title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=157 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome-wide association study reveals the advantaged genes regulating japonica rice grain shape traits in northern China link: https://peerj.com/articles/18746 last-modified: 2024-12-18 description: BackgroundRice, a staple food for over half of the global population, exhibits significant diversity in grain shape characteristics, which impact not only appearance and milling quality but also grain weight and yield. Identifying genes and loci underlying these traits is crucial for improving rice breeding programs. Previous studies have identified multiple quantitative trait loci (QTLs) and genes regulating grain length, width, and length-width ratio; however, further investigation is necessary to elucidate their regulatory pathways and their practical application in crop improvement.MethodsThis study employed a genome-wide association study (GWAS) on 280 japonica rice varieties from northern China to decipher the genetic basis of grain shape traits. Phenotyping included measurements of 11 grain-related traits, such as grain length, width, and area, along with their brown and white rice counterparts. High-density single nucleotide polymorphism (SNP) markers (33,579) were utilized for genotyping, and GWAS was performed using a mixed linear model (MLM) incorporating principal component analysis (PCA) and kinship (K) matrix to account for population structure and relatedness.ResultsOur analysis detected 15 QTLs associated with the 11 grain shape traits, of which five major QTL clusters emerged as crucial. Candidate genes, including LOC_Os01g50720 (qGL1), OsMKK4 (LOC_Os02g54600, influencing qBA2, qWL2, and qWA2), GW5 (LOC_Os05g09520, controlling qGW5, qBW5, qBR5, qWW5, and qWR5), GW6a (LOC_Os06g44100, associated with qGW6, qBW6, qBR6, qWW6, and qWR6), and FZP (LOC_Os07g47330, linked to qWL7), were identified based on functional annotations and haplotype analysis. These findings offer valuable insights into the genetic mechanisms underlying rice grain shape and suggest promising targets for marker-assisted selection to enhance rice quality and yield. creator: Hongwei Chen creator: Xue Zhang creator: Shujun Tian creator: Hong Gao creator: Jian Sun creator: Xiu Pang creator: Xiaowan Li creator: Quanying Li creator: Wenxiao Xie creator: Lili Wang creator: Chengwei Liang creator: Guomin Sui creator: Wenjing Zheng creator: Zuobin Ma uri: https://doi.org/10.7717/peerj.18746 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Chen et al. title: Incidence and risk factors of hepatitis E virus infection in women with gynecological tumors in Eastern China link: https://peerj.com/articles/18747 last-modified: 2024-12-18 description: BackgroundRecently, there has been increasing interest in the exploration of the association between the hepatitis E virus (HEV) infection and malignancies; however, epidemiological data for HEV infection among women with a gynecological tumors (GT) are limited. Herein, we investigated the correlation between HEV and GT in Chinese women.MethodsWe recruited 452 women diagnosed with a primary GT and 452 healthy volunteers to investigate the possible routes and risk factors for HEV infection. The serum antibody levels of anti-HEV IgG and IgM were measured by enzyme-linked immunoassays once a year.ResultsAfter a median follow-up time of 5.4 years (range 4 to 7 years), the overall detection rate of anti-HEV antibodies in patients with GT and in controls were 69/452 (15.27%) and 23/452 (5.09%) (P = 0.001), respectively. The seroprevalence of anti-HEV IgG antibodies was significant higher in patients with GT (15.27%) than in healthy controls (5.09%) (P = 0.001). Moreover, 13 (2.88%) patients with GT were positive for IgM antibodies, while only 4 (0.88%) healthy controls tested positive for anti-HEV IgM antibodies (P = 0.028). The highest prevalence of HEV antibodies were detected in patients with ovarian borderline tumors (40%), followed by patients with ovarian cancer (20.54%) and endometrial cancer (18.46%). Multivariable analysis revealed that contact with dogs (OR, 1.88; 95% CI [1.10–3.22]; P = 0.015) and a history of anti-tumor chemotherapy (OR, 1.85; 95% CI [1.07–3.20]; P = 0.028) were independent risk factors for HEV infection.ConclusionOverall, the present study showed that patients with GT are more susceptible to HEV infection in Eastern China, particularly in patients with ovarian borderline tumors. Thus, effective strategies are needed to reduce HEV infection in patients with GT. creator: