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Abstract Background Burkholderia is a phosphorus solubilizing microorganism discovered in recent years, which can dissolve insoluble phosphorus compounds into soluble phosphorus. To investigate the effects of Burkholderia and calcium phosphate on the composting of Torreya grandis branches and leaves, as well as to explain the nutritional and metabolic markers related to the composting process. Methods In this study, we employed amplicon sequencing and untargeted metabolomics analysis to examine the interplay among phosphorus (P) components, microbial communities, and metabolites during T. grandis branch and leaf waste composting that underwent treatment with calcium phosphate and phosphate-solubilizing bacteria (Burkholderia). There were four composting treatments, 10% calcium phosphate (CaP) or 5 ml/kg (1 × 108/ml Burkholderia) microbial inoculum (WJP) or both (CaP + WJP), and the control group (CK). Results The results indicated that Burkholderia inoculation and calcium phosphate treatment affected the phosphorus composition, pH, EC, and nitrogen content. Furthermore, these treatments significantly affected the diversity and structure of bacterial and fungal communities, altering microbial and metabolite interactions. The differential metabolites associated with lipids and organic acids and derivatives treated with calcium phosphate treatment are twice as high as those treated with Burkholderia in both 21d and 42d. The results suggest that calcium phosphate treatment alters the formation of some biological macromolecules. Conclusion Both Burkholderia inoculation and calcium phosphate treatment affected the phosphorus composition, nitrogen content and metabolites of T. grandis branch and leaf waste compost.These results extend our comprehension of the coupling of matter transformation and community succession in composting with the addition of calcium phosphate and phosphate-solubilizing bacteria.

Introduction: Torreya grandis is a gymnosperm belonging to Taxodiaceae. As an economically important tree, its kernels are edible and rich in oil with high unsaturated fatty acids, such as sciadonic acid. However, the kernels from different T. grandis landraces exhibit fatty acid and oil content variations. Objectives: As a gymnosperm, does T. grandis have special regulation mechanisms for oil biosynthesis? The aim of this study was to dissect the genetic architecture of fatty acid and oil content and the underlying mechanism in T. grandis. Methods: We constructed a high integrity reference sequence of expressed regions of the genome in T. grandis and performed transcriptome-referenced association study (TRAS) for 10 fatty acid and oil traits of kernels in the 170 diverse T. grandis landraces. To confirm the TRAS result, we performed functional validation and molecular biology experiments for oil significantly associated genes. Results: We identified 41 SNPs from 34 transcripts significantly associated with 7 traits by TRAS (−log10 (P) greater than 6.0). Results showed that LOB domain-containing protein 40 (LBD40) and surfeit locus protein 1 (SURF1) may be indirectly involved in the regulation of oil and sciadonic acid biosynthesis, respectively. Moreover, overexpression of TgLBD40 significantly increased seed oil content. The nonsynonymous variant in the TgLBD40 coding region discovered by TRAS could alter the oil content in plants. Pearson’s correlation analysis and dual-luciferase assay indicated that TgLBD40 positively enhanced oil accumulation by affecting oil biosynthesis pathway genes, such as TgDGAT1. Conclusion: Our study provides new insights into the genetic basis of oil biosynthesis in T. grandis and demonstrates that integrating RNA sequencing and TRAS is a powerful strategy to perform association study independent of a reference genome for dissecting important traits in T. grandis.

Background: The most serious manifestation of pulmonary cryptococcosis is complicated with cryptococcal meningitis, while its clinical manifestations lack specificity with delayed diagnosis and high mortality. The early prediction of this complication can assist doctors to carry out clinical interventions in time, thus improving the cure rate. This study aimed to construct a nomogram to predict the risk of cryptococcal meningitis in patients with pulmonary cryptococcosis through a scoring system. Methods: The clinical data of 525 patients with pulmonary cryptococcosis were retrospectively analyzed, including 317 cases (60.38 %) with cryptococcal meningitis and 208 cases (39.62 %) without cryptococcal meningitis. The risk factors of cryptococcal meningitis were screened by univariate analysis, LASSO regression analysis and multivariate logistic regression analysis. Then the risk factors were incorporated into the nomogram scoring system to establish a prediction model. The model was validated by receiver operating characteristic (ROC) curve, decision curve analysis (DCA) and clinical impact curve. Results: Fourteen risk factors for cryptococcal meningitis in patients with pulmonary cryptococcosis were screened out by statistical method, including 6 clinical manifestations (fever, headache, nausea, psychiatric symptoms, tuberculosis, hematologic malignancy) and 8 clinical indicators (neutrophils, lymphocytes, glutamic oxaloacetic transaminase, T cells, helper T cells, killer T cells, NK cells and B cells). The AUC value was 0.978 (CI 96.2 %∼98.9 %), indicating the nomogram was well verified. Conclusion: The nomogram scoring system constructed in this study can accurately predict the risk of cryptococcal meningitis in patients with pulmonary cryptococcosis, which may provide a reference for clinical diagnosis and treatment of patients with cryptococcal meningitis.

Torreya grandis is a characteristic rare economic tree species in subtropical mountainous areas. The nut has a variety of bioactive compounds, such as polyphenols and vitamins. However, the carotenoids compositions and its regulatory mechanisms underlying carotenoid biosynthesis in kernels remain unknown. Here, the major carotenoids in the kernel were analyzed. The result showed that lutein and β-carotene were the predominant carotenoids in the kernel, while low levels of α-carotenoid and zeaxanthin were detected. Lutein and β-carotene were decreased during the maturation of kernel. Expression analysis by RNA-seq and qRT-PCR indicated that the expressions of TgCYP97A3 and TgLCYB were also reduced during the maturation of kernel. The contents of lutein or β-carotene were obviously increased in tobacco transiently overexpressing TgCYP97A3 or TgLCYB. Moreover, DPPH radical scavenging activity and FRAP were also significantly enhanced. In addition, several MYB and WRKY transcription factors TgMYBS3, TgMYB48 and TgWRKY11 were identified to positively regulate the TgCYP97A3 expression, while TgMYB48, TgWRKY2 and TgWRKY11 could upregulate the TgLCYB expression. The illustration of carotenoids biosynthesis and its molecular mechanism in kernels not only provides a basis for understanding carotenoids biosynthesis in kernels, but also enables the use of molecular biotechnology to develop new health products rich in carotenoids based on T. grandis nuts.

