Tritium distribution in the 'water-soil-air' system in the Semipalatinsk Test Site.

This article presents research findings on 3H in abiotic environmental compartments, specifically, the 'water-soil-air' system. All of the research areas are located within the Semipalatinsk Test Site (STS): the perimeter of the 'Degelen' site, the riverside zone of the Shagan river and the 'background' area-the southeastern part of the STS (SEP). As research progressed, numerical values of 3H and its species were revealed in various environmental compartments. The presence of 3H was registered not only in underground nuclear test locations but also in the 'background' area-SEP. Maximum 3H tritium concentrations in the water were detected at the 'Degelen' site (up to 57000±5000 Bq/kg) and the Shagan riv (up to 61500±6000 Bq/kg), in the air of the 'Degelen' site (up to 56±11 Bq/m3), in the soil of the 'Degelen' site (up to 5170±500 Bq/kg) and the Shagan riv (4100±400 Bq/kg) in the free water, at SEP (up to 1710±170 Bq/kg) in the organic constituent. Based upon all of the findings, 3H was found to be readily distributed in abiotic environmental compartments depending on certain conditions. Research suggests that water plays a key role in 3H migration processes in the natural system of interest. The second most but equally important constituent is soil and microorganisms of plant and animal origin living there. These assumptions are indirectly proven by research findings that show the HTO and HT air concentration dynamics depending on the sampling location.

Characterization of geological and lithological features in the area proximal to tritium-contaminated groundwater at the Semipalatinsk test site.

The article presents the results of a study of groundwater contaminated with tritium in the vicinity of the 'Atomic Lake' - a crater filled with water as a result of a thermonuclear explosion on the territory of the former Semipalatinsk test site. This crater was created as part of an experimental thermonuclear explosion in 1965 with the aim of creating an artificial reservoir in arid areas. The study was carried out to identify the source of groundwater contamination near the crater formed from a thermonuclear test. There were two possible factors of pollution: the influence of contaminated water from the crater on the groundwater of the adjacent area, or groundwater polluting the water in the crater. It was necessary to find out the source of groundwater contamination and its connection with the water in the funnel. For this purpose, a study of the geological and lithological conditions of the territory adjacent to the funnel was carried out, which was carried out using drilling operations and hydrological measurements. Drilling work made it possible to study the depth of distribution of groundwater, hydrological work made it possible to determine the conditions of distribution of groundwater, as well as to take samples of groundwater. The assessment of the degree of groundwater contamination was carried out through water sampling and laboratory analysis. As a result, it was established that the geological and lithological conditions of the area limit the flow of contaminated groundwater to the water in the crater - the 'Atomic Lake'. Despite the fact that the waters in the crater from a thermonuclear explosion and the groundwater of the adjacent territory are contaminated with the radionuclide tritium, they have different sources of contamination and are not interconnected. Radionuclide analysis of groundwater showed that increased concentrations of tritium with a specific activity of up to 95 000 Bq/l are found in groundwater near the river bed. Shagan and this is due to the influence of the flow of groundwater coming from other parts of the landfill.

BRACNAC: A BRCA1 and BRCA2 Copy Number Alteration Caller from Next-Generation Sequencing Data.

Detecting copy number variations (CNVs) and alterations (CNAs) in the BRCA1 and BRCA2 genes is essential for testing patients for targeted therapy applicability. However, the available bioinformatics tools were initially designed for identifying CNVs/CNAs in whole-genome or -exome (WES) NGS data or targeted NGS data without adaptation to the BRCA1/2 genes. Most of these tools were tested on sample cohorts of limited size, with their use restricted to specific library preparation kits or sequencing platforms. We developed BRACNAC, a new tool for detecting CNVs and CNAs in the BRCA1 and BRCA2 genes in NGS data of different origin. The underlying mechanism of this tool involves various coverage normalization steps complemented by CNV probability evaluation. We estimated the sensitivity and specificity of our tool to be 100% and 94%, respectively, with an area under the curve (AUC) of 94%. The estimation was performed using the NGS data obtained from 213 ovarian and prostate cancer samples tested with in-house and commercially available library preparation kits and additionally using multiplex ligation-dependent probe amplification (MLPA) (12 CNV-positive samples). Using freely available WES and targeted NGS data from other research groups, we demonstrated that BRACNAC could also be used for these two types of data, with an AUC of up to 99.9%. In addition, we determined the limitations of the tool in terms of the minimum number of samples per NGS run (≥20 samples) and the minimum expected percentage of CNV-negative samples (≥80%). We expect that our findings will improve the efficacy of BRCA1/2 diagnostics. BRACNAC is freely available at the GitHub server.

