title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=448 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Preoperative lymphocyte count, neutrophil to lymphocyte and platelet to lymphocyte ratio predict the recurrence with progression and cancerization in vocal fold lesions—retrospective study link: https://peerj.com/articles/15642 last-modified: 2023-09-20 description: BackgroundsThis study explored the contribution of peripheral blood markers in diagnosis and prognosis estimation of different stages of laryngeal dysplasia and early glottic cancer.MethodsRetrospective analysis of clinical, histopathological and laboratory data of 220 patients including hemoglobin, neutrophil, lymphocyte, monocyte and platelet counts, neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR).ResultsThe mean hemoglobin level and platelets count showed differences between histopathological stages of lesions (p = 0.041 and 0.046, respectively). In patients with recurrent lesions mean level of lymphocyte count, NLR and PLR were significant in assessing progression and cancerization (p = 0.005, 0.028 and 0.023, respectively). The univariate analysis recognized level of PLR ≥ 141.74 as significant risk factor of the recurrence of vocal fold hypertrophic lesions (OR = 1.963).ConclusionsThe levels of blood cells and their ratios seem to be effective in predicting the recurrence of lesion and even more their potential role in indicating malignant progression. creator: Anna Rzepakowska creator: Wioletta Pietruszewska creator: Michał Żurek creator: Maria Molga-Magusiak creator: Michał Leszczyński creator: Kazimierz Niemczyk uri: https://doi.org/10.7717/peerj.15642 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Rzepakowska et al. title: Modelling and analysis of the complement system signalling pathways: roles of C3, C5a and pro-inflammatory cytokines in SARS-CoV-2 infection link: https://peerj.com/articles/15794 last-modified: 2023-09-20 description: The complement system is an essential part of innate immunity. It is activated by invading pathogens causing inflammation, opsonization, and lysis via complement anaphylatoxins, complement opsonin’s and membrane attack complex (MAC), respectively. However, in SARS-CoV-2 infection overactivation of complement system is causing cytokine storm leading to multiple organs damage. In this study, the René Thomas kinetic logic approach was used for the development of biological regulatory network (BRN) to model SARS-CoV-2 mediated complement system signalling pathways. Betweenness centrality analysis in cytoscape was adopted for the selection of the most biologically plausible states in state graph. Among the model results, in strongly connected components (SCCs) pro-inflammatory cytokines (PICyts) oscillatory behaviour between recurrent generation and downregulation was found as the main feature of SARS-CoV-2 infection. Diversion of trajectories from the SCCs leading toward hyper-inflammatory response was found in agreement with in vivo studies that overactive innate immunity response caused PICyts storm during SARS-CoV-2 infection. The complex of negative regulators FI, CR1 and DAF in the inhibition of complement peptide (C5a) and PICyts was found desirable to increase immune responses. In modelling role of MAC and PICyts in lowering of SARS-CoV-2 titre was found coherent with experimental studies. Intervention in upregulation of C5a and PICyts by C3 was found helpful in back-and-forth variation of signalling pattern linked with the levels of PICyts. Moreover, intervention in upregulation of PICyts by C5a was found productive in downregulation of all activating factors in the normal SCCs. However, the computational model predictions require experimental studies to be validated by exploring the activation role of C3 and C5a which could change levels of PICyts at various phases of SARS-CoV-2 infection. creator: Didar Murad creator: Rehan Zafar Paracha creator: Muhammad Tariq Saeed creator: Jamil Ahmad creator: Ammar Mushtaq creator: Maleeha Humayun uri: https://doi.org/10.7717/peerj.15794 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Murad et al. 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.