Mapping the structural landscape of the yeast Ty3 retrotransposon RNA genome.

Long terminal repeat (LTR)-retrotransposons are significant contributors to the evolution and diversity of eukaryotic genomes. Their RNA genomes (gRNA) serve as a template for protein synthesis and reverse transcription to a DNA copy, which can integrate into the host genome. Here, we used the SHAPE-MaP strategy to explore Ty3 retrotransposon gRNA structure in yeast and under cell-free conditions. Our study reveals the structural dynamics of Ty3 gRNA and the well-folded core, formed independently of the cellular environment. Based on the detailed map of Ty3 gRNA structure, we characterized the structural context of cis-acting sequences involved in reverse transcription and frameshifting. We also identified a novel functional sequence as a potential initiator for Ty3 gRNA dimerization. Our data indicate that the dimer is maintained by direct interaction between short palindromic sequences at the 5' ends of the two Ty3 gRNAs, resembling the model characteristic for other retroelements like HIV-1 and Ty1. This work points out a range of cell-dependent and -independent Ty3 gRNA structural changes that provide a solid background for studies on RNA structure-function relationships important for retroelement biology.

Exposure to air pollution and ovarian reserve parameters.

Exposure to air pollution is associated with many different health effects, especially cardiovascular and respiratory diseases. Additionally, highly significant links between exposure to air pollution and fertility, particularly male fertility was observed, however the studies regarding exposure to selected air pollutants and female fertility assessed by ovarian reserve are rare. Hence, the main aim of the study was to analyze relationship between exposure to ambient air pollution and ovarian reserve parameters among Polish women. The study population consisted of 511 women, who attended to infertility clinic because of diagnostic purposes. Participants filled in the questionnaire about social-demographic, lifestyle and health factors. Infertility specialists assessed ovarian parameters such as: antral follicle count (AFC) and concentration of hormones: Anti-Müllerian hormone (AMH), follicle stimulating hormone (FSH) and estradiol (E2). The air pollutants level (sulfur dioxide, nitrogen dioxide, carbon monoxide, ozone, particulate matters) were obtained via National Environmental Protection Inspectorate database. Significant negative association between PM2,5 and AHM (p = 0.032) as well as AFC (p = 0.044) was observed. Moreover, SO2 concentrations decrease AFC (p = 0.038). The results also suggest that PM10, PM2.5, SO2 exposure on antral follicle count may be more pronounced among women with a female factor infertility diagnosis. Additionally, exposure to PM2.5 and NOx on AFC and AMH was stronger among older women (> 35 years of age). To conclude, the present study found that air pollution could lead to decrease in follicle antral count and Anti-Müllerian hormone level, especially exposure to PM2,5 and SO2 thus the evidence suggest negative impact to ovarian reserve.

Sylvian fissure lipoma associated with fusiform aneurysm in the middle cerebral artery trifurcation: A case report and literature review.

Background: The intracranial lipomas are rare congenital malformations accounting for approximately 0.1-1.3% of all intracranial tumors, of which Sylvian fissure lipomas account for <5%. These lesions are frequently associated with dysgenesis of neuronal brain tissues and vascular malformations and in the majority are asymptomatic. Intracranial lipomas on magnetic resonance imaging (MRI) may mimic late subacute hemorrhage due to similar radiological features. Due to the tight adhesion of the lipoma to the surrounding nerve structures and vessels, complete removal is difficult and does not guarantee the disappearance of symptoms. Case Description: We present the case of a 42-year-old woman with chronic headaches and short-term memory impairment who was admitted to the emergency room after an out-of-hospital brain MRI with suspected ruptured right middle cerebral artery (MCA) aneurysm and late subacute intracranial hemorrhage. In the hospital, after clinical evaluation, emergency computed tomography (CT) angiography was performed, which revealed an unruptured fusiform aneurysm located in the right MCA trifurcation surrounded by an extremely hypodense lesion corresponding to fat in the right Sylvian fissure. No features of intracranial hemorrhage were present. The diagnosis of intracranial lipoma was finally confirmed after the MRI of the brain with a fat suppression sequence. Surgical treatment was not attempted, and the patient was treated conservatively with a satisfactory general outcome. Conclusion: A Sylvian fissure lipoma may be associated with a fusiform aneurysm in the MCA trifurcation. By modifying the standard MRI protocol and performing a CT scan, an intracranial lipoma can be detected and a late subacute intracranial hemorrhage can be excluded.

