bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA Identification of Parasitic Copepods Salmincola (Copepoda, Siphonostomatoida, Lernaeopodidae): Variability and Rate of Evolution of the Mitochondrial Cytochrome c Oxidase Subunit I Gene
Authors: Shedko S. V. , Shedko M. B. , Miroshnichenko I. L. , Nemkova G. A.
Published: April 2024

The barcode fragment of the COI gene was sequenced in 91 specimens of five species of parasitic Salmincola copepods, sampled from salmonids mainly from the Russian Far East: S. californiensis (mykiss and masu salmon) and S. edwardsii (various species of chars, sockeye salmon from Lake Kronotskoe), S. carpionis (various species of chars), S. markewitschi (whitespotted char), S. stellata (Sakhalin taimen). A total of 41 haplotypes were found with a maximum level of differences of 0.183 nucleotide substitutions per position. The distance between species varied from 0.139 ± 0.014 in the S. markewitschi–S. carpionis pair to 0.179 ± 0.015 in the S. stellata–S. californiensis pair. The intraspecific nucleotide diversity of the COI gene fragment is much lower: for S. californiensis and S. edwardsii, inhabiting the gill cavity and fins of the host – 0.013 ± 0.003 and 0.015 ± 0.003, and for S. stellata, S. markewitschi, and S. carpionis, localized in the buccal cavity of the hosts – 0.002 ± 0.001, 0.004 ± 0.001, and 0.005 ± 0.001, respectively. A comparison of samples of three Salmincola copepod species from different regions of the Russian Far East revealed a significant (Fst = 0.28–0.42, P \( \ll \) 0.001) genetic subdivision. Three subclades of edwardsii-like copepods – S. edwardsii from the Russian Far East, S. edwardsii from the American brook char of eastern North America, and S. siscowet from the lake char of Michigan (COI sequences of copepods from the last two groups are taken from genetic databases) – differed from each other by an average of 9.3–10.9% nucleotide positions, which means the need for a taxonomic revision of S. edwardsii. According to the molecular dating carried out, the divergence of Salmincola lineages started in the Miocene and ended in the early Pliocene. The phylogenetic substitution rate was 0.0228 (95% interval: 0.0132–0.033) nucleotide substitutions/position/million years/lineage. The rate of nucleotide substitutions at the population level is 3.7 times higher – 0.0849 (0.0212–0.170). The high level of variability of the COI gene fragment makes this marker a useful tool both for developing the taxonomy and phylogeny of Salmincola and Lernaeopodidae copepods at the species and genus levels, and for analyzing the differentiation of their populations.
Determination of G/C Polymorphism at chr20:37352001 Position in Human Blood DNA Preparations by GlaI- and Bst2UI-PCR Analyses Methods
Authors: Akishev A. G. , Netesova N. A. , Abdurashitov M. A. , Degtyarev S. Kh.
Published: April 2024

Single nucleotide polymorphism (SNP) is a change of one nucleotide by another. This change often leads to an emergence (or disappearance) of a site recognized by a certain restriction endonuclease. As a result amplification of DNA fragment using primers surrounding SNP point (containing either N1 or N2 nucleotide) followed by hydrolysis of the amplicon with this restriction enzyme will be different for three possible variants in a diploid genome (genotypes N1/N1, N1/N2 and N2/N2). This method of restriction fragments length polymorphism (RFLP) is widely used in the genetic studies. Earlier we have developed GlaI- and FatI-PCR analyses methods which allowed to carry out real-time PCR and showed it applicability for SNP determination. In the current work a new way to determine the single nucleotide polymorphism G/C by the Bst2UI-PCR analysis is proposed. GlaI- and Bst2UI-PCR analyses have been used to determine the frequency of G/C polymorphism variants at the chr20:37352001 position (according to GRCH38.p14 genomic assembly) in the blood DNA samples of 161 donors. The study included: 1) the isolation of leukocyte DNA from blood cells; 2) GlaI- and Bst2UI-PCR analyses of the DNA fragment chr20:37351957-37352083, 3) determination of cytosine and guanine at the chr20:37352001 position in the analyzed DNA preparations, and 4) comparative analysis of the obtained results. It has been shown that 68 donors (42.2%) have a heterozygous set of G/C at the chr20:37352001 position, 89 donors (55.3%) are homozygous by G, and 4 donors (2.5%) are homozygous by C. Thus, taking into account that blood cells have a diploid set of chromosomes, G to C replacement occurs in 76 out of 322 analyzed cases (23.6%). At the same time, from the results obtained it follows that the cytosine residue complementary to G at the chr20:37352001 position exists in methylated form (5-methylcytosine) in most of the DNA molecules, both in homo- and heterozygotes. The proposed method of Bst2UI-PCR analyses extends the possibilites of SNP determination using real-time PCR.
Study of Genetic Diversity and Population Structure of the Osetin Breed in Comparison with Other Coarse Wool Fat-Tailed Sheep Breeds Based on SNP Genotyping Data
Authors: Deniskova T. E. , Dotsev A. V. , Selionova M. I. , Zinovieva N. A.
Published: April 2024

