Magnetic nanomagnetic nanoparticles combining with Slit2 gene and bone marrow mononuclear cells to improve cognitive dysfunction in rats with chronic cerebral ischemia.

Purpose: Cognitive dysfunction caused by chronic cerebral hypoperfusion (CCH) is the leading cause of vascular dementia. Therefore, it is necessary to explore the mechanism that causes cerebral injury and find an effective therapy. Methods: Bone marrow mononuclear cells (BMMNCs) were extracted to detect the activity by CCK-8 kit and verify the transfection efficiency using reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR). A CCH rat model was established. Superparamagnetic iron oxide nanoparticles (BMPs)-PEI-Slit2/BMMNCs were injected into the tail vein and intervened with an external magnetic field. Hematoxylin and eosin staining was used to observe the pathological changes in brain tissue. The Slit/Robo pathway-related proteins Slit2 and Robo4 were detected by RT-qPCR and Western blotting. Results: The neurological score of the CCH group significantly increased compared with that of the sham group (P<0.05). The levels of brain injury markers S-100ß and NSE were significantly higher in the CCH group than in the sham group (P<0.05). Neuronal apoptosis in the frontal cortex and hippocampus of CCH rats significantly increased compared with that of the sham group (P<0.05). The expression levels of Slit2 and Robo4 mRNAs and proteins in brain tissue of CCH rats significantly increased (P<0.05). The neurological function scores of CCH rats treated with BMP-PEI-Slit2/BMMNC significantly increased after Robo4 siRNA administration (P<0.05). Conclusion: BMP combination with the CCH-related gene Slit2 can effectively improve the efficiency of BMMNC transplantation in treatment.

Phylogenomics and functional analysis of Glycerol-3-Phosphate Acyltransferase (GPAT) Genes: A critical role in lipid biosynthesis.

The tung tree (Vernicia fordii Hemsl.), an economically important woody plant, is widely planted for the production of high-quality tung oil. Glycerol-3-phosphate acyltransferases (GPATs), the rate-limiting enzymes in triacylglycerol synthesis, play an important role in seed oil biosynthesis. In this study, we performed a genome-wide analysis of VfGPATs. A total of 9 VfGPATs were identified from the whole tung genome, and phylogenetic analysis divided the VfGPATs into three major clades: clade II (VfGPAT9), clade III (VfATS1) and clade IV (VfGPAT1 ~ 8). Subcellular localization analysis revealed that five VfGPATs (1, 5, 6, 8, and 9) are localized in the endoplasmic reticulum, and four VfGPATs (3-1, 3-2, 3-3, and ATS1) are localized in the chloroplast. Overexpression of VfGPATs in Arabidopsis thaliana revealed that the oil content in VfGPAT8- and VfGPAT9-transgenic plants were significantly increased by 26.60 and 55.94% compared to the wild-type. Transient expression of VfGPAT8 + VfFADX and VfGPAT9 + VfFADX could promote the synthesis of α-eleostearic acid and enhance the accumulation of lipid droplets in tobacco (Nicotiana benthamiana) leaves. We further tested the enzymatic activities of VfGPAT8 and VfGPAT9 with the yeast double mutant strain ZAFU1. The results showed that VfGPAT8 complemented the phosphatidate biosynthetic defect in the double mutant, while VfGPAT9 could not, suggesting that VfGPAT8 has a high acetyltransferase activity. However, altering serine (S) residue at position 113 of VfGPAT9 to threonine (T) could restore its enzymatic activity. This study provided important insights into the evolutionary history of VfGPATs and will promote the genetic improvement of tung trees and related species.

Metabolic basis for superior antioxidant capacity of red-fleshed peaches.

Peach fruit is an important natural source of phenolic compounds that are well-known to have health benefits, but their metabolic basis remain elusive. Here, we report on phenolic compounds accumulation and antioxidant activity of ripe fruits in peach. A considerable variation in phenolic compounds content was observed among peach germplasm, with significantly higher levels detected in red-fleshed peaches compared to non-red-fleshed peaches. Antioxidant activity of crude extracts from ripe fruits showed significant differences among peach germplasm, with red-fleshed peaches having the strongest antioxidant activity. Intriguingly, it was observed that total phenolics instead of anthocyanins were strongly associated with antioxidant activity. Phenolic compounds content and antioxidant activity showed dynamic changes throughout fruit development, and these were much higher in the peel than in the flesh. Metabolomic analysis unveiled a coordinated accumulation of anthocyanins as well as key components of flavonoids and phenolic acids, which endows red-fleshed peaches with superior antioxidant activity.

