title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=329 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Regulation of endoplasmic reticulum stress on autophagy and apoptosis of nucleus pulposus cells in intervertebral disc degeneration and its related mechanisms link: https://peerj.com/articles/17212 last-modified: 2024-04-22 description: Intervertebral disc degeneration (IVDD) is a common and frequent disease in orthopedics, which seriously affects the quality of life of patients. Endoplasmic reticulum stress (ERS)-regulated autophagy and apoptosis play an important role in nucleus pulposus (NP) cells in IVDD. Hypoxia and serum deprivation were used to induce NP cells. Cell counting kit-8 (CCK-8) assay was used to detect cell activity and immunofluorescence (IF) was applied for the appraisement of glucose regulated protein 78 (GRP78) and green fluorescent protein (GFP)-light chain 3 (LC3). Cell apoptosis was detected by flow cytometry and the expression of LC3II/I was detected by western blot. NP cells under hypoxia and serum deprivation were induced by lipopolysaccharide (LPS), and intervened by ERS inhibitor (4-phenylbutyric acid, 4-PBA) and activator (Thapsigargin, TP). Then, above functional experiments were conducted again and western blot was employed for the evaluation of autophagy-, apoptosis and ERS-related proteins. Finally, NP cells under hypoxia and serum deprivation were stimulated by LPS and intervened using apoptosis inhibitor z-Val-Ala-DL-Asp-fluoromethyl ketone (Z-VAD-FMK) and autophagy inhibitor 3-methyladenine (3-MA). CCK-8 assay, IF, flow cytometry and western blot were performed again. Besides, the levels of inflammatory cytokines were measured with enzyme-linked immunosorbent assay (ELISA) and the protein expressions of programmed death markers were estimated with western blot. It showed that serum deprivation induces autophagy and apoptosis. ERS was significantly activated by LPS in hypoxic and serum deprivation environment, and autophagy and apoptosis were significantly promoted. Overall, ERS affects the occurrence and development of IVDD by regulating autophagy, apoptosis and other programmed death. creator: Jiuming Dai creator: Jin Liu creator: Yucheng Shen creator: Bing Zhang creator: Chaonian Li creator: Zhidong Liu uri: https://doi.org/10.7717/peerj.17212 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dai et al. title: SUMOylation of zebrafish transcription factor Zbtb21 affects its transcription activity link: https://peerj.com/articles/17234 last-modified: 2024-04-22 description: BackgroundPost-translational modification by Small Ubiquitin-like MOdifier (SUMO) is an important mechanism to regulate protein activity, protein stability, and localization of substrates. Zbtb21 is a zinc finger and BTB (Broad-complex, Tram-track and Bric à brac) domain-containing transcription factor. Bioinformatic prediction suggests several putative SUMOylated sites in Zbtb21 protein.MethodsTwo evolutionarily conserved lysine residues in Zbtb21 protein were mutated alone or in combination to disrupt the binding with SUMO molecules. Western blot and co-immunoprecipitation analyses were performed to detect the SUMOylation state of wild type and mutant Zbtb21 proteins, respectively. Luciferase reporter assays were conducted to evaluate their transcription activities. Meanwhile, immunofluorescence staining was carried out to show their sub-nuclear localizations. Finally, co-immunoprecipitation was performed to detect the interaction between Zbtb21 and its partners.ResultsPhylogenetically conserved lysines 419 and 845 of zebrafish Zbtb21 protein can be conjugated with SUMO molecules. SUMOylation does not affect the subcellular localization and protein stability of Zbtb21, as well as the interaction with Zbtb14 or Zbtb21. Nevertheless, luciferase reporter assays revealed that Zbtb21 is a dual-function transcription factor which exerts activation or repression effect on different promoters, and SUMOylation can modulate the transcriptional activity of Zbtb21 in regulating downstream target genes. Hence, Zbtb21 is identified as a novel substrate of SUMOylation, which would be important for its function.ConclusionsZebrafish Zbtb21 protein can be SUMOylated on lysines 419 and 845, which is evolutionary conserved. SUMOylation affects the dual role of Zbtb21 on transcription. creator: Zhou Fang creator: Yun Deng creator: Haihong Wang