Correction: A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana.

[This corrects the article DOI: 10.1371/journal.ppat.1008147.].

Maternal DDB1 regulates apoptosis and lineage differentiation in porcine preimplantation embryos.

CONTEXT: Maternal-effect genes (MEGs) play a critical role in modulating both cellular and molecular biology events in preimplantation embryonic development. Damage-specific DNA binding protein 1 (DDB1) is a gene that participates in meiotic resumption, ovulation, and embryonic stem cell maintenance. Its function in preimplantation development is not well-studied. AIMS: We aimed to explore the expression pattern, genomic heritage, and potential molecular mechanisms of DDB1 in preimplantation embryos in porcine. METHODS: In this study, RNA interference, microinjection, RT-qPCR, immunofluorescence staining and single-cell RNA sequencing were used to explore the molecular function of DDB1 in porcine preimplantation embryos. KEY RESULTS: DDB1 was found to be expressed in germinal vesicle (GV) and Meiosis II (MII) oocytes and in preimplantation embryos. We confirmed it is a MEG. DDB1 -deficient blastocysts had a significantly reduced number of trophectoderm cells, an increased apoptotic cell number and increased apoptosis index. According to a next-generation sequencing (NGS) analysis, 236 genes (131 upregulated and 105 downregulated) significantly changed in the DDB1 -deficient morula. The myeloid leukaemia factor 1 (MLF1 ) and yes-associated protein 1 (YAP1 ) expressions were significantly upregulated and downregulated respectively, in the DDB1 -deficient morula. In combination with the decreased expression of TEAD4 , CDX2 , GATA3 , OCT4 , and NANOG and the increased expression of SOX2 in the blastocyst, DDB1 may play a role in determining lineage differentiation and pluripotency maintenance. CONCLUSIONS: DDB1 is a MEG and it plays a crucial role in porcine preimplantation embryonic development. IMPLICATIONS: This study provides a theoretical basis for further understanding the molecular mechanisms of preimplantation embryo development.

Expression profiles and functions of ferroptosis-related genes in the placental tissue samples of early- and late-onset preeclampsia patients.

BACKGROUND: The accumulation of reactive oxygen species (ROS) resulting from upregulated levels of oxidative stress is commonly implicated in preeclampsia (PE). Ferroptosis is a novel form of iron-dependent cell death instigated by lipid peroxidation that likely plays an important role in PE pathogenesis. This study aimed to investigate the expression profiles and functions of ferroptosis-related genes (FRGs) in early-onset preeclampsia (EOPE) and late-onset preeclampsia (LOPE). METHODS: Gene expression data and clinical information were downloaded from the Gene Expression Omnibus (GEO) database. The "limma" R package was used to screen differentially expressed genes. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction (PPI) network analyses were conducted to investigate the bioinformatics functions and molecular interactions of significantly different FRGs. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to verify the expression of hub FRGs in PE. RESULTS: A total of 4215 differentially expressed genes (DEGs) were identified between EOPE and preterm cases while 556 DEGs were found between LOPE and term controls. Twenty significantly different FRGs were identified in EOPE subtypes, while only 3 FRGs were identified in LOPE subtypes. Functional enrichment analysis revealed that the differentially expressed FRGs were mainly involved in EOPE and enriched in hypoxia- and iron-related pathways, such as the response to hypoxia, iron homeostasis and iron ion binding process. PPI network analysis and verification by RT-qPCR resulted in the identification of the following five FRGs of interest: FTH1, HIF1A, FTL, MAPK8 and PLIN2. CONCLUSIONS: EOPE and LOPE have distinct underlying molecular mechanisms, and ferroptosis may be mainly implicated in the pathogenesis of EOPE. Further studies are necessary for deeper inquiry into placental ferroptosis and its role in the pathogenesis of EOPE.

Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA.

While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). Deep sequencing PSTVd genomes from plants inoculated with a cloned master sequence revealed naturally occurring variants, and showed that G/U pairs are maintained to the same extent as canonical WC base pairs. Comprehensive mutational analysis demonstrated that nearly all G/U pairs are critical for replication and/or systemic spread. Two selected G/U pairs were found to be required for PSTVd entry into, but not for exit from, the host vascular system. This study identifies critical roles for G/U pairs in the survival of an infectious RNA, and increases understanding of structure-based regulation of replication and trafficking of pathogen and cellular RNAs.

[Biomechanical Study of New Biodegradable Esophageal Stent].

The radial force of the degradable esophageal stent before and after degradation is one of the important indicators for effective treatment of esophageal stricture. Based on a combination of in vitro experiments and finite element analysis, this paper studies and verifies the biomechanical properties of a new type of degradable esophageal stent under different esophageal stricture conditions. Under radial extrusion conditions, the maximum stress at the port of the stent is 65.25 MPa, and the maximum strain is 1.98%; The peak values of stress and strain under local extrusion and plane extrusion conditions both appear in the extrusion area and the compression expansion area at both ends, which are respectively 48.68 MPa, 46.40 MPa, 0.49%, 1.13%. The maximum radial force of the undegraded stent was 11.22 N, and 97% and 51% of the maximum radial force were maintained after 3 months and 6 months of degradation, respectively. The research results verify the safety and effectiveness of the radial force of the new degradable esophageal stent, and provide a theoretical basis for the clinical treatment of esophageal stricture.