A PpEIL2/3-PpNAC1-PpWRKY14 module regulates fruit ripening by modulating ethylene production in peach.

WRKY transcription factors play key roles in plant resistance to various stresses, but their roles in fruit ripening remain largely unknown. Here, we report a WRKY gene PpWRKY14 involved in the regulation of fruit ripening in peach. The expression of PpWRKY14 showed an increasing trend throughout fruit development. PpWRKY14 was a target gene of PpNAC1, a master regulator of peach fruit ripening. PpWRKY14 could directly bind to the promoters of PpACS1 and PpACO1 to induce their expression, and this induction was greatly enhanced when PpWRKY14 formed a dimer with PpNAC1. However, the transcription of PpNAC1 could be directly suppressed by two EIN3/EIL1 genes, PpEIL2 and PpEIL3. The PpEIL2/3 genes were highly expressed at the early stages of fruit development, but their expression was programmed to decrease significantly during the ripening stage, thus derepressing the expression of PpNAC1. These results suggested a PpEIL2/3-PpNAC1-PpWRKY14 module that regulates fruit ripening by modulating ethylene production in peach. Our results provided an insight into the regulatory roles of EIN3/EIL1 and WRKY genes in fruit ripening.

Chromosome-level genome of Scolopendra mutilans provides insights into its evolution.

Report the first chromosome level genome of myriapod Scolopendra mutilans. Reveal gene expansions for importance to adapt. Annotate nine Hox cluster genes in this genome.

The SMXL8-AGL9 module mediates crosstalk between strigolactone and gibberellin to regulate strigolactone-induced anthocyanin biosynthesis in apple.

Although the strigolactone (SL) signaling pathway and SL-mediated anthocyanin biosynthesis have been reported, the molecular association between SL signaling and anthocyanin biosynthesis remains unclear. In this study, we identified the SL signal transduction pathway associated with anthocyanin biosynthesis and the crosstalk between gibberellin (GA) and SL signaling in apple (Malus × domestica). ELONGATED HYPOCOTYL5 (HY5) acts as a key node integrating SL signaling and anthocyanin biosynthesis, and the SL response factor AGAMOUS-LIKE MADS-BOX9 (AGL9) promotes anthocyanin biosynthesis by activating HY5 transcription. The SL signaling repressor SUPPRESSOR OF MAX2 1-LIKE8 (SMXL8) interacts with AGL9 to form a complex that inhibits anthocyanin biosynthesis by downregulating HY5 expression. Moreover, the E3 ubiquitin ligase PROTEOLYSIS1 (PRT1) mediates the ubiquitination-mediated degradation of SMXL8, which is a key part of the SL signal transduction pathway associated with anthocyanin biosynthesis. In addition, the GA signaling repressor REPRESSOR-of-ga1-3-LIKE2a (RGL2a) mediates the crosstalk between GA and SL by disrupting the SMXL8-AGL9 interaction that represses HY5 transcription. Taken together, our study reveals the regulatory mechanism of SL-mediated anthocyanin biosynthesis and uncovers the role of SL-GA crosstalk in regulating anthocyanin biosynthesis in apple.

Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network.

Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utilize expression data to identify the most physiologically relevant targets. Although these methods are effective, they typically require a large sample size and high-depth sequencing to detect potential miRNA-target pairs, thereby limiting their applicability in improving plant breeding. In this study, we propose a novel miRNA-target prediction framework named kmerPMTF (k-mer-based prediction framework for plant miRNA-target). Our framework effectively extracts the latent semantic embeddings of sequences by utilizing k-mer splitting and a deep self-supervised neural network. We construct multiple similarity networks based on k-mer embeddings and employ graph convolutional networks to derive deep representations of miRNAs and targets and calculate the probabilities of potential associations. We evaluated the performance of kmerPMTF on four typical plant datasets: Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, and Prunus persica. The results demonstrate its ability to achieve AUPRC values of 84.9%, 91.0%, 80.1%, and 82.1% in 5-fold cross-validation, respectively. Compared with several state-of-the-art existing methods, our framework achieves better performance on threshold-independent evaluation metrics. Overall, our study provides an efficient and simplified methodology for identifying plant miRNA-target associations, which will contribute to a deeper comprehension of miRNA regulatory mechanisms in plants.

A novel C-type lectin protein (BjCTL5) interacts with apoptosis stimulating proteins of p53 (ASPP) to activate NF-κB signaling pathway in primitive chordate.

