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The CRISPR/Cas system is the most promising among genome editing tools. It can provide the development of modified nontransgenic plants with the possibility of simultaneous multiple targeted mutations. The purpose of this review is to analyze published papers describing the utilization of the CRISPR/Cas system for crop gene modification in order to assess the potential of this technology as a new plant breeding technique. The search for “CRISPR & crop name” within article titles, abstracts and keywords in the Scopus database was carried out for 45 crops. Among a total of 206 search results, only 88 have been recognized as original articles describing editing crop genes with the CRISPR/Cas system. A total of 145 target genes of 15 crops are described in these 88 articles, including rice with the largest number of genes modified (78 genes). In these studies, the ability to get transgene-free modified plants was widely demonstrated. However, in most cases research was aimed at the approbation of the technology or was to elucidate target gene function, while modification of just 37 target genes was related with crop improvement. We present here a catalogue of these genes. In most of these cases, modifications resulted in knockout of the genes such as negative growth and development regulators or negative regulators of plant resistance. In most cases, the phenotype of modified plants was assessed, and the presence of desired changes was shown. However, since the estimated number of “negative regulators” is limited in plant genomes, the CRISPR-directed gene knockout has a restricted potential for crop improvement. Intensive application of the CRISPR/Cas system for more complicate modifications such as replacement of defect alleles by functional ones or insertion of a desired gene is required (so far reports about such modifications are very rare in crops). In addition, to provide a basis for broad practical application of CRISPR/Cas-based genome editing, more cultivars of crop species should be involved in ongoing studies. Just a few genotypes of crop species have been used for gene modifications thus far. Nevertheless, in spite of the restrictions mentioned, essential success has been achieved over a short period (3.5 years since the first publications on CRISPR/Cas application in plants).

Great attention is paid to preliminary breeding (prebreeding) when developing triploid apple cultivars. Brief characteristics of diploid gamete donors are given. It should be noted that sometimes donors of diploid gametes with necessary important traits not only have to be selected from among existing tetraploid cultivars, but also developed by a breeding way, especially in the case when in nature there are no cultivars and genotypes (donors of diploid gametes) with given traits. The authors of the paper developed form 30-47-88 (Liberty×13-6-106) by a breeding way. 30-47-88 is a complex donor of diploid gametes and scab immunity (Vf ) at once. During 1970–2015, the following work was done in apple breeding using polyploidy: 455 crossing combinations were performed; 660000 flowers were artificially pollinated; 124700 hybrid seeds were obtained and 47900 one-year-old seedlings were grown, from which after multiple rejections 13200 seedlings were planted in breeding orchards. For the first time in Russia ten apple cultivars (Avgusta, Aleksandr Boiko, Bezhin Lug, Vavilovskoye, Dariona, Maslovskoye, Orlovsky Partizan, Osipovskoye, Patriot and Yablochny Spas) have been developed from intervalence crossings and regionalized. It has been stated that apple cultivars developed at the VNIISPK are characterized, as a rule, by high productivity, better fruit marketability, greater resistance to scab and higher autogamy. Apple cultivars combining triploidy and scab immunity have been developed. Promising breeding is being performed for apple cultivars combining triploidy, scab immunity and columnar habit (Co). Brief characteristics of triploid and scab immune cultivars Vavilovskoye and Yablochny Spas developed from the intervalence crossings as well as three triploid cultivars obtained from crossings of diploid cultivars are given. It is noted that triploid apple cultivars developed at the VNIISPK are inferior to none of foreign cultivars in a complex of commercial traits and they significantly excel foreign cultivars in adaptability. Our apple cultivars may contribute to import substitution of fruit production in the country.

Nowadays, the world’s largest Potato Genebanks, including VIR Potato Genebank, hold about 98 thousand accessions of potato and its wild relatives. This gene pool, which has been accumulated for almost a century, represents a huge genetic diversity of tuber bearing species of the genus Solanum L., which has a great importance for basic and applied research in general, and for human food security. The genebanks of potato and other crops have three highly important tasks such as permanent replenishment of collection material, ensuring its preservation by various storage and maintaining methods, including seed and vegetative propagation, its all-round use in basic and applied research, as well as the improvement of the efficiency of agricultural production. Analysis of performance of the above tasks in genebanks and research institutes in most countries concerned with storage, study and use of potato germplasm, shows great results and achievements, both in terms of its biology and its improvement as a food crop. However, the above three ways to perform tasks still need to be improved in connection with progress made over past decades, in particular in the field of basic and applied sciences. In this paper, a brief analysis of the status of conservation, study and use of potato genetic resources and its wild relatives in the domestic and foreign breeding, as well as solutions of problems in these areas are provided. A great leap forward today is the use of molecular genetic methods for genotyping collection material in gene banks to identify and itemize collection samples, as well as for using this material in basic and applied research, including breeding programs. Coordination of efforts for the collection of wild species that are not in the collections or are represented by a small number of samples, as well as the exchange of material and information about it, will help expand genetic diversity in genebanks and knowledge of the biological features of the potato.

Increasing interest to cytoplasmic male sterility (CMS) and searching for restoration of pollen fertility (Rf) genes in potato is determined by a new way in the modern breeding of this important crop, the development of heterotic hybrids obtained after crosses of inbred diploid lines. The paper reviews the main results of studies on CMS-Rf genetic systems in different species of cultivated plants, the modern methods and approaches of investigating molecular mechanisms of CMS and pollen fertility restoration, and also the available literature data on the status of these studies in potato. The nature of chimeric mitochondrial genes accounting for cytoplasmic male sterility is considered; the peculiarities of the structure and functions of restoration of pollen fertility genes are discussed; examples of CMS-Rf genetic systems in cultivated plant species including representatives of the family Solanaceae are presented. The main results of research on molecular mechanisms of CMS and fertility restoration obtained in the post-genomic era for various plant species using methods of transcriptomic and proteomic analyses are provided. As in many plant species, cytoplasmic male sterility in potato is of hybrid origin. The results of investigating genetic control of male sterility in potato are presented that have been carried out using conventional approaches (hybridological analysis) and led to the formation of the concept of genic cytoplasmic male sterility in some species of section Petota of the genus Solanum. The characteristics of potato cytoplasms types which are associated with male sterility are given. According to classification of Hosaka, Sanetomo (2012), these types include: T/beta, W/gamma and D, each distinguished by the phenotypic appearance of male sterility traits and also by the frequency of occurrence in the breeding varieties gene pool and in various potato species. The results of studies on developing DNA markers for identification of various potato cytoplasm types are presented.

