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Biomedical subjects

M G Samsonova

Publications and source records attributed to M G Samsonova.

14 recordsLinked to original sources
PubMed1999

NetWork: an interactive interface to the tools for analysis of genetic network structure and dynamics.

We designed a Java applet called NetWork which enables a user to interactively construct and visualize a genetic network of interest, and to and to evaluate and explore its dynamics in the framework of a Boolean network model. NetWork displays the mechanism of gene interactions at the level of gene expression and enables the visualization of large genetic networks. NetWork can serve as an interactive interface to tools for the analysis of genetic network structure and behavior.

Algorithms↗
PubMed1999

Spatio-temporal registration of the expression patterns of Drosophila segmentation genes.

The application of image registration techniques resulted in the construction of an integrated atlas of Drosophila segmentation gene expression in both space and time. The registration method was based on a quadratic spline approximation with flexible knots. A classifier for automatic attribution of an embryo to one of the temporal classes according to its gene expression pattern was developed.)

Animals↗
PubMed1998

Graphical interface to the genetic network database GeNet.

UNLABELLED: We designed a Java applet which enables the visualization of genetic networks and can be used as a Web publishing tool by molecular biologists studying the mechanisms of gene interactions. AVAILABILITY: http://www. csa.ru/Inst/gorb_dep/inbios/ genet/Graph/Genes_Graph.html CONTACT: samson@fn.csa.ru

Computational Biology↗
PubMed1997

[Structural and functional chromatin organization of the SUP35 gene in Saccharomyces cerevisiae yeast].

Structural and functional organization of the 5' region of the SUP35 gene was analyzed in Saccharomyces cerevisiae yeast. Indirect DNA end labeling allowed two nuclease-hypersensitive sites and a region involved in nucleosomes to be revealed. DNase I and micrococcal nuclease hypersensitive sites were localized to almost the same regions: -461 ... -372 bp and -271 ... -91 bp for DNase I and -461 ... -356 bp and -231 ... -79 for micrococcal nuclease. Nucleosomes were localized to a region +22 ... +339 bp. Both the location of DNase I and micrococcal nuclease hypersensitive sites within the promoter region and the location of nucleosomes within the coding region remain the same at different cell culture growth phases. However, positioning nucleosomes were revealed within the SUP35 coding region only at the late logarithmic phase; the radioautographic pattern of them does not depend on the extent of nuclease digestion.

Chromatin↗
PubMed1995

Reversions to respiratory competence of omnipotent sup45 suppressor mutants may be caused by secondary sup45 mutations.

The molecular nature of the sup45 respiratory deficient omnipotent suppressor, and of three reversions to respiratory competence which removed the suppressor effect of the initial mutation, was examined. All reversions were caused by secondary sup45 mutations which indicates a direct connection between sup45 "respiratory" and "translational" functions. Computer analysis showed the local changes of Sup45 protein characteristics in the suppressor strain and revertants in comparison to the wild-type protein. The distribution of mutant sites in relation to evolutionary conserved, and tentatively functional, regions in the Sup45 protein is discussed.

Amino Acid Sequence↗
PubMed1994

[The Petergof genetic collection of microorganisms].

The Petergof Genetic Collection (PGC) of microalgae was created in the 1960s during study of the regularities of mutational processes. A collection of yeasts has been maintained at the Department of Genetics and Selection of St. Petersburg State University since 1977. This collection contains some 1000 genetically marked strains of the yeasts Saccharomyces cerevisiae and Pichia methanolica, and the algae collection comprises about 600 strains of Chlamydomonas reinhardtii, Chlorella vulgaris, and Scenedesmus obliquus. The structure of the collection and the employment of strains in basic and applied research, as well as for educational purposes, are discussed. On the basis of the original software GENESTRAIN, a yeast PGC database (DB) was developed. A visual interface that contains information about selection of Ch. reinhardtii strains and crosses made was created in the HyperCard operational system.

Eukaryota↗
PubMed1992

Conservative system for dosage-dependent modulation of translational fidelity in eukaryotes.

Variations in dosage of some genes can alter the level of translational fidelity. The Saccharomyces cerevisiae genes that act as dosage-dependent suppressors and/or modulators of suppression, are the following: some tRNA genes (for example, tRNA(Gln)) inducing readthrough by mispairing; genes coding for either translational elongation factor or other proteins taking part in translation; and some genes of unknown function. We suggest that the SUP35 protein is a factor which may play a major role in balance-dependent regulation of translational fidelity. Homologues of this genes have been identified in other yeast genera (Pichia), green algae (Chlamydomonas) and various animals including man. No homologies have been found in the polychaeta (Nereis) or in insects (Drosophila). Rates of evolution differ for two separate parts of the genes; the N-terminal part, which is important for ambiguous translation in Saccharomyces, is markedly variable in the organisms tested. However, the C-terminal part which is required for yeast viability has a common origin but a separate evolution from that of the EF-Tu protein family.

Animals↗
PubMed1991

Structure comparison and evolutionary relations between elongation factors EF-Tu (EF-1 alpha) and SUP 2 proteins.