For the first time, an analysis of the genetic diversity of the Osetin sheep breed was performed using genome-wide SNP profiles in a comparison with other Russian coarse wool breeds. We established that the Osetin breed has high genetic and allelic diversity indicators. For the first time, the recent and historical population effective sizes of the Osetin breed were calculated. Close genetic relationships between the Osetin and Karachaev sheep breeds were shown, that is confirmed by the low value of differentiation (Fst = 0.009) and the formation of a joint cluster at the Neighbor Net graph. The similarity of the population structure of the Osetin and Karachaev breeds was revealed as well.
Molecular Landscape of Oral Cancer in Young Adults
Authors: Prostakishina E. A. , Dampilova T. D. , Kononova L. A. , Iamshchikov P. S. , Patysheva M. R. , Kolegova E. S. , Choinzonov E. L. , Denisov E. V.
Published: April 2024

Oral cancer (OC) is the most common cancer of the head and neck. Tongue cancer (TC) is the most frequently diagnosed form of OC and is characterized by a high aggressiveness and progression. OC and TC are considered diseases of the elderly, but the incidence among young patients (under 45 years) is increasing every year. The etiological factors and pathogenetic mechanisms of early-onset OC and TC remain unclear. In the present study, based on The Cancer Genome Atlas database, we analyzed the mutational profile, methylome, transcriptome, proteome, and microbiome of OC and TC in young adults (n = 127) compared with older patients. Early-onset OC and TC demonstrated a decrease in the mutation burden, activation of Rap1, PI3K-Akt, MAPK, cGMP-PKG signaling pathways and signaling of Fc-gamma R-mediated phagocytosis, and a specific microbiome profile. In contrast to OC, TC was characterized by activation of such signaling pathways as JAK-STAT, immune response to infectious and parasitic diseases, and PD-L1/PD-1-mediated immunosuppression and inhibition of phagocytosis signaling. The obtained results indicate that early-onset OC demonstrates molecular features different from those in elderly patients, while TC differs from OC in molecular profile and should probably be considered a separate clinical form.
Distribution and Allele Strength of Hybrid Necrosis Genes in the Genotypes of Canadian Cultivars of Spring Bread Wheat (Triticum aestivum L.)
Authors: Pukhalskiy V. A. , Rubets V. S. , Bilinskaya E. N. , Kudryavtsev A. M.
Published: April 2024

The occurrence of two types of cultivars of spring bread wheat of Canada that differ in their necrotic genotypes was shown. The cultivars of one type had the ne1ne1Ne2Ne2 genotype, and the cultivars of the second type had the ne1ne1ne2ne2 genotype. The Ne1Ne1ne2ne2 genotype was not found. The Ne2 genes were represented by medium strength, ms, and strong alleles, s. By pedigree analysis, the donors of the Ne2 gene were identified.
Changes in Lifespan as an Integral Response to the Organism’s Immune Status and Mobile Elements Activity
Authors: Trostnikov M. V. , Malyshev D. R. , Pasyukova E. G.
Published: April 2024

One of the key goals in studying the molecular and genetic basis of many pathologies is to find triggers, which could positively influence the incidence of age-dependent diseases and the rate of aging in general. A possible cause of age-dependent degradation of the organism functions inducing aging is immunosenescence. It is known that the increased activity of mobile elements observed with age may not only affect the level of genome stability, but also play a crucial role in the development of immune response. At the same time, the pivotal role of the nervous system in controlling lifespan has long been proven, and recently it has been shown that components of the machinery that regulate mobile element activity do function in the nervous system, and their functioning affects the development of neurodegenerative diseases. This mini-review presents evidence for complex aging regulation by the nervous and immune systems, involving systems that control mobile element activity and proposes a hypothetical scheme for their joint impact on lifespan.
Assessing the Association of the Degree of DNA Methylation and the Frequency of Chromosomal Aberrations in Human Lymphocytes in a Single Irradiation of Blood in vitro
Authors: Tsymbal O. S. , Isubakova D. S. , Bronikovskaya E. V. , Nikolaeva A. F. , Sigin V. O. , Kalinkin A. I. , Startseva Zh. А. , Litviakov N. V. , Milto I. V. , Takhauov R. M.
Published: April 2024

The most sensitive biomolecule under radiation exposure is DNA, whose damage manifests itself in the form of chromosomal aberrations (CA). The processes of DNA methylation, which are involved in the regulation of gene expression, replication, DNA repair, etc., are also affected by gamma radiation. The aim of the study was to evaluate the relationship between the degree of DNA methylation and the frequency of CA after acute in vitro irradiation of human blood lymphocytes with gamma radiation. The study involved 10 conditionally healthy workers of the Siberian Chemical Combine, in whose blood lymphocytes the degree of methylation of CpG-dinucleotides (wide-genome bisulfite sequencing, XmaI-Reduced representation bisulfite sequencing – XmaI-RRBS) and the frequency of CA (cytogenetic study) after acute in vitro blood irradiation with doses of 0 and 1.5 Gy were evaluated. After acute exposure to gamma radiation in lymphocytes, the frequency of aberrant cells, dicentric chromosomes, chromatid and chromosomal fragments increased. Correlation analysis of the status of CpG-dinucleotide methylation and the frequency of CA revealed changes in the degree of methylation of 97 genes, which strongly correlated positively (56 genes) or negatively (41 genes) with an increased frequency of CA. A primary genome-wide screening of genes whose methylation is correlates with a high frequency of CA was carried out. Many of the identified genes are promising as potential markers of radiation exposure and to study the mechanisms of formation of radiosensitivity of the body and radioresistance of tumors during radiation therapy.
Distribution Peculiarities of Y-Chromosome Haplogroups in the Population of St. Petersburg in Connection with the Problem of Creation Reference Data Bases
Authors: Udina I. G. , Gracheva A. S. , Borinskaya S. A. , Kurbatova O. L.
Published: April 2024