Introduction: Yinchenzhufu decoction (YCZFD) is a traditional Chinese medicine formula with hepatoprotective effects. In this study, the protective effects of YCZFD against cholestatic liver fibrosis (CLF) and its underlying mechanisms were evaluated.Methods: A 3, 5-diethoxycarbonyl-1, 4-dihydro-collidine (DDC)-induced cholestatic mouse model was used to investigate the amelioration of YCZFD on CLF. Data-independent acquisition-based mass spectrometry was performed to investigate proteomic changes in the livers of mice in three groups: control, model, and model treated with high-dose YCZFD. The effects of YCZFD on the expression of key proteins were confirmed in mice and cell models.Results: YCZFD significantly decreased the levels of serum biochemical, liver injury, and fibrosis indicators of cholestatic mice. The proteomics indicated that 460 differentially expressed proteins (DEPs) were identified among control, model, and model treated with high-dose YCZFD groups. Enrichment analyses of these DEPs revealed that YCZFD influenced multiple pathways, including PI3K-Akt, focal adhesion, ECM–receptor interaction, glutathione metabolism, and steroid biosynthesis pathways. The expression of platelet derived growth factor receptor beta (PDGFRβ), a receptor associated with the PI3K/AKT and focal adhesion pathways, was upregulated in the livers of cholestatic mice but downregulated by YCZFD. The effects of YCZFD on the expression of key proteins in the PDGFRβ/PI3K/AKT pathway were further confirmed in mice and transforming growth factor-β-induced hepatic stellate cells. We uncovered seven plant metabolites (chlorogenic acid, scoparone, isoliquiritigenin, glycyrrhetinic acid, formononetin, atractylenolide I, and benzoylaconitine) of YCZFD that may regulate PDGFRβ expression.Conclusion: YCZFD substantially protects against DDC-induced CLF mainly through regulating the PDGFRβ/PI3K/AKT signaling pathway.

Terpene aroma compounds are key quality attributes of postharvest Torreya grandis nuts, contributing to their commercial value. However, terpene biosynthesis and regulatory networks in different T. grandis cvs. are still poorly understood. Here, chief cvs. ‘Xi Fei’ and ‘Xiangya Fei’ were investigated for their differences in terpene biosynthesis and gene expression levels during postharvest ripening using headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography–mass spectrometry (GC-MS) and transcriptomic datasets. A total of 28 and 22 aroma compounds were identified in ‘Xi Fei’ and ‘Xiangya Fei’, respectively. Interestingly, differences in aroma composition between the two cvs. were mostly attributed to D-limonene and α-pinene levels as key determinants in Torreya nuts’ flavor. Further, transcriptome profiling, correlation analysis, and RT-qPCR annotated two novel genes, TgTPS1 in ‘Xi Fei’ and TgTPS2 in ‘Xiangya Fei’, involved in terpene biosynthesis. In addition, six transcription factors (TFs) with comparable expression patterns to TgTPS1 and four TFs to TgTPS2 were identified via correlation analysis of a volatile and transcriptome dataset to be involved in terpene biosynthesis. Our study provides novel insight into terpene biosynthesis and its regulation at the molecular level in T. grandis nut and presents a valuable reference for metabolic engineering and aroma improvement in this less explored nut.

Abstract Background With the advancement of whole‐genome sequencing (WGS) technology, massively parallel sequencing (MPS) remains the mainstream due to its accuracy, low cost, and high throughput. The development of the analytical pipeline corresponding to MPS has always been of great importance. Increasingly large population genomics studies, as a specific type of big data research, pose new challenges for analysis solutions. Results Here, we introduce ZBOLT, a comprehensive analysis system that incorporates both software and hardware advancements, making it an appropriate choice for large‐scale population genomic studies that require extensive data processing. In this study, we first evaluate ZBOLT's calling accuracy using the Genome in a Bottle (GIAB) benchmark dataset. Then we apply ZBOLT to a large‐scale population genomics study with 5,616 high sequencing depth samples totaling 1.16Pbp (base pair). As the results show, ZBOLT demonstrates exceptional efficiency and low energy consumption, processing 100Tbp per day and using 1kWh per 100Gbp sequenced sample. Conclusion This research serves as a valuable reference for analyzing sequencing data from large population cohorts and underscores the significant potential of ZBOLT in large‐scale population genomics studies.

Abstract The nuts of Torreya grandis are abundant in flavonoids, providing potential antioxidant activity. Considering that T. grandis can yield nuts for hundreds or thousands of years, effects of tree age on flavonoids and antioxidant activity of T. grandis nuts were targeted in this study for the first time. Results revealed that antioxidant activity and total flavonoid contents in 100‐ and 1000‐years‐old T. grandis nuts were much higher compared to 10‐years‐old T. grandis. The content of 19 flavonoids showed significant correlations with antioxidant activity in 100‐ and 1000‐years‐old trees using metabolites profiling. Transcriptome and coexpression analysis indicated that seven genes were associated with aged‐related flavonoids biosynthesis. Further analysis showed that abscisic acid and gibberellin might regulate the age‐related differential flavonoids accumulation. Our study provides a novel viewpoint that aged T. grandis is likely to present a better source of natural antioxidants and has yet to be examined in other tree models.

Torreya grandis is a gymnosperm species that produces edible seeds with high level of sciadonic acid (SCA). Here, the authors assemble the genome of this species, preform methylone analysis of seeds at different developmental stages, and reveal two key genes involved in SCA biosynthesis.

The multidrug and toxin efflux (MATE) family participates in numerous biological processes and plays important roles in abiotic stress responses. However, information about the MATE family genes in Torreya grandis remains unclear. In this study, our genome-wide investigation identified ninety MATE genes in Torreya grandis, which were divided into five evolutionary clades. TgMATE family members are located on eleven chromosomes, and a total of thirty TgMATEs exist in tandem duplication. The promoter analysis showed that most TgMATEs contain the cis-regulatory elements associated with stress and hormonal responses. In addition, we discovered that most TgMATE genes responded to abiotic stresses (aluminum, drought, high temperatures, and low temperatures). Weighted correlation network analysis showed that 147 candidate transcription factor genes regulated the expression of 14 TgMATE genes, and it was verified through a double-luciferase assay. Overall, our findings offer valuable information for the characterization of the TgMATE gene mechanism in responding to abiotic stress and exhibit promising prospects for the stress tolerance breeding of Torreya grandis.

