Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements
Stable isotope analysis of skin collagen is useful for detecting short-term or seasonal diet. Preparation of skin for stable isotope analysis varies across laboratories, and this may impact the comparability of data. It is important to understand the effects of different preparatory protocols on the stable isotopic and elemental compositions of skin samples. Using a Eurovector 3,300 elemental analyzer coupled to a Nu Horizon isotope ratio mass spectrometer, we tested the impact of three treatment variants (refluxing at three temperatures to remove non-collagenous proteins, treatment with sodium hydroxide (NaOH), and chemical lipid extraction using 2:1 chloroform:methanol) on the stable isotope (δ13carbon (C) and δ15nitrogen (N)) and elemental (wt% C, and wt% N) composition of pig (Sus scrofa domesticus) skin. The refluxing step produced pig skin with higher δ13C values, lower C:NAtomic ratios, less variable C:NAtomic ratios, wt% C, and wt% N. The chemical lipid extraction also produced higher, more reliable δ13C values and lower, less variable C:NAtomic ratios. The isotopic data in the lipid-extracted and refluxed samples were more consistent in the refluxed samples than the non-refluxed and non-lipid-extracted samples, as determined by the elemental compositions.
Derian et al. (2025) Solubilization of skin collagen improves the accuracy and reliability of stable isotope measurements. PeerJ 13:e20152 https://doi.org/10.7717/peerj.20152
Quality assessment from biobank plasma and serum specimens: a systematic review
Accurate assessment of serum and plasma quality is essential for reliable biobanking and research. This systematic review synthesizes 46 studies and shows that current evaluation methods prioritize sample processing delays, freeze-thaw cycles, storage duration, and temperature variations, while neglecting preanalytical factors like medication and diet. Temperature critically affected stability: non-refrigerated samples (8–37 °C) showed 3.2 times more biomarker alterations than refrigerated samples after >24 h delays. Freeze-thaw cycles caused dose-dependent instability, with >10 cycles triggering severe degradation (70% altered biomarkers) and universal enzyme impairment. Even ≤5 cycles significantly altered enzymes (43% affected). Enzymes also degraded over time at <−20 °C, with alteration rates rising from 20% (1–5 years) to 55% (>10 years). The analysis consolidates stability data for enzymes, sterols, cytokines, and metabolites across conditions, providing an evidence-based foundation for quality control. Standardizing procedures to address these gaps will enhance sample integrity, research reliability, and clinical utility. Critically, this review underscores that preexisting biobank collections may have inherent limitations, necessitating careful evaluation of sample history when designing studies.
Liang et al. (2025) Quality assessment from biobank plasma and serum specimens: a systematic review. PeerJ 13:e20122 https://doi.org/10.7717/peerj.20122
Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer
Background To assess the status of NEUROG1 methylation in the advanced adenoma and colorectal cancer. Methods The NEUROG1 methylation in tissue and stool samples from patients with colorectal cancer (CRC), advanced adenoma (AA), and non-advanced adenoma (NAA) were evaluated using methylation-specific quantitative polymerase chain reaction (PCR). Results In tissue samples, the NEUROG1 methylation detection rates were 36% for CRC, 24% for NAA, and 88% for AA. In stool samples, the NEUROG1 methylation detection had a sensitivity of 63.46% for CRC with a positive predictive value (PPV) of 85.94%. The overall diagnostic specificity of the test for the NAA and the healthy control was 76.32%, with a negative predictive value (NPV) of 40.28%. Conclusion NEUROG1 methylation detection can potentially be used in the CRC and AA screening.
Zhang et al. (2025) Evaluation of NEUROG1 methylation status in stool specimens in the advanced adenomas and colorectal cancer. PeerJ 13:e19968 https://doi.org/10.7717/peerj.19968
Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis
Background Acne is a common skin condition that can cause permanent scarring and profoundly affect patients’ quality of life. Despite the increasing diversity of acne scar treatments, there is a dearth of comprehensive evidence-based guidelines to help clinicians and patients make the best choices. This study aimed to comprehensively assess the efficacy and safety of existing acne scar treatments through a network meta-analysis. Method PubMed, Embase, Cochrane Library, and Web of Science were thoroughly searched for relevant studies from database establishment to September 19, 2024. Outcome included Echelle d’evaluation clinique des cicatrices d’acne (ECCA), Goodman and Baron Scale (GBS), pain, patient satisfaction, and adverse events. Bayesian network meta-analyses were performed using the gemtc package in R. Risk of bias was assessed using Cochrane Risk of Bias (RoB 2) tool, while publication bias was assessed via funnel plots. The study protocol was registered with PROSPERO (CRD42024598780). Results A total of 68 randomized controlled trials were enrolled, comprising 4,480 patients with acne scarring. Laser + platelet-rich plasma (PRP) ranked best in reducing ECCA scores (surface under cumulative ranking curve to the total area (SUCRA): 98.4%), laser + filler injection ranked best in reducing GBS (SUCRA: 72.1%), and laser + chemical peels ranked the best in patient satisfaction (SUCRA: 89.6%). Microneedling was ranked as the most tolerable in terms of pain (SUCRA: 72.6%). In addition, no strong evidence suggesting a treatment reduced the risk of erythema nor post-inflammatory hyperpigmentation compared to the other treatments. Conclusions The evidence suggests laser combined with PRP or filler injections are the best options for reducing scar severity, while laser combined with chemical peeling yields the best patient satisfaction. Laser combined with other therapies should be considered to optimize treatment of acne scarring.
