Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients
Background Stroke is a disease with high morbidity, disability, and mortality. Immune factors play a crucial role in the occurrence of ischemic stroke (IS), but their exact mechanism is not clear. This study aims to identify possible immunological mechanisms by recognizing immune-related biomarkers and evaluating the infiltration pattern of immune cells. Methods We downloaded datasets of IS patients from GEO, applied R language to discover differentially expressed genes, and elucidated their biological functions using GO, KEGG analysis, and GSEA analysis. The hub genes were then obtained using two machine learning algorithms (least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE)) and the immune cell infiltration pattern was revealed by CIBERSORT. Gene-drug target networks and mRNA-miRNA-lncRNA regulatory networks were constructed using Cytoscape. Finally, we used RT-qPCR to validate the hub genes and applied logistic regression methods to build diagnostic models validated with ROC curves. Results We screened 188 differentially expressed genes whose functional analysis was enriched to multiple immune-related pathways. Six hub genes (ANTXR2, BAZ2B, C5AR1, PDK4, PPIH, and STK3) were identified using LASSO and SVM-RFE. ANTXR2, BAZ2B, C5AR1, PDK4, and STK3 were positively correlated with neutrophils and gamma delta T cells, and negatively correlated with T follicular helper cells and CD8, while PPIH showed the exact opposite trend. Immune infiltration indicated increased activity of monocytes, macrophages M0, neutrophils, and mast cells, and decreased infiltration of T follicular helper cells and CD8 in the IS group. The ceRNA network consisted of 306 miRNA-mRNA interacting pairs and 285 miRNA-lncRNA interacting pairs. RT-qPCR results indicated that the expression levels of BAZ2B, C5AR1, PDK4, and STK3 were significantly increased in patients with IS. Finally, we developed a diagnostic model based on these four genes. The AUC value of the model was verified to be 0.999 in the training set and 0.940 in the validation set. Conclusion Our research explored the immune-related gene expression modules and provided a specific basis for further study of immunomodulatory therapy of IS.
Cong et al. (2024) Discovery and validation of molecular patterns and immune characteristics in the peripheral blood of ischemic stroke patients. PeerJ 12:e17208 https://doi.org/10.7717/peerj.17208
Exogenous Hemin enhances the antioxidant defense system of rice by regulating the AsA-GSH cycle under NaCl stress
Abiotic stress caused by soil salinization remains a major global challenge that threatens and severely impacts crop growth, causing yield reduction worldwide. In this study, we aim to investigate the damage of salt stress on the leaf physiology of two varieties of rice (Huanghuazhan, HHZ, and Xiangliangyou900, XLY900) and the regulatory mechanism of Hemin to maintain seedling growth under the imposed stress. Rice leaves were sprayed with 5.0 μmol·L−1 Hemin or 25.0 μmol·L−1 ZnPP (Zinc protoporphyrin IX) at the three leaf and one heart stage, followed by an imposed salt stress treatment regime (50.0 mmol·L−1 sodium chloride (NaCl)). The findings revealed that NaCl stress increased antioxidant enzymes activities and decreased the content of nonenzymatic antioxidants such as ascorbate (AsA) and glutathione (GSH). Furthermore, the content of osmoregulatory substances like soluble proteins and proline was raised. Moreover, salt stress increased reactive oxygen species (ROS) content in the leaves of the two varieties. However, spraying with Hemin increased the activities of antioxidants such as superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) and accelerated AsA-GSH cycling to remove excess ROS. In summary, Hemin reduced the effect of salt stress on the physiological characteristics of rice leaves due to improved antioxidant defense mechanisms that impeded lipid peroxidation. Thus, Hemin was demonstrated to lessen the damage caused by salt stress.