Did everyone change their childbirth plans due to the COVID-19 pandemic? A web-based cross-sectional survey of Polish pregnant women.

BACKGROUND AND AIM: With the worldwide outbreak of coronavirus, a significant impact has been observed on the functioning of healthcare systems and the process of childbirth. Women probably did not even have a choice to adjust their plans accordingly to the current situation. The aim of the study was to examine how the outbreak of the SARS CoV-2 pandemic state affected the decisions of pregnant women about their childbirth plan. DESIGN: This cross-sectional study was performed using a web-based survey published on social media in Poland. METHODS: The cross-sectional study was performed using web-based questionnaires. The study group included Polish women who changed their childbirth plans, compared to a group of women not sure about delivery plan change and those whose plans had not changed. The data were collected from 4 March 2020 to 2 May 2020, when the first rising count of new infections was observed in Poland and worldwide. Statistical analysis was performed using STATISTICA Software, Inc., 13.3 (2020). RESULTS: Of 969 women who completed the questionnaire and were enrolled into the study, 57.2% had not changed their childbirth plans (group I), 28.4% had changed their plans (group II), and 14.4% of respondents answered "not sure" to this question (group III). The majority of women changed their birth plans during the pandemic because of the potential absence of their partner during labour (56% of women who had changed their plans and 48% of those whose answer was "I am not sure", p < .001). Another reason was the fear of separation from the child after delivery (33% of women who had changed their plans and 30% of those whose answer was "I am not sure", p < .001). CONCLUSION: Restrictions due to the COVID-19 outbreak have influenced the childbirth plans of pregnant women. The changes were independent of women's vision of birth before the pandemic. IMPACT: The restriction on births with accompanying person and the risk of separation from their infant after childbirth significantly influenced the decision-making process. As a result, some women were more likely to opt for a home birth with or even without medical assistance. PATIENT OR PUBLIC CONTRIBUTION: The study participants were women who were pregnant at the time of completing the questionnaire, were over 18 years old and spoke Polish.

Comparison of SOX2 and POU5F1 Gene Expression in Leukapheresis-Derived CD34+ Cells before and during Cell Culture.

Bone marrow is an abundant source of both hematopoietic as well as non-hematopoietic stem cells. Embryonic, fetal and stem cells located in tissues (adipose tissue, skin, myocardium and dental pulp) express core transcription factors, including the SOX2, POU5F1 and NANOG gene responsible for regeneration, proliferation and differentiation into daughter cells. The aim of the study was to examine the expression of SOX2 and POU5F1 genes in CD34-positive peripheral blood stem cells (CD34+ PBSCs) and to analyze the influence of cell culture on the expression of SOX2 and POU5F1 genes. The study material consisted of bone marrow-derived stem cells isolated by using leukapheresis from 40 hematooncology patients. Cells obtained in this process were subject to cytometric analysis to determine the content of CD34+ cells. CD34-positive cell separation was conducted using MACS separation. Cell cultures were set, and RNA was isolated. Real-time PCR was conducted in order to evaluate the expression of SOX2 and POU5F1 genes and the obtained data were subject to statistical analysis. We identified the expression of SOX2 and POU5F1 genes in the examined cells and demonstrated a statistically significant (p < 0.05) change in their expression in cell cultures. Short-term cell cultures (<6 days) were associated with an increase in the expression of SOX2 and POU5F1 genes. Thus, short-term cultivation of transplanted stem cells could be used to induce pluripotency, leading to better therapeutic effects.

An exposure to endocrine active persistent pollutants and endometriosis - a review of current epidemiological studies.