In the sample of male residents of St. Petersburg, Y-chromosome haplogroups were determined by genotyping 18 STR Y-chromosome (DYS389I, DYS389II, DYS390, DYS19, DYS385A, DYS385B, DYS456, DYS437, DYS438, DYS447, DYS448, DYS449, DYS391, DYS392, DYS393, DYS439, DYS635 and DYS576) and data on genetic demography were collected by means of a questionnaire. The distribution of Y-chromosome haplogroups in St. Petersburg residents generally corresponds to the published data on Russian gene pool, with the most frequent haplogroups R1a, R1b, E1b1b1, N, T, I1, I2, J1 and J2, and with the predominance of haplogroup R1a. The presence of “southern by origin” haplogroups (C3, G2a, G2c, J1, J2, L, O2, O3, Q, R2 and T) entering the megalopolis with a flow of migrants, with a total frequency of 16% (in Moscow – 18.1%) was noted. A comparative analysis of the frequency distributions of Y-chromosome haplogroups in residents of St. Petersburg and Moscow revealed statistically significant differences in the frequency of haplogroup E1b1b1, and differences in the ratio of I1 and I2, determined by geographic position. Based on the survey data, a sample of Russian men who had no ancestors of another ethnicity in the male line in the two previous generations was formed. Significant differences in the frequency of “southern-origin” haplogroups were established between the initial sample of residents of St. Petersburg (16%) and the sample of men with Russian ancestors in two previous generations (4.1%). The obtained result confirms the spectrum of haplogroups of “southern origin” as penetrating into the gene pool of the population of a megalopolis with migrant flows and indicates the need for genetic and demographic questionnaires when forming reference databases for a megalopolis, as well as for their timely updating due to changes in the gene pool under the influence of migration.
Regulation of Uni-Strand and Dual-Strand piRNA Clusters in Germ and Somatic Tissues in Drosophila melanogaster under Control of rhino
Authors: Milyaeva P. A. , Lavrenov A. R. , Kuzmin I. V. , Kim A. I. , Nefedova L. N.
Published: April 2024

Drosophila melanogaster is a common genetic object for research of RNA-interference pathways and mobile elements regulation. Nowadays taking a part in control of retrotransposon expression the system of piRNA-interfecence well studied in ovary tissues. It is strongly believed that D. melanogaster piRNA-interference is used for retrotransposon suppression only in gonads, and two distinct pathways of piRNA biogenesis exist. Both mechanisms use transcripts of piRNA-clusters (accumulations of truncated and defect mobile elements copies): from unstrand clusters in the first case and from dualstrand clusters in the second, transcribed with one or both DNA chains correspondingly. It is well-known that proper dualstrand clusters function depends on the gene rhino, while unistrand clusters are transcribed rhino-independent and transcripts are spliced. In this paper we show that rhino participates in unistrand flamenco transcripts splicing and the piRNA-interference significance for regulation of several retrotransposons not only in gonads, but in other organs.
Weak Population Genetic Structure of the Eurasian Crane Grus grus L.
Authors: Mudrik E. A. , Markin Yu. M. , Postelnykh K. A. , Kondrakova K. D. , Kashentseva T. А. , Shatokhina A. V. , Kazimirov P. A. , Ilyashenko V. Yu. , Ilyashenko E. I. , Politov D. V.
Published: April 2024

The article presents an extended (as compared with our previous studies) analysis of the population genetic structure of a migratory wide-range bird species with a high abundance, the Eurasian Crane Grus grus L. Using seven highly polymorphic microsatellite loci, high and very similar values of genetic diversity parameters were obtained in the samples of both the western (G. g. grus) and eastern (G. g. lilfordi) subspecies. Coefficients of genetic differentiation between these subspecies (FST = 0.008, GST = 0.002) were also found to be low. According to AMOVA, 99% of genetic variation of G. grus is attributed to individual levels. Using the Bayesian clustering algorithm implemented in STRUCTURE software, no clear population-genetic structuring of the species was revealed. However, visualization of spatial patterns of genetic variability in Geneland showed the presence of a cluster of “pure” subspecies G. g. grus and G. g. lilfordi surrounding a cluster of individuals from the zone of intergradation of these subspecies. This result, along with the observed very low FST values, may indicate subtle genetic differences between cranes from the studied area, possibly having a mutational nature. The lower allelic richness and lack of private alleles in the eastern subspecies suggest that G. g. lilfordi is relatively evolutionary young and suggest its recent origin from some eastern marginal populations of the nominative western subspecies.
Polymorphism of Core and Symbiotically Specialized Genes in the Polytypic Species of Nodule Bacteria
Authors: Provorov N. A. , Kimeklis A. K. , Karasev E. S. , Khosid S. , Onishchuk O. P. , Kurchak O. N. , Andronov E. E.
Published: April 2024

