Arbuscular mycorrhiza (AM) is an ancient mutualistic symbiosis formed by 80–90 % of land plant species with the obligatorily biotrophic fungi that belong to the phylum Glomeromycota. This symbiosis is mutually beneficial, as AM fungi feed on plant photosynthesis products, in turn improving the efficiency of nutrient uptake from the environment. The garden pea (Pisum sativum L.), a widely cultivated crop and an important model for genetics, is capable of forming triple symbiotic systems consisting of the plant, AM fungi and nodule bacteria. As transcriptomic and proteomic approaches are being implemented for studying the mutualistic symbioses of pea, a need for a reference transcriptome of genes expressed under these specific conditions for increasing the resolution and the accuracy of other methods arose. Numerous transcriptome assemblies constructed for pea did not include mycorrhizal roots, hence the aim of the study to construct a reference transcriptome assembly of pea mycorrhizal roots. The combined transcriptome of mycorrhizal roots of Pisum sativum cv. Frisson inoculated with Rhizophagus irregularis BEG144 was investigated, and for both the organisms independent transcriptomes were assembled (coverage 177x for pea and 45x for fungus). Genes specific to mycorrhizal roots were found in the assembly, their expression patterns were examined with qPCR on two pea cultivars, Frisson and Finale. The gene expression depended on the inoculation stage and on the pea cultivar. The investigated genes may serve as markers for early stages of inoculation in genetically diverse pea cultivars.

The color of the grain shell of cereals is an important feature that characterizes the pigments and metabolites contained in it. The grain shell is the main barrier between the grain and the environment, so its characteristics are associated with a number of important biological functions: moisture absorption, grain viability, resistance to pre-harvest germination. The presence of pigments in the shell affects various technological properties of the grain. Color characteristics, as well as the appearance of the grain shell are an important indicator of plant diseases. In addition, the color of the grains serves as a classifying feature of plants. Genetic control of the color formation of both grains and other plant organs is exerted by genes encoding enzymes involved in the biosynthesis of pigments, as well as regulatory genes. For a number of pigments, these genes are well understood, but for some pigments, such as melanin, which causes the black color of grains in barley, the molecular mechanisms of biosynthesis are still poorly understood. When studying the mechanisms of genetic control of grain color, breeders and geneticists are constantly faced with the need to assess the color characteristics of their shell. The technical means of addressing this problem include spectrophotometers, spectrometers, hyperspectral cameras. However, these cameras are expensive, especially with high resolution, both spatial and spectral. An alternative is to use digital cameras that allow you to get high-quality images with high spatial and color resolution. In this regard, recently, in the field of plant phenotyping, methods for evaluating the color and texture characteristics of cereals based on the analysis of two-dimensional images obtained by digital cameras have been intensively developed. This mini-review is devoted to the main tasks related to the analysis of color and texture characteristics of cereals, and to methods of their description based on digital images.

Barley (Hordeum vulgare L.) is the one of the most important cereal species used as food and feed crops, as well as for malting and alcohol production. At the end of the last century, traditional breeding techniques were complemented by the use of DNA markers. Molecular markers have also been used extensively for molecular genetic mapping and QTL analysis. In 2012, the barley genome sequencing was completed, which provided a broad range of new opportunities – from a more efficient search for candidate genes controlling economically important traits to genomic selection. The review summarizes the results of the studies performed after barley genome sequencing, which discovered new areas of barley genetics and breeding with high throughput screening and genotyping methods. During this period, intensive studies aimed at identification of barley genomic loci associated with economically important traits have been carried out; online databases and tools for working with barley genomic data and their deposition have appeared and are being replenished. In recent years, GWAS analysis has been used for large-scale phenotypegenotype association studies, which has been widely used in barley since 2010 due to the developed SNP-arrays, as well as genotyping methods based on direct NGS sequencing of selected fractions of the genome. To date, more than 80 papers have been published that describe the results of the GWAS analysis in barley. SNP identification associated with economically important traits and their transformation into CAPS or KASP markers convenient for screening selection material significantly expands the possibilities of marker-assisted selection of barley. In addition, the currently available information on potential target genes and the quality of the whole barley genome sequence provides a good base for applying genome editing technologies to create material for the creation of varieties with desired properties.