creator: Jun Zhou uri: https://doi.org/10.7717/peerj.17234 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Fang et al. title: Kernel density estimation of allele frequency including undetected alleles link: https://peerj.com/articles/17248 last-modified: 2024-04-22 description: Whereas undetected species contribute to estimation of species diversity, undetected alleles have not been used to estimated genetic diversity. Although random sampling guarantees unbiased estimation of allele frequency and genetic diversity measures, using undetected alleles may provide biased but more precise estimators useful for conservation. We newly devised kernel density estimation (KDE) for allele frequency including undetected alleles and tested it in estimation of allele frequency and nucleotide diversity using population generated by coalescent simulation as well as well as real population data. Contrary to expectations, nucleotide diversity estimated by KDE had worse bias and accuracy. Allele frequency estimated by KDE was also worse except when the sample size was small. These might be due to finity of population and/or the curse of dimensionality. In conclusion, KDE of allele frequency does not contribute to genetic diversity estimation. creator: Satoshi Aoki creator: Keita Fukasawa uri: https://doi.org/10.7717/peerj.17248 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Aoki and Fukasawa title: Fumaric acid production from fermented oil palm empty fruit bunches using fungal isolate K20: a comparison between free and immobilized cells link: https://peerj.com/articles/17282 last-modified: 2024-04-22 description: This study investigated the potential of using steam-exploded oil palm empty fruit bunches (EFB) as a renewable feedstock for producing fumaric acid (FA), a food additive widely used for flavor and preservation, through a separate hydrolysis and fermentation process using the fungal isolate K20. The efficiency of FA production by free and immobilized cells was compared. The maximum FA concentration (3.25 g/L), with 0.034 g/L/h productivity, was observed after incubation with the free cells for 96 h. Furthermore, the production was scaled up in a 3-L air-lift fermenter using oil palm EFB-derived glucose as the substrate. The FA concentration, yield, and productivity from 100 g/L initial oil palm EFB-derived glucose were 44 g/L, 0.39 g/g, and 0.41 g/L/h, respectively. The potential for scaling up the fermentation process indicates favorable results, which could have significant implications for industrial applications. creator: Antika Boondaeng creator: Jureeporn Keabpimai creator: Chanaporn Trakunjae creator: Nanthavut Niyomvong uri: https://doi.org/10.7717/peerj.17282 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Boondaeng et al. title: Predicting central cervical lymph node metastasis in papillary thyroid carcinoma with Hashimoto’s thyroiditis: a practical nomogram based on retrospective study link: https://peerj.com/articles/17108 last-modified: 2024-04-19 description: BackgroundIn papillary thyroid carcinoma (PTC) patients with Hashimoto’s thyroiditis (HT), preoperative ultrasonography frequently reveals the presence of enlarged lymph nodes in the central neck region. These nodes pose a diagnostic challenge due to their potential resemblance to metastatic lymph nodes, thereby impacting the surgical decision-making process for clinicians in terms of determining the appropriate surgical extent.MethodsLogistic regression analysis was conducted to identify independent risk factors associated with central lymph node metastasis (CLNM) in PTC patients with HT. Then a prediction model was developed and visualized using a nomogram. The stability of the model was assessed using ten-fold cross-validation. The performance of the model was further evaluated through the use of ROC curve, calibration curve, and decision curve analysis.ResultsA total of 376 HT PTC patients were included in this study, comprising 162 patients with CLNM and 214 patients without CLNM. The results of the multivariate logistic regression analysis revealed that age, Tg-Ab level, tumor size, punctate echogenic foci, and blood flow grade were identified as independent risk factors associated with the development of CLNM in HT PTC. The area under the curve (AUC) of this model was 0.76 (95% CI [0.71–0.80]). The sensitivity, specificity, accuracy, and positive predictive value of