cpSNP discovery and genotyping for a Pinus taeda breeding population with targeted comparison to related conifers
Pinus taeda (Loblolly pine) is the most important commercial tree species in the southern United States and a significant non-native plantation species in China. Its genetic improvement program has been implemented in South China for 30 years. In this study, the chloroplast (cp) genome of P. taeda was sequenced, assembled, and compared with other available chloroplast genomes of Pin aceae using BLAST. Codon usage among 33 species of Pinaceae was analyzed using the relative synonymous codon usage (RSCU) value. The results were then visualized using the pheatmap v1.0.10 in R. The rates of nonsynonymous (Ka) and synonymous (Ks) substitutions in the chloroplast genomes among five species of Pinus were estimated using the seqinr package in R. Additionally, selected single nucleotide polymorphisms (SNPs) were used to genotype 33 individuals from the P. taeda breeding population. The P. taeda cp genome is 121,530 bp, with certain regions (e.g., ycf1 and ycf2) showing lower sequence conservation compared to other Pinaceae species. Codon usage analysis revealed that codons ending in G or C were not prevalently used, with significant differences in natural selection pressure on chloroplast genes between three species (P. taiwanensis, P. thunbergii, and P. koraiensis) and the other 30 species. Phylogenomic analysis using 36 cp genomes (representing 25 species) resolved Pinus into two subgenera, with P. taeda clustered with P. rigida within the diploxylon pines. Notably, ycf1-based phylogenetic analysis recovered a topology highly congruent (normalized RF = 0.15) with whole-plastome phylogenies. This study validates the single-copy gene ycf1 as a robust and low-cost phylogenetic marker for conifer genus-level reconstruction. The identified SNPs provide valuable molecular markers for genotyping individuals in P. taeda breeding programs, supporting germplasm characterization and management.
Wang et al. (2025) cpSNP discovery and genotyping for a Pinus taeda breeding population with targeted comparison to related conifers. PeerJ 13:e20092 https://doi.org/10.7717/peerj.20092
Eyestalk transcriptome analysis reveals sexually dimorphic host-parasite interactions: divergent molecular strategies of Polyascus sp. for reproductive and growth regulation in Eriocheir sinensis
Background The Chinese mitten crab (Eriocheir sinensis), an economically critical migratory species inhabiting both freshwater and marine environments, is susceptible to parasitization by the rhizocephalan barnacle Polyascus sp. in estuarine ecosystems. In this study, E. sinensis was found to be parasitized by Polyascus sp. in the freshwater waters of the Anqing section of the Yangtze River, which manifested itself as restricted growth and development, hindered gonadal development, and apparent changes in sexual characteristics. Methods Morphological analysis, serological testing, and eyestalk transcriptome analysis were conducted on male and female parasitized and non-parasitized crabs to investigate the molecular mechanisms by which Polyascus sp. affects host growth and reproduction. Results The study revealed that parasitized hosts of both sexes were significantly smaller than normal individuals and exhibited gonadal atrophy. Male hosts displayed feminization of secondary sexual characteristics, whereas females showed no significant alterations. Testosterone and ecdysterone levels decreased in male hosts, whereas estradiol levels declined in female hosts. Transcriptomic profiling revealed differentially expressed genes predominantly associated with metabolic processes, stimulus response, signal transduction, and reproduction. Thirteen key candidate genes related to parasite-induced suppression of host molting and growth, fourteen key candidate genes involved in male reproductive regulation, and ten candidate genes affecting female gonadal development were identified. Key genes involved in gonadal development—including 5-HT1B, CHH, MIH, JHE1, Dmrt family, cytochrome P450 family, Abd-A, and Antp exhibited sex-specific expression patterns. Additionally, critical growth-related genes such as Dib, HR38, and Cht3 exhibited significant alterations in hosts of both sexes. Polyascus sp. parasitism suppresses gonadal development and growth in both sexes, employing distinct regulatory strategies. It uses a “neuroendocrine disruption and reproductive gene regulation” strategy to regulate reproductive development in male hosts, while influencing female reproductive metabolism through a “Nutrient Hijacking-Hormonal Suppression” mechanism. Additionally, the parasitism disrupts host growth via “molting inhibition”. These findings elucidate the sex-specific metabolic, reproductive, and growth disruption strategies of Polyascus sp., providing new insights into host-parasite interactions in decapod crustaceans.