Wenye Bai creator: Xiao Wu creator: Shuchao Zhao creator: Yang Yu creator: Zhongjun Wang creator: Xiu Li creator: Na Zhou uri: https://doi.org/10.7717/peerj.18747 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bai et al. title: Antimicrobial activity of Ruta angustifolia L. Pers against periodontal pathogen: Porphyromonas gingivalis link: https://peerj.com/articles/18751 last-modified: 2024-12-18 description: BackgroundPorphyromonas gingivalis is widely recognised as a periodontal pathogen. In recent years, there has been growing interest in the use of medicinal plant extracts as alternative treatments for periodontitis to combat the emergence of antibiotic-resistant bacteria. Ruta angustifolia L. Pers has been traditionally used to treat various ailments, including oral bacterial infections. However, the antimicrobial potential of R. angustifolia extracts against the periodontal pathogen P. gingivalis remains unexplored. Hence, the aim of this study was to investigate the antimicrobial activity of R. angustifolia extracts against P. gingivalis.MethodsThe antimicrobial activity of R. angustifolia extracts (crude methanol, hexane and chloroform fractionated extracts) against P. gingivalis was evaluated using the well diffusion method. Additionally, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined. Biofilm biomass assessment and live/dead cell viability assays were performed to analyse the effect of R. angustifolia extracts. Ultrastructural morphological changes in P. gingivalis cells were determined using field emission scanning electron microscopy (FE-SEM).ResultsIt was found that P. gingivalis was susceptible to R. angustifolia extracts, with the chloroform fractionated extract exhibiting the highest inhibition zones. The MIC and MBC of chloroform fractionated extract were determined to be 6.25 mg/mL which substantially reduced P. gingivalis biofilm biomass. Live/dead cell viability assays showed the highest percentage of dead P. gingivalis cells after 48 h of incubation. FE-SEM confirmed that the chloroform fractionated extract effectively damaged the bacterial cell wall and altered the ultrastructural morphology of P. gingivalis.ConclusionThe results indicated that extracts of R. angustifolia has the potential to be used as an alternative treatment in addition to conventional periodontal therapies. creator: Husna Hazirah Bakri creator: Syarifah Nur Syed Abdul Rahman creator: Zarith Safinaz Dol Bakri creator: Elly Munadziroh creator: Wan Himratul Aznita Wan Harun uri: https://doi.org/10.7717/peerj.18751 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Bakri et al. title: Non-obese non-alcoholic fatty liver disease and the risk of chronic kidney disease: a systematic review and meta-analysis link: https://peerj.com/articles/18459 last-modified: 2024-12-17 description: BackgroundData on risk of developing chronic kidney disease (CKD) between non-obese and obese non-alcoholic fatty liver disease (NAFLD) patients are limited. We aimed to reveal the risk difference of incident CKD between non-obese and obese NAFLD patients.MethodsWe searched PubMed, Embase, and Web of Science databases for studies which reported the incidence of CKD in non-obese and obese NAFLD from inception to 10 March 2024. The primary and secondary outcomes were pooled. Subgroup analysis was used to examine the heterogeneity.ResultsA total of 15 studies were incorporated. The incidence of CKD in non-obese and obese NAFLD were 1,450/38,720 (3.74%) and 3,067/84,154 (3.64%), respectively. Non-obese NAFLD patients had a comparable risk of CKD as obese NAFLD (odds ratio [OR] 0.92, 95% confidence interval [95% CI] [0.72–1.19], I2 = 88%). No differences in estimated glomerular filtration rate and serum creatinine between non-obese and obese NAFLD were found. The mean differences (MD) and 95% CI were 0.01 [−0.02 to 0.04] and 0.50 [−0.90 to 1.90], respectively. In subgroup analyses, non-obese NAFLD had higher eGFR when diagnosed with ultrasound (MD 1.45, 95% CI [0.11–2.79], I2 = 21%). Non-obese NAFLD had higher creatinine in non-Asian (MD 0.06, 95% CI [0.01–0.11], I2 = 55%) and when taking BMI > 30 as the criterion for obesity (MD 0.06, 95% CI [0.00–0.12], I2 = 76%). The occurrence of CKD did not differ when non-obese NAFLD were categorized into overweight and normal-weight types.ConclusionsNon-obese NAFLD patients experienced the same risk of CKD compared to obese NAFLD. creator: Yixian You creator: Xiong Pei creator: Wei Jiang creator: Qingmin Zeng creator: Lang Bai creator: Taoyou Zhou creator: Xiaoju Lv creator: Hong Tang