The growing global burden of metabolic dysfunction-associated steatohepatitis(MASH)demands a deeper understanding of its underlying mechanisms and risk factors.Recent studies,such as the large population-based case-co...The growing global burden of metabolic dysfunction-associated steatohepatitis(MASH)demands a deeper understanding of its underlying mechanisms and risk factors.Recent studies,such as the large population-based case-control analysis by Abdel-Razeq et al,suggest a significant association between Helicobacter pylori(H.pylori)infection and an increased risk of developing MASH.This study provides compelling data supporting this association,even after adjusting for confounders such as obesity,diabetes,and hyperlipidemia.However,the complexity of this relationship remains unresolved,requiring further investigation into the biological,genetic,and environmental pathways that connect these two conditions.This article critically reviews the study’s findings and identifies its limitations,offering innovative research directions for the future.Key areas of focus include integrating genomic and microbiome analyses,exploring the impact of H.pylori eradication on MASH progression,studying molecular mechanisms at the intersection of infection and liver disease,and developing personalized therapeutic strategies.展开更多
Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.展开更多
Angelica L.has attracted global interest for its traditional medicinal uses and commercial values.However,few studies have focused on the metabolomic differences among the Angelica species.In this study,widely targete...Angelica L.has attracted global interest for its traditional medicinal uses and commercial values.However,few studies have focused on the metabolomic differences among the Angelica species.In this study,widely targeted metabolomics based on gas chromatography-tandem mass spectrometry was employed to analyze the metabolomes of four Angelica species(Angelicasinensis(Oliv.)Diels(A.sinensis),Angelica biserrata(R.H.Shan &Yuan)C.Q.Yuan & R.H.Shan(A.biserrata),Angelica dahurica(Hoffm.)Benth.& Hook.f.ex Franch.& Sav.(A.dahurica)and Angelica keiskei Koidz.(A.keiskei)).A total of 698 volatile metabolites were identified and classified into fifteen different categories.The metabo-lomic analysis indicated that 7-hydroxycoumarin and Z-ligustilide accumulated at significantly higher levels in A.sinensis,whereas bornyl acetate showed the opposite pattern.Furthermore,a high correspondence between the dendrogram of metabolite contents and phylogenetic positions of the four species.This study provides a comprehensive biochemical map for the exploitation,application and development of the Angelica species as medicinal plants or health-related dietary supplements.展开更多
The Jitang metamorphic complex is key to studying the tectonic evolution of the Northern Lancangjiang zone.Through structural-lithological mapping,structural analysis and laboratory testing,the composition of the Jita...The Jitang metamorphic complex is key to studying the tectonic evolution of the Northern Lancangjiang zone.Through structural-lithological mapping,structural analysis and laboratory testing,the composition of the Jitang metamorphic complex was determined.The macro-and microstructural analyses of the ductile detachment shear zone(Guoxuepu ductile shear zone,2–4 km wide)between the metamorphic complex and the overlying sedimentary cap show that the shear sense of the ductile shear zones is top-to-the-southeast.The presence of various deformation features and quartz C-axis electron backscatter diffraction(EBSD)fabric analysis suggests multiple deformation events occurring at different temperatures.The average stress is 25.68 MPa,with the strain rates(έ)ranging from 9.77×10^(−14)s^(−1)to 6.52×10^(−16)s^(−1).The finite strain of the Guoxuepu ductile shear zone indicates an elongated strain pattern.The average kinematic vorticity of the Guoxuepu ductile shear zone is 0.88,implying that the shear zone is dominated by simple shear.The muscovite selected from the protomylonite samples in the Guoxuepu ductile shear zone yields a 40Ar-39Ar age of 60.09±0.38 Ma.It is suggested that,coeval with the initial Indo–Eurasian collision,the development of strike-slip faults led to a weak and unstable crust,upwelling of lower crust magma,then induced the detachment of the Jitang metamorphic complex in the Eocene.展开更多
Thigmotropism and thigmomorphogenesis are two related and pervasive processes that play crucial roles in plant adaptation to the environment.However,there have been few investigations into the molecular regulatory mec...Thigmotropism and thigmomorphogenesis are two related and pervasive processes that play crucial roles in plant adaptation to the environment.However,there have been few investigations into the molecular regulatory mechanisms of these phenomena.Cucumber(Cucumis sativus L.)tendrils are ideal material for studying thigmotropism and thigmomorphogenesis because they display a combination of the two processes.Here,we generated the transcriptome profiles of cucumber tendrils at the young,stretch,and coiling stages.Genes related to receptor proteins,transmembrane transport,and ion transport were significantly enriched among those differentially expressed between stages.Pharmacological assays illustrated that three GLUTAMATE RECEPTOR(GLR)genes might play a vital function in perceiving or transducing touch stimulation signals.Comparing the transcriptomes of tendrils and roots after touch stimulation,we found that genes related to extracellular stimulus and xyloglucan metabolism might have conserved functions in the regulation of thigmomorphogenesis.The transcriptome atlas of thigmotropism and thigmomorphogenesis of cucumber tendrils constructed in this study will help further elucidate the molecular mechanisms behind these processes.展开更多
