Age-related changes in cationic compositions of human cranial base bone apatite measured by X-ray energy dispersive spectroscopy (EDS) coupled with scanning electron microscope (SEM).

One of the most common scientific methods to study the chemical composition of bone matter is energy-dispersive X-ray spectroscopy (EDS). However, interpretation of the data obtained can be quite complicated and require a thorough understanding of bone structure. This is especially important when evaluating subtle changes of chemical composition, including the age-related ones. The aim of current study is to create a method of processing the obtained data that can be utilized in clinical medicine and use it to evaluate the age evolution of bone chemical composition. To achieve this goal, an elemental composition of 62 samples of cadaver compact bone, taken from the skull base (age: Me = 57.5; 21/91(min/max); Q1 = 39.5, Q3 = 73.75), was studied with EDS. We used the original method to estimate the amount of Mg2+ cations. We detected and confirmed an increase of Mg2+ cation formula amount in the bone apatite, which characterizes age-related resorption rate. Analysis of cation estimated ratio in a normative bone hydroxylapatite showed an increase of Mg2+ amount (R = 0.43, p = 0.0005). Also, Ca weight fraction was shown to decrease with age (R = - 0.43, p = 0.0005), which in turn confirmed the age-dependent bone decalcification. In addition, electron probe microanalysis (EPMA) and X-ray diffraction analysis (XRD) were performed. EDS data confirmed the EPMA results (R = 0.76, p = 0.001). In conclusion, the proposed method can be used in forensic medicine and provide additional data to the known trends of decalcification and change of density and crystallinity of mineral bone matter.

[Epidemiological Situation With Main Risk Factors of Cardio-Vascular Diseases Among Young Adults in Russian Federation].

OBJECTIVE: to assess dynamics of cardiovascular risk factors (RF) among young adults in some regions of Russian Federation on the basis of arterial hypertension monitoring conducted in 2003-2010. Data on blood pressure (BP), weight, height, total cholesterol level as well.

[Prevalence of some modified cardiovascular risk factors among young students].

AIM: To estimate the prevalence of some modified cardiovascular risk factors (RFs) among the students of two Moscow higher education institutions to further test the technology of individual medical prevention counseling. SUBJECTS AND METHODS: A questionnaire survey was conducted among 1912 first-year students (boys and girls, mean age 17.7 years) from 2 Moscow higher education institutions to reveal physical activity levels, smoking status, alcohol abuse, and food addictions. RESULTS: Almost one third of the students (mainly girls) lead a sedentary lifestyle. The mean age at onset of smoking is 14.8 years. At the moment, the smoking students are 22% (28% of boys and 18% of girls). 12.2% of the respondents have moderate and high nicotine dependence. Most smokers demonstrate low motivation to give up smoking. The mean age for alcohol consumption is 15.8 years. 60% of the students use alcohol. There are no great differences in the drinking of alcoholic beverages between the girls and boys. 18% of the study sample students eat irregularly. Nearly 50% of the students add salt to cooked foods. 17% of the students eat too much sugar; more than 50% take sugar- and fat-laden foods. 54% of the students use vegetables and fruits insufficiently. CONCLUSION: Among all the modified cardiovascular RFs, alcohol use and irrational nutrition are most common among the students. Smoking and low physical activity are also relevant problems although these indicators among the students of Moscow are lower than among those in other regions of the Russian Federation. The found patterns call for the increased attention of the administrations of higher education institutions.

Structure and luminescence properties of EuF3 and SrF2:Eu nanoparticles after microwave plasma annealing in "methane-hydrogen".

