bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interplay of host genome and tumour genome in bladder cancer
Authors: Smal M. P. , Kuzhir T. D. , Rolevich A. I. , Krasny S. A. , Goncharova R. I. 
Published: November 2019

Aim. To determine the influence of the polymorphic variants of the base (OGG1 and XRCC1) and nucleotide (ERRC2/XPD and ERRC6/CSB) excision repair genes on the mutational and epigenetic status of bladder tumors. Methods. For this study, we used previously obtained data on the polymorphism of DNA repair genes in bladder cancer (BC) patients, whose tumor tissue samples were analyzed for the presence of key mutational and epigenetic changes. Results. Genotypes containing at least one minor OGG1 rs1052133 allele were significantly associated with an increased frequency of RAS family gene mutations and a reduced frequency of PIK3CA mutations. The polymorphisms of both base excision repair genes influenced the epigenetic variability of urothelial carcinomas, the modifying effect of OGG1 rs1052133 manifesting in ISL1 methylation and XRCC1 rs25487 impacting p16 or TIMP3 methylation. The minor ERRC6/CSB rs2228526 allele was associated with RAS mutations and lack of TIMP3 methylation. Likewise, carriers of the genotypes containing at least one minor ERRC2/XPD rs1799793 allele were less frequently found to have methylated RUNX3 gene in tumor tissues. Conclusions. The polymorphisms of the base (OGG1, XRCC1) and nucleotide (ERRC2/XPD, ERRC6/CSB) excision repair genes modify the mutational and epigenetic variability of a number of key BC genes. The study of the mechanisms of such interactions is necessary for understanding the molecular basis of BC pathogenesis.
Keywords: bladder cancer, OGG1, XRCC1, ERRC2/XPD, ERRC6/CSB gene polymorphism, mutation, methylation.
Assessment of genetic resources of medicinal plants collection of M.M. Gryshko National Botanic Garden of the NAS of Ukraine
Authors: Dzhurenko N. I. , Palamarchuk O. P. , Koval I. V. , Chetvernya S. O. 
Published: November 2019

Aim. The purpose of the work was to analyze the collection fund of medicinal plants of the Medical Botany laboratory at M.M. Gryshko National Botanic Garden of the National Academy of Sciences of Ukraine. Methods. We used the methods of information analysis and synthesis and computer methods of information database processing. Results. The stages of collection formation, created by attracting seed and planting material from the natural flora of Ukraine and by exchange with the botanical gardens of Ukraine and the world are shown. Selection of the source material was carried out taking into account the introduction methods of genus complexes and climatic analogues. The carried out analysis of the taxonomic composition was represented by species belonging to 62 families. The collection has 388 species, including 385 flowering plants, 2 gymnosperms, 1 fern. Among them there are: 280 perennials, 52 biennials, 53 annuals. The introduced plants make up the significant percentage of the collections. Considerable attention is paid to the preservation of the collection fund valuable varieties. The rare and endangered medicinal plant species cultivated and conserving in the collection. Conclusions. The collection of the Medical Botany laboratory is a valuable gene pool of medicinal plants, including rare and endangered listed in the Red Data Book of Ukraine; material is not only for scientific research, but it is also is a base of scientific and educational activities for students, post-graduate students and schoolchildren.
Keywords: genetic resources, collection fund, medicinal plants, introduced plants, rare plants.
Influence of photoperiod on morphogenetic processes in near-isogenic lines in PPD genes of soft wheat
Authors: Zubrich O. I. , Avksentievа O. О. 
Published: November 2019

Aim. Investigation of the effects of contrast photoperiodic conditions and the state of the Ppd genes (dominant or recessive) on growth and morphogenetic reactions in NILs of soft winter wheat Myronivska 808 and Mercia cultivars. Methods. Experiments were carried out in field and vegetation chamber conditions. NILs were cultivated in contrast photoperiodic conditions: control group plants – in the conditions of a long photoperiod of 16 hours (LD), experimental group plants – in a short photoperiod – 9 hours (SD). The stages of organogenesis, the height of apical growth cones, the number of tillers and biomass of the above-ground part of plants were determined. Results. In our studies, we found that all NILs of both cultivars respond to a photoperiod reduction as typical long-day plants, namely: they have a two-stage of organogenesis delay in development, growth processes are inhibited (growth of the apical cone, formation of tillering shoots and accumulation of plant biomass). It was shown that NILs with the genotypes Ppd-A1a and Ppd-D1a are characterized by accelerated development due to inhibition of growth processes. Conclusions. The genes responsible for controlling the development and photoperiodic sensitivity of soft wheat plants also determine the pace of development, growth and morphogenetic reactions of common wheat plants as in LD photoperiod conditions (16 hours), as well as in SD photoperiod conditions (9 hours).
Keywords: Triticum aestivum L., Ppd genes, photoperiod, stages of organogenesis, shoot apex.
Plant β-tubulin phosphorylation on Ser172 as canonical suppressing factor of microtubule growth
Authors: Karpov P. A. , Blume Ya. B. 
Published: November 2019