The polytypic species of nodule bacteria Rhizobium leguminosarum (includes biovars viciae and trifolii) and Neorhizobium galegae (biovars orientalis and officinalis) differ in the nucleotide polymorphism of housekeeping genes (hkg) and of symbiotically specialized genes (sym) that control the formation of N2-fixing nodules in leguminous plants. In R. leguminosarum, p-distance values for sym genes are higher than for hkg genes in strains from the same and from different biovars. In N. galegae, differences between biovars in sym genes are higher than in hkg genes while within biovars, polymorphism in sym genes is lower than in hkg genes. Coefficients of biovar differentiation for both groups of genes are higher in N. galegae than in R. leguminosarum, possibly reflecting the spatial isolation of N. galegae biovars. In these species of rhizobia, the phylogenetic congruence of sym and hkg genes is more pronounced in N. galegae than in R. leguminosarum. This difference indicates an active transfer of sym genes in R. leguminosarum populations possibly representing an important factor of the deep diversification for symbiotic traits in this rhizobia species.
Thermodynamic Properties of Pectolite
Authors: Ogorodova L. P. , Gritsenko Yu. D. , Vigasina M. F. , Ksenofontov D. A. , Melchakova L. V.
Published: April 2024

Pectolite H1.00Na0.96Ca2.00Mn2+0.02Si3.00O9 from nepheline−feldspathic veins in the Kovdor massif, Kola Peninsula, Russia, was studied by X-ray diffraction (XRD), IR and Raman spectrometry, microprobe analysis (EPMA), and thermal analysis. The enthalpy of formation of pectolite HNaCa2Si3O9.from elements ∆fH° (298.15 K) = –4651.0 ± 4.3 kJ/mol was determined by melt solution calorimetry on a Setaram Tian–Calvet (France) microcalorimeter. The enthalpy of formation of serandite HNaMn2Si3O9, the manganese end member of the pectolite–serandite isomorphic series, was determined to be ΔH(298.15 K) = −4052.6 ± 4.4 kJ/mol. The absolute entropies and Gibbs energies of pectolite and serandite were calculated.
Geochemical Significance of Bicyclic Sesquiterpanes in Hydrothermal Oil of the Uzon Volcano Caldera (Kamchatka)
Authors: Konopleva I. V. , Sevastianov V. S.
Published: April 2024

The composition and relative content of C14-C16 bicyclic sesquiterpanes in oil seeps from thermal springs of the Uzon Caldera have been studied by GC-MS technique. It is shown that C16 homodrimanes prevail in oil composition, C15 drimane content is insignificant, and C14 nordrimanes are present in trace amounts. Homodrimane with biological configuration 8α(H) was detected. Bicyclic sesquiterpanes of Uzon oil are probably its derivatives. It has been revealed that the relative content of C15 drimanes increases with the oil maturity. A sesquiterpane maturity index, which has not been used previously in organic geochemistry, is proposed.
Peculiarities of CH4 and CO2 Distribution in Sediments of the Arctic Seas
Authors: Sevastyanov V. S. , Fedulova V. Yu. , Kuznetsova O. V. , Naimushin S. G. , Dushenko N. V. , Fedulov V. S. , Krivenko A. P. , Malova A. I. , Tkachenko E. A.
Published: April 2024

The distribution of the concentrations of CH4 and CO2 and other gases in the sediments of the Kara, Laptev and East Siberian seas was studied. A correlation was found between CH4 and CO2 in most sediment cores. The correlation coefficient R for the sediments of the Kara Sea ranges from 0.58 to 0.97 and does not depend on the gas distribution with depth. Methanogenesis in marine sediments is presumably associated with sulfate reduction, and hydrogenotrophic methanogenesis leads to an increase in CH4 concentration against the background of high CO2 concentration. The high concentration of dimethyl sulfide in the sediments indicates the simultaneous formation of CH4 and CO2 through methylotrophic methanogenesis with the participation of CH3SCH3. In the upper layers of the sediment, opposite trends in the CH4 and CO2 distribution can be observed. The fact that the correlation coefficients between CH4 and CO2 gases in the sediments of the Laptev Sea acquire both negative and positive values is probably related to the fact that gas formation processes in the upper layers of the sediment captured by short columns differ from those of deep layers.
Applicability Limits of the Maturity Concept in Organic Geochemistry
Authors: Smirnov M. B. , Fadeeva N. P. , Vanyukova N. A.
Published: April 2024

To find out how various maturity criteria reflect how much OM as a whole approaches the state of chemical equilibrium, correlation analysis of relationships between 27 composition parameters was carried out. The OM was obtained from carbonate, siliceous–carbonate, carbonate–siliceous, and siliceous rocks from the northern and central regions of the Volga–Urals area (more than 100 samples). The data were processed using the apparatus of nonparametric statistics. We analyzed interrelations only between maturity indicators that are based on the same type of reactions (for example, reactions breaking C–C bonds). It has been established that none of the 85 correlation coefficients corresponds to the values characteristic of the functional dependence. The largest absolute value is 0.87. Therefore, maturity can be a factor determining the value only of one of all the parameters. For the rest, two options are possible. First, even for reactions of the same type, it is impossible to judge whether chemical equilibrium is generally approached. Second, the values of almost all the parameters are affected not only by reactions of approaching equilibrium but also by several other comparable and unknown factors. It is shown that, if the difference between the samples is up to five-fold values of any of the parameters, it is impossible to determine whether the OM of one of the samples is more mature than in any other. Thus, the concept of maturity is applicable at best only to roughly subdivide OM samples, with an increment in any parameter corresponding to at least a ten-fold change in it. For a detailed description, the term maturity can be used only with specifying the parameter by which it is determined (for example, maturity based on the Ts/Tm ratio). In this case, several such indicators based on reactions of different type should be used.
Assessment of the Zn, Cu, Ni, and Co Mobility in Soils of the Valday National Park
Authors: Baranov D. Yu.
Published: April 2024