Submillimeter wave radiometers are promising remote sensing tools for sounding ice cloud parameters. The Ice Cloud Imager (ICI) aboard the second generation of the EUMETSAT Polar System (EPS−SG) is the first operational submillimeter wave radiometer used for ice cloud remote sensing. Ice clouds simultaneously contain three species of ice hydrometeors—ice, snow, and graupel—the physical distributions and submillimeter wave radiation characteristics of which differ. Therefore, jointly retrieving the mass parameters of the three ice hydrometeors from submillimeter brightness temperatures is very challenging. In this paper, we propose a multiple species of ice hydrometeor parameters retrieval algorithm based on convolutional neural networks (CNNs) that can jointly retrieve the total content and vertical profiles of ice, snow, and graupel particles from submillimeter brightness temperatures. The training dataset is generated by a numerical weather prediction (NWP) model and a submillimeter wave radiative transfer (RT) model. In this study, an end to end ICI simulation experiment involving forward modeling of the brightness temperature and retrieval of ice cloud parameters was conducted to verify the effectiveness of the proposed CNN retrieval algorithm. Compared with the classical Unet, the average relative errors of the improved RCNN–ResUnet are reduced by 11%, 25%, and 18% in GWP, IWP, and SWP retrieval, respectively. Compared with Bayesian Monte Carlo integration algorithm, the average relative error of the total content retrieved by RCNN–ResUnet is reduced by 71%. Compared with BP neural network algorithm, the average relative error of the vertical profiles retrieved by RCNN–ResUnet is reduced by 69%. In addition, this algorithm was applied to actual Advanced Technology Microwave Sounder (ATMS) 183 GHz observed brightness temperatures to retrieve graupel particle parameters with a relative error in the total content of less than 25% and a relative error in the profile of less than 35%. The results show that the proposed CNN algorithm can be applied to future space borne submillimeter wave radiometers to jointly retrieve mass parameters of ice, snow, and graupel.

The kernel of Torreya grandis cv. ‘Merrillii’ (Cephalotaxaceae) is a rare nut with a variety of bioactive compounds and a high economic value. β-sitosterol is not only the most abundant plant sterol but also has various biological effects, such as antimicrobial, anticancer, anti-inflammatory, lipid-lowering, antioxidant, and antidiabetic activities. In this study, a squalene synthase gene from T. grandis, TgSQS, was identified and functionally characterized. TgSQS encodes a deduced protein of 410 amino acids. Prokaryotic expression of the TgSQS protein could catalyze farnesyl diphosphate to produce squalene. Transgenic Arabidopsis plants overexpressing TgSQS showed a significant increase in the content of both squalene and β-sitosterol; moreover, their drought tolerance was also stronger than that of the wild type. Transcriptome data from T. grandis seedlings showed that the expression levels of sterol biosynthesis pathway-related genes, such as HMGS, HMGR, MK, DXS, IPPI, FPPS, SQS, and DWF1, increased significantly after drought treatment. We also demonstrated that TgWRKY3 directly bound to the TgSQS promoter region and regulated its expression through a yeast one-hybrid experiment and a dual luciferase experiment. Together, these findings demonstrate that TgSQS has a positive role in β-sitosterol biosynthesis and in protecting against drought stress, emphasizing its importance as a metabolic engineering tool for the simultaneous improvement of β-sitosterol biosynthesis and drought tolerance.

Torreya grandis is native Chinese tree species of economic significance, renowned for its long lifespan and the rich nutritional value of its nuts. In this study, we analyzed the morphological characteristics, metabolites, associated gene expressions, and regulatory mechanism in nuts from young (10 years old) and old (1000 years old) T. grandis trees. We observed that the length, width, and weight of nuts from older trees were considerably greater than those from younger trees. Metabolomic analysis revealed that the concentrations of 18 amino acids and derivatives (including histidine and serine) in nuts from older trees were markedly higher than those in nuts from younger trees. Transcriptome and metabolomic correlation analysis identified 16 genes, including TgPK (pyruvate kinase), TgGAPDH (glyceraldehyde 3-phosphate dehydrogenase), and others, which exhibit higher expression levels in older trees compared to younger trees, as confirmed by qRT-PCR. These genes are associated with the biosynthesis of histidine, glutamic acid, tryptophan, and serine. Transient expression of TgPK in tobacco led to increased pyruvate kinase activity and amino acid content (histidine, tryptophan, and serine). Additionally, dual-luciferase assays and yeast one-hybrid results demonstrated that TgWRKY21 positively regulates TgPK expression by directly binding to the TgPK promoter. These findings not only demonstrate the nutritional differences between nuts from young and old trees but also offer fresh insights into the development of nutritional sources and functional components based on nuts from old trees, enriching our understanding of the potential benefits of utilizing nuts from older trees.

As a class of highly dynamic organelles, lipid droplets (LDs) are involved in numerous physiological functions, and the changes in polarity of LDs are closely related to a variety of diseases. In this work, we developed two polarity-sensitive fluorescent probes (CC-CH and CC-Cl) based on curcumin analogs. CC-CH and CC-Cl with a donor–acceptor–donor (D–A–D) structure exhibited the property of intramolecular charge transfer (ICT); thus, their fluorescence emissions were significantly attenuated with increasing ambient polarity. Cell experiments indicated that CC-CH and CC-Cl showed excellent photostability, a low cytotoxicity, and a superior targeting ability regarding LDs. After treatment with oleic acid (OA) and methyl-β-cyclodextrin (M-β-CD), the polarity changes of LDs in living cells could be visualized by using CC-CH and CC-Cl. In addition, CC-CH and CC-Cl could monitor polarity changes of LDs in different pathological processes, including inflammatory responses, nutrient deprivation, and H2O2-induced oxidative stress. Therefore, CC-CH and CC-Cl are promising potential fluorescent probes for tracking intracellular LD polarity changes.

Torreya grandis is a characteristic rare economic tree species in subtropical mountainous areas. The kernels of T. grandis have rich content of organic acids, and malate is the predominant organic acid in T. grandis kernels. However, the contents, biosynthesis/metabolism pathway and transcriptional regulation of malate in developing T. grandis kernels remain completely unknown. Here, the organic acid composition in developing T. grandis kernels was first analyzed. The results showed that the content of malate was increased during the maturation T. grandis kernels. A malate synthase (TgMLS) gene might be involved in the accumulation of malate based on transcriptome data, gene expression and enzyme activity analysis. Transient expression of TgMLS in tobacco resulted in the high malate synthase activity and malate content. Furthermore, a basic helix-loop-helix transcription factor (bHLH), TgbHLH87 was identified to positively regulate the TgMLS expression via directly binding the TgMLS promoter. Our finding contributes to mechanism underlying malate accumulation in T. grandis kernels.