A spectrum of BRCA1 and BRCA2 germline deleterious variants in ovarian cancer in Russia.

PURPOSE: Pathogenic variants (PVs) in BRCA1 and BRCA2 genes are essential biomarkers of an increased breast and ovarian cancer risk and tumor sensitivity to poly ADP ribose polymerase inhibitors. In Russia, eight PVs were thought to be the most common, among which BRCA1 c.5266dup is the most frequently identified one. METHODS: We show the distribution of BRCA1/2 PVs identified with quantitative PCR and targeted next-generation sequencing in 1399 ovarian cancer patients recruited into the study from 72 Russian regions in 2015-2021. RESULTS: The most abundant PVs were c.5266dup (41.0%), c.4035del (7.0%), c.1961del (6.3%), c.181 T > G (5.2%), c.3756_3759del (1.8%), c.3700_3704del (1.5%), and c.68_69del (1.5%), all found in BRCA1 and known to be recurrent in Russia. Several other frequent PVs were identified: c.5152 + 1G > T (1.2%), c.1687C > T (1.0%), c.4689C > G (0.9%), c.1510del (0.6%), c.2285_2286del (0.6%) in the BRCA1 gene; and c.5286 T > G (1.2%), c.2808_2811del (0.8%), c.3847_3848del (0.8%), c.658_659del (0.7%), c.7879A > T (0.6%), in the BRCA2 gene. For the most common PV in the BRCA2 gene c.5286 T > G, we suggested that it arose about 700 years ago and is a new founder mutation. CONCLUSION: This study extends our knowledge about the BRCA1 and BRCA2 pathogenic variants variability.

NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions.

Multiplex polymerase chain reaction (PCR) has multiple applications in molecular biology, including developing new targeted next-generation sequencing (NGS) panels. We present NGS-PrimerPlex, an efficient and versatile command-line application that designs primers for different refined types of amplicon-based genome target enrichment. It supports nested and anchored multiplex PCR, redistribution among multiplex reactions of primers constructed earlier, and extension of existing NGS-panels. The primer design process takes into consideration the formation of secondary structures, non-target amplicons between all primers of a pool, primers and high-frequent genome single-nucleotide polymorphisms (SNPs) overlapping. Moreover, users of NGS-PrimerPlex are free from manually defining input genome regions, because it can be done automatically from a list of genes or their parts like exon or codon numbers. Using the program, the NGS-panel for sequencing the LRRK2 gene coding regions was created, and 354 DNA samples were studied successfully with a median coverage of 97.4% of target regions by at least 30 reads. To show that NGS-PrimerPlex can also be applied for bacterial genomes, we designed primers to detect foodborne pathogens Salmonella enterica, Escherichia coli O157:H7, Listeria monocytogenes, and Staphylococcus aureus considering variable positions of the genomes.

Rathayibacter caricis sp. nov. and Rathayibacter festucae sp. nov., isolated from the phyllosphere of Carex sp. and the leaf gall induced by the nematode Anguina graminis on Festuca rubra L., respectively.

Two novel species, Rathayibacter caricis sp. nov. (type strain VKM Ac-1799T = UCM Ac-618T) and Rathayibacter festucae sp. nov. (type strain VKM Ac-1390T UCM Ac-619T), are proposed for two coryneform actinomycetes found in the phyllosphere of Carex sp. and in the leaf gall induced by the plant-parasitic nematode Anguina graminis on Festuca rubra L., respectively. The strains of the novel species are typical of the genus Rathayibacter in their chemotaxonomic characteristics and fall into the Rathayibacter 16S rDNA phylogenetic cluster. They belong to two separate genomic species and differ markedly from current validly described species of Rathayibacter at the phenotypic level. The most striking feature differentiating Rathayibacter caricis sp. nov. from other species of the genus is the presence of fucose in its cell wall and Rathayibacter festucae sp. nov. can be easily recognized among other yellow-pigmented rathayibacters because of its rose-orange-coloured colonies.