title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=21 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments link: https://peerj.com/articles/20348 last-modified: 2025-11-19 description: Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces—Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance. creator: Xuemei Han creator: Huan Liu creator: Xue Bai creator: Diyan Li creator: Tao Wang creator: Hang Zhong creator: Yongfang Yao creator: Jing Sun uri: https://doi.org/10.7717/peerj.20348 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Han et al. title: Cross-cultural adaptation and psychometric validation of the Chinese quality-of-life questionnaire for patients with systemic sclerosis link: https://peerj.com/articles/20331 last-modified: 2025-11-19 description: BackgroundPatients with systemic sclerosis (SSc) frequently experience symptoms such as pain, fatigue, and functional impairments, leading to a significant decline in their quality of life (QoL). Accurately evaluating the QoL of SSc patients is crucial for developing personalized treatment plans and enhancing prognosis. The Systemic Sclerosis Quality of Life Questionnaire (SScQoL), an internationally recognized SSc-specific tool, is commonly used for QoL assessment. However, this questionnaire has not undergone cross-cultural adaptation in China, and its reliability and validity require further validation.ObjectivesTo localize the Systemic Sclerosis Quality of Life Questionnaire (SScQoL) into Chinese and assess its reliability and validity.MethodsFollowing the principles of scale introduction, the Beaton model was employed to translate and back-translate the English version. The scale underwent cross-cultural adaptation through expert consultation, resulting in the Chinese version of the SScQoL test. From August 2023 to December 2024, a convenience sampling method was used to recruit 160 patients with systemic sclerosis from two hospitals for questionnaire surveys to evaluate questionnaire reliability and validity.ResultsSScQoL comprises five dimensions and 29 items. The content validity index (CVI) at the item level ranges from 0.83 to 1.00, and the CVI at the scale level is 0.97. Exploratory factor analysis identified five common factors, with a cumulative variance contribution rate of 65.761%. The Cronbach’s α coefficient for the total scale is 0.922, and the Cronbach’s α coefficients for the five dimensions range from 0.756 to 0.942. The test-retest reliability for the total scale is 0.969; for the five dimensions, it ranges from 0.710 to 0.961.ConclusionsSScQoL is a reliable and effective tool for evaluating patients’ quality of life with systemic sclerosis. This tool can support nurses and researchers and help them formulate targeted strategies, thereby significantly improving patients’ quality of life with systemic sclerosis. creator: Yinfeng Hu creator: Wenjie Zhong creator: Liqiong Zhou uri: https://doi.org/10.7717/peerj.20331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Hu et al. title: Dissecting antibody-dependent enhancement modulation by Fc-modified cross-neutralizing human monoclonal antibody link: https://peerj.com/articles/20329 last-modified: 2025-11-19 description: BackgroundDengue is a mosquito-borne disease caused by four dengue virus serotypes (DENV1 to DENV4). Secondary infections can generate flavivirus cross-reactive antibodies at sub-neutralizing levels. This phenomenon can significantly increase the severity of secondary infections through antibody-dependent enhancement (ADE). ADE is associated with a high risk of viral infection in immune effector cells, triggering cytokine cascades and activating the complement system, which can lead to severe symptoms. Despite extensive studies, therapeutic antibodies, particularly fully human monoclonal antibodies, which could serve as candidates for immune passive therapy, have not yet been discovered.MethodologyThis study generated LALA-mutated human monoclonal antibody clone B3B9 (LALA-B3B9 HuMAb) which can neutralize all four DENV serotypes without enhancing viral activity. The number of infected cells in the ADE assay was compared among the wild-type antibody (B3B9), LALA-B3B9 HuMAb, and an Fc modified variant at position N297Q (N297Q-B3B9), with or without complement proteins. Moreover, the therapeutic efficacy of these HuMAbs against ADE infection by competing with natural antibodies in patients with acute dengue was evaluated using the in vitro suppression-of-enhancement assay in K562 cells.ResultOur novel Fc-modified antibody LALA-B3B9 (Leu234Ala/Leu235Ala mutations), exhibited neutralizing activity against all dengue virus serotypes without triggering ADE activity at any antibody concentration. This outcome was similar to that observed with the previously developed Fc-modified N297Q-B3B9 antibody (N297Q mutation). We further evaluated the effect of complement protein on the enhancing and neutralizing activities of our Fc-modified antibodies. The results showed that LALA-B3B9 and N297Q-B3B9 HuMAbs were complement-independent, meaning that the reduced binding between complement protein (C1q) and the Fc portion