mRNAs and 4 blocks corresponding to the ontogenetic processes: two-stage replication, integration and exclusion of phage genome, formation of aggregates of regulatory proteins, regulation of bacterial lysis. By means of computer simulation of the RSDP lambda-2 model, the dynamics of concentrations of all main proteins, respective fractions of mRNAs and DNA are described in lytic and lysogenic regimens of phage ontogenesis. The results obtained are in a good agreement with available experimental data. The dependence of portion (%) of lysogenic responses on the mean multiplicity n of phage infection of bacterial culture, is built. This curve has a maximum point in accordance with experimental data of Kourilsky [10].

Bacteriophage lambda↗
PubMed1976

A cybernetic approach to the origin of the genetic coding mechanism. I. Methodological principles.

It is postulated that some quasi-deterministic code features (universality, connectedness, systematic degeneracy, symmetry, regularity and so on) resulted from unique (and therefore universal) relization of a stochastic evolutionary process. The evolution of real genetic systems should satisfy the principle of succession; that is, loss of a feature that is necessary for a genetic system means death to its carrier. The hypothesis of unique key coincidence is proposed which indicates the mechanisms of arising of the primary correspondence between the linear structures of polynucleotides and polypeptides. If the collinear coincidence was to appear in the key positions of pra-protein with, at least, some of the primitive properties of the pra-amino-acyl-t-RNA-synthetase required for the accelerated recognition of the key positions of pra-template, the positive feed-back mechanism in the system would be most short-circuited so that the repetitive reproduction of pra-synthetase would be much accelerated.

Amino Acyl-tRNA Synthetases↗