Meng et al. (2024) Exogenous Hemin enhances the antioxidant defense system of rice by regulating the AsA-GSH cycle under NaCl stress. PeerJ 12:e17219 https://doi.org/10.7717/peerj.17219
Inhibition of SUV39H1 reduces tumor angiogenesis via Notch1 in oral squamous cell carcinoma
Targeting tumor angiogenesis is an important approach in advanced tumor therapy. Here we investigated the effect of the suppressor of variegation 3–9 homolog 1 (SUV39H1) on tumor angiogenesis in oral squamous cell carcinoma (OSCC). The GEPIA database was used to analyze the expression of SUV39H1 in various cancer tissues. The expression of SUV39H1 in OSCC was detected by immunohistochemistry, and the correlation between SUV39H1 and Notch1 and microvascular density (MVD) was analyzed. The effect of SUV39H1 inhibition on OSCC was investigated in vivo by chaetocin treatment. The migration and tube formation of vascular endothelial cells by conditioned culture-medium of different treatments of oral squamous cell cells were measured. The transcriptional level of SUV39H1 is elevated in various cancer tissues. The transcription level of SUV39H1 in head and neck squamous cell carcinoma was significantly higher than that in control. Immunohistochemistry result showed increased SUV39H1 expression in OSCC, which was significantly correlated with T staging. The expression of SUV39H1 was significantly correlated with Notch1 and CD31. In vivo experiment chaetocin treatment significantly inhibit the growth of tumor, and reduce SUV39H1, Notch1, CD31 expression. The decreased expression of SUV39H1 in OSCC cells lead to the decreased expression of Notch1 and VEGF proteins, as well as the decreased migration and tube formation ability of vascular endothelial cells. Inhibition of Notch1 further enhance this effect. Our results suggest inhibition of SUV39H1 may affect angiogenesis by regulating Notch1 expression. This study provides a foundation for SUV39H1 as a potential therapeutic target for OSCC.
Chen et al. (2024) Inhibition of SUV39H1 reduces tumor angiogenesis via Notch1 in oral squamous cell carcinoma. PeerJ 12:e17222 https://doi.org/10.7717/peerj.17222
Unveiling the aesthetic secrets: exploring connections between genetic makeup, chemical, and environmental factors for enhancing/improving the color and fragrance/aroma of Chimonanthus praecox
Floral color and scent profiles vary across species, geographical locations, and developmental stages. The exclusive floral color and fragrance of Chimonanthus praecox is contributed by a range of endogenous chemicals that distinguish it from other flowers and present amazing ornamental value. This comprehensive review explores the intricate interplay of environmental factors, chemicals and genes shaping the flower color and fragrance of Chimonanthus praecox. Genetic and physiological factors control morpho-anatomical attributes as well as pigment synthesis, while environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Specific genes control pigment synthesis, and environmental factors such as temperature, light intensity, and soil composition influence flower characteristics. Physiological processes including plant hormone contribute to flower color and fragrance. Hormones, notably ethylene, exert a profound influence on varioustraits. Pigment investigations have spotlighted specific flavonoids, including kaempferol 3-O-rutinoside, quercetin, and rutin. Red tepals exhibit unique composition with cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside being distinctive components. Elucidating the molecular basis of tepal color variation, particularly in red and yellow varieties, involves the identification of crucial regulatory genes. In conclusion, this review unravels the mysteries of Chimonanthus praecox, providing a holistic understanding of its flower color and fragrance for landscape applications. This comprehensive review uniquely explores the genetic intricacies, chemical and environmental influences that govern the mesmerizing flower color and fragrance of Chimonanthus praecox, providing valuable insights for its landscape applications. This review article is designed for a diverse audience, including plant geneticists, horticulturists, environmental scientists, urban planners, and students, offering understandings into the genetic intricacies, ecological significance, and practical applications of Chimonanthus praecox across various disciplines. Its appeal extends to professionals and enthusiasts interested in plant biology, conservation, and industries dependent on unique floral characteristics.