Chinese Medicine(CM)has been widely used as an important avenue for disease prevention and treatment in China especially in the form of CM prescriptions combining sets of herbs to address patients’symptoms and syndro...Chinese Medicine(CM)has been widely used as an important avenue for disease prevention and treatment in China especially in the form of CM prescriptions combining sets of herbs to address patients’symptoms and syndromes.However,the selection and compatibility of herbs are complex and abstract due to intrinsic relationships between herbal properties and their overall functions.Network analysis is applied to demonstrate the complex relationships between individual herbal efficacy and the overall function of CM prescriptions.To illustrate their connections and correlations,prescription function(PF),prescription herb(PH),and herbal efficacy(HE)intranetworks are proposed based on CM theory to identify relationships between herbs and prescriptions.These three networks are then connected by PF-PH and PH-HE interlayer networks adopting herb dosage to form a multidimensional heterogeneous network,a Prescription-Herb-Function Network(PHFN).The network is applied to 112 classic prescriptions from Treatise on Exogenous Febrile and Miscellaneous Diseases to illustrate the application of PHFN.The PHFN is constructed including 146 functions in PF intra network,89 herbs in the PH intra network,and 163 herbal efficacies in the HE intra network.The results show that herb pairs with synergistic actions have stronger relevance,such as licorice-cassia twig,licorice-Chinese date,fresh ginger-Chinese date,etc.The integration of dosage to the network helps to indicate the main herbs for cluster analysis and automatic formulation.PHFN also reveals the internal relationships between the functions of prescriptions and composed herbal efficacies.展开更多
Chitin is an abundant aminopolysaccharide found in insect pests and phytopathogenic microorganisms but absent in higher plants and vertebrates. It is crucial for mitigating threats posed by chitin-containing organisms...Chitin is an abundant aminopolysaccharide found in insect pests and phytopathogenic microorganisms but absent in higher plants and vertebrates. It is crucial for mitigating threats posed by chitin-containing organisms to human health, food safety, and agriculture. Therefore, targeting the chitin biosynthesisassociated bioprocess holds a promise for developing human-safe and eco-friendly antifungal agents or pesticides. Chitin biosynthesis requires chitin synthase and associated factors, which are involved in the modification, regulation, organization or turnover of chitin during its biosynthesis. A number of enzymes such as chitinases, hexosaminidases, chitin deacetylases are closely related and therefore are promising targets for designing novel agrochemicals that target at chitin biosynthesis. This review summarizes the advances in understanding chitin biology over the past decade by our research group and collaborates,specifically regarding essential proteins linked to chitin biosynthesis that can be exploited as promising pesticide targets. Examples of small bioactive molecules that against the activity of these targets are given.展开更多
Photosynthesis is one the most important chemical reaction in plants,and it is the ultimate energy source of any living organisms.The light and dark reactions are two essential phases of photosynthesis.Light reaction ...Photosynthesis is one the most important chemical reaction in plants,and it is the ultimate energy source of any living organisms.The light and dark reactions are two essential phases of photosynthesis.Light reaction harvests light energy to synthesize ATP and NADPH through an electron transport chain,and as well as giving out O_(2);dark reaction fixes CO_(2) into six carbon sugars by utilizing NADPH and energy from ATP.Subsequently,plants convert optical energy into chemical energy for maintaining growth and development through absorbing light energy.Here,firstly,we highlighted the biological importance of photosynthesis,and hormones and metabolites,photosynthetic and regulating enzymes,and signaling components that collectively regulate photosynthesis in tomato.Next,we reviewed the advances in tomato photosynthesis,including two aspects of genetic basis and genetic improvement.Numerous genes regulating tomato photosynthesis are gradually uncovered,and the interaction network among those genes remains to be constructed.Finally,the photosynthesis occurring in fruit of tomato and the relationship between photosynthesis in leaf and fruit were discussed.Leaves and fruits are photosynthate sources and sinks of tomato respectively,and interaction between photosynthesis in leaf and fruit exists.Additionally,future perspectives that needs to be addressed on tomato photosynthesis were proposed.展开更多
Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomat...Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomato fruit yield.It is necessary to identify transcription factors(TFs)and target genes involved in heat stress response(HSR)signaling cascades in tomato flower buds to improve tomato plant thermotolerance.In this study,we profiled genes expressed in three developmental stages of tomato flower buds.Red and turquoise modules for heat stress(HS)were identified through gene co-expression network analysis,and the genes within these modules were enriched in HS-related pathways.By focusing on the TFs in the two modules,we identified several novel HSR-related TFs,including SlWRKY75,SlMYB117,and SlNAM.Furthermore,homology analysis illustrated a conserved signaling cascade in tomato.Lastly,we identified and experimentally validated four HSF-regulated genes,namely SlGrpE,SlERDJ3A,SlTIL,and SlPOM1,that likely modulate thermotolerance in plants.These results provide a high-resolution atlas of gene expression during tomato flower bud development under HS conditions,which is a valuable resource for uncovering potential regulatory networks associated with the HSR in tomato.展开更多
Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its impor...Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its importance,the lack of a complete genome assembly has been a stumbling block in its biological breeding process.Therefore,we generated deep coverage ultralong Oxford Nanopore Technology(ONT)and PacBio HiFi reads to construct a telomere-to-telomere(T2T)genome assembly.The final assembly spans 537.27 Mb with no gaps,demonstrating a remarkable completeness of 98.1%.We utilized a combination of transcriptome data and homologous proteins to annotate the genome,identifying 36018 protein-coding genes.Furthermore,we profiled global cytosine DNA methylations using ONT sequencing data.Global methylome analysis revealed high methylation levels in transposable element(TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas.By integrating a detailed multi-omics data analysis,we obtained valuable insights into the mechanism underlying endopleura coloration.This investigation led to the identification of eight candidate genes(e.g.ANR)involved in anthocyanin biosynthesis pathways,which are crucial for the development of color in plants.The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.展开更多
