Hepatic nuclear factor 4 alpha promotes the ferroptosis of lung adenocarcinoma via transcriptional activation of cytochrome P450 oxidoreductase
Background Lung adenocarcinoma is one of the most prevalent cancers while ferroptosis is crucial for cancer therapies. This study aims to investigate the function and mechanism of hepatic nuclear factor 4 alpha (HNF4A) in lung adenocarcinomas’ ferroptosis. Materials and Methods HNF4A expression in ferroptotic A549 cells was detected. Then HNF4A was knocked down in A549 cells while overexpressed in H23 cells. Cells with changed HNF4A expression were tested for cytotoxicity and the level of cellular lipid peroxidation. The expression of cytochrome P450 oxidoreductase (POR) expression was examined after HNF4A was knocked down or overexpressed. Chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and dual-luciferase assays were performed to validate the regulation of HNF4A on POR. Finally, POR was restored in HNF4A-altered cells to check whether it restores the effect of HNF4A on ferroptosis. Results We found that HNF4A expression significantly decreased in the ferroptosis of A549 cells, and this change can be blocked by deferoxamine, an inhibitor of ferroptosis. Knockdown of HNF4A inhibited ferroptosis in A549 cells while overexpression of HNF4A promoted ferroptosis in H23 cells. We identified a key ferroptosis-related gene, POR serves as a potential target gene of HNF4A, whose expression was significantly changed in lung adenocarcinoma cells knocking down or overexpressing HNF4A. We demonstrated that HNF4A was bound to the POR’s promoter to enhance POR expression, and identified the binding sites via ChIP-qPCR and luciferase assays. Restoration of POR expression blocked the promoting effect of HNF4A on ferroptosis in lung adenocarcinoma. Conclusion HNF4A promotes POR expression through binding to the POR’s promoter, and subsequently promotes the ferroptosis of lung adenocarcinoma.
Besskaya et al. (2023) Hepatic nuclear factor 4 alpha promotes the ferroptosis of lung adenocarcinoma via transcriptional activation of cytochrome P450 oxidoreductase. PeerJ 11:e15377 https://doi.org/10.7717/peerj.15377
Student perceptions toward virtual reality training in dental implant education
Objectives Both the shortage of professional teaching resources and the expensive dental implant supplies impede the effective training of dental undergraduate in implantology. Virtual reality (VR) technology may provide solutions to solve these problems. This pilot study was implemented to explore the usability and acceptance of a VR application in the training of dental implant among dental students at the Jinan University School of Stomatology. Methods We designed and developed a VR system with head-mounted displays (HMDs) to assist dental implant training. Undergraduate dental students were invited to experience a 30-minute “Introduction to dental implants” VR-HMDs training module. A total of 119 dental students participated the training. Firstly, the VR interactive training on dental implant was described, illustrated and practiced. Next, a system usability scale (SUS) survey was used to verify the usability and feasibility of the VR application on training dental students. Finally, the participants were given a questionnaire to provide their perceptions and feedback of the usefulness of the VR application for training dental implant skills. Results The SUS score was 82.00 ± 10.79, indicating a top 10 percentage ranking of the system’s usabilitys. The participants’ answers to the questionnaire reflected most of them exhibited strong interests in the VR system, with a tendency that the female students were more confident than the male in manipulating the VR system. The participants generally acknowledged the usefulness of VR dental implants, ranking VR value above the traditional laboratory operations, and a preference for using the VR system on learning other skills. They also gave valuable suggestions on VR dental implants for substantial improvement. However, some students were not strongly positive about the VR training in this study, the reason might lie in a more theoretical module was selected for testing, which impacted the students’ ratings. Conclusions In this study we revealed the feasibility and usability of VR applications on training dental implant among undergraduate dental students. This pilot study showed that the participants benefited from the dental implant VR training by practicing the skills repeatedly. The feedback from student participants affirmed the advantages and their acceptance of the VR application in dental education. Especially, the VR-based technology is highly conducive to clinical operating skills and surgical procedures-focused training in medical education, indicating that the VR system should be combined with the traditional practice approach in improving dental students’ practical abilities.
