[Influence of meteorological factors on the activity of the adult taiga tick (Ixodes persulcatus Sch., Ixodinae) in St. Petersburg and its environs].

The article deals with influence of meteorolical factors on the activity of the taiga tick Ixodes persulvatus Sch. in St. Petersburg and its environs. The results of correlation analysis of meteorological data (21 index) and data ticks collected in 1980-2012 allowed determining linear dependence between 11 meteorological indices an average amount of ticks. Factor analysis reduced dimentionality down to 3 indices: sum of temperatures higher than +5.0 °C, sum of precipitation higher than 5 mm per year, and Selyaninov hydrothermal coefficient. It was demonstrated that, at the background of the general tendency for the decrease of the average number of active ticks in the studied territories, correlation between the amount of ticks and meteorological indices can significantly vary as in the correlation density, so in the character and in dependence of microclimatic features of the collecting site. When variability of the mean abundance of ticks during years of investigation is low, the methods of collecting can significantly affect the results of the statistical analysis. This fact must be taken in consideration during prognosis of both dates of the beginning of epidemiological season and its intensity.

[Structural and functional chromatin organization of the SUP35 gene in Saccharomyces cerevisiae yeast]. / Strukturno-funktsional'naia organizatsiia khromatina gena SUP35 drozhzhei Saccharomyces cerevisiae.

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.

Hydrodynamic properties of nucleosomal fibers and chromatin higher-order structure.

We studied the comparative hydrodynamic properties of chromatins differing in transcriptional activity and in linker DNA length. Chromatins were prepared from the nuclei of pigeon brain cortical neurones, rat thymus and sea urchin sperm. The sizes of linker DNA are 20, 50 and 100 base pairs (b.p.), respectively. Oligonucleosomes of different chain length were isolated from micrococcal nuclease-digested nuclei and studied by the method of sedimentation velocity. Rheological behavior of nucleosome oligomers depends on the number of nucleosomes in the chain and on the ionic strength in the range between 5 and 85 mM was analyzed on the basis of a cylinder model using different hydrodynamic theories. It is shown that hydrodynamic properties of oligonucleosomes from all types of investigated chromatins at low ionic strength can be well described by the model of a three-dimensional zig-zag chain with a diameter of about 20 nm, the DNA packing ratio growing with the increase of linker DNA length. Increasing ionic strength induces condensation of the zig-zag-shaped chain of nucleosomes into a two-start double superhelix with densely packed nucleosomes. Linkers are arranged inside the superhelix, which is bent or folded into a loop, depending on its size.

Chromatin higher-order structure: two-start double superhelix formed by zig-zag shaped nucleosome chain with folded linker DNA.

Hydrodynamic properties of chromatins differing in linker DNA length and in transcriptional activity have been studied by the method of sedimentation velocity. Oligonucleosomes of different chain length were isolated from chromatins of pigeon brain cortical neurones, rat thymus and sea urchin sperm characterized by nucleosome DNA repeat length of 165, 198 and 248 base pairs respectively. The hydrodynamic behaviour of oligonucleosomes in the dependence on the number of nucleosomes in the chain and on the ionic strength has been analysed on the basis of cylinder model. The data obtained allows one to calculate the main structural parameters of the oligonucleosomal chain: its mass per unit length, the hydrodynamic diameter of the chain, the length of the chain per nucleosome and DNA packing ratio. It is shown that hydrodynamic behaviour of nucleosome oligomers from all types of chromatins investigated at low ionic strength can be well described by the model of three-dimensional zig-zag chain with similar diameter and length of the chain per nucleosome, DNA packing ratio growing with the increase of linker DNA length. It can be achieved by unfolding the short linker DNA in neurone chromatin and by coiling the long linker DNA of sea urchin sperm chromatin into a loop. With the increase of ionic strength zig-zag shaped nucleosomal chain is condensed into a two-start double superhelix with closely arranged nucleosomes and linker DNA loops packed inside the superhelix. The suggested model is in good agreement with available experimental data and overcomes a number of difficulties which arise for the solenoid model and other models of the 30-nm chromatin fibril.

