The effect of 8-methoxypsoralen (8-MOP) activated by UVA (365 nm) on the expression of the oxidative stress genes soxS and katG and SOS response genes recA and colD in Escherichia coli biosensors was studied. The luxCDABE operon of the luminescent bacterium Photorhabdus luminescens is a reporter for the expression of these genes in biosensors. A statistical method of segmented regressions was used to analyze the dynamics of dose–response relationships. It was established that when irradiated with UVA, 8-MOP induces the formation of superoxide anion and peroxide in the cells of pSoxS-lux and pKatG-lux biosensors, respectively. At the same time, the dynamics of biosensor responses differed significantly, which indicates the activation sequence of the corresponding promoters. pRecA-lux and pColD-lux biosensors are activated under conditions of DNA damage; however, the latter has significantly higher sensitivity. As compared to the recA, soxS, and katG promoters, the colD(cda) promoter shows a wider sensitivity and pronounced effect of signal amplification.
The growth and development of skeletal muscle is an important factor that affects animal body size and weight and is elaborately controlled by numerous genetic and nutritional factors. MiRNAs have been shown to be important regulators and have received extensive attention in relation to the growth and development of skeletal muscle. However, the reports of miRNAs regulating the growth and development of skeletal muscle in A. davidianus remain unclear. In this study, through RNA-seq analysis of skeletal muscles across five development stages of A. davidianus at 0.5Y, 1Y, 2Y, 3Y and 4Y, miRNA transcriptomes were systematically investigated. In total, 474 known miRNAs and 116 novel miRNAs were screened and identified among the five groups. In the 1Y vs. 0.5Y comparison group, 117 significantly differentially expressed miRNAs were found to target 9881 genes; in the 2Y vs. 0.5Y comparison group, 126 significantly differentially expressed miRNAs were found to target 11 200 genes; in the 3Y vs. 0.5Y comparison group, 123 significantly differentially expressed miRNAs were screened to target 9889 genes; in the 4Y vs. 0.5Y comparison group, 116 significantly differentially expressed miRNAs were screened to target 10 458 genes. Subsequently, GO and KEGG analyses revealed that these target genes were associated with energy metabolism and substance metabolism in the muscle development of A. davidianus. Additionally, dual-luciferase reporter assays indicated that cfa-miR-217_R-2 could directly target the beta-actin gene. Our work helps to understand miRNA function across A. davidianus age-related skeletal muscle development stages, and lays a foundation for improving the growth speed of artificial molecular breeding of A. davidianus in the future.
The principles for establishing the centers of diversity and origin of cultivated plants, formulated by N.I. Vavilov, are outlined. The hypotheses are presented, in which Ethiopia is considered by various authors either as a center of origin or as a center of genetic diversity of the cultivated barley. The review provides historical information on the emergence of barley in Ethiopia, as well as data explaining a high botanical diversity of Ethiopian barleys are considered. The results of studying the genetic markers of nuclear (loci of hordein grain storage proteins) and chloroplast DNA markers, indicating the genetic similarity of Ethiopian, Yemeni, and Iraqi barleys, are analyzed. In total, this information supports the statement of N.I. Vavilov that Ethiopia is a secondary center of barley diversity.
The results of genome-wide association studies (GWAS) showed a significant association of several variants localized in the ABO gene, which determines ABO blood groups, with a severe phenotype in coronavirus infection COVID-19. However, the contradictory data on the identified associations indicate the importance of studying the effect of ABO gene variants on the severity of COVID-19 for different populations and ethnic groups. The association analysis for the ABO gene rs505922, rs550057, rs657152, and rs687289, that were previously associated with the development of severe clinical picture in patients with coronavirus infection COVID-19, was performed. It was established that the TT genotype of rs550057 increases the risk of severe COVID-19, while the CT genotype of rs505922 and AC genotype of rs657152 have a protective effect. The combinations of genotypes for the analyzed variants, associated with different course of COVID-19, were also established. The allele frequency distribution for the ABO gene variants is characterized by genogeographic variability, which can contribute to the interpopulation heterogeneity in SARS-CoV-2 severity. The proposed mechanisms of the influence of the ABO genetic system on the severe course of COVID-19 are considered.