Xie et al. (2025) Eyestalk transcriptome analysis reveals sexually dimorphic host-parasite interactions: divergent molecular strategies of Polyascus sp. for reproductive and growth regulation in Eriocheir sinensis. PeerJ 13:e20089 https://doi.org/10.7717/peerj.20089
Hemodynamic outcomes in patients undergoing bidirectional cavopulmonary connection with additional or antegrade pulmonary blood flow: a single-centre retrospective study
Background The bidirectional cavopulmonary connection (BCPC) is a pivotal stage in the surgical palliation of single-ventricle patients. However, there is ongoing debate regarding the benefits and drawbacks of BCPC with additional or antegrade pulmonary blood flow (AAPBF) in optimizing the subsequent stage—total cavopulmonary connection (TCPC). Objective To determine the influence of BCPC with AAPBF on pulmonary artery growth and hemodynamic outcomes. Methods A retrospective review was conducted of 167 single-ventricle patients who underwent BCPC at Siriraj Hospital between 2006 and 2022. Patients were categorized into two groups based on AAPBF status: group 1 (with AAPBF, n = 44) and group 2 (without AAPBF, n = 123). Variables from pre-BCPC and pre-TCPC cardiac catheterization—including pulmonary artery growth, McGoon ratio, Nakata index, mean pulmonary arterial pressure (mPAP), ventricular end-diastolic pressure (EDP), and indexed pulmonary vascular resistance (PVRi)—were compared between groups. Pulmonary artery branch z-scores were analyzed and adjusted using analysis of covariance (ANCOVA). Survival rate, all-cause mortality, and incidence of atrioventricular valve regurgitation (AVVR) and pulmonary arteriovenous malformation (AVM) were also assessed. Results Median ages at pre-BCPC assessment were 1.06 years (group 1) and 2.17 years (group 2), and at pre-TCPC assessment were 6.19 and 7.27 years, respectively. Median age at BCPC operation was similar between groups (1.58 vs. 1.51 years). Over a median follow-up of 64.33 months, group 1 showed significantly greater increases in right and left pulmonary artery size compared to group 2 (RPA: 3.27 vs. 1.6 mm (p = 0.019); LPA: 2.38 vs. 0.88 mm (p = 0.004)). The Nakata index increased in group 1 but decreased in group 2 (26.70 vs. –84.67 mm2/m2, p < 0.001). Z-scores confirmed significant growth in both pulmonary arteries when adjusted for body surface area (p < 0.001). No significant differences were found in pre-BCPC mPAP (16 vs. 15 mmHg, p = 0.38), EDP (12 vs. 12 mmHg, p = 0.584), or PVRi (1.77 vs. 2.03 WU m2, p = 0.890). Survival rates did not differ significantly between groups (p = 0.350). Conclusions BCPC with AAPBF effectively promotes pulmonary artery growth without adversely affecting ventricular volume loading or pulmonary artery pressure. Further investigation into the development of arteriovenous malformations is recommended.
Puthikitakawiwong et al. (2025) Hemodynamic outcomes in patients undergoing bidirectional cavopulmonary connection with additional or antegrade pulmonary blood flow: a single-centre retrospective study. PeerJ 13:e20021 https://doi.org/10.7717/peerj.20021
NT-proBNP serves as a prognostic marker for adverse outcomes in severe immune checkpoint inhibitor-associated myocarditis
Background Immune checkpoint inhibitors (ICIs) have transformed cancer treatment but carry risks of rare, life-threatening immune-related adverse events, particularly myocarditis. Prognostic biomarkers and optimal management strategies for severe ICI-associated myocarditis remain poorly defined. Methods This single-center retrospective cohort study analyzed 71 patients diagnosed with ICI-associated myocarditis among 7,157 ICI-treated individuals at a tertiary center (August 2018–August 2024). Myocarditis severity was graded per American Society of Clinical Oncology (ASCO) guidelines. Cardiac biomarkers, including NT-proBNP and troponin T, were assessed. Binary logistic regression identified predictors of mortality. Treatment protocols and immunotherapy rechallenge outcomes were evaluated. Results Severe myocarditis (Grades 3–4) occurred in 33 patients (46.5%), with an overall mortality rate of 54.5% in this subgroup (18/33). NT-proBNP levels were significantly elevated in fatal cases versus survivors (median: 13,804 vs. 4,050 pg/mL; P < 0.001) and independently predicted mortality risk (odds ratio (OR) 4.3, 95% confidence interval (CI) [1.2–21.9]; P = 0.023). A multimodal regimen combining plasmapheresis with high-dose corticosteroids, intravenous immunoglobulin, and mycophenolate mofetil was associated with improved survival. Among nine patients rechallenged with immunotherapy, seven (77.8%) tolerated subsequent cycles without recurrent immune toxicity, while two with prior Grade 2 myocarditis experienced symptom recurrence. Discussion Elevated NT-proBNP emerges as a critical prognostic marker for risk stratification in severe ICI-associated myocarditis. Immunotherapy rechallenge appears feasible in select patients but warrants caution in those with prior moderate-grade myocarditis. These findings advocate for biomarker-guided escalation of therapies and shared decision-making frameworks to balance oncologic efficacy with cardiovascular safety.
