title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=314 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification of YUC genes associated with leaf wrinkling trait in Tacai variety of Chinese cabbage link: https://peerj.com/articles/17337 last-modified: 2024-05-20 description: Chinese cabbage (Brassica campestris L. ssp. chinensis (L.) Makino) stands as a widely cultivated leafy vegetable in China, with its leaf morphology significantly influencing both quality and yield. Despite its agricultural importance, the precise mechanisms governing leaf wrinkling development remain elusive. This investigation focuses on ‘Wutacai’, a representative cultivar of the Tacai variety (Brassica campestris L. ssp. chinensis var. rosularis Tsen et Lee), renowned for its distinct leaf wrinkling characteristics. Within the genome of ‘Wutacai’, we identified a total of 18 YUCs, designated as BraWTC_YUCs, revealing their conservation within the Brassica genus, and their close homology to YUCs in Arabidopsis. Expression profiling unveiled that BraWTC_YUCs in Chinese Cabbage exhibited organ-specific and leaf position-dependent variation. Additionally, transcriptome sequencing data from the flat leaf cultivar ‘Suzhouqing’ and the wrinkled leaf cultivar ‘Wutacai’ revealed differentially expressed genes (DEGs) related to auxin during the early phases of leaf development, particularly the YUC gene. In summary, this study successfully identified the YUC gene family in ‘Wutacai’ and elucidated its potential function in leaf wrinkling trait, to provide valuable insights into the prospective molecular mechanisms that regulate leaf wrinkling in Chinese cabbage. creator: Xuelian Ye creator: Ji Sun creator: Yuan Tian creator: Jingwen Chen creator: Xiangtan Yao creator: Xinhua Quan creator: Li Huang uri: https://doi.org/10.7717/peerj.17337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ye et al. title: Antibiotics alter development and gene expression in the model cnidarian Nematostella vectensis link: https://peerj.com/articles/17349 last-modified: 2024-05-20 description: BackgroundAntibiotics are commonly used for controlling microbial growth in diseased organisms. However, antibiotic treatments during early developmental stages can have negative impacts on development and physiology that could offset the positive effects of reducing or eliminating pathogens. Similarly, antibiotics can shift the microbial community due to differential effectiveness on resistant and susceptible bacteria. Though antibiotic application does not typically result in mortality of marine invertebrates, little is known about the developmental and transcriptional effects. These sublethal effects could reduce the fitness of the host organism and lead to negative changes after removal of the antibiotics. Here, we quantify the impact of antibiotic treatment on development, gene expression, and the culturable bacterial community of a model cnidarian, Nematostella vectensis.MethodsAmpicillin, streptomycin, rifampicin, and neomycin were compared individually at two concentrations, 50 and 200 µg mL−1, and in combination at 50 µg mL−1 each, to assess their impact on N. vectensis. First, we determined the impact antibiotics have on larval development. Next Amplicon 16S rDNA gene sequencing was used to compare the culturable bacteria that persist after antibiotic treatment to determine how these treatments may differentially select against the native microbiome. Lastly, we determined how acute (3-day) and chronic (8-day) antibiotic treatments impact gene expression of adult anemones.ResultsUnder most exposures, the time of larval settlement extended as the concentration of antibiotics increased and had the longest delay of 3 days in the combination treatment. Culturable bacteria persisted through a majority of exposures where we identified 359 amplicon sequence variants (ASVs). The largest proportion of bacteria belonged to Gammaproteobacteria, and the most common ASVs were identified as Microbacterium and Vibrio. The acute antibiotic exposure resulted in differential expression of genes related to epigenetic mechanisms and neural processes, while constant application resulted in upregulation of chaperones and downregulation of mitochondrial genes when compared to controls. Gene Ontology analyses identified overall depletion of terms related to development and metabolism in both antibiotic treatments.DiscussionAntibiotics resulted in a significant increase to settlement time of N. vectensis larvae. Culturable bacterial species after antibiotic treatments were taxonomically diverse. Additionally, the transcriptional effects of antibiotics, and after their removal result in significant differences in gene expression that may impact the physiology of the anemone, which