of the antibody left the neutralizing and enhancing activities unchanged. Additionally, both LALA-B3B9 and N297Q-B3B9 HuMAbs demonstrated the suppression-of-enhancement activity in K562 cells induced by human anti-DENV serum antibodies. Overall, this study highlights the main advantages of our EDII-specific HuMAbs in inhibiting in vitro ADE, indicating that they are promising candidates for future dengue treatment. creator: Subenya Injampa creator: Surachet Benjathummarak creator: Sujitra Keadsanti creator: Rochanawan Sootichote creator: Wilarat Puangmanee creator: Atsushi Yamanaka creator: Tadahiro Sasaki creator: Pongrama Ramasoota creator: Pannamthip Pitaksajjakul uri: https://doi.org/10.7717/peerj.20329 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Injampa et al. title: Comparison of anti-PD-1/PD-L1-based regimens in relapsed/refractory diffuse large B-cell lymphoma: a meta-analysis link: https://peerj.com/articles/20314 last-modified: 2025-11-19 description: AimTo evaluate the therapeutic value and find out potential combination agents of programmed death 1/programmed death-ligand 1 (PD-1/PD-L1) monoclonal antibody (mAb) in relapsed/refractory (r/r) diffuse large B-cell lymphoma (DLBCL).MethodsWe conducted a meta-analysis to assess the efficacy and safety of PD-1/PD-L1 mAb in r/r DLBCL, potential qualified studies were searched in PubMed, Embase, Web of Science, and ClinicalTrials.gov. This meta-analysis had been registered on the PROSPERO platform (CRD42023340031).ResultsAfter systematic screening, a total of 32 records involving 29 studies were included, pooled survival curves indicated better progression-free survival (PFS) (p < 0.0001; HR = 0.51, 95% CI [0.42–0.62]) and overall survival (OS) (p = 0.013; HR = 0.71, 95% CI [0.57–0.88]) for combination therapy compared with monotherapy. Combination therapy group also achieved a better pooled complete response rate (CRR) (14.6% vs. 3.0%; p < 0.001) and overall response rate (ORR) (30.5% vs. 10.3%; p < 0.001). Analysis of the incidence of adverse events (AEs) did not demonstrate additional toxicities of combination therapy. The limitation was the predominance of single-arm trials, precluding the direct comparison of combination versus partner agents alone.ConclusionsThese findings support further exploration of PD-1/PD-L1-mAb-based combination therapy to identify long-term survival benefits, while application of monotherapy in unselected DLBCL patients is not recommended. creator: Wenxin Jiang creator: Tingyu Wen creator: Peng Liu uri: https://doi.org/10.7717/peerj.20314 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jiang et al. title: Deciphering the role of Hat1 in spermatogenesis: Chromatin organization and beyond link: https://peerj.com/articles/20240 last-modified: 2025-11-19 description: Spermatogenesis, a core process for male fertility, relies heavily on chromatin organization regulated by histone acetyltransferases (HATs). However, the spatiotemporal expression pattern of histone acetyltransferase 1 (Hat1) in mouse testes and its specific role in spermatogenesis via chromatin organization remain unclear. This study employed RT-qPCR, Western blot, immunofluorescence localization, and bioinformatics to explore Hat1’s dynamic expression and regulatory mechanisms during mouse spermatogenesis. Results showed that both Hat1 mRNA and protein were significantly upregulated in the testes of 8-week-old (mature) mice compared to 3-week-old (immature) mice. Immunofluorescence revealed Hat1 was predominantly localized in the nuclei of male germ cells, with stage-specific expression: highest in spermatogonia and sperm, intermediate in primary spermatocytes, and lowest in secondary spermatocytes. Bioinformatics analysis (based on single-cell sequencing data GSE214315) identified 246 differentially expressed genes (DEGs) related to chromatin organization—these DEGs were screened between adjacent stages of male germ cell development during spermatogenesis, including comparisons of leptotene-zygotene vs. pachytene-diplotene cells, pachytene-diplotene vs. round spermatids, round spermatids vs. early elongating spermatids, and early elongating vs. late elongating spermatids (screening criteria: FDR < 0.05, |log2(FC)| ≥ 1). Additionally, 41 Hat1-interacting proteins encoded by these DEGs were identified. Functional enrichment indicated stage-specific roles of Hat1: in the leptotene-zygotene phase, it participated in transcription regulation to initiate meiosis; in round spermatids, it shifted to refined epigenetic regulation and chromatin assembly for subsequent spermiogenesis; in late spermiogenesis and sperm, it was involved in DNA repair and ATP-dependent chromatin remodeling to protect sperm genetic material. In summary, the stage-specific expression patterns of Hat1 and its interactors highlighted the importance of precise control of gene expression and chromatin remodeling, as well as DNA repair in protection of sperm genetic material, in the development of male germ cells. However, future research should conduct functional assays. Overall, this research provides valuable insights into the epigenetic