Widespread exposure to persistent pollutants can disrupt the bodies' natural endocrine functions and contribute to reproductive diseases like endometriosis. In this review, we focus at the relationship between endocrine-disrupting chemicals (EDCs), including metals and trace elements, organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated biphenyls (PBBs), poly-brominated diphenyl ethers (PBDEs), polychlorinated dibenzodioxin (PCDDs), polychlorinated dibenzofurans (PCDFs), and per- and polyfluoroalkyl substances (PFAS) exposure and risk of endometriosis. Relevant studies from the last 10 years by November 2022 were identified by searching Pubmed, Web of Science, and Scopus. The cohort and case-control studies that reported effect size with 95% confidence intervals (CIs) of EDC exposure and endometriosis were selected. Twenty three articles examining the relationship between endometriosis and exposure to persistent EDCs were considered. Most of the studies indicated association with exposure to persistent chemicals and development of endometriosis. The consistent results were found in case of lead, PCB-28, PCB-138, PCB-153, PCB-180, PCB-201, 1,2,3,7,8 - PeCDD, 2,3,4,7,8 - PeCDF and all described OCPs, showing the increased risk of endometriosis. These results support that exposure to certain EDCs, including OCPs, PCBs, PBBs, PBDEs, PFAS, and lead increase the risk of endometriosis.

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.

RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computational 3D structure prediction methods are experiencing an ongoing and thriving development. Such methods can lead to many models; thus, it is necessary to build comparisons and extract common structural motifs for further medical or biological studies. Here, we introduce a computational pipeline dedicated to reference-free high-throughput comparative analysis of 3D RNA structures. We show its application in the RNA-Puzzles challenge, in which five participating groups attempted to predict the three-dimensional structures of 5'- and 3'-untranslated regions (UTRs) of the SARS-CoV-2 genome. We report the results of this puzzle and discuss the structural motifs obtained from the analysis. All simulated models and tools incorporated into the pipeline are open to scientific and academic use.

Cell Compartment-Specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome.

The structural transitions RNAs undergo during trafficking are not well understood. Here, we used the well-developed yeast Ty1 retrotransposon to provide the first structural model of genome (g) RNA in the nucleus from a retrovirus-like transposon. Through a detailed comparison of nuclear Ty1 gRNA structure with those established in the cytoplasm, virus-like particles (VLPs), and those synthesized in vitro, we detected Ty1 gRNA structural alterations that occur during retrotransposition. Full-length Ty1 gRNA serves as the mRNA for Gag and Gag-Pol proteins and as the genome that is reverse transcribed within VLPs. We show that about 60% of base pairs predicted for the nuclear Ty1 gRNA appear in the cytoplasm, and active translation does not account for such structural differences. Most of the shared base pairs are represented by short-range interactions, whereas the long-distance pairings seem unique for each compartment. Highly structured motifs tend to be preserved after nuclear export of Ty1 gRNA. In addition, our study highlights the important role of Ty1 Gag in mediating critical RNA-RNA interactions required for retrotransposition.

The silencing of ets-4 mRNA relies on the functional cooperation between REGE-1/Regnase-1 and RLE-1/Roquin-1.

Regnase-1 is an evolutionarily conserved endoribonuclease. It degrades diverse mRNAs important for many biological processes including immune homeostasis, development and cancer. There are two competing models of Regnase-1-mediated mRNA silencing. One model postulates that Regnase-1 works together with another RNA-binding protein, Roquin-1, which recruits Regnase-1 to specific mRNAs. The other model proposes that the two proteins function separately. Studying REGE-1, the Caenorhabditis elegans ortholog of Regnase-1, we have uncovered its functional relationship with RLE-1, the nematode counterpart of Roquin-1. While both proteins are essential for mRNA silencing, REGE-1 and RLE-1 appear to associate with target mRNA independently of each other. Thus, although the functional interdependence between REGE-1/Regnase-1 and RLE-1/Roquin-1 is conserved, the underlying mechanisms may display species-specific variation, providing a rare perspective on the evolution of this important post-transcriptional regulatory mechanism.

Environmental Exposure to Non-Persistent Endocrine Disrupting Chemicals and Endometriosis: A Systematic Review.

