Single-cell transcriptome analysis reveals cellular reprogramming and changes of immune cell subsets following tetramethylpyrazine treatment in LPS-induced acute lung injury
Background Acute lung injury (ALI) is a disordered pulmonary disease characterized by acute respiratory insufficiency with tachypnea, cyanosis refractory to oxygen and diffuse alveolar infiltrates. Despite increased research into ALI, current clinical treatments lack effectiveness. Tetramethylpyrazine (TMP) has shown potential in ALI treatment, and understanding its effects on the pulmonary microenvironment and its underlying mechanisms is imperative. Methods We established a mouse model of lipopolysaccharide (LPS)-induced ALI and performed single cell RNA sequencing (scRNA-seq). Bioinformatic analyses of the immune, epithelial and endothelial cells were then performed to explore the dynamic changes of the lung tissue microenvironment. We also analyzed the effects of TMP on the cell subtypes, differential gene expression and potential regulation of transcriptional factors involved. Immunohistochemistry and enzyme-linked immunosorbent assay were performed to identify the effects of TMP on immune inflammatory response. Results We found that TMP efficiently protected against LPS-induced acute lung injury. Results of scRNA-seq showed that the cells were divided into seven major cell clusters, including immune cells, fibroblasts, endothelial cells and epithelial cells. Neither dexamethasone (Dex) nor TMP treatment showed any significant protective effects in these clusters. However, TMP treatment in the LPS-induced ALI model significantly increased follicular helper T cells and reduced CD8+ naive T cells, Vcan-positive monocytes and Siva-positive NK cells. In addition, TMP treatment increased the number of basal epithelial cells and lymphatic endothelial cells (LECs), indicating its protective effects on these cell types. Scenic analysis suggested that TMP likely mitigates LPS-induced injury in epithelial and endothelial cells by promoting FOSL1 in basal epithelial cells and JunB in LECs. Conclusions Our findings suggest that TMP appears to alleviate LPS-induced lung injury by regulating the immune response, promoting epithelial cell survival and boosting the antioxidant potential of endothelial cells. This study highlights the potential therapeutic use of TMP in the management of ALI.
Wu et al. (2025) Single-cell transcriptome analysis reveals cellular reprogramming and changes of immune cell subsets following tetramethylpyrazine treatment in LPS-induced acute lung injury. PeerJ 13:e18772 https://doi.org/10.7717/peerj.18772
Unveiling the complex double-edged sword role of exosomes in nasopharyngeal carcinoma
Nasopharyngeal carcinoma (NPC) is a malignancy arising from the epithelium of the nasopharynx. Given its late diagnosis, NPC raises serious considerations in Southeast Asia. In addition to resistance to conventional treatment that combines chemotherapy and radiation, NPC has high rates of metastasis and frequent recurrence. Exosomes are small membrane vesicles at the nanoscale that transport physiologically active compounds from their source cell and have a crucial function in signal transmission and intercellular message exchange. The exosomes detected in the tissues of NPC patients have recently emerged as a potential non-invasive liquid biopsy biomarker that plays a role in controlling the tumor pathophysiology. Here, we take a look back at what we know so far about the complex double-edged sword role of exosomes in NPC. Exosomes could serve as biomarkers and therapeutic agents, as well as the molecular mechanisms by which they promote cell growth, angiogenesis, metastasis, immunosuppression, radiation resistance, and chemotherapy resistance in NPC. Furthermore, we go over some of the difficulties and restrictions associated with exosome use. It is anticipated that this article would provide the reference for the apply of exosomes in clinical practice.
