Vol 59, No 8 (2023)

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become one of the major tools to elucidate gene expression programs. Similar to other molecular profiling methods, ChIP-seq is sensetive to several technical biases which affect downstream results, especially in cases when material quality is difficult to control, for example, frozen post-mortem human tissue. However methods for bioinformatics analysis improve every year and allow to mitigate these effects after sequencing by adjusting for both technical ChIP-seq biases and more general biological biases like post-mortem interval or cell heterogenity of the sample. Here we review a wide selection of ChIP-seq normalization methods with a focus on application in specific experimental settings, in particular when brain tissue is investigated.

Levilactobacillus brevis 47f is a heterofermentative aerotolerant lactic acid bacterium isolated from the microbiota of the gastrointestinal tract of a healthy person. Previously, the strain showed anti-inflammatory properties and protects the murine intestine from enteropathy induced by 5-fluorouracil as part of preclinical studies. At the same time, the molecular mechanisms that account for the properties of the strain and its response to the action of reactive oxygen species, remain unexplored. The aim of this work was to study the response of the strain to the action of oxidizing agents – hydrogen peroxide and oxygen – using the method of transcriptional RNAseq analysis. Both oxidants exhibited a strong effect on the strain, increasing or decreasing the expression of several hundred genes – both general and specific for each oxidant. The characteristics of proteins whose expression was increased the most (DE ≥ 5) are provided. The genes activated under the action of both oxidants encode proteins related to stress, antioxidant activity, protein and nucleotide repair, cell wall, carbohydrate transport and metabolism, and catabolic energy storage pathways. Peroxide mainly activated the transcription of defense proteins, namely, stress response and molecular chaperones, antioxidant activity, DNA repair, and proteins involved in the formation of the cell wall. Under aerobic conditions, the genes that encode proteins involved in energy conversion (the use of fatty acids, nucleosides, fructose in addition to glucose as an energy source; proteins of the phosphoketolase pathway) and the import of peptides, amino acids, and sugars, were activated to a large extent. The data obtained in this work will be used by us to conduct an integrated analysis of transcriptomic, proteomic, and metabolomic data derived from this strain. This will make a significant contribution to the creation of a pharmacobiotic based on L. brevis 47f for the treatment of various inflammatory diseases.

Carotenoids are secondary metabolites that are synthesized and stored in all types of plant plastids. These pigments play a significant role in protection against oxidative stress, as well as in the color of flowers and sink organs. Tubers of potato Solanum tuberosum L. synthesize carotenoids, including during post-harvest storage. The state of physiological dormancy and cold stress response are controlled, among other things, by abscisic acid (ABA), which is an apocarotenoid. In this study, we analyzed the expression of carotenoid biogenesis pathway genes (PSY1, PSY2, PSY3, PDS, ZDS, Z-ISO, CRTISO, LCYB1, LCYB2, LCYE, VDE, ZEP, NSY, NCED1, NCED2, and NCED6), as well as genes putatively involved in initiation of chromoplast differentiation (OR1 and OR2), in the dynamics of long-term cold storage (September, February, April) of tubers of potato cultivars Barin, Utro, Krasavchik, Sevemoe siyanie and Nadezhda. It was shown that OR1, and OR2 mRNAs are present in tubers of all cultivars at all stages of storage. The expression profile of all analyzed carotenoid biosynthesis genes during tuber storage was characterized by a significant decrease in transcript levels in February compared to September, with some exceptions. In the period from February to April, the level of gene transcripts changed insignificantly. The biochemical analysis of the carotenoid content in the dynamics of cold storage showed that at the time of harvesting, the highest carotenoid content was in tubers of the cv. Utro; tubers of other cultivars were characterized by a similar amount of carotenoids. During storage from September to April, the total carotenoids changed in a genotype-dependent manner without any trend common to all cultivars.

Peculiarities of the lncRNA expression – COOLAIR, COLDAIR, and COLDWRAP, which perform an important function in the vernalization-mediated epigenetic mechanism of the transition to flowering in A. thaliana plants of northern natural populations (Karelia), were revealed. The results obtained are partly differ from the data of other authors performing studies on pure lines and other ecotypes of this species. It is suggested that the genetic and epigenetic mechanisms involved in the process of vernalization and control of flowering times may differ in plant populations from different geographic regions.

The hypotheses on colonization history of red-backed vole of Iturup Island comparative analysis of distribution and number of haplotypes of mitochondrial cytochrome b gene (662 bp) in vole sampled at various sites along the Iturup Island perimeter and Hokkaido, Kunashir and Sakhalin Islands and adjacent regions of the mainlandhas been carried out. All studied samples from the Iturup Island (68) belonged to the only one haplotype most close to the haplotypes of voles from the Sakhalin Island. The only sample from the Kunashir Island, nearest to the Iturup Island possessed the same haplotype, three additional samples from this island have haplotypes related to haplotypes of voles from the Sakhalin Island and fall within the so called “Sakhalin” clade, while the majority of haplotypes of voles from the Kunashir Island appeared to be close to haplotypes of voles from the Hokkaido Island and make up with them one independent clade, genetically very different from clade of Sakhalin and Iturup samples. The obtained data on the genetic variability of voles from the Iturup Island provides convincing evidence in favour of the recent introduction of the red-backed vole C. rufocanus to the Iturup Island, most likely with sea transport from Sakhalin.

Genome-wide association studies (GWAS) have proven to be a powerful approach to discovering genes for susceptibility to schizophrenia; their findings are important not only for our understanding of the genetic architecture of a given disease, but also for potential applications in the field of personalized medicine. The aim of this study was to study the genetic risk factors for the development of schizophrenia during a genome-wide association analysis in the Republic of Bashkortostan.

In accordance with the Protocol of the genetic and epidemiological survey of the population, the study of the population-genetic characteristics of the Ingush of North Ossetia-Alania was carried out. The extended nature of reproduction was found (3.62). The Crow index is calculated in two ways – the classical one and according to the method proposed by N.H. Spitsina, which takes into account not only pre-productive, but also prenatal losses. The age parameters of reproduction are within the limits of those for other surveyed populations. A graphical comparative analysis of the components of the Crow’s index obtained by different methods is carried out. Low endogamy was revealed (0.13), positive but low ethnic marital assortativness (1.96). The scheme of the surname landscape shows two clusters corresponding to the Ingush and Ossetian populations.