Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize.

Chromatin in eukaryotes folds into a complex three-dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low-Pi treatment led to greater chromatin volume. Furthermore, low-Pi stress increased the insulation score and the number of TAD-like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD-like boundaries, whereas RdDM peak levels at conserved TAD-like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome-wide RdDM sites near TAD-like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low-Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low-Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP-seq results revealed that ZmDDM1A could bind to Pi- and root development-related genes. Strong associations were found between interacting genes in significantly different chromatin-interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low-Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics.

Transcriptomic and genome-wide association study reveal long noncoding RNAs responding to nitrogen deficiency in maize.

BACKGROUND: Long noncoding RNAs (lncRNAs) play important roles in essential biological processes. However, our understanding of lncRNAs as competing endogenous RNAs (ceRNAs) and their responses to nitrogen stress is still limited. RESULTS: Here, we surveyed the lncRNAs and miRNAs in maize inbred line P178 leaves and roots at the seedling stage under high-nitrogen (HN) and low-nitrogen (LN) conditions using lncRNA-Seq and small RNA-Seq. A total of 894 differentially expressed lncRNAs and 38 different miRNAs were identified. Co-expression analysis found that two lncRNAs and four lncRNA-targets could competitively combine with ZmmiR159 and ZmmiR164, respectively. To dissect the genetic regulatory by which lncRNAs might enable adaptation to limited nitrogen availability, an association mapping panel containing a high-density single-nucleotide polymorphism (SNP) array (56,110 SNPs) combined with variable LN tolerant-related phenotypes obtained from hydroponics was used for a genome-wide association study (GWAS). By combining GWAS and RNA-Seq, 170 differently expressed lncRNAs within the range of significant markers were screened. Moreover, 40 consistently LN-responsive genes including those involved in glutamine biosynthesis and nitrogen acquisition in root were identified. Transient expression assays in Nicotiana benthamiana demonstrated that LNC_002923 could inhabit ZmmiR159-guided cleavage of Zm00001d015521. CONCLUSIONS: These lncRNAs containing trait-associated significant SNPs could consider to be related to root development and nutrient utilization. Taken together, the results of our study can provide new insights into the potential regulatory roles of lncRNAs in response to LN stress, and give valuable information for further screening of candidates as well as the improvement of maize resistance to LN stress.

ED-71 ameliorates bone regeneration in type 2 diabetes by reducing ferroptosis in osteoblasts via the HIF1α pathway.

Eldecalcitol (ED-71), a novel active form of vitamin D, shows potential in treating osteoporosis. However, its underlying mechanisms of action remain to be determined. This study aimed to investigate the effect of ED-71 on bone regeneration and to illustrate its mode of action. The in-vitro model was developed using rat primary osteoblasts cultured under high-glucose conditions, and these cells were treated with ED-71. Additionally, an in vivo model of cranial bone defects was established in type 2 diabetic rats, and ED-71 was administered by gavage. The results demonstrated that ED-71 prevented osteoblast cell death, enhanced rat primary osteoblasts' osteogenic capacity, and attenuated the overexpression of hypoxia-inducible factor 1α (HIF1α) induced by high glucose levels. Furthermore, ED-71 increased glutathione peroxidase 4 (GPX4) levels and inhibited ferroptosis in response to hyperglycemic stimulation. Notably, interference with the HIF1α activator and ferroptosis activator Erastin significantly reduced the therapeutic effects of edetate osteolysis. These findings were further tested in vivo experiments. These results suggest that ED-71 activates the HIF1α pathway in vivo and in vitro, effectively relieving the ferroptosis induced by high glucose. Significantly, ED-71 may improve osteogenic disorders caused by diabetes.

Efficiency and mechanism of the degradation of ciprofloxacin by the oxidation of peroxymonosulfate under the catalysis of a Fe3O4/N co-doped sludge biochar.