Zinc(Zn)is an essential micronutrient for both plants and humans.Zn deficiency is common in many paddy fields and reduces yield and grain Zn content(GZC).To accelerate breeding for improved GZC and Zn deficiency toler...Zinc(Zn)is an essential micronutrient for both plants and humans.Zn deficiency is common in many paddy fields and reduces yield and grain Zn content(GZC).To accelerate breeding for improved GZC and Zn deficiency tolerance(ZDT)rice varieties,it is important to identify genes regulating Zn homeostasis.In this study,a member of the Ser/Thr protein phosphatase family,LOC_Os07g48840(named as OsGZ7),was found to contributed to ZDT and GZC in rice.The expression of OsGZ7 in roots and shoots was inhibited by Zn deficiency and toxicity,but induced by iron(Fe),manganese(Mn),and copper(Cu)deficiency,as well as chromium toxicity.OsGZ7 localized to the cytoplasm and was expressed in all tissues during the tillering,flowering,and grain-filling stages,particularly in the leaf blade and leaf sheath.At the seedling stage,knockout of OsGZ7 enhanced ZDT and increased Zn accumulation in both roots and shoots.At the maturity stage,knockout of OsGZ7 enhanced GZC,while overexpression of OsGZ7 reduced GZC.RNA-seq analysis suggested that OsGZ7 might regulate Zn homeostasis by affecting metal binding,hormone signal transduction,and oxidoreductase activity.Taken together,our findings indicate that OsGZ7 contributes to ZDT and Zn accumulation in rice.展开更多
Objective To predict the potential targets of Qingfu Juanbi Decoction(青附蠲痹汤,QFJBD)in treating rheumatoid arthritis(RA)using an improved Transformer model and investigate the network pharmacological mechanisms und...Objective To predict the potential targets of Qingfu Juanbi Decoction(青附蠲痹汤,QFJBD)in treating rheumatoid arthritis(RA)using an improved Transformer model and investigate the network pharmacological mechanisms underlying QFJBD’s therapeutic effects on RA.Methods First,a traditional Chinese medicine herb-target interaction(TCMHTI)model was constructed to predict herb-target interactions based on Transformer improvement.The per-formance of the TCMHTI model was evaluated against baseline models using three metrics:area under the receiver operating characteristic curve(AUC),precision-recall curve(PRC),and accuracy.Subsequently,a protein-protein interaction(PPI)network was built based on the predicted targets,with core targets identified as the top nine nodes ranked by degree val-ues.Gene Ontology(GO)functional and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses were performed using the targets predicted by TCMHTI and the targets identified through network pharmacology method for comparison.Then,the re-sults were compared.Finally,the core targets predicted by TCMHTI were validated through molecular docking and literature review.Results The TCMHTI model achieved an AUC of 0.883,PRC of 0.849,and accuracy of 0.818,predicting 49 potential targets for QFJBD in RA treatment.Nine core targets were identified:tumor necrosis factor(TNF)-α,interleukin(IL)-1β,IL-6,IL-10,IL-17A,cluster of differentia-tion 40(CD40),cytotoxic T-lymphocyte-associated protein 4(CTLA4),IL-4,and signal trans-ducer and activator of transcription 3(STAT3).The enrichment analysis demonstrated that the TCMHTI model predicted 49 targets and enriched more pathways directly associated with RA,whereas classical network pharmacology identified 64 targets but enriched pathways showing weaker relevance to RA.Molecular docking demonstrated that the active molecules in QFJBD exhibit favorable binding energy with RA targets,while literature research further revealed that QFJBD can treat RA through 9 core targets.Conclusion The TCMHTI model demonstrated greater accuracy than traditional network pharmacology methods,suggesting QFJBD exerts therapeutic effects on RA by regulating tar-gets like TNF-α,IL-1β,and IL-6,as well as multiple signaling pathways.This study provides a novel framework for bridging traditional herbal knowledge with precision medicine,offering actionable insights for developing targeted TCM therapies against diseases.展开更多
In this review,we explore the application of next-generation sequencing in liver cancer research,highlighting its potential in modern oncology.Liver cancer,particularly hepatocellular carcinoma,is driven by a complex ...In this review,we explore the application of next-generation sequencing in liver cancer research,highlighting its potential in modern oncology.Liver cancer,particularly hepatocellular carcinoma,is driven by a complex interplay of genetic,epigenetic,and environmental factors.Key genetic alterations,such as mutations in TERT,TP53,and CTNNB1,alongside epigenetic modifications such as DNA methylation and histone remodeling,disrupt regulatory pathways and promote tumorigenesis.Environmental factors,including viral infections,alcohol consum-ption,and metabolic disorders such as nonalcoholic fatty liver disease,enhance hepatocarcinogenesis.The tumor microenvironment plays a pivotal role in liver cancer progression and therapy resistance,with immune cell infiltration,fibrosis,and angiogenesis supporting cancer cell survival.Advances in immune check-point inhibitors and chimeric antigen receptor T-cell therapies have shown po-tential,but the unique immunosuppressive milieu in liver cancer presents challenges.Dysregulation in pathways such as Wnt/β-catenin underscores the need for targeted therapeutic strategies.Next-generation sequencing is accele-rating the identification of genetic and epigenetic alterations,enabling more precise diagnosis and personalized treatment plans.A deeper understanding of these molecular mechanisms is essential for advancing early detection and developing effective therapies against liver cancer.展开更多
