Metagenomics-based analysis of mobile genetic elements and antibiotic/metal resistance genes carried by treated wastewater
Wastewater treatment plants in Tunisia are recognized as key locations for the spread of antibiotic and heavy metal resistance genes among bacteria. Despite the widespread presence of pollutants in these treatment systems, there is still a significant gap in our understanding of resistance dynamics. This study focused on analyzing the bacterial community and resistome-mobilome profiles of the Charguia wastewater treatment plant (WWTP). Using metagenomics sequencing, six samples from the influent, sludge, and effluent were thoroughly examined. Our research findings indicated the prevalence of Proteobacteria and high levels of Bacteroidota, Firmicutes, Campylobacterota, and Patescibacteria. After conducting a species level analysis, we identified important species such as Pseudomonas psychrophila, Pseudomonas fragi, Pseudomonas lundensis, Acinetobacter johnsonii, and Thiothrix unzii linked to antibiotic resistant genes (ARGs) like mdtA and merR1 and heavy metal resistance genes (MRGs), including czcA and cnrA. Our study illustrated the persistence of specific species in the effluent due to the co-occurrence of ARGs/MRGs and mobile genetic elements (MGE). Notably, IncQ and IncP were found to be associated with mdtA, mexR, arsR1, and merR. The conclusions drawn from our research suggest that the WWTP has been potentially effective in reducing multidrug resistance.
Environmental Contamination and Remediation
Naccache et al. (2025) Metagenomics-based analysis of mobile genetic elements and antibiotic/metal resistance genes carried by treated wastewater. PeerJ 13:e19682 https://doi.org/10.7717/peerj.19682
A study of salivary cortisol and glutamate after the cold pressor task in healthy adults
Nociception related salivary biomolecules can be a useful future aid in the assessment of acute pain. We have investigated changes in the levels of two salivary biomolecules, glutamate and cortisol, following the induction of acute cold pain using the cold pressor task (CPT). Saliva samples were collected from 18 healthy volunteers before, immediately after and then, every 10 minutes for one hour after CPT. Statistical analysis of the biomolecule concentrations across all participants and time points were done. This showed significant differences between salivary cortisol concentration before (median 0.14 µg/dL, Interquartile Range (IQR) = 0.1) and 10 minutes after termination of CPT (median 0.34 µg/dL, IQR = 0.4, p = 0.007). Male participants exhibited a greater increase in cortisol concentration after cold pain compared to females. The timeline and pattern of the rise in salivary cortisol concentration in this study are consistent with existing literature. Salivary glutamate concentration fluctuated but none of the changes were statistically significant except at t = + 50 minutes, when the concentration had dropped below baseline. The findings do not support the use of glutamate as a useful biomarker in acute pain despite evidence that plasma and salivary glutamate levels are higher in people with chronic pain conditions such as migraine and temporomandibular disorder.
Zarnegar et al. (2025) A study of salivary cortisol and glutamate after the cold pressor task in healthy adults. PeerJ 13:e19625 https://doi.org/10.7717/peerj.19625
Impact of P fertilizer and arbuscular mycorrhizal fungi on forage legume growth, chlorophyll content and productivity
Soil phosphorous (P) is the most limiting plant nutrient globally, reducing forage plant productivity. Although inorganic P fertilizers are used, about 75–90% of P becomes unavailable for plant uptake, hence, the strategies to enhance P uptake acquisition, such as the use of arbuscular mycorrhizal fungi (AMF) inoculation, are crucial. A greenhouse pot experiment was conducted under controlled environmental conditions at the University of Fort Hare, where three legume species (Vigna unguiculata, Lablab purpereus and Mucuna pruriens) were grown for 90 days under five P fertilizer levels (0; 0.68; 1.36; 2.04 and 2.72 g P/pot) with or without AMF-inoculation, resulting in 30 treatment factorial arrangement, each replicated 4 times. Agronomic responses to P fertilization and AMF-inoculation were assessed. Plant height, stem diameter, chlorophyll content, and leaf and stem yield were significantly influenced (p < 0.001) by the interaction of phosphorus (P) fertilizer levels, arbuscular mycorrhizal fungi (AMF) inoculation, and legume species. Inoculated plants showed remarkable growth, reaching heights of 94.2 to 159.0 cm compared to 61.1 to 117.0 cm in uninoculated plants. Additionally, inoculated plants had stem diameters twice as large as those of uninoculated plants when grown with 1.36 g P/pot, outperforming other P fertilizer levels by day 90 across all legume species. Likewise, chlorophyll content of inoculated plants (78.1–90.7 soil plant analysis development (SPAD)) was significantly higher than uninoculated plants (56.9–69.1 SPAD) at 1.63 P g/pot compared to 0, 0.68, 2.04 and 2.72 g P/pot. Moreover, inoculated plants attained relatively higher leaf (123.3–144.0 g/pot) and stem yield (75.2–121.8 g/pot) than uninoculated plants at 1.36 g P/pot compared to 0, 0.68, 2.04 and 2.72 g P/pot. Overall, AMF-inoculation improved growth and productivity of forage legumes, but its effects depended on the P fertilizer level, with 1.36 g P/pot being the potential optimum fertilizer rate for soil nutrition of legume pastures.
