Regulatory Mechanisms Research Articles

MoSec13 combined with MoGcn5b modulates MoAtg8 acetylation and regulates autophagy in Magnaporthe oryzae

ABSTRACT Macroautophagy/autophagy is an evolutionarily conserved cellular degradation process that is crucial for cellular homeostasis in Magnaporthe oryzae. However, the precise regulatory mechanisms governing autophagy in this organism remain unclear. In this study, we found a multiregional localization of MoSec13 to the vesicle membrane, endoplasmic reticulum, nucleus, and perinucleus. MoSec13 negatively regulated autophagy through specific amino acid residues in its own WD40 structural domain by interacting with MoAtg7 and MoAtg8. We also found that the histone acetyltransferase MoGcn5b mediated the acetylation of MoAtg8 and regulated autophagy activity. Subsequently, we further determined that MoSec13 regulated the acetylation status of MoAtg8 by controlling the interaction between MoGcn5b and MoAtg8 in the nucleus. In addition, MoSec13 maintained lipid homeostasis by controlling TORC2 activity. This multilayered integration establishes MoSec13 as an essential node within the autophagic regulatory network. Our findings fill a critical gap in understanding the role of Sec13 in autophagy of filamentous fungi and provide a molecular foundation for developing new therapeutic strategies against rice blast fungus. ABBREVIATIONS BFA: brefeldin A; BiFC: bimolecular fluorescence complementation; CM: complete medium; CMAC: 7-amino-4-chloromethylcoumarin; Co-IP: co-immunoprecipitation; COPII: coat complex II; GFP: green fluorescent protein; HPH: hygromycin phosphotransferase; MM-N: nitrogen-starvation conditions; NPC: nuclear pore complex; PAS: phagophore assembly site; PE: phosphatidylethanolamine; UPR: unfolded protein response.

Medulloblastoma’s master regulators and their association with patients’ risk

Medulloblastoma (MB) is the most common malignant pediatric brain tumor, accounting for approximately 20% of all childhood brain tumors. Despite recent advances, current treatments like surgery, radiation, and chemotherapy still lead to severe side effects and high morbidity. Limited knowledge exists regarding the regulatory mechanisms behind the MB transcriptional alterations in high-aggressive subgroups like Group 3 and Group 4, hindering the development of targeted therapies. Identifying key transcriptional regulators, known as master regulators (MRs), can elucidate the dysregulated pathways underlying MB progression and uncover potential treatment targets. In this study, we utilize primary MB gene expression samples to infer its regulatory network. Subsequently, we applied the Master Regulator Analysis identifying the transcription factors BHLHE41, RFX4, and NPAS3 as its main transcriptional regulators, showing tumor suppressor features. We also identified eight risk MRs highly associated with patient outcome: four regulators (MYC, REL, ZSCAN5 A, and ZFAT) with activities associated with poor prognosis, and four (PAX6, ARNT2, ZNF157, and HIVEP3) acting antagonistically, being associated with good outcome. Our results offer key insights into the molecular mechanisms driving these tumors and identify novel potential therapeutic targets, addressing the urgent need for more effective and less toxic treatments.

Sex-Biased Gene Expression of RNAi Pathway Components in the Sea Lice Caligus rogercresseyi.

RNA interference (RNAi) is a conserved mechanism for post-transcriptional gene regulation and a critical process of arthropod immunity. This study investigates RNAi-associated genes in Caligus rogercresseyi, an ectoparasitic sea louse that poses significant challenges to salmon aquaculture. In that regard, 16 RNAi-associated genes were identified by in silico analysis, including Cr-AGO1, Cr-CNOT1, Cr-DCR, Cr-SND1, and Cr-XRN1. Phylogenetic analysis demonstrated clustering with homologous sequences from other arthropods, particularly the ectoparasitic copepod Lepeophtheirus salmonis. RNA-Seq analyses revealed developmentally regulated expression patterns, with RNAi-associated genes clustered into four distinct expression profiles. Quantitative PCR (qPCR) validation confirmed significant male-biased expression for several key genes, including Cr-AGO1 (109-fold increase), Cr-DCR (22-fold), Cr-XRN1 (22-fold), Cr-SND1 (fourfold), and Cr-CNOT1 (threefold), suggesting potential roles in male reproductive processes such as spermatogenesis. Cr-DDX6, Cr-Drosha, and Cr-XPO5, potentially involved in oocyte development and RNA transport, exhibited female-biased expression. These results provide new insights into RNAi-associated gene expression in C. rogercresseyi, uncovering significant developmental and sex-biased expression patterns. Characterizing these critical genes establishes a foundation for exploring control strategies based on the RNAi process, targeting sex-biased and developmentally essential genes. Such treatments could reduce reproductive success in sea lice while minimizing environmental impact, offering a sustainable alternative for managing caligidosis in aquaculture.