may include removal of bacterial signaling on anemone gene expression. Our research suggests that impacts of antibiotics beyond the reduction of bacteria may be important to consider when they are applied to aquatic invertebrates including reef building corals. creator: Quinton Krueger creator: Britney Phippen creator: Adam Reitzel uri: https://doi.org/10.7717/peerj.17349 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Krueger et al. title: Machine learning approaches to debris flow susceptibility analyses in the Yunnan section of the Nujiang River Basin link: https://peerj.com/articles/17352 last-modified: 2024-05-20 description: BackgroundThe Yunnan section of the Nujiang River (YNR) Basin in the alpine-valley area is one of the most critical areas of debris flow in China.MethodsWe analyzed the applicability of three machine learning algorithms to model of susceptibility to debris flow—Random Forest (RF), the linear kernel support vector machine (Linear SVM), and the radial basis function support vector machine (RBFSVM)—and compared 20 factors to determine the dominant controlling in debris flow occurrence in the region.ResultsWe found that (1) RF outperformed RBFSVM and Linear SVM in terms of accuracy, (2) topographic conditions were prerequisites, and geology, precipitation, vegetation, and anthropogenic influence were critical to forming debris flows. Also, the relative elevation difference was the most prominent evaluation factor of debris flow susceptibility, and (3) susceptibility maps based on RF’s debris flow susceptibility (DFS) showed that zones with very high susceptibility were distributed along the mainstream of the Nujiang River. These findings provide methodological guidance and reference for improvement of DFS assessment. It enriches the content of DFS studies in the alpine-valley areas. creator: Jingyi Zhou creator: Jiangcheng Huang creator: Zhengbao Sun creator: Qi Yi creator: Aoyang He uri: https://doi.org/10.7717/peerj.17352 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhou et al. title: Terrestrial wildlife as indicators of microplastic pollution in western Thailand link: https://peerj.com/articles/17384 last-modified: 2024-05-20 description: Plastic pollution in terrestrial wildlife represents a new conservation challenge, with research in this area, especially within protected areas (PAs), being scant. This study documents the accumulation of microplastics (MPs) in terrestrial wildlife both inside and outside PAs in western Thailand. Carcasses of road-killed vertebrates in good condition, as well as live tadpoles, were collected to examine their exposure to plastic pollution. The digestive tracts of the vertebrate carcasses and the entire bodies of tadpoles were analyzed for MPs, which were identified if they measured over 50 µm. A total of 136 individuals from 48 vertebrate species were examined. The sample comprised snakes (44.12%), birds (11.03%), lizards (5.15%), tadpoles (32.25%), amphibians (5.88%), and mammals (1.47%). In total, 387 MPs were found in 44 species (91.67%), with an average occurrence of 3.25 ± 3.63 MPs per individual or 0.05 ± 0.08 MPs per gram of body weight. The quantities of MPs significantly varied among the animal groups, both in terms of number per individual (p < 0.05) and number per gram of body weight (p < 0.01). Furthermore, a significant difference in MP quantities was observed between specimens collected inside and outside PAs on an individual basis (p < 0.05), but not on a body weight basis (p = 0.07). Most MPs were fibers (77%), followed by fragments (22.22%), with only a minimal presence of film (0.52%) and foam (0.26%). Of all the MPs identified, 36.84% were confirmed as plastics or fibers made from natural materials, and 31.58% were plastics, including Polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), Polyvinylidene chloride (PVDC), and polyester (PES). Additionally, fibers made of cotton, and those containing polyurethane (PU), rayon, PES, and combinations of rayon and PU, were identified. The quantities of MPs were significantly influenced by animal body weight, factors associated with human settlement/activity, and land use types. Our findings highlight the prevalence of plastic pollution in terrestrial vertebrates within Thai PAs. Further toxicological studies are required to establish plastic pollution standards. It is proposed that snakes, obtained from road kills, could serve as a non-invasive method for monitoring plastic pollution, thus acting as an indicator of the pollution threat to species within terrestrial ecosystems. There is an urgent need for the standardization of solid waste management at garbage dump sites in remote areas, especially within PAs. Conservation education focusing on MP occurrence, potential