Recently, progress has been made in fabricating diamond-based scintillators with integrated rare-earth luminescent particles. These luminescent particles are integrated into the bulk of diamond during their synthesis by chemical vapor deposition (CVD). However, the growth conditions include a chemically aggressive plasma environment and elevated temperatures, which results in the partial degradation of particles and a decrease in the intensity of their luminescence. Here, we investigate the effect of thermal annealing of luminescent EuF3 and SrF2:Eu powders in microwave plasma that simulates the growth conditions of polycrystalline diamond. It was found that silicon substrates act as efficient reducing agents that lead to the partial reduction of trivalent europium to divalent europium. When annealing occurs on a diamond substrate, the reduction processes proceed at a significantly slower rate. The observed luminescence spectra showed both Eu2+ and Eu3+ luminescence bands, which allows for a targeted tuning of the luminescence spectrum of europium in composites and can be used to fabricate detectors and visualizers of X-ray radiation using a visible signal from the desired combination of Eu2±/Eu3± ions. During plasma annealing in pure hydrogen at moderate temperatures (600 °C), an intensive hydrogenation of particles is observed. Such hydrogen plasma treatment of fluorides may be considered a promising route to fabricate hydrides of various metals.

Classification and monomer-by-monomer annotation dataset of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly.

In the latest hg38 human genome assembly, centromeric gaps has been filled in by alpha satellite (AS) reference models (RMs) which are statistical representations of homogeneous higher-order repeat (HOR) arrays that make up the bulk of the centromeric regions. We analyzed these models to compose an atlas of human AS HORs where each monomer of a HOR was represented by a number of its polymorphic sequence variants. We combined these data and HMMER sequence analysis platform to annotate AS HORs in the assembly. This led to discovery of a new type of low copy number highly divergent HORs which were not represented by RMs. These were included in the dataset. The annotation can be viewed as UCSC Genome Browser custom track (the HOR-track) and used together with our previous annotation of AS suprachromosomal families (SFs) in the same assembly, where each AS monomer can be viewed in its genomic context together with its classification into one of the 5 major SFs (the SF-track). To catalog the diversity of AS HORs in the human genome we introduced a new naming system. Each HOR received a name which showed its SF, chromosomal location and index number. Here we present the first installment of the HOR-track covering only the 17 HORs that belong to SF1 which forms live functional centromeres in chromosomes 1, 3, 5, 6, 7, 10, 12, 16 and 19 and also a large number of minor dead HOR domains, both homogeneous and divergent. Monomer-by-monomer HOR annotation used for this dataset as opposed to annotation of whole HOR repeats provides for mapping and quantification of various structural variants of AS HORs which can be used to collect data on inter-individual polymorphism of AS.

Analysis and development of the computer methods of nucleosome localization on DNA fragments with different AT-content.

Trinucleotide parameter sets published previously were used for the development of the predictive method for the determining the nucleosome positions along the DNA. The choice of the type of parameter sets used depends upon AT-content of the fragment. Some limitations are imposed on these predictions due to the presence of A(n), T(n) tracts (in our case n>5 or =5) within the 145 bp fragment leading to the displacement or even the prohibition for the corresponding site to be occupied by nucleosomes. The predicted nucleosome positioning site with the large potential may influence on the choice of the proximal nucleosome positions with the weaker bending potentials as is revealed by the comparison with the micrococcal nuclease digestion map. Trinucleotide methods may be considered as advantageous in the comparison with the dinucleotide ones.

Mathematical modeling of living cell metabolism using the method of steady-state stoichiometric flux balance.

This approach uses a set of algebraic linear equations for reaction rates (the method of steady-state stoichiometric flux balance) to model the purposeful metabolism of the living self-reproducing biochemical system (i.e. cell), which persists in steady-state growth. Linear programming (SIMPLEX method) is used to derive the solution for the model equations set (determining reaction rates which provide flux balance at given conditions). Here, we demonstrate the approach through the mathematical modeling of steady-state metabolism in Saccharomyces cerevisiae mitochondria.

Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly.