regulatory mechanisms of spermatogenesis and a foundation for male fertility research. creator: Shenni Peng creator: Yulian Tang creator: Ruiqun Lu creator: Shi Huang creator: Yinyin Mo creator: Hailing Huang creator: Genliang Li uri: https://doi.org/10.7717/peerj.20240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Peng et al. title: A Bayesian model for assessing organic matter supply in complex marine food webs using amino acid stable isotope analysis link: https://peerj.com/articles/20220 last-modified: 2025-11-19 description: While several software packages have been developed to solve stable isotope mixing models, none are currently equipped to trace the flow of organic matter through the lower trophic levels of planktonic food webs. To address this gap, we have developed a new Bayesian mixing model tailored for use with δ15N values of individual amino acids. This model simultaneously estimates trophic relationships between consumers and organic matter sources at the base of the food web, determines the relative contributions of these basal organic matter sources to consumers, and accounts for trophic discrimination affecting amino acid δ15N values during protozoan and metazoan trophic steps. This “Organic Matter Supply Model” is uniquely suited for applications where food web structure is unknown and trophic intermediaries, such as protozoan and metazoan grazers with distinct amino acid trophic discrimination factors, play a critical role in nutrient transfer. In this paper, we describe the model’s basic structure, outline key considerations for adapting it to specific applications, evaluate its performance using simulated zooplankton data, discuss its strengths and limitations, and offer recommendations for its further development. By testing the model on simulated zooplankton amino acid δ15N data, we demonstrate that the Organic Matter Supply Model can enhance our understanding of the roles of small particles and diel vertical migration in deep-sea organic matter supply pathways. Furthermore, it provides a new framework for exploring the foundational role of heterotrophic protists in marine ecosystems. We find specific subsets of amino acids to be most useful as markers of trophic ecology (in this case including glutamic acid and proline) and to identify supply from basal organic matter sources (phenylalanine, lysine, and threonine). Other amino acids may be more ideal source tracers in other settings, although amino acids with inconsistent or poorly constrained isotope fractionation behavior (e.g., isoleucine, valine) should be excluded to optimize model reliability. creator: Connor H.H. Shea creator: Jeffrey C. Drazen creator: Brian N. Popp uri: https://doi.org/10.7717/peerj.20220 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Shea et al. title: Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province link: https://peerj.com/articles/20199 last-modified: 2025-11-19 description: BackgroundHongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province.MethodsSurveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing.ResultsThe results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P = 0.038 at the family, P = 0.019 at the genus and P = 0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P < 0.05) than that in the rainy season group according to the Kruskal–Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P = 0.018). The relative abundance of multidrug resistance genes in urban sewage was higher than that in rural sewage, and the relative abundance of most resistance genes in the dry season group was higher than that in the rainy season group.ConclusionsIn general, the abundance and distribution features of the sewage microbial communities in the Hongta District of Yuxi city were affected by site and rainfall factors, with significant regional and temporal specificity. Strengthening the surveillance of environmental sewage and improving discharge methods are highly important for ensuring public health security. creator: Senquan Jia creator: Wenpeng Gu creator: Lili Jiang creator: Yong Zhang creator: Xiaoqing Fu creator: Jianwen Yin creator: Yongming Zhou uri: https://doi.org/10.7717/peerj.20199 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Jia et al. title: AIMP1: multifunctional regulator in physiology and pathology with therapeutic implications link: https://peerj.com/articles/20334 last-modified: 2025-11-18 description: Aminoacyl tRNA synthetase complex interacting multifunctional protein 1 (AIMP1), also referred to as p43, serves as an auxiliary factor of the macromolecular aminoacyl tRNA synthetase complex. Beyond its classical role in the assembling the multisynthetase complex (MSC) for protein translation, growing evidence has elucidated that AIMP1 plays a pivotal role in regulating immune response, brain function and angiogenesis. Furthermore, accumulating studies have demonstrated that AIMP1 is involved in a spectrum of pathological processes, including cancer, immunity associated disorders, and neurological diseases. Herein, we summarize the current research regarding the functions of AIMP1 under both