sources, and impacts could enhance awareness, thereby influencing changes in behaviors and attitudes toward plastic waste management at the household level. creator: Jiraporn Teampanpong creator: Prateep Duengkae uri: https://doi.org/10.7717/peerj.17384 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Teampanpong and Duengkae title: Systematic evaluation and meta-analysis of the prognosis of down-staging human papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma using cetuximab combined with radiotherapy instead of cisplatin combined with radiotherapy link: https://peerj.com/articles/17391 last-modified: 2024-05-20 description: ObjectiveTo evaluate the efficacy and safety of cetuximab instead of cisplatin in combination with downstaging radiotherapy for papillomavirus (HPV) positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC).DesignMeta-analysis and systematic evaluation.Data sourcesThe PubMed, Embase, Web of Science, and Cochrane library databases were searched up to June 8, 2023, as well as Clinicaltrials.gov Clinical Trials Registry, China Knowledge Network, Wanfang Data Knowledge Service Platform, and Wiprojournal.com.Eligibility criteria for selecting studiesRandomized controlled trials reporting results of standard regimens of cetuximab + radiotherapy vs cisplatin + radiotherapy in treating HPV+ OPSCC were included. The primary outcomes of interest were overall survival (OS), progression-free survival (PFS), local regional failure rate (LRF), distant metastasis rate (DM), and adverse events (AE).Data extraction and synthesisTwo reviewers independently extracted data and assessed the risk of bias of the included studies. The HR and its 95% CI were used as the effect analysis statistic for survival analysis, while the OR and its 95% CI were used as the effect analysis statistic for dichotomous variables. These statistics were extracted by the reviewers and aggregated using a fixed-effects model to synthesise the data.ResultsA total of 874 relevant papers were obtained from the initial search, and five papers that met the inclusion criteria were included; a total of 1,617 patients with HPV+ OPSCC were enrolled in these studies. Meta-analysis showed that OS and PFS were significantly shorter in the cetuximab + radiotherapy group of patients with HPV+ OPSCC compared with those in the conventional cisplatin + radiotherapy group (HR = 2.10, 95% CI [1.39–3.15], P = 0.0004; HR = 1.79, 95% CI [1.40–2.29], P < 0.0001); LRF and DM were significantly increased (HR = 2.22, 95% CI [1.58–3.11], P < 0.0001; HR = 1.66, 95% CI [1.07–2.58], P = 0.02), but there was no significant difference in overall grade 3 to 4, acute and late AE overall (OR = 0.86, 95% CI [0.65–1.13], P = 0.28).ConclusionsCisplatin + radiotherapy remains the standard treatment for HPV+ OPSCC. According to the 7th edition AJCC/UICC criteria, low-risk HPV+ OPSCC patients with a smoking history of ≤ 10 packs/year and non-pharyngeal tumors not involved in lymphatic metastasis had similar survival outcomes with cetuximab/cisplatin + radiotherapy. However, further clinical trials are necessary to determine whether cetuximab + radiotherapy can replace cisplatin + radiotherapy for degraded treatment in individuals who meet the aforementioned characteristics, particularly those with platinum drug allergies.Prospero registration numberCRD42023445619. creator: Qiong Hu creator: Feng Li creator: Kai Yang uri: https://doi.org/10.7717/peerj.17391 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Hu et al. title: The effect of rehabilitation time on functional recovery after arthroscopic rotator cuff repair: a systematic review and meta-analysis link: https://peerj.com/articles/17395 last-modified: 2024-05-20 description: ObjectiveWe compared the effects of early and delayed rehabilitation on the function of patients after rotator cuff repair by meta-analysis to find effective interventions to promote the recovery of shoulder function.MethodsThis meta-analysis was registered in PROSPERO (CRD42023466122). We manually searched the randomized controlled trials (RCTs) in the Cochrane Library, Pubmed, Cochrane Library, EMBASE, the China National Knowledge Infrastructure (CNKI), the China VIP Database (VIP), and the Wanfang Database to evaluate the effect of early and delayed rehabilitation after arthroscopic shoulder cuff surgery on the recovery of shoulder joint function. Review Manager 5.3 software was used to analyze the extracted data. Then, the PEDro scale was employed to appraise the methodological quality of the included research.ResultsThis research comprised nine RCTs and 830 patients with rotator cuff injuries. According to the findings of the meta-analysis, there was no discernible difference between the early rehabilitation group and the delayed