C-type lectin proteins (CTLs), a group of pattern recognition receptors (PRRs), play pivotal roles in immune responses. However, the signal transduction and regulation of CTLs in cephalochordates have yet to be explored. In this study, we examined the composition of CTLs in Branchiostoma japonicum, identifying a total of 272 CTLs. These CTLs underwent further analysis concerning domain arrangement, tandem and segmental duplication events. A multidomain C-type lectin gene, designated as BjCTL5, encompassing CLECT, KR, CUB, MAM, and SR domains, was the focal point of our investigation. BjCTL5 exhibits ubiquitous expression across all detected tissues and is responsive to stimulation by LPS, mannose, and poly (I:C). The recombinant protein of BjCTL5 can bind to Escherichia coli and Staphylococcus aureus, inducing their agglutination and inhibiting the proliferation of S. aureus. Yeast two-hybrid, CoIP, and confocal immunofluorescence experiments revealed the interaction between BjCTL5 and apoptosis-stimulating proteins of p53, BjASPP. Intriguingly, BjCTL5 was observed to induce the luciferase activity of the NF-κB promoter in HEK293T cells. These results suggested a potential interaction between BjCTL5 and BjASPP, implicating that they involve in the activation of the NF-κB signaling pathway, which provides an evolutionary viewpoint on NF-κB signaling pathway in primitive chordate.

Functional characterization of NBS-LRR genes reveals an NBS-LRR gene that mediates resistance against Fusarium wilt.

BACKGROUND: Most disease resistance (R) genes in plants encode proteins that contain leucine-rich-repeat (LRR) and nucleotide-binding site (NBS) domains, which belong to the NBS-LRR family. The sequenced genomes of Fusarium wilt-susceptible Vernicia fordii and its resistant counterpart, Vernicia montana, offer significant resources for the functional characterization and discovery of novel NBS-LRR genes in tung tree. RESULTS: Here, we identified 239 NBS-LRR genes across two tung tree genomes: 90 in V. fordii and 149 in V. montana. Five VmNBS-LRR paralogous were predicted in V. montana, and 43 orthologous were detected between V. fordii and V. montana. The orthologous gene pair Vf11G0978-Vm019719 exhibited distinct expression patterns in V. fordii and V. montana: Vf11G0978 showed downregulated expression in V. fordii, while its orthologous gene Vm019719 demonstrated upregulated expression in V. montana, indicating that this pair may be responsible for the resistance to Fusarium wilt in V. montana. Vm019719 from V. montana, activated by VmWRKY64, was shown to confer resistance to Fusarium wilt in V. montana by a virus-induced gene silencing (VIGS) experiment. However, in the susceptible V. fordii, its allelic counterpart, Vf11G0978, exhibited an ineffective defense response, attributed to a deletion in the promoter's W-box element. CONCLUSIONS: This study provides the first systematic analysis of NBS-LRR genes in the tung tree and identifies a candidate gene that can be utilized for marker-assisted breeding to control Fusarium wilt in V. fordii.

Rolling bearing fault diagnosis based on Gramian angular difference field and improved channel attention model.

Fault diagnosis of rolling bearings is a critical task, and in previous research, convolutional neural networks (CNN) have been used to process vibration signals and perform fault diagnosis. However, traditional CNN models have certain limitations in terms of accuracy. To improve accuracy, we propose a method that combines the Gramian angular difference field (GADF) with residual networks (ResNet) and embeds frequency channel attention module (Fca) in the ResNet to diagnose rolling bearing fault. Firstly, we used GADF to convert the signals into RGB three-channel fault images during data preprocessing. Secondly, to further enhance the performance of the model, on the foundation of the ResNet we embedded the frequency channel attention module with discrete cosine transform (DCT) to form Fca, to effectively explores the channel information of fault images and identifies the corresponding fault characteristics. Finally, the experiment validated that the accuracy of the new model reaches 99.3% and the accuracy reaches 98.6% even under an unbalanced data set, which significantly improves the accuracy of fault diagnosis and the generalization of the model.

Eco-friendly managements and molecular mechanisms for improving postharvest quality and extending shelf life of kiwifruit: A review.

Kiwifruit (Actinidia spp.) is a commercially important horticultural fruit crop worldwide. Kiwifruit contains numerous minerals, vitamins, and dietary phytochemicals, that not only responsible for the flavor but can also serve as adjuncts in the treatment of diabetes, digestive disorders, cardiovascular system, cancer and heart disease. However, fruit quality and shelf life affect consumer's acceptance and production chain. Understanding the methods of fruit storage preservation, as well as their biochemical, physiological, and molecular basis is essential. In recent years, eco-friendly (comprehensive and environmentally friendly) treatments such as hot water, ozone, chitosan, quercetin, and antifungal additive from biocontrol bacteria or yeast have been applied to improve postharvest fruit quality with longer shelf life. This review provides a comprehensive overview of the latest advancements in control measures, applications, and mechanisms related to water loss, chilling injury, and pathogen diseases in postharvest kiwifruit. Further studies should utilize genome editing techniques to enhance postharvest fruit quality and disease resistance through site-directed bio-manipulation of the kiwifruit genome.

