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The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid ‘Yuluxiang’ pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm. Using the constructed pangenome, we identified 21 224 gene PAVs (Presence-absence variation) and 1 158 812 SNPs (Single Nucleotide Polymorphism) in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, PAV-based analysis provides additional insights into the pear population structure. In addition, some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in ‘Xuehuali’ which is vital for pear quality. PsbMGH3.1 may play a role in the IAA pathway, contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene. This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.

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.

Abstract 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.

Abstract 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.

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.

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.

Abstract Background MYB transcription factors are widely distributed in the plant kingdom and play key roles in regulatory networks governing plant metabolism and biochemical and physiological processes. Results Here, we first determined the R2R3-MYB genes in five Euphorbiaceae genomes. The three Trp (W) residues from the first MYB domain (R2) were absolutely conserved, whereas the first W residue from the second MYB domain (R3) was preferentially mutated. The R2R3-MYBs were clustered into 48 functional subfamilies, of which 34 had both R2R3-MYBs of Euphorbiaceae species and AtMYBs, and four contained only Euphorbiaceae R2R3-MYBs. The whole-genome duplication (WGD) and/or segmental duplication (SD) played key roles in the expansion of the R2R3-MYB family. Unlike paralogous R2R3-MYB family members, orthologous R2R3-MYB members contained a higher selective pressure and were subject to a constrained evolutionary rate. VfMYB36 was specifically expressed in fruit, and its trend was consistent with the change in oil content, indicating that it might be involved in oil biosynthesis. Overexpression experiments showed that VfMYB36 could significantly provide linolenic acid (C18:3) content, which eventually led to a significant increase in oil content. Conclusion Our study first provides insight into understanding the evolution and expression of R2R3-MYBs in Euphorbiaceae species, and also provides a target for the production of biomass diesel and a convenient way for breeding germplasm resources with high linolenic acid content in the future.

Purpose: 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.

Abstract Glioblastoma (GBM) is the most common primary intracranial tumor in the central nervous system, and resistance to temozolomide is an important reason for the failure of GBM treatment. We screened out that Solute Carrier Family 2 Member 10 (SLC2A10) is significantly highly expressed in GBM with a poor prognosis, which is also enriched in the NF-E2 p45-related factor 2 (NRF2) signalling pathway. The NRF2 signalling pathway is an important defence mechanism against ferroptosis. SLC2A10 related LINC02381 is highly expressed in GBM, which is localized in the cytoplasm/exosomes, and LINC02381 encoded micropeptides are localized in the exosomes. The micropeptide encoded by LINC02381 may be a potential treatment strategy for GBM, but the underlying mechanism of its function is not precise yet. We put forward the hypothesis: “The micropeptide encoded by LINC02381 regulates ferroptosis through the glucose transporter SLC2A10 in GBM.” This study innovatively used machine learning for micropeptide to provide personalized diagnosis and treatment plans for precise treatment of GBM, thereby promoting the development of translational medicine. The study aimed to help find new disease diagnoses and prognostic biomarkers and provide a new strategy for experimental scientists to design the downstream validation experiments.

Woody oil plants are the most productive oil-bearing species that produce seeds with high levels of valuable triacylglycerols (TAGs). TAGs and their derivatives are the raw materials for many macromolecular bio-based products, such as nylon precursors, and biomass-based diesel. Here, we identified 280 genes encoding seven distinct classes of enzymes (i.e., G3PAT, LPAAT, PAP, DGAT, PDCT, PDAT, and CPT) involved in TAGs-biosynthesis. Several multigene families are expanded by large-scale duplication events, such as G3PATs, and PAPs. RNA-seq was used to survey the expression profiles of these TAG pathway-related genes in different tissues or development, indicating functional redundancy for some duplicated genes originated from the large-scale duplication events, and neo-functionalization or sub-functionalization for some of them. Sixty-two genes showed strong, preferential expression during the period of rapid seed lipid synthesis, suggesting that their might represented the core TAG-toolbox. We also revealed for the first time that there is no PDCT pathway in Vernicia fordii and Xanthoceras sorbifolium. The identification of key genes involved in lipid biosynthesis will be the foundation to plan strategies to develop woody oil plant varieties with enhanced processing properties and high oil content.

Estrogen, as a pleiotropic endocrine hormone, not only regulates the physiological functions of peripheral tissues but also exerts vital neuroregulatory effects in the central nervous system (CNS), such as the development of neurons and the formation of neural network connections, wherein rapid estrogen-mediated reactions positively stimulate spinogenesis and regulate synaptic plasticity and synaptic transmission to facilitate cognitive and memory performance. These fast non-genomic effects can be initiated by membrane-bound estrogen receptors (ERs), three best known of which are ERα, ERβ, and G protein-coupled estrogen receptor (GPER). To date, the effects of ERα and ERβ have been well studied in age-associated memory impairment, whereas there is still a lack of attention to the role of GPER in age-associated memory impairment, and there are still disputes about whether GPER indeed functions as an ER to enhance learning and memory. In this review, we provide a systematic overview of the role of GPER in age-associated memory impairment based on its expression, distribution, and signaling pathways, which might bring some inspiration for translational drugs targeting GPER for age-related diseases and update knowledge on the role of estrogen and its receptor system in the brain.

