[Packaging of Subchromosomal-Size DNA Molecules in Chromatin Bodies in the Ciliate Macronucleus].

A fundamental difference between somatic nuclei (macronuclei) of ciliates and cell nuclei of higher eukaryotes is that the macronuclear genome is a huge number (up to tens or hundreds of thousands) of gene-sized (0.5-25 kb) or subchromosomal (up to 2000 kb) minichromosomes. Electron microscopy shows that macronuclear chromatin usually looks like chromatin bodies or fibrils 200-300 nm thick in the interphase. However, the question of how many DNA molecules are contained in an individual chromatin body remains open. The organization of chromatin in macronuclei was studied in the ciliates Didinium nasutum and three Paramecium sp, which differ in pulsed-field gel electrophoresis (PFGE) karyotype, and compared with the model of topologically associated domains (TADs) of higher eukaryotic nuclei. PFGE showed that the sizes of macronuclear DNAs ranged from 50 to 1700 kb, while the majority of the molecules were less than 500 kb in length. A comparative quantitative analysis of the PFGE and electron microscopic data showed that each chromatin body contained one minichromosome in P. multimicronucleatum in the logarithmic growth phase, while bodies in the D. nasutum macronucleus contained two or more DNA molecules each. Chromatin bodies aggregated during starvation, when activity of the macronuclei decreased, leading to an increase of chromatin body size or the formation of 200- to 300-nm fibrils of several chromatin bodies. A model was proposed to explain the formation of such structures. In terms of topological characteristics, macronuclear chromatin bodies with subchromosomal DNA molecules were found to correspond to higher eukaryotic TADs.

Establishment of a FDC-P1 Murine Cell Line with Human KIT N822K Gene Overexpression.

The mechanism of resistance of leukemia cells to chemotherapeutic drugs remains poorly understood. New model systems for studying the processes of malignant transformation of hematopoietic cells are needed. Based on cytokine-dependent murine acute myeloid leukemia (AML) FDC-P1 cells, we generated a new cell line with ectopic expression of the KIT gene encoding mutant human receptor tyrosine kinase (N822K). We investigated the role played by overexpression of the mutant KIT in the survival of leukemia cells and their sensitivity to therapeutic drugs. We also generated a co-culture system consisting of FDC-P1 murine leukemia cells and a HS-5 human stromal cell line. Our data can be used for a further comprehensive analysis of the role of KIT N822K mutation in the cellular response to anti-leukemic drugs, growth factors, and cytokines. These data are of interest in the development of new effective therapeutic approaches to the treatment of acute leukemia.

[Factors Affecting the Labeling of NIH 3T3 Cells with Magnetic Nanoparticles].

The factors that affect the labeling of NIH 3T3 murine fibroblasts with Fe3O4-based magnetic nanoparticles (MNPs) were studied using MNPs produced by the gas condensation and solution precipitation methods and MNPs surface-modified with 3-aminopropylsilane or L-lysine. The production method, surface modifications, the particle concentration and size, the state of the cell population, and the method of MNP introduction were found to substantially affect the efficiency of MNP binding by cells. In particular, large MNP clusters may occur in MNP suspensions in DMSO, and their disruption by sonication increased the percent yield of magnetically labeled cells. Static incubation of a cell suspension led to a more efficient labeling as compared with continuous agitation. Cells attached to a plastic support could be labeled to a higher degree than cells in suspension, but required substantially longer incubations with MNPs. MNP centrifugation on cell layers (magnetic spinoculation) significantly increased the rate and efficiency of labeling. The stability of magnetic labeling was shown to depend on the MNP dose during labeling. Electron microscopy studies demonstrated that MNPs were associated with the cell surface after 20-min incubation with cells and were mostly in the cell interior after 4-h incubation. The results of the study may be useful for preparation and application of magnetized cell samples.

Controlled formaldehyde fixation of fibronectin layers for expansion of mesenchymal stem cells.

Extracellular cell matrices deposited by cells stimulate cell proliferation. However, their generation is cumbersome and time consuming. We show here that controlled fixation of fibronectin layers after coating culture vessels significantly enhances expansion of murine and human mesenchymal stem cells (MSCs) and, to a lesser extent, primary fibroblasts. In contrast, fibronection fixation did not stimulate proliferation of established cancer cell lines. Fixed vitronectin or collagen IV layers also enhanced proliferation of murine MSCs. Thus, controlled formaldehyde fixation of layers formed by fibronectin or some other extracellular matrix components represents a simple and reproducible way to enhance proliferation of primary cells.