Huang et al. (2023) Student perceptions toward virtual reality training in dental implant education. PeerJ 11:e14857 https://doi.org/10.7717/peerj.14857
Identification of key immune-related genes associated with LPS/D-GalN-induced acute liver failure in mice based on transcriptome sequencing
Background The aim of this study was to identify key immune-related genes in acute liver failure (ALF) by constructing an ALF mouse model for transcriptome sequencing. Methods The C57BL/6 mouse with ALF model was induced by lipopolysaccharide (LPS)/ D-galactosamine (D-GalN). After successful modelling, the liver tissues of all mice were obtained for transcriptome sequencing. The key immune-related genes in mice with ALF were identified by differential expression analysis, immune infiltration analysis, weighted gene co-expression network analysis (WGCNA), enrichment analysis, and protein-protein interaction (PPI) analysis. Results An LPS/D-GalN-induced ALF mouse model was successfully constructed, and transcriptome sequencing was performed. Significant differences in the proportions of monocytes, macrophages M0, macrophages M1 and neutrophils were shown by immune infiltration analysis, and 5255 genes highly associated with these four immune cells were identified by WGCNA. These immune genes were found to be significantly enriched in the TNF signalling pathway by enrichment analysis. Finally, PPI analysis was performed on genes enriched in this pathway and three key genes (CXCL1, CXCL10 and IL1B) were screened out and revealed to be significantly upregulated in ALF. Conclusions Key immune-related genes in ALF were identified in this study, which may provide not only potential therapeutic targets for treating ALF and improving its prognosis, but also a reliable scientific basis for the immunotherapy of the disease.
Chen et al. (2023) Identification of key immune-related genes associated with LPS/D-GalN-induced acute liver failure in mice based on transcriptome sequencing. PeerJ 11:e15241 https://doi.org/10.7717/peerj.15241
Retrospective study of influencing factors on the outcomes of luteal phase stimulation in patients with dual stimulation
Background Dual/double stimulation (DS) is an ovarian stimulation strategy that has emerged in recent years; it is characterized by two rounds of ovarian stimulation and oocyte retrieval in the same menstrual cycle. DS can greatly shorten the time required to obtain valid embryos in assisted reproduction. For fertility preservation, DS can speed up oocyte storage process. However, factors influencing luteal phase ovarian stimulation (LPS) outcomes in DS have not been elucidated. Methods A total of 156 cycles from 78 cases were studied. Patients were grouped and analyzed according to their follicular phase ovarian stimulation (FPS) types. Female ages, ovarian stimulation protocols, number of oocytes retrieved, embryo quality were recorded. Comparisons of outcomes were conducted between different groups. Results Our study found that LPS obtained similar outcomes to follicular phase stimulation (FPS), and that the choice of FPS protocol affected the efficiency of LPS, the antagonist protocol and progestin-primed ovarian stimulation (PPOS) protocol resulted in better embryo outcomes in LPS. In LPS of DS, sufficient stimulation duration was the guarantee of embryo quality (number of available embryos: β = 0.145, 95% CI [0.078–0.211], P = 0.000; number of high-quality embryos: β = 0.114, 95% CI [0.057–0.171], P = 0.000). Discussion This study provided ideas for the precise use of DS. We suggest to further expand the sample size of DS in the future, conduct prospective controlled studies, unify the sample size of each subgroup, include the ovarian reserve of patients in the grouping basis, and exclude the influence of male factors. We hope that this study will help further refinement of DS so as to maximize patient benefits from it. Conclusion When the DS strategy is considered in the follicular phase, the antagonist protocol and PPOS protocol are more recommended for better embryo outcomes in LPS. During LPS, adequate ovarian stimulation duration is the most important guarantee for LPS efficiency.
Chen et al. (2023) Retrospective study of influencing factors on the outcomes of luteal phase stimulation in patients with dual stimulation. PeerJ 11:e15296 https://doi.org/10.7717/peerj.15296
Reporting inconsistency between published conference abstracts and article abstracts of randomised controlled trials in prosthodontics presented at IADR general sessions
Background There is commonly a discrepancy between conference abstracts and published article abstracts in prosthodontic randomized controlled trials (RCTs), which may mislead the scholars those attend conferences. Objective To identify the characteristics predicting inconsistency between conference abstracts and published article abstracts in prosthodontic RCTs. Methods The conference abstracts of prosthodontic RCTs presented at the IADR general sessions from 2002 to 2015 were searched. Electronic searches of MEDLINE, EMBASE, the Cochrane Library, and Google Scholar databases were conducted to match full-text publications for conference abstracts. Two investigators extracted basic characteristics and assessed the consistency and reporting quality independently and in duplicate. The linear regression model was used to analyze the predictors of inconsistency. Results A total of 147 conference abstracts were matched with published articles. Results for the secondary outcome measure, Statistical analysis, and precision measure were less than 50% consistent, and even nearly 5% of the studies had opposite conclusions. Multiple linear regression analysis showed that three factors were correlated with lower inconsistency, including continent of origin (p = 0.011), presentation type (p = 0.017), and difference in reporting quality (p = 0.013). Conclusion Conference attendees should cautiously treat the findings of the conference abstracts. Researchers should improve the precision of the information delivered at conferences. We recommend the authors of RCTs to explain the primary difference between conference abstracts and article abstracts.