creator: Dongbo Wu uri: https://doi.org/10.7717/peerj.18459 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 You et al. title: Coral reef rehabilitation following Hurricane Irma using nano-engineered artificial reefs in Sint Maarten link: https://peerj.com/articles/18487 last-modified: 2024-12-17 description: Artificial reefs are being increasingly deployed as a coral reef restoration strategy. Additional reef habitats made from conventional substrates (e.g., metal, concrete, etc.) have had limited success in addressing conservation objectives on degraded coral reefs due to structure size and lack of standardized monitoring, and inability to enhance select ecological, and species variables. Technological advances and new restoration methods must be quickly tested and applied on a large scale to curb further deterioration of coral reefs. Here, we present the results of the first deployment of Oceanite artificial reefs (ARs). We compare the composition of the benthic community and associated fish assemblages on Oceanite ARs 14 months after deployment in a marine protected area (MPA) and two unprotected sites in Philipsburg, Sint Maarten. We also examined fish abundance and behaviour on the ARs. The initial results from this pilot study suggest that Oceanite mineral matrices can enhance local biodiversity, attract coral recruits, provide food and protection for large fish communities, and develop an early stage, healthy coral reef community in 14 months. We suggest that further research and testing of Oceanite capabilities will allow us to develop site-, species-, and function-specific nanotechnology-enabled substrates to optimize AR conservation goals. Oceanite mix designs can be tuned to precise parameters to promote reef restoration and stressor mitigation (e.g., pH, leachate emissions, surface texture, porosity, void structure, and hydrophobic, heat-absorbing, and disease-fighting properties). Using both bottom-up and top-down restoration processes, we suggest that deploying bio-enhancing habitats with targeted microclimate stressor treatments on the world’s critical reefs will allow to build global refuges resilient to climate change and provide much needed ecosystem services. creator: Emily Higgins creator: Kyralai Duppel creator: Megan Connell creator: Guyon Brenna creator: Konstantin Sobolev uri: https://doi.org/10.7717/peerj.18487 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Higgins et al. title: Prognostic value of inflammatory and nutritional indexes among patients with unresectable advanced gastric cancer receiving immune checkpoint inhibitors combined with chemotherapy—a retrospective study link: https://peerj.com/articles/18659 last-modified: 2024-12-17 description: BackgroundRecent studies have revealed that inflammatory factors and nutritional status of patients with advanced gastric cancer (AGC) are related to the efficacy of drug therapy and patient prognosis. This study seeks to evaluate the correlation between inflammatory markers, nutritional status, and clinical outcomes of immune checkpoint inhibitor (ICI)-based therapies among inoperable AGC patients.MethodThis retrospective study included 88 AGC patients who received ICIs combined with chemotherapy. Inflammatory and nutritional indicators from patients before and after two cycles of treatment were collected. Finally, the correlations between these indicators and the clinical response and survival of AGC patients with ICI treatment were examined.ResultsThe results revealed that an Eastern Cooperative Oncology Group performance status (ECOG PS) score of 0, neutrophil count to lymphocyte count ratio (NLR) < 2.84, platelet count to lymphocyte count ratio (PLR) < 82.23, lymphocyte count to monocyte count ratio ≥ 2.35, the hemoglobin, albumin, lymphocyte and platelet score (HALP) ≥ 31.17, prognostic nutritional index (PNI) ≥ 46.53, albumin ≥ 41.65, the decreased HALP group and the decreased PNI group were significantly correlated with improved objective response rate. Additionally, an ECOG PS score of 0, NLR < 2.84 and the decreased HALP group was associated with a superior disease control rate. Meanwhile, an ECOG PS score of 0 (progression-free survival (PFS): P = 0.003; overall survival (OS): P = 0.001) and decreased PLR following treatment (PFS: P = 0.011; OS: P = 0.008) were significant independent predictors of PFS and OS. Lastly, a systemic immune inflammation index ≥ 814.8 was also a positive independent predictor of OS among AGC patients.ConclusionOur study supports the potential of inflammatory and nutritional factors to serve