In recent years, the task of expanding the genetic diversity of common wheat has become a critical priority due to climate change and the considerable narrowing of the gene pool driven by selection for productivity based on a small number of elite founder varieties. Wild relatives of wheat, in particular species of the genus Aegilops, possess a complex of economically valuable traits and are a valuable source of genes for its improvement. However, the formation of distant hybrids is a technically challenging process that results in the so-called genomic shock, whereby genomes combined in a newly emerged allopolyploid suffer a number of changes that can be observed at the chromosomal level. Spontaneous fertile Ae. biuncialis–wheat hybrids detected in the plantings of the Dagestan branch of VIR can serve as a convenient model to study the processes occurring during the formation of a new allopolyploid species, and their molecular and cytogenetic characterization will allow for the use of these hybrids in directed wheat breeding. Analysis of nine hybrids with fluorescence in situ hybridization (FISH) provided characterization of their karyotypes and determination of the genomic composition. According to the FISH patterns, the accessions were divided into two groups. The first group included six accessions and the second group, three accessions. The chromosome number in accessions from group I were close to the octoploid one (2n = 54–56). These hybrids were characterized by similar marker probes distribution patterns on chromosomes and carried identical T7UbL.3MbL translocation. The three remaining lines were also similar to each other in FISH patterns that differed from those in the previous group and apparently arose from hybridization of other parental forms. They were characterized by high variability of chromosome number (2n = 41–52) with substantially different chromosome elimination rates. The most frequent losses were chromosomes 6A, 3Ub, 2Mb, 4Mb, while some chromosomes of the A, B, Ub, and Mb genomes were present in all examined plants. In two plants, each from two accessions from group II, reduction of the mixed genome (2n = 14) that included representatives of all seven homeologous groups belonging to different parental subgenomes was observed. A suggestion on the influence of genotypes on the formation of hybrid genomes and the prospect of using the resulting forms in breeding was made.
Structural and functional organization of multipartite genomes was addressed in two biovars of Neorhizobium galegae (nodule bacteria of goat’s rue), bv. orientalis and bv. officinalis, each forms N2-fixing nodules with only one host plant species, Galega orientalis or G. officinalis. The studied strains (ten of each biovar) isolated from North Caucasian center of G. orientalis origin in addition to chromosome (4380.5–4627.1 kb) contain a chromid, which is more variable in size (1317.1–2107.2 kb) than chromosome, and up to four plasmids, which are more variable (0.9–403.7 kb) than chromids. Bv. orientalis exceeds significantly bv. officinalis for the whole genome and chromosome sizes but it does not differ for the sizes of chromids and plasmids. Bv. orientalis exceeds by 68.2
Marker-assisted selection has only recently begun to be used in the breeding of the Southern Meat breed, and its resistance to diseases has not been studied before. Currently, the work is underway to create a new selective type within this breed, which differs from representatives of the original forms by a high meat productivity. As an additional selection criterion, the effective breeding work should include the analysis of the prion protein gene (PRNP) polymorphism to determine the classes of genetic resistance to classical and atypical forms of scrapie, which will allow us to increase significantly the genetic resistance to scrapie in new generations of Southern Meat breed sheep. In our study, data on genetic resistance to scrapie was for the first time obtained in sheep of the gene pool herd of the Southern Meat breed and in their descendants, crosses with the Katumskaya breed (1/2) of the first generation (F1).
This study analyzes the polymorphism of exons of the MTHFR gene, which encodes 5,10-methylenetetrahydrofolate reductase, a key enzyme involved in folate and methionine metabolism, in indigenous Siberian populations. The analysis of allele and haplotype distributions for the polymorphic loci rs2274976, rs1801131, rs2066462, rs1801133, and rs2066470 revealed the presence of interregional differences among indigenous population of Siberia. A more detailed analysis was performed for loci rs2274976, rs1801131, and rs1801133, nucleotide substitutions in which lead to a decrease in the MTHFR enzyme activity. In addition, according to published data, Canadian Inuit individuals, carriers of the rs2274976-T, rs1801131-G, and rs1801133-G variants, have elevated mercury concentrations in the blood, which can be associated with the peculiarities of traditional Arctic diet containing relatively high levels of toxic metals. Our population genetic analysis revealed an increase in the frequency of the TGG haplotype (at the above indicated loci) from southern to northeastern Siberia, with maximum frequency values in Eskimo populations. The reasons for the identified dynamics of MTHFR gene haplotype distribution in indigenous Siberian populations are discussed, including a possibility of evolutionary compromise related to the protection against mercury neurotoxicity in Arctic populations.