Mpongwana et al. (2025) Impact of P fertilizer and arbuscular mycorrhizal fungi on forage legume growth, chlorophyll content and productivity. PeerJ 13:e18955 https://doi.org/10.7717/peerj.18955
Tertiary lymphoid structures-driven immune infiltration patterns and their association with survival in neuroblastoma
Background Neuroblastoma (NB), a diverse childhood cancer, needs better prognostic markers for personalized treatment. The current clinical risk stratification system does not fully explain the high heterogeneity of tumor patients. Tertiary lymphoid structures (TLS), key in tumor immunity, may serve as new biomarkers, but their impact on NB prognosis is unclear. Methods We combined transcriptome data from NB cohorts GSE49710 and GSE62564, analyzing 37 TLS-related genes. A prognostic signature (CMLS) was created using machine learning and validated with Kaplan-Meier and receiver operating characteristic (ROC) curves. We also studied immune infiltration and gene expression patterns in NB tissues using single-cell sequencing and quantitative real-time polymerase chain reaction (qRT-PCR). Results A 6-gene TLS signature predicted better survival in NB patients. High levels of CCL2, CCL4, CCL21, CD200, CXCR3, and IGSF6 correlated with improved survival. The low-TLS risk group showed better event-free and overall survival. Immune analysis indicated a higher immune cell presence, especially cytotoxic T cells, in this group. Single-cell sequencing revealed lower TLS gene expression in refractory recurrence samples. CD200 downregulation reduced NB cell invasiveness and migration. Conclusion Our study demonstrates that TLS-related genes play a crucial role in NB prognosis, with a 6-gene TLS signature (CCL2, CCL4, CCL21, CD200, CXCR3, and IGSF6) serving as a promising prognostic biomarker for NB. CD200 may be a potential target for inhibiting the biological behavior of NB cells.
Liu et al. (2025) Tertiary lymphoid structures-driven immune infiltration patterns and their association with survival in neuroblastoma. PeerJ 13:e19767 https://doi.org/10.7717/peerj.19767
Preoperative digital 6-minute walk test reveals risk of postoperative pulmonary complications in patients undergoing heart valve surgery: a pilot feasibility study
Background Postoperative pulmonary complications (PPCs) are a significant concern in cardiac surgery, affecting patient prognosis. This pilot study explored the feasibility of developing a machine learning model for preoperative PPCs risk stratification by integrating dynamic respiratory physiology from the six-minute walk test (6MWT) with clinical parameters. Methods A prospective study was conducted at the Department of Cardiovascular Surgery of West China Hospital, Sichuan University, from August 2021 to December 2022. We enrolled 142 consecutive patients undergoing valvular heart surgery. After quality control, 117 patients with complete synchronized respiratory monitoring during 6MWT and clinical data were included. We extracted 94 physiological features across 6MWT phases (baseline, walking, recovery) and clinical variables, developing predictive models using five machine learning algorithms evaluated through rigorous five-fold cross-validation. Results The logistic regression model demonstrated promising discriminative performance (AUC 0.86, 95% CI [0.81–0.89]) in this exploratory cohort. Preliminary physiological patterns emerged, including associations between elevated expiratory tidal volume during recovery (OR 9.70, p = 0.006) and reduced baseline minute ventilation (OR 0.15, p = 0.002) with higher PPCs risk. Conclusion These pilot findings suggest that continuous physiological monitoring during 6MWT, when combined with clinical data, may provide a feasible approach for preoperative PPCs risk assessment. While requiring multi-center validation, the results highlight the potential of wearable-enabled respiratory monitoring to guide prehabilitation strategies in cardiac surgery.
