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относятся Aphelenchoides parasoprophilus, A. trivi-alis, A. capsuloplanus, A. delhiensis, A. submersus, Aphelenchus cylindricaudata. В стеблях и листьях из микохилофагов отмечены Aphelenchus avenae, Aphelenchoides parietinus, A. composticola.
Фитопаразиты в корнях представлены 11 видами; преобладают особи Ditylenchus dipsaci. В эту группу также входят виды: Bitylenchus dubius, Pratylenchus pratensis, P. neglectus, Helicotylenchus dihystera, Tylenchorhynchus tener, T. brassicae, Heli-cotylenchus pseudorobustus.
В стеблях исследуемых культур обнаружено 14 видов девисапробионтов, в том числе Panagro-laimus rigidus, P. mycophilus, P. multidentatus, Eucephalobus oxyuroides, Chiloplacus propinquus, Ch. sclerovaginatus. Первые два вида занимают доминирующее положение и составляют основную массу особей фитонематод. В листьях зарегистрировано 13 видов девисапробионтов, доминируют Panagrolaimus rigidus, P.multidentatus, P. mycophi-lus, P. subelongatus.
Паразитические нематоды в стеблях и листьях очень редки и представлены лишь видом Ditylenchus dipsaci.
Надо отметит, что выше указанные паразитические нематоды были немногочисленные и серьёзную угрозу для пшеницы не представляют. Однако, выявление на пшеничных полях комплекса весьма патогенных паразитических видов нематод - прати-ленхов, геликотиленхов, тиленхоринхов и дитилен-хусов с достаточно высокой плотностью их популяций, вызывает особую тревогу, как широко распространившейся опасной болезни.
Ссылки:
1. Малахов В., Рыжиков К., Сонин М. 1982. "Система крупных таксонов нематод: подклассы, отряды, подотряды." Зоол. журн. -М.: -Т.11.-вып.8.-С. 1125-1134.
2. Парамонов А. 1962. "Основы фитогельмин-тологии." Изд-во. АН СССР.-М.: Т.1.- С.480.
3. Парамонов А. 1952. "Опыт экологической классификации фитонематод." Тр. ГЕЛАН. М.: -Т.6.-С. 338-369.
4. Груздева Л. 1989. "Структура сообществ нематод торфяных почв при внесении минеральных удобрений." Влияние минеральных удобрений на сообщества почвенных нематод., Петрозаводск, - С. 82-97.
O.A.Orlovsky
Ph.D (Biol), D.Sc(MA), staff scientist, R.E.Kavetsky Institute of experimental pathology, oncology and radiobiology
NAS of Ukraine, Kyiv O.A.Samoylenko Principal engineer, the same place of employment
V.O. Shlyakhovenko Doctor of medicine, professor, principal staff scientist, the same place of employment
C-MYC-TFBS-COMPLEMENTARY AND NF-KB-p50-TFBS-COMPLEMENTARY MOTIFS IN MATURE miRNA OF HUMAN AND LABORATORY RODENTS
Abstract
The aim of our study was to evaluate all miRNAs have been discovered in Homo sapiens and in the most widespread laboratory animals - Mus musculus and Rattus norvegicus - in respect to their potential ability to function as alternative agents for such protein transcription factors as c-myc and NF-kB p50.
Methods. C-myc-TFBS-complementary and NF-KB-p50-TFBS-complementary motifs were determined as the short RNA nucleotide sequences, complementary to the c-myc-binding and NF-KB-p50-binding DNA motifs described in our previous paper [7] and were found in the miRNA sequences by the same way as it was described in [7] for the DNA TFBS motifs. Overlaps of the TFBS-complementary motifs were specially noted as a sign of informational redundancy of miRNA-mediated transcription control.
Results. Number of the TFBS-complementary sites, including conventional ones, runs up to a few of tens and even hundreds per each species miRNA set. The sites assortment and distribution in the whole species miRNA sets and in the individual miRNA families suggest that each kind of conventional or modified TFBS and corresponding TFBS-complementary site has its own specific function in the transcription control. Informational redundancy of miRNA-mediated transcription control was shown to be many times more for c-myc than for NF-kB p50 suggesting the first of them is much more evolutionary old than the second.
Keywords: microRNA, transcription factor binding site (TFBS), transcription control.