On the basis of high homology and structural similarity, three genes, SUP2 Saccharomyces cerevisiae, SUP2 Pichia pinus and GST1 Homo sapiens, might be considered as members of one family named SUP2. Comparison of the primary structure of SUP2 proteins and elongation factors EF-Tu(EF-1 alpha) from 19 different species was performed. It was found that SUP2 proteins bear more homology to eukaryotic elongation factor than to procaryotic EF-Tu, though the degree of sequence conservation in SUP2 proteins is smaller than in EF-1 alpha factors. The extensive phylogenetic analysis of SUP2 and EF-Tu(EF-1 alpha) genes was performed by means of 3 methods, 2 phenetic and one cladystic (maximal parsimony). The data support the close relation of SUP2 genes to other elongation factor genes.

Amino Acid Sequence↗
PubMed1991

A new method for finding long consensus patterns in nucleic acid sequences.

We describe a fast computer algorithm for identifying consensus patterns in DNA sequences. The method requires no prior assumptions about the consensus pattern other than its length. In particular no previous knowledge of the frequency or spacing of consensus patterns is required. However, a priori information about the shape of the consensus pattern, or invariability of individual positions, or the overall conservation level, can be utilized to enhance the selectivity and sensitivity of search. As the number of all possible consensus words increases very rapidly with length, comprehensive searches have usually been restricted to a maximum of 10-12 nucleotides, even when large mainframes are used. Our algorithm enables searching for consensus patterns of this order on current mid-range and powerful microcomputers. Searches may be conducted on single, long sequences or a set of possibly aligned shorter sequences. We give examples of identified consensus patterns in both prokaryotic and eukaryotic DNA sequences, along with some typical program timings.

Base Sequence↗
PubMed1980

[Genetico-biochemical study of the acid phosphatases of Saccharomyces cerevisiae yeasts. X. Analysis of mutations arising in gene acp3].

Mutations leading to decrease or absence of orthophosphate-repressible acid phosphatase activity have been studied. It is shown that these mutations can arise in three genes: acp1, acp2 and acp3, which are not linked. Genes acp1 and acp2 have been studied previously; the existence of the gene acp3 is demonstrated in this paper. It is established that all mutations in the acp3 gene are recessive, are leaky and epistatic to the constitutive mutations in all known regulatory genes for acid phosphatase II synthesis - acp4, acp80, acp81, acp82, acp83, and acp84. The gene acp3 is not linked with these regulatory genes, but it is closely linked with the structural gene for constitutive acid phosphatase - pho1 (D=0.33+/-0.20 cM). The pho1 gene has been recently located on the right arm of chromosome II on the left of the gene lys2. Mutations lacking activity of constitutive and repressible acid phosphatases simultaneously have been found. It is shown that these mutations are allelic to mutations in the gene acp3 and pho1 simultaneously. Two hypotheses are proposed about the role of the gene acp3: the gene controls the positive factor for the repressible acid phosphatase synthesis or the structure of the enzyme.

Acid Phosphatase↗
PubMed1975

[Genetico-biochemical study of acid phosphatases in Saccharomyces cerevisiae yeast. V. Genetic control of regulation of acid phosphatase II synthesis].

Regulation of exocellular enzyme acid phosphatase 2 synthesis is studied. 21 mutants with consitutive synthesis of this enzyme are obtained by UV-irradiation. All mutants were recessive and were distributed among 3 complementation groups ACP80, ACP81, ACP82. Two groups, ACP80 and ACP81 corresponded to two different genes, which showed no linkage with ACP1, ACP2 and PHO1 genes. The type of synthesis of acid phosphatase 2 in strains acp1 acp80, acp1 acp81, acp2 acp80, acp2 acp81 is determined, and a conclusion is made about the participation of ACP2 gene in the regulation of acid phosphatase 2 synthesis. It is shown that some mutations in PHO1 gene, which block the activity of acid phosphatase 1, influence the activity and regulation of acid phosphatase 2.

Acid Phosphatase↗
PubMed1975

[Genetic-biochemical study of acid phosphatases from Saccharomyces cerevisiae yeasts. IV. Genetic control of acid phosphatase II activity].

Genetic control of exocellular acid phosphatase of yeast Saccharomyces cerevisiae (acph 2) is studied. 64 mutants with the impaired activity of acid phosphatase have been obtained by UV-irradiation. All the mutations have been distributed among 4 genes: ACP1, ACP2, ACP3, ACP4 using functional and recombinational tests for allelism. It is shown that mutations in genes ACP1--ACP3 are recessive, but in the gene ACP4--dominant. The gene ACP4 is found to be located 0.41+/-0.064 in strains from centromere and to have no linkage with ACP1. Possible functions of genes studied are under discussion.

Acid Phosphatase↗
PubMedDate not supplied

[Spatial registration of data on gene expression in situ].

For registering data on the in situ expression of segmentation genes, a method of image registration was developed basing on the spline approximation. The reference points for the registration were the coordinates of extrema in one-dimensional patterns of gene expression. This registration method is characterized by a very high accuracy. A method of creating a generalized pattern of gene expression in single cells is proposed. Such patterns were constructed for nine segmentation genes belonging to the gap and pair-rule classes of genes.

Gene Expression Profiling↗