Zhao et al. (2024) Unveiling the aesthetic secrets: exploring connections between genetic makeup, chemical, and environmental factors for enhancing/improving the color and fragrance/aroma of Chimonanthus praecox. PeerJ 12:e17238 https://doi.org/10.7717/peerj.17238
Meta-analysis of the correlation between pulmonary hypertension and echocardiographic parameters in patients with chronic kidney disease
Objective To investigate the correlation between pulmonary hypertension (PH) and echocardiographic parameters in patients with chronic kidney disease (CKD). Methods PubMed, Embase, Web of Science, Cochrane, VIP, CNKI, and Wanfang databases were systematically searched for articles published from inception to 19 May 2023. Study quality was estimated using the Quality Assessment of Case-Control Studies tool. Forest plots were drawn using R language software. The “metacor” function in the “meta” package was utilized for meta-analysis of the r-values and their standard errors. Heterogeneity and sensitivity analyses were carried out, with the main outcomes as r-value, p-value, and I2 value. Results Eleven studies were included, with 1,809 CKD patients. The correlations between 12 echocardiographic parameters and PH were analyzed. Except for FS and LVEF which were negatively correlated with CKD-PH, the other 10 parameters were positively correlated with CKD-PH. Among them, LA was highly correlated with CKD-PH (0.70 < r < 0.89); LVDD, RA, RV, LVMI, and LVDS were moderately correlated with CKD-PH (0.40 < r < 0.69); while PA, IVS, LVPW, SV, FS, and LVEF were lowly correlated with CKD-PH (0.20 < r < 0.39). The synthesized estimates were stable against heterogeneity. Conclusion CKD-PH patients may have large cardiac chambers, thickened septal tissue on both sides of the chambers, reduced pulmonary artery flow rates, and decreased left ventricular function.
Jin et al. (2024) Meta-analysis of the correlation between pulmonary hypertension and echocardiographic parameters in patients with chronic kidney disease. PeerJ 12:e17245 https://doi.org/10.7717/peerj.17245
The effect of obesity on the outcome of thoracic endovascular aortic repair: a systematic review and meta-analysis
Background Obesity is a well-known predictor for poor postoperative outcomes of vascular surgery. However, the association between obesity and outcomes of thoracic endovascular aortic repair (TEVAR) is still unclear. This systematic review and meta-analysis was performed to assess the roles of obesity in the outcomes of TEVAR. Methods We systematically searched the Web of Science and PubMed databases to obtain articles regarding obesity and TEVAR that were published before July 2023. The odds ratio (OR) or hazard ratio (HR) was used to assess the effect of obesity on TEVAR outcomes. Body mass index (BMI) was also compared between patients experiencing adverse events after TEVAR and those not experiencing adverse events. The Newcastle–Ottawa Scale was used to evaluate the quality of the enrolled studies. Results A total of 7,849 patients from 10 studies were included. All enrolled studies were high-quality. Overall, the risk of overall mortality (OR = 1.49, 95% CI [1.02–2.17], p = 0.04) was increased in obese patients receiving TEVAR. However, the associations between obesity and overall complications (OR = 2.41, 95% CI [0.84–6.93], p = 0.10) and specific complications were all insignificant, including stroke (OR = 1.39, 95% CI [0.56–3.45], p = 0.48), spinal ischemia (OR = 0.97, 95% CI [0.64–1.47], p = 0.89), neurological complications (OR = 0.13, 95% CI [0.01–2.37], p = 0.17), endoleaks (OR = 1.02, 95% CI [0.46–2.29], p = 0.96), wound complications (OR = 0.91, 95% CI [0.28–2.96], p = 0.88), and renal failure (OR = 2.98, 95% CI [0.92–9.69], p = 0.07). In addition, the patients who suffered from postoperative overall complications (p < 0.001) and acute kidney injury (p = 0.006) were found to have a higher BMI. In conclusion, obesity is closely associated with higher risk of mortality after TEVAR. However, TEVAR may still be suitable for obese patients. Physicians should pay more attention to the perioperative management of obese patients.