[Structure of the chromatin with long linker DNA]. / Struktura khromatina s dlinnoi linkernoi DNK.

The method of velocity sedimentation have been used to investigate ionic-strength-induced compaction of sea urchin sperm chromatin characterized by extremely long linker DNA (100 b.p.). The dependence of sedimentation coefficients of oligonucleosomes on the number of nucleosomes in the chain have been studied in the range of ionic strength from 0.005 to 0.085. Analysis of these data indicates that such structural parameters of sea urchin sperm chromatin fibre as the diameter of the chain and the length of the chain per nucleosome are quite similar to those of chromatin with shorter linker DNA, but the DNA packing ratio is higher. The structure of sea urchin sperm oligonucleosomes agrees well with the model of three-dimensional zig-zag-shaped chain with linker DNA forming a loop. The possible role of alpha-helical regions of the C-terminal domain of sea urchin sperm histone H1 in the long linker DNA folding is discussed.

Structural differences between histone H1 molecules from sea urchin (Strongylocentrotus intermedius) sperm and calf thymus: hydrodynamic and c.d. studies.

Comparative sedimentation, diffusion and circular dichroism (c.d.) measurements have been performed on two histones H1 from sperm of the sea urchin Strongylocentrotus intermedius (H1S) and from calf thymus (H1T), at a high salt concentration of M NaCl. Both the Stokes radius and the frictional ratio derived from the hydrodynamic parameters were found to be somewhat smaller for H1S than the corresponding values for H1T. In view of the considerably higher molar mass of H1S compared with that of H1T, this result indicates that H+S in 2 M NaCl has a more compact conformation than H1T, probably due to a higher degree of secondary structure in the flanking domains of H1S. The c.d. measurements likewise show that H1S has a higher content of ordered structures than H1T. Model considerations indicate that the C-terminal tail of H1S is the main candidate for accommodation of these additional secondary structure regions.

[Structural transformations of oligonucleosomes from pigeon erythrocyte chromatin]. / Strukturnye prevrashcheniia oligonukleosom khromatina éritrotsitov golubia.

The methods of velocity sedimentation and circular dichroism have been used to investigate structural rearrangements of pigeon erythrocyte oligonucleosomes isolated after digestion with micrococcal nuclease (oligonucleosomes-M) or pancreatic DNase I (oligonucleosomes-D), in the wide range of ionic strength (mu from 0.005 to 0.5). The electrophoretic analysis of DNA isolated from the oligonucleosomes has revealed internal cuts in the DNA chain of oligonucleosomes-D. In spite of this fact the conformational parameters of DNA in both types of oligonucleosomes are practically indistinguishable, and their optical and hydrodynamic properties vary in a similar way with increasing ionic strength of the solution. The specificity of DNase I action results in the ability of oligonucleosomes-D to form homogeneous associates at mu = 0.065, which seems to be due to the existence of elongated intact ends of linker DNA in oligonucleosomes-D. It has been shown that the integrity of oligonucleosomes-D in a wide range of ionic strength is maintained by histones H1 and H5, because after their dissociation the sedimentation coefficient sharply decreases. The results obtained reveal the multifunctional role of lysine-rich histones and intact linker in the processes of compaction and association of oligonucleosomes.

[The structure of chromatin from the pigeon brain. II. Sedimentation analysis of oligonucleosome density]. / Struktura khromatina mozga golubia. II. Sedimentatsionnyi analiz kompaktizatsii oligonukleosom.

