title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=417 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: YAP1 affects the prognosis through the regulation of stemness in endometrial cancer link: https://peerj.com/articles/15891 last-modified: 2023-09-20 description: BackgroundEndometrial cancer stem-like cells (ECSCs) have been proven to be responsible for recurrence, metastasis, and drug-resistance in patients with endometrial cancer. The HIPPO pathway has been shown to play an important role in the development and maintenance of stemness in a variety of tumors. While there was less research about its function in ECSCs. The aim of this study was to explore the role of YAP1, a core molecular of HIPPO pathway, in the stemness of endometrial cancer and to reveal its influence on prognosis.MethodsWe collected specimens and clinical data from 774 patients with endometrial cancer to analyze the correlation between YAP1 expression and prognosis. We then examined the expression of YAP1 in ECSCs and EC cell lines (Ishikawa; HEC1-A) in vitro experiments. Changes in the stemness of cell lines were detected after YAP1 silencing by siRNA. Finally, high-throughput sequencing was used to predict the potential molecular interactions and mechanisms of YAP1’s effect on stemness.ResultDown-regulation of YAP1 significantly suppresses the stemness of EC cell lines. High expression of YAP1 leads to poor prognosis in EC by regulation of stemness.ConclusionYAP1 plays an important role in the prognosis of patients with EC by regulation of stemness. creator: Wei Kong creator: Yuzhen Huang creator: Peng Jiang creator: Yuan Tu creator: Ning Li creator: Jinyu Wang creator: Qian Zhou creator: Yunfeng Zheng creator: Shikai Gou creator: Chenfan Tian creator: Rui Yuan uri: https://doi.org/10.7717/peerj.15891 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kong et al. title: Iron and copper on Botrytis cinerea: new inputs in the cellular characterization of their inhibitory effect link: https://peerj.com/articles/15994 last-modified: 2023-09-20 description: Certain metals play key roles in infection by the gray mold fungus, Botrytis cinerea. Among them, copper and iron are necessary for redox and catalytic activity of enzymes and metalloproteins, but at high concentrations they are toxic. Understanding the mechanism requires more cell characterization studies for developing new, targeted metal-based fungicides to control fungal diseases on food crops. This study aims to characterize the inhibitory effect of copper and iron on B. cinerea by evaluating mycelial growth, sensitivity to cell wall perturbing agents (congo red and calcofluor white), membrane integrity, adhesion, conidial germination, and virulence. Tests of copper over the range of 2 to 8 mM and iron at 2 to 20 mM revealed that the concentration capable of reducing mycelial growth by 50% (IC50) was 2.87 mM and 9.08 mM for copper and iron, respectively. When mixed at equimolar amounts there was a significant inhibitory effect mostly attributable to copper. The effect of Cu50, Fe50, and Cu50–Fe50 was also studied on the mycelial growth of three wild B. cinerea strains, which were more sensitive to metallic inhibitors. A significant inhibition of conidial germination was correlated with adhesion capacity, indicating potential usefulness in controlling disease at early stages of crop growth. Comparisons of the effects of disruptive agents on the cell wall showed that Cu, Fe, and Cu–Fe did not exert their antifungal effect on the cell wall of B. cinerea. However, a relevant effect was observed on plasma membrane integrity. The pathogenicity test confirmed that virulence was correlated with the individual presence of Cu and Fe. Our results represent an important contribution that could be used to formulate and test metal-based fungicides targeted at early prevention or control of B. cinerea. creator: Fátima Rodríguez-Ramos creator: Vilbett Briones-Labarca creator: Verónica Plaza creator: Luis Castillo uri: https://doi.org/10.7717/peerj.15994 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Rodríguez-Ramos et al. title: Chorein sensitive microtubule organization in tumor cells link: https://peerj.com/articles/16074 last-modified: 2023-09-20 description: BackgroundThe purpose of this study is to analyzed the involvement of chorein in microtubules organization of three types of malignant; rhabdomyosarcoma tumor cells (ZF), rhabdomyosarcoma cells (RH30), and rhabdomyosarcoma cells (RD). ZF are expressing high chorein levels. Previous studies revealed that chorein protein silencing in ZF tumor cells persuaded apoptotic response followed by cell death. In addition, in numerous malignant and non-malignant