Li et al. (2024) The effect of obesity on the outcome of thoracic endovascular aortic repair: a systematic review and meta-analysis. PeerJ 12:e17246 https://doi.org/10.7717/peerj.17246
Association of time-averaged serum uric acid level with clinicopathological information and long-term outcomes in patients with IgA nephropathy
Objective Whether serum uric acid (SUA) at baseline could been identiûed as a risk factor for progression in IgA nephropathy (IgAN) patients remains unclear, therefore, long- term SUA control levels must be monitored. We aimed to investigate the relevant factors affecting time-averaged SUA (TA-SUA) and to assess the prognostic value of TA-SUA in IgAN. Methods This retrospective study included 152 patients with IgAN. The relationships between TA-SUA and clinicopathological features and renal outcomes (defined as the doubling of the baseline serum creatinine level or end-stage renal disease) were analyzed in groups divided by quartiles of TA-SUA levels, the presence of hyperuricemia, and sex. Results Patients with high TA-SUA levels had higher levels of baseline SUA, blood urea nitrogen (BUN), triglycerides, serum C3 and serum C4 and were more likely to be male and have hypertension, proteinuria, poor renal function, and pathological injuries including high grades of tubular atrophy/interstitial fibrosis (T1–T2). These patients had a poorer prognosis compared with patients with low TA-SUA levels. The TA-SUA level was positively correlated with baseline age and BUN, triglycerides, serum C3, and serum C4 levels, and negatively correlated with baseline eGFR. Survival curve analysis indicated that persistent hyperuricemia was associated with significantly poorer renal outcomes than normo-uricemia in both men and women. The TA-SUA level also was an independent predictor of renal outcome in patients with IgAN, with optimal cutoû values of 451.38 µmol/L (area under the curve (AUC) = 0.934) for men and 492.83 µmol/L (AUC = 0.768) for women. Conclusions The TA-SUA level is associated with triglyceride level, complement component levels, renal function, and pathological severity of IgAN, and it may be a prognostic indicator in male and female patients with IgAN.
Weng et al. (2024) Association of time-averaged serum uric acid level with clinicopathological information and long-term outcomes in patients with IgA nephropathy. PeerJ 12:e17266 https://doi.org/10.7717/peerj.17266
Non-significant influence between aerobic and anaerobic sample transport materials on gut (fecal) microbiota in healthy and fat-metabolic disorder Thai adults
Background The appropriate sample handling for human fecal microbiota studies is essential to prevent changes in bacterial composition and quantities that could lead to misinterpretation of the data. Methods This study firstly identified the potential effect of aerobic and anaerobic fecal sample collection and transport materials on microbiota and quantitative microbiota in healthy and fat-metabolic disorder Thai adults aged 23–43 years. We employed metagenomics followed by 16S rRNA gene sequencing and 16S rRNA gene qPCR, to analyze taxonomic composition, alpha diversity, beta diversity, bacterial quantification, Pearson’s correlation with clinical factors for fat-metabolic disorder, and the microbial community and species potential metabolic functions. Results Our study successfully obtained microbiota results in percent and quantitative compositions. Each sample exhibited quality sequences with a >99% Good’s coverage index, and a relatively plateau rarefaction curve. Alpha diversity indices showed no statistical difference in percent and quantitative microbiota OTU richness and evenness, between aerobic and anaerobic sample transport materials. Obligate and facultative anaerobic species were analyzed and no statistical difference was observed. Supportively, the beta diversity analysis by non-metric multidimensional scale (NMDS) constructed using various beta diversity coefficients showed resembling microbiota community structures between aerobic and anaerobic sample transport groups (P = 0.86). On the other hand, the beta diversity could distinguish microbiota community structures between healthy and fat-metabolic disorder groups (P = 0.02), along with Pearson’s correlated clinical parameters (i.e., age, liver stiffness, GGT, BMI, and TC), the significantly associated bacterial species and their microbial metabolic functions. For example, genera such as Ruminococcus and Bifidobacterium in healthy human gut provide functions in metabolisms of cofactors and vitamins, biosynthesis of secondary metabolites against gut pathogens, energy metabolisms, digestive system, and carbohydrate metabolism. These microbial functional characteristics were also predicted as healthy individual biomarkers by LEfSe scores. In conclusion, this study demonstrated that aerobic sample collection and transport (<48 h) did not statistically affect the microbiota and quantitative microbiota analyses in alpha and beta diversity measurements. The study also showed that the short-term aerobic sample collection and transport still allowed fecal microbiota differentiation between healthy and fat-metabolic disorder subjects, similar to anaerobic sample collection and transport. The core microbiota were analyzed, and the findings were consistent. Moreover, the microbiota-related metabolic potentials and bacterial species biomarkers in healthy and fat-metabolic disorder were suggested with statistical bioinformatics (i.e., Bacteroides plebeius).