The article considers the distribution of mobile forms and bulk concentrations of Zn, Cu, Ni, Co in the genetic horizons of the studied soils at the studied area in the central part of the Valday Upland. The contents of easily soluble, exchangeable, and sum of potentially mobile forms of elements were determined by extraction method. It was found that in all genetic soil horizons, the bulk Zn content and the concentration of its mobile forms are higher than those of other elements, but Cu demonstrates the most intense migration. The predominant form of Cu migration is complexes with organic compounds. According to the calculated data of the extraction criterion (EC), the studied soils are background. The availability of Zn, Cu, and Co in the soils was estimated, which characterizes the potential reserves of elements as plant nutrients.
Assessment of Hydrocarbon Potential Conversion in Source Rocks in the Southwestern Flank of the Korotaikha Depression, Timan–Pechora Basin
Authors: Galushkin Yu. I. , Kotik I. S.
Published: April 2024

The 1-D burial and thermal history of the Korotaikha depression in the Timan–Pechora basin was numerically simulated for the sedimentary sequences of three wells: Korotaikhinskaya 1, Labogeyskaya 15, and Khavdeiskaya 1. This made it possible to numerically assess the conversion history of the hydrocarbon (HC) potential of source rocks in the southwestern flank of the Korotaikha depression in the northeastern Timan−Pechora basin. The modern modified kinetic spectrum of vitrinite maturation was used in calculations of the vitrinite reflectance to clarify the thermal history of the sedimentary cover of the study area. The occurrence of episodes of hydrothermal activity follows from comparison of the calculated and measured values of the vitrinite reflectance and explains the jumps in the maturity of organic matter at the boundaries of the unconformity of Quaternary and Triassic sediments, as well as the Permian and Carboniferous sediments. The simulations suggest a high conversion of the initial HC potential of the source rocks of the Silurian and Domanic horizons, Tournaisian, and Visean ages in the Korotaikhinskaya and Labogeiskaya areas and moderate generation in the Havdeyskaya area. The simulation shows that the high grades of the catagenesis (MC5 and higher) of the main source rocks and the significant role of secondary cracking of liquid HC fractions in the central part of the Korotaikha depression (wells Korotaikhinskaya 1 and Labogeyskaya 15) suggest that the possible HC accumulations should contain only gas. Accumulations in the southern part of the depression (Khavdeiskaya area), where secondary cracking was minimal and source rocks occur within the oil window, should contain both oil and gas (due to Permian rocks with terrigenous organic matter).
Physicogeochemical Mechanisms of the Genesis of Matryoshka-Type Diamonds on the Basis of the Mantle-Carbonatite Theory
Authors: Litvin Yu. A.
Published: April 2024

A physicochemical analysis of the genesis of a unique Matryoshka-type diamond from the Nyurbinskaya kimberlite pipe of the Nakyn kimberlite field, Yakutia, Russia, was performed. The specimen consists of a host diamond with a cavity containing a loose diamond inclusion; two through holes with a width of 0.1–0.4 mm emerge from the cavity. The analysis is based on the mantle-carbonatite theory of the genesis of diamonds and associated phases developed on the basis of consistent results of a physicochemical experiment and an analytical study of paragenetic inclusions in natural diamonds from kimberlite deposits. The published data of crystal morphological and physical studies of the Matryoshka diamond were used as well. As a result, the physicogeochemical mechanisms of nucleation and crystallization of the host diamond with a cavity and diamond inclusion under the conditions of mass genesis of diamonds in completely miscible carbonate–eclogite–carbon melts of the upper-mantle diamond-forming chamber are substantiated. The initially closed cavity was filled with a diamond-forming carbonate–silicate melt with dissolved carbon. In addition, an analysis of the conditions of etching and dissolution of the host diamond and diamond inclusion during the kimberlite transport of diamond-bearing material from the mantle chamber to the depths of the Earth’s crust was performed. The reasons for the explosive formation of cone-shaped through holes in the main diamond, which was accompanied by the ejection of the diamond-forming medium and the filling of the cavity with (С–О–Н)-fluid-containing kimberlite melt, are considered. The final episodes of partial dissolution of diamonds from the Matryoshka sample by kimberlite and assimilated melts continued during the formation of a cumulative chamber in the Earth’s crust and its solidification with the release of a highly compressed C–O–H fluid. “Fluid drilling” of the top of the cumulative chamber stimulated the explosive formation of the Nyurbinskaya pipe and its filling with kimberlite and assimilated diamondiferous matter. With prolonged compaction of this substance, the Matryoshka diamond was subjected to atmospheric and hydrothermal factors, as is evidenced by fine-grained sedimentary barite, a mineral of barium sulphate, found in the through holes of the host diamond.
Environment-Forming Effect of Bubble Gas Emissions in the Golubaya Bay, Black Sea: Oxygen Regime and Bacterial Mats
Authors: Malakhova T. V. , Murashova A. I. , Ivanova I. N. , Budnikov A. A. , Malakhova L. V. , Krasnova E. A. , Rylkova O. A. , Pimenov N. V.
Published: April 2024

