Genome-wide identification of TPS and TPP genes in cultivated peanut (Arachis hypogaea) and functional characterization of AhTPS9 in response to cold stress

IntroductionTrehalose is vital for plant metabolism, growth, and stress resilience, relying on Trehalose-6-phosphate synthase (TPS) and Trehalose-6-phosphate phosphatase (TPP) genes. Research on these genes in cultivated peanuts (Arachis hypogaea) is limited.MethodsThis study employed bioinformatics to identify and analyze AhTPS and AhTPP genes in cultivated peanuts, with subsequent experimental validation of AhTPS9’s role in cold tolerance.ResultsIn the cultivated peanut genome, a total of 16 AhTPS and 17 AhTPP genes were identified. AhTPS and AhTPP genes were observed in phylogenetic analysis, closely related to wild diploid peanuts, respectively. The evolutionary patterns of AhTPS and AhTPP genes were predominantly characterized by gene segmental duplication events and robust purifying selection. A variety of hormone-responsive and stress-related cis-elements were unveiled in our analysis of cis-regulatory elements. Distinct expression patterns of AhTPS and AhTPP genes across different peanut tissues, developmental stages, and treatments were revealed, suggesting potential roles in growth, development, and stress responses. Under low-temperature stress, qPCR results showcased upregulation in AhTPS genes (AhTPS2-5, AhTPS9-12, AhTPS14, AhTPS15) and AhTPP genes (AhTPP1, AhTPP6, AhTPP11, AhTPP13). Furthermore, AhTPS9, exhibiting the most significant expression difference under cold stress, was obviously induced by cold stress in cultivated peanut, and AhTPS9-overexpression improved the cold tolerance of Arabidopsis by protect the photosynthetic system of plants, and regulates sugar-related metabolites and genes.DiscussionThis comprehensive study lays the groundwork for understanding the roles of AhTPS and AhTPP gene families in trehalose regulation within cultivated peanuts and provides valuable insights into the mechanisms related to cold stress tolerance

Genome-wide analysis reveals regulatory mechanisms and expression patterns of TGA genes in peanut under abiotic stress and hormone treatments

IntroductionThe TGA transcription factors, plays a crucial role in regulating gene expression. In cultivated peanut (Arachis hypogaea), which faces abiotic stress challenges, understanding the role of TGAs is important.MethodsIn this study, we conducted a comprehensive in analysis of the TGA gene family in peanut to elucidate their regulatory mechanisms and expression patterns under abiotic stress and hormone treatments. Furthermore, functional studies on the representative AhTGA gene in peanut cultivars were conducted using transgenic Arabidopsis and soybean hair roots.ResultsThe genome-wide analysis revealed that a total of 20 AhTGA genes were identified and classified into five subfamilies. Collinearity analysis revealed that AhTGA genes lack tandem duplication, and their amplification in the cultivated peanut genome primarily relies on the whole-genome duplication of the diploid wild peanut to form tetraploid cultivated peanut, as well as segment duplication between the A and B subgenomes. Promoter and Protein-protein interaction analysis identified a wide range of cis-acting elements and potential interacting proteins associated with growth and development, hormones, and stress responses. Expression patterns of AhTGA genes in different tissues, under abiotic stress conditions for low temperature and drought, and in response to hormonal stimuli revealed that seven AhTGA genes from groups I (AhTGA04, AhTGA14 and AhTGA20) and II (AhTGA07, AhTGA11, AhTGA16 and AhTGA18) are involved in the response to abiotic stress and hormonal stimuli. The hormone treatment results indicate that these AhTGA genes primarily respond to the regulation of jasmonic acid and salicylic acid. Overexpressing AhTGA11 in Arabidopsis enhances resistance to cold and drought stress by increasing antioxidant activities and altering endogenous hormone levels, particularly ABA, SA and JA.DiscussionThe AhTGA genes plays a crucial role in hormone regulation and stress response during peanut growth and development. The findings provide insights into peanut's abiotic stress tolerance mechanisms and pave the way for future functional studies

Border row effects improved the spatial distributions of maize and peanut roots in an intercropping system, associated with improved yield

BackgroundBorder row effects impact the ecosystem functions of intercropping systems, with high direct interactions between neighboring row crops in light, water, and nutrients. However, previous studies have mostly focused on aboveground, whereas the effects of intercropping on the spatial distribution of the root system are poorly understood. Field experiments and planting box experiments were combined to explore the yield, dry matter accumulation, and spatial distribution of root morphological indexes, such as root length density (RLD), root surface area density (RSAD), specific root length (SRL), and root diameter (RD), of maize and peanut and interspecific interactions at different soil depths in an intercropping system.ResultsIn the field experiments, the yield of intercropped maize significantly increased by 33.45%; however, the yield of intercropped peanut significantly decreased by 13.40%. The land equivalent ratio (LER) of the maize–peanut intercropping system was greater than 1, and the advantage of intercropping was significant. Maize was highly competitive (A = 0.94, CR=1.54), and the yield advantage is mainly attributed to maize. Intercropped maize had higher RLD, RSAD, and SRL than sole maize, and intercropped peanut had lower RLD, RSAD, and SRL than sole peanut. In the interspecific interaction zone, the increase in RLD, RSAD, SRL, and RD of intercropped maize was greater than that of intercropped peanut, and maize showed greater root morphological plasticity than peanut. A random forest model determined that RSAD significantly impacted yield at 15–60 cm, while SRL had a significant impact at 30–60 cm. Structural equation modeling revealed that root morphology indicators had a greater effect on yield at 30–45 cm, with interactions between indicators being more pronounced at this depth.ConclusionThese results show that border-row effects mediate the plasticity of root morphology, which could enhance resource use and increase productivity. Therefore, selecting optimal intercropping species and developing sustainable intercropping production systems is of great significance