Hepatitis C virus: The role of N-glycosylation sites of viral genotype 1b proteins for formation of viral particles in insect and mammalian cells.

Hepatitis C virus (HCV) is characterized by considerable genetic variability and, as a consequence, it has 6 genotypes and multitude of subtypes. HCV envelope glycoproteins are involved in the virion formation; the correct folding of these proteins plays the key role in virus infectivity. Glycosylation at certain sites of different genotypes HCV glycoproteins shows substantial differences in functions of the individual glycans (Goffard et al., 2005; Helle et al., 2010) [1], [2]. In this study, differential glycosylation sites of HCV genotype 1b envelope proteins in insect and mammalian cells was demonstrated. We showed that part of glycosylation sites was important for folding of the proteins involved in the formation of viral particles. Point mutations were introduced in the protein N-glycosylation sites of HCV (genotype 1b) and the mutant proteins were analyzed using baculovirus expression system in mammalian and insect cells. Our data showed that, in contrast to HCV 1a and 2a, the folding of HCV 1b envelope proteins E2 (sites N1, N2, N10) and E1 (sites N1, N5) was disrupted, however that did not prevent the formation of virus-like particles (VLP) with misfolded glycoproteins having densities typical for HCV particles containing RNA fragments. Experimental data are supported by mathematical modeling of the structure of E1 mutant variants.

[Superparamagnetic Cobalt Ferrite Nanoparticles "Blow up" Spatial Ordering of Double-stranded DNA Molecules].

The formation of cholesteric liquid-crystalline dispersions formed by double-stranded DNA molecules, handled by positively charged superparamagnetic cobalt ferrite nanoparticles, as well as action of these nanoparticles on DNA dispersion, are considered. The binding of magnetic nanoparticles to the linear double-stranded DNA in solution of high ionic strength (0.3 M NaCl) and subsequent phase exclusion of these complexes from polyethylene glycol-containing solutions lead to their inability to form dispersions, whose particles do possess the spatially twisted arrangement of neighboring double-stranded DNA molecules. The action of magnetic nanoparticles on DNA dispersion (one magnetic nanoparticle per one double-stranded DNA molecule) results in such "perturbation" of DNA structure at sites of magnetic nanoparticles binding that the regular spatial structure of DNA dispersion particles "blows up"; this process is accompanied by disappearance of both abnormal optical activity and characteristic Bragg maximum on the small-angle X-ray scattering curve. Allowing with the fact that the physicochemical properties of the DNA liquid-crystalline dispersion particles reflect features of spatial organization of these molecules in chromosomes of primitive organisms, it is possible, that the found effect can have the relevant biological consequences.

The peculiarities of piRNA expression upon heat shock exposure in Drosophila melanogaster.

Different types of stress including heat shock may induce genomic instability, due to the derepression and amplification of mobile elements (MEs). It remains unclear, however, whether piRNA-machinery regulating ME expression functions normally under stressful conditions. The aim of this study was to explore the features of piRNA expression after heat shock (HS) exposure in Drosophila melanogaster. We also evaluated functioning of piRNA-machinery in the absence of major stress protein Hsp70 in this species. We analyzed the deep sequence data of piRNA expression after HS treatment and demonstrated that it modulates the expression of certain double-stranded germinal piRNA-clusters. Notable, we demonstrated significant changes in piRNA levels targeting a group of MEs after HS only in the strain containing normal set of hsp70 genes. Surprisingly, we failed to detect any correlation between the levels of piRNAs and the transcription of complementary MEs in the studied strains. We propose that modulation of certain piRNA-clusters expression upon HS exposure in D. melanogaster occurs due to HS-induced altering of chromatin state at certain chromosome regions.

[Role of N-linked glycans in HCV glycoprotein E1 in the folding of structural proteins and formation viral particles].

