Browsing by Author "Kalendar, Ruslan"

Sort by: Order: Results:

Now showing items 1-10 of 10
  • Trebichalsky, Andrej; Kalendar, Ruslan; Schulman, Alan; Stratula, Olga; Galova, Zdenka; Balazova, Zelmira; Chnapek, Milan (2013)
  • Hosid, Elena; Brodsky, Leonid; Kalendar, Ruslan; Raskina, Olga; Belyayev, Alexander (Genetics Society of America, 2012)
    Background: The environment can have a decisive influence on the structure of the genome, changing it in a certain direction. Therefore, the genomic distribution of environmentally sensitive transposable elements may vary measurably across a species area. In the present research, we aimed to detect and evaluate the level of LTR retrotransposon intraspecific variability in Aegilops speltoides (2n=2x=14), a wild cross-pollinated relative of cultivated wheat. Results: The inter-retrotransposon amplified polymorphism (IRAP) protocol was applied to detect and evaluate the level of LTR retrotransposon intraspecific variability in Ae. speltoides and closely related species of sect. Sitopsis. IRAP analysis revealed significant diversity in TE distribution. Various genotypes from the same population significantly differ with respect to the patterns of the four explored LTR retrotransposons (WIS2, Wilma, Daniela, and Fatima). This diversity points to a constant ongoing process of LTR retrotransposon fraction restructuring in populations of Ae. speltoides throughout the species’ range and within single populations in time. Maximum changes were recorded in genotypes from small stressed populations. Principal component analysis showed that the dynamics of the Fatima element in populations of Ae. speltoides significantly differ from those of WIS2, Wilma, and Daniela. In terms of relationships between Sitopsis species, IRAP analysis of WIS2, Wilma, and Daniela elements revealed a grouping similar to groupings determined by other methods, with Ae. sharonensis and Ae. longissima forming a separate unit, Ae. speltoides appearing as a dispersed group, and Ae. bicornis being in an intermediate position. Conclusions: IRAP display data revealed dynamic changes in LTR retrotransposon fractions in the genome of Ae. speltoides. The process is permanent and population-specific, ultimately leading to the separation of small stressed populations from the main bunch.
  • Bublyk, Olena M.; Andreev, Igor O.; Kalendar, Ruslan; Spiridonova, Kateryna V.; Kunakh, Viktor A. (Springer-Verlag, 2013)
  • Kalendar, Ruslan; Lee, David; Schulman, Alan H. (ACADEMIC PRESS, 2011)
    The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict properties oligonucleotides based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.
  • Zachepilo, Tatiana; Kalendar, Ruslan; Schulman, Alan; Vaido, Alexander; Dyuzhikova, Natalia (2014)
    Stress can induce structural changes in the brain and contribute to a variety of chronic diseases from post-traumatic stress disorder to depression. The hippocampus is a highly plastic brain region particularly susceptible to the effects of environmental stress. A genomic stress response partly consists in changes in insertion activity of transposable elements. Retrotransposons account for ~45% of the mammalian genome. Mechanisms of action of stress and the formation of posttraumatic stress disorder (PTSD) in hu-man are associated with retrotransposons (LINE1, L1) activity in various tissues. Endogenous retrotransposition of L1 elements has been proposed as one potential mechanism generating neuronal genome diversity. They are capable of inserting into new genomic locations, which can result in deleterious outcomes. The greatest interest is the study of these processes in the brain due to indi-vidual variability of neural processes to effective pharmacotherapy path finding. The purpose of this work was to investigate the effect of stress on the LINE1 insertion pattern in the hippocampus. We used the model of emotional stress for the PTSD-like state formation in two lines of rats with genetically determined differ-ences in the level of excitability of the nervous system (low and high) to study of emotionally painful stress (3 types: short-term, long-term and massive stress) effect on LINE1 retrotransposon insertion polymorphism in the dentate gyrus of the hippocampus. L1 insertions in the promoter of gene GRIN1 [glutamate receptor ionotropic N-methyl-D-aspartate (NMDA) subtype, subunit 1] examined by two-step PCR (general and directed). Glutamate NMDA receptors play a key role in synaptic plasticity, synap-togenesis, excitotoxicity, memory acquisition and learning. These receptors mediate neuronal functions in glutamate neurotransmis-sion. NMDAR-mediated neurotransmission in the hippocampus is implicated in cognitive and emotional disturbances during stress-related disorders. NMDA receptor subunit 1 is a core molecule in the NMDA receptor complex. GRIN1 expression is associated with neurotransmission efficiency and state of the nervous system. We suppose that L1 retrotransposon insertions to promoter of GRIN1 gene will alter GRIN1 expression. It was shown that L1 insertion pattern depends on the level of excitability of the nervous system, intensity and duration of stress exposure. The most variable spectrum of L1 transposable elements activity (L1 insertion pattern) is detected under the influence of massive stress in the rats with low excitability of the nervous system. We assume that L1 retrotransposon insertions take part in the regulation of expression of candidate genes associated with the stress response and the formation of psychopathology.