Huang et al. (2025) Unveiling the complex double-edged sword role of exosomes in nasopharyngeal carcinoma. PeerJ 13:e18783 https://doi.org/10.7717/peerj.18783
To stay or to go: resource diversity alters the dispersal behavior of sympatric cryptic marine nematodes
Animals can use specific environmental cues to make informed decisions about whether and where to disperse. Patch conditions are known to affect the dispersal behavior of animals, but empirical studies investigating the impact of resource diversity on the dispersal of closely related species are largely lacking. In this study, we investigated how food diversity affects the dispersal behavior of three co-occurring cryptic species of the marine bacterivorous nematode complex Litoditis marina (Pm I, Pm III and Pm IV). Using microcosms composed of a local patch (inoculation plate), a connection tube, and a distant patch (dispersal plate), we examined nematode dispersal patterns with bacteria serving as the food source. Food treatments included low-, medium-, and high-diversity bacterial mixtures of 5, 10, and 15 bacterial strains, respectively. Additionally, a single-strain food resource Escherichia coli was used as a control treatment. Both local and distant patches had either identical food treatments (‘homogeneous patches’) or E. coli in the local patches and more diverse food (low-, medium-, or high-diversity food) in distant patches (‘heterogeneous patches’). Our results show that the dispersal behavior of the cryptic species varies depending on food diversity, indicating that L. marina acquire information about their environment when making dispersal decisions. All three cryptic species tend to disperse faster toward food patches that increase fitness. Pm I and Pm IV exhibited faster dispersal toward patches with a more diverse food source, while Pm III showed similar dispersal rates toward E. coli, medium-diversity, and high-diversity food. This indicates that resource diversity can alter the dispersal behavior of cryptic species and may be an important mechanism to achieve species coexistence in the field.
Guden et al. (2025) To stay or to go: resource diversity alters the dispersal behavior of sympatric cryptic marine nematodes. PeerJ 13:e18790 https://doi.org/10.7717/peerj.18790
Social presence effect in language comprehension: evidence from event-related potential (ERP) research
Objective This study aimed to examine the impact of social presence on Chinese reading comprehension and associated neural responses. Methods Participants tasked with reading Chinese sentences either alone or in the presence of others and subsequently assessing the accuracy of the sentences’ meanings. Concurrently, we recorded the participants’ electrical brain responses to critical word processing. Results Behavioral results indicated no significant effect of social presence on the judgment of sentence accuracy. Electroencephalogram (EEG) results, however, revealed that reading in the presence of others elicited more pronounced left anterior negativity (LAN) components in the left front of the scalp compared to reading alone. Additionally, incorrect meanings triggered larger N400 and P600 amplitudes in the mid-parietal region than correct meanings. Conclusion Social presence intensifies early neural responses during the reading of Chinese sentences, although it does not influence semantic integration or conflict resolution. These findings support the notion that social context affects language processing.
Yu et al. (2025) Social presence effect in language comprehension: evidence from event-related potential (ERP) research. PeerJ 13:e18798 https://doi.org/10.7717/peerj.18798
Effects of tropical fruit blends on fermentative and pigmentation aspects of probiotic native cultured goat milk
Background Fruits are sources of bioactive compounds such as phenolics that bring health benefits to consumers. The addition of fruit products and microorganisms with probiotic potential in fermented goat milk can facilitate the acquisition of these benefits through diet. In this sense, the objective of this study was to evaluate the effect of incorporating a mixture of ingredients from jaboticaba (Myrciaria cauliflora), jambolana (Syzygium cumini), and mandacaru (Cereus jamacaru) fruits on fermentation parameters (pH, titratable acidity, viability of the native culture Lactiplantibacillus plantarum CNPC003 and the starter culture), associated with pigmentation (phenolic compound content and color) through experimental mixture design. Methods A simplex-centroid experimental design was conducted, comprised of seven trials totaling the addition of 30% of the fruit preparations in the final formulation of fermented milk and one control trial (without addition of preparations), with the response being the total phenolic content and the instrumental color parameter a*. Fermentations were carried out with the addition of the native culture Lactiplantibacillus plantarum CNPC003 and the starter culture Streptococcus thermophilus. Subsequently, analyses of pH, titratable acidity, viability of the native and starter cultures, total phenolic compound content, and the instrumental color parameter a* were performed. Results The final pH among trials ranged from 4.55 to 4.69, titratable acidity ranged from 0.59 to 0.64, the population of L. plantarum CNPC003 reached levels exceeding 8 log CFU/g, as did the population of Streptococcus thermophilus. The content of phenolic compounds was higher in trials T1, T5, and T7, as well as the color parameter (a*). The use of experimental mixture design contributed to the development of products with high viability of L. plantarum, high content of phenolic compounds, and a characteristic color of the added fruits, bringing benefits to consumer health.
