Vavilov Institute of General Genetics

In the present study, the consolidation of horse breed groups was assessed using the microsatellite marker fragment analysis. Interbreed and intrabreed genetic distances were used as key indices. Intrabreed genetic distances were calculated by using the inverse of an identity-by-state (IBS) matrix. The level of genetic differentiation between populations was determined using the Fst method. Factory-bred and indigenous horse (Equus caballus) breeds, common in Russia and Europe, were used as model objects. An isolated horse population inhabiting Vodny Island located in the Rostovsky State Nature Biosphere Reserve (Rostov oblast) served as a control group, characterized by minimum genetic distance values typical of isolated populations. Randomized samples, including one random specimen from each studied breed, were artificially created to represent the group with maximum diversity. The results of the study revealed statistically significant differences in genetic distances (Dist(IBS)) and the fixation coefficient (Fst) between horse breeds and groups that differ in their breeding status.

Large interstitial telomeric regions are considered remnants and markers of chromosomal rearrangements or a result of several suggested molecular mechanisms of telomere repeats accumulation. More rare are cases when large interstitial repeats are found not close to, but at a distance from the centromere. However, synapsis, recombination, and effects on chromatin near these regions during meiotic prophase I have not been sufficiently studied. Using the model of three snake species of the genus Vipera: V. berus, V. nikolskii, V. renardi, we studied interstitial telomere sites (ITSs) in the pachytene nuclei of primary spermatocytes. We discovered an unusual composite chromosome in the species under study with two ITSs located far from the centromere. In V. berus, two very large adjacent ITS blocks were found on bivalent 5. In the other two species, V. nikolskii and V. renardi, two ITSs are also present on bivalent 5, but they are significantly smaller and barely distinguishable by FISH on pachytene bivalents. The possibility of forming crossing-over sites is shown between the two ITSs. Apparently, the three studied viper species received this complex structure of chromosome 5 from their common ancestor. However, the transformation of these telomeric repeat regions during evolution in the species under study occurred differently. Possible mechanisms of modifications of the telomeric regions are discussed.

Abstract Biofilm formation in Escherichia coli arises from regulatory programs that can diverge even among genetically identical cultures. Exploiting spontaneous replicate-to-replicate variation in E. coli K-12 MG1655, we mapped expression modules whose behavior tracks biofilm abundance across four genetic backgrounds: wild type; strain with deleted gene for hexuronate regulator UxuR Δ uxuR ; an uxuR translation-disrupted retaining locus-derived sRNAs (Δ uxuR -tr), and strain with deleted gene for global carbon regulator cAMP-CRP (Δ crp ). In the wild type, regulator EcpR/MatA demonstrated the highest correlation with the biofilm intensity, and its role was, in particular, seemingly reinforced by stress/pH-homeostasis and c-di-GMP-linked factors. Δ uxuR exhibited the strongest stochasticity in biofilm formation, while in Δ uxuR -tr, replicate dispersion was mostly muted, indicating that uxuR -derived sRNAs buffer motility-adhesion switching. In Δ crp , pgaA was de-repressed due to the absence of CsrA, with expression being highly consistent with intensity of biofilm formation, alongside stress/ion-homeostasis genes. This is in line with the suggestion that CRP regulates biofilms and motility indirectly via regulation of more local transcription factors. Overall, replicate-resolved clustering converts apparent “noise” into structured regulatory patterns, which include genes whose role in biofilm formation was not yet evident, and helps identify switch nodes between planktonic and biofilm bacterial states.