Wu et al. (2025) Optimal treatment options for acne scars in patients with historic acne: a systematic review and network meta-analysis. PeerJ 13:e19938 https://doi.org/10.7717/peerj.19938
Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis
Background Groundwater is a critical water resource in the Poyang Lake basin, especially given the increasing frequency of extreme drought events. However, comprehensive assessments of its chemical characteristics and associated health risks remain insufficient. This study aims to provide a comprehensive assessment of groundwater quality and associated health risks in the Poyang Lake basin, China. Methods This study collected 670 groundwater samples from domestic and agricultural wells across the basin during the 2022 dry season. Hydrochemical parameters, including manganese (Mn), ammonia nitrogen (NH4+), iron (Fe3+), aluminum (Al3+), chemical oxygen demand (COD), fluoride (F−), and nitrate (NO3−), were analyzed and compared against China’s Class III groundwater quality standards. Spatial variations in water quality were evaluated using the Entropically Weighted Water Quality Index (EWQI). Non-carcinogenic health risks via ingestion and dermal contact pathways were quantified through deterministic risk assessment models, with uncertainty and probability analyzed via Monte Carlo simulations (10,000 iterations). Sensitivity analysis was conducted to identify dominant factors influencing risk outcomes, ensuring a robust probabilistic interpretation of health hazards. Results The results unveils pronounced spatial variability across key hydrochemical parameters: pH ranges from 3.05 to 11.09, total dissolved solids (TDS) from 25.38 to 1,635.21 mg/L, Mn from below detection limits to 19.93 mg/L, COD from below detection limits to 8.57 mg/L, and TH from 9.47 to 905.78 mg/L. A notable proportion of samples breach the Class III groundwater quality standards, with 38% for Mn, 39% for COD, and 15% for NH4+. The Piper diagram analysis categorizes the primary groundwater type as HCO3− -Ca, with a secondary Cl-Ca-Mg type. Through the EWQI assessment, while the overall water quality is deemed acceptable, we identify 56 sites with EWQI values indicative of poor to very poor quality, predominantly influenced by Mn and NH4+. The irrigation risk assessment highlights extensive areas unsuitable for irrigation, particularly within the Ganjiang River basin. Health risk assessments utilizing a deterministic model reveal significant non-carcinogenic risks from F− and NO3− in groundwater, especially for children. However, our Monte Carlo simulation indicates that the probabilities of F− and NO3− posing non-carcinogenic health risks are virtually zero, suggesting that the deterministic assessment may have overestimated the health risks. This study provides critical insights into the groundwater quality and health risks in the Poyang Lake basin and underscores the necessity for targeted water management strategies to mitigate pollution sources and safeguard public health.
Environmental Contamination and Remediation
Chu et al. (2025) Unveiling water quality and health risks from groundwater chemicals in Poyang Lake basin of China: a sophisticated analysis. PeerJ 13:e19937 https://doi.org/10.7717/peerj.19937
From lowlands to highlands: how elevation and habitat complexity drive anuran multidimensional diversity?