Isadora Kaline Camelo Pires de Oliveira Galdino
© 2025 Kaline Camelo Pires de Oliveira Galdino et al.
Oliveira Galdino et al. (2025) Effects of tropical fruit blends on fermentative and pigmentation aspects of probiotic native cultured goat milk. PeerJ 13:e18813 https://doi.org/10.7717/peerj.18813
©2025 Kaline Camelo Pires de Oliveira Galdino et al.
Kaline Camelo Pires de Oliveira Galdino et al.
Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence
Acer palmatum is a deciduous shrub or small tree. It is a popular ornamental plant because of its beautiful leaves, which change colour in autumn. This study revealed 116 ApNAC genes within the genome of A. palmatum. These genes are unevenly distributed on the 13 chromosomes of A. palmatum. An analysis of the phylogenetic tree of Arabidopsis thaliana NAC family members revealed that ApNAC proteins could be divided into 16 subgroups. A comparison of ApNAC proteins with NAC genes from other species suggested their potential involvement in evolutionary processes. Studies suggest that tandem and segmental duplications may be key drivers of the expansion of the ApNAC gene family. Analysis of the transcriptomic data and qRT‒PCR results revealed significant upregulation of most ApNAC genes during autumn leaf senescence compared with their expression levels in summer leaves. Coexpression network analysis revealed that the expression profiles of 10 ApNAC genes were significantly correlated with those of 200 other genes, most of which are involved in plant senescence processes. In conclusion, this study contributes to elucidating the theoretical foundation of the ApNAC gene family and provides a valuable basis for future investigations into the role of NAC genes in regulating leaf senescence in woody ornamental plants.
Meng et al. (2025) Genome-wide analyses of the NAC transcription factor gene family in Acer palmatum provide valuable insights into the natural process of leaf senescence. PeerJ 13:e18817 https://doi.org/10.7717/peerj.18817
The impact of induced stress on reactive and proactive control in depression
Background Depression, a widespread mental health issue, is often marked by impaired cognitive control, particularly in managing proactive and reactive processes. The Dual Mechanisms of Control (DMC) framework differentiates between these two modes of cognitive control: proactive control involves sustained goal maintenance, while reactive control is more stimulus-driven and transient. Stress, known to exacerbate cognitive dysfunction in depression, may influence the balance between these control processes, though the specific effects remain poorly understood. This study aimed to investigate how acute stress influences proactive and reactive control in individuals with depressive symptoms. Methods A total of 142 participants were divided into high-stress and control conditions and further categorized based on their depression levels, measured using the Beck Depression Inventory-II (BDI-II). Cognitive control was assessed using the AX-Continuous Performance Task (AX-CPT), both before and after exposure to a stress-inducing anagram task, which was designed to differentiate between high-stress and low-stress conditions. Results Participants exposed to the high-stress condition reported significantly greater stress and fatigue levels compared to the control group, validating the stress manipulation. Although the balance between reactive and proactive control, as measured by the Proactive Behavioral Index (PBI), did not show significant changes, depressive individuals in the high-stress condition exhibited a significant decline in their ability to retain contextual information, as indicated by a reduction in the d’-context index. This suggests that depressive individuals may be more prone to stress-induced difficulties in proactive control. Discussion These findings highlight the selective impact of stress on proactive cognitive control in individuals with depressive symptoms, shedding light on a potential cognitive vulnerability in depression. While the balance between reactive and proactive control remained stable, the impaired retention of contextual information post-stress points to a specific deficit in proactive control. This could have implications for targeted cognitive interventions, such as cognitive control training, aimed at enhancing resilience against stress in depressive populations. Future research should explore the long-term effects of stress on cognitive control, particularly in clinically diagnosed individuals.
Masuyama (2025) The impact of induced stress on reactive and proactive control in depression. PeerJ 13:e18821 https://doi.org/10.7717/peerj.18821
Genome-wide association study on color-image-based convolutional neural networks
Background Convolutional neural networks have excellent modeling abilities to complex large-scale datasets and have been applied to genomics. It requires converting genotype data to image format when employing convolutional neural networks to genome-wide association studies. Existing studies converting the data into grayscale images have shown promising. However, the grayscale image may cause the loss of information of the genotype data. Methods In order to make full use of the information, we proposed a new method, color-image-based convolutional neural networks, by converting the data into color images. Results The experiments on simulation and real data show that our method outperforms the existing methods proposed by Yue and Chen for converting data into grayscale images, in which the model accuracy is improved by an average of 7.61%, and the ratio of disease risk genes is increased by an average of 18.91%. The new method has better robustness and generalized performance.