Chitin is an abundant natural biopolymer that plays a crucial role in insect growth and development as a fundamental structural component of the exoskeleton.The membrane-integralβ-glycosyltransferase,chitin synthase,...Chitin is an abundant natural biopolymer that plays a crucial role in insect growth and development as a fundamental structural component of the exoskeleton.The membrane-integralβ-glycosyltransferase,chitin synthase,has been identified as the central component in chitin biosynthesis.However,the precise roles of other proteins in facilitating chitin synthase in chitin biosynthesis remain unclear.In this study,we employed split-ubiquitin membrane yeast two-hybrid(MYTH)and pull-down assays to demonstrate the physical interaction between Twinstar(Tsr),a small molecular protein in the actin-depolymerizing factor ADF/Cofilin protein family,and chitin synthase Krotzkopf verkehrt(Kkv)in Drosophila melanogaster in vitro.The RNA interference(RNAi)-mediated global knockdown of Tsr in D.melanogaster resulted in larval lethality.Furthermore,targeted suppression of Tsr in the tracheal and epidermal tissues also led to larval mortality,while knocking down Tsr in the wing tissues led to wrinkled wings.Additionally,silencing Tsr not only reduced the chitin content in the first longitudinal vein of the wings but also led to the absence of the chitin lamellar structure.To validate the functional conservation of Tsr in other insect orders,the two agricultural pests Ostrinia furnacalis and Tribolium castaneum,representing lepidoptera and coleoptera insects,respectively,were investigated.Knockdown experiments targeting the Drosophila Tsr orthologues OfTsr in O.furnacalis and TcTsr in T.castaneum produced abnormal larvae during molting or pupation in O.furnacalis and lethality in T.castaneum.Our findings not only improve ourknowledge of the chitin biosynthesis machinery in insect cuticles but also provide new potential targets for the control of major agricultural pests.展开更多
Potato(Solanum tuberosum)is a globally important staple crop.However,cultivated potato varieties are highly sensitive to low temperatures.The molecular mechanisms underlying freezing resistance in potatoes remain poor...Potato(Solanum tuberosum)is a globally important staple crop.However,cultivated potato varieties are highly sensitive to low temperatures.The molecular mechanisms underlying freezing resistance in potatoes remain poorly understood.Through comparative metabolome and transcriptome analyses of freezing-tolerant(CM,Solanum commersonii)and freezing-sensitive(DM,DM1-3516R44)varieties,we identified a coldinduced UDP-glycosyltransferase gene,ScUGT73B4,which is associated with the accumulation of glycosylated flavonoids in wild CM varieties.Overexpression of ScUGT73B4 led to increased accumulation of glycosylated flavonoids and enhanced antioxidant capacity,resulting in improved freezing tolerance in potato plantlets.These findings reveal a UDP-glycosyltransferase in the flavonoid pathway and offer a potential valuable genetic resource for breeding potatoes with improved freezing tolerance.展开更多
Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lac...Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.展开更多
oluble solids content(SSC) plays an important role in determining the flavor of tomato fruits. Tomato fruit SSC is transcriptionally regulated via sugar metabolism. Previous studies have predominantly focused on the r...oluble solids content(SSC) plays an important role in determining the flavor of tomato fruits. Tomato fruit SSC is transcriptionally regulated via sugar metabolism. Previous studies have predominantly focused on the role of C2H2-type zinc finger proteins in tomato growth and development. However, the specific regulatory mechanisms of C2H2 in the accumulation of soluble solids in tomato fruits are not fully understood. This study used eight tomato accessions with varying levels of SSC to study the expression of SlC2H2 family genes in red ripe fruits. The levels of SlC2H2-71 expression were found to be significantly reduced in high-SSC accessions compared to low-SSC accessions. Several Slc2h2-71 mutant lines were developed using the CRISPR-Cas9 system, which led to elevated levels of soluble solids, fructose, glucose, malic acid, and citric acid in mature red ripe fruits. However, the sucrose content in the edited Slc2h2-71 mutant lines was generally lower. RNA-seq analysis revealed that fruits from the mutant lines had altered expression of genes related to the sugar and acid metabolic pathways, which was further confirmed by quantitative real-time PCR. Specifically, the expression of SlLIN5 encoding the cell wall invertase(CWIN) was elevated. The yeast one-hybrid(Y1H) assay, 35S::UAS-GUS, dual-luciferase reporter systems and electrophoretic mobility shift assay(EMSA) demonstrated that C2H2-71 regulates tomato sugar metabolism by directly binding to the promoter region of Sl LIN5, culminating in the repression of its transcriptional activity. The activity of acid invertase exhibited a significantly higher level in the SlC2H2-71 knock-out lines compared to the control lines. In summary, the regulation of tomato fruit SSC by C2H2-71 involves the inhibition of SlLIN5 expression.展开更多
Graph neural networks(GNNs)have demonstrated excellent performance in graph representation learning.However,as the volume of graph data grows,issues related to cost and efficiency become increasingly prominent.Graph d...Graph neural networks(GNNs)have demonstrated excellent performance in graph representation learning.However,as the volume of graph data grows,issues related to cost and efficiency become increasingly prominent.Graph distillation methods address this challenge by extracting a smaller,reduced graph,ensuring that GNNs trained on both the original and reduced graphs show similar performance.Existing methods,however,primarily optimize the feature matrix of the reduced graph and rely on correlation information from GNNs,while neglecting the original graph’s structure and redundant nodes.This often results in a loss of critical information within the reduced graph.To overcome this limitation,we propose a graph distillation method guided by network symmetry.Specifically,we identify symmetric nodes with equivalent neighborhood structures and merge them into“super nodes”,thereby simplifying the network structure,reducing redundant parameter optimization and enhancing training efficiency.At the same time,instead of relying on the original node features,we employ gradient descent to match optimal features that align with the original features,thus improving downstream task performance.Theoretically,our method guarantees that the reduced graph retains the key information present in the original graph.Extensive experiments demonstrate that our approach achieves significant improvements in graph distillation,exhibiting strong generalization capability and outperforming existing graph reduction methods.展开更多