the model were determined to be 88%, 51%, 67%, and 57%, respectively.ConclusionsThe proposed clinic-ultrasound-based nomogram in this study demonstrated a favorable performance in predicting CLNM in HT PTCs. This predictive tool has the potential to assist clinicians in making well-informed decisions regarding the appropriate extent of surgical intervention for patients. creator: Lirong Wang creator: Lin Zhang creator: Dan Wang creator: Jiawen Chen creator: Wenxiu Su creator: Lei Sun creator: Jue Jiang creator: Juan Wang creator: Qi Zhou uri: https://doi.org/10.7717/peerj.17108 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wang et al. title: Magnification in preclinical procedures: effect on muscle activity and angular deviations of the neck and trunk link: https://peerj.com/articles/17188 last-modified: 2024-04-19 description: ObjectivesThis study aimed to assess the effects of different magnification systems on the angular deviations of the neck and trunk and the muscle activities of the upper back and neck during preclinical cavity preparation.MethodsThis was an experimental laboratory study, with the angular deviations from the neutral positions of the neck and trunk and the activities of the bilateral upper back (the descending and ascending trapezius) and neck (sternocleidomastoid) muscles as the dependent variables. The independent variables were the different magnification systems used (Simple, Galilean, and Keplerian loupes, with direct vision as the control) and prepared teeth (teeth 16, 26, 36, and 46). A dental mannequin phantom head with artificial resin teeth was used, and Class I cavity preparations for composite resin were performed on teeth 16, 26, 36, and 46 using a 1012 round diamond bur at low speed. To analyze the angular deviations, the postures adopted during the procedure were recorded using a tripod-mounted camera positioned to provide a lateral view of the operator. A trained researcher measured the angular deviations using the software entitled “Software for Postural Assessment”—SAPO (version 0.69). Bilateral muscle activity was assessed using surface electromyography. Descriptive statistical analysis was performed, and after verifying the assumptions of normality and homoscedasticity, two-way analysis of variance and the Tukey and Games-Howell post-hoc tests were used to compare the data (α=0.05).ResultsThe angular deviation from the neutral position of the neck was found to be significantly higher during cavity preparations performed with the naked eye and the Simple loupe, irrespective of the prepared tooth. With regard to tooth location, the angular deviation of the neck was significantly greater during cavity preparation on teeth 16 and 26, and the angular deviation of the trunk was significantly greater during cavity preparation on tooth 26, regardless of the magnification system used. There were significant differences in right sternocleidomastoid muscle activity between the Simple, Galilean, and Keplerian loupes, with activity being the lowest for the Galilean loupe (p = 0.008). There were no significant differences in left sternocleidomastoid muscle activity between the loupes, regardless of the prepared tooth (p = 0.077). The activities of the bilateral descending trapezius and the right ascending trapezius muscles were significantly lower when the Galilean loupe was used (p < 0.010).ConclusionThese results suggest that the Galilean loupe resulted in lower muscle activity in the neck and back regions and that the Galilean and Keplerian loupes resulted in less angular deviations of the neck and trunk during cavity preparation. creator: Júlia Margato Pazos creator: Ana Flávia Ribeiro Monteiro Fernandes creator: Edson Donizetti Verri creator: Guilherme Gallo Costa Gomes creator: Simone Cecílio Hallak Regalo creator: Patricia Petromilli Nordi Sasso Garcia uri: https://doi.org/10.7717/peerj.17188 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pazos et al. title: Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients link: https://peerj.com/articles/17208 last-modified: 2024-04-19 description: BackgroundStroke is a disease with high morbidity, disability, and mortality. Immune factors play a crucial role in the occurrence of ischemic stroke (IS), but their exact mechanism is not clear. This study aims to identify possible immunological mechanisms by recognizing immune-related biomarkers and evaluating the