Liu et al. (2025) Genome-wide association study on color-image-based convolutional neural networks. PeerJ 13:e18822 https://doi.org/10.7717/peerj.18822
Cloning and functional verification of Geraniol-10-Hydroxylase gene in Lonicera japonica
Background Geraniol 10-hydroxylase (G10H) is a cytochrome P450 monooxygenase involved in regulation, which is involved in the biosynthesis of monoterpene. However, G10H is not characterized at the enzymatic mechanism and regulatory function in Lonicera japonica. Methods and Results A gene related to the biosynthesis of monoterpenoid, geraniol 10-hydroxylase, has been cloned from the medicinal plant Lonicera japonica. The gene, LjG10H, encodes a peptide of 498 amino acids with a predicted molecular weight of 54.45 kDa. LjG10H shares a homology of 72.93–83.90% with G10H from other plants. Phylogenetic analysis suggests that the protein encoded by this gene belongs to the cytochrome P450 monooxygenase family. Tissue-specific expression analysis revealed that LjG10H is most highly expressed in flowers. Through heterologous expression in E. coli, the LjG10H protein was purified and its catalytic activity was studied. The results show that the enzyme can catalyze the hydroxylation of geraniol to 10-hydroxygeraniol. Additionally, analysis of Lonicera japonica seedlings with silenced LjG10H revealed a reduction in monoterpenoid content. Conclusions This study demonstrates that LjG10H plays an important role in the biosynthetic pathway of iridoids. This is the first article that ascribes G10H to be associated with the biosynthetic pathway of iridoid. This study provides a theoretical basis for the functional mechanism of LjG10H in regulating iridoid synthesis and provides a valuable resource for molecular breeding studies.
Zhang et al. (2025) Cloning and functional verification of Geraniol-10-Hydroxylase gene in Lonicera japonica. PeerJ 13:e18832 https://doi.org/10.7717/peerj.18832
Association between maternal rectovaginal group B streptococcus and the risk of stillbirth: a meta-analysis
Background Group B streptococcus (GBS) colonization in pregnant women is associated with adverse perinatal outcomes, including stillbirth. This meta-analysis investigated the relationship between maternal rectovaginal GBS colonization and the risk of stillbirth. Methods We conducted a comprehensive literature search across several databases, including PubMed, Embase, Web of Science, Wanfang, and China National Knowledge Infrastructure, covering studies published from the inception of the database until September 9, 2024. The search focused on observational studies comparing the risk of stillbirth in pregnant women with and without rectovaginal GBS colonization. Results were summarized using odds ratios (ORs) and 95% confidence intervals (CIs), and a random-effects model was used to account for potential heterogeneity. Results A total of ten studies comprising 121,195 pregnant women were included in the analysis. The pooled results indicated no significant overall association between maternal rectovaginal GBS colonization and the risk of stillbirth (OR: 1.66, 95% CI [0.95–2.91], p = 0.08; I2 = 84%). However, sensitivity analyses revealed a significant association in studies that included intrapartum antibiotic prophylaxis (IAP) (OR: 1.36, 95% CI [1.02–1.80], p = 0.03). Subgroup analyses demonstrated a significant association between maternal rectovaginal GBS colonization and stillbirth risk in retrospective studies (OR: 2.62, p = 0.04) and in studies employing multivariate analysis (OR: 2.11, p = 0.04). Conclusions While the meta-analysis did not find a significant overall association between maternal rectovaginal GBS colonization and stillbirth, significant associations were noted under specific conditions, such as studies using IAP, retrospective designs, and multivariate analyses. Further research is needed to clarify these associations.
Wang et al. (2025) Association between maternal rectovaginal group B streptococcus and the risk of stillbirth: a meta-analysis. PeerJ 13:e18834 https://doi.org/10.7717/peerj.18834