Hybrid generations usually face either a heterosis advantage or a breakdown, that can be expressed by the level of parasite infection in hybrid hosts. Hybrids are less infected by parasites than parental species (especially F1 generations) or more infected than parental species (especially post-F1 generations). We performed the experiment with blood-feeding gill parasite Paradiplozoon homoion (Monogenea) infecting leuciscid species, Abramis brama and Rutilus rutilus, their F1 generation and two backcross generations. Backcross generations tended to be more parasitized than parental lines and the F1 generation. The number of differentially expressed genes (DEGs) was lower in F1 hybrids and higher in backcross hybrids when compared to each of the parental lines. The main groups of DEGs were shared among lines; however, A. brama and R. rutilus differed in some of the top gene ontology (GO) terms. DEG analyses revealed the role of heme binding and erythrocyte differentiation after infection by blood-feeding P. homoion. Two backcross generations shared some of the top GO terms, representing mostly downregulated genes associated with P. homoion infection. KEGG analysis revealed the importance of disease-associated pathways; the majority of them were shared by two backcross generations. Our study revealed the most pronounced DEGs associated with blood-feeding monogeneans in backcross hybrids, potentially (but not exclusively) explainable by hybrid breakdown. The lower DEGs reported in F1 hybrids being less parasitized than backcross hybrids is in line with the hybrid advantage.

• Klíčová slova
• Monogenea, Paradiplozoon homoion, RNA seq, differential gene expression, freshwater fish, hybrid breakdown, hybrid heterosis, hybridization,
• Publikační typ
• časopisecké články MeSH

Landfills, especially those poorly managed, can negatively affect the environment and human beings through chemical contamination of soils and waters. This study investigates the soils of a historical municipal solid waste (MSW) landfill situated in the heart of a residential zone in the capital of Slovakia, Bratislava, with an emphasis on metal (loid) contamination and its consequences. Regardless of the depth, many of the soils exhibited high metal (loid) concentrations, mainly Cd, Cu, Pb, Sb, Sn and Zn (up to 24, 2620, 2420, 134, 811 and 6220 mg/kg, respectively), classifying them as extremely contaminated based on the geo-accumulation index (Igeo >5). The stable lead isotopic ratios of the landfill topsoil varied widely (1.1679-1.2074 for 206Pb/207Pb and 2.0573-2.1111 for 208Pb/206Pb) and indicated that Pb contained a natural component and an anthropogenic component, likely municipal solid waste incineration (MSWI) ash and construction waste. Oral bioaccessibility of metal (loid)s in the topsoil was variable with Cd (73.2-106%) and Fe (0.98-2.10%) being the most and least bioaccessible, respectively. The variation of metal (loid) bioaccessibility among the soils could be explained by differences in their geochemical fractionation as shown by positive correlations of bioaccessibility values with the first two fractions of BCR (Community Bureau of Reference) sequential extraction for As, Cd, Mn, Ni, Pb, Sn and Zn. The results of geochemical fractionation coupled with the mineralogical characterisation of topsoil showed that the reservoir of bioaccessible metal (loid)s was calcite and Fe (hydr)oxides. Based on aqua regia metal (loid) concentrations, a non-carcinogenic risk was demonstrated for children (HI = 1.59) but no risk taking into account their bioaccessible concentrations (HI = 0.65). This study emphasises the need for detailed research of the geochemistry of wastes deposited in urban soils to assess the potentially hazardous sources and determine the actual bioaccessibility and human health risks of the accumulated metal (loid)s.

• Klíčová slova
• Bioaccessibility, Contamination, Health risks, Landfill, Soil, Trace metals,
• MeSH
• hodnocení rizik MeSH
• kovy analýza   MeSH
• látky znečišťující půdu * analýza   MeSH
• lidé MeSH
• monitorování životního prostředí * metody   MeSH
• odpadky - odstraňování MeSH
• půda * chemie   MeSH
• skládková zařízení * MeSH
• těžké kovy analýza   MeSH
• tuhý odpad * analýza   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Slovenská republika MeSH
• Názvy látek
• kovy MeSH
• látky znečišťující půdu * MeSH
• půda * MeSH
• těžké kovy MeSH
• tuhý odpad * MeSH

Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. However, currently available resources, 'Telomerase database' and 'Plant rDNA database', contain just fragments of all relevant literature published over decades of telomere research as they have a different primary focus and limited updates. To fill this gap, we gathered data about telomere DNA sequences from a thorough literature screen as well as by analysing publicly available NGS data, and we created TeloBase (http://cfb.ceitec.muni.cz/telobase/) as a comprehensive database of information about telomere motif diversity. TeloBase is supplemented by internal taxonomy utilizing popular on-line taxonomic resources that enables in-house data filtration and graphical visualisation of telomere DNA evolutionary dynamics in the form of heat tree plots. TeloBase avoids overreliance on administrators for future data updates by having a simple form and community-curation system for application and approval, respectively, of new telomere sequences by users, which should ensure timeliness of the database and topicality. To demonstrate TeloBase utility, we examined telomere motif diversity in species from the fungal genus Aspergillus, and discovered (TTTATTAGGG)n sequence as a putative telomere motif in the plant family Chrysobalanaceae. This was bioinformatically confirmed by analysing template regions of identified telomerase RNAs.

• MeSH
• databáze genetické * MeSH
• nukleotidové motivy MeSH
• rostliny genetika   MeSH
• telomerasa * genetika   MeSH
• telomery genetika   metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• telomerasa * MeSH

Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm5U34) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U-containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.

• Klíčová slova
• ALKBH8, HITS-CLIP, Trm9, mcm5U, mcm5s2U, wobble uridine modification,
• MeSH
• AlkB homolog 8, tRNA methyltransferasa genetika   MeSH
• antikodon MeSH
• ChiP sekvenování * MeSH
• lidé MeSH
• nekódující RNA genetika   MeSH
• RNA transferová * genetika   metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• AlkB homolog 8, tRNA methyltransferasa MeSH
• ALKBH8 protein, human MeSH Prohlížeč
• antikodon MeSH
• nekódující RNA MeSH
• RNA transferová * MeSH

INTRODUCTION: Parasite-mediated selection is considered one of the potential mechanisms contributing to the coexistence of asexual-sexual complexes. Gibel carp (Carassius gibelio), an invasive fish species in Europe, often forms populations composed of gynogenetic and sexual specimens. METHODS: The experimental infection was induced in gynogenetic and sexual gibel carp using eye-fluke Diplostomum pseudospathaceum (Trematoda), and the transcriptome profile of the spleen as a major immune organ in fish was analyzed to reveal the differentially expressed immunity-associated genes related to D. pseudospathaceum infection differing between gynogenetic and sexual gibel carp. RESULTS: High parasite infection was found in gynogenetic fish when compared to genetically diverse sexuals. Although metacercariae of D. pseudospathaceum are situated in an immune-privileged organ, our results show that eye trematodes may induce a host immune response. We found differential gene expression induced by eye-fluke infection, with various impacts on gynogenetic and sexual hosts, documenting for the majority of DEGs upregulation in sexuals, and downregulation in asexuals. Differences in gene regulation between gynogenetic and sexual gibel carp were evidenced in many immunity-associated genes. GO analyses revealed the importance of genes assigned to the GO terms: immune function, the Notch signaling pathway, MAP kinase tyrosine/threonine/phosphatase activity, and chemokine receptor activity. KEGG analyses revealed the importance of the genes involved in 12 immunity-associated pathways - specifically, FoxO signaling, adipocytokine signaling, TGF-beta signaling, apoptosis, Notch signaling, C-type lectin receptor signaling, efferocytosis, intestinal immune network for IgA production, insulin signaling, virion - human immunodeficiency virus, Toll-like receptor signaling, and phosphatidylinositol signaling system. DISCUSSION: Our study indicates the limited potential of asexual fish to cope with higher parasite infection (likely a loss of capacity to induce an effective immune response) and highlights the important role of molecular mechanisms associated with immunity for the coexistence of gynogenetic and sexual gibel carp, potentially contributing to its invasiveness.