He et al. (2025) NT-proBNP serves as a prognostic marker for adverse outcomes in severe immune checkpoint inhibitor-associated myocarditis. PeerJ 13:e20020 https://doi.org/10.7717/peerj.20020
Oropharyngeal microbiome dysbiosis in esophageal squamous cell carcinoma: taxonomic shifts, metabolic reprogramming, and geographic disparities in a high-incidence cohort
Background Esophageal squamous cell carcinoma (ESCC) is a leading cause of cancer mortality globally, with pronounced geographic disparities in incidence. Emerging evidence links oral microbiome dysbiosis to ESCC pathogenesis, yet comprehensive insights into microbial diversity, taxonomic shifts, and functional alterations in high-risk populations remain limited. Methods Using 16S rRNA amplicon sequencing, we compared the oral microbiome of ESCC patients and healthy controls from a high-incidence region in Northwest China. Alpha and beta diversity metrics, taxonomic composition, and predicted functional pathways were analyzed to identify microbial signatures associated with ESCC. Results ESCC patients exhibited significantly elevated microbial richness (observed amplicon sequence variants (ASVs), Chao1, ACE; p < 0.05) but comparable Shannon/Simpson diversity to controls. Unique amplicon sequence variants (ASVs) were more prevalent in ESCC samples, and principal component analysis confirmed distinct community structures (p < 0.05). Taxonomically, Streptococcus and Neisseria dominated both groups, but ESCC patients showed enrichment of Gemella (p = 0.0003) and Corynebacterium (p < 0.00001), alongside depletion of Prevotella_7 (p = 0.0002) and Moraxella (p < 0.001). Functional profiling revealed upregulated amino acid metabolism (e.g., beta-alanine and valine degradation) and downregulated carbohydrate metabolism in ESCC-associated microbiota. Conclusion This study uncovers unique oral microbial signatures in ESCC patients from a high-incidence region, characterized by increased richness, taxon-specific shifts, and metabolic reprogramming favoring amino acid catabolism. These findings highlight the potential of microbial biomarkers for ESCC detection and provide mechanistic insights into microbiome-driven carcinogenesis. The geographic specificity of the cohort underscores the urgency of tailored interventions in high-risk populations and advances our understanding of microbial contributions to esophageal cancer.
Liu et al. (2025) Oropharyngeal microbiome dysbiosis in esophageal squamous cell carcinoma: taxonomic shifts, metabolic reprogramming, and geographic disparities in a high-incidence cohort. PeerJ 13:e20009 https://doi.org/10.7717/peerj.20009
The 12-LOX/12-HETE/GPR31 metabolic pathway promotes tumor-associated macrophage M2 polarization mediated pancreatic cancer development
Background The 12-lipoxygenase (12-LOX)/12-hydroxyeicosatetraenoic acid (12-HETE) pathway is associated with various tumors. M2 macrophages in the tumor microenvironment promote tumorigenesis and progression. However, the role of the 12-LOX/12-HETE/G protein-coupled receptor 31 (GPR31) metabolic pathway and its relationship with M2 macrophages remains unclear in pancreatic cancer (PC). Methods The expression levels of 12-LOX, GPR31, and 12-HETE were detected in PC and mouse PC models using western blot and enzyme-linked immunosorbent assays (ELISA). In vivo and in vitro experiments were conducted using the 12-LOX inhibitor ML355 to investigate the role of the 12-LOX/12-HETE/GPR31 metabolic pathway in M2 macrophage polarization and tumor progression through flow cytometry, reverse transcription polymerase chain reaction (RT-PCR), 5-Ethynyl-20-deoxyuridine (EdU) assays, and Transwell experiments. Results The 12-LOX/12-HETE/GPR31 metabolic pathway is expressed actively in PC. Inhibition of 12-LOX in a mouse model of pancreatic cancer suppressed the expression of this metabolic pathway, retarded tumor growth, and reduced the polarization of macrophages towards the M2 type. In vitro, co-culturing PC cell line PANC-1 with macrophages and selectively inhibiting 12-LOX influenced the proliferation, migration, and invasion of PC cells. Inhibiting 12-LOX did not suppress the function of individual PC cells, but it inhibited the development of PC cells co-cultured with macrophages. Moreover, inhibiting 12-LOX reduced the co-cultured M2 macrophages. Conclusion This study, through in vivo and in vitro experiments, reveals that the 12-LOX/12-HETE/GPR31 metabolic pathway affects the growth, migration, and invasion of PC by modulating M2 macrophage polarization patterns.