Envelope proteins of HCV play a major role in virus lifecycle. These proteins are main components of the virion. They are involved in virus assembly. Envelope proteins are modified by N-linked glycosylation which is supposed to play a role in their stability, in the assembly of the functional HCV glycoprotein heterodimer, protein folding and viral entry. The role of N-linked glycosylation sites in HCV E1 protein in structural proteins assembly was analyzed by site-directed mutagenesis in a model system--insect cells producing three viral structural proteins with formation of virus-like particles. Removing of single N-linked glycosylation sites in HCV E1 protein does not affect the efficiency of its expression in insect Sf9 cells. E1 electrophoretic mobility is increasing in parallel with decreasing the number of glycosylation sites. The destroying of glycosylation sites N1 or N5 in E1 influences the assembly of noncovalent glycoprotein heterodimer E1E2--the prototype of natural complex incorporated in virion. The lack of glycans in N1 and N5 sites of E1 was shown to affect the efficiency of its expression in mammalian HEK293 T cells.

[Immunocytochemical visualization of P185(HER2) receptor by antibody fused with dibarnase and conjugate of barstar with colloidal gold].

We studied the localization of transmembrane receptor P185(HER2) in SKOV-3 and BT-474 cancer cells by fluorescence, confocal and electron immunomicroscopy. P185(HER2) is a marker of breast and ovarian tumors, it is considered as a target for anticancer therapy. It is extremely important to choose a universal immunicytotoxic agent applicable, first, to study the distribution of P185(HER2) in cancer cells, secondly, to remove P185(HER2) from the cell surface and, thirdly, to eliminate target cells. In this work for visualization of P185HER2 We prOposed immunocytotoxic system, consisting of the monoclonal miniantibody 4D5 scFv to extracellular P185E domain fused with two molecules of barnase (ribonuclease from Bacillus amyloliquefaciens) and of its specific inhibitor barstar. Fluorescence microscopy has showed that the module 4D5 scFv-dibarnase:barstar efficiently identified P185(HER2) on the surface of cancer cells. It was revealed by confocal microscopy that interaction with 4D5 scFv-dibarnase lead to internalization of P185(HER2). The localization of P185(HER) in human ovarian carcinoma cells SKOV-3 and breast carcinoma cells BT-474 was compared by electron microscopy using 4D5 scFv-dibarnase:barstar-Au and 4D5 scFv-dibarnase-Au complexes. P185(HER) distributed on the cell surface unequally with preferential localization on protrusions or close to their bases and in contacts between protrusions and cell membrane. At 37 degrees C, P185(HER2) internalized through coated pits and vesicles and concentrated in the endosomes and multivesicular bodies in the cells of both cell lines, as well as in lysosomes in cells BT-474.

[Dynamics of penetration of "solid" nanoconstructions based on double-stranded DNA complexed with gadolinium into CHO cells].

Currently, neutron capture therapy is a promising cancer treatment. This method is based on the reaction of the thermal neutron capture by some non-radioactive elements (e.g., Gds57), which results in subsequent emission of electrons and gamma rays. An effective instrument for delivery of gadolinium into the tumor tissue are the particles of the "rigid" nanostructures (NS) based on double-stranded DNA complexes with gadolinium (NS-Gd). The local concentration of Gd in such nanostructures may reach 40%. To optimize the process of neutron capture therapy it is very important to investigate possible penetration mechanisms of NS-Gd particles into the tumor cells. In this work, the dynamics of interaction NS-Gd with cultivated chinese hamster ovary cells (CHO) was studied by confocal and electron microscopy. It is shown that NS-Gd are able to enter CHO cells. This process begins in about 1 hour after the start ofincubation. After 6 h NS-Gd particles were detected in almost all cells. A further increase of the incubation time does not lead to significant changes in cell morphology, although the number NS-Gd inside the cells increases. The plasma membrane of the cells remains intact. The NS-Gd particles, which entered the cells, remain inside the cells for a long time. The data obtained show that NS-Gd are relatively low-toxic and suggest that the presence of NS-Gd in the tumor cells does not prevent their division. The data obtained are important for improving the efficiency of the neutron capture therapy method.

[Affect of deoxynojirimycin derivatives on hepatitis C virus morphogenesis].