Background: The CCN family of stromal proteins is involved in the regulation of many important biological functions. However, the role of dysregulated CCN proteins in lower-grade glioma (LGG) remain less understand.Methods: The clinical significance of the CCN proteins was explored based on RNA-seq profiles from multiple cohorts. A CCNScore was constructed using LASSO regression analysis. The PanCanAtlas data and MEXPRESS database were employed to elucidate molecular underpinnings.Results: The expression of CCN4 was associated with poor prognosis in LGG. The CCNScore (CCN1 = 0.06, CCN4 = 0.86) showed implication in prognosis prediction, subtype assessment and therapy selection. The gene mutation pattern of the high-CCNScore group was similar with glioblastoma, including EGFR, PTEN, and NF1 mutation frequently. Besides, the high-CCNScore group was comprised of samples mainly classic-like and mesenchymal-like, had lower methylation levels, higher stemness, higher inflammation, higher levels of extracellular matrix remodel and dysfunction of metabolic pathways. On the other hand, the low-CCNScore group consisted mainly of IDH-mutation LGG, and was characterized by TP53, CIC, and ATRX gene mutations, hyper-methylation status, lower stemness, lower proliferation, immune quietness and low extracellular matrix stiffness.Conclusion: In summary, these results outlined the role of CCN family in LGG and provided a potential and promising therapeutic target.

BackgroundThe IGFBP family of insulin-like growth factor binding proteins has important biological functions in the organism. However, the role of the IGFBP family in low-grade glioma (LGG) has not been fully explored.MethodsWe validated the clinical value of the IGFBP family using RNA-seq and clinical data of LGG in the TCGA and constructed an IGFBPScore using LASSO-regression analysis for prognosis prediction, subtype determination, and treatment sensitivity determination. Subsequently, we explored the role of the IGFBP family in the development of LGG using PanCanAtlas data.ResultsOur results suggest that most IGFBP family members were aberrantly expressed and were strongly associated with poor prognosis in LGG. By constructing an IGFBPScore representing the IGFBP family, we found that tumor samples with a high IGFBPScore had a glioblastoma-like mutation pattern characterized by IDH1wt, EGFRmut, PTENmut, and NF1mut with hypo-methylation and glioma stem cell (GSC) diversity. In contrast, the low IGFBPScore group was characterized by IDH1mut accompanied by TP53mut, CICmut, and ATRXmut, and had hyper-methylation status as well as the GSC restriction. Additionally, the high-IGFBPScore group had a high inflammation phenotype with increased immune antigenicity and increased infiltration of immune molecules and cells, as well as a high extracellular matrix phenotype and enhanced multiple metabolic pathways compared with the immune-quiet phenotype of the low-IGFBPScore group, which was strongly associated with poor prognosis.ConclusionOur study provides a summary analysis and a theoretical basis for the biological role and clinical value of the IGFBP family in LGG, providing an important therapeutic target for LGG.

Epithelial-mesenchymal transition (EMT) confers high invasive and migratory capacity to cancer cells, which limits the effectiveness of tumor therapy. Long non-coding RNAs (lncRNAs) can regulate the dynamic process of EMT at different levels through various complex regulatory networks. We aimed to comprehensively analyze and screen EMT-related lncRNAs to characterize lower-grade glioma (LGG) tumor biology and provide new ideas for current therapeutic approaches. We retrieved 1065 LGG samples from the Cancer Genome Atlas and Chinese Glioma Genome Atlas by machine learning algorithms, identified three hub lncRNAs including CRNDE, LINC00665, and NEAT1, and established an EMT-related lncRNA signature (EMTrLS). This novel signature had strong prognostic value and potential clinical significance. EMTrLS described LGG genomic alterations and clinical features including gene mutations, tumor mutational burden, World Health Organization (WHO) grade, IDH status, and 1p/19q status. Notably, stratified analysis revealed activation of malignancy-related and metabolic pathways in the EMTrLS-high cohort. Moreover, the population with increased EMTrLS scores had increased cells with immune killing function. However, this antitumor immune function may be suppressed by increased Tregs and macrophages. Meanwhile, the relatively high expression of immune checkpoints explained the immunosuppressive state of patients with high EMTrLS scores. Importantly, we validated this result by quantifying the course of antitumor immunity. In particular, EMTrLS stratification enabled assessment of the responsiveness of LGG to chemotherapeutic drug efficacy and PD1 blockade. In conclusion, our findings complement the foundation of molecular studies of LGG, provide valuable insight into our understanding of EMT-related lncRNAs, and offer new strategies for LGG therapy.

Nitrogen enters the terrestrial ecosystem through deposition. High nitrogen levels can affect physical and chemical properties of soil and inhibit normal growth and reproduction of forest plants. Nitrogen modulates the composition of soil microorganisms. Strigolactones inhibits plant branching, promotes root growth, nutrient absorption, and promotes arbuscular fungal mycelia branching. Plants are subjected to increasing atmospheric nitrogen deposition. Therefore, it is imperative to explore the relationship between strigolactone and nitrogen deposition of plants and abundance of soil microorganisms. In the present study, the effects of strigolactone on genetic responses and soil microorganisms of Torreya grandis, under simulated nitrogen deposition were explored using high-throughput sequencing techniques. T. grandis is a subtropical economic tree species in China. A total of 4,008 differentially expressed genes were identified in additional N deposition and GR24 treatment. These genes were associated with multiple GO terms and metabolic pathways. GO enrichment analysis showed that several DEGs were associated with enrichment of the transporter activity term. Both additional nitrogen deposition and GR24 treatment modulated the content of nutrient elements. The content of K reduced in leaves after additional N deposition treatment. The content of P increased in leaves after GR24 treatment. A total of 20 families and 29 DEGs associated with transporters were identified. These transporters may be regulated by transcription factors. A total of 1,402,819 clean reads and 1,778 amplicon sequence variants (ASVs) were generated through Bacterial 16S rRNA sequencing. Random forest classification revealed that Legionella, Lacunisphaera, Klebsiella, Bryobacter, and Janthinobacterium were significantly enriched in the soil in the additional N deposition group and the GR24 treatment group. Co-occurrence network analysis showed significant differences in composition of soil microbial community under different treatments. These results indicate a relationship between N deposition and strigolactones effect. The results provide new insights on the role of strigolactones in plants and composition of soil microorganisms under nitrogen deposition.