Yang et al. (2025) The 12-LOX/12-HETE/GPR31 metabolic pathway promotes tumor-associated macrophage M2 polarization mediated pancreatic cancer development. PeerJ 13:e19963 https://doi.org/10.7717/peerj.19963
The BAF53A-BACH1-GCLM axis regulates glutathione metabolism and enhances ferroptosis resistance in esophageal squamous cell carcinoma
Objective Esophageal squamous cell carcinoma (ESCC), a highly lethal malignancy, exhibits poor survival rates and limited treatment options. Ferroptosis, a regulated form of cell death driven by lipid peroxidation, emerges as a potential therapeutic target. However, the mechanisms suppressing ferroptosis in ESCC remain poorly understood. Methods Short hairpin RNA (shRNA) was employed to knock down BAF53A and BACH1 in ESCC cell lines, followed by assessments of cell proliferation, colony formation, and ferroptosis sensitivity. Glutathione (GSH) metabolism was evaluated by measuring GSH/GSSG and NADP+/NADPH ratios, reactive oxygen species (ROS) levels, and lipid peroxidation through flow cytometry and fluorescence imaging. Molecular interactions were evaluated using co-immunoprecipitation and chromatin immunoprecipitation sequencing (ChIP-seq) to identify transcriptional targets of the BAF53A-BACH1 complex. Results BAF53A was elevated in ESCC, and its depletion impaired cell proliferation and colony formation ability of cells. Knockdown of BAF53A disrupted GSH metabolism, leading to increased ROS levels, reduced GSH/GSSG and NADP+/NADPH ratios, and enhanced ferroptosis sensitivity. Mechanistically, BAF53A collaborated with BACH1 to transcriptionally activate glutamate-cysteine ligase modifier subunit (GCLM), a key enzyme in GSH biosynthesis. Overexpression of GCLM restored redox balance and cell viability in BAF53A- or BACH1-silenced cells. Conclusions The BAF53A-BACH1-GCLM axis constitutes a novel egulatory pathway that integrates chromatin remodeling, transcriptional regulatione, and ferroptosis resistance in ESCC. Targeting this axis may offer a promising approach to exploit metabolic vulnerabilities and enhance ferroptosis sensitivity in ESCC treatment.
Jiang et al. (2025) The BAF53A-BACH1-GCLM axis regulates glutathione metabolism and enhances ferroptosis resistance in esophageal squamous cell carcinoma. PeerJ 13:e20156 https://doi.org/10.7717/peerj.20156
The association between ADIPOQ gene variants (rs266729, rs2241766, rs1501299) and acute myocardial infarction in Vietnamese patients with type 2 diabetes mellitus
Background Type 2 diabetes mellitus (T2DM) significantly increases the risk of acute myocardial infarction (AMI). Polymorphisms in the ADIPOQ gene, which encodes the adiponectin hormone, are believed to influence cardiovascular disease risk. This study aims to evaluate the association between three ADIPOQ gene variants—rs266729, rs2241766, and rs1501299—and the risk of AMI in Vietnamese patients with T2DM. Methods A case–control study was conducted from January 2023 to June 2024 at the University Medical Center, Ho Chi Minh City. The study included 275 T2DM patients with a history of AMI (case group) and 275 T2DM patients without AMI (control group). Participants were matched by age, gender, smoking status, and duration of T2DM to control for potential confounding factors. DNA was extracted from peripheral blood samples, and the three polymorphisms were genotyped using Sanger sequencing. Results Significant associations were found between ADIPOQ gene polymorphisms and AMI risk. The G/G genotype of rs266729 and the T/T genotype of rs1501299 were associated with a reduced risk of AMI (OR = 0.45, 95% CI [0.23–0.89], p = 0.021; OR = 0.45, 95% CI [0.22–0.90], p = 0.025, respectively). In contrast, the T/G genotype of rs2241766 was significantly associated with an increased risk of AMI (OR = 2.07, 95% CI [1.44–2.97], p < 0.001). Conclusion This study suggests that rs266729 and rs1501299 may have protective effects, while rs2241766 may increase the risk of AMI in Vietnamese patients with T2DM. These findings highlight the importance of further research into adiponectin levels and long-term monitoring, and support the potential use of genetic variants in personalized cardiovascular risk management for patients with T2DM.