cells this protein regulates actin cytoskeleton structure and cellular signaling. However, the function of chorein protein in microtubular organization is yet to be established.MethodsIn a current research study, we analyzed the involvement of chorein in microtubules organization by using three types of malignant rhabdomyosarcoma cells. We have applied confocal laser-scanning microscopy to analyze microtubules structure and RT-PCR to examine cytoskeletal gene transcription.ResultsWe report here that in rhabdomyosarcoma cells (RH30), chorein silencing induced disarrangement of microtubular network. This was documented by laser scanning microscopy and further quantified by FACS analysis. Interestingly and in agreement with previous reports, tubulin gene transcription in RH cells was unchanged upon silencing of chorein protein. Equally, confocal analysis showed minor disordered microtubules organization with evidently weakened staining in rhabdomyosarcoma cells (RD and ZF) after silencing of chorein protein.ConclusionThese results disclose that chorein silencing induces considerable structural disorganization of tubulin network in RH30 human rhabdomyosarcoma tumor cells. Additional studies are now needed to establish the role of chorein in regulating cytoskeleton architecture in tumor cells. creator: Saad Alkahtani creator: Abdullah A. Alkahtane creator: Christos Stournaras creator: Saud Alarifi uri: https://doi.org/10.7717/peerj.16074 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Alkahtani et al. title: Metabolomics profiling reveals differences in proliferation between tumorigenic and non-tumorigenic Madin-Darby canine kidney (MDCK) cells link: https://peerj.com/articles/16077 last-modified: 2023-09-20 description: BackgroundMadin-Darby canine kidney (MDCK) cells are a cellular matrix in the production of influenza vaccines. The proliferation rate of MDCK cells is one of the critical factors that determine the vaccine production cycle. It is yet to be determined if there is a correlation between cell proliferation and alterations in metabolic levels. This study aimed to explore the metabolic differences between MDCK cells with varying proliferative capabilities through the use of both untargeted and targeted metabolomics.MethodsTo investigate the metabolic discrepancies between adherent cell groups (MDCK-M60 and MDCK-CL23) and suspension cell groups (MDCK-XF04 and MDCK-XF06), untargeted and targeted metabolomics were used. Utilizing RT-qPCR analysis, the mRNA expressions of key metabolites enzymes were identified.ResultsAn untargeted metabolomics study demonstrated the presence of 81 metabolites between MDCK-M60 and MDCK-CL23 cells, which were mainly affected by six pathways. An analysis of MDCK-XF04 and MDCK-XF06 cells revealed a total of 113 potential metabolites, the majority of which were impacted by ten pathways. Targeted metabolomics revealed a decrease in the levels of choline, tryptophan, and tyrosine in MDCK-CL23 cells, which was in accordance with the results of untargeted metabolomics. Additionally, MDCK-XF06 cells experienced a decrease in 5’-methylthioadenosine and tryptophan, while S-adenosylhomocysteine, kynurenine, 11Z-eicosenoic acid, 3-phosphoglycerate, glucose 6-phosphate, and phosphoenolpyruvic acid concentrations were increased. The mRNA levels of MAT1A, MAT2B, IDO1, and IDO2 in the two cell groups were all increased, suggesting that S-adenosylmethionine and tryptophan may have a significant role in cell metabolism.ConclusionsThis research examines the effect of metabolite fluctuations on cell proliferation, thus offering a potential way to improve the rate of MDCK cell growth. creator: Na Sun creator: Yuchuan Zhang creator: Jian Dong creator: Geng Liu creator: Zhenbin Liu creator: Jiamin Wang creator: Zilin Qiao creator: Jiayou Zhang creator: Kai Duan creator: Xuanxuan Nian creator: Zhongren Ma creator: Xiaoming Yang uri: https://doi.org/10.7717/peerj.16077 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sun et al. title: Identification of anthropogenic debris in the stomach and intestines of giant freshwater prawns from the Trang River in southern Thailand link: https://peerj.com/articles/16082 last-modified: 2023-09-20 description: BackgroundAnthropogenic waste, especially microplastics, is becoming more prevalent in the environment and marine ecosystems, where it has the potential to spread through food chains and be consumed by humans. Southeast Asian countries are home to giant freshwater prawns, a common freshwater species that is eaten around the world. Microplastic pollution in river water, sediment, and commercially significant aquatic species such as fish and mollusks has been observed, yet few