Endothelial major vault protein alleviates vascular remodeling via promoting Parkin-mediated mitophagy

Many important vascular diseases including neointimal hyperplasia and atherosclerosis are characterized by the endothelial cell (EC) injury-initiated pathological vascular remodeling. However, the endogenous regulatory mechanisms underlying it are not fully understood. The present study investigates regulatory role of major vault protein (MVP) in the pathogenesis of vascular remodeling via controlling EC injury. By generating male murine vascular disease models, we find that ablation of endothelial MVP increases neointima formation and promotes atherosclerosis. Mechanistically, MVP directly binds with Parkin and inhibits the ubiquitination and proteasomal degradation of Parkin by dissociating the E3 ligase NEDD4L from Parkin, leading to activation of Parkin-mediated mitophagy pathway in the EC. Genetic modulation of endothelial MVP and Parkin influences the mitophagy, apoptosis, and neointima formation. These results demonstrate that MVP acts as an intracellular regulator promoting Parkin-mediated mitophagy. Our findings suggest that MVP/NEDD4L/Parkin axis may serve as the therapeutic target for treating intimal hyperplasia and atherosclerosis.

A tubby-like protein, MdTLP7 enhances drought and salt stresses tolerance of Malus domestica

BackgroundDrought and salt stresses as common abiotic stresses have a significant impact on the yield and quality of Malus domestica (apple). The tubby-like proteins (TLPs), as a family of transcription factors, play an important role in plant response to abiotic stresses, but the regulatory mechanisms involved remain unclear.ResultsHere, we investigated how apple TLP7 (MdTLP7) and its interacting genes regulate apple response to drought and salt stresses. The results shows that overexpression of MdTLP7 significantly increased the drought and salt tolerance of apple through regulating gene transcription. Yeast two-hybrid screening, together with DNA affinity purification sequencing (DAP-seq), revealed that MdTLP7 interacted with MdNAC72L to regulate the expression of MdHsp70-8 and MdAGP, and that the overexpression of these two genes significantly enhanced the drought and salt stresses tolerance of apple.ConclusionThe apple protein MdTLP7 could interact with MdNAC72L and promoted the expression of MdHsp70-8 and MdAGP, thus improved drought and salt tolerance of apple calli. These results provide insights into the molecular mechanism of MdTLP7 increasing the drought and salt stresses tolerance of apple as well as a theoretical basis for the expansion of apple cultivation and related research.

Synergistic effect of grassland plants and beneficial rhizosphere bacteria helps plants cope with overgrazing stress

BackgroundOvergrazing (OG) is an important driver of grassland degradation and productivity decline. Highly effective synergy between plants and rhizosphere growth-promoting rhizobacteria (PGPR) may be a major way for grassland plants to effectively cope with OG stress. There have been few reports providing solid evidence on how this synergy occurs.ResultThis study combined with multi-omics analysis and the interaction effect of specific root exudate with PGPR B68, aiming to reveal the synergistic effect and regulatory mechanism of L. chinensis and PGPR under overgrazing stress. The results showed that Leymus chinensis plants with OG history can recruit the beneficial Phyllobacterium sp. B68 by regulating specific root exudate compounds(such as amino acid L-leucyl-L-alanine and alkaloid cordycepin). These compounds enhanced B68 rhizosphere colonization by promoting B68 chemotaxis and biofilm formation. The pot study experiments indicated that the bacterial isolates used as bio inoculants increased L. chinensis growth (mainly including plant height and biomass) by significantly increasing the chlorophyll content, RuBisCO activity, soluble sugar, plant hormones and nutrient content. Metagenomics results show that B68 inoculation significantly altered rhizosphere soil bacterial community composition and function. Additionally, B68 systemically upregulated the expression level of genes involved in plant hormone signaling, nutrient and sugar transporters, nitrogen metabolism, cell division, cell wall modification and photosynthesis to promote plant growth. The above results indicate that the PGPR B68 recruited by the root exudates of L. chinensis under OG helps the plant adapt to stress by promoting nutrient uptake and transport, maintaining hormone homeostasis, and enhancing the expression of genes related to plant growth and nutrient metabolism.ConclusionThis study provides new insights into the positive interactions between grassland plants and rhizosphere bacteria under OG stress, offering valuable knowledge for developing new fertilizers and better management practices for degraded rangeland restoration and sustainable agriculture development.Clinical trial numberNot applicable.