As contemporary literature shows, miRNA role in cases, miRNA-mediated transcription control is not di-the protein expression control is, at least, dual. Com- rect, namely is based on post-transcriptional affect of monly known for today is post-transcriptional pathway protein transcription factor (TF) expression. Neverthe-based on miRNA interaction with mRNA. But there are less, there are some data showing direct miRNA-medi-also some experimental works showing the miRNA ated transcription control.
ability to regulate transcription of several genes, as well At the same time, we could not find any publica-
as some reviews of such works [1 — 3]. In certain tions about global evaluation of the total miRNA set,
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known in one or another biological species, in respect to their potential ability to function as alternative transcription factors. Although, it must be noted at least one opposite investigation [4], in which the authors have searched for the transcription factor binding sites (TFBS) in the miRNAs themselves.
The aim of our study was to evaluate all miRNAs have been discovered in Homo sapiens and in the most widespread laboratory animals - Mus musculus and Rattus norvegicus - in respect to their potential ability to function as alternative agents for such protein transcription factors as c-myc and NF-kB p50.
Materials and methods Nucleotide sequences of the mature miRNAs were retrieved in the miRBase — the officially main miRNA database in the world being supported by Manchester University (UK) [5, 6] - and saved in the Microsoft Word format (.doc or .docx).
C-myc-TFBS-complementary and NF-KB-p50-TFBS-complementary motifs were determined as the short RNA nucleotide sequences, complementary to the c-myc-binding and NF-KB-p50-binding DNA motifs described in our previous paper [7] and were found in the miRNA sequences by the same way as it was described in [7] for the DNA TFBS motifs. Overlaps of the TFBS-complementary motifs were specially noted as a sign of informational redundancy of miRNA-me-diated transcription control.
Note 1. We name the TFBS variations as "deletions", "insertions" or "exchanges", i.e., such as mutations are named commonly. But we can't know, are they real mutations or constitutional variations. Indeed, we can establish a true mutation only if we know that certain nucleotide sequence was previously without the
Table 1.
Total number of c-myc-TFBS-complementary sites in miRNAs of Homo sapiens, Mus musculus and Rattus
variation we observe now and only later got it. Moreover, some our finds (see below) suggest that most of the TFBS and TFBS-complementary site variations are just constitutional, not true mutant.
Statistical evaluations. If it was necessary, significance of the differences was calculated using the exact Fisher's method. But, since such factorials of big numbers as, for example 435! or 2558!, in practice may be used only in the rough, in a*10n form, where a is a rational number [8], the final results where also evaluated approximately, as P<0.001, etc.
Results and discussion
Interpreting the search results, it must be pointed that, in contrast to the [7] paper, in this case we have studied not a material obtained from single donor or single inbred strain of mice but total species sets of the material (miRNA) as they were known at a time point when the study was initiated, i.e., on October 12, 2016.
Since the miRNAs studied number was enough high (2558 for Homo sapiens, 1915 for Mus musculus and 765 for Rattus norvegicus) and, in addition, the miRBase data are compiled from a few hundreds of the works have been performed on manifold materials with quite different aims, these species sets may be regarded as statistically representative samples.
The integrated search results are given in the Tables 1and 2. The supplementary materials (full schemes and tables, near 700 pages) one can obtain by request on one of the following e.mails: orlova-leks1955 @ukr.net, orlovaleks 1955 @mail.ru, orlova-leks@rambler.ru.
Number of sites (% of Esites) Overlaps
Conventional Deletion Insertion Exchange Inner inversion
Homo sapiens, 2558 mature miRNAs, Esites=435 (E/NmiRNA~0.17)
51 (11.7) 325 (74,7) 49 (11.3) 0 (0) 10 (2.3) 2
Mus musculus, 1915 mature miRNAs, Esites=256 (E/NmiRNA~0.13)
23 (9.0) 190 (74.2) 39 (15.2) 0 (0) 4 (1.6) 0
Rattus norvegicus, 765 mature miRNAs, Esites=150 (E/NmiRNA~0.20)
20 (13.3) 106 (70.7) 22 (14.7) 0 (0) 2 (1.3) 0
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Table 2.