A novel and recyclable composite material, Fe3O4/N co-doped sludge biochar (FNBC), was developed from original sludge biochar (BC) and found to have excellent stability and superior catalytic capacity during the ciprofloxacin (CIP) degradation under the action of peroxymonosulfate (PMS). In the FNBC/PMS system, an approximately complete removal of CIP was achieved within 60 min under the condition of 1.0 g/L FNBC, 3.0 mM PMS, and 20 mg/L CIP, which was about 2.08 times of that in BC/PMS system (48.01%). Besides, FNBC/PMS system could effectively remove CIP under the influence of wide pH (2.0-10.0) or inorganic ions compared with BC/PMS system. Moreover, it was found that there were radical produced under the effect of Fe element, defects, functional groups, pyridinic N and pyrrolic N and non-radical caused by graphitic N, carbon atoms next to the iron atoms and better adsorption capacity in the FNBC/PMS system. It was observed that the contribution of hydroxyl radical (•OH), sulfate radical (SO4•-) and singlet oxygen (1O2), which were the main reactive oxygen species, during the CIP degradation, were 75.80%, 11.49% and 10.26%, respectively. Furthermore, total organic carbon (TOC) variation was analyzed and the degradation pathway of CIP was speculated. The application of this material could combine the recycling of sludge with the effective degradation of refractory organic pollutant, providing an environmentally friendly and economic method.

[Degradation of Ciprofloxacin by Activating Peroxymonosulfate with Sludge Biochar].

Sludge biochar(BC), which was prepared by the pyrolysis of waste-activated sludge at 450℃, was applied for peroxymonosulfate(PMS) activation to construct a BC/PMS system for ciprofloxacin(CIP) degradation. The physical and chemical properties of BC were studied using scanning electron microscopy(SEM), an energy dispersive spectrometer(EDS), a Fourier transform infrared spectrometer(FTIR), X-ray diffraction(XRD), a Zeta potential analyzer, and electron paramagnetic resonance spectroscopy(EPR). The effects of BC dosage, PMS dosage, initial pH value, and inorganic anions on CIP removal in the BC/PMS system were investigated. Further, the degradation mechanism of the BC/PMS system was speculated through the free radical quenching experiment and X-ray photoelectron spectroscopy(XPS) analysis. The results showed that the CIP degradation rate was 49.09% at a BC dosage of 1.0 g·L-1, PMS of 3.0 mmol·L-1, CIP of 20 mg·L-1, and pH of 6.0 in 120 min. SO42- and NO3- had no obvious effect on the removal of CIP in the BC/PMS system, whereas HCO3- and Cl-could inhibit CIP degradation significantly. The CIP removal in the BC/PMS system was attributed to the common function of the radical pathway dominated by ·OH and SO4-· and the non-radical pathway dominated by 1O2. The CIP degradation pathway mainly included piperazine ring opening and hydroxylation reaction.

Functional analysis of ZmG6PE reveals its role in responses to low-phosphorus stress and regulation of grain yield in maize.

A previous metabolomic and genome-wide association analysis of maize screened a glucose-6-phosphate 1-epimerase (ZmG6PE) gene, which responds to low-phosphorus (LP) stress and regulates yield in maize's recombinant inbred lines (RILs). However, the relationship of ZmG6PE with phosphorus and yield remained elusive. This study aimed to elucidate the underlying response mechanism of the ZmG6PE gene to LP stress and its consequential impact on maize yield. The analysis indicated that ZmG6PE required the Aldose_epim conserved domain to maintain enzyme activity and localized in the nucleus and cell membrane. The zmg6pe mutants showed decreased biomass and sugar contents but had increased starch content in leaves under LP stress conditions. Combined transcriptome and metabolome analysis showed that LP stress activated plant immune regulation in response to the LP stress through carbon metabolism, amino acid metabolism, and fatty acid metabolism. Notably, LP stress significantly reduced the synthesis of glucose-1-phosphate, mannose-6-phosphate, and ß-alanine-related metabolites and changed the expression of related genes. ZmG6PE regulates LP stress by mediating the expression of ZmSPX6 and ZmPHT1.13. Overall, this study revealed that ZmG6PE affected the number of grains per ear, ear thickness, and ear weight under LP stress, indicating that ZmG6PE participates in the phosphate signaling pathway and affects maize yield-related traits through balancing carbohydrates homeostasis.