Loquat (Eriobotrya japonica Lindl.) is an evergreen fruit tree species of the Rosaceae, and its unique flowering time greatly hinders its production. To explore the artificial regulation of loquat flowering time, we removed the main inflorescence (by cutting it) to induce reflowering. For different loquat tree cultivars with different stages, the inflorescence was removed by cutting the main floral axis at two alternative positions: the upper or the lower position beneath the inflorescence, and it was found that the proportion of reflowering resulting from removing the upper position of the main floral axis of yellow-flesh loquat cultivars during the full-bloom stage was the highest. In addition, compared with those of the normal-growing panicles, the number of flower buds and branch axes of the reflowering panicles decreased significantly after cutting. Importantly, these newly produced inflorescences flowered 2–4 months later than normal-growing inflorescences did, effectively prolonging both the flowering and fruiting time. In addition, qRT-PCR results showed that EjFT1, EjFT2, EjAP1–1 and EjAP1–2 were highly expressed in the floral axis. These findings highlighted a new method for extending the production cycle of loquat and provided a reference for the flowering regulation of loquat and other economically important fruit tree species.

The plant hormone ABA (abscisic acid) plays an extremely important role in plant growth and adaptive stress, including but are not limited to seed germination, stomatal closure, pathogen infection, drought and cold stresses. Reactive oxygen species (ROS) are response molecules widely produced by plant cells under biotic and abiotic stress conditions. The production of apoplast ROS is induced and regulated by ABA, and participates in the ABA signaling pathway and its regulated plant immune system. In this review, we summarize ABA and ROS in apoplast ROS production, plant response to biotic and abiotic stresses, plant growth regulation, ABA signal transduction, and the regulatory relationship between ABA and other plant hormones. In addition, we also discuss the effects of protein post-translational modifications on ABA and ROS related factors.

The tung tree is a woody oil plant native to China and widely distributed in the subtropics. The three main species commonly known as Vernicia are V. fordii, V. montana, and V. cordata. The growth and development of V. fordii are affected by a large number of plant pathogens, such as Fusarium wilt caused by Fusarium sp. In contrast, V. montana shows significant resistance to Fusarium wilt. The leucine-rich repeat receptor-like protein kinase (LRR-RLK) is the largest class of receptor-like kinases associated with plant resistance to Fusarium wilt. Here, we identified 239 VmLRR-RLKs in V. montana, and found that there were characteristic domains of resistance to Fusarium wilt in them. Phylogenetic analysis suggested that the VmLRR-RLKs are divided into 14 subfamilies, indicating that homologous genes in the same group may have similar functions. Chromosomal localization analysis showed that VmLRR-RLKs were unevenly distributed on chromosomes, and segment duplications were the main reason for the expansion of VmLRR-RLK family members. The transcriptome data showed that six orthologous pairs were up-regulated in V. montana in response to Fusarium wilt, while the corresponding orthologous genes showed low or no expression in V. fordii in resistance Fusarium wilt, further indicating the important role of LRR-RLKs in V. montana’s resistance to infection by Fusarium spp. Our study provides important reference genes for the future use of molecular breeding to improve oil yield and control of Fusarium wilt in tung tree.

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.

The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms.

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.

DICER-likes (DCLs) proteins are the core component for non-coding RNA (ncRNA) biogenesis, playing essential roles in some biological processes. The DCL family has been characterized in model plants, such as Arabidopsis, rice, and poplar. However, the evolutionary aspect and the expression mechanism under drought stress were scarce and have never been reported and characterized in one of the most important worldwide cultivated fruit trees, peach (Prunus persica). Eight DCLs genes in the Prunus persica genome were detected, in addition to 51 DCLs in the other seven Rosaceae genomes. The phylogenetic analysis with Arabidopsis thaliana and RTL1 gene as outgroups suggested that DCL members are divided into four clades: DCL1, DCL2, DCL3, and DCL4 with several gene gain/loss events of DCL gene copies through the evolutionary tract of the Rosacea family. The number of homologous DCL copies within each clade, along with the chromosomal location indicated gene duplication event of the DCL2 gene occurred once for the subfamily Amygdaloideae and twice for Pyrus communis and Prunus dulics and trice for the P. persica on Chromosome number 7 genes. Another duplication event was found for the DCL3 gene that occurred once for all the eight Rosaceae species with no match in A. thaliana. The DCL genetic similarity and activity was evaluated using BLASTp and previously published RNA-seq data among different tissues and over different time points of peach trees exposed to drought conditions. Finally, the expression pattern of PrupeDCLs in response to drought stress was identified, and two of these members, Prupe.7G047900 and Prupe.6G363600, were found as main candidate genes for response to drought stress. Our data presented here provide useful information for a better understanding of the molecular evolution of DCL genes in Rosaceae genomes, and the function of DCLs in P. persica.

Nitrogen-containing organic compounds and nitrogenous disinfection by-products (N-DBPs) in drinking water have attracted attention in the field of water treatment. Metabolites released during algae growth contain a variety of organic nitrogen species, which are called N-DBP precursors. The aim of this paper is to elucidate how N-DBP precursors are released under UV radiation, as well as investigate the variations of their chemical properties. The results show that through UV radiation, the physiological metabolism of algal cells was disordered and the properties of their metabolites were changed. The dissolved organic nitrogen (DON) compound concentration increased rapidly from 5.38 at the beginning to 11.11 mg/L after 30 min of radiation, and then increased steadily from 11.11 to 23.71 mg/L during a further 210 min of radiation. Derivation results of the curves for algae and DON concentration variations shows that when 1 × 1010 algal cells were destroyed, 8.31 mg DON was released into the solution during the first 30 min of radiation. Low dose UV radiation brought a slight decline of the specific N-DBP formation potential due to changes in the extracellular organic matter (EOM) structure without destroying the algal cells, which was conducive to controlling the formation potential of N-DBPs. Long-time UV radiation can bring a significant increase in N-DBP formation potential. After 4 hours of ultraviolet radiation, the total formation potential of N-DBPs in the solution increased from about 84.9 μg/L to about 213.5 μg/L, 2.5 times higher than the initial solution. The N-DBP formation potential increases obviously during the first 10–30 min UV radiation, and then decreases slightly in the subsequent 30–240 min radiation. HIGHLIGHTS After ultraviolet radiation, the physiological metabolism of algal cells is disturbed and the metabolic properties are changed.; The concentration of will increase rapidly after 30 min of irradiation, and then steadily during a further 210 min of irradiation.; Under UV irradiation, the total formation potential of N-DBPs in the solution first increases then decreases with time.;