Total number of NF-KB-p50-TFBS-complementary sites in miRNAs of Homo sapiens, Mus musculus and _Rattus norvegicus__
Number of sites (% of Esites) Overlaps
Conventional Deletion Insertion Exchange In total (% of total sites) Double (% of total overlaps)
Homo sapiens, 2558 mature miRNAs, Esites=132 (E/NmiRNA~0.05)
16 (12.1) 55 (41.7)* 22 (16.7) 39 (29.5)# 25* (19%) 10** (40%)
Mus musculus, 1915 mature miRNAs, Esites=77 (E/NmiRNA~0.04)
9 (11.7) 39 (50.6)* 8 (10.4) 21 (27.3)# 19* (25%) 4** (21%)
Rattus norvegicus, 765 mature miRNAs, Esites=31 (E/NmiRNA~0.04)
2 (6.5) 18 (58.1)* 2 (6.5) 9 (29.0)# 5* (16%) 0**
Notes: * - P<0.05 versus the corresponding cell of the Table 1; # - P<0.001 versus the corresponding cell of the Table 1; ** - P<0.01 versus each of two other species miRNA sets.
As one can see in the Tables 1 and 2, regulatory potential of miRNA with respect to transcription of the c-myc-dependent and NF-kB-dependent genes is rather high, because number of correspondent TFBS-complementary sites, including conventional ones, runs up to a few of tens and even hundreds per each species miRNA set.
Note 2. Naturally, we can not know at the point, how frequently and under what conditions this potential would be realized. But one can be sure such conditions really exist and this potential is realizing, because there is nothing in nature that is possible and never realizing.
Of a special interest is similarity among these data and the data on the corresponding DNA TFBS [7, Supplementary materials] in regard to the following points:
а) in each of the species have been studied, number of the modified TFBS-complementary sites is multiple higher than conventional ones;
б) in each species miRNA set, number of the c-myc-TFBS-complementary sites is significantly more than NF-KB-p50-TFBS-complementary ones.
Of a special interest is a strong dependence of the TFBS-complementary site spectra on both biological species and TF kind. In particular:
- in all cases, the sites with deletions essentially prevail among all modified sites, and this predominance is significantly more for the c-myc-TFBS-complementary sites than for NF-KB-p50-TFBS-complementary ones;
- for c-myc, the sites with exchanges are completely absent, wheres number of such sites for NF-kB p50 amounts 27-29% in each of three species, and this difference is of high statistical significance;
- among the miRNA families [Supplementary materials to this paper], there are some ones containing certain kind of TFBS-complementary sites (in some cases, more than one copy per a member) in all their known members (for example, miR-941 family in
Homo sapiens contains conventional c-myc-TFBS-complementary sites in each of its 5 members - in twos in four of them and one - in the fifth); miR-3118 family contains one c-myc-TFBS-complementary site with deletion in each of its 4 members; miR6724 family -one c-myc-TFBS-complementary site with inner inversion in each of its 4 members; miR-3689 family (4 known members) is rich in the NF-KB-p50-TFBS-complementary sites, both conventional and deleted or inserted, etc.).
These data are of fundamental importance because they suggest a new look on the nature of TFBS variations and miRNA classification. Namely:
- contrary to the contemporary common opinion, the TFBS variations are not accidental, but each kind of TFBS in DNA and TFBS-complementary site in miRNA has its specialized function in the transcription control;
- miRNA families and individual miRNAs specialization in the transcription control must constitute a new complementary principle of their classification.
A special kind of data makes calculation of the overlaps between the TFBS-complementary sites. We have registered only 2 overlaps between the c-myc-TFBS-complementary sites, and both of them - in the Homo sapiens miRNA set (Table 1 and Supplementaru materials). Double overlaps were not found there. In contrast to this, the overlaps of the NF-KB-p50-TFBS-complementary sites mount 16-25% of total TFBS-complementary sites number in each species miRNA set (Table 2 and Supplementaru materials). Moreover, there were found enough multiple cases of the double overlaps, and just this kind of finds makes essential in-terspecies difference (Table 2).
The overlaps data show:
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Wschodnioeuropejskie Czasopismo Naukowe (East European Scientific Journal)^ 1(17), 2017
a) many times higher level of informational redundancy of miRNA-mediated transcription control realizing through NF-kB p50 TFBS versus c-myc TFBS; this suggest c-myc to be much more evolutionary old than NF-kb;
b) significantly higher level of informational redundancy of miRNA-mediated transcription control in Homo sapients than in the rodents.