Regulatory Mechanism of CRTC1 on Autophagy and GluA2 Expression in Epilepsy.

We initially established a magnesium-free epilepsy cell model and recorded cellular discharges using the whole-cell patch clamp technique. Next, we experimentally activated autophagy and identified effective methods for silencing the CRTC1 gene using RNA interference technology. Furthermore, we developed an animal models of status epilepticus and employed immunofluorescence and Western Blot to elucidate CRTC1's role in regulating autophagy-related genes and GluA2 expression in epilepsy. We observed mouse hippocampal neurons under magnesium-free extracellular conditions. Treatment with an autophagy activator decreased GluA2 expression; however, CRTC1 was not dephosphorylated. CRTC1 siRNA suppressed LC3 and PSD95 expression, whereas CRTC1siRNA intervention restored GluA2 expression. CRTC1 indirectly influences the expression of synaptic-related proteins and GluA2 by directly modulating autophagy during the pathological process of epilepsy. The findings of this study reveal novel molecular targets for the treatment of epilepsy.

Comparative transcriptome analysis of oat varieties with different flowering performances under a short-day photoperiod

BackgroundInsensitivity to day length is an essential trait for oat cultivation and its geographical spread to a wide range of latitudes. Daylength-insensitive oat cultivars can flower normally from low to high latitudes and may be especially well suited for a double-cropping system. However, few studies have investigated the regulatory mechanisms involved in flowering in photoperiod-insensitive oats.ResultsIn this study, we compared the developmental stages of shoot apical meristems (SAMs) and transcriptome profiles between the photoperiod-insensitive oat cultivar VAO-8 and the photoperiod-sensitive oat cultivar Baiyan 2 at four time points under a short-day photoperiod. The development of Baiyan 2 was affected by short-day length, and SAMs persisted in the vegetative stage. VAO-8 responded less to photoperiod and matured normally under a short-day photoperiod. Comparative transcriptome data of the two cultivars revealed a total of 824, 1,189, 646 and 1,145 differentially expressed genes (DEGs) between VAO-8 and Baiyan 2 at four time points. Functional enrichment analysis revealed that metabolic processes related to chlorophyll biosynthesis, photosynthesis, carbohydrate metabolism and the secondary metabolism were significantly enhanced in VAO-8 compared with those in Baiyan 2. The upregulated genes involved in these processes may contribute to the flowering of VAO-8 under a short-day photoperiod. Furthermore, the differential expression of 93 transcription factor genes involved in multiple flowering pathways was observed, and these genes may play important roles in the regulation of VAO-8 flowering.ConclusionsThe results provide a comprehensive understanding of the photoperiod-insensitive molecular mechanism of oats at the transcriptional level under a short-day photoperiod, which lay a foundation for breeding photoperiod-insensitive oat cultivars.

Resistance mechanism of Abies beshanzuensis under heat stress was elucidated through the integration of physiological and transcriptomic analyses

Elevated temperatures significantly impaired the normal growth and development of plants. This study combined physiological and transcriptomic analyses to explore the potential mechanisms of response to heat stress in Abies beshanzuensis M. H. Wu. Under heat stress, A. beshanzuensis exhibited reduced photosynthetic rates and chlorophyll content, accompanied by marked downregulation of photosynthesis-associated genes, suggesting heat-induced photoinhibition and compromised carbon assimilation capacity. Furthermore, the increased activities of MDA, SOD, POD, and CAT suggested that A. beshanzuensis could withstand heat stress by enhancing the activity of antioxidant enzymes to mitigate excess reactive oxygen species and anions. Transcriptome analysis revealed the induction of genes related to heat shock proteins, plant hormone signaling, and antioxidants, which could enhance the tolerance of A. beshanzuensis to high temperatures. In summary, the research demonstrated that A. beshanzuensis could not tolerate high temperatures, which was identified as one of the primary reasons for its endangerment. This study offers a novel approach to investigating the regulatory mechanisms of heat stress.