Overexpression of TIMP3 Protects Against Cardiac Ischemia/Reperfusion Injury by Inhibiting Myocardial Apoptosis Through ROS/Mapks Pathway

Background/Aims: Myocardial ischemia/reperfusion (I/R) injury remains a great challenge in clinical therapy. Tissue inhibitor of metalloproteinases 3 (TIMP3) plays a crucial role in heart physiological and pathophysiological processes. However, the effects of TIMP3 on I/R injury remain unknown. Methods: C57BL/6 mice were infected with TIMP3 adenovirus by local delivery in myocardium followed by I/R operation or doxorubicin treatment. Neonatal rat cardiomyocytes were pretreated with TIMP3 adenovirus prior to anoxia/reoxygenation (A/R) treatment in vitro. Histology, echocardiography, in vivo phenotypical analysis, flow cytometry and western blotting were used to investigate the altered cardiac function and underlying mechanisms. Results: The results showed that upregulation of TIMP3 in myocardium markedly inhibited myocardial infarct areas and the cardiac dysfunction induced by I/R or by doxorubicin treatment. TUNEL staining revealed that TIMP3 overexpression attenuated I/R-induced myocardial apoptosis, accompanied by decreased Bax/Bcl-2 ratio, Cleaved Caspase-3 and Cleaved Caspase-9 expression. In vitro, A/R-induced cardiomyocyte apoptosis was abrogated by pharmacological inhibition of reactive oxygen species (ROS) production or MAPKs signaling. Attenuation of ROS production reversed A/R-induced MAPKs activation, whereas MAPKs inhibitors showed on effect on ROS production. Furthermore, in vivo or in vitro overexpression of TIMP3 significantly inhibited I/R- or A/R-induced ROS production and MAPKs activation. Conclusion: Our findings demonstrate that TIMP3 upregulation protects against cardiac I/R injury through inhibiting myocardial apoptosis. The mechanism may be related to inhibition of ROS-initiated MAPKs pathway. This study suggests that TIMP3 may be a potential therapeutic target for the treatment of I/R injury

Changes in Lignin Content and Activity of Related Enzymes in the Endocarp During the Walnut Shell Development Period

Lignification was observed using the phloroglucinol–HCl method and the content of lignin, cellulose, and polyphenol and the activity of related enzymes were measured during development with the materials of walnut of ‘Zanmei’ and ‘Zhenzhuxiang’. Results showed that lignification occurred at the beginning of June, initially took shape in mid-June and finished in late July. From shell lignification to harvest, the concentrations of lignin, cellulose, and phenolic content increased before harvest, but phenolic content decreased slightly. The activities of both POD and PAL decreased and PPO varied somewhat. Correlation analysis showed lignin content to be significantly positively correlated with the cellulose content. Phenolic content had a significant positive correlation with that of lignin. Phenolic content was positively correlated with cellulose. The activity of POD had a significant negative correlation with lignin, cellulose, and phenolic content, but it was positively correlated with the activity of PAL

MicroRNA-29b Regulates the Mitochondria-Dependent Apoptotic Pathway by Targeting Bax in Doxorubicin Cardiotoxicity

Background/Aims: Myocardial apoptosis plays an important role in doxorubicin (Dox) cardiotoxicity. MicroRNA-29 (miR-29) is suggested to function as an anti-fibrotic factor with potential therapeutic effects on cardiac fibrosis. However, it has not been shown whether there is an association between miR-29b and myocardial apoptosis. Methods: Male Wistar rats were transfected with miR-29b agomir by local delivery to the myocardium prior to Dox treatment. Rat cardiomyocytes were pretreated with miR-29b mimics or inhibitor followed by Dox incubation in vitro. Cardiac function and underlying mechanisms were evaluated by echocardiography, immunofluorescence, flow cytometry, real-time PCR, and western blotting. Results: Our results revealed that miR-29b is the only member of the miR-29 family that was significantly downregulated in myocardium from Dox-treated rats. Delivery of miR-29b agomir to myocardium resulted in a marked improvement of cardiac function. Terminal deoxynucleotidyl transferase dUTP nick end labeling staining showed that rescue of miR-29b expression inhibited Dox-induced myocardial apoptosis, concomitantly with increased Bcl-2 expression and decreased Bax expression and caspase-3 activity. In vitro, miR-29b overexpression mitigated, whereas inhibition of miR-29b promoted, Dox-induced cardiomyocyte apoptosis. Mechanistically, miR-29b negatively regulated Bax expression by directly targeting the 3′ untranslated region of Bax. In Dox-treated cardiomyocytes, upregulation of miR-29b resulted in a significant decrease in Bax expression, with an increase in Bcl-2 expression, accompanied by inhibition of mitochondrial membrane depolarization, cytochrome c release, and caspase activation. However, inhibition of miR-29b produced the opposite effects by further augmenting the effects of Dox. Conclusions: These data demonstrate that miR-29b prevents Dox-induced myocardial apoptosis through inhibition of the mitochondria-dependent pathway by directly targeting Bax, suggesting that miR-29b is a potential novel therapeutic target for the treatment of Dox cardiotoxicity