References
1. Martins F.M.M. In silico analysis of miRNA promoters / Mestrado em Bioinformatica e Biologia Computational.- Universidade de Lisboa.- 2011.- 41p. (In English, titles and abstract in Portugal).
2. Somel M., Liu X., Tang L., et al. MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates // PLOS Biology.- 9(12).- e1001214.- doi: 10.1371/journal.plbio.1001214
3. Liu Z-P., Wo C., Miao H., Wo H. RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse // Database.- Vol. 2015.- Article ID 095.- doi:
10.1093/database/bav095.
4. Putta P., Orlov Yu.L., Podkolodnyy N.L., Mitra C.K. Relatively conserved common short sequences in transcription factor binding sites and miRNA // Вавиловский журнал генетики и селекции.- 2011.-Т.15, №4.- С. 750-756.
5. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data // Nucl. Acids Res.- 2011.- 39 (Database issue).-P. 152-157.
6. Aushev V.N. MicroRNA: small molecules of great significance // Klin. Oncohematol.- 2015.- V. 8, #1.- P. 1-12 (in Russian).
7. Orlovsky O.A., Samoylenko O.A., Shlyakhovenko V.O. Transcription factor binding sites in a structural gene: what may be this? (by the example of the genes encoding the main enzymes of the polyamines metabolism) // East Eur. Sci. J. - 2016.- No 6(10), Part 3.- P. 62-68.
8. Factorial tables (in Russian) http://chursinvb.ucoz.ru/load/tablica faktorialov ot 1
do 2000/7-1-0-113
Paulouski M.B.
PhD in Biology
Central Botanical Gardens of the National Academy of Sciences of Belarus
Павловский Николай Болеславович
кандидат биологических наук, заведующий лабораторией Центральный ботанический сад Национальной академии наук Беларуси
PHENOLOGICAL DEVELOPMENT OF HIGHBUSH BLUEBERRY VARIOUS CULTIVARS IN
BELARUS
Summary: Drawing on a decade of stationary observation of seasonal growth rhythms and development, the paper demonstrates peculiarities of phenological development stages in 20 highbush blueberry cultivars and 3 halfhighbush blueberry cultivars. The calendar periods for the beginning of vegetation and duration of the spring phenological development stages in the cultivars differ considerably from year to year and depend on weather conditions. Cultivar differences in the development of blueberry show more vividly in the blooming period, and especially at the fruit ripening stage. The climatic conditions in the central agro-climatic region of Belarus ensure the completion of the entire cycle of seasonal development in highbush blueberry cultivars of the entire crop ripening range.
Key words: Vaccinium corymbosum, Highbush blueberry; Cultivars; Phenology; Temperature conditions; Correlation; Belarus.
Аннотация: На основании данных десятилетних стационарных наблюдений за ритмами сезонного роста и развития показаны особенности прохождения фаз фенологического развития 20 сортов голубики высокорослой и 3 сортов голубики полувысокорослой. Календарные сроки начала вегетации и продолжительность весенних фаз фенологического развития сортов по годам значительно варьируют и зависят от погодных условий. Сортовые различия развития голубики проявляются существенней в сроках цветения, а особенно созревания плодов. На основании результатов корреляционного анализа показаны особенности термической зависимости фенологического развития сортов голубики высокорослой в течение вегетационного периода. У подавляющего числа сортов голубики установлена сильная положительная корреляция между урожайностью и продолжительностью периода созревания плодов. Климатические условия центральной агроклиматической области Беларуси обеспечивают прохождение полного цикла сезонного развития сортами голубики высокорослой всего спектра созревания урожая.
Ключевые слова: Vaccinium corymbosum, голубика высокорослая, сорта, фенология, температурные условия, корреляция, Беларусь.
Introduction
Highbush blueberry (Vaccinium corymbosum) is a relatively new small-fruit crop introduced in Belarus from the Atlantic coast of North America. There are no absolutely identical regions in terms of climatic and soil
conditions. Therefore, plants are normally transferred to conditions that differ from their places of origin and their introduction can be successful when alien crops possess phenotypic adaptive flexibility. In order to identify the applicability of a plant in new conditions,