Over the past few years, the CRISPR/Cas techniques have become a revolution in genome editing. Since the original paper on CRIPSR/Cas9 genome editing, researches have proposed numerous modifications of the key components of the CRISPR/Cas9 system to make it extremely efficient. Nowadays, CRISPR/Cas systems can be used not only to modify genomes, but also to control expression levels of defined genes, visualize loci of interest in the space of living cell nuclei, change methylation status of mammalian CpG sites, and to serve many other purposes. Due to an extremely high efficacy and ease of usage, the CRISPR/ Cas system has been employed in a large number of studies in various areas of biology and biotechnology. We have recently published a review describing various CRISPR/Cas systems, mechanisms of their functioning, and applications of the techniques in details. Despite the broad range of potential applications of CRISPR/Cas systems, they are mostly used for genome editing. And, however simple the system may be, there is a number of potential pitfalls on the way towards its use in CRISPR/Cas- naïve laboratory settings. In this article, we describe protocols of CRISPR/Cas9 system generation. We start with a short description of theoretical aspects underlying Cas9-mediated genome editing. Next, we describe a step-by-step protocol of guide RNA vector design and assembly, and several ways of qualitative and quantitative evaluations of the system. Finally, we report protocols of genome editing for modification of embryonic stem cells and zygotes.

Fungi belong to the major plant pathogens and investigation of plant resistance genes is a quite important task. During the last years many wheat resistance genes were identified. However, the sequencing of the Triticum aestivum L. genome is still going on and the nucleotide sequences of most resistance genes are not yet known. In addition, the study of allelic variants of resistance genes is important for better understanding of the molecular mechanisms of their action. In this paper we present an information resource for accumulation of data on sequenced genes of wheat and its relatives providing resistance against diseases caused by fungal pathogens. The database (Pathogenesis-Related Genes, PRG) contains information on gene chromosomal localizations and functional activities, nucleotide sequences and single nucleotide polymorphisms associated with their effects. PRG provides data on the proteins encoded, pathogens and diseases, as well as on the resistance gene expression patterns in response to pathogen inoculations, exposure to hormones and various external stimuli. It also has cross-references with related entries from the databases on nucleotide sequences (GenBank) and proteins (UniProt). Information entered into the database is a result of the annotation of scientific publications and manual curation. Currently PRG compiles data on 75 allelic variants of 66 resistance genes. The PRG database was developed on the basis of the SRS (Sequence Retrieval System) platform. This system allows the use of complex queries and visualization tools and automatically generates www-interface with the information in table or text formats. PRG may be useful for researchers studying plant biology or breeding new plant cultivars resistant to fungal diseases. It is available at the address: http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+top+-newId.

Transgenesis has become a routine for modern biological studies. The most popular method for producing transgenic animals–pronuclear microinjection–frequently leads to host gene disruption due to a random transgene integration. In this paper, we report our analysis of morphophysiological parameters of the transgenic mouse line GM9, in which a transgene designed for milk-specific expression of the human granulocyte-macrophage colony-stimulating factor (GM-CSF) gene was integrated into the intron of the Contactin 5 gene (Cntn5). We studied Cntn5 expression with RT-PCR and discovered that its expression in the brain, the primary organ of Cntn5 activity, was unperturbed. However, transgenic animals had less Cntn5 transcripts in other tissues such as the kidney and heart. In addition, we observed a decreased amount of splice variants of Cntn5 exons that flank the transgene integration site. These data suggest that the transgene integration event might affect proper Cntn5 splicing in some tissues. Publications exist that imply that some polymorphisms in the Cntn5 gene are associated with obesity and arterial hypertension in humans. We evaluated core parameters of lipid metabolism and heart activity in mice homozygous and heterozygous for Cntn5 mutation using wild- type animals as control. Our results uncovered that homozygous mutant mice have lower body weight than controls and that it is caused by slower accumulation of fat tissue. Cntn5 mutants also exhibit abnormalities in blood circulation: homozygous Cntn5 mutants are characterized by a higher blood pressure and heart beat rate, as well as faster blood flow in the tail vessels. Heterozygous animals showed intermediate results for all of these parameters.

Retention of lactase activity in adulthood (lactase persistence) is one of the most important adaptive traits for human populations that consume fresh milk from domestic animals. At a molecular-genetic level, lactase persistence is determined by the presence of specific alleles of polymorphic sites in cis-regulatory elements of the LCT gene located on chromosome 2q21. Ascertainment of the molecular-genetic causes of lactase persistence has made this trait one of the most convenient for studying mechanisms of human population adaptation to environmental conditions. But the populations of many regions remain insufficiently investigated in relation to the genetic variability of the LCT loci. This paper presents the results of polymorphism analysis of loci, including the enhancer element for the LCT gene and its flanking regions, in two Turkic-speaking populations from southern Siberia, Altaian Kazakhs and Khakasses. It was found that the “European” allele LCT-13910T is the most characteristic of the Turkic-speaking populations from Altai-Sayan regions among all the polymorphic variants associated with lactase persistence. The expansion of the “European” allele LCT-13910T to the gene pool of the populations in southern Siberia could be related to migration waves of ancient herders form western Eurasia during the Bronze Age (in III – II millennium BC). A decrease of the LCT-13910T allele frequency and the total frequency of its carriers in the Turkic-speaking populations of southern Siberia in comparison with the majority of European populations and the Kazakhs from southern Central Asia can be attributed to: (1) a significant influence on the Altai- Sayan population’s gene pool by Eastern Eurasian populations, for which the LCT-13910T allele is rare; (2) a lesser adaptive significance of lactase persistence for south Siberian populations, compared to the populations of Europe. Rare and unique SNPs in the locus under consideration that were found in the Altaian Kazakhs (LCT-13895G > C and LCT-13927C > G) and Khakasses (LCT-14011C > T) potentially play a role in regulation of LCT gene expression, because they are located within the enhancer, regulating activity of its promoter.

Short read next generation sequencing (NGS) has significant impacts on modern genomics, genetics, cell biology and medicine, especially on meta-genomics, comparative genomics, polymorphism detection, mutation screening, transcriptome profiling, methylation profiling, chromatin remodelling and many more applications. However, NGS are prone for errors which complicate scientific conclusions. NGS technologies consist of shearing DNA molecules into collection of numerous small fragments, called a ‘library’, and their further extensive parallel sequencing. These sequenced overlapping fragments are called ‘reads’, they are assembled into contiguous strings. The contiguous sequences are in turn assembled into genomes for further analysis. Computational sequencing problems are those arising from numerical processing of sequenced samples. The numerical processing involves procedures such as: quality-scoring, mapping/assembling, and surprisingly, error-correction of a data. This paper is reviewing post-processing errors and computational methods to discern them. It also includes sequencing dictionary. We present here quality control of raw data, errors arising at the steps of alignment of sequencing reads to a reference genome and assembly. Finally this work presents identification of mutations (“Variant calling”) in sequencing data and its quality control.