Centromeric alpha satellite (AS) is composed of highly identical higher-order DNA repetitive sequences, which make the standard assembly process impossible. Because of this the AS repeats were severely underrepresented in previous versions of the human genome assembly showing large centromeric gaps. The latest hg38 assembly (GCA_000001405.15) employed a novel method of approximate representation of these sequences using AS reference models to fill the gaps. Therefore, a lot more of assembled AS became available for genomic analysis. We used the PERCON program previously described by us to annotate various suprachromosomal families (SFs) of AS in the hg38 assembly and presented the results of our primary analysis as an easy-to-read track for the UCSC Genome Browser. The monomeric classes, characteristic of the five known SFs, were color-coded, which allowed quick visual assessment of AS composition in whole multi-megabase centromeres down to each individual AS monomer. Such comprehensive annotation of AS in the human genome assembly was performed for the first time. It showed the expected prevalence of the known major types of AS organization characteristic of the five established SFs. Also, some less common types of AS arrays were identified, such as pure R2 domains in SF5, apparent J/R and D/R mixes in SF1 and SF2, and several different SF4 higher-order repeats among reference models and in regular contigs. No new SFs or large unclassed AS domains were discovered. The dataset reveals the architecture of human centromeres and allows classification of AS sequence reads by alignment to the annotated hg38 assembly. The data were deposited here: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&hgt.customText=https://dl.dropboxusercontent.com/u/22994534/AS-tracks/human-GRC-hg38-M1SFs.bed.bz2.

Isolation of transposon TnA from plasmid RP4 carrying two copies of this element.

Employing heteroduplex and restriction analyses, two inverted copies of a 3.2.10(6) dalton transposable sequence, TnA, were found in RP4::TnA, a spontaneously arisen derivative of the plasmid RP4. Integration of the second copy of TnA causes loss of the conjugative properties of RP4. Both TnA sequences in RP4::TnA were localized and found to have opposite orientations. The DNA fragment corresponding to the individual transposon TnA was isolated after the endonuclease S1 digestion of RP4::TnA molecules annealed under conditions favoring intramolecular renaturation. The attempts to transform the cells of Escherichia coli QD5003, HB101[pCRI] and JC7623 with the isolated transposon were unsuccessful.

Comparison of smoking prevalence in school students sampled from the United States of America and the Union of Soviet Socialist Republics.

To assess the smoking prevalence among adolescents in the USA and the USSR, students in Moscow and Minneapolis were surveyed by common protocol and identically trained staff. Smoking habits were measured by a self-report questionnaire and an expired air sample of carbon monoxide (CO). Significant gender differences were found between the two national groups. Among girls in the USA, there was a significantly higher rate of weekly smoking as compared to girls in the USSR. Among boys in the USSR as compared to those in the USA, there was a significantly higher rate of ever smokers and daily smokers, but also of ex-smokers. These gender differences may reflect cultural differences in smoking patterns between the two countries. Cigarette smoking is clearly a public health problem in both countries with its onset in adolescence.

Statistical analysis of nucleotide runs in coding and noncoding DNA sequences.

A statistical analysis of the occurrence of particular nucleotide runs in DNA sequences of different species has been carried out. There are considerable differences of run distributions in DNA sequences of procaryotes, invertebrates and vertebrates. There is an abundance of short runs (1-2 nucleotides long) in the coding sequences and there is a deficiency of such runs in the noncoding regions. However, some interesting exceptions from this rule exist for the run distribution of adenine in procaryotes and for the arrangement of purine-pyrimidine runs in eucaryotes. The similarity in the distributions of such runs in the coding and noncoding regions may be due to some structural features of the DNA molecule as a whole. Runs of guanine (or cytosine) of three to six nucleotides occur predominantly in noncoding DNA regions in eucaryotes, especially in vertebrates.

Small circles of helical DNA obtained on the basis of transcriptional pause sites sequence.

The 21-base pair synthetic DNA duplexes with basic 'pause-motif site ('CATGC') were ligated head-to-tail to produce linear and circular multimers. This also was done from other closely related sequences. Electrophoretic mobilities of the linear multimers in polyacrylamide gels were determined under the standard and modified conditions. We revealed that small linear multimers (approximately 90 bp) were characterized by comparable value of gel retardation relative to the well known curved DNA, while longer multimers (130 to approximately 170 bp) had only slightly expressed mobility anomaly. Nevertheless these multimers containing nontruncated 'pause-motif were capable of cyclization, in particular, formation of unusually small circles while truncated ones were not. We conclude that basic 'pause-motif site increases the closure ability while the multimers based on truncated 'pause motif fail to curve into the small circles. We tend to explain this situation as a result of intrinsic bending as well as the influence of the thermal fluctuations of DNA, the latter most probably can be associated with 'pause motif'. We have estimated the equilibrial and maximal bend angles per 10.5 bp to be 12 degrees to approximately 16 degrees and 32 degrees accordingly under experimental conditions of our study.