Gastric cancer(GC),the fifth most common malignancy worldwide,poses a substantial challenge in clinical oncology,particularly in its advanced stages.Despite advancements in immunotherapy,patient prognosis remains poor...Gastric cancer(GC),the fifth most common malignancy worldwide,poses a substantial challenge in clinical oncology,particularly in its advanced stages.Despite advancements in immunotherapy,patient prognosis remains poor,underscoring the need for reliable prognostic tools to refine treatment strategies.A study by Yao et al explores the role of the triglyceride-glucose(TyG)index as a prognostic marker for advanced GC patients receiving immunotherapy combined with chemotherapy.The results of the study demonstrate that the TyG index correlates with improved survival outcomes,including better progression-free survival and overall survival.This editorial critically evaluates the significance of these findings,discusses their implications for future research,and highlights innovative directions that could drive further breakthroughs in the application of the TyG index to cancer therapy.This editorial also highlights the potential of TyG in advancing precision oncology and advocates for global validation and mechanistic investigations to further solidify its clinical utility.Future research should focus on validating the TyG index across various malignancies,exploring its potential to influence immunotherapy through metabolic interventions,and developing multi-biomarker models that integrate TyG with immune and genomic profiles.展开更多
基金Supported by Scientific Research Project of Putian University,No.2022059.
文摘The growing global burden of metabolic dysfunction-associated steatohepatitis(MASH)demands a deeper understanding of its underlying mechanisms and risk factors.Recent studies,such as the large population-based case-control analysis by Abdel-Razeq et al,suggest a significant association between Helicobacter pylori(H.pylori)infection and an increased risk of developing MASH.This study provides compelling data supporting this association,even after adjusting for confounders such as obesity,diabetes,and hyperlipidemia.However,the complexity of this relationship remains unresolved,requiring further investigation into the biological,genetic,and environmental pathways that connect these two conditions.This article critically reviews the study’s findings and identifies its limitations,offering innovative research directions for the future.Key areas of focus include integrating genomic and microbiome analyses,exploring the impact of H.pylori eradication on MASH progression,studying molecular mechanisms at the intersection of infection and liver disease,and developing personalized therapeutic strategies.
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金supported by the National Science Foundation of China,Grant 32470245.
文摘Angelica L.has attracted global interest for its traditional medicinal uses and commercial values.However,few studies have focused on the metabolomic differences among the Angelica species.In this study,widely targeted metabolomics based on gas chromatography-tandem mass spectrometry was employed to analyze the metabolomes of four Angelica species(Angelicasinensis(Oliv.)Diels(A.sinensis),Angelica biserrata(R.H.Shan &Yuan)C.Q.Yuan & R.H.Shan(A.biserrata),Angelica dahurica(Hoffm.)Benth.& Hook.f.ex Franch.& Sav.(A.dahurica)and Angelica keiskei Koidz.(A.keiskei)).A total of 698 volatile metabolites were identified and classified into fifteen different categories.The metabo-lomic analysis indicated that 7-hydroxycoumarin and Z-ligustilide accumulated at significantly higher levels in A.sinensis,whereas bornyl acetate showed the opposite pattern.Furthermore,a high correspondence between the dendrogram of metabolite contents and phylogenetic positions of the four species.This study provides a comprehensive biochemical map for the exploitation,application and development of the Angelica species as medicinal plants or health-related dietary supplements.
基金financially supported by the China Geological Survey Scientific Research Project(Grant Nos.DD20190167 and DD20190053)the National Natural Science Foundation of China(Grant No.42172259).
文摘The Jitang metamorphic complex is key to studying the tectonic evolution of the Northern Lancangjiang zone.Through structural-lithological mapping,structural analysis and laboratory testing,the composition of the Jitang metamorphic complex was determined.The macro-and microstructural analyses of the ductile detachment shear zone(Guoxuepu ductile shear zone,2–4 km wide)between the metamorphic complex and the overlying sedimentary cap show that the shear sense of the ductile shear zones is top-to-the-southeast.The presence of various deformation features and quartz C-axis electron backscatter diffraction(EBSD)fabric analysis suggests multiple deformation events occurring at different temperatures.The average stress is 25.68 MPa,with the strain rates(έ)ranging from 9.77×10^(−14)s^(−1)to 6.52×10^(−16)s^(−1).The finite strain of the Guoxuepu ductile shear zone indicates an elongated strain pattern.The average kinematic vorticity of the Guoxuepu ductile shear zone is 0.88,implying that the shear zone is dominated by simple shear.The muscovite selected from the protomylonite samples in the Guoxuepu ductile shear zone yields a 40Ar-39Ar age of 60.09±0.38 Ma.It is suggested that,coeval with the initial Indo–Eurasian collision,the development of strike-slip faults led to a weak and unstable crust,upwelling of lower crust magma,then induced the detachment of the Jitang metamorphic complex in the Eocene.