Gas seep and fluid flows from the seabed are an environment-forming factor of the aquatic environment, mainly due to their influence on the dissolved gases in the water, including dissolved oxygen. During the summer seasons from 2019 to 2021 in the area of shallow water gas emission site off the southern coast of the Heracles Peninsula, series of vertical probing profiles were carried out to determine hydrological parameters of the water: dissolved oxygen concentration (O2), temperature (T), salinity (S), and flow velocity (U). The study area is an underwater ledge with faults in the form of three canyons composed of dense limestones, two of which contained bubble gas emissions. Significant variability in O2 was identified in canyons where gas emissions are observed: from 1 to 80% saturation in the bottom layer, in contrast to normoxia at the background sites. Hypoxia was observed in the bottom layer above the emission sites in the absence of turbulence at temperature stratification. The values S decreased with depth, and the maximum difference reached 0.4‰. The bubble gas was dominated by methane (68.5–75.5%), and the carbon isotope composition of the bubble methane gas varied from –67.9 to –59.8‰ VPDB in 2019 and 2020, respectively. This generally indicates that the CH4 is of predominantly microbial genesis, was formed under different conditions, and matured in various periods of research during the monitoring period. Bacterial mats (mostly sulfur-oxidizing bacteria) were found in the areas of gas emissions.
Crystallogenetic Causes of the Unique Shape of the Matryoshka Diamond: The Effect of Capturing a Diamond Inclusion of Twin Diamond Crystals
Authors: Pavlushin A. D. , Konogorova D. V.
Published: April 2024

The unusual shape of the Matryoshka diamond, which is a diamond crystal with a cavity containing a diamond crystal freely moving in it, continues to attract keen interest of many researchers in the context of its seemingly paradoxical origin for a mantle mineral. The discovery sparked lively discussions and multiple attempts to explain the nature of the unique shape of this crystal. A comprehensive mineralogical and crystallographic analysis of the unusual specimen, as well as other analogous diamond crystals, suggests that it was formed as a consequence of the mutual disorientation of the crystals during their growth and the presence of a twin of diamond subindividuals that formed both the core (inclusion) and the sheath (host) diamonds. The twinning planes (111) in the contacting crystals of the inclusion and the host were in a sub-perpendicular position to each other during their simultaneous growth. The captured diamond of the inclusion prevented the normal development of the diamond that became the host. The diamond host rapidly grew along the direction of its own twin boundary and constantly generated new growth layers, which eventually converged around the small captured twin crystal cluster during metric selection. Analysis of diamond crystals of similar shape from the Nyurbinskaya pipe and from elsewhere worldwide confirms the ontogenic model of their origin as a consequence of the capture of diamond inclusions that hampered the rapid growth of the twin crystal (spinel-law twins) in the direction of the twin boundary.
Evaluation of Mineralogical Composition and Organic Matter Content of Oil Shales by IR Microscopy
Authors: Tanykova N. G. , Petrova Yu. Yu. , Spasennykh M. Yu. , Vtorushina E. A. , Kul’kov M. G. , Vtorushin M. N. , Kuklina V. M. , Nekhoroshev S. V. , Kozlova E. V. , Kostina Yu. V.
Published: April 2024

Sedimentary rocks with different contents of organic matter (oil shales of the Bazhenov Formation and sandstones of the Tyumen Formation) from the West Siberian oil and gas province were used to demonstrate the simultaneous study of the mineralogical and structural-group composition, as well as semi-quantitative evaluation of mineral and organic matter contents in rocks by Fourier transform infrared (FTIR) microscopy. The following bands characterizing the stretching vibrations were used: Si–O and Al–O–Si of clay minerals (990–1090 cm–1), Si–O–Si of quartz (798 cm–1), CO2−3 of carbonates (1460 cm–1), as well as aliphatic C–H stretch (2800–3000 cm–1) and C=C ring stretch (1600–1650 cm–1) of organic matter. The obtained results are in good agreement with data obtained by traditional methods of bulk rock analysis: programmed pyrolysis, X-ray diffraction (XRD), and X-ray fluorescence (XRF) analyses. FTIR-ATR (attenuation total reflection) microscopy also provides the possibility of the distribution analysis of sample surface with color mapping, demonstrating the heterogeneity of the rock composition using the Bazhenov Formation as an example of unconventional reservoir. In addition, the method makes it possible to estimate the organic matter maturity and the rock residual generation potential based on the ratio of stretching band intensities of aliphatic and aromatic fragments.
Study of the Chemical Composition of Ash Nanoparticles from the Volcanoes of Kamchatka
Authors: Ermolin M. S. , Shilobreeva S. N. , Fedotov P. S.
Published: April 2024