Regulating post-treatment of polyamide nanofiltration membranes: The role of solvent polarity and miscibility on membrane performance

ABSTRACT Solvent post-treatment is an effective strategy for regulating polyamide nanofiltration membranes. However, the regulatory mechanism behind this process requires further supplementation and improvement. In this study, different polar solvents (polarity order: acetonitrile > methanol > ethanol > acetone > n-butanol > n-hexane) were used for post-treatment of PEI nano-filtration membranes to compare and analyze the influence of solvent post-treatment on the performance of PEI nano-filtration membranes (flux, salt and heavy metal retention). Combined with the comprehensive physicochemical characterization (SEM, FTIR, XPS, contact angle), the regulatory mechanisms of different solvent post-treatments on PEI nanofiltration membranes were analyzed and summarized. The results revealed that the effect of solvent post-treatment on PEI-TMC polyamide is different from that of the MPD and PIP systems, possibly due to the larger molecular weight and acyclic molecular chain structure of PEI. Moreover, the solvent post-treatment mainly modulates the polyamide structure through two mechanisms: the swelling effect and the miscibility-promoted further reaction or hydrolysis. The former is the primary mechanism that determines the changes in separation properties. And the chemical structure of the polyamide surface is primarily influenced by the mutual dissolution promoted reaction or hydrolysis. This study improves the understanding of solvent post-treatment of interfacial polymerization and provides inspiration for performance modulation of positively charged PEI NF membranes.

Biological and Analytical Perspectives on D-Amino Acids in Cancer Diagnosis and Therapy

For a long time, D-amino acids remained unexplored in mammalian physiology. The technological advances in enantioseparation over the past 50 years have revealed that D-amino acids not only exist in human tissues and fluids but also play important roles in neurotransmission, immune regulation, and cellular proliferation. The present review provides a comprehensive assessment of the role of D-amino acids in cancer, including their endogenous and exogenous production pathways, along with the analytical methodologies used for detection and quantification, from liquid chromatography to biosensors. These methods have underlined how altered levels of D-amino acids can be helpful in early detection, progression, or response to treatment in several malignancies, including gastric, hepatic, colorectal, or breast cancer. The present review also explores how manipulation of D-amino acids can regulate cell proliferation, their mechanisms in cancer regulation, including the modulation of N-methyl-D-aspartate (NMDA) receptors and the production of hydrogen sulphide (H2S), and the role of specific D-amino acids in cancer onset, immune defence, and protection against chemotherapy-induced toxicity. Finally, several underexplored research directions are outlined, such as potential correlations with gut microbiota composition, the impact of processed food consumption, and the integration of multiomics strategies.

Metabolic Pathways and Molecular Regulatory Mechanisms of Fruit Color Change During Greening Stage of Peppers (Capsicum annuum L.)

Our multi-omics investigation of pepper fruit coloration dynamics demonstrates that the coordinated regulation of flavonoid accumulation and chlorophyll retention underpins the distinct pigmentation patterns between dark green (XHB) and light green (QL2017) cultivars. Through the integrated analysis of three developmental stages (10–30 DPA), we identified 989 differentially accumulated metabolites (DAMs) and 810 differentially expressed genes (DEGs), with flavonoid biosynthesis, phenylpropanoid metabolism, and chlorophyll turnover pathways pinpointed as central regulatory hubs. Notably, key metabolites such as quercitrin, kaempferol-3-O-rhamnoside, and cinnamic acid were significantly enriched in dark green fruits (XHB), coinciding with enhanced antioxidant activity and delayed chlorophyll degradation. Transcriptomic data revealed the coordinated upregulation of chlorophyll biosynthesis genes (COX15, POR) and light-harvesting complex components (Lhcb1, Lhcb2), while PAO—a pivotal chlorophyll catabolism gene—also exhibited elevated expression. Co-expression network analysis highlighted scopoletin GTase, F5H, CCR, and CAD as hub genes regulating flavonoid biosynthesis. qRT-PCR validation confirmed high consistency with transcriptomic trends (r > 0.85, p < 0.01). Our findings propose a synergistic model wherein flavonoid accumulation and chlorophyll metabolic dynamics jointly orchestrate green fruit pigmentation, offering novel insights and molecular targets for the precision breeding of pepper fruit coloration.

Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis.

Angiogenesis, the formation of new blood vessels, is a fundamental biological process with implications for both physiological functions and pathological conditions. While the transcriptional regulation of angiogenesis, mediated by factors such as HIF-1α (hypoxia-inducible factor 1-alpha) and VEGF (vascular endothelial growth factor), is well-characterized, the translational regulation of this process remains underexplored. Bioinformatics has emerged as an indispensable tool for advancing our understanding of translational regulation, offering predictive models that leverage large data sets to guide research and optimize experimental approaches. However, a significant gap persists between bioinformatics experts and other researchers, limiting the accessibility and utility of these tools in the broader scientific community. To address this divide, user-friendly bioinformatics platforms are being developed to democratize access to predictive analytics and empower researchers across disciplines. Translational control, compared with transcriptional control, offers a more energy-efficient mechanism that facilitates rapid cellular responses to environmental changes. Furthermore, transcriptional regulators themselves are often subject to translational control, emphasizing the interconnected nature of these regulatory layers. Investigating translational regulation requires advanced, accessible bioinformatics tools to analyze RNA structures, interacting micro-RNAs, long noncoding RNAs, and RBPs (RNA-binding proteins). Predictive platforms such as RNA structure, human internal ribosome entry site Atlas, and RBPSuite enable the study of RNA motifs and RNA-protein interactions, shedding light on these critical regulatory mechanisms. This review highlights the transformative role of bioinformatics using widely accessible user-friendly tools with a Web-browser interface to elucidate translational regulation in angiogenesis. The bioinformatics tools discussed extend beyond angiogenesis, with applications in diverse fields, including clinical care. By integrating predictive models and experimental insights, researchers can streamline hypothesis generation, reduce experimental costs, and find novel translational regulators. By bridging the bioinformatics knowledge gap, this review aims to empower researchers worldwide to adopt bioinformatics tools in their work, fostering innovation and accelerating scientific discovery.

How the Structure of Signaling Regulation Evolves: Insights from an Evolutionary Model.

To monitor environmental changes, signaling pathways attenuate their activity with negative feedback loops (NFLs), where proteins produced upon stimulation downregulate the response. NFLs function both upstream of signaling to reduce input and downstream to reduce output. Unlike upstream NFLs, downstream NFLs regulate gene expression without the involvement of intermediate proteins. Thus, we hypothesized that downstream NFLs evolve under more stringent selection than upstream NFLs. Indeed, genes encoding downstream NFLs evolve at a slower and more consistent rate than upstream genes, suggesting that the latter may be under weaker or more context-specific selection. This suggests that downstream NFLs evolve more robustly, whereas upstream NFLs are more susceptible to changes in signaling proteins and stimuli. We tested these assumptions using a minimal model of immune signaling, which predicts robust evolution of downstream NFLs to changes in model parameters. This is consistent with their critical role in regulating signaling and the conservative rate of evolution. Furthermore, we show that the number of signaling steps needed to activate a downstream NFL is influenced by the cost of signaling. Our model predicts that upstream NFLs are more likely to evolve under a shorter half-life of signaling proteins, absence of host-pathogen co-evolution, and a high infection rate. Although it has been proposed that NFLs evolve to reduce the cost of signaling, we show that a high cost does not necessarily predict the evolution of upstream NFLs. The insights from our model have broad implications for understanding the evolution of regulatory mechanisms across signaling pathways.

The sneeze reflex in physiological and pathological states: a mini review

The sneeze reflex serves as a protective response of the human body to environmental stimuli, with its regulatory mechanism largely depending on a complex nervous system. Current research indicates that the sneeze reflex can be triggered by both internal and external stimuli, including light and temperature. The composition of its reflex arc involves the coordinated action of multiple neural structures. Recent in-depth studies on the mechanism of the sneeze reflex have revealed a growing association between this reflex and various diseases, such as allergic rhinitis and infectious diseases. However, existing research primarily focuses on elucidating the neurophysiological basis of the sneeze reflex and its related neural pathways. The manifestations and mechanisms of the sneeze reflex under different pathological states remain underexplored, thereby limiting the potential application of the sneeze reflex in clinical diagnosis and treatment. This review aims to discuss the physiological mechanisms and pathological manifestations associated with the sneeze reflex.