as predictors of the efficacy and prognosis in patients undergoing ICI-based therapies for AGC. However, further investigations are necessary to validate these findings. creator: Meiqin Zhu creator: Lin-Ting Zhang creator: Wenjuan Lai creator: Fang Yang creator: Danyang Zhou creator: Ruilian Xu creator: Gangling Tong uri: https://doi.org/10.7717/peerj.18659 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhu et al. title: The relationship between mitochondrial DNA haplotype and its copy number on body weight and morphological traits of Wuliangshan black-bone chickens link: https://peerj.com/articles/17989 last-modified: 2024-12-16 description: Mitochondria play a pivotal role as carriers of genetic information through their circular DNA molecules. The rapid evolution of the D-loop region in mitochondria makes it an ideal molecular marker for exploring genetic differentiation among individuals within species and populations with close kinship. However, the influence of mtDNA D-loop region haplotypes and mtDNA copy numbers on phenotypic traits, particularly production traits in chickens, remains poorly understood. In this comprehensive study, we conducted D-loop region amplification and sequencing in the blood mitochondria of 232 female Wuliangshan black-bone chickens. Our investigation identified a total of 38 haplotypes, with a focus on 10 haplotypes that included more than five individuals. We meticulously analyzed the correlations between these haplotypes and a range of traits, encompassing body weight, tibial length, tibial circumference, body oblique length, chest width, and chest depth. The results unveiled significant disparities in specific tested traits across different haplotypes, indicating a tangible association between mtDNA haplotypes and traits in chickens. These findings underscore the potential impact of mitochondrial DNA variations on energy metabolism, ultimately leading to divergent chicken phenotypes. Furthermore, our examination revealed positive correlations between mtDNA copy numbers and tested traits for select haplotypes, while other haplotypes exhibited non-uniform relationships between traits and mtDNA copy numbers. In addition, phylogenetic analysis disclosed the involvement of two subspecies of red jungle chicken in the origin of Wuliangshan black-bone chickens. Consequently, our research contributes novel insights into mitochondrial genomic selection, augments comprehension of the roles played by haplotypes and mtDNA copy numbers in chicken population genetics and phylogenetic analysis, and furnishes fundamental data crucial for the preservation and provenance determination of black-bone chickens. creator: Wenpeng Li creator: Zhen Yang creator: Chao Yan creator: Siyu Chen creator: Xingbo Zhao uri: https://doi.org/10.7717/peerj.17989 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Li et al. title: Hydrogen gas inhalation prior to high-intensity training reduces attenuation of nitric oxide bioavailability in male rugby players link: https://peerj.com/articles/18503 last-modified: 2024-12-16 description: BackgroundInhalation of hydrogen gas (H2) as an antioxidant supplement may alleviate exercise-induced oxidative damage and protect post-exercise hydrogen peroxide signaling, which may help mediate beneficial exercise adaptation. The aims of this study were to determine the effects of H2 inhalation on plasma nitric oxide (NO) level and its synthesis precursor in professional athletes.MethodsA randomized, placebo-controlled, double-blind, crossover trial was conducted with professional male rugby players for 3 weeks. Participants underwent 1 week of H2 supplementation and 1 week of placebo treatment prior to daily sessions of high-intensity exercise training, separated by 1 week of low-intensity training as a washout.ResultsTwo-way (supplementation and time) repeated-measures analyses of variance showed that NO, L-arginine, and tetrahydrobiopterin levels in the H2 inhalation group were significantly higher than those in the placebo group after exercise (D6) and remained higher after 24 h of rest (D7). Levels of hydroxydeoxyguanosine and interleukin 6 were lower in the H2 inhalation week than in the placebo week on D6 and D7. In addition, total antioxidant levels were significantly higher with H2 inhalation than with placebo.SignificanceThese results suggest that H2 inhalation helps to maintain NO signaling after exercise and to alleviate inflammation and oxidative stress induced by high-intensity exercise training in professional athletes. creator: Yuqi Zhao creator: Chaoqun