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T V Nasedkina

Publications and source records attributed to T V Nasedkina.

At least 19 recordsLinked to original sources
PubMed2006

[Comparative analysis of N-acetylation polymorphism in humans as determined by phenotyping and genotyping].

The N-acetylation polymorphisms of volunteers from the Moscow population analyzed by phenotyping and genotyping have been compared. The ratios between the proportions of fast acetylators (FAs) and slow acetylators (SAs) estimated by phenotyping and genotyping do not differ significantly from each other (47 and 44%, respectively). The absolute acetylation rate widely varies in both FAs and SAs. The NAT2 genotype and allele frequencies in the population sample have been calculated. The most frequent alleles are NAT2*4 (a "fast" allele), NAT2*5, and NAT2*6 ("slow" alleles); the most frequent genotypes are NAT2*5/*5, NAT2*4/*6, and NAT2*4/*5. Comparative analysis of N-acetylation polymorphism estimated by phenotyping and genotyping in the same subjects has shown a complete concordance between the phenotype and genotype in only 62 out of 75 subjects (87%). Comparative characteristics and presumed applications of the two approaches (quantitative estimation of acetylation rate and qualitative determination of the acetylator genotype) to the identification of individual acetylation status are presented.

Acetylation↗
PubMed2005

Biosensing and monitoring of cell populations using the hydrogel bacterial microchip.

Advanced development of the hydrogel bacterial microchip (HBMChip) technique is proposed. The microchip represents an array of hemispherical gel elements 0.3-60 nl in volume attached to hydrophobic glass surface and containing live immobilized microbial cells. Separate gel elements contain each up to 10(5) cells and retain them inside even while the cells are dividing. Porous structure of the gel provides easy access of nutrients and tested substances to the immobilized cells. Optical signals from the cells are easily measurable and allow monitoring of intracellular metabolism using vital fluorescent stains or engineered constructs encoding bioluminescent or fluorescent reporters. Two possible application modes of the HBMChip have been investigated, i.e. the observation of bacteria and biosensing. The dynamics of nucleic acids synthesis in growing E. coli cells has been analyzed using vital fluorescent stain SYTO 9. A special function has been suggested for evaluation of the cell growth parameters. Biosensing properties of the HBMChip have been illustrated by quantitative analysis of antibiotics and the detection of sodium meta-arsenite.

Anti-Bacterial Agents↗
PubMed1998

[Use of photo-anchoring of DNA probes for fluorescent in situ hybridization].

A possibility was investigated to use photo-crosslinking DNA probes for fluorescent in situ hybridization (FISH). DNA probes were modified by incorporating photonucleotides in these, containing a photoreactive group (tetrafluorobenzazid) and capable of making covalent bonds with the examined DNA, when irradiated in 300-330 nm region. The photonucleotide was incorporated into the probe either by nick-translation, or upon elongation of the hybridized probe by the Kljonow fragment. It has been shown that the DNA probe, cross-linking to a chromosome as a result of covalent bonds, is not removed from the place of hybridization under consequent denaturating washing, which makes it possible to carry out the following DNA hybridization with selective conservation of signals obtained due to previous hybridization. This peculiarity of photo-linking DNA probes makes it possible to use them for the two-step DNA hybridization. To demonstrate this, preparations of human chromosomes were investigated. On the first step, chromosomal DNA was hybridized by means of DNA probe having nucleotide sequences of centromeric regions of chromosomes 13 and 21, the probe being linked to chromosomal DNA by the photonucleotide. Following the denaturation treatment of the preparation, and after the second chromosomal DNA hybridization with cosmid DNA, containing chromosome 13 DNA nucleotide sequence, the signal in chromosome 13 centromeric region was retained to serve a marker of this chromosome, thus fascilitating its easier identification following the hybridization of its DNA with cosmic DNA. The denaturation stability of photo-crosslinking probes opens some new possibilities in technology of DNA in situ hybridization.

Chromosomes, Human↗
PubMed1997

[The isolation and analysis of lymphoblastoid cell lines from patients with xeroderma pigmentosum and progeria].