• Klíčová slova
• RNA seq, asexual and sexual reproduction, differential gene expression, fish, immunity-associated pathways, invasive species, parasites,
• MeSH
• infekce červy třídy Trematoda * veterinární   imunologie   parazitologie   MeSH
• interakce hostitele a parazita imunologie   MeSH
• kapři parazitologie   imunologie   genetika   MeSH
• nemoci ryb * imunologie   parazitologie   MeSH
• regulace genové exprese MeSH
• rozmnožování imunologie   MeSH
• stanovení celkové genové exprese MeSH
• transkriptom MeSH
• Trematoda * fyziologie   MeSH
• zavlečené druhy * MeSH
• zvířata MeSH
• Check Tag
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Plant sexual reproduction is highly sensitive to elevated ambient temperatures, impacting seed development and production. We previously phenotyped this effect on three rapeseed cultivars (DH12075, Topas DH4079, and Westar). This work describes the transcriptional response associated with the phenotypic changes induced by heat stress during early seed development in Brassica napus. RESULTS: We compared the differential transcriptional response in unfertilized ovules and seeds bearing embryos at 8-cell and globular developmental stages of the three cultivars exposed to high temperatures. We identified that all tissues and cultivars shared a common transcriptional response with the upregulation of genes linked to heat stress, protein folding and binding to heat shock proteins, and the downregulation of cell metabolism. The comparative analysis identified an enrichment for a response to reactive oxygen species (ROS) in the heat-tolerant cultivar Topas, correlating with the phenotypic changes. The highest heat-induced transcriptional response in Topas seeds was detected for genes encoding various peroxidases, temperature-induced lipocalin (TIL1), or protein SAG21/LEA5. On the contrary, the transcriptional response in the two heat-sensitive cultivars, DH12075 and Westar, was characterized by heat-induced cellular damages with the upregulation of genes involved in the photosynthesis and plant hormone signaling pathways. Particularly, the TIFY/JAZ genes involved in jasmonate signaling were induced by stress, specifically in ovules of heat-sensitive cultivars. Using a weighted gene co-expression network analysis (WGCNA), we identified key modules and hub genes involved in the heat stress response in studied tissues of either heat-tolerant or sensitive cultivars. CONCLUSIONS: Our transcriptional analysis complements a previous phenotyping analysis by characterizing the growth response to elevated temperatures during early seed development and reveals the molecular mechanisms underlying the phenotypic response. The results demonstrated that response to ROS, seed photosynthesis, and hormonal regulation might be the critical factors for stress tolerance in oilseed rape.

• Klíčová slova
• Brassica napus, Embryo, Ovule, Seed, Thermomorphogenesis, Transcriptomics,
• MeSH
• Brassica napus * metabolismus   MeSH
• reaktivní formy kyslíku metabolismus   MeSH
• regulace genové exprese u rostlin MeSH
• semena rostlinná metabolismus   MeSH
• stanovení celkové genové exprese MeSH
• transkriptom MeSH
• vajíčko rostlin MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• reaktivní formy kyslíku MeSH

Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries) and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling, and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allows the populations of C. gibelio to combine the evolutionary and ecological advantages of the two reproductive strategies. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.

• Klíčová slova
• Asexual reproduction, Carassius gibelio, Differential expression analysis, Evolution of sexual reproduction, Gynogenesis, Meiosis, Oogenesis, Reproduction, Transcriptomics,
• MeSH
• jednonukleotidový polymorfismus MeSH
• kapři * genetika   fyziologie   MeSH
• nepohlavní rozmnožování * genetika   MeSH
• ovarium metabolismus   MeSH
• rozmnožování * genetika   MeSH
• stanovení celkové genové exprese MeSH
• transkriptom MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the determination of the length of telomeres is of high importance for many studies. Over the last years, new methods for the analysis of the length of telomeres have been developed, including those based on PCR or analysis of NGS data. Despite that, terminal restriction fragment (TRF) method remains the gold standard to this day. However, this method lacks universally accepted and precise tool capable to analyse and statistically evaluate TRF results. RESULTS: To standardize the processing of TRF results, we have developed WALTER, an online toolset allowing rapid, reproducible, and user-friendly analysis including statistical evaluation of the data. Given its web-based nature, it provides an easily accessible way to analyse TRF data without any need to install additional software. CONCLUSIONS: WALTER represents a major upgrade from currently available tools for the image processing of TRF scans. This toolset enables a rapid, highly reproducible, and user-friendly evaluation of almost any TRF scan including in-house statistical evaluation of the data. WALTER platform together with user manual describing the evaluation of TRF scans in detail and presenting tips and troubleshooting, as well as test data to demo the software are available at https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51/tab?tabId=125#WALTER and the source code at https://github.com/mlyc93/WALTER .