基金National Key R&D Program of China(Grant No.2019YFA0906200)the Science and Technology Innovation Team of Shaanxi(Grant No.2021TD-32)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(Grant Nos.CAAS-ASTIP and CAAS-ZDRW202009).
文摘Thigmotropism and thigmomorphogenesis are two related and pervasive processes that play crucial roles in plant adaptation to the environment.However,there have been few investigations into the molecular regulatory mechanisms of these phenomena.Cucumber(Cucumis sativus L.)tendrils are ideal material for studying thigmotropism and thigmomorphogenesis because they display a combination of the two processes.Here,we generated the transcriptome profiles of cucumber tendrils at the young,stretch,and coiling stages.Genes related to receptor proteins,transmembrane transport,and ion transport were significantly enriched among those differentially expressed between stages.Pharmacological assays illustrated that three GLUTAMATE RECEPTOR(GLR)genes might play a vital function in perceiving or transducing touch stimulation signals.Comparing the transcriptomes of tendrils and roots after touch stimulation,we found that genes related to extracellular stimulus and xyloglucan metabolism might have conserved functions in the regulation of thigmomorphogenesis.The transcriptome atlas of thigmotropism and thigmomorphogenesis of cucumber tendrils constructed in this study will help further elucidate the molecular mechanisms behind these processes.
文摘Chinese Medicine(CM)has been widely used as an important avenue for disease prevention and treatment in China especially in the form of CM prescriptions combining sets of herbs to address patients’symptoms and syndromes.However,the selection and compatibility of herbs are complex and abstract due to intrinsic relationships between herbal properties and their overall functions.Network analysis is applied to demonstrate the complex relationships between individual herbal efficacy and the overall function of CM prescriptions.To illustrate their connections and correlations,prescription function(PF),prescription herb(PH),and herbal efficacy(HE)intranetworks are proposed based on CM theory to identify relationships between herbs and prescriptions.These three networks are then connected by PF-PH and PH-HE interlayer networks adopting herb dosage to form a multidimensional heterogeneous network,a Prescription-Herb-Function Network(PHFN).The network is applied to 112 classic prescriptions from Treatise on Exogenous Febrile and Miscellaneous Diseases to illustrate the application of PHFN.The PHFN is constructed including 146 functions in PF intra network,89 herbs in the PH intra network,and 163 herbal efficacies in the HE intra network.The results show that herb pairs with synergistic actions have stronger relevance,such as licorice-cassia twig,licorice-Chinese date,fresh ginger-Chinese date,etc.The integration of dosage to the network helps to indicate the main herbs for cluster analysis and automatic formulation.PHFN also reveals the internal relationships between the functions of prescriptions and composed herbal efficacies.
基金supported by the National Key Research and Development Program of China (No. 2022YFD1700200)the National Natural Science Foundation of China (Nos. 32161133010, 3230170969)+1 种基金the Innovation Program of Chinese Academy of Agricultural Sciences, the Shenzhen Science and Technology Program (No. KQTD20180411143628272)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District (No. PT202101–02)。
文摘Chitin is an abundant aminopolysaccharide found in insect pests and phytopathogenic microorganisms but absent in higher plants and vertebrates. It is crucial for mitigating threats posed by chitin-containing organisms to human health, food safety, and agriculture. Therefore, targeting the chitin biosynthesisassociated bioprocess holds a promise for developing human-safe and eco-friendly antifungal agents or pesticides. Chitin biosynthesis requires chitin synthase and associated factors, which are involved in the modification, regulation, organization or turnover of chitin during its biosynthesis. A number of enzymes such as chitinases, hexosaminidases, chitin deacetylases are closely related and therefore are promising targets for designing novel agrochemicals that target at chitin biosynthesis. This review summarizes the advances in understanding chitin biology over the past decade by our research group and collaborates,specifically regarding essential proteins linked to chitin biosynthesis that can be exploited as promising pesticide targets. Examples of small bioactive molecules that against the activity of these targets are given.
基金supported by grants from the National Key Research&Development Plan(Grants Nos.2022YFF10030022022YFD1200502)+7 种基金National Natural Science Foundation of China(Grant Nos.3237269631991182)Wuhan Biological Breeding Major Project(Grant No.2022021302024852)Key Project of Hubei Hongshan Laboratory(2021hszd007)HZAU-AGIS Cooperation Fund(Grant No.SZYJY2023022)Funds for High Quality Development of Hubei Seed Industry(HBZY2023B004)Hubei Agriculture Research System(2023HBSTX4-06)Hubei Key Research&Development Plan(Grants Nos.2022BBA0066,2022BBA0062)。
文摘Photosynthesis is one the most important chemical reaction in plants,and it is the ultimate energy source of any living organisms.The light and dark reactions are two essential phases of photosynthesis.Light reaction harvests light energy to synthesize ATP and NADPH through an electron transport chain,and as well as giving out O_(2);dark reaction fixes CO_(2) into six carbon sugars by utilizing NADPH and energy from ATP.Subsequently,plants convert optical energy into chemical energy for maintaining growth and development through absorbing light energy.Here,firstly,we highlighted the biological importance of photosynthesis,and hormones and metabolites,photosynthetic and regulating enzymes,and signaling components that collectively regulate photosynthesis in tomato.Next,we reviewed the advances in tomato photosynthesis,including two aspects of genetic basis and genetic improvement.Numerous genes regulating tomato photosynthesis are gradually uncovered,and the interaction network among those genes remains to be constructed.Finally,the photosynthesis occurring in fruit of tomato and the relationship between photosynthesis in leaf and fruit were discussed.Leaves and fruits are photosynthate sources and sinks of tomato respectively,and interaction between photosynthesis in leaf and fruit exists.Additionally,future perspectives that needs to be addressed on tomato photosynthesis were proposed.