Lodging is one of the main factors in reducing the yield and grain quality of winter and spring wheat varieties. The resistance of wheat cultivars to lodging largely depends on environmental factors, biological and morphological features of the stem and root systems. Selection of the varieties for resistance to lodging is relevant in many countries of the world and has a number of achievements. Plant height is one of the most important morphological characters associated with lodging resistance. Breeding of the varieties carrying the dwarfing genes (Rht) is the main direction to reduce the risk of lodging. The Rht-B1b, Rht-D1b, Rht8 and Rht11 genes are widely used throughout the world due to their significant influence on agronomically valuable traits, including lodging. It turned out to be important to study the anatomical and morphological features and chemical composition of stem tissues, which complement the assessment of resistance to lodging and allow the varietal material to be more fully characterized. The thickness of stem internodes and their anatomical structure play an important role in the stem strength. The diameter of the stem, its thickness and weight, a large number of vascular bundles and a wide ring of mechanical tissues correlate with resistance to lodging. The content of lignin, silicon and cellulose are important structural components and provide the stem strength of wheat plants. Molecular genetic analysis and mapping of genes and quantitative trait loci are of great importance in identifying the genetic basis of the relationship between the anatomical and morphophysiological characters of the stem and root system and lodging. Genetic factors reflecting correlations between the lodging and the thickness of the stem wall, the number of vascular bundles and other characters were mapped to chromosomes 1A, 1B, 2A, 2D, 3A, 4B, 4D, 5A, 5D, 6D and 7D. It has been found that loci with high phenotypic effects on lodging tolerance are colocalized with loci responsible for plant height, stem diameter and stem strength. To increase resistance to lodging, it is necessary to develop a set of agrotechnical methods that reduce the influence of soil and climatic factors and create wheat varieties tolerant to lodging.

The active expansion of foreign potato cultivars on the territory of the Russian Federation has led to a change in the dominant pathogen species and to the emergence of new pathotypes of causal agents of harmful potato diseases. The aim of the study was to evaluate resistance to Phytophthora infestans and Globodera rostochiensis of modern potato cultivars and determine the distribution of fungal and oomycetic diseases on potato cultivars in various agroclimatic zones of Russia. The resistance of 41 foreign cultivars was evaluated to pathotype Ro1 G. rostochiensis and to isolate VZR17 P. infestans with virulence genes 1.2.3.4.5.6.7.8.9.10.11. Resistant to G. rostochiensis were 38 cultivars. 57R marker of the H1 gene conferring resistance to the Ro1 pathotype of G. rostochiensis was detected in 96.6 % of the nematode resistant cultivars studied; susceptible varieties did not possess this marker. Absolute resistance to the causative agent of late blight was demonstrated by the cultivars Alouette and Sarpo Mira (score 9); high levels of resistance (score 6 and 7) were determined for the cultivars Evolution, Red Fantasy and Ricarda. The cultivars Baltic Rose, Damaris, Desiree, Gala, Labella, Laperla, Mia, Sanibel, Zekura, Queen Anne, Red Lady and ‘7 for 7’ were classified as susceptible, although the characteristics of originators indicated average resistance to late blight. A phytopathological test was conducted on 92 samples of 39 varieties of seed potatoes from four federal districts of the Russian Federation: Volga, NorthWest, Central and North Caucasus. Rhizoctonia solani, Fusarium spp. and Helminthosporium solani are most common on all varieties. 100 % defeat of tubers by H. solani was recorded in various regions on the cultivars Red Scarlett, Evolution, Labella, Colombo, Gala and Nevsky. Widespread Colletotrichum coccodes on tubers of the elite and 2nd reproductions of the potato cultivar Red Scarlett (50.0–71.4 %) was recorded in the Central District.

For accurate species-level identification of microorganisms, researchers today increasingly use a combination of standard microbiological cultivation and visual observation methods with molecular biological and genetic techniques that help distinguish between species and strains of microorganisms at the level of DNA or RNA molecules. The aim of this work was to identify microorganisms from the ICG SB RAS Collection using an integrated approach that involves a combination of various phenotypic and genotypic characteristics. Key molecular-genetic and phenotypic characteristics were determined for 93 microbial strains from the ICG SB RAS Collection. The strains were characterized by means of morphological, physiological, moleculargenetic, and mass-spectrometric parameters. Specific features of the growth of the strains on different media were determined, and cell morphology was evaluated. The strains were tested for the ability to utilize various substrates. The strains studied were found to significantly differ in their biochemical characteristics. Physiological characteristics of the strains from the collection were identified too, e. g., the relationship with oxygen, type of nutrition, suitable temperature and pH ranges, and NaCl tolerance. In this work, the microorganisms analyzed were combined into separate groups based on the similarities of their phenotypic characteristics. This categorization, after further refinement and expansion of the spectrum of taxa and their metabolic maps, may serve as the basis for the creation of an “artificial” classification that can be used as a key for simplified and quicker identification and recognition of microorganisms within both the ICG SB RAS Collection and other collections.