To analyze the association of the rs2241766 polymorphism in the ADIPOQ gene with the risk of obesity, quantitative indices of body mass index (BMI), and indices of fat tissue distribution (waist–hip ratio, WHR; waist–height ratio, WHtR) in individuals of Yakut ethnicity. A total of 418 participants of Yakut ethnicity (mean age 48.6 ± 14.2 years) were examined, including 170 with obesity (BMI ≥ 30 kg/m2), 96 with overweight (BMI 25.0–29.9 kg/m2), and 152 with normal BMI (18.5–24.9 kg/m2). Genotyping of rs2241766 was performed using the PCR-RFLP method. Statistical analysis included the χ2, Kruskal–Wallis, Mann–Whitney tests, logistic and linear regression. In the total sample, the genotype frequencies were: GG—1.9
The analysis of 50 patients with a clinical diagnosis of MUTYH-associated polyposis (more than 20 colorectal polyps) with genetic confirmation was conducted. Twenty-six different pathogenic/likely pathogenic variants were detected in the MUTYH gene, including four new ones. A predominance of four variants was demonstrated: c.1103G>A (p.Gly368Asp), c.650G>A (p.Arg217His), c.452A>G (p.Tyr151Cys), c.464G>A (p.Gly155Asp), that together account for 68
It is known that the distribution of allele frequencies of the thermogenesis genes UCP1 (rs1800592) and UCP3 (rs1800849) correlates with climatic parameters of the environment. In the present work, the influence of previously unstudied factor (traditional lifestyle) on the distribution of the alleles of these genes was assessed among 14 indigenous populations of Siberia. A total of 1819 individuals were included in the analysis of the UCP1 gene rs1800592; 1868 individuals, for the UCP3 gene rs1800849. The populations were divided into the groups according to their lifestyle: pastoralists (Yakuts, Buryats, Altaians), reindeer herders (Evenks, Evens, Khanty, Mansi, Nenets), hunter-gatherers (Yukaghirs, Nivkhs, Kets, Coastal Chukchi, Nanai, and Ulchi). The frequency of the rs1800592 A allele, associated with increased expression of the UCP1 gene, was significantly higher in the groups of pastoralists (60
Mass spectrometric analysis confirms gene expression at the proteome level, which represents the physical basis of cell phenotype. However, for many proteins, knowledge of their functions, cellular location, and medical significance is currently lacking, while these poorly studied components of the human proteome may be key regulators of fundamental processes, such as all-trans retinoic acid (ATRA)-induced granulocytic differentiation. In the proteome of nuclear fractions of HL-60 cells, we identified 114 proteins with low annotation scores in the Uniprot database (1–4). Among them were 14 proteins containing zinc finger motifs, indicating DNA-binding capacity and a potential role in transcriptional regulation, as well as 39 proteins for which, according to Uniprot, information on their biological functions is lacking. Among proteins with low Uniprot annotation scores, zinc finger domains, and/or unknown biological function, increased mRNA expression was detected for alternative protein isoforms compared to the main, canonical isoform for BTF3L4, C19orf53, CCDC12, GLOD4, KNOP1, RBM26, ZKSCAN1, ZNF38, and ZNF512. Moreover, differential expression under ATRA treatment was determined for 13 proteins with insufficiently studied biological function and/or zinc finger domains. The most pronounced decrease in expression was observed for the WDR70 protein starting from 6 h after ATRA treatment and up to 72 h. Meanwhile, the levels of ZKSCAN1 and ZNF787 proteins were increased at early time points after ATRA addition. The identified molecules may represent new regulators of induced granulocytic differentiation of leukemia cells or molecular targets for the development of alternative approaches to the treatment of acute myeloid leukemia (AML).
Climate change has led to drought stresses recurring in different crops. Drought stress adversely impacts ground nut production. Ground nuts need to be explored for genetic variation for drought tolerance. This study evaluated 60 groundnut genotypes of three growth habits (Spanish bunch, Virginia bunch and Virginia runner) to identify drought-tolerant genotypes. Artificial drought was induced using PEG-6000 (10 and 20
Non-fatal suicidal behavior (SB, comprising suicidal ideation and attempted suicide) is a serious public health problem. It is most often associated with depression and is partly heritable. Recent GWAS studies have been searching for genomic markers of SB associated with affective disorders or independent of them, most conclusive results being produced by large-scale meta-analyses. However, associations from limited but clinically well-defined monoethnic samples may substantially augment existing knowledge by utilizing replication strategy. Here we present results of GWAS on suicidal ideation (SI) and suicide attempts (SA) among 245 patients with major depressive disorder (MDD) and 132 healthy volunteers (67.7
Bread wheat Triticum aestivum L. (2n = 6x = 42, BBAADD) is one of the most important agricultural crops that has accompanied humans since the first human civilizations. It emerged nearly 10 000 BP presumably in the northwestern part of Iran from natural hybridization of tetraploid wheat (2n = 4x = 28, BBAA) and wild goatgrass Ae. tauschii (2n = 2x = 14, DD) and then gradually spread along with human migrations to Europe, Asia and Africa, and later to America and Australia. The routes and time of wheat expansion have been the subject of numerous studies using both archaeological and historical, as well as modern molecular genetic methods. At the same time, the history of the appearance and spread of bread wheat over Russian territory was poorly reflected in these works, mainly because most papers in this area were published in local Russian journals that are not translated into English and are not accessible to the world scientific community. In this regard, we tried to summarize the data accumulated so far on the history of wheat cultivation in Russia from the emergence of agriculture in Ancient Rus’ until the advent of scientific breeding (early 20th century).