DNMT3B promotes the progression of pheochromocytoma by mediating the hypermethylation of LRP1B promoter

BackgroundPheochromocytoma (Pheo) represents a potential metastatic neuroendocrine tumor. As a tumor suppressor gene, LRP1B is involved in the regulation of tumor progression. However, the precise regulatory mechanism of LRP1B in Pheo remains elusive.MethodsRT-QPCR, western blot and immunohistochemistry (IHC) were used to identify the expression levels of DNMT3B and LRP1B. Biochemistry assays including luciferase and ChIP were utilized to detect the interaction between the methyltransferase DNMT3B and LRP1B promoter. LRP1B or DNMT3B were knock-down in Pheo cell line by shRNAs. Functional experiments including clonal formation, migration, and in vivo transplantation were performed to evaluate the regulation of LRP1B or DNMT3B on tumor growth.ResultsLRP1B was down-regulated, while DNMT3B was up-regulated in Pheo.Overexpression of LRP1B or inhibition of DNMT3B inhibited the progress of Pheo. DNMT3B was responsible for the hypermethylation of LRP1B promoter in Pheo. At the same time, overexpression of DNMT3B reversed the inhibitory effect of overexpression of LRP1B on Pheo progression.ConclusionDNMT3B mediated the hypermethylation of the tumor suppressive gene LRP1B and promotes Pheo progression.

Positive regulation Asperosaponin VI accumulation by DaERF9 through JA signaling in Dipsacus asper

The ERF transcription factor can regulate the biosynthesis of various secondary metabolites, including triterpenoid saponins, in plants. DaERF9 has been found to be a potential regulatory factor in the accumulation of asperosaponin VI in Dipsacus asper. However, its underlying molecular mechanisms remain unclear. Here, we cloned the transcription factor DaERF9, which promotes the accumulation of asperosaponin VI in D.asper. Metabolomic analysis showed that wound stress significantly increased the content of asperosaponin VI and jasmonic acid, while the expression level of DaERF9 was markedly enhanced during this process, suggesting that DaERF9 plays a regulatory role in the wound-induced synthesis of asperosaponin VI by JA signaling pathway. Transgenic DaERF9 promoted the synthesis of precursor compounds of asperosaponin VI in Arabidopsis, activating the triterpenoid saponin biosynthesis pathway. MeJA induction enhanced the expression of the key enzyme gene DaHMGCR, which is involved in the synthesis of asperosaponin VI in transgenic DaERF9. Wound treatment markedly increased the transcriptional level of DaERF9 and the content of JA, and DaERF9 was able to interact with the DaHMGCR promoter, activating the activity of DaHMGCR. Overall, our findings suggest that DaERF9 plays a crucial role in the synthesis of asperosaponin VI in D. asper and elucidate the transcriptional regulatory mechanism of JA-induced accumulation of asperosaponin VI.

Biomarkers Related to Interferon-γ Pathway in Myocardial Ischemia-Reperfusion Injury and the Potential Molecular Mechanisms.

Although reperfusion therapy can reduce the mortality of myocardial infarction, it results in myocardial ischemia-reperfusion injury (MIRI). The molecular mechanism by which the interferon-γ pathway affects MIRI is unclear, so we addressed this problem by mining transcriptome and single-cell sequencing data. The GSE160516 and GSE83472 datasets, single cell RNA sequencing (scRNA-seq) data of GSE227088 dataset and 182 interferon-γ pathway related genes (IRGs) were retrieved and incorporated into this study. The differentially expressed genes (DEGs) between MIRI and control samples were searched, the candidate genes were obtained by intersecting DEGs with IRGs. The protein-protein interaction (PPI) analysis was utilized for selecting key genes from candidate genes. Moreover, key genes with significant expression and consistent trend in GSE160516 and GSE83472 datasets were selected as biomarkers. The biological functions and regulatory mechanism of biomarkers were investigated by enrichment analysis and predicting the upstream molecules targeting them. Ulteriorly, cell clusters were identified via unsupervised cluster analysis and merged into different cell types by cell annotation. Cell types in which biomarkers observably and differentially expressed were selected as crucial cell types. Finally, cell communication and pseudo-time analysis were implemented based on crucial cell types. Totally 34 candidate genes were searched by overlapping 1,930 DEGs with 182 IRGs. Nine key genes were singled out from candidate genes, of which Myd88 and Trp53 were significantly upregulated in the MIRI samples of GSE160516 and GSE83472 datasets, so they were identified as biomarkers. Besides, they participated in pathways such as ribosome, spliceosome and cell cycle. Myd88 might be simultaneously regulated by mmu-miR-361-3p and mmu-miR-421-3p, and Trp53 could be regulated by Abl1 and Tead2. Totally 25 cell clusters were merged into six cell types, of which three crucial cell types (cardiomyocyte, fibroblast, and macrophage) could interact with each other through receptor-ligand. Pseudo-time analysis revealed states 1, 2, and 5 of macrophages might be associated with MIRI. Two biomarkers (Myd88 and Trp53) related to IRGs in MIRI were mined, providing a reference for elucidating the mechanism of interferon-γ pathway on MIRI.