基金supported by grants from the National Natural Science Foundation of China(Grant No.32072571)the 111 Project(Grant No.B17043)the Construction of Beijing Science,and Technology Innovation and Service Capacity in Top Subjects(Grant No.CEFF-PXM2019_014207_000032)。
文摘Tomato(Solanum lycopersicum)is an important fruit and vegetable crop in worldwide.The fertility of tomato reproductive organs can be dramatically decreased when ambient temperatures rise above 35°C,reducing tomato fruit yield.It is necessary to identify transcription factors(TFs)and target genes involved in heat stress response(HSR)signaling cascades in tomato flower buds to improve tomato plant thermotolerance.In this study,we profiled genes expressed in three developmental stages of tomato flower buds.Red and turquoise modules for heat stress(HS)were identified through gene co-expression network analysis,and the genes within these modules were enriched in HS-related pathways.By focusing on the TFs in the two modules,we identified several novel HSR-related TFs,including SlWRKY75,SlMYB117,and SlNAM.Furthermore,homology analysis illustrated a conserved signaling cascade in tomato.Lastly,we identified and experimentally validated four HSF-regulated genes,namely SlGrpE,SlERDJ3A,SlTIL,and SlPOM1,that likely modulate thermotolerance in plants.These results provide a high-resolution atlas of gene expression during tomato flower bud development under HS conditions,which is a valuable resource for uncovering potential regulatory networks associated with the HSR in tomato.
基金supported by the Yunnan Seed Laboratory,China(202205AR070001-15)the National Natural Science Foundation of China,China(Grant No.32160697)。
文摘Juglans sigillata is an economically valuable nut crop renowned for its nutritional richness,including essential nutrients,antioxidants,and healthy fats,which boost human cardial,brain and gut health.Despite its importance,the lack of a complete genome assembly has been a stumbling block in its biological breeding process.Therefore,we generated deep coverage ultralong Oxford Nanopore Technology(ONT)and PacBio HiFi reads to construct a telomere-to-telomere(T2T)genome assembly.The final assembly spans 537.27 Mb with no gaps,demonstrating a remarkable completeness of 98.1%.We utilized a combination of transcriptome data and homologous proteins to annotate the genome,identifying 36018 protein-coding genes.Furthermore,we profiled global cytosine DNA methylations using ONT sequencing data.Global methylome analysis revealed high methylation levels in transposable element(TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas.By integrating a detailed multi-omics data analysis,we obtained valuable insights into the mechanism underlying endopleura coloration.This investigation led to the identification of eight candidate genes(e.g.ANR)involved in anthocyanin biosynthesis pathways,which are crucial for the development of color in plants.The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.
基金supported by the National Key R&D Program of China(Grant No.2022YFE0139400)the National Natural Science Foundation of China(Grant No.31961143016)the Shenzhen Science and Technology Program,China(Grant No.JCYJ20200109150650397).
文摘Zinc(Zn)is an essential micronutrient for both plants and humans.Zn deficiency is common in many paddy fields and reduces yield and grain Zn content(GZC).To accelerate breeding for improved GZC and Zn deficiency tolerance(ZDT)rice varieties,it is important to identify genes regulating Zn homeostasis.In this study,a member of the Ser/Thr protein phosphatase family,LOC_Os07g48840(named as OsGZ7),was found to contributed to ZDT and GZC in rice.The expression of OsGZ7 in roots and shoots was inhibited by Zn deficiency and toxicity,but induced by iron(Fe),manganese(Mn),and copper(Cu)deficiency,as well as chromium toxicity.OsGZ7 localized to the cytoplasm and was expressed in all tissues during the tillering,flowering,and grain-filling stages,particularly in the leaf blade and leaf sheath.At the seedling stage,knockout of OsGZ7 enhanced ZDT and increased Zn accumulation in both roots and shoots.At the maturity stage,knockout of OsGZ7 enhanced GZC,while overexpression of OsGZ7 reduced GZC.RNA-seq analysis suggested that OsGZ7 might regulate Zn homeostasis by affecting metal binding,hormone signal transduction,and oxidoreductase activity.Taken together,our findings indicate that OsGZ7 contributes to ZDT and Zn accumulation in rice.