Le et al. (2025) The association between ADIPOQ gene variants (rs266729, rs2241766, rs1501299) and acute myocardial infarction in Vietnamese patients with type 2 diabetes mellitus. PeerJ 13:e20145 https://doi.org/10.7717/peerj.20145
Optimizing legume green manure applications for enhanced forage sorghum-sudangrass performance and soil property improvements
Background Legume-based green manuring is an environmentally sustainable and economically viable approach that enhances soil fertility by improving organic matter content, facilitating biological nitrogen fixation, and stimulating microbial activity. These benefits collectively reduce reliance on mineral fertilizers, which are associated with environmental degradation. While the soil-enhancing properties of legumes are well-established, limited information is available regarding how the timing of green manure incorporation affects the growth performance and forage quality of subsequent crops. This study aimed to assess the effects of incorporating different legume species at various phenological stages on the growth, yield, and forage quality of sorghum × sudangrass under Mediterranean climatic conditions. Methods A field experiment was conducted from 2022 to 2024 at Aydın Adnan Menderes University, Türkiye, using a randomized complete block design with three replicates. Eleven treatments were implemented, consisting of three legume species (common vetch, narbon vetch, and forage pea) incorporated at three distinct phenological stages (pre-flowering, 10% flowering, and full flowering), along with unfertilized and fertilized controls. Following incorporation, sorghum × sudangrass was sown without additional fertilization, except in the fertilized control. Key response variables included fresh forage yield (FFY), hay yield (HY), plant height, leaf number, leaf area index (LAI), chlorophyll content (SPAD), and crude protein yield (CPY). Soil organic matter and total nitrogen levels were also measured before and after treatments. Results Green manure application significantly enhanced the growth, biomass accumulation, and forage quality of sorghum × sudangrass. The incorporation of common vetch and narbon vetch at the 10% flowering stage led to up to a 50% increase in fresh forage yield compared to the unfertilized control. Forage pea maintained consistent yield performance across all incorporation stages. Improvements in soil organic matter and nitrogen content were particularly notable in legume-amended plots. Furthermore, the highest SPAD and LAI values were recorded at early flowering stages, suggesting enhanced photosynthetic efficiency. These findings underscore the effectiveness of legume green manuring, particularly with optimal incorporation timing, as a sustainable strategy to improve soil health, forage productivity, and resource-use efficiency in Mediterranean agroecosystems.
Kara (2025) Optimizing legume green manure applications for enhanced forage sorghum-sudangrass performance and soil property improvements. PeerJ 13:e20137 https://doi.org/10.7717/peerj.20137
Reconstruction of masked sequences via inverse mapping of incomplete information natural vectors
Alignment-free embedding methods, which map biological sequences into a fixed-dimensional space using mathematical techniques, hold significant value in biology. A key challenge in this field is constructing an inverse mapping to recover sequences from embedded vectors. The natural vector approach uniquely provides a theoretical one-to-one correspondence between sequences and high-order natural vectors, but reconstructing sequences from lower-order vectors remains unsolved. Moreover, when sequences contain masked regions, extracting features and constructing the inverse mapping to restore the original sequence, including the masked parts, becomes even more challenging. In this article, we define incomplete information natural vectors for masked sequences and develop a long short-term memory model that achieves over 99.9% accuracy in reconstructing unmasked positions in original sequences on SARS-CoV-2 and HIV-1 datasets, while also providing predictions for masked sites that significantly outperform random prediction. Our model can robustly handle sequences with varying masked nucleotides. Overall, our approach expands the scope of alignment-free embedding methods by enabling bidirectional conversion and addressing challenges posed by incomplete information.
Ding et al. (2025) Reconstruction of masked sequences via inverse mapping of incomplete information natural vectors. PeerJ 13:e20126 https://doi.org/10.7717/peerj.20126