The epithelial-mesenchymal transition (EMT) is an important process that drives progression, metastasis, and oncology treatment resistance in cancers. Also, the adjacent non-tumor tissue may affect the biological properties of cancers and have potential prognostic implications. Our study aimed to identify EMT-related genes in LGG samples, explore their impact on the biological properties of lower grade gliomas (LGG) through the multi-omics analysis, and reveal the potential mechanism by which adjacent non-tumor tissue participated in the malignant progression of LGG. Based on the 121 differentially expressed EMT-related genes between normal samples from the GTEx database and LGG samples in the TCGA cohort, we identified two subtypes and constructed EMTsig. Because of the genetic, epigenetic, and transcriptomic heterogeneity, malignant features including clinical traits, molecular traits, metabolism, anti-tumor immunity, and stemness features were different between samples with C1 and C2. In addition, EMTsig could also quantify the EMT levels, variation in prognosis, and oncology treatment sensitivity of LGG patients. Therefore, EMTsig could assist us in developing objective diagnostic tools and in optimizing therapeutic strategies for LGG patients. Notably, with the GSVA, we found that adjacent non-tumor tissue might participate in the progression, metastasis, and formation of the tumor microenvironment in LGG. Therefore, the potential prognostic implications of adjacent non-tumor tissue should be considered when performing clinical interventions for LGG patients. Overall, our study investigated and validated the effects of EMT-related genes on the biological properties from multiple perspectives, and provided new insights into the function of adjacent non-tumor tissue in the malignant progression of LGG.

5-Methylcytosine (m5C) methylation is an important RNA modification pattern that can participate in oncogenesis and progression of cancers by affecting RNA stability, expression of oncogenes, and the activity of cancer signaling pathways. Alterations in the expression pattern of long non-coding RNAs (lncRNAs) are potentially correlated with abnormalities in the m5C regulation features of cancers. Our aim was to reveal the mechanisms by which lncRNAs regulated the m5C process, to explore the impact of aberrant regulation of m5C on the biological properties of lower-grade gliomas (LGG), and to optimize current therapeutic. By searching 1017 LGG samples from the Cancer Genome Atlas and Chinese Glioma Genome Atlas, we first clarified the potential impact of m5C regulators on LGG prognosis in this study and used univariate Cox analysis and least absolute shrinkage and selection operator regression to explore clinically meaningful lncRNAs. Consequently, we identified four lncRNAs, including LINC00265, CIRBP-AS1, GDNF-AS1, and ZBTB20-AS4, and established a novel m5C-related lncRNAs signature (m5CrLS) that was effective in predicting prognosis. Notably, mutation rate, WHO class II, IDH mutation, 1p/19q co-deletion and MGMT promoter methylation were increased in the low m5CrLS score group. Patients with increased m5CrLS scores mostly showed activation of tumor malignancy-related pathways, increased immune infiltrating cells, and decreased anti-tumor immune function. Besides, the relatively high expression of immune checkpoints also revealed the immunosuppressed state of patients with high m5CrLS scores. In particular, m5CrLS stratification was sensitive to assess the efficacy of LGG to temozolomide and the responsiveness of immune checkpoint blockade. In conclusion, our results revealed the molecular basis of LGG, provided valuable clues for our understanding of m5C-related lncRNAs, and filled a gap between epigenetics and tumor microenvironment.

In recent years, an increasing number of people have myopia in China, especially the younger generation. Common myopia may develop into high myopia. High myopia causes visual impairment and blindness. Parapapillary atrophy (PPA) is a typical retinal pathology related to high myopia, which is also a basic clue for diagnosing high myopia. Therefore, accurate segmentation of the PPA is essential for high myopia diagnosis and treatment. In this study, we propose an optimized Unet (OT-Unet) to solve this important task. OT-Unet uses one of the pre-trained models: Visual Geometry Group (VGG), ResNet, and Res2Net, as a backbone and is combined with edge attention, parallel partial decoder, and reverse attention modules to improve the segmentation accuracy. In general, using the pre-trained models can improve the accuracy with fewer samples. The edge attention module extracts contour information, the parallel partial decoder module combines the multi-scale features, and the reverse attention module integrates high- and low-level features. We also propose an augmented loss function to increase the weight of complex pixels to enable the network to segment more complex lesion areas. Based on a dataset containing 360 images (Including 26 pictures provided by PALM), the proposed OT-Unet achieves a high AUC (Area Under Curve) of 0.9235, indicating a significant improvement over the original Unet (0.7917).

Torreya grandis ‘Merrillii’ is a famous nut with great nutritional value and high medicinal value. Aril cracking is an important process for seed dispersal, which is also an indicator of seed maturation. However, the cracking mechanism of T. grandis aril during the maturation stage remains largely unknown. Here, we provided a comprehensive view of the physiological and molecular levels of aril cracking in T. grandis by systematically analyzing its anatomical structure, physiological parameters, and transcriptomic response during the cracking process. These results showed that the length of both epidermal and parenchymatous cell layers significantly increased from 133 to 144 days after seed protrusion (DASP), followed by a clear separation between parenchymatous cell layers and kernel, which was accompanied by a breakage between epidermal and parenchymatous cell layers. Moreover, analyses of cell wall composition showed that a significant degradation of cellular wall polysaccharides occurred during aril cracking. To examine the global gene expression changes in arils during the cracking process, the transcriptomes (96 and 141 DASP) were analyzed. KEGG pathway analysis of DEGs revealed that 4 of the top 10 enriched pathways were involved in cell wall modification and 2 pathways were related to ethylene biosynthesis and ethylene signal transduction. Furthermore, combining the analysis results of co-expression networks between different transcription factors, cell wall modification genes, and exogenous ethylene treatments suggested that the ethylene signal transcription factors (ERF11 and ERF1A) were involved in aril cracking of T. grandis by regulation of EXP and PME. Our findings provided new insights into the aril cracking trait in T. grandis.