Compaction of pigeon brain and rat thymus chromatin differing in the length of the linker DNA has been studied by the method of velocity sedimentation. The dependence of sedimentation coefficients of oligonucleosomes on the number of nucleosomes in the chain in solution of different ionic strength (0.005-0.085) has been analyzed. The analyses of these dependences showed that the structure of oligonucleosomes of both cell types at low ionic conditions may be described by the model of a zig-zag-shaped nucleosomal chain. The process of compaction of the oligonucleosomes at higher ionic strength (0.045-0.085) proceeds similarly for brain and thymus chromatin. The formation of a superhelical structure is determined by the interaction of no less than 6 nucleosomes; the compactness of the structure is significantly increased when the number of nucleosomes in the chain exceeds 10. The ability of the brain oligonucleosomes to form a compact structure despite the short linker allow the suggestion that in brain short chromatin the DNA chain does not form two complete turns in the nucleosome. This provides necessary flexibility of brain chromatin.

Interaction of histone H1 from sea urchin sperm with superhelical and relaxed DNA.

Complexes of histone H1 from sea urchin sperm (H1S) and calf thymus (H1T) with superhelical DNA I and relaxed circular DNA II have been analyzed by analytical sedimentation. Similar to H1T, the highly basic and relatively arginine-rich histone H1S preferentially interacts with DNA I compared to DNA II under competition conditions. However, H1S induces a stronger aggregation of both forms of DNA than H1T. Below 0.05 M NaCl, the soluble complexes formed by both histones have similar properties, but aggregation proceeds in a different manner: H1S induces a stronger aggregation of DNA II as compared to DNA I, whereas H1T fails to aggregate DNA I. The results are explained on the basis of differences in amino acid sequence and structure of the two histones and related to the special chromatin condensing ability of histone H1S.

The role of histone H2B from sea urchin sperm in the association of reconstituted minichromosomes.

A comparative study of the condensation of reconstituted complexes of circular SV40 DNA with core histones from calf thymus and sea urchin sperm was performed using sedimentation and electron microscopic techniques. It is shown that in low ionic strength solutions both types of complexes are similar to native 'minichromosomes'. In the region from 0.08 to 0.16 M NaCl the complexes of SV40 DNA with thymus histones form small compact particles. By contrast, the compaction of the SV40 DNA complexes with sperm histones results in the formation of giant intermolecular associates. The results obtained may mean that histone H2B of sea urchin sperm participates in the formation of a higher order structure in sperm chromatin.

[Conformational peculiarity of H1 histones of calf thymus and sea urchin sperm]. / Konformatsionnye osobennosti gistonov H1 iz timusa telenka i spermiev morskogo ezha.

The secondary structure, sizes and form of H1 histone molecules of calf thymus (H1-T) and sea urchin sperm (H1-S) were studied by circular dichroism, sedimentation and diffusion. An increase in the ionic strength of solution is shown to result in the formation of alpha-helical parts in H1-T and both alpha-helical and beta-structural parts of H1-S. An analysis of amino acid composition of histones and their compaction under these conditions enables a conclusion that the resulting B-structure is antiparallel and intramolecular. The above properties of H1-S can result in a more dense compactness of the sea urchin sperm chromatin.

Ionic strength dependent structural changes of nucleosomes.

Rat thymus nucleosomes were studied as to their sedimentation behaviour and molecular weight Mr in NaCl and (NH)2SO4 solutions of different ionic strengths. The sedimentation coefficient s20,w decreases in two steps at ionic strengths of about 0.45-0.6 and of 1-1.2 and amounts to 11.0 S in salt-free buffer and to 5.5 S in 2 M NaCl-solution. This decrease in s20,w is paralleled by an analogous decrease in Mr. There is, however, an additional decline in Mr from 233 000 to 200 000 between the ionic strengths of 0.005 and 0.4. These changes are accompanied by conformational changes of nucleosomes as shown by varying molar frictional ratios f/f0. The decrease in Mr could be attributed to the successive release of histones as checked by electrophoretic analysis. Furthermore, nucleosomes in (NH4)SO4-solution proved to be more stable against increasing salt concentration than nucleosomes in NaCl-solution.