A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana.

Potato spindle tuber viroid (PSTVd) is a circular non-coding RNA of 359 nucleotides that replicates and spreads systemically in host plants, thus all functions required to establish an infection are mediated by sequence and structural elements in the genome. The PSTVd secondary structure contains 26 Watson-Crick base-paired stems and 27 loops. Most of the loops are believed to form three-dimensional (3D) structural motifs through non-Watson-Crick base pairing, base stacking, and other local interactions. Homology-based prediction using the JAR3D online program revealed that loop 27 (nucleotides 177-182) most likely forms a 3D structure similar to the loop of a conserved hairpin located in the 3' untranslated region of histone mRNAs in animal cells. This stem-loop, which is involved in 3'-end maturation, is not found in polyadenylated plant histone mRNAs. Mutagenesis showed that PSTVd genomes containing base substitutions in loop 27 predicted by JAR3D to disrupt the 3D structure were unable to replicate in Nicotiana benthamiana leaves following mechanical rub inoculation, with one exception: a U178G/U179G double mutant was replication-competent and able to spread within the upper epidermis of inoculated leaves, but was confined to this cell layer. Remarkably, direct delivery of the U178G/U179G mutant into the vascular system by needle puncture inoculation allowed it to spread systemically and enter mesophyll cells and epidermal cells of upper leaves. These findings highlight the importance of RNA 3D structure for PSTVd replication and intercellular trafficking and indicate that loop 27 is required for epidermal exit, but not epidermal entry or transit between other cell types. Thus, requirements for RNA trafficking between epidermal and underlying palisade mesophyll cells are unique and directional. Our findings further suggest that 3D structure and RNA-protein interactions constrain RNA sequence evolution, and validate JAR3D as a tool to predict RNA 3D structure.

Chinese patients' clinical and psychosocial outcomes in the 6 months following percutaneous coronary intervention.

BACKGROUND: In China, there has been a precipitous increase in the number of percutaneous coronary interventions (PCI) conducted. We sought to characterize the clinical and psychosocial trajectory of PCI patients from the time of procedure through 6 months post, and correlates of adverse cardiovascular events (ACEs). METHODS: In this prospective, observational study, patients from 2 hospitals in Shanghai, China were assessed. At follow-up visits at 1, 3 and 6 months post-PCI, clinical indicators were again extracted from patients' clinical records, including ACEs, and they completed validated surveys assessing self-management, as well as psychosocial indicators (Hospital Anxiety and Depression Scale; Pittsburgh Sleep Quality Index; quality of life [QoL]: SF-12, Seattle Angina Questionnaire [SAQ]). Repeated measures analysis of variance, adjusted for Barthel index and PCI indication, was used to assess change over time in risk factors and psychosocial indicators. Logistic regression was used to explore correlates of ACEs. RESULTS: 610 participants (mean age = 63.3; n = 150, 18.2% female) were recruited, of which 491 (80.5%) were retained at 6 months. 82 (16.7%) had an ACE at any time point, including most commonly angina and stroke (only 1 death). Clinical indicators such as blood pressure (p < 0.031 for both), symptom burden (p < .01 on all subscales) and QoL (p < 0.001 for both, but started quite low) improved over 6 months. Anxiety and depressive symptoms were above threshold, and the latter worsened over time (p < 0.001). With adjustment for age and indication, patients with any ACEs had higher sleep latency (odds ratio [OR] = 1.48; 95% confidence interval [CI] = 1.03-2.10]), and depressive symptoms (OR = 1.20; 95% CI = 1.02-1.41), but lower anxiety (OR = 0.79; 95% CI = 0.67-0.93) compared to those without. CONCLUSION: Centers may wish to re-visit patient selection criteria and processes for PCI, as well as implement mental health screening and treatment protocols, as can be achieved through cardiac rehabilitation, given how hazardous psychosocial distress is in this population.

Cardiac Rehabilitation Perceptions Among Healthcare Providers in China: A Mixed-Methods Study.

BACKGROUND: Cardiac rehabilitation (CR) in China has not been widely adopted for a variety of reasons, including healthcare provider (HCP)s' lack of awareness and beliefs. OBJECTIVE: To explore HCP's perceptions of CR in China. METHODS: An exploratory, sequential design was used in this mixed-methods study. Face-to-face semi-structured interviews were performed; this was followed by a cross-sectional survey. SETTING: The interviews were conducted in a university-affiliated hospital and a rehabilitation hospital in Shanghai. The survey was conducted in the cardiac departments of primary, secondary, or tertiary hospitals in Shanghai or Yunnan Province, China. PARTICIPANTS: Saturation was achieved upon interviewing 13 HCPs (5 doctors, and 8 nurses). A total of 610 HCPs (185 doctors [30.5%], 417 nurses [68.8%]) completed the survey. RESULTS: Analysis of the interviews revealed 4 themes: the perceived value of CR, the need for pro-CR policy, variability in CR awareness, and obstacles to CR delivery. HCP approaches to the treatment of patients with cardiac conditions did not universally include exercise training (only approximately 60% of HCPs), or all other recommended domains of secondary prevention, and assessment of the major risk factors was quite low. Familiarity with CR was moderate (48.7%). HCPs perceived that philosophies of Traditional Chinese Medicine (TCM) were highly compatible with, and could add value to, CR. HCP approaches to secondary preventive care and CR perceptions varied significantly according to their highest level of education, clinical profession, job seniority, type of hospital where they worked, whether the hospital had a CR program and the hospital's location. CONCLUSION: HCPs recognize the value of CR, particularly considering secondary preventive care practices were not comprehensive. Education is needed to improve HCPs CR awareness.