infiltration pattern of immune cells.MethodsWe downloaded datasets of IS patients from GEO, applied R language to discover differentially expressed genes, and elucidated their biological functions using GO, KEGG analysis, and GSEA analysis. The hub genes were then obtained using two machine learning algorithms (least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE)) and the immune cell infiltration pattern was revealed by CIBERSORT. Gene-drug target networks and mRNA-miRNA-lncRNA regulatory networks were constructed using Cytoscape. Finally, we used RT-qPCR to validate the hub genes and applied logistic regression methods to build diagnostic models validated with ROC curves.ResultsWe screened 188 differentially expressed genes whose functional analysis was enriched to multiple immune-related pathways. Six hub genes (ANTXR2, BAZ2B, C5AR1, PDK4, PPIH, and STK3) were identified using LASSO and SVM-RFE. ANTXR2, BAZ2B, C5AR1, PDK4, and STK3 were positively correlated with neutrophils and gamma delta T cells, and negatively correlated with T follicular helper cells and CD8, while PPIH showed the exact opposite trend. Immune infiltration indicated increased activity of monocytes, macrophages M0, neutrophils, and mast cells, and decreased infiltration of T follicular helper cells and CD8 in the IS group. The ceRNA network consisted of 306 miRNA-mRNA interacting pairs and 285 miRNA-lncRNA interacting pairs. RT-qPCR results indicated that the expression levels of BAZ2B, C5AR1, PDK4, and STK3 were significantly increased in patients with IS. Finally, we developed a diagnostic model based on these four genes. The AUC value of the model was verified to be 0.999 in the training set and 0.940 in the validation set.ConclusionOur research explored the immune-related gene expression modules and provided a specific basis for further study of immunomodulatory therapy of IS. creator: Lin Cong creator: Yijie He creator: Yun Wu creator: Ze Li creator: Siwen Ding creator: Weiwei Liang creator: Xingjun Xiao creator: Huixue Zhang creator: Lihua Wang uri: https://doi.org/10.7717/peerj.17208 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Cong et al. title: Exogenous Hemin enhances the antioxidant defense system of rice by regulating the AsA-GSH cycle under NaCl stress link: https://peerj.com/articles/17219 last-modified: 2024-04-19 description: Abiotic stress caused by soil salinization remains a major global challenge that threatens and severely impacts crop growth, causing yield reduction worldwide. In this study, we aim to investigate the damage of salt stress on the leaf physiology of two varieties of rice (Huanghuazhan, HHZ, and Xiangliangyou900, XLY900) and the regulatory mechanism of Hemin to maintain seedling growth under the imposed stress. Rice leaves were sprayed with 5.0 μmol·L−1 Hemin or 25.0 μmol·L−1 ZnPP (Zinc protoporphyrin IX) at the three leaf and one heart stage, followed by an imposed salt stress treatment regime (50.0 mmol·L−1 sodium chloride (NaCl)). The findings revealed that NaCl stress increased antioxidant enzymes activities and decreased the content of nonenzymatic antioxidants such as ascorbate (AsA) and glutathione (GSH). Furthermore, the content of osmoregulatory substances like soluble proteins and proline was raised. Moreover, salt stress increased reactive oxygen species (ROS) content in the leaves of the two varieties. However, spraying with Hemin increased the activities of antioxidants such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) and accelerated AsA-GSH cycling to remove excess ROS. In summary, Hemin reduced the effect of salt stress on the physiological characteristics of rice leaves due to improved antioxidant defense mechanisms that impeded lipid peroxidation. Thus, Hemin was demonstrated to lessen the damage caused by salt stress. creator: Fengyan Meng creator: Naijie Feng creator: Dianfeng Zheng creator: Meiling Liu creator: Hang Zhou creator: Rongjun Zhang creator: XiXin Huang creator: Anqi Huang uri: https://doi.org/10.7717/peerj.17219 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Meng et al. title: Inhibition of SUV39H1 reduces tumor angiogenesis via Notch1 in oral squamous cell carcinoma link: https://peerj.com/articles/17222 last-modified: 2024-04-19 description: Targeting tumor angiogenesis is an important approach in advanced tumor therapy. Here we investigated the effect of the suppressor of