BGLU β-glucosidases in glycoside hydrolase family 1 (GH1) are involved in many processes of plant secondary metabolism. In particular, its de-glycosylation function plays an important role in the transport of lignin monolignols. No comprehensive study of the BGLU family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported yet. In this study, the 50 BGLU family members from Chinese white pear were identified. Three candidate genes, PbBGLU1, PbBGLU15, and PbBGLU16, that may be involved in lignin synthesis were screened by bioinformatics analysis and qRT-PCR. Subcellular localization showed that all three of these candidate genes were expressed in the extracellular region. Then, we analyzed the functions of PbBGLU1 and PbBGLU16. In situ hybridization analysis showed that PbBGLU1 transcripts were not only localized to some pulp cell walls, lignin deposition, and stone cell areas of a pear fruit, but that was also a small amount of enrichment in normal pear flesh cells. PbBGLU16 transcripts were only enriched in lignin deposition and stone cell areas of pear fruit. Enzyme activity analysis revealed that GST-PbBGLU1 and GST-PbBGLU16 had a stronger activity and higher catalytic efficiency for coniferin than syringin. In addition, GST-PbBGLU16 exhibited the higher activity and catalytic efficiency for the two substrates compared with GST-PbBGLU1. The transformation of PbBGLU1 and PbBGLU16 into Arabidopsis identified that the lignin contents of Arabidopsis BGLU-45 mutant, PbBGLU1-RE, and PbBGLU16-RE were not changed than that of wild-type. However, compared with wild-type Arabidopsis, the overexpression of the plant’s lignin increased in varying degrees. The effect of PbBGLU16 on the lignin increment was greater than that of PbBGLU1 in Arabidopsis. In pear fruits, with transient overexpression of PbBGLU1, the contents of lignin and stone cells were significantly higher (0.01 < P < 0.05) than those with empty vector injection pear fruits. After transient expression of PbBGLU16, lignin in pear fruit increased significantly (0.01 < P < 0.05) and stone cells showed a very significant difference (P < 0.01) compared with the control group. However, RNA interference silenced these two genes in pear fruit, which seemed to have no impression on lignin and stone cells. This study provides a molecular biological basis for improving pear fruit quality at the molecular level.

Environmental stress is one of the major restrictions on plant development and foodstuff production. The adaptive response in plants largely occurs through an intricate signaling system, which is crucial for regulating the stress-responsive genes. Myelocytomatosis (MYC) transcription factors are the fundamental regulators of the jasmonate (JA) signaling branch that participates in plant development and multiple stresses. By binding to the cis-acting elements of a large number of stress-responsive genes, JA-responsive transcription factors activate the stress-resistant defense genes. The mechanism of stress responses concerns myriad regulatory processes at the physiological and molecular levels. Discovering stress-related regulatory factors is of great value in disclosing the response mechanisms of plants to biotic or abiotic stress, which could guide the genetic improvement of plant resistance. This review summarizes recent researches in various aspects of MYC2-mediated JA signaling and emphasizes MYC2 involvement in plant growth and stress response.

The virtual cluster needs to deploy virtual nodes with different computing modes for Large-scale data computing jobs including many tasks with different computing modes. There are resource unbalance among the virtual cluster subsets, which is consisted of virtual nodes with the same computing mode. So the resource utilization of virtual cluster is poor due to the time-varying and complexity of workloads. To solve these issues, a novel dynamic deployment model based on Docker was proposed to optimize resource configuration of virtual cluster. Hybrid deployment scheme includes coarse-grained deployment and fine-grained deployment in order to absorb the mutation of resource demand when processing the jobs encapsulated with complex computing logic. This deployment model can reduce job waiting time and improve performance by providing more resource for running jobs. The coarse-grained deployment mechanism has the ability of decreasing deploying overhead and improving stability from global optimal perspective. And the fine-grained deployment mechanism can increases the deploying accuracy from local optimal perspective. The experiments show that this model can improve the execution efficiency of job by 2.3 percent compared with static deploying scheme and improve the virtual CPU utilization about 7.9 to 25.9 percent compared with other approaches.

Aiming to address the problems of a low fault detection rate and poor diagnosis performance under different loads and noise environments, a rolling bearing fault diagnosis method based on switchable normalization and a deep convolutional neural network (SNDCNN) is proposed. The method effectively extracted the fault features from the raw vibration signal and suppressed high-frequency noise by increasing the convolution kernel width of the first layer and stacking multiple layers’ convolution kernels. To avoid losing the intensity information of the features, the K-max pooling operation was adopted at the pooling layer. To solve the overfitting problem and improve the generalization ability, a switchable normalization approach was used after each convolutional layer. The proposed SNDCNN was evaluated with two sets of rolling bearing datasets and obtained a higher fault detection rate than SVM and BP, reaching a fault detection rate of over 90% under different loads and demonstrating a better anti-noise performance.