Lymphoblastoid cell lines from patients with xeroderma pigmentosum (2 forms) and progeria (unusual form) were established using transformation of peripheral blood lymphocytes by Epstein--Barr virus. The influence of different UV doses on cell vitality, proliferation and cell cycle progression was studied by means of flow cytometry. The cell vitality was determined after incubation of cells with etidium bromide and FDA. We used cytograms with two logarithmic signals (log green/log red) to discriminate the cell cycle status. Cell cultures were used with density of 500,000 cells per 1 ml, previously synchronized at G-phase by the incubation in a medium with low serum content. The effect of UV irradiation was followed during 72 h. Among four analysed cell lines only line XP2SP demonstrated enhanced UV sensitivity, expressed by decreasing of the amount of living cells after the UV dose of 2.5 J/m2 and higher. The cell cycle studies showed that cells were blocked in S-phase and simultaneously the amount of apoptotic cells with both reduced DNA content and ability to bind FDA was seen increased. Similar events were observed in the control line only after the dose of 20 J/m2 and higher.

Cell Line↗
PubMed1985

[Patterns in the occurrence and the submicroscopic organization of elongated metaphase chromosomes isolated from the cell].

Chinese hamster metaphase chromosomes were investigated under different conditions of isolation. Light microscopic study demonstrated different forms of stretched chromosomes, from those in which merely a small region is stretched to rope-like structures 20-25 microns long with diameter of about 0.4 micron. The ratio between the number of stretched and of compact chromosomes is dependent on the concentration of bivalent cations, on the pH and temperature of the isolation buffer. A study of the submicroscopic organization of stretched chromosomes revealed lengthwise fibrils that disappeared after the treatment with 0.6 NaCl and staphylococcal nuclease. Distinct aggregates were seen, whose array is maintaining the stretched chromosome structure. It is suggested that stretched chromosomes appear due to the existing in vivo lability of bonds between the main chromosome components involved in organization of chromatin fiber packing. It is proposed that the structure obtains rigidity in the course of isolation with bivalent cations.

Animals↗
PubMed1984

[Residual structures revealed after the action of staphylococcal nuclease on decondensed metaphase chromosomes].

The isolated Chinese hamster metaphase chromosomes were decondensed in 0.6 M NaCl solution and digested by staphylococcal nuclease on electron microscope grids. The residual structures as seen in electron microscope as isolated aggregates scattered over the entire area occupied by the chromosome. Prior to digestion, the material in the chromosome did not form presumably an integral protein structure similar to a scaffold.

Animals↗
PubMed1983

[Changes in the structure of the chromosomal nucleohistone fibrils on removal of divalent cations and histone H1].

A technique of freeze--drying was applied in studies on submicroscopic organization of metaphase chromosomes from Chinese hamster. In the buffer without bivalent cations the chromosomes increased in size; the removal of bivalent cations with EDTA resulted in a large swelling of chromosomes. Regularly organized nucleosomal filaments of a "beads-on-a-string" type appeared on the periphery of chromosomes. The regular organization of the fibers is damaged as soon as histone H1 is removed. An increase in the ionic strength of solution in the absence of bivalent cations results in chromosome compactization, although the regular fibrillar structure being not restored.

Animals↗
PubMed1982

The structure of partly decondensed metaphase chromosomes.

The technique of freeze-drying was applied to examine the submicroscopic organisation of metaphase chromosomes from Chinese hamster after removal of bivalent cations with EDTA and removal of histone HI with 0,6 M NaCl. Treated chromosomes increased in size, and nucleosomal filaments appeared at the periphery of the chromosomes. Removal of bivalent cations is accompanied with the appearance of regularly organized structures of the "beads-on-a-string" type. The regular organization of the fibers is damaged as soon as histone H1 is removed. After decondensation in a 0.6 M NaCl solution the metaphase chromosomes were treated with staphylococcal nuclease in situ on EM grids nd the residual structures analysed using electron microscopy. Nucleohistone fibers wer visible at the periphery of the chromosomes at the beginning of digestion. After complete elimination of the nucleohistone fibers in the course of digestion the remaining proteinaceous material was represented by aggregates of irregular shape and of varying size. These were either concentrated along the central axis of the chromatids or, at the final step of digestion, scattered evenly over the entire area that had been occupied by the chromosome. Presumably, in the chromosome prior to digestion, the material did not form an integral protein structure similar to a scaffold in dehistonised and spread chromosomes. An alternative interpretation for the fragmentation of protein material in the chromosome considers possible degradation of the protein scaffold in the course of digestion.