Rice is a staple food for nearly one-half of the world’s population. Rice is a thermophilic crop and temperature conditions is an important factor that restricts the area of its cultivation. The south of the European part of Russia is one of the most northern regions of rice cultivation in the world. Therefore, studies of specimens cultivated in this region can play an important role in understanding the mechanisms responsible for adaptation to temperature conditions and other abiotic and biotic environmental factors, improving the breeding process and expanding the boundaries of cultivation of the crop. However, no systematic research on the genetic diversity of Russian rice varieties using modern methods has been performed so far. The analysis of whole-plastome sequences is an important source of data on plant phylogeny and evolution. In the present study, we analyzed the complete sequences of chloroplast genomes of 56 rice accessions, including Russian and European varieties, varieties from the former Soviet Union countries, and some other varieties and lines of different origins. It was shown that all the studied samples could be classified into only three out of five previously identified groups of chloroplast genomes of cultivated rice. The most represented group of all was group 1 (Or-wj-I). A significantly large part of the analysed samples had identical haplotypes. Thus, our data lead to the conclusion about the low genetic diversity of the studied sample. This may be explained by the limited set of parental forms used to create genotypes adapted to cultivation at the northern border of the cropping area.
Bronchial asthma (BA) is a common heterogeneous chronic disease of the respiratory tract. In numerous genome-wide association studies (GWAS), a large number of associated genes were detected, but they cannot be considered as an exhaustive spectrum. Repair proteins are involved in the maturation of B and T lymphocytes, switching of immunoglobulin classes, and somatic hypermutation, which directly connects them with the pathogenesis of infectious–allergic diseases, including BA. In adult patients, BA is often combined with cardiovascular pathology, primarily with hypertension. In this work, associations of variants of the genes of DNA repair systems with “isolated” BA and with BA combined with hypertension were studied. Markers of the ATM (rs189037 and rs1801516), NBN (rs709816 and rs1805800), MRE11 (rs473297), TP53BP1 (rs560191), MLH1 (rs1799977), PMS2 (rs1805321) genes were investigated. Associations with the “isolated” form of bronchial asthma were found for three markers: rs560191 in the TP53BP1 gene, rs1799977 in the MLH1 gene, and rs189037 in the ATM gene. The rs1801516 in the ATM gene was associated with bronchial asthma in combination with hypertension. In addition, the results of the study indicate a genetically determined heterogeneity of the combination of bronchial asthma and hypertension depending on the primary manifestation of one or another of the studied diseases.
In this paper, we have shown that the origin of genetic and epigenetic information is connected with the origin of organisms. The Crick diagram describing the sequence hypothesis and the central dogma of molecular biology is modified so as to describe the origin of genes and regulation; epigenetic interactions and differential gene expression; and genome, transcriptome and proteome evolution. We also formulated three corresponding statements about the evolution of biological information flow after the origin of organisms that may be considered as the extension of the sequence hypothesis and the central dogma. These statements are valid during the evolution of organisms. The origin of new genetic and epigenetic information is connected with frozen accidents that accompany every step of progressive evolution.
This review is devoted to diagonal integration of multi-omics data, an approach enabling to combine data from different molecular modalities obtained in independent studies without pairwise measurements. Twenty-two diagonal integration methods classified by mathematical basis are analyzed. A comparative analysis of international and Russian platforms is presented. A concept of a biocentric approach based on coupled Laplacians and kernel methods in reproducing Hilbert space is substantiated.
This article has been retracted. Please see the Retraction Notice for more detail: https://doi.org/10.1134/S102279542607001X