Aim. The estimation of potential role of plant β-tubulin Ser172 phosphorylation for correct function of microtubules and cell division due to selection of protein kinases, most probable associated with phosphorylation of Ser172 in Arabidopsis thaliana (L.) Heynh. Methods. Literature and database search. Comparison of protein sequences and structures: multiple sequence alignment, phylogenetic profiling, protein structure modeling, etc. Results. Comparison of Ser172 site region from all known β-tubulins from Homo sapiens, Sus scrofa, Saccharomyces cerevisiae, Drosophila melanogaster and A. thaliana confirms its significant similarity. Joint clusterization of all Ser172 site regions (in S±10 a.a. format) reveals that plant site is most similar to Ser172±10 fragment of β-tubulin from S. cerevisiae. At the same time, sequences and catalytic domain structures of cyclin-dependent kinases 1 and YAK1-related kinases (MNB/DYRK1a/YAK1) associated with Ser172 phosphorylation, found maximal similarity in A. thaliana and S. cerevisiae. Сonclusions. The results confirm similarity of amino acid environment of Ser172 in β-tubulin isotypes in human, pig, fruit fly, yeast and arabidopsis. This suggests similar effect of β-tu­bulin phosphorylation at Ser172 for inhibition of microtubule assembly onto their protofilaments and its association with CDK1 and YAK1-related protein kinases. Similarity of Ser172 sites and associated protein kinases, allows us to expect similar effect of this modification on structure of microtubules in A. thaliana and S. cerevisiae. Keywords: β-tubulin, Ser172, phospho­rylation, CDK1, DYRK1, MNB, YAK1.
Formation of the L1Hs retroelement in the intron of the MGMT gene of hominoidea
Authors: Pidpala O. V. , Lukash L. L. 
Published: November 2019

Aim. Analyze the formation of a human-specific L1Hs element in the intron 3 of the MGMT gene on an example of a hominid. Methods. The results of the search and identification of mobile genetic elements were performed using the CENSOR program. The homology between nucleotide sequences was determined by BLAST 2.6.1. Results. The components of the cluster, where the L1Hs element in the human being was formed, are fragments of the L1PA6 element, which are common in the monkeys of the Old and New World. In the gibbon, among the L1 element groups, there are representatives of older subfamilies (L1PB, L1MC, L1MD and L1ME), and the partial homology to the L1Hs of the element is predominantly of elements of groups that have arisen in the mammalian genomes. Conclusions. Formation of a human-specific L1Hs element occurred during the evolution of Hominoidea in parallel with the formation of the cluster structure of MGE in humans from different subfamilies of LINE1-elements whose component components, obviously, also involved in the formation of the L1Hs element.
Keywords: Hominoidea, MGMT gene, intron 3, human-specific L1Hs element.
Izozyme polymorphism of alpha-amylase in soft wheat
Authors: Radchenko O. M. , Sandetska N. V. , Dykun M. O. , Sirant L. V. 
Published: November 2019