Background Montane environments in Neotropical regions are known for their rich diversity of amphibians, but the ecological drivers behind this diversity along altitudinal gradients remain poorly understood. We investigated the effects of the altitudinal range and local environmental variables on the taxonomic, phylogenetic, and functional alpha and beta diversity of anuran assemblages along an altitudinal gradient in the Atlantic Forest of northeastern Brazil. Methods We characterized the richness, abundance, taxonomic, functional, and phylogenetic diversity of anurans in 24 transects within the interior of the forest along an altitudinal range of 200–950 m in the Private Reserve of Natural Heritage (RPPN) Serra Bonita, southern Bahia state, northeastern Brazil. For each transect, we measured the following environmental variables: altitude, leaf litter depth and cover, canopy opening, number of tank-bromeliads, number of trees, and mean air temperature. Results We found 36 anuran species distributed in 10 families. Altitudinal strata plays an important role in explaining anuran abundance, with direct-developing frogs being the most abundant species. The number of tank-bromeliads was interpreted as having the most substantial support to explain the anuran abundance, lineage richness and functional diversity, whereas leaf litter depth influenced the dominant lineages. Additionally, altitude significantly influenced taxonomic and phylogenetic dissimilarity. Lastly, we found an inverse pattern of altitudinal Rapoport’s rule, in which species with optimal altitudes in the highlands exhibit a lower range-size distribution, likely due to habitat specialization or micro-endemism at higher altitudes. Conclusion Altitude significantly influenced the abundance, taxonomic composition, and phylogenetic diversity of anuran communities, with higher elevations supporting a greater number of individuals and distinct evolutionary lineages. In contrast, functional diversity did not vary with altitude, suggesting functional redundancy, where different species perform similar ecological roles, thereby maintaining community resilience. Local factors, such as the number of tank-bromeliads and leaf litter depth, were also key variables shaping community structure. Given the high species turnover and the presence of unique evolutionary lineages, especially in the highlands, conservation efforts should prioritize the protection of the entire montane habitat to sustain the ecological and evolutionary processes that support this exceptional biodiversity. Understanding how species are distributed and identifying the most important filters of anuran diversity along altitudinal gradients in the Atlantic Forest is essential for developing management plans and conservation actions in this threatened region that harbors one of the world’s most remarkable assemblages of anurans.
Dias et al. (2025) From lowlands to highlands: how elevation and habitat complexity drive anuran multidimensional diversity?. PeerJ 13:e19561 https://doi.org/10.7717/peerj.19561
The safety and efficacy of phosphodiesterase type 5 inhibitors in the treatment of diabetic erectile dysfunction: a systematic review and meta-analysis
Background Previous studies have confirmed the efficacy of phosphodiesterase type 5 inhibitors (PDE-5 inhibitors) in treating diabetic erectile dysfunction (DED), but they still have research value in terms of efficacy comparison and individualized safety. This study, while evaluating safety and efficacy, also focused on the sources of heterogeneity and innovatively explored the nonlinear relationship between therapeutic effect and age. Aim This study aimed to systematically evaluate the safety and efficacy of PDE-5 inhibitors for the treatment of DED and the related application effects and to provide a clinical basis for its treatment. Methods By searching PubMed, Embase, Web Of Science, Cochrane Library, China Knowledge Network (CNKI), Wipro (VIP), Wanfang, and China Biomedical Literature Database (CBM) before December 31, 2024, and reading the retrieved articles and references, PDE-5 inhibitors for diabetic erectile dysfunction in randomized controlled trials (RCTs). The literature of the included studies was evaluated using the Cochrane Literature Quality Assessment Tool. The meta-analysis was registered to PROSPERO (CRD42025637725). Outcomes The International Index of Erectile Function (IIEF-5) overall and related evaluation questionnaires were used as the primary efficacy evaluation indicators, and adverse events were used as secondary indicators. Results Meta-analysis was performed using Rever Manager 5.3 and STATA18 software. A total of 10 studies were included, and random-effects model meta-analysis analyzed the post-treatment efficacy of the 10 articles with a combined RR = 2.91, 95% CI of [1.95–4.34], P < 0.001. Fixed-effects model meta-analysis investigated adverse effects with RR = 2.0, 95% CI of [1.53–2.61], P < 0.001. There was a non-linear relationship between age and PDE-5 inhibitors. Conclusion PDE-5 inhibitors can safely and effectively improve diabetic erectile dysfunction, but the degree of effectiveness of different types of drugs, the occurrence of related adverse effects, and the differences that exist between individuals still need to be taken into account during use.
Zhu et al. (2025) The safety and efficacy of phosphodiesterase type 5 inhibitors in the treatment of diabetic erectile dysfunction: a systematic review and meta-analysis. PeerJ 13:e20147 https://doi.org/10.7717/peerj.20147
Comprehensive analysis of DNA methylation patterns in recurrent miscarriage: imprinted/non-imprinted genes and their regulation across sperm and fetal-maternal tissues
Background Epigenetic regulation, including DNA methylation, is essential for normal embryonic development and maternal-fetal interactions. Recurrent miscarriage (RM), defined as the loss of two or more consecutive pregnancies, poses significant clinical and emotional challenges. However, the role of epigenetic alterations in RM, particularly in gametes and placental tissues, remains underexplored. This study aims to investigate global DNA methylation profiles and imprinting gene expression in the context of RM, providing insights into epigenetic mechanisms that contribute to pregnancy failure. Methods Genome-wide DNA methylation profiling was performed on sperm and chorionic villi from RM patients and control couples undergoing artificial abortion using the Illumina HumanMethylation 450 BeadChip platform. Genes related to differentially methylated probes (DMPs) in functionally critical genomic regions, including enhancers, promoters, and DNase hypersensitive sites (DHS), were identified and submitted to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Key imprinting genes (CPA4 and PRDM16) were validated at the protein level using Western blotting. Results RM samples exhibited a significant increase in hypermethylated DMPs across all analyzed tissues, with villi and decidua showing the highest numbers of epigenetic changes. Enrichment analyses highlighted pathways implicated in tissue morphogenesis, immune regulation, and cell signaling, including the PI3K-Akt, TGF-beta, and Wnt signaling pathways. Among imprinting genes, CPA4 and PRDM16 showed distinct hypomethylation at enhancer regions, corresponding to elevated protein expression in RM villi tissues. Conclusions This study identifies profound epigenetic dysregulation in RM-associated tissues, emphasizing the contribution of imprinting gene methylation abnormalities to pregnancy loss. Future studies incorporating functional assays and animal models are essential to elucidate the causal roles of candidate genes in RM pathogenesis and maternal-fetal health.
