Improved Measurement of Solar Neutrinos from the Carbon-Nitrogen-Oxygen Cycle by Borexino and Its Implications for the Standard Solar Model.

We present an improved measurement of the carbon-nitrogen-oxygen (CNO) solar neutrino interaction rate at Earth obtained with the complete Borexino Phase-III dataset. The measured rate, R_{CNO}=6.7_{-0.8}^{+2.0} counts/(day×100 tonnes), allows us to exclude the absence of the CNO signal with about 7σ C.L. The correspondent CNO neutrino flux is 6.6_{-0.9}^{+2.0}×10^{8} cm^{-2} s^{-1}, taking into account the neutrino flavor conversion. We use the new CNO measurement to evaluate the C and N abundances in the Sun with respect to the H abundance for the first time with solar neutrinos. Our result of N_{CN}=(5.78_{-1.00}^{+1.86})×10^{-4} displays a ∼2σ tension with the "low-metallicity" spectroscopic photospheric measurements. Furthermore, our result used together with the ^{7}Be and ^{8}B solar neutrino fluxes, also measured by Borexino, permits us to disfavor at 3.1σ C.L. the "low-metallicity" standard solar model B16-AGSS09met as an alternative to the "high-metallicity" standard solar model B16-GS98.

[Analysis of genetic diversity of Russian regional populations based on common STR markers used in DNA identification].

We conducted the first genetic analysis of a wide a range of rural Russian populations in European Russia with a panel of common DNA markers commonly used in criminalistics genetic identification. We examined a total of 647 samples from indigenous ethnic Russian populations in Arkhangelsk, Belgorod, Voronezh, Kursk, Rostov, Ryazan, and Orel regions. We employed a multiplex genotyping kit, COrDIS Plus, to genotype Short Tandem Repeat (STR) loci, which included the genetic marker panel officially recommended for DNA identification in the Russian Federation, the United States, and the European Union. In the course of our study, we created a database of allelic frequencies, examined the distribution of alleles and genotypes in seven rural Russian populations, and defined the genetic relationships between these populations. We found that, although multidimensional analysis indicated a difference between the Northern gene pool and the rest of the Russian European populations, a pairwise comparison using 19 STR markers among all populations did not reveal significant differences. This is in concordance with previous studies, which examined up to 12 STR markers of urban Russian populations. Therefore, the database of allelic frequencies created in this study can be applied for forensic examinations and DNA identification among the ethnic Russian population over European Russia. We also noted a decrease in the levels of heterozygosity in the northern Russian population compared to ethnic populations in southern and central Russia, which is consistent with trends identified previously using classical gene markers and analysis of mitochondrial DNA.

[An unusual case of investigation into the child's disputable descent complicated by manifestation of a rare genomic mutation (disomy)].

This investigation was carried out in the framework of a criminal case concerning substitution of a newborn infant. The subjects involved in the case were the child and its putative mother. Solution of the problem required typing two hypervariable mitochondrial DNA markers and 82 chromosomal markers. Moreover, we had to depart from the current norms according to which parentage can be excluded if two loci of the child contain alleles absent in the reputed parent. The present examination was complicated by the manifestation of a rare genomic mutation (unipaternal disomy) that necessitated extensive studies and taking non-trivial decisions. Details of this unusual case are highlighted and difficulties encountered in the course of investigation discussed to promote future analyses of chromosomal DNA mutations in parental gametes that hamper unambiguous interpretation of results of forensic examination.

[Combined use of molecular genetic technologies to identify the Russian citizens died during tsunami in Thailand].

Main stages, methodological aspects and practical results of molecular genetic research to identify the citizens of Russia died during tsunami in Thailand are considered.

[Strategy of multiplex analysis of STR-loci polymorphism of Y-chromosome on the basis of "minimal haplotype"].