Studies of the last decade reveal a new sight on the possible link between aging processes and circadian rhythm. New data on the role of the NAD+-dependent histone deacetylase SIRT1 in the integration of regulation pathways for circadian rhythms and metabolism as well as data on a new function of the NAD+ as the ”metabolic oscillator” open a promising direction in this area. In the paper we suggested a modification and extension of the most detailed model for the circadian oscillator developed by Kim and Forger (2012). We included the additional feedback of the oscillator which concerns genes/proteins NAMPT, SIRT1, and also NAM, NAD+. The regulation of transcription for gene NAMPT by transcription factor CLOCK/BMAL1 determine the appropriate rhythm of mRNA and protein NAMPT expression. Since an enzyme product of this gene is a key in the pathway of biosynthesis and recycling of NAD+, therefore the circadian rhythm is also characteristic for the fluctuations in the level of this coenzyme and in the activity of NAD+-dependent histone deacetylase SIRT1. The deacetylation of circadian oscillator components by this enzyme closes the feedback mediated through this pathway. In particular, the effects of SIRT1 in circadian oscillator are the gain of degradation of protein Per2, increasing of the gene Bmal1 transcription, deacetylation of chromatin in regulatory regions of circadian oscillator genes in the E-boxes area with subsequent suppression of transcription. We took into account all of these processes in our extended model of the circadian oscillator. Based on the experimental data on the aging changes in the activity of SIRT1 and the level of NAD+, we attempted to study the effect of these age-related changes on the functioning of the circadian oscillator. Simulation data showed a decrease in expression level of several genes of the circadian oscillator, in particular, Bmal1 and Per2, in the older age groups. In addition, our extended model predicted an increase in the period of oscillations. The results indicate that decrease in SIRT1 activity deal with agerelated NAD+ metabolic disorder may be one of the reasons for the circadian oscillator dysfunctions in the suprachiasmatic nuclei. Such disorders may result in a breaking of the circadian rhythms in the body as a whole.

Various mutationally impaired genes are often found in malignant tumors of animals and humans. At the same time, a large number of carcinogens demonstrate positive activity in different in vitro tests for mutagenicity. These findings are indicative of a geno- toxic mechanism of carcinogen action. It is considered that chemically active carcinogens induce mutations (and tumors) directly interacting with DNA, while inactive substances are mutagenically activated in the processes of cellular metabolism in target tissues. The aminoazo dyes was found to be activated by N-hydroxilation and subsequent conjugation with sulfuric acid catalyzed by the enzyme sulfotransferase. Previously we found that it is activated metabolites of ortho-aminoazotoluene that are responsible for its inhibitory effect on hormonal induction of tyrosinaminotransferase activity in the liver of sensitive mice. Inhibition of sulfoconjugation of 4-aminoazobenzene, another hepatocarcinogen for mice, by pentaclorophenol was reported to reduce its both mutagenic and carcinogenic activity. In this paper, we confirmed this observation. But we found that, when used ortho-aminoazotoluene, pentaclorophenol inhibited its mutagenic activity, but significantly stimulated the hepatocarcinogenic potency. It seems that carcinogenic action is provoked by unmetabolysed ortho-aminoazotoluene per se or some of its nonsulfated derivatives. The results of our comparative study with ortho-aminoazotoluene and 3.4-benzopyrene are in contradiction with the genotoxic theory of carcinogenesis: both are similarly activated by mouse liver enzymes, but induce tumors in different tissues: the former, hepatocellular carcinomas and the latter, splenic lymphoma. The conclusion was made that the accepted notion about the mechanism of carcinogenesis has to be revised.

This paper presents the results of studying the inheritance of protein markers in different generations of interspecific hybrids of cotton Gossypium hirsutum L. × G. barbadense L. and G. barbadense L. × G. hirsutum L. While these hybrids were in development, the species G. hirsutum was represented by dwarf plants and the species G. barbadense, by variety C-6037 plants. G. hirsutum plants had protein marker H-0.13 and G. barbadense plants had the homologous marker, protein B-0.18. Previous studies demonstrated that in interspecific crosses these markers behave as alleles of the same locus. This allowed these markers to be used for analysis of the ratios of phenotypic classes in the succession of generations of interspecific hybrids, including F2, F9 and F10. In these studies, the plants with only one type of protein (H-0.13 or B-0.18) were regarded as homozygous for the corresponding gene, while plants with both proteins (H-0.13 and B-0.18), as heterozygous. Some polymorphic progeny showed a significant shift in the ratios of phenotypic classes. These changes were observed as an increased or a decreased share of a particular phenotypic class, or as a significant increase or decrease in the proportion of the heterozygotes. The electrophoretic protein composition of cotton seed samples remained unchanged until the tenth generation of hybrids, but in the tenth generation, some heterozygous plants gave offspring, the seeds of which lacked protein with an electrophoretic mobility of 0.70. Plants in which this protein was absent belonged to the homozygous phenotypic class with marker H-0.13.

The use of monosomic lines significantly increases the effectiveness of molecular-genetic analysis and the development of superior quality breeding lines via substitutions by alien chromosomes. A complete set of aneuploid series for each cotton chromosome was required. Simple sequence repeats (SSR) have been applied as useful markers for understanding cotton genetics. Several DNA markers have already been assigned to the individual chromosomes of Gossypium hirsutum. The primary objective of this paper is to report the creation of new monosomic lines and the use of chromosome specific simple sequence repeat (SSR) markers and translocation lines for chromosome identification to confirm chromosome specificity of monosomic lines in the Uzbek collection. Here, we summarize data on the development of a monosomic stock collection of cotton (G. hirsutum L.) from Uzbekistan, including the origin of 95 primary monosomics, their cytogenetic characteristics, morphological features and their identification by translocation tests and chromosome SSR-markers. Our results indicated several different monosomic lines identified by chromosomes 2, 4, 6 and telosome 11 of the At subgenome and chromosomes 18 and 22 of the Dt subgenome, 22 monosomes were identified as duplicates of three monosomes (chromosomes 2, 4 and 6). Chromosome 4 of the At subgenome was recovered more frequently (18 times) than chromosome 2 of the At subgenome (4 times) and chromosome 6 of the At subgenome (3 times) during pollen irradiation at different doses and in the progeny of the desynaptic plants. These lines will be useful for molecular mapping and enhancement of Upland cotton.