physiological and pathological conditions, with a particular focus on its therapeutic potential in these diseases. creator: Xunan Yuan creator: Xinmiao Wang creator: Xiaodan Ma creator: Yaping Mao creator: Qinqin Wang uri: https://doi.org/10.7717/peerj.20334 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Yuan et al. title: Machine learning classification of mango maturity based on carotene content from Raman spectra link: https://peerj.com/articles/20288 last-modified: 2025-11-18 description: Determining mango ripeness is essential for ensuring its delicious taste, enticing aroma, and rich nutritional value. For farmers, harvesting mangoes too early can result in stunted fruit and lower yields compared to those harvested at a ripe stage. This study aims to develop a potentially non-invasive and efficient method for detecting mango ripeness using Raman spectroscopy. Traditional methods, which rely on human assessment and color evaluation with image processing, are inconsistent, inaccurate, and time-consuming due to variations in mango color and individual differences in vision and perception. To address these limitations, this study pursued three main objectives: extracting data characteristics of organic compounds in mangoes based on raw Raman spectrum data, identifying the correlation between carotene characteristics and mango ripeness levels, and evaluating the performance of machine learning models in classifying mango ripeness levels. A total of  29 mango fruit spectra were analyzed, with 13 samples selected to represent three ripeness categories: underripe, ripe, and overripe. Raman spectra peak signal analysis revealed that mango peel contains lycopene, β-carotene, lutein, and neoxanthin, all of which are derived from carotenoid molecules in the range of 1,480 cm−1 to 1,550 cm−1. Statistical analysis confirmed the significance (p < 0.05) of extracted Raman Peak Intensity features in distinguishing ripeness levels, supported by high correlation coefficients between carotenoid peak intensity and mango maturity. This study achieved 100% accuracy in classifying mango ripeness levels using three classifier models: the Medium Gaussian Support Vector Machine, the Cubic Support Vector Machine, and the Weighted K-Nearest Neighbors. Raman spectroscopy has proven to be a reliable and robust method, immune to external factors such as light, humidity, and noise, which makes it a promising approach for assessing mango ripeness. creator: Ji Loun Tan creator: Fazida Hanim Hashim creator: Jahariah Sampe creator: Aqilah Baseri Huddin creator: Ghassan Maan Salim creator: Sawal Hamid Md Ali uri: https://doi.org/10.7717/peerj.20288 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Tan et al. title: Identification of mitochondrial-related genes to evaluate the immune infiltration and prognosis of lung adenocarcinoma link: https://peerj.com/articles/20262 last-modified: 2025-11-18 description: BackgroundMitochondrial dysfunction critically impacts lung adenocarcinoma (LUAD) progression and tumor microenvironment (TME) remodeling, highlighting the urgent need to identify predictive biomarkers with clinical utility.MethodsRNA-seq data sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to identify mitochondrial-related (MTR) genes associated with LUAD progression. A three-gene prognostic signature, consisting of SFXN1, CPS1, and MTFR2, was developed through univariate, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. Functional enrichment, immune infiltration, and tumor mutation burden (TMB) analyses were performed to characterize the TME. Experimental studies were conducted in LUAD cell lines via siRNA-mediated knockdown, assessing mitochondrial dynamics, mitochondrial membrane potential (ΔΨm), reactive oxygen species (ROS) levels, and mitochondrial DNA (mtDNA) stability.ResultsThe signature stratified patients into high-risk and low-risk groups with significant survival differences (TCGA: HR = 1.476, P < 0.001; GSE31210: P < 0.001; GSE30219: P = 0.001). High-risk patients exhibited features of immunosuppressive TME, including elevated tumor purity, higher TIDE scores, increased TMB, and immune checkpoint expression (CD274, CD276, PDCD1, RELT). Functional analyses revealed that siRNA-mediated knockdown of CPS1 triggered mitochondrial fission, as evidenced by ΔΨm↓/ROS↑. Conversely, SFXN1 knockdown induced mitochondrial fusion accompanied by hyperpolarization (ΔΨm↑/ROS↓). Notably, MTFR2 knockdown promoted mitochondrial fusion, contributing to ΔΨm↑/ROS↓. All three siRNA treatments compromised mtDNA integrity, with CPS1 knockdown uniquely inducing the release of cytosolic mtDNA.ConclusionThis study has successfully established a mitochondrial-related prognostic signature that predicts survival outcomes and immune phenotypes of LUAD patients, providing a clinically relevant predictive tool and laying the foundation for developing mitochondrial-targeted therapeutic strategies. creator: Yutong Ge creator: Ao Sun creator: Tao Yu creator: Shaokun Yu creator: Kaihua Lu uri: https://doi.org/10.7717/peerj.20262 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2025 Ge et al.