The causative agent of opisthorchiasis, the liver fluke Opisthorchis felineus (Rivolta, 1884) is one of the helminths of humans and animals in Russia. Together with closely related species of trematodes O. viverrini (Poirier, 1886) and Clonorchis sinensis (Loos, 1907), O. felineus is a part of a triad of epidemiologically important trematodes in the family Opisthorchiidae. Adult O. felineus worms infest the hepatobiliary system of warm-blooded animals and might provoke the development of severe pathologies, including malignancy of bile duct epithelium. The high medical importance of O. felineus attracts the attention of researchers. This review briefly summarizes the data about O. felineus genomics and proteomics. The review provides a comparative analysis of the number of genes and sizes of nuclear genomes of a number of flatworms, the distribution of intron lengths, as well as results of synteny between the O. felineus, O. viverrini and C. sinensis genomes. Special attention is paid to a particular form of RNA processing known as trans-splicing, widely presented in the opisthorchiid genomes. We also provide the results of a comparative analysis of the xenobiotic metabolizing system between parasitic and free-living flatworms. Moreover, data on parasitic granulins, which are potential promoters of cholangiocyte neoplasia, are also presented. Data on the O. felineus genomics and proteomics provide first insights into the structural and functional organization of the genome of this parasitic flatworm with a complex life cycle as well as provide a significant contribution to our understanding of “host-parasite” interaction and evolution of this group of parasitic flatworms.

Asthma is a common severe disease of the respiratory tract, it leads to a significant impairment in the quality of a patient’s life unless effectively treated. Uncontrolled asthma symptoms are a cause of disease progression and development, they lead to an increase in the patient’s disability. The sensitivity to asthma therapy largely depends on the interaction of genetic and epigenetic factors, which account for about 50–60 % of variability of therapeutic response. Beta-2-agonists are some of the major class of bronchodilators used for asthma management. According to published data, allelic variants of the arginase ARG1 and ARG2 genes are associated with a risk of asthma development, spirometry measures and efficacy of bronchodilator therapy. High arginase activity results in a low level of plasma L-arginine and in a decrease in nitric oxide, and, as a result, in an increase in airway inflammation and remodeling. Arginase genetic polymorphisms (rs2781667 of the ARG1 gene, rs17249437, rs3742879, rs7140310 of the ARG2 gene) were studied in 236 children with asthma and 194 unrelated healthy individuals of Russian, Tatar and Bashkir ethnicity from the Republic of Bashkortostan. Association analysis of the studied polymorphisms with asthma development and course, the sensitivity to therapy in patients was carried out. It was found that the rs2781667*C allele of the ARG1 gene is a marker of an increased risk of asthma in Tatars. In Russians, the association of rs17249437*TT and rs3742879*GG genotypes of the ARG2 gene with a decrease in spirometry measures (FEV1, MEF25) was established. In Russians and Tatars receiving glucocorticoid monotherapy or combination therapy, the association of the rs17249437*T allele and rs17249437*TT genotype of the ARG2 gene with a partially controlled and uncontrolled course of asthma was shown.

It is known that ionizing radiation influences the expression of the genes that play a key role in the mechanisms of maintaining the stability of cellular homeostasis. As a rule, changes in the transcriptome of an exposed cell occur within the first 24 hours following radiation exposure. And it predetermines early response in the case of genome damage. Later on modulations in gene transcription activity are also possible and could result in a carcinogenic effect. However, in order to find the role of exogenous factors (ionizing radiation), it is also necessary to take into account the contribution of endogenous factors that are able to modify gene transcription activity. This is especially important for long after the onset of radiation exposure. Single nucleotide polymorphisms located in regulatory regions of the genes may belong to this group of factors. The objective of the current study was to analyze the influence of ionizing radiation on the transcription activity of the STAT3, GATA3, NFkB1, PADI4 genes, which regulate proliferation and differentiation of immune competent human cells; and to assess the potential influence of single nucleotide polymorphisms located in regulatory regions of the genes on the amount of mRNA. The study involved people who had been chronically exposed due to releases of radioactive waste into the Techa River. It was observed that 60 years after the onset of radiation exposure changes in the transcription activity of the NFkB1 and PADI4 genes were registered in people with cumulative doses to RBM within the range 78–3510 mGy. In people who had been chronically exposed, the effect of allelic variations in rs1053023, rs4143094, rs28362491, rs874881 on the level of mRNAs of the STAT3, GATA3, PADI4, NFkB1 genes has not been established.