variegation 3–9 homolog 1 (SUV39H1) on tumor angiogenesis in oral squamous cell carcinoma (OSCC). The GEPIA database was used to analyze the expression of SUV39H1 in various cancer tissues. The expression of SUV39H1 in OSCC was detected by immunohistochemistry, and the correlation between SUV39H1 and Notch1 and microvascular density (MVD) was analyzed. The effect of SUV39H1 inhibition on OSCC was investigated in vivo by chaetocin treatment. The migration and tube formation of vascular endothelial cells by conditioned culture-medium of different treatments of oral squamous cell cells were measured. The transcriptional level of SUV39H1 is elevated in various cancer tissues. The transcription level of SUV39H1 in head and neck squamous cell carcinoma was significantly higher than that in control. Immunohistochemistry result showed increased SUV39H1 expression in OSCC, which was significantly correlated with T staging. The expression of SUV39H1 was significantly correlated with Notch1 and CD31. In vivo experiment chaetocin treatment significantly inhibit the growth of tumor, and reduce SUV39H1, Notch1, CD31 expression. The decreased expression of SUV39H1 in OSCC cells lead to the decreased expression of Notch1 and VEGF proteins, as well as the decreased migration and tube formation ability of vascular endothelial cells. Inhibition of Notch1 further enhance this effect. Our results suggest inhibition of SUV39H1 may affect angiogenesis by regulating Notch1 expression. This study provides a foundation for SUV39H1 as a potential therapeutic target for OSCC. creator: Yan Chen creator: Xiuhong Weng creator: Chuanjie Zhang creator: Simin Wang creator: Xuechen Wu creator: Bo Cheng uri: https://doi.org/10.7717/peerj.17222 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Unveiling the aesthetic secrets: exploring connections between genetic makeup, chemical, and environmental factors for enhancing/improving the color and fragrance/aroma of Chimonanthus praecox link: https://peerj.com/articles/17238 last-modified: 2024-04-19 description: Floral color and scent profiles vary across species, geographical locations, and developmental stages. The exclusive floral color and fragrance of Chimonanthus praecox is contributed by a range of endogenous chemicals that distinguish it from other flowers and present amazing ornamental value. This comprehensive review explores the intricate interplay of environmental factors, chemicals and genes shaping the flower color and fragrance of Chimonanthus praecox. Genetic and physiological factors control morpho-anatomical attributes as well as pigment synthesis, while environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Specific genes control pigment synthesis, and environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Physiological processes including plant hormone contribute to flower color and fragrance. Hormones, notably ethylene, exert a profound influence on varioustraits. Pigment investigations have spotlighted specific flavonoids, including kaempferol 3-O-rutinoside, quercetin, and rutin. Red tepals exhibit unique composition with cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside being distinctive components. Elucidating the molecular basis of tepal color variation, particularly in red and yellow varieties, involves the identification of crucial regulatory genes. In conclusion, this review unravels the mysteries of Chimonanthus praecox, providing a holistic understanding of its flower color and fragrance for landscape applications. This comprehensive review uniquely explores the genetic intricacies, chemical and environmental influences that govern the mesmerizing flower color and fragrance of Chimonanthus praecox, providing valuable insights for its landscape applications. This review article is designed for a diverse audience, including plant geneticists, horticulturists, environmental scientists, urban planners, and students, offering understandings into the genetic intricacies, ecological significance, and practical applications of Chimonanthus praecox across various disciplines. Its appeal extends to professionals and enthusiasts interested in plant biology, conservation, and industries dependent on unique floral characteristics. creator: Haoyu Zhao creator: Hafiza Ayesha Masood creator: Sher Muhammad uri: https://doi.org/10.7717/peerj.17238 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhao et al.