[Periodicities in nucleotide distribution in the locus of the light chain of Gallus gallus immunoglobulins].

Fourier spectra of nucleotide sequences from chromosome 15 of Gallus gallus have been obtained. The periodical structures of several Ig locus fragments have been characterized. The uniqueness of Fourier spectra of the locus of the Ig light chain and its fragments (such as a variable region, a constant region, an enhancer, and several other fragments) among Fourier spectra of other fragments of chromosome 15 is demonstrated.

[The specificity in promoter recognition by the Bacillus subtilis RNA polymerase deltaA and deltaH holoenzymes is connected with periodicities in the promoter nucleotide sequences].

Promoters recognized by deltaA-RNA and deltaH-RNA polymerase have different periodic patterns their nucleotide disposition. By using the special method of Fourier analysis for symbolic sequences. Fourier spectra of the primary structure of promoters transcribed bv deltaA-RNA and deltaH-RNA polymerase were obtained. For two data sets, a small one and a big one, a stepwise discriminant analysis with jackknife test based on the spectral characteristics of each of the promoters was performed. It was shown that it is possible to classify the data with the accuracy of 100% sets into classes: promoters that are recognized by the deltaA-RNA polymerise and promoters that are recognized by the deltaH-RNA polymerase. Significant correlations between the promoter strength and the characteristics of their Fourier spectra were obtained. Thus, the periodicity in nucleotide distribution along the polynucleotide chain is the attribute sufficient for promoter recognition by RNA polymerase holoenzyme.

[Optimization of conditions for isolating chromosomes in flow sorting]. / Optimizatsiia uslovii vydeleniia khromosom pri ikh sortirovke v potoke.

Factors for purity and efficiency of flow chromosome sorting were analysed on the base of quantitative analysis. The sorting rate and relative purity of individual chromosome fractions are determined both by the quality of initial chromosome suspension, instrument parameters and gate position on experimental histograms. The described procedure of analysing sorting efficiency and fraction purity allowed to formulate general tips for optimization of sorting conditions depending on a given strategy: maximization of quantity of obtained material, or achieving maximum purity for sorted fraction. The analysis is carried out on the bases of chromosome distribution parameters: their relative halfwidths and distances. These parameters can be obtained by the quantitative analysis programs for flow cytometry data. It is shown that the critical parameter for sorting purity is the level of contaminated objects in a zone of sorted chromosome signal registration. In addition, the fraction purity depends on the cover extent between different chromosome distributions. Created procedure allows to build up nomograms linking the sorting efficiency with fraction purity, depending on the position of sorting gates. These monograms permit to determine the position of sorting gates in relation to one or another strategy: 1) maximum rate for chromosome material obtaining, 2) maximum fraction purity, or 3) compromise between the two. The presented analysis allows to optimize the chromosome sorting process for subsequent genome investigations providing chromosome material with controlled characteristics.

[A novel method of chromosome distribution analysis in saccharose density gradient]. / Primenenie novogo metoda k analizu raspredeleniia khromosom v gradiente plotnosti sakharozy.

The human chromosomes distribution in a sucrose density gradient was studied using a new computer method of the quantitative analysis of flow karyotypes. The dual-parameter flow distributions of human chromosomes fluorescence intensities of the sucrose density gradient fractions were analyzed to obtain the quantity of each chromosome. The chromosomes were found to distribute over sucrose density gradient as follows: 1) fractions with low sucrose density mostly contain chromosomes 1-7, and their quantity is increased between 1.4- to 3.2-fold in comparison with the control unfractionated suspension; 2) medium density fractions are enriched with chromosomes 8-20 up to 2.4-fold; 3) fractions with a high sucrose density mostly contain small chromosomes 21-22 and fragments of broken chromosomes. So the new method of quantitative analysis of flow karyotypes allows one to determine the efficiency of enrichment and the maximally enriched fraction for any chosen chromosome. Maximally enriched fractions maximize the rate of preparative flow sorting of individual chromosomes for research or biotechnology purposes.

[Two-parameter flow fluorescence analysis of human chromosomes. Quantitative processing]. / Dvukhparametricheskii fluprestsentnyi analiz khromosom cheloveka v potoke. Kolichestvennaia obrabotka.

A procedure for the quantitative analysis of the results of fluorimetric studies on human chromosomes in a flow is described. The procedure enables one to simultaneously follow two parameters by using two fluorochromes, one of which is selective to the GC-, and the other, to AT base pairs of DNA. Thus, it becomes possible to derive from the experimentally obtained distributions an information on the relative DNA content in individual chromosomes, differences in DNA content between homologous chromosomes, the relative number of chromosomes of each type in the sample tested, as well as on the percent ratio of AT and GC base pairs in a particular chromosome. In addition, the procedure enables one to assign, with a high degree of accuracy, the peaks on experimental distributions to the objects of analysis chromosomes. The analysis cutting off the extreme combines the method of components with the least square method, as applied to the peaks of the Gaussian shape. The first step involves the filtration of the starting experimental data from contaminating signals from both the parts of degraded chromosomes and stained cytoplasm fragments, and from chromosome aggregates. The procedure is realized as a package of programs for IBM-compatible PC/AT computers (486 and later versions), which permits one to perform a comprehensive analysis of two-parameter distributions of chromosome fluorescence signals to solve a number of problems, such as the identification of chromosome aberrations in cell lines tested, quantitative comparison of distinguishing features of homologous chromosomes and whole chromosome sets.

[Quantitative processing of results of uniparametric fluorescent flow analysis of human chromosomes]. / Kolichestvennaia obrabotka rezul'tatov odnoparametricheskogo fluorestsentnogo analiza khromosom cheloveka v potoke.

The proposed procedure of computer analysis of the flow karyotype data, obtained in human chromosomes studies, is able to provide information about the basic parameters of the karyotypes: the positions of the peaks (corresponding to the relative size of chromosomes), peaks areas (relative number of chromosomes in the sample), coefficients of variation (CV) of the peaks--possible differences between homologous chromosomes. The analysis is based on the assumption that all chromosomal components of the experimental distributions are normal (Gaussians). The algorithm of the analysis uses a combination of two approaches: truncation method and least squares method. As the flow data are "contaminated" by background components, special tools for filtering off the contaminating signals were designed including the original integral Fourier filtering procedure. This analysis is realized in a program package utilizing IBM-compatible PCs. The user is able to get the desired parameters for most chromosomes of the karyotype under study from univariate flow data: differences between particular homologous chromosomes, presence of chromosome aberrations, extra chromosomes, etc., since structural aberrations and chromosome number variation lead to specific changes of the parameters of chromosome-related components.