Abstract N⁶-methyladenosine (m⁶A) role in translation control and, particularly, in cap-independent initiation has attracted major attention. A common approach is to study the impact of m⁶A depending on its particular location in the transcripts, but the global impact of m⁶A along mRNAs remains unclear. Here, we combined ribosome profiling under conditions of mTOR inhibition and m⁶A mapping to identify distinct subsets of mRNAs that differ in their sensitivity to the suppression of cap-dependent initiation. The sensitivity was strongly correlated with the total m⁶A methylation of the transcripts. Further, we demonstrated that upon decreased mTOR activity, m⁶A methylation facilitated the enhanced association of mRNAs with components of the eIF4F complex. Thus, the efficiency of cap-independent translation initiation is primarily defined not by precise localization but by the total level of m⁶A methylation, and m⁶A has a compensatory role in maintaining translation when the canonical cap-dependent pathway is impaired. All in all, our findings underscore the significance of contemplating global m⁶A methylation status as a pivotal element in translational control, particularly under stress or signaling perturbations.

Seed shattering is a crucial adaptive trait in wild plant species but is undesirable in domesticated crops. In this study, we investigated the anatomical and molecular mechanisms underlying seed shattering in common buckwheat (Fagopyrum esculentum) and explored its genetic control. Previous research has shown that seed shattering in F. esculentum follows a monogenic inheritance pattern. To pinpoint the genomic region associated with this trait, we analyzed an F₂ progeny derived from a cross between wild ancestor of common buckwheat - Fagopyrum esculentum ssp. ancestrale and the cultivated variety - Fagopyrum esculentum cv. Dasha. Anatomical analysis revealed that both shattering and non-shattering phenotypes possess an abscission zone (AZ); however, in non-shattering plants, the AZ remains underdeveloped and inactive. Histological observations indicated that AZ formation begins during early bud development. Transcriptomic analysis across four developmental stages (early bud, late bud, flower, and fruit) identified abscisic acid regulation, ethylene signaling, and cell wall modification as key factors in AZ differentiation. Unexpectedly, many genes typically associated with abscission layer activation showed increased expression at the flower stage rather than the fruit stage, suggesting that AZ activation occurs earlier than anticipated. We also provided preliminary data on the localization of the gene responsible for shattering in wild buckwheat and reviewed candidate genes. Our results provide new insights into the structure of abscission zone in buckwheat and into molecular mechanisms underlying seed shattering in buckwheat. We identified key pathways involved in abscission zone differentiation and performed the initial localization of the causative gene.

The paper presents a review of taxa within the salmon subfamily, based on consideration of morpho-biological characteristics, paleontological, genetic data, and features of the history of morphogenesis. It is noted that along with the Salmo and Salvelinus branches, the Parasalmo branch identified by Vladykov is part of the main macroevolutionary trunk in the evolution of salmon, taking into account diadromy and polycyclicity as the main features. At the same time, using the advantages of polycyclicity in terms of resistance to changes in environmental factors, they realized a wide settlement in the northern waters of the Atlantic and Pacific oceans, and a circumpolar distribution in the Arctic. A large group of monocyclic Pacific salmon (Oncorhynchus) prevails in the North Pacific waters with fairly stable (compared to the North Atlantic and Arctic waters) climatic and oceanographic conditions in interstadials and even more stable conditions in stadials against the background of the cessation of Arctic waters entering the region during the “drying up” of the Bering Strait during the ocean regression. Using a set of data when considering the specifics of macroevolutionary processes, based on and in development of the views of researchers on the features of the formation of the taxonomic composition of genera within the subfamily Salmoninae, a position is substantiated with a proposal to introduce in addition to the g. Parasalmo and Oncorhynchus and the g. Masou.

Advances in high-throughput sequencing have illuminated the complexity of transcriptome landscape in eukaryotes. An inherent part of this complexity is the presence of multiple isoforms generated by the alternative splicing and the use of alternative transcription start and polyadenylation sites. However, currently available tools have limited capacity to infer full-length isoforms. We developed a new pipeline, FLIC (full-length isoform constructor). FLIC is based on the long-read transcriptome data and integrates several key features: (1) utilizing biological replicate concordance to filter out noise and artifacts; (2) employing peak calling to precisely identify transcription start and polyadenylation sites; (3) enabling robust isoform reconstruction with minimal reliance on existing annotations. We evaluated FLIC using a dedicated set of real and simulated data of Arabidopsis thaliana cDNA sequencing. Results demonstrate that FLIC accurately reconstructs known and novel isoforms, outperforming existing tools, especially in the absence of reference annotations. A direct comparison with CAGE, currently regarded as the gold standard for transcription start site identification, shows that FLIC is equally accurate, while being much less time-consuming. Thus, FLIC provides a valuable tool for comprehensive transcript characterization, particularly for non-model organisms or when dealing with incomplete or inaccurate annotations. FLIC is available at https://github.com/albidgy/FLIC.