studies have been conducted on giant freshwater prawns in the rivers of southern Thailand, where microplastics may contaminate prawns via the food they ingest. The purpose of this research was to investigate the accumulation of anthropogenic material in the organs of river prawns (Macrobrachium rosenbergii).MethodsMicroplastics in the stomachs and intestines of giant freshwater prawns were the focus of this study. Samples were digested with 30 ml of 10% potassium hydroxide (KOH), heated for 5 min at 60 °C, and then digested at room temperature. The quantity, color, and appearance of microplastics were assessed using a stereomicroscope after 12 h. Furthermore, polymers were examined using a Fourier transform infrared spectrophotometer (FTIR). Microplastic counts were compared between sexes. A T-test was used to compare male and female microplastic counts in the stomach and intestine, and the Pearson correlation was used to compare the association between microplastic counts in the stomach and intestine and carapace length (CL), length of abdomen (LA), and body weight (BW) of male and female giant freshwater prawns. The threshold of significance was fixed at p < 0.05.ResultsBased on the study results, a total of 370 pieces of anthropogenic debris were discovered in the stomachs and intestines of both female and male prawns. The average number of microplastics per individual was 4.87 ±  0.72 in female stomachs and 3.03 ± 0.58 in male stomachs, and 1.73 ± 0.36 in female intestines and 2.70 ± 0.57 in male intestines. The majority of microplastics found in females were within the <100 µm range, while males contained microplastics in the range of 100–500 µm. Both male and female prawns contained fibers (72.70%) and fragments (27.30%). Various polymers were identified, including cotton, rayon, and polyvinyl chloride (PVC). The study also explored the relationship between carapace length, length of abdomen, body weight, stomach weight, and the number of microplastics. The findings reveal a significant association between the number of microplastics and stomach weight in male prawns (R = 0.495; p = 0.005). These findings provide alarming evidence of anthropogenic debris ingestion in prawns and raise concerns about the future effects of anthropogenic pollution on giant freshwater prawns. creator: Kanyarat Tee-hor creator: Thongchai Nitiratsuwan creator: Siriporn Pradit uri: https://doi.org/10.7717/peerj.16082 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Tee-hor et al. title: Surgical vs. transcatheter aortic valve replacement in patients over 75 years with aortic stenosis: sociodemographic profile, clinical characteristics, quality of life and functionality link: https://peerj.com/articles/16102 last-modified: 2023-09-20 description: BackgroundAortic valve stenosis (AVS) affects 25% of the population over 65 years. At present, there is no curative medical treatment for AVS and therefore the surgical approach, consisting of transcatheter aortic valve replacement (TAVR) or surgical aortic valve replacement (SAVR), is the treatment of choice.MethodologyThe aim of this study was to analyze the sociodemographic and clinical characteristics, quality of life and functionality of a sample of patients with AVS over 75 years of age, who underwent TAVR or SAVR, applying standard clinical practice. A prospective multicenter observational study was conducted in two hospitals of the Spanish National Health System. Data were collected at baseline, 1, 6 months and 1 year.ResultsIn total, 227 participants were included, with a mean age of 80.6 [SD 4.1]. Statistically significant differences were found in terms of quality of life, which was higher at 1 year in patients who underwent SAVR. In terms of functionality, SAVR patients obtained a better score (p < 0.01). However, patients who underwent TAVR began with a worse baseline situation and managed to increase their quality of life and functionality after 1 year of follow-up.ConclusionThe individualized choice of TAVR or SAVR in patients with AVS improves patients’ quality of life and function. Moreover, the TAVR procedure in patients with a worse baseline situation and a high surgical risk achieved a similar increase in quality of life and functionality compared to patients undergoing SAVR with a better baseline situation. creator: Víctor Fradejas-Sastre creator: Paula Parás-Bravo creator: Manuel Herrero-Montes creator: María Paz-Zulueta creator: Ester Boixadera-Planas creator: Luis Manuel Fernández-Cacho creator: Gabriela Veiga-Fernández creator: Maria Elena Arnáiz-García creator: Jose María De-la-Torre-Hernández uri: https://doi.org/10.7717/peerj.16102 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fradejas-Sastre