The potential of molecular approaches in the management of the technological properties of wheat grain affecting the quality of the end product of bread industry is considered. Currently, along with the growth of grain production, the traditional range of staples is crowded out, the quality of most popular bread varieties deteriorates, and dozens of different substances of biological and chemical origin are used as bread improvers. Meanwhile, the genetic potential of wheat allows the development of varieties with technological parameters of grain suitable for production of high-quality bread. In Russia, multiple examples of the creation of varieties for the production of first and second-class grain are known, and modern molecular genetics offers techniques that can supplement classical breeding approaches and accelerate the development of new varieties adapted to the conditions and requirements of the baking industry, using the natural genetic potential of wheat. We summarize the diversity of requirements for grain and flour for different end-use products. Statistics on the volume and structure of grain quality in Russia in 2011–2014 is analyzed. An essential deformation of the quality structure of the produced wheat grain in favor of less valuable classes is observed. A brief retrospective analysis of research in wheat genetics, demonstrating the contribution of genetic factors to grain and flour technological properties, is performed. Various approaches to rapid breeding of varieties with desired properties are considered in relation with the development of plant molecular genetics. The paper provides examples illustrating the feasibility of using methods of DNA diagnostics in various stages of the process, during which the genetic potential of food crops expresses itself and affects the quality of the end product. The results of molecular studies on the localization and isolation of genes determining technological properties (protein and wet gluten contents, milling properties, rheological properties, flour color, and starch properties) are reviewed. The data on diagnostic DNA markers, which are suitable for efficient selection of genotypes instead of the time-consuming analysis of technological properties during breeding process, are summarized. Thus, the information about the genetic potential of bread wheat and modern technologies that provide grounds for moving from excessive use of chemicals to a more benign and organic effect on the quality of the products throughout the "grain – flour – bread" chain, is summarized.

The Michurinsk Department of the Vavilov Society of Geneticists and Breeding Scientists (VOGiS) was formed in 1966 after the constituent congress of VOGiS and nowadays includes 54 members. The scientists are engaged in 4 scientific institutions affiliated with FASO of Russia. The paper presents investigations of the individual genetics of leading fruit crops (pear, cherry, apple), identified genes, regularities of inheriting resistance to low temperatures, the most harmful diseases and several characters responsible for fruit quality. Some genes were identified for the first time. These are genes regulating Coccomyces hiemalis Higg. resistance (A), retarded growth habit in cherry (O2), astringency (Ta) and juiciness (Su) of fruit in pear. On the base of hybridological analysis and DNA marking, genotypes were identified. These genotypes carry target alleles of the following genes: columnar growth habit (Co) in apple, dwarf trait (PcDw) in pear, retardant growth (O2) in cherry. It was found that the markers C18470-25831, Mdo.chr 10.12, Co04R12 do not always show robust results for screening of young apple seedlings with columnar growth habit (Co) because they are identified as non-columnar forms. The primer pairs of 29f1 и jwi1r are the most robust ones for identification of columnar genotypes. These primers amplify specific PCR product of 586 bp (5’CR). On the basis of molecular-genetic analysis of apple initial forms and hybrid seedlings, there were identified targeted alleles of monogenic scab resistance genes including dominant homozygous genotype (Rvi6Rvi6) and also alleles of genes involved in the control of the biosynthesis of ethylene (Md-ACS1 and Md-ACO1) and expansin (Md-Exp7) controlling fruit long shelf life and pulp firmness.

Monogenic scab resistance and columnar growth habit are important breeding traits of apple. The use of molecular markers very accurately determines the presence of necessary genes in the genome early during ontogenesis and reduces the time of selection. The purpose of this study was molecular genetic testing of initial forms of apple and hybrid seedlings of apple to identify carriers of the target alleles of genes for monogenic scab resistance (Rvi6) and columnar growth habit (Co) and the clarification of the pattern of inheritance of the Co and Rvi6 genes in hybrid progeny populations. This paper presents the results of molecular genetic analysis of varieties Valuta, Uspenskoe, Belarusskoe sladkoe and seedlings of the Valuta×Uspenskoe and Valuta×Belarusskoe sladkoe hybrid families for genes controlling columnar growth habit (Co) and scab resistance (Rvi6). The presence of the dominant allele of the Co gene was diagnosed with primers 29f1 and JWI1r flanking the 5’-end of the insert at the Co locus controlling columnar genotypes. Allelic status of the Rvi6 gene was determined with the AL07-SCAR marker mapping at about 0.2 cM from the Rvi6 locus. The correlation frequency of inheritance of the allelic states of these genes has been determined. Valuta×Uspenskoe crosse yielded 48.1 % columnar genotypes and 77.8 % scab-immune genotypes; Valuta×Belarusskoe sladkoe crosses, 46.8 % and 68.0 %, respectively. The observed segregation conforms to the expected Mendelian ratios: 1:1 for columnar habit and 3:1 for scab resistance. The joint inheritance of columnar growth habit and monogenic resistance to scab has been analyzed. The hybrid seedlings that had the dominant Co allele together with the Rvi6 gene in the homozygous dominant state (Rvi6 Rvi6) in their genome have been identified, which can significantly intensify the selection process and run it into 100 % of hybrid seedlings with monogenic scab resistance and up to 50 % of genotypes with columnar growth habit.

Common vetch Vicia sativa L. is one of the major annual fodder legume crops in Russia. Like other legumes, it can enter into symbiosis with nodule bacteria of the genus Rhizobium and to fix molecular nitrogen from the air. This ability contributes to the enrichment of soils with nitrogen and the possibility of growing crops on poor soils. Vetch symbiotic genes have not yet been identified, so the breeding of this crop is confined to the assessment of breeding material with regard to nodulation and very rarely to the activity of nitrogen fixation measured by the acetylene method. This paper presents the results of studies of nodulation and nitrogen-fixing activity that we conducted with four spring vetch cultivars raised at the Siberian Research Institute for Plant Industry and Breeding. Two varieties of forage pea, namely Druzhnaya and traditional cv. Falenskaya 42, were taken as references. The activity of nitrogen fixation was assessed from nitrogenase activity, assayed by the acetylene method. The study revealed significant varietal differences in nodulation and nitrogen fixation, determined on a gas chromatograph Tsvet 500, Russia. The nitrogenase activity rates in vetch cultivars under study varied from 2811 to 6890 С2Н4 nmol/ plant/h. Two of them, Lena and Priobskaya 25, were prominent in high nodulation nitrogen fixation rates. Nodulation in the two reference pea cultivars was weaker than in vetch. However, their nitrogen fixation activities were higher.