Aim. Study of alpha amylase polymorphism in winter wheat varieties. Methods. Isoenzymes of alpha-amylase were detected by electrophoretic protein separation in a polyacrylamide gel. The fall number on the Falling Number 1700 was determined. Results. Strains from various collections were explored: Institute of Plant Physiology and Genetics of the National Academy of Sciences of Ukraine, Kiev, The Plant Breeding and Genetics Institute – National Center of Seed and Cultivar Investigation of the National Academy of Agricultural Sciences of Ukraine, Odesa and german strains. The polymorphism of wheat grain alpha-amylase was detected by the method of electrophoretic protein separation. We searched associations between variants of alpha-amylase and resistance to pre-harvest germination, the falling number in the examined samples was determined. Conclusions. The frequency of the prevalence of variants for isoenzymes of alpha-amylase in soft wheat varieties was estimated. It was shown that genotypes containing the variant of the isoenzymes АbC are more resistant to pre-harvest germination. Among the studied varieties of PBGI NAAS and IPPG NAS of Ukraine, the variant of alpha-amylase AbC.
Keywords: α-amylase, isoenzymes, soft wheat, electrophoresis, falling number.
Xerotolerant strain of Penicillium chrysogenum MF18_10 isolated from the damaged walls of Saint Sophia’s Cathedral, Kyiv
Authors: Lutsenko V. A. , Polishchuk L.V. , Hong J. , Fomina M.A. 
Published: November 2019

Aim. The aim of this work is to determine the taxonomic position of the fungal strain MF18_10 isolated from the damaged wall with medieval painting of St. Sophia’s Cathedral (Kyiv, Ukraine). Methods. The fungus was isolated on selective medium for xerophilic fungi (70% sucrose Czapek agar). Мacro- and micro-morphological phenotypic characterization was carried out using light and scanning electron microscopy. Molecular-biological identification was performed using nucleotide sequences of the ITS-fragment. Results. On the basis of phenotypical characteristics of the fungal isolate MF18_10, it was established its affiliation to the genus Penicillium. ITS analysis revealed that the isolate belongs to the species P. chrysogenum demonstrating 100% identity with other 78 P. chrysogenum strains in GenBank database including the type strains NR_077145 and AY373902, also sharing several distinct differences in substitutions, deletions and insertions within this group. Conclusions. The isolated xerotolerant fungus was identified as P. chrysogenum, the typical representative of the indoor environments and dust, and also common for mycobiota of damaged historic-cultural artifacts. The differences in the analyzed P. chrysogenum ITS primary structures did not correlate with the source of isolation. Keywords: Penicillium chrysogenum, xero-tolerant fungi, ITS, scanning electron microscopy.
Population genetic analysis of the population of Transcarpathian region based on surname data
Authors: Gorpynchenko M. Yu. , Atramentova L. A. 
Published: November 2019

Aim. The purpose of research is to analyse the populations of Transcarpathian region, finding out, as ability of surnames changes to differentiate the populations of area level as compared with regional. Methods. The base of total list of surnames of the population of Transcarpathian region is used. The way of description of genetic structure of the population offered I. Barrai. Material is analysed with use of methodical approaches developed of Е.В. Balanovskaya. Results. Population genetic ratings for area as a whole - index of isonymy (І=6,1×10-4), index of inbreeding (FST=15,2×10-5), migration index (v=12,8×10-4), rate of names diversity (a=16,4×102), index of entropy (H=12,8) and redundancy of surnames (R=36,7), as well as for thirteen areas of Transcarpathian region are designed. Conclusions. Index isonymy, inbreeding and migration in a few times above in the populations of area level, than regional, the rating of diversity in area populations has more low values, than in regional population.
Keywords: quasigenetic markers, population, isonymy, inbreeding, migration.
Crow’s index in ethnic and social groups of urban population
Authors: Kozak N. O. , Atramentova L. A. 
Published: November 2019

Aim. According to the data characterizing reproductive behavior of women, assess an impact of ethnicity and level of education on the intensity of selection in the urbanized multinational population of Kharkiv city. Methods. Data from obstetric history of 532 post-reproductive age women was studied. Results. For indicators of the number of pregnancies with favorable and unfavorable outcomes, universally valid statistical indicators were calculated. Crow’s indexes were calculated as indicators of the intensity of selection. The total selection index for Ukrainians living in Kharkiv equal 0.26, for Russians it is 0.32, and for the group formed from representatives of rare nationalities this index is 0.75. In a group of women with secondary education total selection index is 0.26, in a group with highest education it is 0.35. Conclusions. Ethnicity and level of education of women affects reproductive behavior and determine number of pregnancies and their outcomes. Selection indexes differ in ethnic groups and in groups with different levels of education.
Keywords: reproductive characteristics, Kharkiv population, Crow's index, selection, nationality, education.
Karyological and cytogenetic research of the conifers of boreal zone by classic and new methods
Authors: Muratova E. N. , Sedel’nikova T. S. , Pimenov A. V. , Goryachkina O. V. 
Published: November 2019