Niu et al. (2025) Comprehensive analysis of DNA methylation patterns in recurrent miscarriage: imprinted/non-imprinted genes and their regulation across sperm and fetal-maternal tissues. PeerJ 13:e20125 https://doi.org/10.7717/peerj.20125
Sucking lice in bandicoot rats with first complete description of Hoplopleura malabarica nymphs
Background Studies of insect biodiversity and parasitism are often based on adult stages, as immature stages are poorly known and often cannot be identified to species level. However, sucking lice (Anoplura) are permanent, hematophagous parasites with single-host life cycles, making it possible to track the occurrence of all life stages. Only the complete identification of all life stages provides a full picture of parasitism, including infestation levels, parasite topography preferences on the host, and host specificity. The detection of different development stages on a host provides strong evidence that lice of a particular species are actively reproducing and completing their life cycle on that host, making full use of its resources. Conversely, the presence of adult lice alone, particularly when found sporadically, may suggest a failed or incidental attempt at host colonization rather than an established parasitic association. Methodology The description of the nymphal stages of Hoplopleura malabarica is based on specimens of sucking lice from the greater bandicoot rat Bandicota indica from Southeast Asia, specifically from the Vientiane area of Lao PDR. The study used morphometric analysis and scanning microscopy techniques. Results This study presents the first description of the nymphal stages of Hoplopleura malabarica, an oligoxenous parasite of rodents of the genus Bandicota. In addition, a global checklist of Anoplura parasitizing rodents of the genus Bandicota was provided. Conclusions The detection of different life stages of lice within the host confirms that they reproduce and develop on a given host species, fully utilizing its resources.
Kozina et al. (2025) Sucking lice in bandicoot rats with first complete description of Hoplopleura malabarica nymphs. PeerJ 13:e20115 https://doi.org/10.7717/peerj.20115
Transcriptome reveals differential expression of flavor and color in closely related strains of tomato (Solanum lycopersicum)
Fruit flavor and color are critical quality characteristics of tomatoes (Solanum lycopersicum). Numerous studies have demonstrated that tomato flavor is primarily linked to the sugar-acid content and its ratio, while fruit color is predominantly determined by the composition and concentration of carotenoids and flavonoids. To elucidate the regulatory mechanisms underlying the differences in sugar-acid and color formation during fruit ripening, transcriptome analysis was conducted for the first time on the breaker stage (Br) and mature fruit stage (MF) of the closely related strains yellow-fruited tomato (No. 19) and red-fruited tomato (No. 20). This analysis aimed to identify key regulatory genes and biosynthetic pathways associated with the formation of flavor and color in tomato fruits. The transcriptome analysis revealed that 1,546 differentially expressed genes (DEGs) were identified in the Br19_vs_Br20 comparison, of which 507 were up-regulated and 1,039 were down-regulated. In the MF19_vs_MF20 comparison, 2,178 DEGs were detected, with 1,235 up-regulated and 943 down-regulated. Upon further analysis of the DEGs, we identified several key genes in the sugar-acid metabolic pathway, including sucrose synthase (SUS), phosphofructokinase (PFK), fructose-bisphosphate aldolase (FBA), citrate synthase (CS), and succinate dehydrogenase (SuDH), which may significantly influence tomato flavor. Additionally, differential genes related to carotenoid and flavonoid metabolism, such as cytochrome P450 98A (CYP98A), caffeoyl-CoA3-O-methyltransferase (CCoAMT), carotenoid isomerase (CRTISO), lycopene beta cyclase (LCYB), zeaxanthin epoxidase (ZEP), violaxanthin deepoxidase (VDE), and 9-cis-epoxycarotenoid dioxygenase (NCED), as well as genes linked to ethylene synthesis, such as 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), may play a role in the color changes observed in tomatoes. The findings of this study provide insights into the underlying mechanisms of flavor and color development in tomato fruit, offering valuable information for the genetic improvement of tomatoes.
Guo et al. (2025) Transcriptome reveals differential expression of flavor and color in closely related strains of tomato (Solanum lycopersicum). PeerJ 13:e20113 https://doi.org/10.7717/peerj.20113