Peptide-Conjugated Aggregation-Induced Emission Fluorogenic Probe for Glypican-3 Protein Detection and Hepatocellular Carcinoma Cells Imaging

Hepatocellular carcinoma (HCC) is a malignant tumor with high morbidity and mortality on a global scale, and the development of accurate detection and imaging methods for HCC cells is urgently needed. Herein, by connecting peptide L5, which can specifically bind to the overexpressed Glypican-3 (GPC-3) protein of HCC cells with aggregation-induced emission (AIE) moiety ammonium cation-functionalized 9,10-distyrylanthracene (NDSA) via the “click” reaction, we synthesized a fluorescent probe NDSA-L5. In an aqueous solution, the probe shows weak emission, whereas, in the presence of the GPC-3 protein, bright fluorescence can be obtained since NDSA-L5 binds to the GPC-3 protein, leading to the restricted intramolecular movement of AIE-active NDSA-L5. The imaging and flow cytometry experiments demonstrate that the NDSA-L5 probe can rapidly accumulate in the subcutaneous HCC cells and liver tumor tissue and shows a potential application in early detection and surgical navigation for HCC cancer

Cross-Talk between N6-Methyladenosine and Their Related RNAs Defined a Signature and Confirmed m6A Regulators for Diagnosis of Endometriosis

An RNA modification known as N6-methyladenosine (m6A) interacts with a range of coding and non-coding RNAs. The majority of the research has focused on identifying m6A regulators that are differentially expressed in endometriosis, but it has ignored their mechanisms that are derived from the alterations of modifications among RNAs, affecting the disease progression primarily. Here, we aimed to investigate the potential roles of m6A regulators in the diagnostic potency, immune microenvironment, and clinicopathological features of endometriosis through interacting genes. A GEO cohort was incorporated into this study. Variance expression profiling was executed via the “limma” R package. Pearson analysis was performed to investigate the correlations among 767 interacting lncRNAs, 374 interacting mRNAs, and 23 m6A regulators. K-means clustering analysis, based on patterns of mRNA modifications, was applied to perform clinical feature analysis. Infiltrating immune cells and stromal cells were calculated using the Cibersort method. An m6A-related risk model was created and supported by an independent risk assay. LASSO regression analysis and Cox analyses were implemented to determine the diagnostic genes. The diagnostic targets of endometriosis were verified using PCR and the WB method. Results: A thorough investigation of the m6A modification patterns in the GEO database was carried out, based on mRNAs and lncRNAs related to these m6A regulators. Two molecular subtypes were identified using unsupervised clustering analysis, resulting in further complex infiltration levels of immune microenvironment cells in diversified endometriosis pathology types. We identified two m6A regulators, namely METTL3 and YTHDF2, as diagnostic targets of endometriosis following the usage of overlapping genes to construct a diagnostic m6A signature of endometriosis through multivariate logistic regression, and we validated it using independent GSE86534 and GSE105764 cohorts. Finally, we found that m6A alterations might be one of the important reasons for the progression of endometriosis, especially with significant downregulation of the expressions of METTL3 and YTHDF2. Finally, m6A modification patterns have significant effects on the diversity and complexity of the progression and immune microenvironment, and might be key diagnostic markers for endometriosis

KIF26B and CREB3L1 Derived from Immunoscore Could Inhibit the Progression of Ovarian Cancer

Background. Ovarian cancer (OV) is characteristic of high incidence rate and fatality rate in the malignant tumors of female reproductive system. Researches on pathogenesis and therapeutic targets for OV need to be continued. This study mainly analyzed the immune-related pathogenesis and discovered the key immunotherapy targets for OV. Methods. WGCNA was used for excavating hub gene modules and hub genes related to the immunity of OV. Enrichment analysis was aimed to analyze the related pathways of hub gene modules. Biological experiments were used for exploring the effect of hub genes on SKOV3 cells. Results. We identified two hub gene modules related to the immunoscore of OV and found that these genes in the modules were related to the extracellular matrix and viral infections. At the same time, we also discovered six hub genes related to the immunity of OV. Among them, KIF26B and CREB3L1 can affect the proliferation, migration, and invasion of SKOV3 cells by the Wnt/β-catenin pathway. Conclusions. The local infection or inflammation of ovarian may affect the immunity of OV. KIF26B and CREB3L1 are expected to be potential targets for the immunotherapy of OV