Functional and kinetics of two efficient phenylalanine ammonia lyase from Pyrus bretschneideri.

BACKGROUND: The enzyme phenylalanine ammonia lyase (PAL) controls the transition from primary to secondary metabolism by converting L-phenylalanine (L-Phe) to cinnamic acid. However, the function of PAL in pear plants (Pyrus bretschneideri) has not yet been fully elucidated. RESULTS: We identified three PAL genes (PbPAL1, PbPAL2 and PbPAL3) from the pear genome by exploring pear genome databases. The evolutionary tree revealed that three PbPALs were classified into one group. We expressed PbPAL1 and PbPAL2 recombinant proteins, and the purified PbPAL1 and PbPAL2 proteins showed strict substrate specificity for L-Phe, no activity toward L-Tyr in vitro, and modest changes in kinetics and enzyme characteristics. Furthermore, overexpression of PbAL1 and PbPAL1-RNAi, respectively, and resulted in significant changes in stone cell and lignin contents in pear fruits. The results of yeast one-hybrid (Y1H) assays that PbWLIM1 could bind to the conserved PAL box in the PbPAL promoter and regulate the transcription level of PbPAL2. CONCLUSIONS: Our findings not only showed PbPAL's potential role in lignin biosynthesis but also laid the foundation for future studies on the regulation of lignin synthesis and stone cell development in pear fruit utilizing molecular biology approaches.

Competitive binding of circCCDC6 to microRNA-128-3p activates TXNIP/NLRP3 pathway and promotes cerebral ischemia-reperfusion defects.

OBJECTIVE: Circular RNAs (circRNAs) are enriched in the brain and involved in various central nervous system diseases. The potential role of circCCDC6 in cerebral ischemia-reperfusion defects was partly elucidated in the work. METHODS: A middle cerebral artery occlusion/reperfusion (MCAO/R) rat model and an oxygen-glucose deprivation and re-oxygenation (OGD/R)-treated SH-SY5Y cell model were constructed. CircCCDC6 expression in the two models was examined, and circCCDC6-involved mechanisms in neuronal pyroptosis and inflammation were analyzed through loss- and gain-of-function assays. RESULTS: MCAO/R rat brain tissues and OGD/R-treated SH-SY5Y cells exhibited upregulated circCCDC6. Silencing circCCDC6 attenuated neuronal pyroptosis and inflammation in the brain tissue of MCAO/R rats. Overexpressing circCCDC6 or inhibiting miR-128-3p stimulated OGD/R-induced pyroptosis and inflammation in SH-SY5Y cells, while upregulating miR-128-3p attenuated OGD/R injury. CircCCDC6 silencing-induced effects on SH-SY5Y cells were antagonized by TXNIP overexpression. CONCLUSION: Mechanistically, circCCDC6 mediates miR-128-3p and activates TXNIP/NLRP3, thereby promoting OGD/R-induced neuronal pyroptosis and inflammation. CircCCDC6 may provide a new strategy for the treatment of MCAO/R.

Nomogram-based prediction model for survival of COVID-19 patients: A clinical study.

The study aim to construct an effective model for predicting the survival period of COVID-19 patients. METHODS: Clinical data of 386 COVID-19 patients were collected from December 2022 to January 2023. The patients were randomly divided into training and validation cohorts in a 7:3 ratio. LASSO regression and multivariate Cox regression analyses were used to identify prognostic factors, and a nomogram was constructed. Nomogram was evaluated using decision curve analysis, receiver operating characteristic curve, consistency index (c-index), and calibration curve. RESULTS: 86 patients (22.3%) died. A new nomogram for predicting the survival was established based on age, resting oxygen saturation, Blood urea nitrogen (BUN), c-reactive protein-to-albumin ratio (CAR), and pneumonia visual score. The decision curve indicated high clinical applicability. The nomogram c-indexes in the training and validation cohorts were 0.846 and 0.81, respectively. The area under the curves (AUCs) for the 15-day and 30-day survival probabilities were 0.906 and 0.869 in the training cohort, and 0.851 and 0.843 in the validation cohort. The calibration curves demonstrated consistency between predicted and actual survival probabilities. CONCLUSIONS: Our nomogram has the capacity to assist clinical practitioners in estimating the survival rate of COVID-19 patients, thereby facilitating more optimal management strategies and therapeutic interventions with substantial clinical applicability.