Objective: The PRAME antigen (Preferentially Expressed Antigen in Melanoma), a cancer-testis antigen expressed in various tumor types, represents an attractive target for targeted cancer therapy. Methods: A humanized antibody (6H8Hu) was developed based on the monoclonal antibody 6H8 specific to the PRAME protein. The antibody was produced in CHO cells. Results and Discussion: The humanized antibody retains the high affinity of the parental mAb to the antigen (1.2 nM), binds to both recombinant and native PRAME protein, inhibits the proliferation of the PRAME-positive human melanoma cell line Mel Ibr, and suppresses tumor nodule growth in vivo to a degree comparable to that of the murine antibody 6H8 and the cytostatic agent melphalan. Conclusions: The humanized antibody 6H8Hu is a promising candidate for targeted therapy against PRAME-positive melanoma, showing potential comparable to murine antibodies and conventional cytotoxic treatments.

The aim of this study was to synthesize, characterize, and investigate the biomedical effects of nanoscale cerium phosphate obtained via different synthesis techniques, as well as to evaluate the influence of various CePO4 concentrations on cells involved in skin structure regeneration (human mesenchymal stem cells, keratinocytes, and fibroblasts) and establish their antioxidant properties. Methods and Results: Cerium(III) orthophosphate was obtained by precipitation with ammonium dihydrogen phosphate from a nitrate solution. By changing the initial concentrations of the solutions and the drying and annealing temperatures, the best conditions for obtaining nanosized phosphate powders were established. The structure of rhabdophane was obtained by X-ray diffraction analysis, and the particle sizes were measured by transmission electron microscopy. The particle sizes ranged from 2 to 10 nm in the transverse direction and 20 to 50 nm in the longitudinal direction. Studies on cell lines have shown a high level of safety, as well as the regenerative potential of CePO4 nanoparticles, which have a stimulating effect on the proliferation of MSCs at concentrations of 10−2 to 10−3 M for 48 h after application and stimulate the metabolism of human keratinocytes and fibroblasts at a wide range of concentrations (10−3 to 10−5 M). A dose-dependent antioxidant effect of small CePO4 nanoparticles at a concentration of 10−2 to 10−5 has been established, which is stronger than ascorbic acid. Conclusions: A method for obtaining cerium phosphate nanoparticles with beneficial biomedical effects was developed. The non-cytotoxicity and regenerative potential of CePO4 were established at a wide range of concentrations on different cell lines that are involved in the healing of skin wounds, as were their antioxidant properties.

The history of Ancient Rus’ is inextricably linked with the history of ancient Vladimir, the capital of North-Eastern Rus’ in the 12th–14th centuries. Historical, anthropological, and archaeological data suggest a complex composition of the population of Ancient Rus’ cities, however, the genetic structure of this population is currently practically unexplored. We performed whole-genome sequencing with high coverage for an individual from a burial with a stone pillow from the necropolis “Patriarch's Garden” in Vladimir, dated to the second half of the 13th–14th centuries. Based on this, the individual was identified as a male. Identified haplogroups of mitochondrial DNA (H1ba) and Y-chromosome (R-L21) of the buried man have not been previously described in burials from the territory of Ancient Rus’. The paternal lineage of the individual is likely traced to the territory of Northwest Europe. In combination with data on autosomal markers, these results testify to the genetic connection of the man buried in Vladimir with the Western European populations.