WRKY transcription factors participate in various regulation processes at different developmental stages in higher plants. Here, 98 WRKY I genes were identified in seven Rosaceae species. The WRKY I genes are highly enriched in some subgroups and are selectively expanded in Chinese pear [Pyrus bretschneideri (P. bretschneideri)] and apple [Malus domestica (M. domestica)]. By searching for intra-species gene microsynteny, we found the majority of chromosomal segments for WRKY I-containing segments in both P. bretschneideri and M. domestica genomes, while paired segments were hardly identified in the other five genomes. Furthermore, we analyzed the environmental selection pressure of duplicated WRKY I gene pairs, which indicated that the strong purifying selection for WRKY domains may contribute to the stability of its structure and function. The expression patterns of duplication PbWRKY genes revealed that functional redundancy for some of these genes was derived from common ancestry and neo-functionalization or sub-functionalization for some of them. This study traces the evolution of WRKY I genes in Rosaceae genomes and lays the foundation for functional studies of these genes in the future. Our results also show that the rates of gene loss and gain in different Rosaceae genomes are far from equilibrium.

Background: Glioblastoma (GBM) is the most common and aggressive primary intracranial tumor of the central nervous system, and the prognosis of GBM remains a challenge using the standard methods of treatment—TMZ, radiation, and surgical resection. Traditional Chinese medicine (TCM) is a helpful complementary and alternative medicine. However, there are relatively few studies on TCM for GBM.Purpose: We aimed to find the connection between TCM and anti-GBM.Study design: Network pharmacology and inflammatory microenvironment strategy were used to predict Siraitia grosvenorii (Luo Han Guo) target for treating glioblastoma.Methods: We mainly used network pharmacology and bioinformatics.Results: CCL5 was significantly highly expressed in GBM with poor prognostics. Uni-cox and randomForest were used to determine that CCL5 was especially a biomarker in GBM. CCL5 was also the target for SG and TMZ. The active ingredient of Luo Han Guo — squalene and CCL5 —showed high binding efficiency. CCL5, a chemotactic ligand, was enriched and positively correlated in eosinophils. CCL5 was also the target of Luo Han Guo, and its effective active integrate compound –— squalene — might act on CCL5.Conclusion: SG might be a new complementary therapy of the same medicine and food, working on the target CCL5 and playing an anti-GBM effect. CCL5 might affect the immune microenvironment of GBM.

The transient receptor potential plays a critical role in the sensory nervous systems of vertebrates in response to various mechanisms and stimuli, such as environmental temperature. We studied the physiological adaptive evolution of the TRP gene in the saurian family and performed a comprehensive analysis to identify the evolution of the thermo-TRPs channels. All 251 putative TRPs were divided into 6 subfamilies, except TRPN, from the 8 saurian genomes. Multiple characteristics of these genes were analyzed. The results showed that the most conserved proteins of TRP box 1 were located in motif 1, and those of TRP box 2 were located in motif 10. The TRPA and TRPV in saurian tend to be one cluster, as a sister cluster with TRPC, and the TRPM is the root of group I. The TRPM, TRPV, and TRPP were clustered into two clades, and TRPP were organized into TRP PKD1-like and PKD2-like. Segmental duplications mainly occurred in the TRPM subfamily, and tandem duplications only occurred in the TRPV subfamily. There were 15 sites to be under positive selection for TRPA1 and TRPV2 genes. In summary, gene structure, chromosomal location, gene duplication, synteny analysis, and selective pressure at the molecular level provided some new evidence for genetic adaptation to the environment. This result provides a basis for identifying and classifying TRP genes and contributes to further elucidating their potential function in thermal sensors.

Abstract Background Studies have demonstrated that BBX (B-BOX) genes play crucial roles in regulatory networks controlling plant growth, developmental processes and stress response. Nevertheless, comprehensive study of BBX genes in orchids (Orchidaceae) is not well studied. The newly released genome sequences of Dendrobium officinale and Phalaenopsis equestris have allowed a systematic analysis of these important BBX genes in orchids. Results Here we identified 19 (DoBBX01–19) and 16 (PeBBX01–16) BBX genes from D. officinale and P. equestris, respectively, and clustered into five clades (I-V) according to phylogenetic analysis. Thirteen orthologous, two DoBBXs paralogous and two PeBBXs paralogous gene pairs were validated. This gene family mainly underwent purifying selection, but five domains experienced positive selection during evolution. Noteworthy, the expression patterns of root, root_tips, stem, leaf, speal, column, lip, and flower_buds revealed that they might contribution to the formation of these tissues. According to the cis-regulatory elements analysis of BBX genes, qRT-PCR experiments were carried out using D. officinale PLBs (protocorm-like bodies) and displayed that these BBX genes were differentially regulated under AgNO3, MeJA (Methyl Jasmonate), ABA (abscisic acid) and SA (salicylic acid) treatments. Conclusions Our analysis exposed that DoBBX genes play significant roles in plant growth and development, and response to different environmental stress conditions of D. officinale, which provide aid in the selection of appropriate candidate genes for further functional characterization of BBX genes in plants.