Wang et al. (2023) Reporting inconsistency between published conference abstracts and article abstracts of randomised controlled trials in prosthodontics presented at IADR general sessions. PeerJ 11:e15303 https://doi.org/10.7717/peerj.15303
Genome-wide transcriptomic analysis identifies candidate genes involved in jasmonic acid-mediated salt tolerance of alfalfa
Soil salinity imposes a major threat to plant growth and agricultural productivity. Despite being one of the most common fodder crops in saline locations, alfalfa is vulnerable to salt stress. Jasmonic acid (JA) is a phytohormone that influences plant response to abiotic stimuli such as salt stress. However, key genes and pathways by which JA-mediated salt tolerance of alfalfa are little known. A comprehensive transcriptome analysis was performed to elucidate the underlying molecular mechanisms of JA-mediated salt tolerance. The transcripts regulated by salt (S) compared to control (C) and JA+salt (JS) compared to C were investigated. Venn diagram and expression pattern of DEGs indicated that JS further altered a series of genes expression regulated by salt treatment, implying the roles of JA in priming salt tolerance. Enrichment analysis revealed that DEGs exclusively regulated by JS treatment belonged to primary or secondary metabolism, respiratory electron transport chain, and oxidative stress resistance. Alternatively, splicing (AS) was induced by salt alone or JA combined treatment, with skipped exon (SE) events predominately. DEGs undergo exon skipping involving some enriched items mentioned above and transcription factors. Finally, the gene expressions were validated using quantitative polymerase chain reaction (qPCR), which produced results that agreed with the sequencing results. Taken together, these findings suggest that JA modulates the expression of genes related to energy supply and antioxidant capacity at both the transcriptional and post-transcriptional levels, possibly through the involvement of transcription factors and AS events.
Yang et al. (2023) Genome-wide transcriptomic analysis identifies candidate genes involved in jasmonic acid-mediated salt tolerance of alfalfa. PeerJ 11:e15324 https://doi.org/10.7717/peerj.15324
Using DNA metabarcoding to assess insect diversity in citrus orchards
Background DNA metabarcoding is rapidly emerging as a cost-effective approach for large-scale biodiversity assessment and pest monitoring. The current study employed metabarcoding to assess insect diversity in citrus orchards in Ganzhou City, Jiangxi, China in both 2018 and 2019. Insects were sampled using Malaise traps deployed in three citrus orchards producing a total of 43 pooled monthly samples. Methods The Malaise trap samples were sequenced following DNA metabarcoding workflow. Generated sequences were curated and analyzed using two cloud databases and analytical platforms, the barcode of life data system (BOLD) and multiplex barcode research and visualization environment (mBRAVE). Results These platforms assigned the sequences to 2,141 barcode index numbers (BINs), a species proxy. Most (63%) of the BINs were shared among the three sampling sites while BIN sharing between any two sites did not exceed 71%. Shannon diversity index (H′) showed a similar pattern of BIN assortment at the three sampling sites. Beta diversity analysis by Jaccard similarity coefficient (J) and Bray-Curtis distance matrix (BC) revealed a high level of BIN similarity among the three sites (J = 0.67–0.68; BC = 0.19–0.20). Comparison of BIN records against all those on BOLD made it possible to identify 40% of the BINs to a species, 57% to a genus, 97% to a family and 99% to an order. BINs which received a species match on BOLD were placed in one of four categories based on this assignment: pest, parasitoid, predator, or pollinator. As this study provides the first baseline data on insect biodiversity in Chinese citrus plantations, it is a valuable resource for research in a broad range of areas such as pest management and monitoring beneficial insects in citrus gardens.