et al. title: Identification of Dioscorea opposite Thunb. CDPK gene family reveals that DoCDPK20 is related to heat resistance link: https://peerj.com/articles/16110 last-modified: 2023-09-20 description: Temperature affects the growth and yield of yam (Dioscorea opposite Thunb.), and calcium-dependent protein kinases (CDPKs) play an important role in the plant stress response. However, there has been a lack of system analyses of yam’s CDPK gene family. In this study, 29 CDPK transcriptome sequences with complete open reading frames (ORFs) were identified from yam RNA sequencing data. The sequences were classified into four groups (I–VI) using phylogenetic analysis. Two DoCDPK genes were randomly selected from each group and the gene patterns of yam leaves were determined using quantitative real-time PCR (qRT-PCR) under high and low temperature stress in order to show their unique functions in mediating specific responses. Among them, DoCDPK20 was significantly induced in high temperatures. The pPZP221-DoCDPK20 was transformed into tobacco leaves using an agrobacterium-mediated method. Under high temperature stress, DoCDPK20 overexpression reduced photosynthesis and improved heat tolerance in transgenic tobacco. Our research offers meaningful perspectives into CDPK genes and new avenues for the genetic engineering and molecular breeding of yam. creator: Yuanli Gao creator: Yanfang Zhang creator: Xiang Ji creator: Jinxin Wang creator: Ningning Suo creator: Jiecai Liu creator: Xiuwen Huo uri: https://doi.org/10.7717/peerj.16110 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gao et al. title: Genome-wide identification of putative dihydroflavonol 4-reductase (DFR) gene family in eight Solanaceae species and expression analysis in Solanum lycopersicum link: https://peerj.com/articles/16124 last-modified: 2023-09-20 description: Dihydroflavonol 4-reductase (DFR; EC1.1.1.219) is an important rate-limiting enzyme in the plant flavonoid pathway toward both anthocyanins and proanthocyanidins. Although DFR genes have been isolated from multiple plants and their functions have been well characterized in some plants, little is known about DFRs in Solanaceae species. Therefore, in this study, we performed genome-wide analysis and identified 6, 5, 4, 5, 5, 6, 6 and 5 DFR gene family members in eight Solanaceae species (S. lycopersicum, S. pennellii, S. tuberosum, S. melongena, C. annuum, N. tabacum, P. inflata, and P. axillaris) respectively. The putative DFR genes were systematically identified using bioinformatics to predict their protein properties, cellular location, phylogenetic relationships, gene structure, conserved motifs, and cis-acting elements in the promoters. Furthermore, quantitative real-time PCR (qRT-PCR) was used to identify the expression pattern of DFRs in tomato. We classified all DFRs into five groups based on their phylogenetic features. Sequence analysis showed that all encoded DFR protein sequences possess a highly conserved NAD-dependent epimerase/dehydratase. In addition, almost all the members of each group displayed similar gene structures and motif distributions, which might be related to their identical executive functions. All 42 DFRs possess a series of light-responsive, phytohormone-responsive, MYB-responsive, stress-responsive, and tissue-specific expression-related cis-elements in the promoter sequences. qRT-PCR analysis showed that tomato DFRs were expressed in many different organs. This study will provide a theoretical basis for further investigation of the function of DFRs in Solanaceae. creator: Wenjing Li creator: Yiming Zhang creator: Hualiang Liu creator: Qiuping Wang creator: Xue Feng creator: Congyan Wang creator: Yanxiang Sun creator: Xinye Zhang creator: Shu Zhu uri: https://doi.org/10.7717/peerj.16124 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Inclusion of up to 20% Black Soldier Fly larvae meal in broiler chicken diet has a minor effect on caecal microbiota link: https://peerj.com/articles/15857 last-modified: 2023-09-19 description: BackgroundThe Black Soldier Fly larvae (BSFL) are a source of nutrients and bioactive compounds in broiler diets. Some components of the BSFL may serve as a prebiotic or may impact the intestinal microbiota of the broilers by other modes of action, which in turn can affect the health and performance of broilers. Here, we investigate the impact of up to 20% BSFL in broiler diets on the diversity and composition of the broiler’s microbiota.MethodsFour hundred broilers were fed five iso-nutritious experimental diets with increasing levels of BSFL meal reaching 0%, 5%, 10%, 15%, 20% in the finisher diets. Eight caecal content samples coming from each of the