A molecular-genetic analysis of Y chromosome is a convenient tool of paternal affinity determination. This method is now widely introduced in expert practice. Previous experience in typing of Y chromosome is outlined. Strategy of development and experience in operating a multiplex system for a simultaneous analysis of seven STR loci of Y chromosome is discussed.

Mitochondrial DNA sequence diversity in Russians.

The article presents the results of the first regular study of Russian populations by sequencing the control region of mitochondrial DNA (mtDNA). The sequenced region is the most variable on mtDNA molecule and is commonly used for population and evolutionary studies. Russians form one of the largest ethnic groups (more than 129 million). However, their genetic diversity had only been characterized with RFLP and biochemical markers, although there are already established mtDNA sequence databases for many ethnic groups of the world. We have obtained sequence data from 103 individuals living in three Russian regions: Kostroma, Kursk, and Rjazan. The sequenced fragment analyzed is 360 bp in length (positions from 16024 to 16383). Fifty nine nucleotide positions have been found polymorphic in Russians, among those were 57 transitions and two transversions. One individual is found having two insertions of two cytosines between positions 16184 and 16193. Among 64 different mitotypes identified in the study 52 were unique in these samples. The index of genetic diversity (Nei, 1987) for Russians is 0.96. This value is within the established range for European populations (0.93 to 0.98). Genetic distances calculated from our data show that Russians form a cluster with Germans, Bulgarians, Swedes, Estonians, and Volgo-Finns are more distant from Karelians and Finns, and much more differ from Turks and especially Mongolians.

Backbone dynamics of the channel-forming antibiotic zervamicin IIB studied by 15N NMR relaxation.

The backbone dynamics of the channel-forming peptide antibiotic zervamicin IIB (Zrv-IIB) in methanol were studied by 15N nuclear magnetic resonance relaxation measurements at 11.7, 14.1 and 18.8 T magnetic fields. The anisotropic overall rotation of the peptide was characterized based on 15N relaxation data and by hydrodynamic calculations. 'Model-free' analysis of the relaxation data showed that the peptide is fairly rigid on a sub-nanosecond time-scale. The residues from the polar side of Zrv-IIB helix are involved in micro-millisecond time-scale conformational exchange. The conformational exchange observed might indicate intramolecular processes or specific intermolecular interactions of potential relevance to Zrv-IIB ion channel formation.

Model-free approach beyond the borders of its applicability.

Model calculations presented in this article show that commonly used methodology of 15N relaxation data analysis completely fails in detecting nanosecond time scale motions if the major part of the molecule is involved in these motions. New criteria are introduced for the detection of such cases, based on the dependence of the apparent overall correlation time, derived from the T1/T2 ratio, on the spectrometer frequency. Correctly estimating the overall rotation correlation time tauR was shown to play the key role in model-free data analysis. It is found, however, that in cases of slow internal motions with characteristic times of more than 3-4 ns, the effective tauR provided by the T1/T2 ratio for individual amide nitrogens can be used for the characterization of the fast picosecond internal dynamics.

Sampling of protein dynamics in nanosecond time scale by 15N NMR relaxation and self-diffusion measurements.

