Vol 54, No 7 (2018)

In silico analysis of open reading frames of genomic islands of Sinorhizobium meliloti Rm1021 was performed. This strain is a typical representative of soil bacteria forming nitrogen-fixing symbiosis with legume host plants from the alfalfa cross-inoculation group. It was demonstrated that genomic islands had mosaic structure, in which blocks of functional genes, IS-elements and noncoding RNA alternated. Genomic islands contained as well the components of T4SS and T4CP systems, and lacked systems of conjugative mobilization of islands. It was concluded that two of the three islands could be the variants of reduced integrative conjugative elements, and the third island represented a reduced integrated conjugative transposon. Site-specific integration of islands occurred into a 15–31 bp sequence (depending on the island) localized at the 3′-end of the tRNA gene, which is then shifted rightward, while the remaining part of the tRNA gene is completed by a similar sequence that exists in the island. A suggestion on the existence of “speciesspecific insertion hotspots” for genomic islands of root nodule bacteria was put forward.

Current problems and some future perspectives of molecular genetic study of connective tissue diseases (CTDs) are reviewed. The corresponding clinical manifestation and mode of heritable disorders of connective tissue (HDCT) inheritance are subdivided into inherited, mostly monogenic, forms and mixed or multifactorial dysplasia of connective tissue (MDCTs). Both forms, especially MDCT, pose significant problems for precise clinical diagnostics. Implementation of modern DNA technologies includes new generation sequencing and clinical exome sequencing which provided a substantial impact in understanding the complex molecular genetic background of CTDs. Owing to new technologies, hundreds of new causative genes of CTDs were found and many commercial gene panels were designed for more precise and objective diagnostics of different CTDs. The results of implementation of NGS for analysis of both HDCTs and especially MDCTs complicated with common syntropic diseases as well as some new data on epigenetic causes of CTDs are briefly summarized. Special attention is paid to biological models and cell culture technologies complemented results of NGS in CTDs. Obvious advantages, relevant problems, and definite limitations in clinical implication of NGS for CTDs studies are discussed.

Breeding practice defined the main ways to increase crop yield: morphotype change, exploitation of heterosis, and increase in photosynthesis effectiveness. We identified donors and sources of high photosynthetic potential genetic system and polymorphic loci controlling photosynthetic efficiency in Russian rice cultivars. Thirty-two Russian rice cultivars were used as material. The content of chlorophyll a and b and carotenoids was measured at the beginning of tillering, heading, and flowering stages by a Genesys 8 spectrophotometer. Twenty plants of each cultivar in two replications were used for measurement. SSR markers were used. DNA was extracted by the STAB method. Polymerase chain reaction (PCR) and visualization of amplification products were performed under the International Rice Research Institute (IRRI) protocol. Donors of high contents of each pigment were found. A high level of polymorphism for the loci connected with photosynthesis effectiveness in Russian rice cultivars will allow us to create new cultivars with improved characters by hybridization. Six markers significantly divided cultivar groups with different photosynthetic rate, three of them (RM154, RM600, RM5508) were related to the content of carotenoids, two markers (RM347, RM240) were related to specific leaf weight (SLW) control, and two others (RM154, RM509) were related to the chlorophyll a content.

Genetic and genotypic variabilities of a rare relict aquatic plant Nelumbo komarovii Grossh. from six natural populations of Primorsky krai (Russia) were assessed using isozyme analysis. The highest genetic and genotypic diversities were observed in the Razdol’noe and Okeanskaya populations, which can be explained by cross-pollination participation in the seed formation for maintenance of the Razdol’noe population size and by sowing seeds from different habitats for the Okeanskaya population. Low polymorphism at the population level (P = 8.97, H_O = 0.055, H_E = 0.039) is determined by the history of existence of the species from the Tertiary Period as well as by the influence of gene drift. Clonal renewal plays a decisive role in the propagation of N. komarovii in most natural populations.

Sequence analysis of the mtDNA cytochrome b gene (974 bp) was performed using 139 roe deer specimens from different regions of the European part of Russia and Ukraine. The data obtained showed that, at present, both European and Siberian roe deer inhabit this part of the range with predominance of the later: about 60% of individuals carry various Siberian haplotypes, most of which are similar to those in the populations of Capreolus pygargus from the Urals, Siberia, and the Far East. A great variety of mtDNA haplotypes of Siberian roe deer in Eastern Europe is undoubtedly caused by the heterogeneity of founder individuals (immigrants) that were imported from different parts of Asia. Some problems of coexistence of closely related species are discussed.