Liu et al. (2023) Using DNA metabarcoding to assess insect diversity in citrus orchards. PeerJ 11:e15338 https://doi.org/10.7717/peerj.15338
Pollination efficacy of stingless bees, Tetragonula pagdeni Schwarz (Apidae: Meliponini), on greenhouse tomatoes (Solanum lycopersicum Linnaeus)
The stingless bee Tetragonula pagdeni is distributed over a vast Southeast Asian territory. This species is commonly used as a commercial insect pollinator. Pollination efficacy of T. pagdeni was investigated with tomato (Solanum lycopersicum L.) cultivated in greenhouse environments. In the first experiment, the number of fruit sets, number of seeds, fresh weight, and fruit height were quantified in the greenhouse with stingless bees, without stingless bees, and with pollination by mechanical vibration by hand. In the second experiment, the treatments were conducted with tomatoes of indeterminate growth in the greenhouse with and without stingless bees to prevent variation among the different tomato plants. The obtained results showed that a greenhouse with stingless bees presented 85 ± 4.24 fruits per 100 flowers, more than a greenhouse with mechanical vibration (79.5 ± 2.12 fruits per 100 flowers) or a greenhouse without stingless bees (15 ± 0.00 fruits per 100 flowers). In addition, fruit produced in a greenhouse with stingless bees showed greater fruit weight and number of seeds than fruit produced in a greenhouse without stingless bees or pollinated by mechanical vibration. According to the obtained results, we suggest that T. pagdeni could be beneficial as an insect pollinator of greenhouse tomatoes in tropical regions, where the use of honeybees and bumblebees would be more difficult.
Wongsa et al. (2023) Pollination efficacy of stingless bees, Tetragonula pagdeni Schwarz (Apidae: Meliponini), on greenhouse tomatoes (Solanum lycopersicum Linnaeus). PeerJ 11:e15367 https://doi.org/10.7717/peerj.15367
Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses
Abscisic acid (ABA) is a plant hormone that plays an important regulatory role in plant growth and stress response. The AREB (ABA-responsive element binding protein)/ABF (ABRE-binding factor) are important ABA-signaling components that participate in abiotic stress response. However, genome-scale analysis of ABF/AREB has not been systemically investigated in tomato. This study was conducted to identify tomato ABF/AREB family members and analyze their response to ABA and abiotic stresses. The results show that a total of 10 ABF/AREB members were identified in tomato, which are randomly distributed on five chromosomes. Domain analysis showed that these members exhibit high protein similarity, especially in the basic leucine zipper (bZIP) domain region. Subcellular localization analysis indicated that all 10 ABF/AREB members are localized in the nucleus. Phylogenetic tree analysis showed that tomato ABF/AREB genes are divided into two groups, and they are similar with the orthologs of other plants. The analysis of cis-acting elements showed that most tomato ABF/AREB genes contain a variety of hormones and stress-related elements. Expression profiles of different tissues indicated that SlABF2 and SlABF10 play an important role in fruit ripening. Finally, qRT-PCR analysis revealed that 10 tomato ABF/AREB genes respond to ABA, with SlABF3 being the most sensitive. SlABF3, SlABF5 and SlABF10 positively respond to salt and cold stresses. SlABF1, SlABF3 and SlABF10 are significantly induced under UV radiation treatment. SlABF3 and SlABF5 are significantly induced in osmotic stress. Overall, this study may provide insight into the role of tomato ABF/AREB homologues in plant response to abiotic stresses, which laid a foundation for future functional study of ABF/AREB in tomato.
Pan et al. (2023) Identification of ABF/AREB gene family in tomato (Solanum lycopersicum L.) and functional analysis of ABF/AREB in response to ABA and abiotic stresses. PeerJ 11:e15310 https://doi.org/10.7717/peerj.15310
Variation of choroidal thickness during the waking period over three consecutive days in different degrees of myopia and emmetropia using optical coherence tomography
Purpose To investigate the diurnal variation in subfoveal choroidal thickness (SFCT) during the waking period over three consecutive days in different degrees of myopia and emmetropia. Methods A total of 60 adult volunteers were grouped into low, moderate, high myopia, and emmetropia subgroups. SFCT, axial length (AL), anterior chamber depth (ACD), and intraocular pressure (IOP) were measured every 2 h from 8 AM to 8 PM for three successive days. Results The mean values of daily change amplitude were 3.18 mmHg (IOP), 0.05 mm (AL), 0.17 mm (ACD), and 13.51 μm (SFCT). The values of AL and ACD increased simultaneously with spherical equivalent refraction (SER), but SFCT was the opposite. IOP had a diurnal variation, and there was no difference among the four groups. AL of the high myopia group, ACD of the emmetropia group, and SFCT of each myopia group had diurnal variation over three consecutive days. AL had a high mean value at noon every day, and SFCT had a low mean value at noon every day. Conclusion The choroid thickness of subjects with different degrees of myopia had a significant diurnal variation. The change of diurnal variation between emmetropic and myopic subjects may be one of the causes of myopia.
Jiang et al. (2023) Variation of choroidal thickness during the waking period over three consecutive days in different degrees of myopia and emmetropia using optical coherence tomography. PeerJ 11:e15317 https://doi.org/10.7717/peerj.15317