This paper presents a procedure for detection of intermediate nanosecond internal dynamics in globular proteins. The procedure uses 1H-15N relaxation measurements at several spectrometer frequencies and hydrodynamic calculations based on experimental self-diffusion coefficients. New heteronuclear experiments, using pulse field gradients, are introduced for the measurement of translation diffusion coefficients of 15N labeled proteins. An advanced interpretation of recently published (Luginbühl et al., Biochemistry, 36, 7305-7312 (1997)) backbone amide 15N relaxation data, measured at two spectrometers (400 and 750 MHz for 1H) for N-terminal DNA-binding domain (1-63) of 434 repressor, is presented. Non-applicability of commonly used fast (picosecond) dynamics model (FD) was justified by (i) poor fit of relaxation data by the FD model-free spectral density function both for isotropic and anisotropic models of the overall molecular tumbling; (ii) specific dependence of the overall rotation correlation times calculated from T1/T2 ratio on the spectrometer frequency; (iii) mismatch of the ratio of longitudinal 15N relaxation times T1, measured at different spectrometer frequencies, in comparison with that anticipated for the FD model; (iv) significantly underestimated overall rotation correlation time provided by the FD model (5.50+/-0.15 and 5.80+/-0.15 ns for 750 and 400 MHz spectrometer frequency respectively) in comparison with correlation time obtained from hydrodynamics. On the other hand, all relaxation and hydrodynamics data are in good correspondence with the model of intermediate (nanoseconds) dynamics. Overall rotation correlation time of 7.5+/-0.7 ns was calculated from experimental translation self-diffusion rate using hydrodynamics formalism (Garcia de la Torre, J. and Bloomfield, V.A. Quart. Rev. Biophys., 14, 81-139 (1981)). The statistical analysis of 15N relaxation data along with the hydrodynamic consideration clearly revealed that most of the residues in 434(1-63) repressor are involved in the nanosecond internal dynamics characterized by the the mean order parameters of 0.59+/-0.06 and the correlation times of ca. 5 ns.

[Refinement of the spatial structure of the gramicidin A ion channel]. / Utochnenie prostranstvennoi struktury ionnogo kanala gramitsidina A.

The spatial structure of the gramicidin A (GA) transmembrane ion-channel was refined on the base of cross-peak volumes measured in NOESY spectra (mixing time tau m = 100 and 200 ms). The refinement methods included the comparison of experimental cross-peak volumes with those calculated for low-energy GA conformations, dynamic averaging of the low-energy conformation set and restrained energy minimization. Accuracy of the spatial structure determination was estimated by the penalty function Fr defined as a root mean square deviation of interproton distances corresponding to the calculated and experimental cross-peak volumes. As the initial conformation we used the right-handed pi 6,3 LD pi 6,3 LD helix established on the base of NMR data regardless of the cross-peak volumes. The conformation is in a good agreement with NOE cross-peak volumes (Fr 0.2 to 0.5 A depending on NOESY spectrum). For a number of NOEs formed by the side chain protons, distances errors were found as much as 0.5-2.0 A. Restrained energy minimization procedure had little further success. However some of these errors were eliminated by the change in torsional angle chi 2 of D-Leu12 and dynamic averaging of the Val7 side chain conformations. Apparently, majority of deviations of the calculated and experimental cross-peak volumes are due to the intramolecular mobility of GA and cannot be eliminated within the framework of rigid globule model. In summary the spatial structure of GA ion-channel can be thought as a set of low-energy conformations, differing by the side chain torsion angles chi 1 Val7 and chi 2 D-Leu4 and D-Leu10 and the orientation of the C-terminal ethanolamine group. Root mean square differences between the atomic coordinates of conformations are in the range of 0.3-0.8 A.

[1H-15N NMR signal assignment and secondary structure of bacteriorhodopsin (1-231) in solution]. / Otnesenie 1H-15N signalov i vtorichnaya struktura Des-(232-248) bacteriorodopsina v rastvore.

15N-Labeled de-(232-248)-bacteriorhodopsin [BR(1-231)] was solubilized in 1:1 chloroform-methanol solvent mixture that contained 1.0 M 2HCO2N2H4 and mimic membrane medium. Resonances in the 1H-15N heteronuclear multiple-quantum coherence (HMQC) spectrum of BR (1-231) were assigned using the data of two- and three-dimensional NMR experiments. Of 117 cross-peaks present in the 1H-15N HMQC spectrum, 98 were assigned to residues in 1-75 and 193-231 segments of the protein. Almost all cross-peaks that correspond to the 76-192 segment were absent in the HMQC spectrum (except for six cross-peaks from the side chains and 14 cross-peaks from the backbone). Deuterium exchange rates of amide protons and cross-peaks of nuclear Overhauser effect helped to localize helices A (residues 8-30), B (residues 40-65), and G (residues 198-226). The periodicity in the rates of deuterium exchange of NH protons of helices A, B, and G was explained by the compact arrangement of these helices in the protein globule. The broadening of signals from six residues in helix G, which, according to the electron cryomicroscopy model of bacteriorhodopsin, is in contact with the NMR-unobservable bundle of helices CDEF, indicates specific interactions of the helices in BR(1-231). These data suggest that BR(1-231) solubilized in an organic medium has a spatial structure similar to that in the electron cryomicroscopy model of BR.