Li et al. (2025) Preoperative digital 6-minute walk test reveals risk of postoperative pulmonary complications in patients undergoing heart valve surgery: a pilot feasibility study. PeerJ 13:e19732 https://doi.org/10.7717/peerj.19732
Non-agriculturalization of cultivated land in densely populated areas at the watershed scale: a case study of the Minjiang River Basin, China
Zero hunger is a top priority in the Sustainable Development Goals, however, millions of people worldwide still face hunger. Over the years, China has experienced rapid population growth, industrialization and urbanization, leading to significant agricultural land loss, which threats the nation’s food supply. Understanding the patterns and driving factors of non-agriculturalization is crucial for its protection. The Minjiang River Basin, the largest tributary of the Yangtze River, is densely populated and experiencing rapid urbanization, making it a typical snapshot of the non-agriculturalization in China. This study comprehensively examines the characteristics and trends in the spatiotemporal evolution of cultivated land in the Minjiang River Basin, along with the drivers of non-agriculturalization. The results reveal the findings: (1) From 1990 to 2020, the cultivated land in the Minjiang River Basin has decreased and mainly concentrated in flat areas. The spatiotemporal evolution of cultivated land exhibits low dispersion and strong directionality, predominantly shifting northward, and the migration of cultivated land can be divided into three stages. (2) A consistent positive spatial correlation is observed in the non-agriculturalization areas of cultivated land in the Minjiang River Basin, with high-high (HH) clustering analysis revealing an aggregation pattern radiating outward from the city center. (3) Population growth and economic factors are the primary drivers of non-agriculturalization in the Minjiang River Basin.
Spatial and Geographic Information Science
Zhao et al. (2025) Non-agriculturalization of cultivated land in densely populated areas at the watershed scale: a case study of the Minjiang River Basin, China. PeerJ 13:e19722 https://doi.org/10.7717/peerj.19722
Regulatory role of transcription factor c-Myc in the pathogenesis of psoriasis
Psoriasis is a chronic relapsing dermatosis characterized by hyperproliferation and poor differentiation of keratinocytes (KCs). The c-Myc gene is one of the main members of the Myc family and exerts multiple biological functions. C-Myc is highly expressed in psoriatic lesions. The co-expressed genes and coexisting factors of c-Myc determine the final survival of cells. The high expression levels of c-Myc in the skin lesions of psoriatic patients are associated with the continuous proliferation of KCs, and form an abnormal state of epidermal dynamics. C-Myc is also involved in the induction of metabolic reprogramming of cells in the development of psoriasis, thus exacerbating the excessive proliferation of psoriatic epidermis. In this review, we focus on the mechanisms of the transcription factor c-Myc in the pathogenesis of psoriasis and its clinical implications.
Cao et al. (2025) Regulatory role of transcription factor c-Myc in the pathogenesis of psoriasis. PeerJ 13:e19706 https://doi.org/10.7717/peerj.19706
A SNP-based genome-wide association study (GWAS) of seed-yield related traits in Psathyrostachys juncea using wheat as a reference genome
Background Psathyrostachys juncea is an popular perennial grass for both mowing and grazing when used for pasture establishment in high latitude regions. P. juncea has the advantages of high yield, high quality, good palatability and high nutritional value. It is widely used in artificial grassland construction and ecological restoration in Inner Mongolia and other regions. Methods The current study aimed to identify genetic signals associated with seed yield in P. juncea germplasm through a genome-wide association study (GWAS) using wheat as a reference genome. 300 accessions of P. juncea germplasm from different countries were used as materials to assess eight seed yield-related traits in two environments for two consecutive years. Results All the trait values varied considerably across genotypes. Across different locations, the coefficient of variation among genotypes was the highest for seed yield per plant, which exceeded 70%. Further correlation analysis of seed yield factors showed that seed yield per plant had a significant positive correlation with reproductive tiller number. The population exhibited five population structures (Q) assessed by using 84,024 single-nucleotide polymorphisms (SNPs). After controlling Q and K (subgroups), GWAS identified 121 SNPs significantly associated with eight traits. Among them, 19 SNPs were detected in multiple environments, and a total of 91 candidate genes were annotated, which involve the synthesis of cell wall polysaccharides and proteins, plant growth and development, photosynthesis, gibberellin regulation, hormone signal transduction, phenylalanine metabolism, and amino acid metabolism processes. The identification of SNP signals and related candidate genes could enrich the existing genomic resources and lay a foundation for the study of molecular breeding, mapping, and cloning of important genes in P. juncea.