The role of histone H1 in compaction of nucleosomes. Sedimentation behaviour of oligonucleosomes in solution.

The dependence of sedimentation coefficients of oligonucleosomes on the number of nucleosomes in the chain in solutions of different ionic strength has been studied for oligonucleosomes both containing and lacking histone H1. The analysis of these dependencies has shown that oligonucleosomes with H1 at low concentration (I = 0.01 mol/l) may be described by the model of a short cylinder with an average length of the chain per nucleosome l0 = 11 nm where the neighbouring nucleosomes are in close contact. Oligonucleosomes without H1 at I = 0.01 mol/l can be described by the model of a worm-like chain with l0 = 27 nm. This suggests that when H1 is removed the linker DNA unfolds completely. In 0.15 M NaCl the oligonucleosome chain without H1 folds up to a compact configuration typical of oligonucleosomes with H1 at I = 0.01 mol/l. Thus, the linker DNA, with charges being screened, may fold due to interactions with core histones. Oligonucleosomes with H1 in 0.15 M NaCl form a supercoiled structure, whose stable conformation is accounted for by cooperative interactions of no less than five nucleosomes.

[Structure of the nucleosome chain. I. Role of histone H1 in oligonucleosome compaction]. / Struktura nukleosomnoi tsepi. I. Rol' gistona H1 v kompaktizatsii oligonukleosom.

The method of sedimentation velocity has been used to study the changes of the oligonucleosome compact state under the influence of various NaCl concentrations and to investigate the role of histone H1 in compaction of nucleosomes. Analysis of dependencies of the sedimentation coefficients on the number of nucleosomes in the chain has demonstrated that histone H1 stabilizes the compact structure of oligonucleosomes in the solution of low ionic strength (mu = 0.01). Removal of histone H1 leads to partial unfolding of the chains of oligonucleosomes. In 0.15 M NaCl solution H1-depleted oligonucleosomes are folded into the compact structure, which is similar to that of oligonucleosomes with histone H1 in solutions of low ionic strength. Further compaction of H1-containing oligonucleosomes in 0.15 M NaCl solution leads to formation of supercoiled structure, stabilized by cooperative interaction of at least five nucleosomes.

[Structure of the nucleosome chain. II. Hydrodynamic models of oligonucleosomes]. / Struktura nukleosomnoi tsepi. II. Gidrodinamicheskie modeli oligonukleosom.

Theoretical analysis of the dependencies of sedimentation coefficients of oligonucleosomes on the number of nucleosomes in the chain presented in the first part of the work has been carried out. The analysis has shown that the oligonucleosomes with H1 at mu 0.01 may be described by the model of a short cylinder with ML = 2600 dalton/A and d = 90 A. Oligonucleosomes without H1 at mu 0.01 can be described by the model of a wormlike chain with ML = 880 dalton/A and d = 70 A. In 0.15 M NaCl the oligonucleosome chain without H1 folds up to a compact configuration typical of oligonucleosomes with H1 at mu 0.01. Further compaction of oligonucleosomes with H1 in 0.15 M NaCl results in the formation of a supercoiled structure, whose stable conformation is accounted for by cooperative interactions of at least 5 nucleosomes.

[Investigation of DNA complexes with histones F3 and F3+F2a2]. / Issledovanie kompleksov DNK s gistonami F3 i F3+F2A2.

Characteristic viscosity, sedimentation constant and optical anisotropy were studied of the complexes formed between DNA and histone fractions F3 and F3+F2a2. The parameters mentioned continuously change with the increase of protein content within the complex. Analysis of experimental data shows that binding of a histone bads to a decrease of size and thermodynamic rigidity of the DNA molecule. On the basis of results obtained a model of F3 histone binding with DNA is suggested, amino acid sequence of this protein being taken into account. Comparison of behaviour of nucleohistones DNA+F3 and DNA+F1 studied previously testifies different way of binding of these histones to DNA.