Endometriosis is a disease characterized by the presence of the uterine endometrium outside of its normal location. As the etiology of endometriosis is not well known and hormonal imbalance is central to disease pathogenesis, the potential contribution of exposure to endocrine-disrupting chemicals (EDCs) has been hypothesized in endometriosis. A systematic search of the literature was carried out to identify relevant studies using: PubMed, Scopus, Elsevier, Springer; EBSCO, and Web of Science. A total of 22 studies were considered. Most of the studies reviewed in this paper showed an association between exposure to BPA and phthalates and endometriosis. In the case of phthalate exposure, the reviewed studies found an association between the concentration of at least one phthalate metabolite and endometriosis. Only one study was performed to assess the exposure to parabens and a significant relationship with endometriosis was found. Additionally, only one study assessed the relationship of non-persistent pesticide exposure with endometriosis, observing a significant association between endometriosis and the urinary concentration of diazinon, chlorpyrifos, and chlorpyrifos-methyl. Studies struggled to provide a conclusion on the effect of exposure to benzophenones on endometriosis. Despite the numerous limitations of the results, the reviewed studies suggest that exposure to non-persistent endocrine disruptors, especially bisphenol A and phthalates may affect endometriosis. The results of the studies on exposure to parabens, benzophenones, and non-persistent insecticides are inconclusive.

RNA Binding Properties of the Ty1 LTR-Retrotransposon Gag Protein.

A universal feature of retroelement propagation is the formation of distinct nucleoprotein complexes mediated by the Gag capsid protein. The Ty1 retrotransposon Gag protein from Saccharomyces cerevisiae lacks sequence homology with retroviral Gag, but is functionally related. In addition to capsid assembly functions, Ty1 Gag promotes Ty1 RNA dimerization and cyclization and initiation of reverse transcription. Direct interactions between Gag and retrotransposon genomic RNA (gRNA) are needed for Ty1 replication, and mutations in the RNA-binding domain disrupt nucleation of retrosomes and assembly of functional virus-like particles (VLPs). Unlike retroviral Gag, the specificity of Ty1 Gag-RNA interactions remain poorly understood. Here we use microscale thermophoresis (MST) and electrophoretic mobility shift assays (EMSA) to analyze interactions of immature and mature Ty1 Gag with RNAs. The salt-dependent experiments showed that Ty1 Gag binds with high and similar affinity to different RNAs. However, we observed a preferential interaction between Ty1 Gag and Ty1 RNA containing a packaging signal (Psi) in RNA competition analyses. We also uncover a relationship between Ty1 RNA structure and Gag binding involving the pseudoknot present on Ty1 gRNA. In all likelihood, the differences in Gag binding affinity detected in vitro only partially explain selective Ty1 RNA packaging into VLPs in vivo.

In vivo structure of the Ty1 retrotransposon RNA genome.

Long terminal repeat (LTR)-retrotransposons constitute a significant part of eukaryotic genomes and influence their function and evolution. Like other RNA viruses, LTR-retrotransposons efficiently utilize their RNA genome to interact with host cell machinery during replication. Here, we provide the first genome-wide RNA secondary structure model for a LTR-retrotransposon in living cells. Using SHAPE probing, we explore the secondary structure of the yeast Ty1 retrotransposon RNA genome in its native in vivo state and under defined in vitro conditions. Comparative analyses reveal the strong impact of the cellular environment on folding of Ty1 RNA. In vivo, Ty1 genome RNA is significantly less structured and more dynamic but retains specific well-structured regions harboring functional cis-acting sequences. Ribosomes participate in the unfolding and remodeling of Ty1 RNA, and inhibition of translation initiation stabilizes Ty1 RNA structure. Together, our findings support the dual role of Ty1 genomic RNA as a template for protein synthesis and reverse transcription. This study also contributes to understanding how a complex multifunctional RNA genome folds in vivo, and strengthens the need for studying RNA structure in its natural cellular context.

Decontamination of microbiologically contaminated abiotic porous surfaces in an oral surgery clinic using vaporised hydrogen peroxide (VHP).