Two independent regulatory mechanisms synergistically contribute to P450-mediated insecticide resistance in a lepidopteran pest, Spodoptera exigua

BackgroundCytochrome P450 enzymes play a pivotal role in the detoxification of plant allelochemicals and insecticides. Overexpression of P450 genes has been proven to be involved in insecticide resistance in insects. However, the molecular mechanisms underlying the regulation of P450 genes in insects are poorly understood.ResultsHere, we determine that upregulation of CYP321B1 confers resistance to organophosphate (chlorpyrifos) and pyrethroid (cypermethrin and deltamethrin) insecticides in the resistant Spodoptera exigua strain. Enhanced expression of transcription factors CncC/Maf contributes to the increase in the expression of CYP321B1 in the resistant strain. Reporter gene assays and site-directed mutagenesis analyses confirm that a specific binding site is crucial for binding CncC/Maf to activate the expression of CYP321B1. In addition, creation of a new binding site resulting from the cis-mutations in the promoter region of CYP321B1 in the resistant strain facilitates the binding of the POU/homeodomain transcription factor Nubbin, and further enhances the expression of this P450 gene. Furthermore, we authenticate that changes in both trans- and cis-regulatory elements in the promoter region of CYP321B1 act in combination to modulate the promoter activity in a synergistic manner.ConclusionsCollectively, these results demonstrate that two distinct but synergistic mechanisms coordinately result in the overexpression of CYP321B1 involved in insecticide resistance in an agriculturally important insect pest, S. exigua. The information on mechanisms of metabolic resistance could help to understand the development of resistance to insecticides by other pests and contribute to designing effective integrated pest management strategies for the pest control.

Molecular regulation of whole genome DNA methylation in heat stress response of dairy cows

BackgroundHeat stress seriously affects the production and health of dairy cows and is a key factor limiting the sustainable development of the dairy industry. DNA methylation serves as an important epigenetic regulatory mechanism closely associated with an animal's response to heat stress. However, the specific molecular mechanism of DNA methylation in cows' heat stress response is not fully understood.ResultsIn this study, whole genome bisulfite sequencing analysis of blood identified 49861 specific differentially methylated regions corresponding to 7613 differentially methylated genes between spring and summer dairy cows. Among them, 4069 the promoter region of differentially methylated genes were significantly enriched in key biological pathways such as substance transport, reactive oxygen species metabolism, signal transduction, and energy metabolism. By integrating the expression data of 4069 promoter differentially methylated genes, 157 genes were further screened, and their DNA methylation levels were negatively correlated with gene expression. The changes in DNLZ, GNAS, and SMAD5 genes were most significant, and network analysis showed that DNLZ gene has high connectivity in the protein–protein interaction network, indicating its potential key function in heat stress response. Experimental verification shows that under heat stress conditions, the methylation level of CpG islands in the promoter region of DNLZ gene significantly increases, and its methylation level is significantly negatively correlated with gene expression level. The Dual-luciferase reporter assays using constructs containing the DNLZ promoter reporter gene experiment further confirms that promoter methylation significantly inhibits DNLZ transcriptional activity, and the higher the degree of methylation, the stronger the inhibitory effect.ConclusionsThe research results provide new insights into the mechanism of heat stress-related DNA methylation in dairy cows, clarify the key roles of genes such as DNLZ, and provide potential target genes and epigenetic markers for the cultivation of heat-resistant dairy cows.