The majority of large-scale data intensive applications designed by MapReduce model are deployed and executed on a large-scale distributed Hadoop system. Running such application on a large cluster requires a large amount of energy. Therefore improving energy efficiency and minimizing energy consumption when executing each MapReduce job is a critical concern for data centers. We propose a control model based on model prediction control (MPC) for improving energy efficiency of Hadoop cluster while satisfying performance goal. The controller can dynamically scale CPU frequency in facing the workloads changes. The wavelet neural network is utilized to build the prediction model, which can accurately estimate energy efficiency ratio based on the features extracting from the variation of Hadoop workloads. With the help of a wavelet neural network, the controller can guarantee the energy efficiency ratio converges to an ideal set point within a finite settling time. We perform the extensive experiments on a Hadoop cluster to compare our controller with the previous MPC controller. The results demonstrate that our controller outperforms the baseline on energy efficiency control and adapts to workloads of Hadoop cluster.

Most eukaryotic genes are interrupted by one or more introns, and only prokaryotic genomes are composed of mainly single-exon genes without introns. Due to the absence of introns, intronless genes in eukaryotes have become important materials for comparative genomics and evolutionary biology. There is currently no cohesive database that collects intronless genes in plants into a single database, although many databases on exons and introns exist. In this study, we constructed the Rosaceae Intronless Genes Database (RIGD), a user-friendly web interface to explore and collect information on intronless genes from different plants. Six Rosaceae species, Pyrus bretschneideri, Pyrus communis, Malus domestica, Prunus persica, Prunus mume, and Fragaria vesca, are included in the current release of the RIGD. Sequence data and gene annotation were collected from different databases and integrated. The main purpose of this study is to provide gene sequence data. In addition, attribute analysis, functional annotations, subcellular localization prediction, and GO analysis are reported. The RIGD allows users to browse, search, and download data with ease. Blast and comparative analyses are also provided through this online database, which is available at http://www.rigdb.cn/.

BZR transcription factors play essential roles in plant growth and environmental stimuli, and they are also the positive regulators of Brassinosteroid (BR) signal transduction in diverse plants. In addition, BZR TFs, as crucial regulators of BR synthesis, may have multiple stress-resistance functions and their related regulatory mechanisms have been well illustrated in model plants. Here, we carried out a genome-wide identification of BZR members in Chinese pear (Pyrus bretschneideri) and identified 13 members. By comparative analysis in five Rosaceae genomes, BZR members in the pear genome may have undergone large-scale duplication events during evolution. Purifying selection played an important role in almost all of the orthologous and paralogous gene pairs. According to the expression analysis of the PbBZRs during fruit development, three PbBZRs were selected for detailed analysis. Transcriptional activation assays presented that PbBZR1 repressed the promoters of P. bretschneideri lignin biosynthetic genes, such as PbCES9, PbCOMT3, and PbHCT6. Our study traces the evolution of BZR gene family members in Rosaceae genomes and illustrates that the rates of gene loss and gain are far from equilibrium in different species. At the same time, our results suggest that PbBZR1 may be involved in the negative regulation of lignin biosynthesis.

Abstract Background The B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, there still lack a genome-wide survey of BBX genes in pear. Results In the present study, a total of 25 BBX genes were identified in pear (Pyrus bretschneideri Rehd.). Subsequently, phylogenetic relationship, gene structure, gene duplication, transcriptome data and qRT-PCR were conducted on these BBX gene members. The transcript analysis revealed that twelve PbBBX genes (48%) were specifically expressed in pear pollen tubes. Furthermore, qRT-PCR analysis indicated that both PbBBX4 and PbBBX13 have potential role in pear fruit development, while PbBBX5 should be involved in the senescence of pear pollen tube. Conclusions This study provided a genome-wide survey of BBX gene family in pear, and highlighted its roles in both pear fruits and pollen tubes. The results will be useful in improving our understanding of the complexity of BBX gene family and functional characteristics of its members in future study.

NADPH oxidases (NOXs) have been known as respiratory burst oxidase homologues (RBOHs) in plants. To characterize the evolutionary relationships and functions of RBOHs in Brassica rapa, 134 RBOH homologues were identified from 13 plant species, including 14 members (namely BrRBOH01–14) from B. rapa. There presented 47 gene-pairs among 14 BrRBOHs and other RBOHs, consisting of five pairs within B. rapa, and 15 pairs between B. rapa and Arabidopsis thaliana. Together with phylogenetic analysis, the results suggested that whole-genome duplication might have played an important role in BrRBOH gene expansion, and these duplication events occurred after the divergence of the eudicot and the monocot lineages examined. Furthermore, gene expression of RBOHs in both A. thaliana and B. rapa were assayed via qRT–PCR. An RBOH gene, BrRBOH13 in B. rapa, was transformed into wild-type Arabidopsis plants. The transgenic lines with the overexpressed level of BrRBOH13 conferred to be more tolerant to heavy metal lead (0.05 mM) than wild-type plants. Overall, this integrated analysis at genome-wide level has provided some information on the evolutionary relationships among plant-specific NOXs and the coordinated diversification of gene structure and function in B. rapa.