PURPOSE: The aims of the study were to identify microorganisms, including those in the VBNC state, inhabiting porous surfaces in oral surgery offices and to assess the biocidal effectiveness and impact of 300 ppm vaporised hydrogen peroxide (VHP) for 20 min on decontaminated materials. METHODS: From the surfaces of textured armrests of dental chairs, pinewood doors and window frames and cotton medical aprons, 30 swabs were taken with moistened sponges. The identification of isolated microorganisms was performed using molecular methods with MALDI-TOF MS, DNA Sanger sequencer and Illumina MiSeq. To evaluate the impact of VHP decontamination (independent variable) on the number of microorganisms (response variable) ANOVA and LSD tests were used. After application of 10 processes of VHP decontamination, changes in the properties of the materials were assessed using FTIR spectroscopy, SEM microscopy and XPS spectrometry. RESULTS: The concentration of microorganisms was 101-104 CFU/100 cm2 on the tested surfaces and 102 CFU/m3 in the air. Twenty species of bacteria, one yeast and 16 filamentous fungi were identified, with the predominance of Bacillus, Staphylococcus, Alternaria, Aspergillus and Penicillium. Moreover, Janthinobacterium, Acremonium, Aureobasidium, Coprinellus and Cosmospora in the VBNC state were metagenomically detected. VHP decontamination resulted in a reduction in the majority of tested microbial strains by a minimum of 3 log, and all tested mixed cultures inhabiting porous surfaces were above 98% and in the air, 100%. VHP decontamination did not affect the structural and morphological properties of cotton fibres, wood or stainless steel. CONCLUSIONS: VHP decontamination at a concentration of 300 ppm for 20 min can be used for the holistic disinfection of air, surfaces and equipment in oral surgery offices.

RNAthor - fast, accurate normalization, visualization and statistical analysis of RNA probing data resolved by capillary electrophoresis.

RNAs adopt specific structures to perform their functions, which are critical to fundamental cellular processes. For decades, these structures have been determined and modeled with strong support from computational methods. Still, the accuracy of the latter ones depends on the availability of experimental data, for example, chemical probing information that can define pseudo-energy constraints for RNA folding algorithms. At the same time, diverse computational tools have been developed to facilitate analysis and visualization of data from RNA structure probing experiments followed by capillary electrophoresis or next-generation sequencing. RNAthor, a new software tool for the fully automated normalization of SHAPE and DMS probing data resolved by capillary electrophoresis, has recently joined this collection. RNAthor automatically identifies unreliable probing data. It normalizes the reactivity information to a uniform scale and uses it in the RNA secondary structure prediction. Our web server also provides tools for fast and easy RNA probing data visualization and statistical analysis that facilitates the comparison of multiple data sets. RNAthor is freely available at http://rnathor.cs.put.poznan.pl/.

On the Way to Understanding the Interplay between the RNA Structure and Functions in Cells: A Genome-Wide Perspective.

RNAs adopt specific structures in order to perform their biological activities. The structure of RNA is an important layer of gene expression regulation, and can impact a plethora of cellular processes, starting with transcription, RNA processing, and translation, and ending with RNA turnover. The development of high-throughput technologies has enabled a deeper insight into the sophisticated interplay between the structure of the cellular transcriptome and the living cells environment. In this review, we present the current view on the RNA structure in vivo resulting from the most recent transcriptome-wide studies in different organisms, including mammalians, yeast, plants, and bacteria. We focus on the relationship between the mRNA structure and translation, mRNA stability and degradation, protein binding, and RNA posttranscriptional modifications.

For good and for bad: the role of endogenous retroelements in humans / Na dobre i na zle: rola endogennych retroelementów u czlowieka.

Transposable elements (TEs) are the sequences that are able to "jump" across the genome. They are found in virtually all organisms including human. Although in human, the majority of TEs lost their ability to autonomous transposition, they make up almost half of our genome, and played important roles in genome evolution. Fast progress in deep sequencing and functional analysis has revealed the importance of domes­ticated copies of transposable elements, including their regulatory sequences, transcripts and proteins in normal cells functioning. However, a growing numer of evidence suggest the involvment of TEs in development and progression of autoimmune and neurodegenerative disaeses as well as in many types of cancer. In this review we summarize the current state of knowledge about the LTR retroelements: endogenous retroviruses (ERVs) and Ty3/Gypsy retrotransposons, and their role in human organism.