Obtained data on the composition and properties of ash nanoparticles from Klyuchevskoy, Tolbachik, Kizimen, and Shiveluch volcanoes (Kamchatka, Russia) are generalized. It has been shown that the concentration of toxic and potentially toxic metals and metalloids (Ni, Cu, As, Se, Ag, Cd, Sn, Te, Hg, Tl, Pb, Bi) in volcanic ash nanoparticles can be 10–535 times higher than their concentration in bulk polydisperse samples. The most volatile elements such as As, Sn, Te, Hg, Tl, and Bi have the highest concentration factors in the range of 100–535. Based on the data on single particle inductively coupled plasma mass spectrometry, it is assumed that the listed metals and metalloids are accumulated in the fraction of volcanic ash nanoparticles mainly through the condensation of these elements or their compounds from the gaseous phase and the formation of individual (single) nanophases with an average size in the range of 12–74 nm. It should be noted that approximately an order of magnitude less nanoparticles have been isolated from the acidic volcanic ashes of the Kizimen and Shiveluch volcanoes as compared to those of basic ashes of the Tolbachik and Klyuchevskoy volcanoes. This fact is inconsistent with published data showing that the fraction of fine ash is usually larger for acidic explosive eruptions compared to basaltic eruptions. The Pearson correlation coefficients between the basicity index of volcanic ash and the concentration of more than 50 elements in the ash and ash nanoparticles have been calculated. Some elements have a correlation coefficient |R| 0.7, which, according to the Chaddock scale, indicates the high degree of correlation. It is noted that a number of elements have an opposite correlation between the basicity index of ash and the concentration of elements in ash and ash nanoparticles. For example, Hg and Tl content in ash have a negative correlation with basicity index, that is, their concentration decreases with increasing basicity index of the ash, whereas their concentrations in nanoparticles positively correlate with ash basicity index. The concentration of Ca, Ho, and Er in the ash increases with an increase in the ash basicity index, whereas ash nanoparticles show an opposite correlation. The revealed regularities are unexpected and confirm the unique features of nanostructures and raise new questions of nanogeochemistry.
Trace Element Partitioning between Olivine and Melt: Analysis of Experimental Data
Authors: Girnis A. V.
Published: April 2024

Knowledge of mineral–melt partition coefficients (D) is necessary for geochemical modeling of magma formation and evolution. The main source of these parameters is experiments on equilibrium between minerals and silicate melt. The database on mineral–melt equilibrium experiments has grown continuously, which allows one to refine partition coefficients and reveal the most important factors affecting them. This paper reports the analysis of available experimental data on trace element partitioning between olivine and melt (7000 experiments from 587 publications were used). Based on the statistical processing of the data array, the dependence of D on melt and olivine composition and P–T conditions was evaluated. It was found that most of incompatible elements are either insensitive or moderately sensitive to these parameters. Among the compositional parameters, CaO content in melt is most significant. It was shown that D estimates can be significantly improved by using ratios of D values for different elements. Such ratios are often independent of experimental parameters and much less variable than D values for particular elements. The obtained D estimates for basaltic compositions vary within six orders of magnitude, from 10–5 (U, Th, and La) to ~5–10 (Co and Ni). The low D values for most elements (0.1) indicate that many trace element ratios in melts do not change significantly even at high degrees of olivine crystallization. The obtained estimates were compared with data on element partitioning between high-pressure (Mg,Fe)2SiO4 phases (wadsleyite and ringwoodite) and silicate melt and between olivine and carbonate–silicate melts. In both cases, there is a close similarity to element partitioning between olivine and silicate melt. One exception is REE. DREE values for the wadsleyite/ringwoodite–melt and olivine–carbonate melt systems are approximately one order of magnitude lower than those for olivine–silicate melt partitioning.
Biogeochemical Changes in Arctic Lakes at Climate Warming: Regional Features
Authors: Moiseenko T. I. , Bazova M. M. , Lummens E. O.
Published: April 2024

The problem of eutrophication of the waters in remote Arctic regions is discussed as a consequence of climate warming and global dispersion of phosphorus. The analysis of long-term monitoring results of water quality from 1990 through 2018 (once every four to five years) provides evidence that the total concentrations of phosphorus and nitrogen, as well as organic matter, had increased by the last decade, which is confirmed by reliable relationships with temperature conditions. The fluxes of phosphorus into lakes from drainage areas were calculated using V.V. Bouillon’s model and turned out to grow during the last decade. The trophic status indicator (TSI) of the lakes shows that the number of oligotrophic lakes has decreased and the number of meso- and eutrophic ones has increased even where no influence of any anthropogenic factors was identified.
Differentiated Estimation of the 137Cs Content on the Biogenic and Lithogenic Suspended Matter in the Black Sea
Authors: Sidorov I. G. , Miroshnichenko O. N. , Poskurnin V. Yu. , Paraskiv A. A.
Published: April 2024

Sedimentation transport of 137Cs can lead to the significant accumulation of this radionuclide at depths that could not be reached through the vertical water exchange alone; therefore, a comparative assessment of its contents for different types of suspended matter (SM) and regions of the Black Sea is of particular interest. For this purpose, we have collected samples of SM and seawater at deep-water and coastal stations for the subsequent determination of the 137Cs activity in the surface water layer. To calculate the fraction of lithogenic matter, the potassium content in the SM was additionally determined. The range of 137Cs content on SM at different stations differed by more than an order of magnitude: from 7 to 111 Bq/kg for specific activity, and from 0.03 to 0.69% for its content on SM, in % of the total content in the surface water layer. Stations located farther away from the coast were characterized by the lowest percentage of 137Cs in SM, while its content at the coastal stations was more variable. The comparison of the lithogenic and biogenic contribution to SM and data on 137Cs for different stations suggests that the content of this radionuclide on SM is primarily determined by the dynamic variations of the lithogenic matter. Based on the 137Cs migration on SM, the Black Sea is divided into at least two types of regions. One regions are water areas far removed from sources of lithogenic matter where SM is formed mainly due to the hydrobiont activity. The 137Cs content in SM due to the predominance of biogenic matter and an insignificant concentration of lithogenic matter in this case accounts for hundredths of a percent of its total content in the surface water layer. Other regions are coastal and shelf water basins, which, on the one hand, are subjected to the significant coastal and river lithogenic runoff, and on the other, they are characterized by the elevated trophicity and biological productivity. In these water areas, 137Cs content on SM owing to the variability of biotic and abiotic factors is more variable and can fluctuate from values typical for the open sea to an order of magnitude higher.
Transfer of Metals under Hydrothermal Conditions in the Form of Colloidal Particles and Supersaturated True Solutions
Authors: Alekseyev V. A.
Published: April 2024