Metacaspase (MC), which is discovered gene family with distant caspase homologs in plants, fungi, and protozoa, may be involved in programmed cell death (PCD) processes during plant development and respond abiotic and biotic stresses. To reveal the evolutionary relationship of MC gene family in Rosaceae genomes, we identified 8, 7, 8, 12, 12, and 23 MC genes in the genomes of Fragaria vesca, Prunus mume, Prunus persica, Pyrus communis, Pyrus bretschneideri and Malus domestica, respectively. Phylogenetic analysis suggested that the MC genes could be grouped into three clades: Type I*, Type I and Type II, which was supported by gene structure and conserved motif analysis. Microsynteny analysis revealed that MC genes present in the corresponding syntenic blocks of P. communis, P. bretschneideri and M. domestica, and further suggested that large-scale duplication events play an important role in the expansion of MC gene family members in these three genomes than other Rosaceae plants (F. vesca, P. mume and P. persica). RNA-seq data showed the specific expression patterns of PbMC genes in response to drought stress. The expression analysis of MC genes demonstrated that PbMC01 and PbMC03 were able to be detected in all four pear pollen tubes and seven fruit development stages. The current study highlighted the evolutionary relationship and duplication of the MC gene family in these six Rosaceae genomes and provided appropriate candidate genes for further studies in P. bretschneideri.

In order to achieve accurate fault diagnosis of rolling bearings, a hierarchical decision fusion diagnosis method for rolling bearings is proposed. The hierarchical back propagation neural networks (BPNNs) architecture includes a fault detection layer, fault isolation layer and fault degree identification layer, which reduce the calculation cost and enhance the maintainability of the fault diagnosis algorithm. By wavelet packet decomposition and signal reconstruction of the raw vibration signal of a rolling bearing, the time-domain features of the reconstructed signals are extracted as the input of each BPNN and the accuracy of fault detection, fault isolation and degree estimation are improved. By using the majority voting method, the diagnosis results of multiple BPNNs are fused, which avoids the missed diagnosis and misdiagnosis caused by the insensitivity of a vibration characteristic to a specific fault. Finally, the proposed method is verified experimentally. The results show that the proposed method can accurately detect the fault of rolling bearings, recognize the fault location and estimate the fault severity under different operating conditions.

MYB transcription factors (TFs), as one of the largest gene families in plants, play important roles in multiple biological processes, such as plant growth and development, cell morphology and pattern building, physiological activity metabolism, primary and secondary metabolic reactions, and responses to environmental stresses. The function of MYB TFs in crops has been widely studied, but few studies have been done on medicinal plants. In this review, we summarized the MYB TFs that play important roles in secondary metabolism and emphasized the possible mechanisms underlying how MYB TFs are regulated at the protein, posttranscriptional, and transcriptional levels, as well as how they regulate the downstream target gene networks related to secondary metabolism in plants, especially in medicinal plants.

Zinc finger-homeodomain (ZHD) genes encode a family of plant-specific transcription factors that not only participate in the regulation of plant growth and development but also play an important role in the response to abiotic stress. The ZHD gene family has been studied in several model plants, including Solanum lycopersicum, Zea mays, Oryza sativa, and Arabidopsis thaliana. However, a comprehensive study of the genes of the ZHD family and their roles in fiber development and pigmentation in upland cotton has not been completed. To address this gap, we selected a brown fiber cultivar for our study; brown color in cotton is one of the most desired colors in the textile industry. The natural colored fibers require less processing and little dying, thereby eliminating dye costs and chemical residues. Using bioinformatics approaches, we identified 37 GhZHD genes from Gossypium hirsutum and then divided these genes into seven groups based on their phylogeny. The GhZHD genes were mostly conserved in each subfamily with minor variations in motif distribution and gene structure. These genes were largely distributed on 19 of the 26 upland cotton chromosomes. Among the Gossypium genomes, the paralogs and orthologs of the GhZHD genes were identified and further characterized. Furthermore, among the paralogs, we observed that the ZHD family duplications in Gossypium genomes (G. hirsutum, G. arboreum, and G. raimondii) were probably derived from segmental duplication or genome-wide duplication (GWD) events. Through a combination of qRT-PCR and proanthocyanidins (PA) accumulation analyses in brown cotton fibers, we concluded that the candidate genes involved in early fiber development and fiber pigment synthesis include the following: GhZHD29, GhZHD35, GhZHD30, GhZHD31, GhZHD11, GhZHD27, GhZHD18, GhZHD15, GhZHD16, GhZHD22, GhZHD6, GhZHD33, GhZHD13, GhZHD5, and GhZHD23. This study delivers insights into the evolution of the GhZHD genes in brown cotton, serves as a valuable resource for further studies, and identifies the conditions necessary for improving the quality of brown cotton fiber.

The SQUAMOSA promoter binding protein (SBP)-box proteins are plant-specific transcriptional factors in plants. SBP TFs are known to play important functions in a diverse development process and also related in the process of evolutionary novelties. SBP gene family has been characterized in several plant species, but little is known about molecular evolution, functional divergence and comprehensive study of SBP gene family in Rosacea. We carried out genome-wide investigations and identified 14, 32, 17, and 17 SBP genes from four Rosacea species (Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume, respectively). According to phylogenetic analysis arranged the SBP protein sequences in seven groups. Localization of SBP genes presented an uneven distribution on corresponding chromosomes of Rosacea species. Our analyses designated that the SBP genes duplication events (segmental and tandem) and divergence. In addition, due to highly conserved structure pattern of SBP genes, recommended that highly conserved region of microsyneteny in the Rosacea species. Type I and II functional divergence was detected among various amino acids in SBP proteins, while there was no positive selection according to substitutional model analysis using PMAL software. These results recommended that the purifying selection might be leading force during the evolution process and dominate conservation of SBP genes in Rosacea species according to environmental selection pressure analysis. Our results will provide basic understanding and foundation for future research insights on the evolution of the SBP genes in Rosacea.