[Content of components GABA metabolism in the brain of cats and rats]. / Soderzhanie komponentov metabolizma GAMK v golovnom mozge koshek i krys.

The activity of glutamate decarboxylase (L-glutamate carboxy-1-lyase; EC 4.1.1.15), GABA-transaminase (GABA-alpha-ketoglutarate aminotransferase, EC 2.6.1.19), content of gamma-aminobutyric, glutamic and aspartic acids were studied in different parts and subcellular particles of the cat and rat brain. It is shown that regional and subcellular distribution of the GABA metabolic components in the cat and rat brain are mainly similar, but quantitative indices are different.

[Possible differentiation of mitotypes in mixed biological subjects based on phylogenetic analysis of mitochondrial DNA]. / O vozmozhnosti differentsirovaniia mitotipov v smeshannykh biologicheskikh ob''ektakh na osnove filogeneticheskogo analiza mitokhondrial'noi DNK.

A possibility was investigated to use the phylogenetic analysis of mitochondrial (mt) DNA to differentiate between the mito-types in mixed subjects in forensic medical examinations. The suggested methodological approach is based on the use of electrophoregram and on the comparison of such data with the information about phylogenic individual (mt) DNA lines.

[Mitochondrial DNA typing--a new level for solving identification problems in forensic medical expert identification of unidentified remains of victims of terrorist acts in Moscow and the armed conflict in the Chechen Republic]. / Tipirovanie mitokhondrial'noi DNK--novyi uroven' resheniia identifikatsionnykh zadach pri sudebno-medintsinskoi ékspertize neopoznannykh ostankov zhertv terroristicheskikh aktov v Moskve i vooruzhennogo konflikta v Chechenskoi Respublike.

Two large-scale episodes described in this paper reflect the first in Russia use of molecular genetic matrilinear markers (analysis of polymorphism of sequences of amplified fragments of mitochondrial DNA hypervariable locuses) in solution of a complex identification problem: forensic medical identification of unidentified fragments of victims of explosions of houses in Moscow in September, 1999, and of soldiers dead in the war conflict in the Chechen Republic in 1994-1996. The results of this work and methodological experience gained in it essentially extend the potentialities of expert studies as regards forensic medical identification of victims of large scale disasters, terroristic acts, and war conflicts.

[Analysis of genetic diversity of the mitochondrial DNA in the forensic medical expert identification of individuals]. / Analiz geneticheskogo raznoobraziia mitikhondrial'noi DNK v aspekte sudebno-ékspertnoi identifikatsii lichnosti.

Spectra of haplotype frequencies were studied for locuses of hypervariable segments 1 and 2 (HVS1 and HVS2), separately for each, and for linked segment HVS1-HVS2. The obtained data were used to determine the values and to evaluate comparatively the discriminating characteristics of the corresponding individualizing systems based on the typing of mtDNA. The system of typing, based on HVS2 (mv = 0.098), was found to possess the least discriminating potential; while the highest information rate is ensured in the analysis of HVS1 (m omega = 0.02) and in the joint analysis of HVS1 and HVS2 (mw = 0.007). The frequency rates of the key haplogroups were estimated within a random sampling of Russian citizens. A random population sampling of Russian citizens was shown not to differ essentially from an ethnically homogeneous population sampling of Russians selected with regard for a genetic diversity and for a spectrum of mitochondrial lines. The results point at the most rational algorithm of examinations in a forensic expert's analysis of mtDNA. The studied sampling can trigger the development of a referential data base designed for conducting, in the Russian Federation, the forensic-medical expert's examinations based on the mtDNA typing.