Computer analysis of R-looped DNA from electron micrographs.

The algorithms of the analysis of R-looped DNA molecules from electron micrographs are presented. We propose a two-dimensional R-loop distribution map with abscissa and ordinate axes corresponding to the positions of the left and right ends of the loop respectively. A transcription analysis of the hybrid plasmid pSCV1, which comprises heterologous genes from SV40 and pBR322, based on this map illustrates the program application.

Cytochrome P450 pattern revision.

The pattern suggested for the structure-function superfamily of cytochromes P450 is composed by combining the conserved amino acid motifs. The sizes of P450 cytochromes were estimated according to their length. The empirical coefficients reflecting the peculiarities of the primary structure of these enzymes are calculated. We propose an approach for determining novel proteins sequences to the mentioned superfamily on the ground of the complex of these parameters. A number of the hypothetical proteins from the international databases is related to the cytochromes P450 by means of our pattern.

The enzyme activity allosteric regulation model based on the composite nature of catalytic and regulatory sites concept.

A new kinetic model of enzymatic catalysis is proposed, which postulates that enzyme solutions are equilibrium systems of oligomers differing in the number of subunits and in the mode of their assembly. It is suggested that the catalytic and regulatory sites of allosteric enzymes are of composite nature and appear as a result of subunits joining. Two possible joining modes are postulated at each oligomerization step. Catalytic site may arise on oligomer formed only by one of these modes. Effector acts by fastening together components of certain oligomeric form and increases the life time of this form. It leads to a shift of oligomer equilibrium and increases a proportion of effector-binding oligomers. Effectors-activators bind the oligomers carrying composite catalytic sites and effectors-inhibitors bind the oligomers, which do not carry active catalytic sites. Thus, catalytic activity control in such system is explained by effector-induced changes of a catalytic sites number, but not of a catalytic site activity caused by changes of subunit's tertiary structure. The postulates of the model do not contradict available experimental data and lead to a new type of general rate equation, which allows to describe and understand the specific kinetic behavior of allosteric enzymes as well as Michaelis type enzymes. All known rate equations of allosteric The equation was tested by modeling the kinetics of human erythrocyte phosphofructokinase. It enabled to reproduce quantitatively the 66 kinetic curves experimentally obtained for this enzyme under different reaction conditions.

Molecular mechanisms of protein-protein recognition: whether the surface placed charged residues determine the recognition process?

We studied the structure and composition of contact areas in 812 different kind dimeric protein-protein complexes from Brookhaven data base (PDB ) in order to reveal their pecularities with regard to protein-protein recognition. We have found, that the large portion of complexes (approximately 70%) have oppositely charged residues in the contact areas (interfaces) on the subunits surfaces, which form electrostatic contacts - R:E, R:D, K:E, K:D, H:E, H:D. These results are consistent with the current view that high rate complex formation may be driven by the long-range electrostatic interaction between charged AA residues of subunits surfaces. However, there are many complexes among the studied ones (approximately 30%), which have no electrostatic contacts at all in their contact area. Thus a question arises: what forces account for high complex formation rates (i.e. for the distant orienting of subunits before encounter) by forming complexes where the surface contact areas lack electrostatic contacts? We believe that the long-range orienting electrostatic interaction of subunits may account for all cases of efficient complex formation if one drops the traditional view that protein subunits interact mainly through their surfaces. We suggest that the distant orienting being due to the electrostatic interaction between the whole aggregates of partial electric charges of atoms of each complex subunits. Our preliminary model calculations (unpublished) made for ribonuclease dimer (does not have electrostatic contacts) conform this suggestion.

Role of the electrostatic interactions in pre-orientation of subunits in the formation of protein-protein complexes.