Paleontologists define global extinctions on Earth as a loss of about three-quarters of plant and animal species over a relatively short period of time. At least five global extinctions are documented in the Phanerozoic fossil record (~500-million-year period): ~65, 200, 260, 380, and 440 million years ago. In addition, there is evidence of global extinctions in earlier periods of life on Earth – during the Late Cambrian (~500 million years ago) and Ediacaran periods (more than 540 million years ago). There is still no common opinion on the causes of their occurrence. The current study is a systematized review of the data on recorded extinctions of complex life forms on Earth from the moment of their occurrence during the Ediacaran period to the modern period. The review discusses possible causes for mass extinctions in the light of the influence of abiogenic factors, planetary or astronomical, and the consequences of their actions. We evaluate the pros and cons of the hypothesis on the presence of periodicity in the extinction of Phanerozoic marine biota. Strong evidence that allows us to hypothesize that additional mechanisms associated with various internal biotic factors are responsible for the emergence of extinctions in the evolution of complex life forms is discussed. Developing the idea of the internal causes of periodicity and discontinuity in evolution, we propose our own original hypothesis, according to which the bistability phenomenon underlies the complex dynamics of the biota development, which is manifested in the form of global extinctions. The bistability phenomenon arises only in ecosystems with predominant sexual reproduction. Our hypothesis suggests that even in the absence of global abiotic catastrophes, extinctions of biota would occur anyway. However, our hypothesis does not exclude the possibility that in different periods of the Earth’s history the biota was subjected to powerful external influences that had a significant impact on its further development, which is reflected in the Earth’s fossil record.

In ancient freshwater lakes, an abnormally large species diversity is observed. The mechanisms that g nerated extremely high biodiversity in the ancient lakes have not been sufficiently studied and remain only partially known. Sequences of environmental changes in highly complex ecosystems such as Lake Baikal, may induce sophisticated combinations of microevolutionary processes. These processes are likely to result in unusual “patterns” of genetic variability of species. The most unusual patterns include the ones when speciation is followed by incomplete lineage sorting as well as mitochondrial or nuclear introgression. All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. Mitochondrial and nuclear introgression is a particularly interesting and complex case, which is the process of incorporating the gene alleles of one species into the gene pool of a sister species due to interspecific hybridization (introgressive hybridization). In many cases, existing methods for molecular phylogenetic analysis do not automatically allow the observed patterns of polymorphism to be explained and, therefore, cannot provide hypotheses that would explain the mechanisms which resulted to these patterns. Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. We propose and justify a set of criteria for detecting how two evolutionary trees may differ, with a special focus on comparing a tree inferred from nuclear DNA to one from mitochondrial DNA. The criteria react to branching pattern and branch lengths, including relative distances from ancestral lineages. Simulations show that the criteria allow fast and automated detection of various types of introgression, secondary breaches of reproductive barriers, and incomplete lineage sorting.