rehabilitation group at six and twelve months after the surgery in terms of the VAS score, SST score, follow-up rotator cuff healing rate, and the rotator cuff retear rate at the final follow-up. There was no difference in the ASES score between the early and delayed rehabilitation groups six months after the operation. However, although the ASES score in the early rehabilitation group differed significantly from that in the delayed rehabilitation group twelve months after the operation, according to the analysis of the minimal clinically important difference (MCID), the results have no clinical significance.ConclusionsThe improvement in shoulder function following arthroscopic rotator cuff surgery does not differ clinically between early and delayed rehabilitation. When implementing rehabilitation following rotator cuff repair, it is essential to consider the paradoxes surrounding shoulder range of motion and tendon anatomic healing. A program that allows for flexible progression based on the patient’s ability to meet predetermined clinical goals or criteria may be a better option. creator: Yang Chen creator: Hui Meng creator: Yuan Li creator: Hui Zong creator: Hongna Yu creator: HaiBin Liu creator: Shi Lv creator: Liang Huai uri: https://doi.org/10.7717/peerj.17395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Chen et al. title: USP22 as a key regulator of glycolysis pathway in osteosarcoma: insights from bioinformatics and experimental approaches link: https://peerj.com/articles/17397 last-modified: 2024-05-20 description: BackgroundOsteosarcoma is the most common primary malignant bone tumor, but its pathogenesis remains unclear. Ubiquitin-specific processing peptidase 22 (USP22) is reported to be highly expressed and associated with tumor malignancy and prognosis in cancers. However, the role and mechanism of USP22 in osteosarcoma is not fully understood. This study aims to investigate the function and potential mechanism of USP22 in osteosarcoma using bioinformatics analysis combined with experimental validation.MethodsWe first integrated transcriptomic datasets and clinical information of osteosarcoma from GEO and TCGA databases to assess the expression and prognostic value of USP22 in osteosarcoma. Then, differential expression analysis and weighted gene co-expression network analysis (WGCNA) were conducted to identify USP22-related co-expressed genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore the biological functions and signaling pathways of USP22 co-expressed genes. To validate the accuracy of bioinformatics analyses, we downregulated USP22 expression in osteosarcoma cell line Sao-2 using siRNA and assessed its effect on cell proliferation, migration, invasion, apoptosis, and regulation of key signaling pathways.ResultsWe found that USP22 was highly expressed in osteosarcoma tissues and correlated with poor prognosis in osteosarcoma patients. USP22 also showed potential as a diagnostic marker for osteosarcoma. In addition, 344 USP22-related co-expressed genes were identified, mainly involved in signaling pathways such as glycolysis, oxidative phosphorylation, spliceosome, thermogenesis, and cell cycle. The in vitro experiments confirmed the accuracy and reliability of bioinformatics analyses. We found that downregulation of USP22 could inhibit Sao-2 cell proliferation, migration, invasion, and induce apoptosis. Furthermore, downregulation of USP22 significantly reduced aerobic glycolysis levels in Sao-2 cells and inhibited the expression of key enzymes and transporters in aerobic glycolysis pathways such as HK2, PKM2, and GLUT1.ConclusionsUSP22 plays a critical role in the occurrence, development, and prognosis of osteosarcoma. USP22 could influence Sao-2 cell proliferation, apoptosis, migration, and invasion by regulating the glycolysis pathway, thereby promoting osteosarcoma progression. Therefore, USP22 may be a potential therapeutic target for the treatment of osteosarcoma. creator: Qiao Zhang creator: Jinwei Zhu creator: Jian Xie creator: Yurong Gu creator: Lu Chen uri: https://doi.org/10.7717/peerj.17397 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: Vaccine refusal in pregnant women in Kahramanmaraş: a community-based study from Türkiye link: https://peerj.com/articles/17409 last-modified: 2024-05-20 description: BackgroundThe global health landscape is increasingly challenged by the rejection of childhood vaccines. This study investigates vaccination reservations and refusal among pregnant women.MethodsA cross-sectional study was conducted in Kahramanmaraş, Türkiye, spanning January to March 2019, entailing face to face interviews with 938 pregnant women. The questionnaire collected sociodemographic data and probed vaccination attitudes. The decision to vaccinate the