Abstract Angiogenic signaling pathway is a major contributing factor in cancer recurrence and progression, which can cause significantly reduced treatment outcomes, especially in the oxygen‐dependent photo‐ and sonodynamic therapies. VEGF and its receptor (VEGFR) play a crucial role in angiogenesis progression; precisely, upregulated VEGF signaling is mainly associated with angiogenesis progression in many types of cancers. Herein, we report a sunitinib‐conjugated sonosensitizer (TK‐RB: tyrosine kinase‐rose bengal) to enhance the anticancer efficacy through VEGF inhibition‐mediated antiangiogenesis in conjunction with cellular/tumor damage by ROS generated under ultrasound irradiation. TK‐RB reveals good selectivity and cytotoxicity toward VEGFR‐positive cells (U87MG) over VEGFR‐negative cells (MCF‐7). The fluorescent imaging analysis in vivo/ex vivo and the tumor growth investigation in nude mice with U87MG glioblastoma tumor xenografts demonstrate that rose bengal having tyrosine kinase inhibitor (TK‐RB) provides an enhanced antitumor effect. The current strategy will make a great contribution to optimizing anticancer performance by utilizing sonodynamic therapy together with antiangiogenics in several different malignancies.

Federated incremental learning best suits the changing needs of common Federal Learning (FL) tasks. In this area, the large sample client dramatically influences the final model training results, and the unbalanced features of the client are challenging to capture. In this paper, a federated incremental learning framework is designed; firstly, part of the data is preprocessed to obtain the initial global model. Secondly, to help the global model to get the importance of the features of the whole sample of each client, and enhance the performance of the global model to capture the critical information of the feature, channel attention neural network model is designed on the client side, and a federated aggregation algorithm based on the feature attention mechanism is designed on the server side. Experiments on standard datasets CIFAR10 and CIFAR100 show that the proposed algorithm accuracy has good performance on the premise of realizing incremental learning.

Background: Hepatic stellate cell (HSC) activation induced by transforming growth factor β1 (TGF-β1) plays a pivotal role in fibrogenesis, while the complex downstream mediators of TGF-β1 in such process are largely unknown. Methods: We performed pharmacoproteomic profiling of the mice liver tissues from control, carbon tetrachloride (CCl4)-induced fibrosis and NPLC0393 administrated groups. The target gene MAT2A was overexpressed or knocked down in vivo by tail vein injection of AAV vectors. We examined NF-κB transcriptional activity on MAT2A promoter via luciferase assay. Intracellular SAM contents were analyzed by LC-MS method. Findings: We found that methionine adenosyltransferase 2A (MAT2A) is significantly upregulated in the CCl4-induced fibrosis mice, and application of NPLC0393, a known small molecule inhibitor of TGF-β1 signaling pathway, inhibits the upregulation of MAT2A. Mechanistically, TGF-β1 induces phosphorylation of p65, i.e., activation of NF-κB, thereby promoting mRNA transcription and protein expression of MAT2A and reduces S-adenosylmethionine (SAM) concentration in HSCs. Consistently, in vivo and in vitro knockdown of MAT2A alleviates CCl4- and TGF-β1-induced HSC activation, whereas in vivo overexpression of MAT2A facilitates hepatic fibrosis and abolishes therapeutic effect of NPLC0393. Interpretation: This study identifies TGF-β1/p65/MAT2A pathway that is involved in the regulation of intracellular SAM concentration and liver fibrogenesis, suggesting that this pathway is a potential therapeutic target for hepatic fibrosis. Fund: This work was supported by National Natural Science Foundation of China (No. 81500469, 81573873, 81774196 and 31800693), Zhejiang Provincial Natural Science Foundation of China (No. Y15H030004), the National Key Research and Development Program from the Ministry of Science and Technology of China (No. 2017YFC1700200) and the Key Program of National Natural Science Foundation of China (No. 8153000502).

Federated learning (FL) is a distributed machine learning (ML) framework. In FL, multiple clients collaborate to solve traditional distributed ML problems under the coordination of the central server without sharing their local private data with others. This paper mainly sorts out FLs based on machine learning and deep learning. First of all, this paper introduces the development process, definition, architecture, and classification of FL and explains the concept of FL by comparing it with traditional distributed learning. Then, it describes typical problems of FL that need to be solved. On the basis of classical FL algorithms, several federated machine learning algorithms are briefly introduced, with emphasis on deep learning and classification and comparisons of those algorithms are carried out. Finally, this paper discusses possible future developments of FL based on deep learning.

Federated Learning (FL) can combine multiple clients for training and keep client data local, which is a good way to protect data privacy. There are many excellent FL algorithms. However, most of these can only process data with regular structures, such as images and videos. They cannot process non-Euclidean spatial data, that is, irregular data. To address this problem, we propose a Federated Learning-Based Graph Convolutional Network (FedGCN). First, we propose a Graph Convolutional Network (GCN) as a local model of FL. Based on the classical graph convolutional neural network, TopK pooling layers and full connection layers are added to this model to improve the feature extraction ability. Furthermore, to prevent pooling layers from losing information, cross-layer fusion is used in the GCN, giving FL an excellent ability to process non-Euclidean spatial data. Second, in this paper, a federated aggregation algorithm based on an online adjustable attention mechanism is proposed. The trainable parameter ρ is introduced into the attention mechanism. The aggregation method assigns the corresponding attention coefficient to each local model, which reduces the damage caused by the inefficient local model parameters to the global model and improves the fault tolerance and accuracy of the FL algorithm. Finally, we conduct experiments on six non-Euclidean spatial datasets to verify that the proposed algorithm not only has good accuracy but also has a certain degree of generality. The proposed algorithm can also perform well in different graph neural networks.

Temperature and relative humidity (RH) influence post-harvest ripening, a crucial stage for quality promotion in some oil plants or fruits. Torreya grandis cv. Merrillii nuts, which are rich in unsaturated fatty acids (UFA), are easily affected by temperature and humidity, and they oxidize quickly during the post-harvest ripening stage, leading to the deterioration of nut quality. In this study, the main nutraceutical components, fatty acid composition, and related metabolic parameters of lipid rancidity under four treatments (20°C and 70% RH, T20-LH; 30°C and 70% RH, T30-LH; 20°C and 90% RH, T20-HH; 30°C and 90% RH, T30-HH) were measured. The post-harvest ripening process was advanced under HH treatments (T20-HH and T30-HH) compared to LH treatments (T20-LH and T30-LH) and was associated with a shorter time for the seed coat to turn dark black and a faster reduction in starch content. The amount of unsaturated fatty acids significantly increased under the T20-HH treatment, but significantly decreased under the T30-HH treatment from 12 to 16 d of ripening time. The acid value (AV) and lipase activity under the T30-HH treatment remained virtually constant from 12 to 16 d of ripening time, and this was accompanied by a dramatic increase in peroxide value (POV), lipoxygenase (LOX) activity, and relative expression of the LOX2 gene. Meanwhile, a significant positive correlation between LOX activity and POV, malondialdehyde (MDA) content, and O2⋅– content was observed. The results imply that the lower amount of oxidative rancidity induced by the T20-HH treatment is related to the LOX activity induced by down-regulation of the LOX2 gene during the late after-ripening stage. Therefore, the T20-HH treatment not only promoted the post-harvest process of T. grandis ‘Merrillii’ nuts but also delayed lipid oxidation, which was ultimately associated with better oil quality at the late after-ripening stage.