Existence of a small subset of cancer cells referred to as tumor initiating stem cells (TISCs) largely responsible for tumor progression and resistance to chemotherapeutic cytostatic drugs reperesent an important recent paradigm shift. The present work is the first report in the series of papers from our group where we describe the development of anticancer therapy based on the selective targeting of TISCs. Here were characterize a cytoreductive activity of cyclophosphamide (CP), double-stranded DNA (dsDNA) and combinations thereof against the TISC population present in mouse Krebs-2 ascites. We evaluated engraftment potential of Krebs-2 cancer cells treated in ascites-bearing mice in vivo, followed by re-engraftment to congenic recipient mice in a form of a solid graft. These data indicate that with our approach TISCs can be completely eliminated even from a well-established ascites. We demonstrate that dsDNA-internalizing and CD34-positive cells are more sensitive to the synergistic effects of CP and dsDNA. When Krebs-2 ascites are treated with human DNA 1-12 hours post CP injection, this results in either elimination of cells that internalize TAMRA-labeled DNA (TISCs) or alters their phenotype, which is accompanied with the loss of surface expression of CD34. Next, we show that the timepoint 18 hrs post CP treatment is critical to the ongoing repair process in that it divides the repair into two phases: nucleotide excision repair + dsDNA break repair and homologous recombination. Importantly, both of these phases can be conveniently used for targeting the tumorigenic potential of the graft. In the context of monotherapy, CP is most effective against ascites grafts when administered as serial injections. To achieve maximum efficiency, the timing of consecutive injections must match the time when cancer cells found at G2/M during the first injection enter G1/S and/or the time of active repair via homologous recombination.

In the present paper, we report on the series of experiments where multiple regimens of CP and dsDNA injections were tested for targeting the ascites form of murine Krebs-2 cancer in situ. We show that combining CP with cross-linked human and salmon dsDNA results in a synergistic toxicity for ascites-bearing mice, an observation supported by the histopathology analysis of organs and tissues of experimental animals. In contrast, using a composite mixture of native and cross-linked human and salmon DNA after CP injections leads to a significant increase in average lifespan of the treated mice. Further, we demonstrate that repeated rounds of CP+dsDNA injections result in dramatic anticancer effect. The timing of injections is chosen so that they target the cells that were insensitive to the previous treatments as they were in the G2/M phase. 3-4 rounds of injections are needed to eliminate the subpopulation of tumor-initiating cancer stem cells. Our experiments identified the regimen when complete resorption of the primary Krebs-2 ascites occurs in all of the treated animals, followed by a remarkable remission period lasting 7-9 days. Yet, this regimen does not prevent secondary site metastases (either solid or ascites form) from developing, which is likely caused by the migration of ascites cells into adjacent tissues or by incomplete eradication of cancer stem cells. To address these and other questions, we expanded the study and performed histopathology analysis, which indicated that secondary metastases is not the only cause of death. In fact, many animals displayed unfolding systemic inflammatory reaction which was culminated by multiple organ failure. Thus, we developed the concept for treating ascites form of Krebs-2 cancer, which allows elimination of the primary ascites.

A somatic mutation and recombination test (SMART) on the wing cells of Drosophila melanogaster is described in this article in detail. SMART can be used to evaluate the effect of various factors on the genome: physical (temperature, various types of radiation, electromagnetic fields), biogenic (genetic, physiological, infectious factors) and a wide range of chemical compounds. SMART is used as an in vivo version of the method for evaluating promutagenic and mutagenic properties of food, food supplements, potential drugs and cosmetics, and environmental pollutants. The method is based on the influence of the agents under study on the dividing cells of the wing imaginal discs of larvae heterozygous for recessive mutations, marking the wing cells. The mutations, multi wing hairs (mwh; 3 – 0.3) and flare (flr; 3 – 38.8), are located on the left arm of chromosome 3. The Drosophila melanogaster wing contains 24,400 cells arranged in two layers. Each normal cell has only one wing fiber. Recombination or mutational events in the cell leads to the formation of mutant spots/clones visible by microscopic analysis of the wing surface. The Drosophila and mammalian detoxication system is arranged on similar principles, which are based on the action of cytochrome P450. There are modifications to SMART, based on elevated cytochrome P450 expression, allowing more reliable extrapolation of the test results to mammals. Detailed recommendations for the use of the SMART method on the wing cells of Drosophila melanogaster presented in the paper can be used as a textbook in practice and for training purposes.

A large number of studies showed that the gene EPAS1 may serve as a possible predictor of success in sports because of its influence on the processes of oxygen transportation and consumption. However, data concerning the impact of EPAS1 polymorphisms on sports achievements in the modern research literature are very scarce and contradictory. The aim of the present paper was to study genetic selection in the polymorphic system of the EPAS1 gene (rs1867785) in a group of male sambo practitioners. 312 Russian males from 18 to 30 years of age were studied. Of them, 220 were professional athletes and 92 were non-athletes, who served as the control group. The genotype of a single nucleotide G/A polymorphic system of the EPAS1 gene was determined for each participant of the study. Analysis of genotype frequencies revealed statistically significant differences between the two groups. An increase of АА and AG genotype frequencies was revealed in the group of athletes (χ2 = 8.68, p = 0.01). Thus, for sambo practitioners, who reached high levels, the presence of the minor А-allele in the genotypes was typical. The odd ratio (OR) calculated for this group was 1.800 (95 % CI 1.227–2.641), demonstrating that the carriers of the А-allele of the EPAS1 gene had some advantages over the carriers of the G-allele. OR for the highest-rank wrestlers was even higher, 1.990 (95 % CI 1.195–3.313). These results suggest directed genetic selection in the А-allele carriers of the EPAS1 gene among sambo practitioners.

In Western Siberia, intense flowering of Fragaria vesca occurs in the first ten days of June and fruiting takes place from the end of June till early July. During our expeditions investigating natural Fragaria vesca L. populations of Western Siberia in 2002–2013, we registered cases of reflowering, or repeated flowering in August-October. The paper concerns the genetic control of re-flowering in natural populations of Fragaria vesca. The study was conducted with accessions collected in the expeditions and seedlings grown from seeds taken in August-October from natural populations of woodland strawberry reflowering. Genetic analysis of seedlings obtained by self-pollination of collected accessions was also made. It involved 1486 seedlings from plants with seasonal fruiting (representing 32 Western Siberian populations) and 856 seedlings from 10 populations showing reflowering and refruiting. Genetic analysis of reflowering Fragaria vesca plants growing in natural conditions showed that they were usually homozygous for the dominant allele of seasonal fruiting. Reflowering in Fragaria vesca in Western Siberia is considered to be a provisional response of the genotype to certain growth conditions specific for a particular vegetation season. The only woodland strawberry population in the foothills of Kuznetsk Alatau displayed plants heterozygous for fruiting habit. Segregation in the progeny of self-fertilized plants from this population evidences monogenic control of day neutrality with a recessive type of inheritance. Its nature is similar to that in Alpine Fragaria vesca populations.