Mitochondria-Associated Endoplasmic Reticulum Membranes: Inextricably Linked with Autophagy Process.

Mitochondria-associated membranes (MAMs), physical connection sites between the endoplasmic reticulum (ER) and the outer mitochondrial membrane (OMM), are involved in numerous cellular processes, such as calcium ion transport, lipid metabolism, autophagy, ER stress, mitochondria morphology, and apoptosis. Autophagy is a highly conserved intracellular process in which cellular contents are delivered by double-membrane vesicles, called autophagosomes, to the lysosomes for destruction and recycling. Autophagy, typically triggered by stress, eliminates damaged or redundant protein molecules and organelles to maintain regular cellular activity. Dysfunction of MAMs or autophagy is intimately associated with various diseases, including aging, cardiovascular, infections, cancer, multiple toxic agents, and some genetic disorders. Increasing evidence has shown that MAMs play a significant role in autophagy development and maturation. In our study, we concentrated on two opposing functions of MAMs in autophagy: facilitating the formation of autophagosomes and inhibiting autophagy. We recognized the link between MAMs and autophagy in the occurrence and progression of the diseases and therefore collated and summarized the existing intrinsic molecular mechanisms. Furthermore, we draw attention to several crucial data and open issues in the area that may be helpful for further study.

Mining synergistic genes for nutrient utilization and disease resistance in maize based on co-expression network and consensus QTLs.

Nutrient restrictions and large-scale emergence of diseases are threatening the maize production. Recent findings demonstrated that there is a certain synergistic interaction between nutrition and diseases pathways in model plants, however there are few studies on the synergistic genes of nutrients and diseases in maize. Thus, the transcriptome data of nitrogen (N) and phosphorus (P) nutrients and diseases treatments in maize, rice, wheat and Arabidopsis thaliana were collected in this study, and four and 22 weighted co-expression modules were obtained by using Weighted Gene Co-expression Network Analysis (WGCNA) in leaf and root tissues, respectively. With a total of 5252 genes, MFUZZ cluster analysis screened 26 clusters with the same expression trend under nutrition and disease treatments. In the meantime, 1427 genes and 22 specific consensus quantitative trait loci (scQTLs) loci were identified by meta-QTL analysis of nitrogen and phosphorus nutrition and disease stress in maize. Combined with the results of cluster analysis and scQTLs, a total of 195 consistent genes were screened, of which six genes were shown to synergistically respond to nutrition and disease both in roots and leaves. Moreover, the six candidate genes were found in scQTLs associated with gray leaf spot (GLS) and corn leaf blight (CLB). In addition, subcellular localization and bioinformatics analysis of the six candidate genes revealed that they were primarily expressed in endoplasmic reticulum, mitochondria, nucleus and plasma membrane, and were involved in defense and stress, MeJA and abscisic acid response pathways. The fluorescence quantitative PCR confirmed their responsiveness to nitrogen and phosphorus nutrition as well as GLS treatments. Taken together, findings of this study indicated that the nutrition and disease have a significant synergistic response in maize.

Effects of seepage and weak interlayer on the failure modes of surrounding rock: model tests and numerical analysis.

The presence of weak interlayers and groundwater are common adverse geological conditions in tunnels. To investigate the modes of failure of rock masses surrounding tunnels owing to weak interlayers and groundwater, model tests and numerical simulations were conducted in this study based on two cases, and a model that considers only the weak interlayer was conducted for comparison. Based on the tests, differences between two models in terms of rock pressure, displacement, cracks and strain were analysed. The results reveal that the presence of groundwater has a significant effect on the space-time distribution of stress, displacement and cracks in the surrounding rock. Furthermore, based on the numerical model, the seepage field was analysed in terms of pore water pressure, permeability and the seepage process to understand the joint action of groundwater and weak interlayer on the failure mechanism of tunnels. The results show that the groundwater and interlayer complement each other to induce the failure mode of the surrounding rock. The water accelerates slip in the interlayer and the development of cracks. Conversely, low strength, muddy weak interlayers serve as the channels of water flow, resulting in deformations and cracks at different locations and different failure modes.