• Klíčová slova
• Online toolset, Telomere length, Terminal restriction fragments,
• MeSH
• software * MeSH
• telomery * genetika   MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Plasma donor-derived cell-free DNA (dd-cfDNA) is used to screen for rejection in heart transplants. We launched the Trifecta-Heart study ( ClinicalTrials.gov No. NCT04707872), an investigator-initiated, prospective trial, to examine the correlations between genome-wide molecular changes in endomyocardial biopsies (EMBs) and plasma dd-cfDNA. The present report analyzes the correlation of plasma dd-cfDNA with gene expression in EMBs from 4 vanguard centers and compared these correlations with those in 604 kidney transplant biopsies in the Trifecta-Kidney study ( ClinicalTrials.gov No. NCT04239703). METHODS: We analyzed 137 consecutive dd-cfDNA-EMB pairs from 70 patients. Plasma %dd-cfDNA was measured by the Prospera test (Natera Inc), and gene expression in EMBs was assessed by Molecular Microscope Diagnostic System using machine-learning algorithms to interpret rejection and injury states. RESULTS: Top transcripts correlating with dd-cfDNA were related to genes increased in rejection such as interferon gamma-inducible genes (eg, HLA-DMA ) but also with genes induced by injury and expressed in macrophages (eg, SERPINA1 and HMOX1 ). In gene enrichment analysis, the top dd-cfDNA-correlated genes reflected inflammation and rejection pathways. Dd-cfDNA correlations with rejection genes in EMB were similar to those seen in kidney transplant biopsies, with somewhat stronger correlations for TCMR genes in hearts and ABMR genes in kidneys. However, the correlations with parenchymal injury-induced genes and macrophage genes were much stronger in hearts. CONCLUSIONS: In this first analysis of Trifecta-Heart study, dd-cfDNA correlates significantly with molecular rejection but also with injury and macrophage infiltration, reflecting the proinflammatory properties of injured cardiomyocytes. The relationship supports the utility of dd-cfDNA in clinical management of heart transplant recipients.

• MeSH
• biologické markery krev   MeSH
• biopsie MeSH
• dárci tkání * MeSH
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• myokard * patologie   metabolismus   MeSH
• prediktivní hodnota testů MeSH
• prospektivní studie MeSH
• rejekce štěpu * genetika   imunologie   patologie   krev   diagnóza   MeSH
• senioři MeSH
• stanovení celkové genové exprese MeSH
• transplantace ledvin škodlivé účinky   MeSH
• transplantace srdce * škodlivé účinky   MeSH
• volné cirkulující nukleové kyseliny * krev   genetika   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• multicentrická studie MeSH
• pozorovací studie MeSH
• srovnávací studie MeSH
• Názvy látek
• biologické markery MeSH
• volné cirkulující nukleové kyseliny * MeSH

In our previous work, we designed and implemented a synthetic metabolic pathway for 1,2,3-trichloropropane (TCP) biodegradation in Escherichia coli. Significant effects of metabolic burden and toxicity exacerbation were observed on single cell and population levels. Deeper understanding of mechanisms underlying these effects is extremely important for metabolic engineering of efficient microbial cell factories for biotechnological processes. In this paper, we present a novel mathematical model of the pathway. The model addresses for the first time the combined effects of toxicity exacerbation and metabolic burden in the context of bacterial population growth. The model is calibrated with respect to the real data obtained with our original synthetically modified E. coli strain. Using the model, we explore the dynamics of the population growth along with the outcome of the TCP biodegradation pathway considering the toxicity exacerbation and metabolic burden. On the methodological side, we introduce a unique computational workflow utilising algorithmic methods of computer science for the particular modelling problem.

• Klíčová slova
• biodegradation, computational modelling, environmental pollutants, metabolic burden, population growth,
• Publikační typ
• časopisecké články MeSH