The paper by the Augustinian friar Gregor Johann Mendel “Experiments on Plant Hybridization” laid the foundation of the new field of knowledge, genetics, 150 years ago. It claimed that any character was determined by two factors. On the one hand, the Mendelian idea of binary coding of a character was inspired by Christian Doppler, with whose department Mendel was contacting for seven years. On the other hand, the regularities discovered by Mendel confirmed the intuitive notion of the divine principle based on rational foundations. Pythagoras was the first to point to the spiritual grounds of being. The world had been created by the number, and the number is a nonmaterial and insensuous entity. All students of heredity before Mendel traced the fate of a character in a succession of generations. Instead, to unveil the heredity mechanism, Mendel traced the fates of two invisible factors that determined the character. Probably, the ideas of binary combinations and mathematical probabilistic variants arose from Mendel’s long meditation and an imaginary experiment. Experiments on pea crosses were undertaken just in order to test the idea of a set of invisible determinants. Methods borrowed from statistical physics allowed Mendel to decrypt the process occurring in experiments with the pea model: The fate of a character was determined by action of two invisible factors.

Aminoazo dyes and other hepatocarcinogenic substances inhibit glucocorticoid-mediated induction of adaptive enzymes, including tyrosine aminotransferase (TAT), in mouse and rat liver. There is a specific relationship between the effect of a carcinogen on TAT induction and its liver carcinogenicity in animals. Presuming tumor development being initiated not directly by the chemicals employed but their metabolically activated derivatives, the question arises whether TAT induction is inhibited by carcinogen metabolites or by their parent compounds. The goal of this paper is to shed some light on the issue. Mouse strains differing in the sensitivity to both carcinogenic and antiglucocorticoid (TAT induction inhibitory) effects of the mouse-specific carcinogen ortho- aminoazotoluene (OAT) underwent a set of experimental procedures: ablation of gonadal and adrenal glands, administration of inhibitors (CoCl2, pentachlorophenol), inducers (3,4- benzopyrene, Aroclor 1254, 20-methylcholanthrene) of xenobiotic-metabolizing enzyme activities, and others. The results unequivocally confirm that glucocorticoid induction of TAT activity in mouse liver is inhibited by activated metabolite(s) of OAT rather than by its intact molecules. In contrast, nonspecific genotoxic agents such as cyclophosphamide and cisplatin exert no effect on TAT induction by glucocorticoids. The wide occurrence (practically in each TAT-expressing hepatocyte) and rapidly reversible inhibition of enzyme induction by the carcinogen point to the epigenetic nature of this phenomenon.

The aim of the present paper is to describe the main metaphors presented in genetic discourse: DNA as text, information, language, book, code, project/blueprint, map, computer, music, and cooking. It also analyses the social implication of these metaphors. The author of this article argues that metaphors are double-edged swords: while they brighten difficult and abstract genetic concepts, they also lead to the misunderstanding and misinterpretation of the reality. The reason for this is that most of these metaphors are of deterministic, reductionist, and fatalistic character. Consequently, they shift the attention from complexity of genetic processes. Moreover, as they appeal to emotions, ascetics, and morality they may involve exaggeration: while they bring hope, they also create an atmosphere of fear over the misuse of genetic knowledge. The author of this article states that the genetic metaphors do not simply reflect the social ideas on DNA, but also shape our understanding of genetics and imagination on the social application of genetic knowledge. Due to this reason, DNA should be understood not only as a biological code, but as a cultural as well.

A 40-year work on apple breeding on a polyploidy level has shown that the most promising crosses for reliable regular development of triploid varieties are 2x × 4x and 4x × 2x.Cytological control shows that reciprocal combinations are unequal in the output of seedlings with different ploidy. In crosses 2x × 4x the output of triploid seedlings is higher than in crosses 4x × 2x. The cause is the different degrees of autogamy in parental tetraploid forms: when nonemasculated flowers are pollinated, highly autogamous forms are preferably pollinated with their own pollen. When larger number of triploid plants is required in crosses 4x × 2x flowers of these forms should be emasculated.The production and biological characteristics of eight apple varieties with stable fruit-bearing and highly marketable fruit, are given in this paper.

This paper introduces classes of segregation models, which describe the inheritance of a quantitative trait, in extended diallelic recombinant inbred crosses. The distinctive feature of the method is usage of the multiple-QTL approach and incorporation of epistatic interactions of loci groups. Solutions that would describe experimental data set to an accuracy of environmental variance are sought in the constructed classes of models. Then linkage analysis is performed: model loci positions of the found solutions are mapped on chromosomes. The search procedure and linkage analysis have been tested with real data on cerebellum weight in laboratory mice as a quantitative trait. The developed software is briefly described.

This paper describes the SNP-MED modular computer-based information system for estimation of the influence of single nucleotide polymorphisms (SNPs) on the function of genes associated with the risk of socially significant diseases. The system includes software components Genomics, Proteomics, Gene networks and the Information resource database (BDIR).

It is believed that the heterochromatic locus flamenco, controlling transposition of retrotransposon/retrovirus gypsy in Drosophila melanogaster, is a source of Piwi-interacting RNA. Piwi is the primary component of the RNA interference machinery. Mutations in piwi and flamenco have the same phenotype – an enhanced transcription and frequency of transposition of the retrotransposon/retrovirus gypsy. This paper discusses the results of the complementation test, which involves crossing strains MS and SS, mutant for the flamenco locus, with the piwi strain 3, heterozygous for a mutation in the piwi gene, followed by study of the transcription level of gypsy in the ovaries and testes of hybrids derived from these crosses. Genetic (hybridological) and molecular analysis of the interaction of the flamenco and piwi loci has been conducted. It has been revealed that transcription of gypsy is differently regulated in testis and ovaries of strains SS and MS, apparently owing to the different activity of piRNA clusters in these tissues. It has been also shown that the piwi and flamenco genes interact complementarily in testis tissue.

We present a computer package for analyzing the structure-functional organization and evolution of biological, social and other networks. The programs allows investigation of not only the global network architecture, but also its local properties, revealing key regulators and structure-functional modules. Also, the network evolution can be traced. The package has been tested with two gene networks: the co-authorship network of biomedical papers and the biomedical term network.

Alien chromatin introgression into the genome of common wheat Triticum aestivum L. is the most efficient way to enrich the gene pool of this crop. To improve the breeding value of wheat accessions, rye Secale cereale L is used as a donor of characters. Transfer of rye genetic material has certain specific features. The combination of the two cereal genomes in a single nucleus results in imbalance in all genetic systems. Fertility restoration in amphihaploids is the first step in the formation of introgression accessions. It is followed by the hybrid genome reorganization, which leads to cytological and genetic stability in the diploid progeny. In this paper, we present and analyze results that were obtained in the study of the two steps of wheat-rye hybrid genome reorganization: (1) breaching of F1 hybrid sterility (cytogenetic mechanisms of unreduced gamete formation) and (2) reorganization of wheat subgenomes during the introgression of single rye chromosomes.