  • Kalendar, Ruslan (Novi Sad Institute of Field and Vegetable Crops, 2011)
    Molecular markers play an essential role in all aspects of genetics, modern plant breeding, in human forensics, for map-based cloning of genes, ranging from the identification of genes responsible for desired traits to the management of backcrossing programs. Retrotransposons are well suited as molecular markers. As dispersed and ubiquitous transposable elements, their “copy and paste” life cycle of replicative transposition leads to new genome insertions without excision of the original element. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. Following the demonstration that retrotransposons are ubiquitous, active, and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of genetic diversity in plants and the way for the rapid isolation of retrotransposon termini.
  • Baranova, Tatyana; Kalendar, Ruslan; Kalaev, V (V. N. Sukachev Institute of Forest, Russian Academy of Sciences, Siberian Branch, 2014)
    The first and second internal transcribed spacer (ITS1 and ITS2) regions of the ribosomal DNA and 5.8S rRNA gene from Rhododendron L. were analysed. This study reveals phylogenetic relationships and collation of data on the phylogeny of the genus Rhododendron L . according to the research of other authors using molecular and classical methods. Sequence analysis of ribosomal spacer showed low variability between species of the genus Rhododendron series of Dauricum. Rh. mucronulatum Turcz., Rh. dauricum L. and some other studied species had identical nucleotide ITS1-ITS2 sequence indicating the artificial division into separate species. Found species differing from each other by 1-2 or few nucleotides, which allows assuming their common phylogenetic affiliation or excluding one taxonomic unit. According to the analysis of ITS1-ITS2 sequences identified 16 groups of species with similar sequence ITS1-ITS2. When comparing the morphological descriptions of some species of the genus Rhododendron L. with a similar sequence of ITS1-ITS2 marked their small differences. Based on the results of molecular genetic analysis it has been assumed that Rhododendron dauricum L., Rh. ledebourii Pojark, Rh. sichotense Pojark and Rh. mucronulatum Turcz belong to the same species. The establishment phylogenetic relationships based on sequence ITS1-ITS2, applicable only in respect of highly isolated species Rhododendron L. To clarify the phylogenetic relationships of the genus Rhododendron L. necessary to expand the comparative analysis of the DNA sequences of universal genes or complex repeats elements (retrotransposons).
  • Belyayev, Alexander; Kalendar, Ruslan; Brodsky, Leonid; Nevo, Eviatar; Schulman, Alan; Raskina, Olga (2010)
    Background<br/>How new forms arise in nature has engaged evolutionary biologists since Darwin's seminal treatise on the origin of species. Transposable elements (TEs) may be among the most important internal sources for intraspecific variability. Thus, we aimed to explore the temporal dynamics of several TEs in individual genotypes from a small, marginal population of Aegilops speltoides. A diploid cross-pollinated grass species, it is a wild relative of the various wheat species known for their large genome sizes contributed by an extraordinary number of TEs, particularly long terminal repeat (LTR) retrotransposons. The population is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA) sites. We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation. <br/><br/>Results<br/>Significant temporal fluctuation in the copy number of TEs was detected when processes that take place in small, marginal populations were simulated. It is known that under critical external conditions, outcrossing plants very often transit to self-pollination. Thus, three morphologically different genotypes with chromosomal aberrations were taken from a wild population of Ae. speltoides, and the dynamics of the TE complex traced through three rounds of selfing. It was discovered that: (i) various families of TEs vary tremendously in copy number between individuals from the same population and the selfed progenies; (ii) the fluctuations in copy number are TE-family specific; (iii) there is a great difference in TE copy number expansion or contraction between gametophytes and sporophytes; and (iv) a small percentage of TEs that increase in copy number can actually insert at novel locations and could serve as a bona fide mutagen. <br/><br/>Conclusions<br/>We hypothesize that TE dynamics could promote or intensify morphological and karyotypical changes, some of which may be potentially important for the process of microevolution, and allow species with plastic genomes to survive as new forms or even species in times of rapid climatic change.
  • Boronnikova, Svetlana; Kalendar, Ruslan (M A I K NAUKA - INTERPERIODICA, 2010)
    Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.