Viral hepatitis C is one of the wide-spread and dangerous human diseases. The choice of drugs for treatment of chronic hepatitis C virus (HCV) infection is limited and prophylactic vaccines do not exist. Thus, the development of new antiviral strategies and substances are of great importance. The targeting of viral morphogenesis might be used as an alternative approach to existing strategies of HCV blocking. The glycosylation of viral envelope proteins is an important step of viral particle morphogenesis that determines the correct assembly of HCV virions. The derivatives of glucose analog deoxynojirimycin (DNJ)--inhibitors of alpha-glucosidase can impair the assembly of structural proteins and HCV particle formation. In the present work the affect of alkylated derivatives of DNJ N-pentyl-DNJ and N-benzyl-DNJ to HCVmorphogenesis in a model system insect cells producing three viral structural proteins with formation of virus-like particles was studied. Intracellular N-glycosylation of HCV envelope glycoproteins was shown to be impaired by DNJ derivatives. At 1 mM concentrations of these substances the level of gpE1 and gpE2 glycoproteins increase and their electrophoretic mobility decrease which seems to be due to inhibition of a-glucosidase in endoplasmic reticulum and accumulation of hyperglycosylated N-glycans in HCV glycoproteins. The interaction of the latters with calnexin leads to formation of unproductive dimers and bloks productive assembly of virus-like particles.

[Study of the positional relationship of nucleolar chromatin and nucleolar compartments in somatic nuclei OPF the ciliate Didinium nasutum].

We showed earlier that nucleoli in interphase ciliates Didinium nasutum, appearing on single ultrathin sections as individual structures, actually are parts of more complex network-like structures in which fibrillar component is located on periphery, and granular--in the central part of a nucleolus. It is known, that nucleolar organizers in D. nasutum are represented by chromatin bodies connected with nucleoli. In this work we used 3D reconstruction on the basis of serial ultrathin sections to study localization of chromatin bodies which by morphological criteria might correspond to nucleolar organizers. Our data showed, that all such chromatin bodies settled down outside of nucleoli, near the periphery of fibrillar component. Even those chromatin bodies which on single sections looked completely surrounded by fibrillar nucleolar component, actually settled down in fibrillar component cavities open to nucleoplasm. Analysis of distribution of nucleolar chromatin bodies allowed us to conclude that activity in different parts of interphase complex network-like nucleoli of D. nasutum is approximately the same.

[Effect of nucleocapsid on multimerization of gypsy structural protein Gag].

The structural protein (Gag) of the gypsy Drosophila retrovirus lacks matrix, but contains capsid and nucleocapsid domains. The Gag forms virus-like particles in a bacterial cell; besides, its capsid alone is able to form aggregates. However, aggregates assembled from the capsid were variable in size and displayed much less organization than particles formed by the whole Gag. The nucleocapsid exerts influence on the organization and structure of particles, and this function is directed by sequence of amino acid residues at its N-terminus (a nucleocapsid proximal part). The particle assembling occurs in the presence of any RNAs or single stranded DNA oligonucleotides.

[Novel bidirectional promoter from human genome].

In human and other mammalian genomes a number of closely linked gene pairs transcribed in opposite directions are found. According to bioinformatic analysis up to 10% of human genes are arranged in this way. In present work the fragment of human genome was cloned that separates genes localized at 2p13.1 and oriented "head-to-head", coding for hypothetical proteins with unknown functions--CCDC (Coiled Coil Domain Containing) 142 and TTC (TetraTricopeptide repeat Containing) 31. Intergenic CCDC142-TTC31 region overlaps with CpG-island and contains a number of potential binding sites for transcription factors. This fragment functions as bidirectional promoter in the system ofluciferase reporter gene expression upon transfection of human embryonic kidney (HEK293) cells. The vectors containing genes of two fluorescent proteins--green (EGFP) and red (DsRed2) in opposite orientations separated by the fragment of CCDC142-TTC31 intergenic region were constructed. In HEK293 cells transfected with these vectors simultaneous expression of two fluorescent proteins is observed. Truncated versions of intergenic region were obtained and their promoter activity measured. Minimal promoter fragment contains elements Inr, BRE, DPE characteristic for TATA-less promoters. Thus, from the human genome the novel bidirectional promoter was cloned that can be used for simultaneous constitutive expression of two genes in human cells.

[The structural protein Gag of the gypsy retrovirus forms virus-like particles in the bacterial cell].