The causality principle in the reconstruction of sparse NMR spectra.

Non-uniform sampling offers a dramatic increase in the power and efficiency of magnetic resonance techniques in chemistry, molecular structural biology, and other fields. Here we show that use of the causality property of an NMR signal is a general approach for major reduction of measuring time and quality improvement of the sparsely detected spectra.

Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition.

Highly resolved multi-dimensional NOE data are essential for rapid and accurate determination of spatial protein structures such as in structural genomics projects. Four-dimensional spectra contain almost no spectral overlap inherently present in lower dimensionality spectra and are highly amenable to application of automated routines for spectral resonance location and assignment. However, a high resolution 4D data set using conventional uniform sampling usually requires unacceptably long measurement time. Recently we have reported that the use of non-uniform sampling and multi-dimensional decomposition (MDD) can remedy this problem. Here we validate accuracy and robustness of the method, and demonstrate its usefulness for fully protonated protein samples. The method was applied to 11 kDa protein PA1123 from structural genomics pipeline. A systematic evaluation of spectral reconstructions obtained using 15-100% subsets of the complete reference 4D 1H-13C-13C-1H NOESY spectrum has been performed. With the experimental time saving of up to six times, the resolution and the sensitivity per unit time is shown to be similar to that of the fully recorded spectrum. For the 30% data subset we demonstrate that the intensities in the reconstructed and reference 4D spectra correspond with a correlation coefficient of 0.997 in the full range of spectral amplitudes. Intensities of the strong, middle and weak cross-peaks correlate with coefficients 0.9997, 0.9965, and 0.83. The method does not produce false peaks. 2% of weak peaks lost in the 30% reconstruction is in line with theoretically expected noise increase for the shorter measurement time. Together with good accuracy in the relative line-widths these translate to reliable distance constrains derived from sparsely sampled, high resolution 4D NOESY data.

MUNIN: a new approach to multi-dimensional NMR spectra interpretation.

A new method, MUNIN (Multi-dimensional NMR spectra interpretation), is introduced for the automated interpretation of three-dimensional NMR spectra. It is based on a mathematical concept referred to as three-way decomposition. An NMR spectrum is decomposed into a sum of components, with each component corresponding to one or a group of peaks. Each component is defined as the direct product of three one-dimensional shapes. A consequence is reduction in dimensionality of the spectral data used in further analysis. The decomposition may be applied to frequency-domain or time-domain data, or to a mixture of these. Features of MUNIN include good resolution in crowded regions and the absence of assumptions about line shapes. Uniform sampling of time-domain data, a prerequisite for discrete Fourier transform, is not required. This opens an avenue for the processing of NMR data that do not follow oscillating behaviour, e.g. from relaxation measurements. The application of MUNIN is illustrated for a 1H-15N-NOESY-HSQC, where each component is defined as the set of all NOE peaks formed by a given amide group. As a result, the extraction of structural information simply consists of one-dimensional peak picking of the shape along the NOE-axis obtained for each amide group.

[The treatment of neurogenic hyperreflexic bladder dysfunctions in girls with low-intensity laser radiation]. / Lechenie neirogennykh giperreflektornykh disfunktsii mochevogo puzyria u devochek nizkointensivnym lazernym izlucheniem.

120 girls were investigated for the efficacy of three methods of treatment: conventional, infrared laser radiation on the projection of the bladder plus He-Ne laser radiation on biologically active points (BAP), red He-Ne laser BAP radiation. All the patients suffered from neurogenic hyperreflexic dysfunctions of the bladder, 99.8% had the diagnosis of vegetovascular dystonia, 94.9% had sympathetic-tonic or mixed patterns. The combined laser exposure brought about the greatest response rate-90.0%.