Colloids of metals have been studied much more poorly in hydrothermal solutions than in surface and underground waters. Nevertheless, literature data indicate that colloidal particles containing metals are present in hydrothermal minerals, in geogas, in groundwaters above orebodies, in fluid inclusions of minerals, and in geothermal solutions. These particles are usually thought to be formed at nucleation in supersaturated solution, which is generated in conversion reactions of minerals or when fluids boil. Published experimental data confirm that colloidal particles can be formed and preserved in hydrothermal conditions. Experimental data on the filtration of supersaturated and colloidal solutions in porous media at elevated temperatures are still too scarce to enable a comprehensive and reasonably accurate assessment of the mobility of colloidal particles under these conditions. The involvement of colloids in the hydrothermal ore-forming process is most clearly manifested at formation of rich epithermal Au deposits. The example of a quartz geothermometer is employed to demonstrate that metals can be transferred in true supersaturated solution, and this mechanism may be even more efficient than colloidal transfer. Metals can thus be transferred in the hydrothermal process in significantly higher concentrations than it follows from the traditional approach based on equilibrium thermodynamics.
Peculiarities of the Extraterrestrial Basalts of the Solar System with Reference to the Exoplanet Science: a Brief Review
Authors: Demidova S. I. , Badyukov D. D.
Published: April 2024

The formation of basalts is a global stage in the evolution of differentiated cosmic body (planet or asteroid) of the Solar System. The paper presents the main chemical and mineralogical features of basaltic meteorites of the SNC, HED group, angrites and lunar mare basalts based on literature data. Despite the differences in the products of basaltic volcanism on different cosmic bodies and significant compositional variations in major minerals of basaltic rocks, most of them belong to low-alkaline basalts, suggesting the prevalence of this type of rocks at least among small bodies of the Solar System. All of them are characterized by the presence of such rock-forming minerals as pyroxene, olivine, and plagioclase, and their spectral characteristics can be used to search for basalts on exoplanets. The main factors affecting the spectral characteristics of atmosphere-free bodies and larger planets with an atmosphere are shown, and the possibility of searching for products of basalt volcanism on exoplanets during future missions is considered.
Conversion of the Oil and Gas Generation Potential of the Deep Source Formations of the West Siberian Basin: An Example of Well Tyumen SG-6
Authors: Galushkin Yu. I.
Published: April 2024

A model of the thermal evolution of the lithosphere of the West Siberian Basin in the area of Superdeep Well SG-6, which was drilled through the Koltogor–Urengoi graben, is used to numerically estimate the generation of various hydrocarbon (HC) fractions by the Triassic and Jurassic source rocks. The thermal model assumes the emplacement of a sill into the subsurface layers of the basement in the Early Jurassic and hydrothermal activity in the Late Pliocene–Lower Pleistocene, which noticeably impacted the conversion history of the HC potential of the Triassic and Jurassic source rocks. For the Triassic Pur formation, the emplacement of the sill into the subsurface layers of the basement in the Lower Jurassic drastically intensified the conversion of the HC potential to 84% and the degradation of more than 97% of the generated light oil mass. Calculations show that the heavy oil generated by the rocks of the Pur, Togur, and lower horizons of the Tyumen formations has degraded almost completely as a result of secondary cracking, while heavy oil predominates among the generated HC fractions in the upper horizons of the Tyumen Formation and in the rocks of the Bazhenovo Formation. The light oil remaining nowadays in the matrix of the source rocks has completely degraded in the Triassic rocks but makes up much of the HC products in rocks at the bottom of the Togur Formation and the top of the Tyumen Formation. This oil is the dominant in the upper horizons of the Togur Formation and in the bottom part of the Tyumen Formation. According to calculations, gas hydrocarbons account for a significant proportion of HC products in the Togur and Tyumen formations, and they dominate in the Middle Triassic Pur Formation. At the relatively low initial potential of HC generation and a low content of organic matter in the rocks of the Pur, Togur, and Tyumen formations, no primary expulsion threshold of liquid HC has been reached, and the generated liquid HC probably did not leave the rock matrix, while the gaseous HC likely migrated. The threshold of primary expulsion of liquid HC for the Bazhenov rocks was calculated to be reached at about 65 My.
On the Formation of Diasteranes in Oil and Organic Matter of Rocks
Authors: Yusupova A. A. , Giruts M. V. , Vasil’eva A. V. , Vylekzhanina D. S. , Gordadze G. N.
Published: April 2024

Data obtained on the distribution patterns of biomarker hydrocarbons (n-alkanes, isoprenanes, steranes, and terpanes) in oils, organic matter in rocks, prokaryotes, and thermolysis products of the insoluble part of prokaryotic biomass indicate that the relatively high concentration of diasteranes (rearranged steranes) in the organic matter of rocks and in oils generated by clay strata is caused by characteristics of the original organic matter but not by the process of isomerization of regular steranes, as has been previously thought.