In plants, plant fructokinases (FRKs) are considered to be the main gateway of fructose metabolism as they can phosphorylate fructose to fructose-6-phosphate. Chinese white pears (Pyrus bretschneideri) are one of the popular fruits in the world market; sugar content is an important factor affecting the quality of the fruit. We identified 49 FRKs from four Rosaceae species; 20 of these sequences were from Chinese white pear. Subsequently, phylogenic relationship, gene structure and micro-collinearity were analysed. Phylogenetic and exon–intron analysis classified these FRKs into 10 subfamilies, and it was aimed to further reveal the variation of the gene structure and the evolutionary relationship of this gene family. Remarkably, gene expression patterns in different tissues or different development stages of the pear fruit suggested functional redundancy for PbFRKs derived from segmental duplication or genome-wide duplication and sub-functionalization for some of them. Additionally, PbFRK11, PbFRK13 and PbFRK16 were found to play important roles in regulating the sugar content in the fruit. Overall, this study provided important insights into the evolution of the FRK gene family in four Rosaceae species, and highlighted its roles in both pear tissue and fruits. Results presented here provide the appropriate candidate of PbFRKs that might contribute to fructose efflux in the pear fruit.

WUSCHEL-related homeobox (WOX) family is one of the largest group of transcription factors (TFs) specifically found in plant kingdom. WOX TFs play an important role in plant development processes and evolutionary novelties. Although the roles of WOXs in Arabidopsis and rice have been well-studied, however, little are known about the relationships among the main clades in the molecular evolution of these genes in Rosaceae. Here, we carried out a genome-wide analysis and identified 14, 10, 10, and 9 of WOX genes from four Rosaceae species (Fragaria vesca, Prunus persica, Prunus mume, and Pyrus bretschneideri, respectively). According to evolutionary analysis, as well as amino acid sequences of their homodomains, these genes were divided into three clades with nine subgroups. Furthermore, due to the conserved structural patterns among these WOX genes, it was proposed that there should exist some highly conserved regions of microsynteny in the four Rosaceae species. Moreover, most of WOX gene pairs were presented with the conserved orientation among syntenic genome regions. In addition, according to substitution models analysis using PMAL software, no significant positive selection was detected, but type I functional divergence was identified among certain amino acids in WOX protein. These results revealed that the relaxed purifying selection might be the main driving force during the evolution of WOX genes in the tested Rosaceae species. Our result will be useful for further precise research on evolution of the WOX genes in family Rosaceae.

The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) proteins are a type of nuclear-localized protein with DNA-binding activity in plants. Although the EIN3/EIL gene family has been studied in several plant species, little is known about comprehensive study of the EIN3/EIL gene family in Rosaceae. In this study, ten, five, four, and five EIN3/EIL genes were identified in the genomes of pear (Pyrus bretschneideri), mei (Prunus mume), peach (Prunus persica) and strawberry (Fragaria vesca), respectively. Twenty-eight chromosomal segments of EIL/EIN3 gene family were found in four Rosaceae species, and these segments could form seven orthologous or paralogous groups based on interspecies or intraspecies gene colinearity (microsynteny) analysis. Moreover, the highly conserved regions of microsynteny were found in four Rosaceae species. Subsequently it was found that both whole genome duplication and tandem duplication events significantly contributed to the EIL/EIN3 gene family expansion. Gene expression analysis of the EIL/EIN3 genes in the pear revealed subfunctionalization for several PbEIL genes derived from whole genome duplication. It is noteworthy that according to environmental selection pressure analysis, the strong purifying selection should dominate the maintenance of the EIL/EIN3 gene family in four Rosaceae species. These results provided useful information on Rosaceae EIL/EIN3 genes, as well as insights into the evolution of this gene family in four Rosaceae species. Furthermore, high level of microsynteny in the four Rosaceae plants suggested that a large-scale genome duplication event in the EIL/EIN3 gene family was predated to speciation.

Calreticulin is down-regulated in the cortical neurons of patients with Alzheimer’s disease (AD) and may be a potential biomarker for the diagnosis of AD. A total of 128 AD patients were randomly recruited from May 2012 to July 2013. The mRNA levels of calreticulin were measured from the serum of tested subjects using real-time quantitative reverse transcriptase-PCR (real-time qRT-PCR). Serum levels of calreticulin were determined by ELISA and Western Blot. Serum levels of calreticulin in AD patients were significantly lower than those from a healthy group (p < 0.01). The baseline characters indicated that sample size, gender, mean age, diabetes and BMI (body mass index) were not major sources of heterogeneity. The serum levels of mRNA and protein of calreticulin were lower in AD patients than those from a healthy group, and negatively associated with the progression of AD according to CDR scores (p < 0.01). Thus, there is a trend toward decreased serum levels of calreticulin in the patients with progression of AD. Serum levels of calreticulin can be a negative biomarker for the diagnosis of AD patients.