Li et al. (2025) A SNP-based genome-wide association study (GWAS) of seed-yield related traits in Psathyrostachys juncea using wheat as a reference genome. PeerJ 13:e19617 https://doi.org/10.7717/peerj.19617
Genome-wide characterization and expression analysis of the JRL gene family in response to hormones and abiotic stress in tomato (Solanum lycopersicum L.)
Jacalin-related lectins (JRLs), a newly discovered subfamily of plant lectins, play an important role in plant growth and development and abiotic stress response. However, in the most important model and economic plant, the tomato, little is known about this gene family. Here, we conducted a genome-wide identification and characterization of the JRL gene family in tomato. A total of eight JRL gene family members (SlJRL1–SlJRL8) were identified based on the tomato genome through bioinformatics analyses, which were unevenly distributed on four chromosomes. Chromosomal localization revealed four pairs of tandemly duplicated genes. Genome collinearity analyses showed that tomato JRL genes were more closely related to Arabidopsis than to rice and maize. Phylogenetic analysis showed that tomato JRL could be divided into seven subgroups, and members within each subgroup shared similar gene structures and conserved motifs. Promoter analysis revealed abundant cis-acting elements associated with stress-responsive and phytohormone-responsive. Finally, real-time quantitative polymerase chain reaction (qRT-PCR) was used to analyze the expression profile of SlJRL gene under various plant hormone and abiotic stress treatments. The results show that the SlJRL gene family exhibits tissue-specific expression patterns and responds to a variety of hormonal and stress conditions. This study systematically analyzed the genomic characteristics of tomato JRL family. Our results lay the foundation for further studies on the biological functions of tomato JRL genes.
Li et al. (2025) Genome-wide characterization and expression analysis of the JRL gene family in response to hormones and abiotic stress in tomato (Solanum lycopersicum L.). PeerJ 13:e19724 https://doi.org/10.7717/peerj.19724
P21 activated kinase 6: a promising tool for predicting small cell lung cancer diagnosis and treatment response
Objective Building upon the established role of P21 Activated Kinase 6 (PAK6) in tumor progression and chemoresistance pathways, we postulate its potential as a dual-function biomarker for small cell lung cancer (SCLC). This investigation aims to conduct a comprehensive evaluation of PAK6’s diagnostic validity and prognostic significance through comparative analysis of PAK6 serological levels across distinct clinical cohorts to determine diagnostic thresholds, and its clinical correlation with therapeutic responsiveness. Patients and Methods This study included 109 patients diagnosed with SCLC, 92 patients with non-small cell lung cancer (NSCLC), 85 patients with pulmonary nodules (PN), and 94 healthy individuals undergoing routine physical examinations as the normal control group (NC). Serum PAK6 concentrations were measured using enzyme-linked immunosorbent assay (ELISA). Additionally, levels of neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), carbohydrate antigen 19-9 (CA19-9), and pro-gastrin-releasing peptide (ProGRP) were quantified via chemiluminescence assays. Progression-free survival (PFS) data for SCLC patients were collected through case review and telephone follow-up. Results Serum PAK6 levels were significantly higher in the SCLC group compared to the other three groups (p < 0.01). Similarly, NSE and ProGRP levels were markedly elevated in the SCLC group compared to the other groups (p < 0.01). Correlation analysis revealed a positive association between PAK6 and variables such as gender, VA (Veteran’s Administration Lung Cancer Study Group) stage, age, smoking status, CEA, CA19-9, NSE, and ProGRP. The serum tumor markers (STMs) PAK6, NSE, and ProGRP exhibited superior diagnostic performance, with AUCs of 0.892, 0.834, and 0.935, respectively (95% confidence interval (CI) [0.857–0.927], [0.778–0.890], and [0.909–0.960]), compared to CEA and CA19-9 (AUCs = 0.676 and 0.611, respectively; 95% CI [0.622–0.731] and [0.547–0.675]) (p < 0.01). Furthermore, PAK6, NSE, and ProGRP levels significantly decreased after three months of treatment, while CEA and CA19-9 showed no significant changes. Survival analysis demonstrated that higher PAK6 levels were associated with poorer SCLC prognosis. Increased serum PAK6 expression correlated with shorter PFS (HR = 2.02 [1.33–3.07], P = 0.001). Conclusion Serum PAK6 holds significant clinical value for the diagnosis, treatment monitoring, and prognosis evaluation of SCLC and may serve as a potential therapeutic target for the disease.
Chen et al. (2025) P21 activated kinase 6: a promising tool for predicting small cell lung cancer diagnosis and treatment response. PeerJ 13:e19714 https://doi.org/10.7717/peerj.19714