Animals↗
PubMedDate not supplied

5-[3-(E)-(4-azido-2,3,5,6-tetrafluorobenzamido)propenyl-1]-2'-deoxy- uridine-5'-triphosphate substitutes for thymidine-5'-triphosphate in the polymerase chain reaction.

The DNA targets may be labeled and simultaneously amplified in the polymerase chain reaction (PCR) using a pair of respective primers after elongation with nucleoside-5'-triphosphates carrying photoreactive groups. The amplified DNA may be subsequently photoactivated by irradiation above 300 nm, resulting in photo-cross-linking of the strands. For this goal 5-[3-(E)-(4-azido-2,3,5,6-tetrafluorobenzamido)propenyl-1]-, 5-{N-[N'-(4-azido-2,3,5, 6-tetrafluorobenzoyl)-3-aminopropionyl]aminomethyl}-, and 5-{N-[N'-(2-nitro-5-azidobenzoyl)-3-aminopropionyl]aminomethyl}-2'-de oxyuridine-5'-triphosphate (VII, VIa, and VIb) derivatives have been synthesized. It was found that VII is capable of efficiently elongating DNA primers with both Klenow fragment DNA polymerase I and Thermus aquaticus DNA polymerase. Thereto, it turned out to provide quantitative incorporation in DNA as revealed by the formation of the full-length amplificate by PCR in the presence of this photoreactive analogue without any dilution with natural dTTP. On the contrary, it was found, that incorporation of VIa and VIb do not permit further DNA replication.

DNA↗
PubMedDate not supplied

[Microchips based on three dimensional gel cells: history and perspective].

The review describes the history of creation and development of the microchip technology and its role in the human genome project in Russia. The emphasis is placed on the three-dimensional gel-based microchips developed at the Center of Biological Microchips headed by A.D. Mirzabekov since 1988. The gel-based chips of the last generation, IMAGE chips (Immobilized Micro Array of Gel Elements), have a number of advantages over the previous versions. The microchips are manufactured by photo-initiated copolymerization of gel components and immobilized molecules (DNA, proteins, and ligands). This ensures an even distribution of the immobilized probe throughout the microchip gel element with a high yield (about 50% for oligonucleotides). The use of methacrylamide as a main component of the polymerization mixture resulted in a substantial increase of gel porosity without affecting its mechanical strength and stability, which allowed one to work with the DNA fragments of up to 500 nt in length, as well as with rather large protein molecules. At present, the gel-based microchips are widely applied to address different problems. The generic microchips containing a complete set of possible hexanucleotides are used to reveal the DNA motifs binding with different proteins and to study the DNA-protein interactions. The oligonucleotide microchips are a cheap and reliable tool of diagnostics designed for mass application. Biochips have been developed for identification of the tuberculosis pathogen and its antibiotic-resistant forms; for diagnostics of orthopoxviruses, including the smallpox virus; for diagnostics of the anthrax pathogen; and for identification of chromosomal rearrangements in leukemia patients. The protein microchips can be adapted for further use in proteomics. Bacterial and yeast cells were also immobilized in the gel, maintaining their viability, which open a wide potential for creation biosensors on the basis of microchips.

Gels↗
PubMedDate not supplied

[Analysis of chromosome translocations involving MML by hybridization with an oligonucleotide microarray].

Identification of chromosome rearrangements is of importance for exact diagnosis, risk assessment, and therapy in blood malignancies. A new method was proposed for rapid and accurate identification of leukemia forms caused by chromosome rearrangements involving MLL (11q23). The method combines reverse transcription-multiplex PCR and hybridization with an oligonucleotide microarray. The microarray was designed to detect the five most common MLL rearrangements: t(4;11) MLL/AF4, t(9;11) MLL/AF9, t(11;19) MLL/ELL, t(11;19) MLL/ENL, and dup(11) MLL/MLL. With clinical specimens, the method was shown to efficiently identify the chromosome translocations in leukemia patients.

Base Sequence↗
PubMedDate not supplied

[Alginate gel microchip for real-time monitoring of intracellular processes in bacterial and yeast cells].