The amino acid sequence of the drosophila retrovirus MDG4 (gypsy) structural protein Gag does not contain a canonical motif known for the majority of vertebrate retroviruses. Moreover, the protein translation can theoretically begin with two separated initiation codons located within its unique open reading frame. We designed constructs for expression of two theoretically possible variants of Gag polypeptide and investigated an ability of the each product to form virus-like particles in the bacterial cell, i.e. in the absence of eukaryotic cell factors. The results obtained showed that the both variants of the gypsy protein Gag form globular particles in the bacterial cell.

[Characteristics of chromatin structural organization in somatic nucleus of the ciliate Didinium nasutum].

Structural organization of macronuclear chromatin of the ciliate Didinium nasutum was studied. Macronuclear genome of D. nasutum is represented by DNA molecules of subchromosomal size. At interphase, macronuclear chromatin is organized into chromatin clumps approximately 100-200 nm in size and some of them form short thick fibres consisting of several chromatin clumps. Using differential staining of nucleic acids on ultrathin sections we revealed perichromatin fibres and granules on the surface of many chromatin clumps. 3D models of spatial distribution of chromatin clumps in the macronucleus were reconstructed on the basis of serial ultrathin sections and peculiar features of their organization were studied.

[Liquid-crystalline dispersions formed by complexes of linear double-stranded DNA molecules with dendrimers].

The formation of liquid-crystalline dispersions as a result of interaction of linear, double-stranded DNA molecules with poly(propyleneimine) dendrimers in water-salt solutions was studied. It was shown, that this process does not depend on the ionic strength of solution and molecular structure of dendrimer. By means of the atomic force microscopy, it was established, that in the case of the dendrimer molecules of the 4th generation (G4), the mean size of particles of (DNA-dendrimer G4) liquid-crystalline dispersion is equal to 300-400 nm. The "boundary" conditions (ionic strength of solutionand molecular mass of dendrimer) of formation of optically active (cholesteric) and optically inactive of the (DNA-dendrimer) dispersions were determined using circular dichroism spectroscopy. The interaction of dendrimers of 1st, 2nd, 3rd and 5th generations with DNA molecules results in the obtaining of the optically inactive dispersions. Dendrimer molecules of 4th generation induce the formation of two types dispersions: in solutions of high ionic strength (micro > 0.4) they induce the formation of cholesteric liquid-crystalline dispersions, and in solutions of low or intermediate ionic strength (micro < 0.4) they can form the optically inactive one. The "molecular crowding" affects both the efficiency of binding of dendrimer molecules of 4th generation to DNA, and the mode of spatial packing of (DNA-dendrimer G4) complexes in particles of liquid-crystalline dispersion. The possible reasons capable of explaining the structural polymorphism of (DNA-dendrimer) liquid-crystalline dispersions are discussed.

[Three-dimensional organization of nucleoli of Didinium nasutum (Ciliata)].

A comparative study of nucleolar organization in the somatic nuclei of the ciliate Didinium nasutum was carried out using 3D reconstruction on the basis of serial ultrathin sections. Recently fed interphase ciliates, starved interphase ciliates and cysts were studied. The nucleoli at the interphase stage were shown to have a complex architecture: the fibrillar component forms a complicated network, the granular component is located inside of it. It was shown that nucleoli, which look like individual structures in single sections, are in fact parts of branched nucleolar networks. A 30-h starvation doesn't lead to disintegration of these networks. However in the starved cells the granular component becomes more dense and vacuolized. In the fed ciliates there are many holes in the fibrillar component, whereas in starved ones the fibrillar component is virtually devoid of them. These holes can be proposed to ensure the transport of newly synthesized rRNP. The nucleolar networks didn't occur in D. nasutum cysts. Nucleoli in the cysts look like small individual structures, mainly consisting of fibrogranular component.

[Complexes of gadolinium with linear and liquid-crystalline forms of DNA].

The binding of Gd3+ ions to linear double-stranded DNA molecules in water-salt solutions or in liquid-crystalline dispersions is accompanied by sharp changes in their optical and X-ray characteristics. Depending on the initial conditions of complex formation, the binding of Gd3+ ions either to DNA bases or phosphate groups occurs, which leads to changes in the properties of the liquid-crystalline dispersions. The packing of neighboring DNA molecules in particles of the liquid-crystalline dispersion of the complex DNA-Gd3+ depends strongly on the concentration of Gd3+ ions. This process is accompanied by a decrease in the amplitude of Bragg's reflection maximum. The unique properties of the developed material open the possibilities for its practical use.