The peculiarities of the dynamics of malaria mosquito species proportions were studied in natural populations. Twenty-one collections from five larval habitats of the Anopheles maculipennis complex malaria mosquitoes were taken in the vicinity of Novosibirsk (Russia). It was detected that the Anopheles messeae and An. daciae are dominant species in the collected samples. Three An. beklemishevi individuals were also detected. The dynamics of the species proportions within the reproduction seasons for a number of years and also the differences between localities in the species composition were studied. It was revealed that the An. daciae proportion is maximal in July and falls in August. The species proportions can change sharply from year to year. For example, the An. messeae species prevailed in localities on the left bank of Novosibirsk Reservoir in 2013 and 2014 with the frequency of 54–68%, while An. daciae began to prevail on this territory in 2016 with the frequency of 73–85%. Our data on the proportions of species in different reservoirs were compared with data of other authors for the collections of malaria mosquitoes of the Anopheles maculipennis complex in Russia (Tomsk oblast) and in Germany. A high correspondence of models provided by these authors for the territory that we studied was demonstrated. Thus, the ecological peculiarities of the An. messeae and An. daciae species are highly stable even in geographically and climatically distant localities. An increase in the portion of relatively anthropophilic An. daciae in the middle of summer can be a risk factor relative to malaria transmission in this period of time.

The aim of this study was to investigate associations between genotypes of UCP2 and UCP3 genes, milk, and reproduction traits in dairy cattle. The study included two herds: Jersey cows and Polish Holstein-Friesian (Red and White strain) cows. All cows were genotyped using the PCR-RFLP method and allele frequencies were determined. Statistical analysis showed a significant association between polymorphism in the UCP3 gene and the milk yield and fat content of milk (P ≤ 0.05, P ≤ 0.01) and between the UCP2 gene and the calving interval (P ≤ 0.05). Information contained in this study may be useful in further analysis to define the role of analysed genes in relation to functional traits in dairy cattle, nevertheless, the obtained results should be verified by conducting research on a larger group of animals and various cattle breeds.

The diversity and prevalence of hereditary diseases (HDs) among Nogais of the Karachay-Cherkess Republic (KChR) are described. The size of the surveyed KChR population was 387231 individuals, including 3.81% Nogais (14741 individuals). We revealed 36 nosological forms of HDs (110 patients from 81 families): 22 with autosomal dominant (AD) inheritance, 10 with autosomal recessive (AR) inheritance, and 4 with X-linked inheritance. The prevalence of HDs in Nogais was 1: 134. The features of HD diversity in Nogais were determined in comparison with the previously surveyed populations of Russia. The accumulation of Ehlers–Danlos syndrome (1: 388), AD amelogenesis imperfecta (1: 3685), AD ichthyosis (1: 4914), AR nonsyndromic mental retardation (1: 1340), AR Gilbert syndrome (1: 4914), and X-linked inherited deficit of glucose-6-dehydrogenase (1: 1774 males) was established. The analysis of heterozygous carriage of mutations “major” for Russia in the genes of the four following AR diseases in 118 unrelated clinically healthy Nogais (236 analyzed chromosomes) was performed: cystic fibrosis (13 mutations in the CFTR gene: CFTRdele2,3 (21 kb), F508del, I507del, 1677delTA, 2184insA, 2143delT, 2183AA>G, 2184delA, 394delTT, 3821delT, L138ins, E92K, W1282X); phenylketonuria (six frequent mutations in the PAH gene: R261X, R408W, R413P, F331S, P211T, P211L); nonsyndromic sensorineural hearing loss (35delG mutation in the GJB2 gene); and Gilbert syndrome (an increase in the number of TA repeats in the UGT1A1 gene). Allelic specificity for all studied genes in the Nogai people was revealed.

Comparative sequence analysis of symbiotic genes (nodA, nodC, nodD, nifH), which are elements of accessory component of the rhizobial genome, demonstrated that the strains of Rhizobium leguminosarum bv. viciae, isolated from the nodules of a relic legume, Vavilovia formosa, the closest relative of hypothetical common ancestor of the tribe Fabeae, represented a group separated from the strains of R. leguminosarum bv. viciae, isolated from other representatives of this tribe (Vicia, Lathyrus, Pisum, Lens). No isolation was observed relative to the genes representing the core component of the rhizobial genome (16S rDNA, ITS, glnII) or relative to host specificity of the rhizobia. The data obtained suggest that sequence divergence of symbiotic genes marks the initial stage of sympatric speciation, which can be classified as the isolation of the relic “vaviloviae” symbiotype, a possible evolutionary precursor of the “viciae” biotype.

The multimammate rats of the genus Mastomys are widespread throughout sub-Saharan Africa. They are the major agricultural pests and reservoirs of many infections dangerous to humans. A simple and accurate species identification of multimammate rats is crucial in ecological and epidemiological studies; however, it is complicated by the absence of pronounced morphological differentiation between Mastomys species. We describe a simple molecular assay based on PCR typing of the cytochrome b gene fragments as a method that allows fast genotyping of a large number of samples without sequencing to distinguish Mastomys species of East Africa.