Tunsakul et al. (2024) Non-significant influence between aerobic and anaerobic sample transport materials on gut (fecal) microbiota in healthy and fat-metabolic disorder Thai adults. PeerJ 12:e17270 https://doi.org/10.7717/peerj.17270
Metabolome and transcriptome integration reveals insights into petals coloration mechanism of three species in Sect. Chrysantha chang
Background Sect. Chrysantha Chang, belonging to the Camellia genus, is one of the rare and precious ornamental plants distinguished by a distinctive array of yellow-toned petals. However, the variation mechanisms of petal color in Sect. Chrysantha Chang remains largely unclear. Methods We conducted an integrated analysis of metabolome and transcriptome to reveal petal coloration mechanism in three species, which have different yellow tones petals, including C. chuongtsoensis (CZ, golden yellow), C. achrysantha (ZD, light yellow), and C. parvipetala (XB, milk white). Results A total of 356 flavonoid metabolites were detected, and 295 differential metabolites were screened. The contents of 74 differential metabolites showed an upward trend and 19 metabolites showed a downward trend, among which 11 metabolites were annotated to the KEGG pathway database. We speculated that 10 metabolites were closely related to the deepening of the yellowness. Transcriptome analysis indicated that there were 2,948, 14,018 and 13,366 differentially expressed genes (DEGs) between CZ vs. ZD, CZ vs. XB and ZD vs. XB, respectively. Six key structural genes (CcCHI, CcFLS, CcDFR1, CcDFR2, CcDFR3, and CcCYP75B1) and five candidate transcription factors (MYB22, MYB28, MYB17, EREBP9, and EREBP13) were involved in the regulation of flavonoid metabolites. The findings indicate that flavonoid compounds influence the color intensity of yellow-toned petals in Sect. Chrysantha Chang. Our results provide a new perspective on the molecular mechanisms underlying flower color variation and present potential candidate genes for Camellia breeding.
Yan et al. (2024) Metabolome and transcriptome integration reveals insights into petals coloration mechanism of three species in Sect. Chrysantha chang. PeerJ 12:e17275 https://doi.org/10.7717/peerj.17275
Relationships among barodontalgia prevalence, altitude, stress, dental care frequency, and barodontalgia awareness: a survey of Turkish pilots
Background Gas expansion in body cavities due to pressure changes at high altitudes can cause barodontalgia. This condition may compromise flight safety. Aim To investigate relationships among barodontalgia awareness, dental visit frequency, and barodontalgia prevalence in civilian and military pilots operating at high altitudes. Materials and Methods Civilian pilots from Turkish Airlines and military pilots from the Turkish Air Force, flying between November 2022 and January 2023, participated in this study. A 20-question survey was administered to 750 pilots, covering topics such as barodontalgia awareness, dental visit frequency, breaks after dental treatments, in-flight pain, and pain type and severity. The voluntary surveys were distributed by email. Results Of the 750 pilots, 526 completed the survey; 61% were aware of barodontalgia, and 81% of pilots who had experienced it reported pain at altitudes <2000 feet. The study revealed higher barodontalgia awareness among pilots who had experienced it, with the highest prevalence among jet pilots. Pilots with barodontalgia also showed a higher frequency of dental visits (p < 0.001). Additionally, this group reported more frequent interruption of flight due to dental treatment (IFDT), more problems experienced in flights after treatment (PFAT), and higher instances of bruxism or teeth clenching during flight, suggesting stress and anxiety (p < 0.05). Conclusions Barodontalgia, a type of pain linked to stress, significantly impacts pilot performance, and can threaten flight safety, even at lower altitudes. Thus, there is a need to educate pilots about stress management, barodontalgia awareness, and the importance of regular dental check-ups.
Topbaş et al. (2024) Relationships among barodontalgia prevalence, altitude, stress, dental care frequency, and barodontalgia awareness: a survey of Turkish pilots. PeerJ 12:e17290 https://doi.org/10.7717/peerj.17290