A Land Plant-Specific Transcription Factor Directly Enhances Transcription of a Pathogenic Noncoding RNA Template by DNA-Dependent RNA Polymerase II.

Some DNA-dependent RNA polymerases (DdRPs) possess RNA-dependent RNA polymerase activity, as was first discovered in the replication of Potato spindle tuber viroid (PSTVd) RNA genome in tomato (Solanum lycopersicum). Recent studies revealed that this activity in bacteria and mammals is important for transcriptional and posttranscriptional regulatory mechanisms. Here, we used PSTVd as a model to uncover auxiliary factors essential for RNA-templated transcription by DdRP PSTVd replication in the nucleoplasm generates (-)-PSTVd intermediates and (+)-PSTVd copies. We found that the Nicotiana benthamiana canonical 9-zinc finger (ZF) Transcription Factor IIIA (TFIIIA-9ZF) as well as its variant TFIIIA-7ZF interacted with (+)-PSTVd, but only TFIIIA-7ZF interacted with (-)-PSTVd. Suppression of TFIIIA-7ZF reduced PSTVd replication, and overexpression of TFIIIA-7ZF enhanced PSTVd replication in planta. Consistent with the locale of PSTVd replication, TFIIIA-7ZF was found in the nucleoplasm and nucleolus, in contrast to the strictly nucleolar localization of TFIIIA-9ZF. Footprinting assays revealed that only TFIIIA-7ZF bound to a region of PSTVd critical for initiating transcription. Furthermore, TFIIIA-7ZF strongly enhanced the in vitro transcription of circular (+)-PSTVd by partially purified Pol II. Together, our results identify TFIIIA-7ZF as a dedicated cellular transcription factor that acts in DdRP-catalyzed RNA-templated transcription, highlighting both the extraordinary evolutionary adaptation of viroids and the potential of DdRPs for a broader role in cellular processes.

Comprehensive Transcriptome Analyses Reveal that Potato Spindle Tuber Viroid Triggers Genome-Wide Changes in Alternative Splicing, Inducible trans-Acting Activity of Phased Secondary Small Interfering RNAs, and Immune Responses.

Many pathogens express noncoding RNAs (ncRNAs) during infection processes. In the most extreme case, pathogenic ncRNAs alone (such as viroids) can infect eukaryotic organisms, leading to diseases. While a few pathogenic ncRNAs have been implicated in regulating gene expression, the functions of most pathogenic ncRNAs in host-pathogen interactions remain unclear. Here, we employ potato spindle tuber viroid (PSTVd) infecting tomato as a system to dissect host interactions with pathogenic ncRNAs, using comprehensive transcriptome analyses. We uncover various new activities in regulating gene expression during PSTVd infection, such as genome-wide alteration in alternative splicing of host protein-coding genes, enhanced guided-cleavage activities of a host microRNA, and induction of the trans-acting function of phased secondary small interfering RNAs. Furthermore, we reveal that PSTVd infection massively activates genes involved in plant immune responses, mainly those in the calcium-dependent protein kinase and mitogen-activated protein kinase cascades, as well as prominent genes involved in hypersensitive responses, cell wall fortification, and hormone signaling. Intriguingly, our data support a notion that plant immune systems can respond to pathogenic ncRNAs, which has broad implications for providing new opportunities for understanding the complexity of immune systems in differentiating "self" and "nonself," as well as lay the foundation for resolving the long-standing question regarding the pathogenesis mechanisms of viroids and perhaps other infectious RNAs.IMPORTANCE Numerous pathogens, including viruses, express pathogenic noncoding transcripts during infection. In the most extreme case, pathogenic noncoding RNAs alone (i.e., viroids) can cause disease in plants. While some work has demonstrated that pathogenic noncoding RNAs interact with host factors for function, the biological significance of pathogenic noncoding RNAs in host-pathogen interactions remains largely unclear. Here, we apply comprehensive genome-wide analyses of plant-viroid interactions and discover several novel molecular activities underlying nuclear-replicating viroid infection processes in plants, including effects on the expression and function of host noncoding transcripts, as well as the alternative splicing of host protein-coding genes. Importantly, we show that plant immunity is activated upon infection of a nuclear-replicating viroid, which is a new concept that helps to understand viroid-based pathogenesis. Our finding has broad implications for understanding the complexity of host immune systems and the diverse functions of noncoding RNAs.