Aim. Establishing of karyological features and conducting of cytogenetic analysis on conifer plants for biological diversity studies, solving of problems of taxonomics, evolutionary and population genetics. Methods. Classic methods with acetohematoxylin staining of slides and fluorescent in situ hybridization (FISH). Results. More than 150 populations and provenances of representatives of different conifer genera from the Pinaceae and Cupressaceae families were studied. The studies were carried out in natural populations and during the introduction, in optimal and extreme conditions, in disturbed ecosystems, botanical gardens and parks; in addition, various intraspecific forms have been studied. The variability of chromosome numbers and a wide range of chromosomal mutations have been revealed. Fluorescence in situ hybridization (FISH) with the 45S and 5S ribosomal RNA gene probes and DAPI staining allows to identify of homologous chromosome pairs in the karyotypes of conifers and to facilitate the comparative karyotype analysis of these species. Conclusions. The studies of chromosomes in species of the Pinaceae and Cupressaceae families showed a karyotypic diversity and chromosomal anomalies in extreme conditions and under introduction. The use of molecular cytogenetic markers made it possible to obtain new information on the structure of conifer chromosomes.
Keywords: chromosomes, nucleolar loci, chromosome mutations, Pinaceae, Cupressaceae.
Sequencing of cytochrome c oxidase subunit I (COI) gene and elongation factor 1-alpha (EF1α) gene in aphids of the Belarussian fauna
Authors: Varabyova M. M. , Voronova N. V. 
Published: November 2019

Aim. Cytochrome c oxidase subunit I gene (COI) and elongation factor 1-alpha gene (EF1α) are frequently used for a correct species diagnostics of aphids forms that are correct diagnosis of the species, studying of species genetic structure, assessment of intraspecies and interspecies genetic polymorphism assessment and construction of phylogenetic systems. Methods. Aphids samples were collected in Belarus. Genetic sequences of COI and EF1α genes were sequenced using primes LCO and EF3. Results. Sequences of COI and EF1α genes of 18 aphid species of Belarussian fauna including 6 aphid species of COI gene (Aphis fabae mordvilkoi Börn. & Janisch,, Aphis pomi Deg., Aphis spiraecola Patch, Colopha compressa Koch, Panaphis juglandis (Gz.) и Uroleucon hypochoeridis (F.)) and 15 species of EF1α gene (Anoecia corni (Fabr.), Aphis euphorbiae Kalt., C. compressa, Drepanosiphum platanoidis (Schr.), Gyphina jacutensis Mordv., Hyalopterus pruni (Geoffr.), Longicaudus trirhodus (Walk.), Monaphis antennata (Kalt.), P. juglandis, Periphyllus aceris (L.), Schizolachmus pineti (F.), Sipha maydis Pass., Therioaphis tenera Aiz., Trichosiphonaphis corticis (Aiz.), U. hypochoeridis) were obtained. Conclusions. COI gene and EF1α gene sequences were decoded and deposited to GenBank.
Keywords: aphids, COI, EF1α, nucleotide sequence, GenBank, BOLD.
Interactions of invadopodia scaffold protein TKS4 with intersectin family proteins
Authors: Kropyvko S. V. , Gryaznova T. A. , Rynditch A. V. 
Published: November 2019

Aim. TKS4 is one of the key proteins of invadopodies, specialized membrane structures that provide invasiveness and metastatic potential of malignant cells. This protein is a substrate for the tyrosine kinase SRC, which is involved in the formation of the membrane bends, affects cellular production of active forms of oxygen, interacts with membrane metallоproteinases causing degradation of the extracellular matrix, but its role in invasive structures has not yet been fully understood. Further study of molecular components of invadopodies and their specific interactions provides better understanding of mechanisms of cellular invasion. Methods. Protein-protein interactions were identified by in vitro precipitation of protein complexes using GST-fused proteins and co-immunoprecipitation. Results. Adapter proteins ITSN1 and ITSN2 are new partners of TKS4. Interactions between intersectins and TKS4 are mediated by the SH3A, SH3C and SH3E domains of ITSN1 or ITSN2. TKS4 phosphorylation on tyrosine residues does not affect interactions between TKS4 and intersectins. Conclusions. In this study, we have showed that TKS4 interacts with endocytic adaptor proteins of the intersectin family, ITSN1 and ITSN2. We have also demonstrated that TKS4 and ITSN1 can form a complex in invasive MDA-MB-231 breast cancer cell line.
Keywords: TKS4, ITSN1, ITSN2, protein-protein interactions.
On the nature of non-protein receptors from the conceptual point of view. Paradigm for abscisic acid
Authors: Kurchii B. A. 
Published: November 2019