A method of alginate-based hydrogel cell microchip manufacturing is proposed. The development of mild conditions for cell immobilization in microvolumes of non-toxic alginate gel allows extending the range of microorganisms used. Different approaches to cell analysis using microchip have been approved in pilot studies. By the example of Escherichia coli, Bordetella bronchiseptica and Saccharomyces cerevisiae it is shown that cell microchip can be successfully applied for monitoring of nucleic acid and protein synthesis in growing cells simultaneously using two fluorescent dyes. The influence of chloramphenicol on the nucleic acids and protein synthesis in five bacterial strains has been studied on the microchip. The microchip was also applied for the analysis of inducible fluorescent protein EGFP synthesis in E. coli cells, the correlation between the level of EGFP synthesis and concentration of the inductor in the medium has been established.

Alginates↗
PubMedDate not supplied

[Biochip development for polymorphism analysis in biotransformation system genes].

Large-scale population researches, diagnostics of genetic predisposition to multifactorial diseases, screening of the polymorphic loci associated with individual sensitivity to pharmaceutical preparations, require the development of effective, exact and rapid methods of analysis for detection of many mutations simultaneously. One of the most perspective methods to solve these problems is a method of allele-specific hybridization with biochips. Taking the analysis of mutations in genes CYP1A1, CYP2D6, GSTM1, GSTT1, NAT2, CYP2C9, CYP2C19 and MTHFR as an example we showed the efficiency of using the approach for identification of individual genetic polymorphism. We believe that the biochips can be also a convenient tool in pharmacogenetics researches.

Biotransformation↗
PubMedDate not supplied

[Analysis of point mutations in BRCA1 gene using hybridization on hydrogel microchips].

Germ-line mutations in BRCA1 gene account for a substantial proportion of inherited breast and ovarian cancers. Identification of these mutations allows molecular diagnosis for breast cancer susceptibility. We have developed method for identification of 185delAG, 300T>G, 4153delA, 4158A>G and 5382insC mutations in BRCA1 gene using hybridization with microarray of geL-immobilized oligonucleotides (microchip). The microchip was tested with 36 control samples, carrying the above-mentioned mutations and 65 clinical cases with breast cancer. Our data demonstrated that developed microchip can be very effective and realible tool, easily introduced in ordinary medical and genetic laboratories.

Adult↗
PubMedDate not supplied

[Electron microscopic study of changes in chromosomal structural organization under the effect of formamide].

Isolated human metaphase chromosomes were treated with formamide at different (0-70%) concentrations and examined electronmicroscopically by protein monolayer technique. At increasing formamide concentration chromosomes gradually decondense, the scaffold becomes more clearly visible, the loops of chromatin fibres coming off the central part of chromosomes lose their nucleosomal appearance. Electrophoretic analysis of chromosomal proteins data show that formamide-treated chromosomes have approximately the same histone content as those before treatment, although chromosomes treated with 70% formamide look very similar to histone-depleted ones described elsewhere.

Chromosomes, Human↗
PubMedDate not supplied

[Uniparametric analysis of chromosomes from human fibroblasts using flow cytofluorometry].

Metaphase chromosomes from human diploid fibroblasts were isolated by the polyamine method and stained with different fluorochromes: propidium iodide, chromomycine A2, bisbensimide H33258, and DAPI. The fluorescently stained chromosomes were analyzed using a cell sorter ATC-3000 ("Bruker-Spectrospine"), and the flow histograms were investigated to identify the peaks of individual chromosomes and to choose the chromosomes which can be isolated to a high purity. High resolution was obtained with H33258 or DAPI. It was demonstrated that the peaks of chromosomes 13, 17, 20 are well distinguished from the adjacent peaks, so that these chromosomes can be sorted with a high purity. The peaks formed by chromosomes 5, 6, 8, 14, 15 are slightly overlapped by the adjacent peaks, and the sorting on the basis of monovariate analysis cannot provide sufficient purity of the sorted fractions (< 0.5). Chromosomes 1-2, 3-4, 7-X, 9-12, 16-18, 19, 21-22 cannot be discriminated for successful sorting of an individual chromosome type. The data obtained provided an experimental basis for choosing the chromosomes to be sorted with high purity for the subsequent cloning of their DNA.

Cells, Cultured↗