Abstract The integration of diagnosis and therapy based on natural products has been receiving considerable attention in recent years because nature can contribute many fantastic functional molecules with good biocompatibility and low toxicity. Diagnostic and therapeutic agents combined with the technique of photodynamic therapy (PDT) and sonodynamic therapy (SDT) have been extensively developed thanks to the advantages of PDT and SDT, such as good selectivity, low toxicity, and noninvasive treatment for cancers and other diseases compared with traditional treatments. In this review, we summarize the recent advances in theranostic agents for natural products categorized as porphyrins, perylenequinone, curcumin, and others. Some representative examples of disease diagnosis in fluorescence/photoacoustic imaging and disease treatment in PDT/SDT were introduced. Potential limitations and future perspectives of these natural products for theranostic agents were also discussed.

Among abiotic stressors, drought and salinity seriously affect crop growth worldwide. In plants, research has aimed to increase stress-responsive protein synthesis upstream or downstream of the various transcription factors (TFs) that alleviate drought and salinity stress. TFs play diverse roles in controlling gene expression in plants, which is necessary to regulate biological processes, such as development and environmental stress responses. In general, plant responses to different stress conditions may be either abscisic acid (ABA)-dependent or ABA-independent. A detailed understanding of how TF pathways and ABA interact to cause stress responses is essential to improve tolerance to drought and salinity stress. Despite previous progress, more active approaches based on TFs are the current focus. Therefore, the present review emphasizes the recent advancements in complex cascades of gene expression during drought and salinity responses, especially identifying the specificity and crosstalk in ABA-dependent and -independent signaling pathways. This review also highlights the transcriptional regulation of gene expression governed by various key TF pathways, including AP2/ERF, bHLH, bZIP, DREB, GATA, HD-Zip, Homeo-box, MADS-box, MYB, NAC, Tri-helix, WHIRLY, WOX, WRKY, YABBY, and zinc finger, operating in ABA-dependent and -independent signaling pathways.

Seed oil content is an important trait of nut seeds, and it is affected by the import of carbon from photosynthetic sources. Although green leaves are the main photosynthetic organs, seed sarcotesta photosynthesis also supplies assimilates to seed development. Understanding the relationship between seed photosynthesis and seed development has theoretical and practical significance in the cultivation of Torreya grandis cv. “Merrillii.” To assess the role of seed sarcotesta photosynthesis on the seed development, anatomical and physiological traits of sarcotesta were measured during two growing seasons in the field. Compared with the attached current-year leaves, the sarcotesta had higher gross photosynthetic rate at the first stage of seed development. At the late second stage of seed development, sarcotesta showed down-regulation of PSII activity, as indicated by significant decrease in the following chlorophyll fluorescence parameters: the maximum PSII efficiency (Fv/Fm), the PSII quantum yield (ΦPSII), and the photosynthetic quenching coefficient (qP). The ribulose 1, 5—bisphosphate carboxylase (Rubisco) activity, the total chlorophyll content (Chl(a+b)) and nitrogen content in the sarcotesta were also significantly decreased during that period. Treatment with DCMU [3-(3,4-dichlorophenyl)-1,1-dimethylurea] preventing seed photosynthesis decreased the seed dry weight and the oil content by 25.4 and 25.5%, respectively. We conclude that seed photosynthesis plays an important role in the dry matter accumulation at the first growth stage. Our results also suggest that down-regulation of seed photosynthesis is a plant response to re-balance the source-sink ratio at the second growth stage. These results suggest that seed photosynthesis is important for biomass accumulation and oil synthesis of the Torreya seeds. The results will facilitate achieving higher yields and oil contents in nut trees by selection for higher seed photosynthesis cultivars.

Atmospheric nitrogen (N) deposition can increase the susceptibility of vascular plants to other stresses, but the physiological basis of such a response remains poorly understood. This study was designed to clarify the physiological mechanisms and to evaluate bioindicators of N deposition impact on vascular plants. We evaluate multiple physiological responses to ~4 years of simulated additional N deposition (30–90 kg N ha−1 year−1) on three age-classes (1a, 3a, and 5a) of Moso bamboo. A saturating response to the additional N deposition was found both in foliar N concentration and in Pn. However, 3- and 5-year-old bamboo seemed to be less tolerant to extremely high N deposition than 1-year-old bamboo since they were saturated at a lower N addition. Furthermore, C/N/P stoichiometric ratios were very sensitive to N deposition in all three-age classes of bamboo, but the responses to N deposition in the various age-classes were diverse. We also found that the highest additional N deposition suppressed stomatal conductance and transpiration rate, suggesting an induced water stress. The stress induced by the high N load was also seen in photochemistry, where it reduced potential and actual photosynthetic use of light energy, diminished photo-protection capacity, and increased risk of the photo-damage. High additional N deposition contributed to a decrease in the foliar soluble protein contents and to an increase in the peroxidase activity (POD). Our study suggested, for the first time, that although the photosynthetic rate was enhanced by the increased N deposition in Moso bamboo, long-term high N load causes negative effects, such as damage to photosystem II. In Moso bamboo photochemical parameters are more sensitive to N deposition than photosynthetic rate or foliar N concentration. Furthermore, plant age should be taken into account when assessing plants' susceptibility to changes in global change drivers, such as N deposition. These findings facilitate the revealing of the risks potentially caused to vascular plants by increased N deposition before any visible symptoms of injury are seen.

