Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

Background During Drosophila spermatogenesis, testis-specific meiotic arrest complex (tMAC) and testis-specific TBP-associated factors (tTAF) contribute to activation of hundreds of genes required for meiosis and spermiogenesis. Intriguingly, tMAC is paralogous to the broadly expressed complex Myb-MuvB (MMB)/dREAM and Mip40 protein is shared by both complexes. tMAC acts as a gene activator in spermatocytes, while MMB/dREAM was shown to repress gene activity in many cell types. Results Our study addresses the intricate interplay between tMAC, tTAF, and MMB/dREAM during spermatogenesis. We used cell type-specific DamID to build the DNA-binding profiles of Cookie monster (tMAC), Cannonball (tTAF), and Mip40 (MMB/dREAM and tMAC) proteins in male germline cells. Incorporating the whole transcriptome analysis, we characterized the regulatory effects of these proteins and identified their gene targets. This analysis revealed that tTAFs complex is involved in activation of achi, vis, and topi meiosis arrest genes, implying that tTAFs may indirectly contribute to the regulation of Achi, Vis, and Topi targets. To understand the relationship between tMAC and MMB/dREAM, we performed Mip40 DamID in tTAF- and tMAC-deficient mutants demonstrating meiosis arrest phenotype. DamID profiles of Mip40 were highly dynamic across the stages of spermatogenesis and demonstrated a strong dependence on tMAC in spermatocytes. Integrative analysis of our data indicated that MMB/dREAM represses genes that are not expressed in spermatogenesis, whereas tMAC recruits Mip40 for subsequent gene activation in spermatocytes. Conclusions Discovered interdependencies allow to formulate a renewed model for tMAC and tTAFs action in Drosophila spermatogenesis demonstrating how tissue-specific genes are regulated

Complex evaluation of the modern atmospheric air of city ecosystems

The results of studies of the chemical composition of atmospheric air showed that the concentration of ammonia (0.2520 mg/m3), nitrogen dioxide (0.3942 mg/m3) and hydrogen sulfide (0.0269 mg/m3) exceeded the MPC requirements. The seasonal dynamics of the spread of aerogenic pollutants revealed a decrease in NO, NO2, H2S, SO2 from winter to the spring-summer season. However, the content of such pollutants as NH3, CO and dust increased significantly in summer to 0.0816, 3.7140 and 0.0289 mg/m3 respectively. During bio-indication of 363 trees only 4 species of the 16 studied ones were characterized as healthy (K<1.5). The overall level of attenuation was 2.16 (“weakened forest”). Evaluation of the fluctuating asymmetry showed high resistance of the maple (Acer Platanoides) to environmental pollution (the level of asymmetry in the transport zone was 0.039 against 0.077–0.078 in the silver birch (Betula pendula) and the fragrant poplar (Populus suaveolens). The high level of anthropogenic pollution in the transport zones of the city adversely affected roadside biotopes. It has been proven that roadside phytocenosis is significantly sparse and the population density drops sharply by 50–100 %, compared to cleaner functional areas. The results of lichenoid indication showed that in most of the sites studied, the air was highly polluted (pollution class 1) and the concentration of SO2 was 0.10–0.30 mg/m3

The study of the nature of the inheritance of quantitative traits in F

In the conditions of the south of the Nonchernozem Zone, intraspecific hybridization of winter soft wheat was carried out. When selecting parental forms used in crossing, special attention was paid to such economically valuable traits as productive tilling capacity, the number of grains and the mass of grain per spike. The true (Htru) and hypothetical heterosis (Hhyp) on the basis of “plant height”, “length of the lower internode”, “length of the upper internode”, “general tilling capacity”, “productive tilling capacity”, “spike length”, “number of spikelets”, “number of grains” and “grain weight per spike” were determined. It was established that the inheritance of quantitative traits in hybrids of the first generation was distinguished by the complex nature of distribution by types. Studies have made possible to identify 5 hybrid combinations F1, in which the effect of heterosis manifests itself simultaneously on five quantitative characteristics (ear length, number of spikelets per ear, number of grains per ear, grain weight per ear, mass grain from a plant)

Analysis of consequences of the relationship between man, nature and technology in the context of technogenesis intellectualization

The paper presents the results of the analysis of demographic and medico-social data characterizing the dynamics of morbidity and mortality from environmental diseases, in particular, diseases of the cardiovascular system. The trend of negative natural population growth was revealed, amounting to -6.9 per 1,000 persons by 2019. The number of patients with cardiovascular diseases was 13 817,4 persons, with the overwhelming majority of the working-age population (9020,2 persons). Ischemic heart disease had the largest share in the structure of the studied diseases (62,25 %). There was also a decrease in life expectancy over the past 30 years and an increase in mortality of young and middle-aged people

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Additional file 6: Fig. 5. Averaged DamID profiles of Can, Comr, and Mip40 at the TSS of genes. The genes having the peaks of Can, Comr, and Mip40 within 1 kb around their TSS were selected. Then, for each coordinate within this area the normalized number of peaks was calculated. Ordinate–relative abundance of each protein. Black line represents the randomized set of peaks

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Additional file 10: Fig. 8. Overlap between direct gene targets of Comr, Can, and Mip40

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Additional file 14: Fig. 11. Analysis of short motifs in the CG9879 peaks. Top three most frequent motifs found in CG9879 peaks using DREME [24] are shown. AT-rich motifs are similar to TATA-box sequences

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Additional file 23: Fig. 19. Targeted deletion of CG9879 gene using CRISPR/Cas9. A The strain with the insertion of transposon containing yellow reporter gene 600 bp upstream CG9879 gene was used. chiRNAs were designed flanking the transposon and CG9879 gene. Targeted sequences are shown. Cas9 introduced the double-strand breaks within the targeted sequences as shown. Upon repair, the fragment containing transposon with the yellow reporter and CG9879 gene was deleted and the new junction appeared. Deletion was confirmed by Sanger sequencing (B)

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Additional file 12: Fig. 9. RNA in situ hybridization localization of CG9879, Trf, and Trf2 transcripts. Upper row—in wild-type testis; lower row—in meiosis arrest mutants. CG9879 transcript is not expressed in aly mutants, while Trf and Trf2 retain their expression in mutant spermatocytes

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Additional file 21: Fig. 17. Performance of peak calling algorithm illustrated by Can DamID data. A Numbers of Can peaks and false positive peaks at different significance levels. FDR=0.05 is reached at the P = 1.7 × 10−7 (dashed line). B Specificity of peak calling at different FDR values. At high FDR values, there is no prevalence of Can to the genes that are down-regulated in can mutants over the genes that are up-regulated. At FDR = 0.05, the number of down-regulated genes is about fourfold higher than the number of up-regulated genes