Identification and Characterization of the Very-Low-Density Lipoprotein Receptor Gene from Branchiostoma belcheri: Insights into the Origin and Evolution of the Low-Density Lipoprotein Receptor Gene Family.

Low-density lipoprotein receptors (LDLRs) are a class of cell-surface endocytosis receptors that are mainly involved in cholesterol homeostasis and cellular signal transduction. Very-low-density lipoprotein receptors (VLDLRs), which are members of the LDLR family, have been regarded as multi-function receptors that fulfill diverse physiological functions. However, no VLDLR gene has been identified in protochordates to date. As a representative protochordate species, amphioxi are the best available example of vertebrate ancestors. Identifying and characterizing the VLDLR gene in amphioxi has high importance for exploring the evolutionary process of the LDLR family. With this study, a new amphioxus VLDLR gene (designated AmphiVLDLR) was cloned and characterized using RACE-PCR. The 3217 nt transcript of the AmphiVLDLR had a 2577 nt ORF, and the deduced 858 amino acids were highly conserved within vertebrate VLDLRs according to their primary structure and three-dimensional structure, both of which contained five characteristic domains. In contrast to other vertebrate VLDLRs, which had a conserved genomic structure organization with 19 exons and 18 introns, the AmphiVLDLR had 13 exons and 12 introns. The results of a selective pressure analysis showed that the AmphiVLDLR had numerous positive selection sites. Furthermore, the tissue expression of AmphiVLDLR using RT-qPCR showed that AmphiVLDLR RNA expression levels were highest in the gills and muscles, moderate in the hepatic cecum and gonads, and lowest in the intestines. The results of the evolutionary analysis demonstrated that the AmphiVLDLR gene is a new member of the VLDLR family whose family members have experienced duplications and deletions over the evolutionary process. These results imply that the functions of LDLR family members have also undergone differentiation. In summary, we found a new VLDLR gene homolog (AmphiVLDLR) in amphioxi. Our results provide insight into the function and evolution of the LDLR gene family.

Two monolignoid biosynthetic genes 4-coumarate:coenzyme A ligase (4CL) and p-coumaric acid 3-hdroxylase (C3H) involved in lignin accumulation in pear fruits.

One of the most important factors impacting the quality of pear fruit is the presence of stone cells and lignin. Lignin is the main component of stone cells in pear fruits. Two monolignoid biosynthetic genes 4-coumarate:coenzyme A ligase (4CL) and p-coumaric acid 3-hdroxylase (C3H) are involved in lignin accumulation in pear fruits. However, the functions of these genes in lignin biosynthesis were excluded in pear. In our study, we isolated and cloned Pb4CL11 (GenBank: KM455955.1) and PbC3H1 (GenBank: KM373790.1) from pear, which contained 1644 bp encoded 54 amino acids (AA), and 1539 bp encoded 513 AA, respectively. The expression of Pb4CL11 and PbC3H1 in Arabidopsis thaliana led to an increase in cell wall thickness for intervascular fibers and xylem cells and lignin content. Overexpression of Pb4CL11 and PbC3H1 in A. thaliana can significantly increase the expression of AtPAL, AtC4H, AtHCT, AtC3H, AtCCOMT, AtCCR, AtF5H, AtCOMT, AtCAD4 and AtCAD5 with promotion of lignin biosynthesis. Taken together, our study's findings not only demonstrated the probable function of Pb4CL11 and PbC3H1 in lignin biosynthesis but also laid the groundwork for future studies using molecular biological methods to control lignin production and the formation of stone cells in pear fruits.

Review: WRKY transcription factors: Understanding the functional divergence.

WRKY transcription factors (TFs) play crucial roles in the growth and development of plants and their response to environmental changes. WRKY TFs have been detected in sequenced plant genomes. The functions and regulatory networks of many WRKY TFs, especially from Arabidopsis thaliana (AtWRKY TFs), have been revealed, and the origin of WRKY TFs in plants is clear. Nonetheless, the relationship between WRKY TFs function and classification is unclear. Furthermore, the functional divergence of homologous WRKY TFs in plants is unclear. In this review, WRKY TFs were explored based on WRKY-related literature published from 1994 to 2022. WRKY TFs were identified in 234 species at the genome and transcriptome levels. The biological functions of ∼ 71 % of AtWRKY TFs were uncovered. Although functional divergence occurred in homologous WRKY TFs, different WRKY TF groups had no preferential function.