In most natural populations, intraspecies competition for natural resources is supplemented by a predator impact. We suppose that the mode and intensity of the interaction between a prey and its predator affects the course of competitive or sympatric speciation among the prey and processes of co-evolution or cospeciation. Mathematical methods allow development of models precisely describing all sides of intra and interspecies interactions. In this paper, we use mathematical modeling to investigate the effect of the intensity of interspecies interactions on competitive or sympatric speciation inside a prey population. The iIntensity of the interaction is the average number of prey which predators eat in a unit of time: the higher is the number of prey eaten by predators, the greater is the intensity of the interaction. In mathematical models, the intensity of such interaction is determined by many parameters. Changes in these parameters will affect the intensity of the interaction. It was found that sufficiently high intensity of interaction slows down competitive speciation among the prey. The preys in this case, seeking to avoid the impact of predators by altering their adaptive traits. Another important result was that the speciation of predators follows prey speciation when the probability of mutational changes in adaptive traits of predators exceeds that in the prey.

The experimental data obtained to date provided grounds for certain concepts of the stem cell niche regulation in shoot apical meristem. Mathematical modeling is used for checking their consistency and coherence with experimental evidence. In this paper, we summarize mathematical models of stem cell niche regulation offered by different authors, analyze the experimental base and working hypotheses formalized in these models, and identify methodological differences in the approaches to the construction of these models.

The intron located between the first and second nucleotide of the leucine tRNA anticodon is the only representative of group I introns in higher plants. In this paper, for the first time the intron sequence of the plastid trnL gene is described in 16 legume species, and putative secondary structures of the entire intron and some of its functional domains are reconstructed. It has been found that genera of the Fabaceae family, as well as species within a single genus, are highly diverse in this sequence. Single nucleotide polymorphisms have been found in sequences of the catalytic center, believed to be highly conserved.

The development of high-throughput sequencing technologies dramatically accelerated the accumulation of data on genome structure, distribution of gene regulatory regions in the genome and specific features of their interaction. Technologies associated with chromatin immunoprecipitation are reviewed: ChIP-PET, ChIP-seq, and ChIA-PET. Computer-assisted methods for the analysis of transcription factor binding sites (TFBSs) and regulatory region structures throughout the genome are described. The paper demonstrates approaches to the solution of tasks related to genomic data annotation and identification of TFBSs and regulatory regions.

Gene networks controlling plant defense against pathogens are rather complex. They may involve hundreds of genes. Infection induces considerable changes at different levels: molecular-genetic, biochemical, physiological, and morphological. These changes manifest themselves locally (near the invasion site) or systemically. The reconstruction of particular gene networks responsible for defense against pathogenic bacteria, fungi, and viruses is an important step in the elucidation of the underlying molecular mechanisms as well as for the development of new approaches to crop improvement. The transcription levels of genes involved in the defense mechanisms commonly increase in response to pathogen invasion. Thus, investigation of their promoters is important for detection of new transcriptional factors controlling their activity and for search for new genes involved in pathogen response. It seems desirable to employ pathogen-responsive promoters to make plant cultivars resistant to various pathogens by gene engineering techniques. In this paper, we present data on promoters of pathogen-responsive genes with experimentally verified transcription patterns annotated in the TGP (TransGene Promoters) database. TGP may be used as a source of information for both interpretation of transcriptomic data and design of gene engineering constructs to obtain agricultural plants with improved resistance against various pathogens.

The chemical composition of the Soranovskii Miscanthus variety harvested in 2011 and 2012 was separately determined in the whole plant, leaves, and stem. In all cases, cellulose was found to prevail in the Miscanthus stem, and non-cellulosic components (the fat-wax fraction, ash, and lignin), in leaves. Cellulose samples were for the first time obtained from leaves and stems separately by two methods (nitric-acid and combined). The best quality cellulose was derived from stems. For instance, cellulose isolated from stems by the nitric-acid process was better than that from leaves, which was expressed as a higher α cellulose content (94,4 % versus 91,7 %) and polymerization degree (800 versus 580), as well as low weight fractions of non-cellulosic components: ash (0,07 % versus 1,01 %) and acid-insoluble lignin (0,45 % versus 1,51 %). The same tendency is observed in celluloses produced by the combined method: Cellulose from stems had better quality than that from leaves; specifically, it had a greater polymerization degree (1040 versus 640) and lower weight fractions of non-cellulosic components: ash (0,14 % versus 0,75 %), acid-insoluble lignin (0,88 % versus 4,2 %), and pentosans (6,8 % versus 8,53 %). It is obvious that cellulose obtained by the nitric-acid method can be suitable for chemical modifications, including nitration. Cellulose from the combined process can be utilized in paper industry.

Mass spectrometry is a physical method, which can be applied to the investigation of proteomes of different organisms. It allows us both to solve the problem of identification of biological macromolecules and to sequence peptide chains in cases where information on the genomes is scarce or absent. Currently, there are many software programs to support research in this area. Nevertheless, in spite of all efforts, there is little progress in the development of programs able to solve the problem for de novo sequencing of cyclic peptides, which are most effective antibiotics, antitumor agents, immunosuppressants, toxins, and a vast number of nonribosomal peptides with unknown functions. In this paper, an effective algorithm for solving the problem of de novo sequencing cyclic peptides is proposed. The algorithm allows us to reconstruct sequences of lengths up to 160 amino acid residues.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease, which affects motor neurons in the brain and spinal cord and leads to patients’ death. One of the causes of motor neuron degeneration and death is the formation of intracellular protein aggregates formed by a mutant SOD1 protein. Recently, it has been shown that the survival time of ALS patients with specific mutation in SOD1 gene inversely correlates with thermodynamic stability of the SOD1 mutant protein. In the present paper, we hypothesize that mutant SOD1 aggregation can be facilitated by not only destabilization due to hydrogen bonds disruption but also by formation of new hydrogen bonds, which can stabilize intermediate “pathogenic” conformations of the mutant SOD1 protein. Molecular dynamics simulations were conducted to estimate frequencies of hydrogen bond occurrence in the protein structure. It was shown that the regression model based on frequencies of hydrogen bond occurrence significantly better correlated with patients’ survival time (R = 0.89, p < 0.00001) than the estimation based on thermodynamic stability analysis of mutant SOD1 proteins.