Li creator: Shi Zhou creator: Zhiguang Xu creator: Xin Huang creator: Li Wen uri: https://doi.org/10.7717/peerj.18503 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Zhao et al. title: Characteristics, source apportionment and health risks of indoor and outdoor fine particle-bound polycyclic aromatic hydrocarbons in Jinan, North China link: https://peerj.com/articles/18553 last-modified: 2024-12-16 description: To investigate the pollution characteristics of polycyclic aromatic hydrocarbons (PAHs) indoors and outdoors and their influencing factors, PM2.5 samples were systematically collected from both environments in Jinan during the summer and autumn seasons. During the observation period, the concentration of ∑ 19PAHs was 18.57 ± 10.50 ng/m3 indoors and 23.79 ± 16.13 ng/m3 outdoors. Most PAHs exhibited indoor-to-outdoor (I/O) ratios less than 1, indicating that indoor PAHs were primarily derived from the infiltration of outdoor sources. Correlation analysis underscored the significant influence of temperature on both outdoor concentrations and I/O ratios of PAHs. By utilizing diagnostic ratios and principal component analysis (PCA), vehicle emissions were identified as the predominant source of outdoor PAHs. Our study found that the toxic equivalents of benzo[a]pyrene (TEQBaP) values exceeded the European Commission’s standard of 1 ng/m3, with indoor values at 2.78 ng/m3 and outdoor values at 3.57 ng/m3. Moreover, the total incremental lifetime cancer risk (ILCRTotal) associated with exposure to PM2.5-bound PAHs surpassed the acceptable level of 10E-6, indicating potential adverse health effects. These results underscore the urgent necessity for more stringent regulatory measures to reduce PAH emissions. Additionally, our findings provide valuable insights into how environmental factors shape the relationship between indoor and outdoor PAHs. creator: Xiaomei Gao creator: Ziyi Wang creator: Xiaoyan Sun creator: Weidong Gao creator: Wei Jiang creator: Xi Wang creator: Fenfen Zhang creator: Xinfeng Wang creator: Lingxiao Yang creator: Yang Zhou uri: https://doi.org/10.7717/peerj.18553 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Gao et al. title: Length-mass relationships of pond macroinvertebrates do not hold between Southern and Northern Europe link: https://peerj.com/articles/18576 last-modified: 2024-12-16 description: The lack of reliable data on length-mass relationships, essential to obtain accurate biomass estimates, limits our ability to easily assess secondary production by aquatic invertebrates. In the absence of published equations from similar habitat conditions, authors often borrow equations developed in geographic regions with different climate conditions, which may bias biomass estimates. A literature overview of published size-mass relationships for Portugal and Sweden highlights the need for further data within these biogeographic regions. We increased the number of equations available to Southern and Northern Europe, developing 18 new length-mass relationships for two families and 10 genera in Portugal and Sweden. All equations were published for the first time for these countries, except the genus Asellus. Our length-mass relationships were obtained from specimens collected on a one-time sampling of eight ponds in Portugal and five ponds in Sweden during late spring in 2023. Dry mass (DM) was modelled as a function of body length (BL), using the natural log-linear function with a power model (ln DM = ln a + b × ln BL). The equations obtained were compared with linear mixed models testing the fixed effects of “body length” and “country”, as well as their interaction. A comparison of the equations developed in this study showed country-specific differences for all taxa, expect the genus Caenis, indicating a low potential transferability of the equations between Southern and Northern Europe. In contrast, the comparison of the equation obtained for A. aquaticus in this study with an equation published for this taxon in Sweden showed great similarities, suggesting a high transferability. Recommending caution in the borrowing of published length-mass equations, that can differ drastically between different geographic and climatic regions, especially at larger sizes, we provide a series of guidelines and good practices in this field. creator: Vladimíra Dekanová creator: Marek Svitok creator: Sara Bento creator: João Caramelo creator: Pedro Peixe e Sousa creator: Bruno M. Carreira uri: https://doi.org/10.7717/peerj.18576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dekanová et al.