eight replicates per treatment were collected at two time points (day 21 and day 42) for DNA extraction and sequencing of the V3–V4 regions using Illumina MiSeq 2 × 300 bp pair-end sequencing with 341f and 805r primers. Analysis of variance and Spearman’s correlation were performed, while QIIME2, DADA2, and Calypso were used for data analysis.ResultsWhen broilers were 21 days of age, the abundance of two groups of sequence variants representing Enterococcus and unclassified Christensenellaceae was significantly lower (p-value = 0.048 and p-value = 0.025, respectively) in the 20% BSFL group compared to the 0% BSFL group. There was no relevant alteration in the microbiota diversity at that stage. On day 42, the Spearman correlation analysis demonstrated that the sequence variants representing the genus Coprococcus showed a negative relationship with the BSFL inclusion levels (p-value = 0.043). The sequence variants representing the genus Roseburia and Dehalobacterium demonstrated a positive relationship with the BSFL dietary inclusion (p-value = 0.0069 and p-value = 0.0034, respectively). There was a reduction in the dissimilarity index (ANOSIM) caused by the 20% BSFL dietary inclusion.ConclusionThe addition of up to 20% BSFL in broiler diets did not affect the overall caeca microbiota diversity or composition at day 21. On day 42, there was a reduction in the beta diversity caused by the 20% BSFL dietary inclusion. The abundance of the bacterial group Roseburia was increased by the BSFL dietary inclusion, and it may be beneficial to broiler immunity and performance. creator: Jessica de Souza Vilela creator: Sarbast K. Kheravii creator: Yadav Sharma Bajagai creator: Manisha Kolakshyapati creator: Terence Zimazile Sibanda creator: Shu-Biao Wu creator: Nigel R. Andrew creator: Isabelle Ruhnke uri: https://doi.org/10.7717/peerj.15857 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 de Souza Vilela et al. title: Climate change and carnivores: shifts in the distribution and effectiveness of protected areas in the Amazon link: https://peerj.com/articles/15887 last-modified: 2023-09-19 description: BackgroundCarnivore mammals are animals vulnerable to human interference, such as climate change and deforestation. Their distribution and persistence are affected by such impacts, mainly in tropical regions such as the Amazon. Due to the importance of carnivores in the maintenance and functioning of the ecosystem, they are extremely important animals for conservation. We evaluated the impact of climate change on the geographic distribution of carnivores in the Amazon using Species Distribution Models (SDMs). Do we seek to answer the following questions: (1) What is the effect of climate change on the distribution of carnivores in the Amazon? (2) Will carnivore species lose or gain representation within the Protected Areas (PAs) of the Amazon in the future?MethodsWe evaluated the distribution area of 16 species of carnivores mammals in the Amazon, based on two future climate scenarios (RCP 4.5 and RCP 8.5) for the year 2070. For the construction of the SDMs we used bioclimatic and vegetation cover variables (land type). Based on these models, we calculated the area loss and climate suitability of the species, as well as the effectiveness of the protected areas inserted in the Amazon. We estimated the effectiveness of PAs on the individual persistence of carnivores in the future, for this, we used the SDMs to perform the gap analysis. Finally, we analyze the effectiveness of PAs in protecting taxonomic richness in future scenarios.ResultsThe SDMs showed satisfactory predictive performance, with Jaccard values above 0.85 and AUC above 0.91 for all species. In the present and for the future climate scenarios, we observe a reduction of potencial distribution in both future scenarios (RCP4.5 and RCP8.5), where five species will be negatively affected by climate change in the RCP 4.5 future scenario and eight in the RCP 8.5 scenario. The remaining species stay stable in terms of total area. All species in the study showed a loss of climatic suitability. Some species lost almost all climatic suitability in the RCP 8.5 scenario. According to the GAP analysis, all species are protected within the PAs both in the current scenario and in both future climate scenarios. From the null models, we found that in all climate scenarios, the PAs are not efficient in protecting species richness. creator: Camila Ferreira Leão creator: Matheus S. Lima Ribeiro creator: Kauê Moraes creator: Gabriela Silva Ribeiro Gonçalves creator: Marcela Guimarães Moreira Lima uri: https://doi.org/10.7717/peerj.15887 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ferreira Leão et al.