Magnesium (Mg2+) has been shown to reduce the physiological and biochemical stress in plants caused by heavy metals. To date our understanding of how Mg2+ ameliorates the adverse effects of heavy metals in plants is scarce. The potential effect of Mg2+ on lead (Pb2+) toxicity in plants has not yet been studied. This study was designed to clarify the mechanism of Mg2+-induced alleviation of lead (Pb2+) toxicity. Torreya grandis (T. grandis) seedlings were grown in substrate contaminated with 0, 700 and 1400 mg Pb2+ per kg-1 and with or without the addition of 1040 mg kg-1 Mg2+. Growth parameters, concentrations of Pb2+ and Mg2+ in the plants’ shoots and roots, photosynthetic pigment, gas exchange parameters, the maximum quantum efficiency (Fv/Fm), root oxidative activity, ultrastructure of chloroplasts and root growth were determined to analyze the effect of different Pb2+ concentrations in the seedlings as well as the potential ameliorating effect of Mg2+ on the Pb2+ induced toxicity. The growth of T. grandis seedlings cultivated in soils treated with 1400 mg kg-1 Pb2+ was significantly reduced compared with that of plants cultivated in soils treated with 0 or 700 mg kg-1 Pb2+. The addition of 1040 mg kg-1 Mg2+ improved the growth of the Pb2+-stressed seedlings, which was accompanied by increased chlorophyll content, the net photosynthetic rate and Fv/Fm, and enhanced chloroplasts development. In addition, the application of Mg2+ induced plants to accumulate five times higher concentrations of Pb2+ in the roots and to absorb and translocate four times higher concentrations of Mg2+ to the shoots than those without Mg2+ application. Furthermore, Mg2+ addition increased root growth and oxidative activity, and protected the root ultrastructure. To the best of our knowledge, our study is the first report on the mechanism of Mg2+-induced alleviation of Pb2+ toxicity. The gener¬ated results may have important implications for understanding the physiological interactions between heavy metals and plants, and for successful management of T. grandis plantations grown on soils contaminated with Pb2+.

In recent years, it has been found that the service life of cemented carbide shield machine tools used in uneven soft and hard strata is substantially reduced in engineering practice. The study found that thermal stress is the main reason for the failure of cemented carbide shield tunneling tools when shield tunneling is carried out in uneven soft and hard soil. To maintain the hardness of cemented carbide, improving the thermal conductivity of the shield machine tool is of great importance for prolonging its service life and reducing engineering costs. In this study, graphene and carbon nanotubes were mixed with WC–Co powder and sintered by spark plasma sintering (SPS). The morphology was observed by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). The Rockwell hardness, bending strength, and thermal conductivity of the samples were tested. The results show that adding a small amount of graphene or carbon nanotubes could increase the bending strength of the cemented carbide by approximately 50%, while keeping the hardness of the cemented carbide constant. The thermal conductivity of the cemented carbide could be increased by 10% with the addition of 0.12 wt % graphene alone.

BACKGROUND: Salt stress is a major factor limiting plant growth and productivity. Salicylic acid (SA) has been shown to ameliorate the adverse effects of environmental stress on plants. To investigate the protective role of SA in ameliorating salt stress on Torreya grandis (T. grandis) trees, a pot experiment was conducted to analyze the biomass, relative water content (RWC), chlorophyll content, net photosynthesis (Pn), gas exchange parameters, relative leakage conductivity (REC), malondialdehyde (MDA) content, and activities of superoxide dismutase (SOD) and peroxidase (POD) of T. grandis under 0.2% and 0.4% NaCl conditions with and without SA. METHODOLOGY/PRINCIPAL FINDINGS: The exposure of T. grandis seedlings to salt conditions resulted in reduced growth rates, which were associated with decreases in RWC and Pn and increases in REC and MDA content. The foliar application of SA effectively increased the chlorophyll (chl (a+b)) content, RWC, net CO2 assimilation rates (Pn), and proline content, enhanced the activities of SOD, CAT and POD, and minimized the increases in the REC and MDA content. These changes increased the capacity of T. grandis in acclimating to salt stress and thus increased the shoot and root dry matter. However, when the plants were under 0% and 0.2% NaCl stress, the dry mass of the shoots and roots did not differ significantly between SA-treated plants and control plants. CONCLUSIONS: SA induced the salt tolerance and increased the biomass of T. grandis cv. by enhancing the chlorophyll content and activity of antioxidative enzymes, activating the photosynthetic process, and alleviating membrane injury. A better understanding about the effect of salt stress in T. grandis is vital, in order gain knowledge over expanding the plantations to various regions and also for the recovery of T. grandis species in the future.

Previously, we screened a proteoglycan for anti-hyperglycemic, named FYGL, from Ganoderma Lucidum. For further research of the antidiabetic mechanisms of FYGL in vivo, the glucose homeostasis, activities of insulin-sensitive enzymes, glucose transporter expression and pancreatic function were analyzed using db/db mice as diabetic models in the present work. FYGL not only lead to a reduction in glycated hemoglobin level, but also an increase in insulin and C-peptide level, whereas a decrease in glucagons level and showed a potential for the remediation of pancreatic islets. FYGL also increased the glucokinase activities, and simultaneously lowered the phosphoenol pyruvate carboxykinase activities, accompanied by a reduction in the expression of hepatic glucose transporter protein 2, while the expression of adipose and skeletal glucose transporter protein 4 was increased. Moreover, the antioxidant enzyme activities were also increased by FYGL treatment. Thus, FYGL was an effective antidiabetic agent by enhancing insulin secretion and decreasing hepatic glucose output along with increase of adipose and skeletal muscle glucose disposal in the late stage of diabetes. Furthermore, FYGL is beneficial against oxidative stress, thereby being helpful in preventing the diabetic complications.

Proper development of a seed requires coordinated exchanges of signals among the three components that develop side by side in the seed. One of these is the maternal integument that encloses the other two zygotic components, i.e., the diploid embryo and its nurturing annex, the triploid endosperm. Although the formation of the embryo and endosperm contains the contributions of both maternal and paternal parents, maternally and paternally derived alleles may be expressed differently, leading to a so-called parent-of-origin or imprinting effect. Currently, the nature of how genes from the maternal and zygotic genomes interact to affect seed development remains largely unknown. Here, we present a novel statistical model for estimating the main and interaction effects of quantitative trait loci (QTLs) that are derived from different genomes and further testing the imprinting effects of these QTLs on seed development. The experimental design used is based on reciprocal backcrosses toward both parents, so that the inheritance of parent-specific alleles could be traced. The computing model and algorithm were implemented with the maximum likelihood approach. The new strategy presented was applied to study the mode of inheritance for QTLs that control endoreduplication traits in maize endosperm. Monte Carlo simulation studies were performed to investigate the statistical properties of the new model with the data simulated under different imprinting degrees. The false positive rate of imprinting QTL discovery by the model was examined by analyzing the simulated data that contain no imprinting QTL. The reciprocal design and a series of analytical and testing strategies proposed provide a standard procedure for genomic mapping of QTLs involved in the genetic control of complex seed development traits in flowering plants.