Theoretical estimation of contribution of the electrostatic interactions to pre-orientation of ribonuclease subunits in process of complex formation was carried out. The subunit was considered as a multipole consisting of partial charges of all atoms of the molecule. The object of investigation was a system of two subunits with their centers of gravity fixed at some distance in vacuum. It was proposed that each subunit independently could rotate freely around its fixed center of gravity. The relative orientation states of the subunits in such system were searched at which the system has electrostatic energy minima (equilibrium states). In first approximation the equilibrium states were found using especially designed approximate method for electrostatic interaction energy calculation, which permitted to calculate and compare the energies of the system in 24(5) (approximately 8 10(6)) states with different mutual orientation of subunits. The angular coordinates of the found equilibrium states were further specified by calculation with gradient sliding method. Angular coordinates of the equilibrium states and the shapes of energy surface cuts along each coordinate angle were calculated also for the intersubunits distances diminished down to 50 angstroms. The dispersions of the angular coordinates of equilibrium states caused by heat movement (at T=300 degrees) and their changes with shortening the distance between centers of gravity of subunits were estimated. Mutual orientation of subunits in the equilibrium states of the system under consideration was found to be similar to their mutual orientations in complex. Also it was found that relaxation time of the system, caused by electrostatic interaction of subunits, after removing the system from an equilibrium state, is much less in vacuum than the mean time between their Brownian collisions at room temperature. It follows from these results that in the case of ribonuclease in vacuum the electrostatic interactions of its subunits must be strong enough to realize the effective pre-orientation of subunits during their Brownian approach from distances of the order 100 angstroms. Preliminary consideration taking into account the effect of surrounding water molecules on the electrostatic interactions of ribonuclease subunits showed that weakening of the interaction must be much less than in the case when one uses in its calculation the macroscopic dielectric permeability value equal to 80. So the results obtained for vacuum seem to be true for water solution also. More strict theoretical analysis of this problem will be carried out in the following publication.

About factors providing the fast protein-protein recognition in processes of complex formation.

A package of programs for the examination of areas of subunit contacts (interface) in protein-protein (PP) complexes has been created and used for a detailed study of amino acid (AA) composition and interface structure in a large number of PP complexes from Brookhaven database (PBD). It appeared that in about 75% of the complexes, the AA composition of the subunit surface is not important. This suggests that, along with the surface AA composition, interactions between AA from the inner parts of protein globules may play a significant role in PP recognition. Such interactions between relatively distant AA residues can only be of electrostatic nature and contribute to the total electric field of the protein molecule. The configuration of the electric field itself appears to determine the PP recognition. The total electric field created by protein molecules can be calculated as a result of superimposition of the fields created by the protein multipole (i.e. by the totality of partial electric charges assigned to each atom of the molecule). We performed preliminary calculations for the distant electrostatic interaction of ribonuclease subunits in a vacuum. The results reveal that the effect of the electric fields of the protein multipole is strong enough to orient protein molecules prior to their Brown collision.

Large-scale periodicity of nucleosome positioning signal in pericentric regions of chromosomes (Drosophila melanogaster).

Nucleosome positioning signal (NPS) in heterochromatin is not uniform. We suggest the analysis of its heterogeneity by correlation with periodic function (analog of Furrier analysis). It was established the periodical repetition of the nucleosome clusters of large size in pericentric regions in a discontinuous manner. In the 3L pericentric region, it was revealed the domination of 78-85 kbp wavelength in the correlation coefficient profile and also strong presentation of 50 kbp signal. In further to centromere position, the 69 kbp value strongly dominates as well as the 50 kbp value in the closest proximity. In addition to the long wavelength signals, there are plenty of short wavelengths signals especially in the closest vicinity to centromere. In some positions throughout pericentric region of 2L chromosome, there are two sizes of repeated intermingled correlation signals (50, and 75 kbp) with dominating value of 75 kbp in proximity and 50 kbp distantly to centromere, the situation for 2R is analogous. Some genes with long introns support these quantitative characteristics of NPSs and to some extent their dominating character in each region. The characteristic repeat periods for 3L pericentric region coincide with the distances between heterochromatin epigenetic mark clusters and their distribution throughout this region for fly embryos, larvae, and some cell lines.