A positive effect of estradiol on insulin sensitivity has been shown for females and males. Insulin sensitivity is higher in females than in males, and males show a greater tendency to develop metabolic disorders. It is believed that these sex differences are due to a protective effect of estradiol in females, but not in males. Estradiol is a steroid hormone, and its effect is due to the modulation of target gene expression, but the effect of estradiol on the expression of genes encoding insulin signal transduction and glucose transport has not been sufficiently studied. The aim of the study was to compare the molecular mechanisms of the estradiol influence on insulin sensitivity in mice of both sexes. The effect of gonadectomy and estradiol (1 μg/animal, three days) on the expression of insulin signaling cascade genes in muscle, adipose tissue, and liver, as well as on the expression of Fgf21, estradiol receptors (Esr1/2), and transcription factor Stat3 in the liver in female and male mice was investigated. Estradiol levels were lower and glucose blood levels and insulin resistance were higher in Sham operated (Sham) males compared to Sham females. Irs2, Pik3cd, and Esr1/2 mRNA levels were lower in the liver of Sham males than in Sham females. In females, gonadectomy reduced the level of estradiol in the blood, increased insulin resistance and blood glucose levels compared to Sham females. Administration of estradiol to gonadectomized females decreased blood insulin levels and insulin resistance. In males, gonadectomy, on the contrary, increased the blood estradiol level, decreased blood insulin level and insulin resistance. Estradiol did not affect the parameters studied in males. The development of insulin resistance in gonadectomized females was associated with a decreased expression of the Irs2 gene in the liver. Increased insulin sensitivity in gonadectomized males was associated with increased levels of Irs2 and Pik3cd mRNA in the liver. It can be assumed that increasing the level of estradiol in the blood activates the expression of the Irs2 gene in the liver regardless of animal sex. Also, estradiol seems to regulate the transport of glucose in adipose tissue regardless of animal sex: in females and males, an increase in the blood estradiol level was associated with a decrease in the expression of the Slc2a4 gene in adipose tissue. Thus, the effects of estradiol on the expression of insulin cascade genes do not seem to depend on animal sex, but have tissue specificity. Since the molecular mechanism of estradiol influence on the expression of insulin cascade genes in females and males is the same, the cause of sexual differences in insulin sensitivity and the rate of development of metabolic disorders may be a decrease in the level of estradiol in the blood, as well as a decrease in the expression of estradiol receptors in the liver in males compared to females.

Obesity and diabetes mellitus are known to lead to the development of metabolic syndrome and non-alcoholic fatty liver disease (NAFLD). The mechanisms of programmed cell death are actively involved in maintaining cellular homeostasis along development of NAFLD. Proteins of the BCL-2 family are key regulators of physiological and pathological apoptosis. Homozygous males of BKS.Cg-Dock7^mLepr^db/+/+/J mice (db/db mice) are characterized by progressive obesity and the development of type 2 diabetes mellitus (DM2) with severe hyperglycemia at 4–8 weeks and organ lesions at 8–10 weeks of age. The aim of this research was to study the expression of molecular cell regulators of apoptosis in liver cells of db/db mice males at different stages of obesity and diabetes development (at the age of 10 and 18 weeks). Immunohistochemical analysis (using the indirect avidin-biotin peroxidase method) and morphometric evaluation of the expression of the antiapoptotic protein Bcl-2 and the proapoptotic protein Bad in liver cells of studied animals at different stages of obesity and DM2 were carried out. An excess of the value of the Bcl-2 protein staining area over the Bad protein staining area was revealed in the liver of 10-week-old animals. The Bcl-2/Bad expression area ratio in 10-week-old animals was twice as high as in 18-week-old animals, which indicates the presence of conditions for blocking apoptosis in the liver of younger db/db mice. At the 18th week of life, db/db mice displayed an almost threefold increase in the expression area of the Bad protein against the background of an unchanged expression of the Bcl-2 protein. The decrease in the Bcl-2/Bad staining area ratio in 18-week-old animals was due to the increase in the Bad expression area, which indicates the absence of antiapoptotic cell protection and creates conditions for activation of the mitochondrial pathway of apoptosis in the liver of male db/db mice with pronounced signs of obesity and DM2.

Lipid metabolism is crucial in physiology. In recent decades the model object Drosophila melanogaster has been actively used in the study of the fundamental issues of lipid metabolism and its disorders, including obesity, as well as in the search for therapeutic goals for the treatment of metabolic disorders in humans. Quick and accurate quantification of lipid content is an important step in solving these problems. For the first time the method of quantitative measurement of total lipids with the use of the sulfophosphovanillin (SPV) method was described by Zöllner and colleagues in 1962, and adapted for insects by Van Handel on females of the yellow fever mosquito Aedes aegypti. The advantages of this method compared to traditional gravimetric and chromatographic methods of analysis are the use of a small amount of biological material, lack of need for complex manipulations with the sample, its high sensitivity, reproducibility and simplicity of implementation with a minimum set of equipment. Here, a modification of the Van Handel protocol is described, which allows the method to be adapted for quantitative determination of total lipids for various organisms as exemplified a widely used model, D. melanogaster. To test the effectiveness of the modified method, we measured the content of total lipids in D. melanogaster females carrying hypomorphic mutations of the dilp6 and dfoxo insulin signaling pathway genes compared to the wild-type Canton-S line, and showed that dilp6 took part in the regulation of fat metabolism, while dfoxo did not. The results obtained emphasize the effectiveness of the colorimetric method with the use of SPV reaction and spectrophotometry for the quantitative analysis of total lipids.