Abscisic acid (ABA) is a biologically active substance that takes part in the various biochemical and physiological processes in the plants. There is currently limited knowledge about how these biochemical and physiological processes are triggered and regulated by ABA. Dozens of receptors have been described for ABA signaling but there is no any information why does ABA have so many receptors and how they act at the molecular levels. In this connection I would like to stress that not all cell proteins conjugated with ABA necessarily can be represented as hormone-receptors complexes. In this paper I proposed that physiological processes in plants are performed at molecular level by elementary chemical reactions (redox reactions) that trigger the cascade of subsequent reactions and that can be caused by various chemical and physical factors. Gene keys (fragments of polynucleotides, non-protein receptors) and gene locks (start fragment of genes) are also described.
Keywords: abscisic acid, free radicals, receptors, gene keys, gene locks.
β-glucosidase PYK 10 gene expression in Arabidopsis thaliana (L.) Heynh. seedlings under clinorotation and X-radiation
Authors: Romanchuk S. M. 
Published: November 2019

Aim. Among plants used in spaceflight experiments, species of family Brassicaceae are considered as the most resistant to radiation exposure. It is supposed that ER-bodies, which are derivative of granular endoplasmic reticulum and selectively accumulate an enzyme β-glucosidase, may be responsible for this resistance. We firstly investigated expression of β-glucosidase PYK10 gene in A. thaliana seedlings under slow horizontal clinorotation and Х-radiation of doses 0.5 Gy, 1 Gy, 2 Gy, 4 Gy, 6 Gy, 8 Gy, 10 Gy, and 12 Gy. Methods. Seedlings were grown on agar nutrient medium. PYK 10 expression was determined using a method of real-time PCR. Results. Significant enhancement of PYK 10 expression and increasing a number of ER-bodies in A. thaliana seedlings under the influence of clinorotation and X-radiation in comparison with control was established. An increase in the number of ER-bodies was due to PYK 10 high expression and β-glucosidase synthesis without a rise of enzyme activity under clinorotation, while β-glucosidase activity increased under X-radiation. Plant responses to X-radiation became adaptive during 10 days after radiation, in which β-glucosidase plays a crucial role. Conclusions. Increased PYK 10 expression in A. thaliana seedlings under clinorotation and X-radiation is a part of the internal program of plant protection against the action of environmental factors. ER-bodies containing β-glucosidase may be one of the main components of the plant protection system from the influence of clinorotation and X-radiation.
Keywords: Arabidopsis thaliana (L.) Heynh., ER-bodies, β-glucosidase, gene expression, clinorotation, Х-radiation.
Efficiency of spring barley haploid production in anther culture in vitro: comparison of basic and improved technologies
Authors: Bilinska O. V. , Dulnyev P. G. 
Published: November 2019

Aim. Evaluation of innovative methodological approaches elaborated on model genotypes for usability to increase frequencies of morphogenic structure induction and plant regeneration in anther culture in vitro in spring barley diverse material. Methods. Spikes isolated from F1 and F2 hybrids of four crosses were pretreated using an improved method (4ºC, 28 days), and anthers were inoculated onto nutrient media containing chemically modified starches D5-M and D5a-1 instead of agar. In control cut tillers were emerged in water and pretreated at 4ºC for 5 days. Anthers were cultivated on agar solidified medium. Results. Positive effects of the improved method of cold pretreatment and cultivation of anthers on media solidified with starches were confirmed. The advantage of new gelling agent D5a-1 was proved. Particularly, its usage resulted in a three-fold increase in the frequency of green plant regeneration. Conclusions. In order to increase spring barley androgenic haploid yield, combination of prolonged cold pretreatment with anther cultivation on media solidified with chemically modified starches instead of agar in an integrated technological process is reasonable.
Keywords: Hordeum vulgare L., anther culture in vitro, cold pretreatment, starch, agar, embryo formation, plant regeneration.