This paper presents the results of the reconstruction and analysis of gene regulatory network of the circadian clock in mammals. Application of graph theory methods makes it possible to analyze the structure of the gene network and identify the central component of circadian clock regulation, which includes the basic regulatory circuits passing through the key element of the circadian clock, the Clock/Bmal1 protein. Cluster analysis has revealed subsystems with clear biological interpretation, which are involved in the functioning of the circadian clock by interacting with the central component. This structural model, which includes the central component and functional subsystems that interact with the central component, can provide grounds for the construction of a mathematical model of the dynamics of the gene network regulating the circadian rhythm.

The paper deals with the theoretical issues of biological oxidation of oil hydrocarbons from alkanes to polycyclic aromatics. We analyze the mechanisms of biochemical processes of decomposition of oil components and provide an overview of data from common databases. Studies of microbial communities of natural oil seeps in the Uzon caldera are described in detail. It is the first study of ecophysiological characteristics of oil-degrading microorganisms isolated from thermal oil seeps of the caldera.

The interaction diversity within the communities of living matter, from bacterial colonies to human societies, makes them inherently more complex than ensembles of particles in inanimate nature. Co-authorship networks are a particular case of intra- and inter-group social interactions. In this paper, we analyze the Novosibirsk biomedical scientific community as an example of such a network. Using the PubMed database, we have built a community network and calculated its statistics. The distribution of organizations by scientific activity has a fat tail and obeys the Pareto principle: 83% of publications and 75% of authors belong to the 20% of the most active organizations. A comparison of their networks shows that networks of the universities have a more pronounced core rather than those of research institutions. We have plotted the “demographic” structure of currently active authors and found out two facts: (1) an abundance of authors with short “publication experience” and (2) a deficit of authors whose first publication is dated back to 1991-1997. In general, the network dynamics is non-steady, and the activity tends to increase.

Parkinson’s disease (PD) is the second most common human neurodegenerative disorder. Genetically, PD may be considered as both a monogenous and multifactorial disease. At the moment, much consideration is being given to a search for genetic markers for the LRRK2 6055G>T mutation in exon 41, which plays a role in the development of both monogenous and sporadic cases of PD. The paper presents the results of a 4-year epidemiological study of PD in the town of Zheleznogorsk (Krasnoyarsk Territory).Objective: to study the epidemiology and clinical and genetic features of PD.Patients and methods. There were three observation groups: 1) 135 patients with PD, including 72.6% with previously diagnosed PD and 27.4% with new-onset PD; 2) 44 patients (75% of women and 25% of men) with PD who underwent molecular genetic examination; 3) 30 healthy volunteers (66.7% of women and 33.3% of men) – a control group. The observation groups were matched for gender and age (p>0.05). The study included a retrospective analysis of medical documentation, a prospective clinical and epidemiological study, and a cohort study of genetic predictors for PD.Results and discussion. The weighted mean prevalence of PD in Zheleznogorsk was 124.2 per 100,000 population; morbidity, 13.8 per 100,000 in 2013; mortality was minimal (0 case per 100,000 in 2010 and 2012 and 1.1 case in 2012 and 2013. The genetic markers rs1427263, rs11176013, and rs11564148 of the LRRK2 6055G>T mutation linked to the PARK8 locus on chromosome 12q12 were unassociated with the development of PD among the dwellers of Zheleznogorsk. The frequency of the genetic marker rs7966550 (the homozygous genotype C/C) in the group of PD patients was higher than in that of healthy volunteers (44.5% vs 16.5%). No specific features were found in the pattern and clinical presentations of PD with regard to single-nucleotide polymorphism markers.

The paper is dedicated to the fundamental book «Biology in St. Petersburg. 1703–2008». The reviewer underlines the main advantages of the book and makes some remarks and wishes. The conclusion about a notable role of the new publication for further studies in the history of biology is made.

The paper presents an overview of studies of genetic polymorphism of loci determining bread-making quality among Ukrainian wheat varieties by means of electrophoretic analysis of storage proteins (Gli and Glu) and PCR. The results of analysis of polymorphism in the Gli-A1, Gli-B1, Gli-D1, Glu-A3 loci, as well as the allelic compositions of the Pina-D1 and Pinb-D1 genes, determining grain hardness, and Wx genes, controlling amylose content in the starch of the endosperm, are presented. Comparison of the results obtained with allele-specific primers to the γ gliadin loci and by storage protein electrophoresis shows that the former method can identify some alleles, but the level of polymorphism revealed by this method is lower than that revealed by electrophoresis of storage proteins. Most of the varieties under consideration have PCR alleles characteristic for hard wheat, and only three varieties have alleles specific for soft wheat. Varieties originating from different Ukrainian breeding-centers differ in grain hardness. PCR analysis has not revealed the presence of null alleles of Wx genes in the studied Ukrainian genetic pool but allowed selection of breeding material for further development of low-amylose varieties.

Pathogenesis-related (PR) proteins participate in complex plant defense response to pathogens. It is known that members of two PR-proteins families (PR-4 and PR-10) exhibit ribonuclease activity in some cases. These proteins were found to be able to inhibit the growth of pathogenic fungi, and the ribonuclease activity is necessary for manifestation of this effect. This paper presents current data on molecular mechanisms governing the antifungal activity of PR-ribonucleases connected both with their direct cytotoxic impact on pathogen cells and with possible participation in induction of plant cell apoptosis and development of the hypersensitive reaction (HR).

The first visit of NI Vavilov to the United States in 1921 is the least studied period of the scientist’s life. The documents and photographs first published in this paper provide a more detailed view of this trip, its objectives and results.

Ukraine played an important role in N.I. Vavilov’s personality formation and implementation of his ideas. The National Plant Gene Bank of Ukraine is the most significant embodiment of his heritage. The paper considers the history, directions and results of Ukrainian scientists’ activity in the formation, introduction, and registration of gene bank collections; their accessioning; preservation in life and genetic invariance; study and use in plant breeding, research, and education.

By now, a huge body of experimental data on gene transcription regulation has been accumulated. Transcription is controlled by a great number of proteins acting at various steps of the process; thus, a diversity of regulatory mechanisms can be realized. This paper presents approaches to building knowledge domain ontology, formalized description of the mechanisms of transcriptional regulation and the development of methods for integration of heterogeneous information on the features of the regulation of gene expression on this base. The pilot version of the knowledge base on the transcriptional regulation of eukaryotic genes includes: (1) description of basic terms related to transcription regulation and relationships between them; (2) hierarchical classification of transcription regulators; (3) classification of phases and steps of transcription; (4) a database of transcriptional regulators of three mammalian species (human, mouse, and rat); and (5) dictionaries for molecular processes involved in transcriptional regulation. The knowledge base is designed for information support of computer analysis of transcriptional regulatory mechanisms. Approaches to reconstruction of eukaryotic transcriptional regulatory mechanisms with the new knowledge base are presented.