Retroviral-like determinants and functions required for dimerization of Ty1 retrotransposon RNA.

During replication of long terminal repeat (LTR)-retrotransposons, their proteins and genome (g) RNA assemble into virus-like particles (VLPs) that are not infectious but functionally related to retroviral virions. Both virions and VLPs contain gRNA in a dimeric form, but contrary to retroviruses, little is known about how gRNA dimerization and packaging occurs in LTR-retrotransposons. The LTR-retrotransposon Ty1 from Saccharomyces cerevisiae is an informative model for studying LTR-retrotransposon and retrovirus replication. Using structural, mutational and functional analyses, we explored dimerization of Ty1 genomic RNA. We provide direct evidence that interactions of self-complementary PAL1 and PAL2 palindromic sequences localized within the 5'UTR are essential for Ty1 gRNA dimer formation. Mutations disrupting PAL1-PAL2 complementarity restricted RNA dimerization in vitro and Ty1 mobility in vivo. Although dimer formation and mobility of these mutants was inhibited, our work suggests that Ty1 RNA can dimerize via alternative contact points. In contrast to previous studies, we cannot confirm a role for PAL3, tRNAiMet as well as recently proposed initial kissing-loop interactions in dimer formation. Our data also supports the critical role of Ty1 Gag in RNA dimerization. Mature Ty1 Gag binds in the proximity of sequences involved in RNA dimerization and tRNAiMet annealing, but the 5' pseudoknot in Ty1 RNA may constitute a preferred Gag-binding site. Taken together, these results expand our understanding of genome dimerization and packaging strategies utilized by LTR-retroelements.

Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.

RNA-binding proteins regulate all aspects of RNA metabolism. Their association with RNA is mediated by RNA-binding domains, of which many remain uncharacterized. A recently reported example is the NHL domain, found in prominent regulators of cellular plasticity like the C. elegans LIN-41. Here we employ an integrative approach to dissect the RNA specificity of LIN-41. Using computational analysis, structural biology, and in vivo studies in worms and human cells, we find that a positively charged pocket, specific to the NHL domain of LIN-41 and its homologs (collectively LIN41), recognizes a stem-loop RNA element, whose shape determines the binding specificity. Surprisingly, the mechanism of RNA recognition by LIN41 is drastically different from that of its more distant relative, the fly Brat. Our phylogenetic analysis suggests that this reflects a rapid evolution of the domain, presenting an interesting example of a conserved protein fold that acquired completely different solutions to RNA recognition.

Filamin A upregulation correlates with Snail-induced epithelial to mesenchymal transition (EMT) and cell adhesion but its inhibition increases the migration of colon adenocarcinoma HT29 cells.

Filamin A (FLNA) is actin filament cross-linking protein involved in cancer progression. Its importance in regulating cell motility is directly related to the epithelial to mesenchymal transition (EMT) of tumor cells. However, little is known about the mechanism of action of FLNA at this early stage of cancer invasion. Using immunochemical methods, we evaluated the levels and localization of FLNA, pFLNA[Ser2152], ß1 integrin, pß1 integrin[Thr788/9], FAK, pFAK[Y379], and talin in stably transfected HT29 adenocarcinoma cells overexpressing Snail and looked for the effect of Snail in adhesion and migration assays on fibronectin-coated surfaces before and after FLNA silencing. Our findings indicate that FLNA upregulation correlates with Snail-induced EMT in colorectal carcinoma. FLNA localizes in the cytoplasm and at the sites of focal adhesion (FA) of invasive cells. Silencing of FLNA inhibits Snail-induced cell adhesion, reduces the size of FA sites, induces the relocalization of talin from the cytoplasm to the membrane area and augments cell migratory properties. Our findings suggest that FLNA may not act as a classic integrin inhibitor in invasive carcinoma cells, but is involved in other pro-invasive pathways. FLNA upregulation, which correlates with cell metastatic properties, maybe an additional target for combination therapy in colorectal carcinoma tumor progression.