Stone cell content is an important factor affecting pear fruit flavor. Lignin, a major component of pear stone cells, hinders the quality and value of commercial fruit. The completion of the Chinese white pear (Pyrus bretschneideri) genome sequence provides an opportunity to perform integrative analysis of the genes encoding the eleven protein families (i.e., PAL, C4H, 4CL, HCT, C3H, CSE, CCoAOMT, CCR, F5H, COMT, and CAD) in the phenylpropanoid pathway. Here, a systematic study based on expression patterns and phylogenetic analyses was performed to identify the members of each gene family potentially involved in the lignification in the Chinese white pear. The phylogenetic analysis suggested that 35 P. bretschneideri genes belong to bona fide lignification clade members. Compared to other plants, some multigene families are expanded by tandem gene duplication, such as HCT, C3H, COMT, and CCR. RNA sequencing was used to study the expression patterns of the genes in different tissues, including leaf, petal, bud, sepal, ovary, stem, and fruit. Eighteen genes presented a high expression in fruit, indicating that these genes may be involved in the biosynthesis of lignin in pear fruit. Similarly to what has been observed for Populus trichocarpa, a bimolecular fluorescence complementation (BiFC) experiment indicated that P. bretschneideri C3H and C4H might also interact with each other to regulate monolignol biosynthesis in P. bretschneideri, ultimately affecting the stone cell content in pear fruits. The identification of the major genes involved in lignin biosynthesis in pear fruits provides the basis for the development of strategies to improve fruit quality.

Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In the present study, we investigate the rates of synonymous substitution (Ks) and the rates of non-synonymous substitution (Ka) by comparing the orthologous genes of two sequenced Pyrus species, Pyrus bretschneideri and Pyrus communis. Subsequently, we compared the evolutionary rates, gene structures, and expression profiles during different fruit development between PSGs and NSGs. Compared with the NSGs, the PSGs have fewer exons, shorter gene length, lower synonymous substitution rates and have higher evolutionary rates. Remarkably, gene expression patterns between two Pyrus species fruit indicated functional divergence for most of the orthologous genes derived from a common ancestor, and subfunctionalization for some of them. Overall, the present study shows that PSGs differs from NSGs not only under environmental selective pressure (Ka/Ks), but also in their structural, functional, and evolutionary properties. Additionally, our resulting data provides important insights for the evolution and highlights the diversification of orthologous genes in two Pyrus species.

Aiming at the nonlinear and nonstationary characteristics of bearing vibration signals as well as the complexity of condition-indicating information distribution in the signals, a novel rolling element bearing fault diagnosis approach based on improved generalized fractal box-counting dimension and adaptive gray relation algorithm was proposed in this article. First, an improved generalized fractal box-counting dimension algorithm was developed to extract the characteristic vectors of fault features from the bearing vibration signals, to offer more useful and distinguishing information imaging different bearing health status in comparison with traditional fractal box-counting dimension. After feature extraction by improved generalized fractal box-counting dimension algorithm, an adaptive gray relation algorithm, in which the concept of weight coefficient and adaptive distinguishing coefficient was introduced into the calculation of the relation degree, was employed to fulfill an intelligent bearing fault diagnosis. The experimental results demonstrate that the proposed approach can more effectively and accurately identify different bearing fault types as well as severities compared with the existing intelligent methods, and it can solve the learning problem with an extremely small number of samples.

Bearing failure is one of the dominant causes of failure and breakdowns in rotating machinery, leading to huge economic loss. Aiming at the nonstationary and nonlinear characteristics of bearing vibration signals as well as the complexity of condition-indicating information distribution in the signals, a novel rolling element bearing fault diagnosis method based on multifractal theory and gray relation theory was proposed in the paper. Firstly, a generalized multifractal dimension algorithm was developed to extract the characteristic vectors of fault features from the bearing vibration signals, which can offer more meaningful and distinguishing information reflecting different bearing health status in comparison with conventional single fractal dimension. After feature extraction by multifractal dimensions, an adaptive gray relation algorithm was applied to implement an automated bearing fault pattern recognition. The experimental results show that the proposed method can identify various bearing fault types as well as severities effectively and accurately.

Gas-path analysis method has been widespread applied to gas turbine engine health control and has become one of the key techniques in favor of condition-oriented maintenance strategy. Theoretically, gas-path analysis method (especially nonlinear gas-path analysis) can easily quantify gas-path component degradations. However, when the number of components within engine is large which highly expands the dimension of fault coefficient matrix, maybe leading to strong smearing effect (i.e. predicted degradations are located almost in all component health parameters, although some of them are not really degraded), the degraded components may not be accurately identified. In order to improve the robustness of gas turbine gas-path fault diagnosis, a hybrid gas-path analysis approach integrating gray relation algorithm into gas-path analysis method has been proposed in this study. The gray relation algorithm and gas-path analysis method approach includes two steps. First, the faulty components are recognized and isolated by gray relation algorithm, which deeply reduces the dimension of fault coefficient matrix, and second, the magnitudes of detected component faults are quantified by the gas-path analysis. The fault classification analyses and case studies have shown that the confidence level of the fault classification can reach more than 95%, when single and multiple components are degraded, and the predicted degradations are almost same as that of implanted fault patterns.

To ensure reliable and efficient operation of gas turbines, multiple model (MM) approaches have been extensively studied for online fault detection and isolation (FDI). However, current MM-FDI approaches are difficult to directly apply to gas path FDI, which is one of the common faults in gas turbines and is understood to mainly be due to the high complexity and computation in updating hypothetical gas path faults for online applications. In this paper, a fault contribution matrix (FCM) based MM-FDI approach is proposed to implement gas path FDI over a wide operating range. As the FCM is realized via an additive term of the healthy model set, the hypothetical models for various gas path faults can be easily established and updated online. In addition, a gap metric analysis method for operating points selection is also proposed, which yields the healthy model set from the equal intervals linearized models to approximate the nonlinearity of the gas turbine over a wide range of operating conditions with specified accuracy and computational efficiency. Simulation case studies conducted on a two-shaft marine gas turbine demonstrated the proposed approach is capable of adaptively updating hypothetical model sets to accurately differentiate both single and multiple faults of various gas path faults.