baby was treated as the dependent variable, analyzed alongside sociodemographic factors and other variables. Data underwent evaluation via descriptive analysis, the Chi-square test, and binary logistic regression.ResultsParticipants had a mean age of 27.6 years. Among them 20 (2.1%) expressed intent to either abstain from or partially vaccinate their babies, with 70% citing apprehensions regarding potential vaccine-related harm. Statistical analysis unveiled that higher economic income, elevated parental education level, fewer than two children, reliance on the Internet for vaccination information, and a lack of trust in physicians significantly correlated with vaccine refusal among pregnant women (p < 0.05).ConclusionsThe study concludes that dissemination of vaccination information by the healthcare professionals, complemented by the enactment of pro-vaccine internet policies holds promise in shaping vaccination behavior. creator: Ramazan Azim Okyay creator: Erhan Kaya creator: Ayşegül Erdoğan uri: https://doi.org/10.7717/peerj.17409 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Okyay et al. title: Clinical value of serum polyunsaturated fatty acids in patients with gastric polyps link: https://peerj.com/articles/17413 last-modified: 2024-05-20 description: Polyunsaturated fatty acids (PUFAs) are vital nutrients in human physiology and are implicated in various chronic diseases. However, the relationship between PUFAs and gastric polyps remains unclear. This study employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to assess PUFA levels in the serum of 350 patients, along with analyzing the ω-6 to ω-3 ratio. The results revealed significant differences in the levels of C16:1, C18:1, C18:2, α-C18:3, γ-C18:3, C20:1, C20:4, C20:5, ω-3-C22:5, ω-6-C22:5, and C22:6, as well as ω-6 to ω-3 ratio between the control and gasteic polyp groups. Moreover, setting the threshold for ω-6: ω-3 at 10 revealed a close correlation between polyp occurrence and this ratio. These findings suggest that PUFAs and the ω-6 to ω-3 ratio hold promise as potential early screening markers for gastric polyps. However, further research is imperative to elucidate the underlying mechanisms and therapeutic potential of PUFAs in managing gastric polyps. creator: Nan Li creator: Qiliu Qian creator: Jun Ouyang creator: Mingyue Hu creator: Juan Liu creator: Hailu Wu creator: Ruihua Shi creator: Shiya Zheng uri: https://doi.org/10.7717/peerj.17413 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Nucleolin myocardial-specific knockout exacerbates glucose metabolism disorder in endotoxemia-induced myocardial injury link: https://peerj.com/articles/17414 last-modified: 2024-05-20 description: BackgroundSepsis-induced myocardial injury, as one of the important complications of sepsis, can significantly increase the mortality of septic patients. Our previous study found that nucleolin affected mitochondrial function in energy synthesis and had a protective effect on septic cardiomyopathy in mice. During sepsis, glucose metabolism disorders aggravated myocardial injury and had a negative effect on septic patients.ObjectivesWe investigated whether nucleolin could regulate glucose metabolism during endotoxemia-induced myocardial injury.MethodsThe study tested whether the nucleolin cardiac-specific knockout in the mice could affect glucose metabolism through untargeted metabolomics, and the results of metabolomics were verified experimentally in H9C2 cells. The ATP content, lactate production, and oxygen consumption rate (OCR) were evaluated.ResultsThe metabolomics results suggested that glycolytic products were increased in endotoxemia-induced myocardial injury, and that nucleolin myocardial-specific knockout altered oxidative phosphorylation-related pathways. The experiment data showed that TNF-α combined with LPS stimulation could increase the lactate content and the OCR values by about 25%, and decrease the ATP content by about 25%. However, interference with nucleolin expression could further decrease ATP content and OCR values by about 10–20% and partially increase the lactate level in the presence of TNF-α and LPS. However, nucleolin overexpression had the opposite protective effect, which partially reversed the decrease in ATP content and the increase in lactate level.ConclusionDown-regulation of nucleolin can exacerbate glucose metabolism disorders in endotoxemia-induced myocardial injury. Improving glucose metabolism by regulating nucleolin was expected to provide new therapeutic ideas for patients with septic cardiomyopathy. creator: Yuting Tang creator: Leijing Yin creator: Ludong Yuan creator: Xiaofang Lin creator: Bimei Jiang uri: https://doi.org/10.7717/peerj.17414 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Tang et al.