基金General Program of the National Natural Science Foundation of China (82474352)Natural Science Foundation of Hunan Province (2023JJ60124)。
文摘Objective To predict the potential targets of Qingfu Juanbi Decoction(青附蠲痹汤,QFJBD)in treating rheumatoid arthritis(RA)using an improved Transformer model and investigate the network pharmacological mechanisms underlying QFJBD’s therapeutic effects on RA.Methods First,a traditional Chinese medicine herb-target interaction(TCMHTI)model was constructed to predict herb-target interactions based on Transformer improvement.The per-formance of the TCMHTI model was evaluated against baseline models using three metrics:area under the receiver operating characteristic curve(AUC),precision-recall curve(PRC),and accuracy.Subsequently,a protein-protein interaction(PPI)network was built based on the predicted targets,with core targets identified as the top nine nodes ranked by degree val-ues.Gene Ontology(GO)functional and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses were performed using the targets predicted by TCMHTI and the targets identified through network pharmacology method for comparison.Then,the re-sults were compared.Finally,the core targets predicted by TCMHTI were validated through molecular docking and literature review.Results The TCMHTI model achieved an AUC of 0.883,PRC of 0.849,and accuracy of 0.818,predicting 49 potential targets for QFJBD in RA treatment.Nine core targets were identified:tumor necrosis factor(TNF)-α,interleukin(IL)-1β,IL-6,IL-10,IL-17A,cluster of differentia-tion 40(CD40),cytotoxic T-lymphocyte-associated protein 4(CTLA4),IL-4,and signal trans-ducer and activator of transcription 3(STAT3).The enrichment analysis demonstrated that the TCMHTI model predicted 49 targets and enriched more pathways directly associated with RA,whereas classical network pharmacology identified 64 targets but enriched pathways showing weaker relevance to RA.Molecular docking demonstrated that the active molecules in QFJBD exhibit favorable binding energy with RA targets,while literature research further revealed that QFJBD can treat RA through 9 core targets.Conclusion The TCMHTI model demonstrated greater accuracy than traditional network pharmacology methods,suggesting QFJBD exerts therapeutic effects on RA by regulating tar-gets like TNF-α,IL-1β,and IL-6,as well as multiple signaling pathways.This study provides a novel framework for bridging traditional herbal knowledge with precision medicine,offering actionable insights for developing targeted TCM therapies against diseases.
文摘In this review,we explore the application of next-generation sequencing in liver cancer research,highlighting its potential in modern oncology.Liver cancer,particularly hepatocellular carcinoma,is driven by a complex interplay of genetic,epigenetic,and environmental factors.Key genetic alterations,such as mutations in TERT,TP53,and CTNNB1,alongside epigenetic modifications such as DNA methylation and histone remodeling,disrupt regulatory pathways and promote tumorigenesis.Environmental factors,including viral infections,alcohol consum-ption,and metabolic disorders such as nonalcoholic fatty liver disease,enhance hepatocarcinogenesis.The tumor microenvironment plays a pivotal role in liver cancer progression and therapy resistance,with immune cell infiltration,fibrosis,and angiogenesis supporting cancer cell survival.Advances in immune check-point inhibitors and chimeric antigen receptor T-cell therapies have shown po-tential,but the unique immunosuppressive milieu in liver cancer presents challenges.Dysregulation in pathways such as Wnt/β-catenin underscores the need for targeted therapeutic strategies.Next-generation sequencing is accele-rating the identification of genetic and epigenetic alterations,enabling more precise diagnosis and personalized treatment plans.A deeper understanding of these molecular mechanisms is essential for advancing early detection and developing effective therapies against liver cancer.
基金supported by the National Natural Science Foundation of China(32161133010)the National Key Research and Development Program of China(2022YFD1700200)+2 种基金the Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-CSCB-202302)the Shenzhen Science and Technology Program,China(KQTD20180411143628272)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District,China(PT202101-02).
文摘Chitin is an abundant natural biopolymer that plays a crucial role in insect growth and development as a fundamental structural component of the exoskeleton.The membrane-integralβ-glycosyltransferase,chitin synthase,has been identified as the central component in chitin biosynthesis.However,the precise roles of other proteins in facilitating chitin synthase in chitin biosynthesis remain unclear.In this study,we employed split-ubiquitin membrane yeast two-hybrid(MYTH)and pull-down assays to demonstrate the physical interaction between Twinstar(Tsr),a small molecular protein in the actin-depolymerizing factor ADF/Cofilin protein family,and chitin synthase Krotzkopf verkehrt(Kkv)in Drosophila melanogaster in vitro.The RNA interference(RNAi)-mediated global knockdown of Tsr in D.melanogaster resulted in larval lethality.Furthermore,targeted suppression of Tsr in the tracheal and epidermal tissues also led to larval mortality,while knocking down Tsr in the wing tissues led to wrinkled wings.Additionally,silencing Tsr not only reduced the chitin content in the first longitudinal vein of the wings but also led to the absence of the chitin lamellar structure.To validate the functional conservation of Tsr in other insect orders,the two agricultural pests Ostrinia furnacalis and Tribolium castaneum,representing lepidoptera and coleoptera insects,respectively,were investigated.Knockdown experiments targeting the Drosophila Tsr orthologues OfTsr in O.furnacalis and TcTsr in T.castaneum produced abnormal larvae during molting or pupation in O.furnacalis and lethality in T.castaneum.Our findings not only improve ourknowledge of the chitin biosynthesis machinery in insect cuticles but also provide new potential targets for the control of major agricultural pests.
基金supported by the National Natural Science Foundation of China(Grant Nos.U2002204 and 32272725)the China National Key Research and Development Program(Grant No.2022YFF1002500)+2 种基金the China Postdoctoral Science Foundation(Grant No.2024M753583)the Guangdong Major Project of Basic and Applied Basic Research(Grant No.2021B0301030004)Natural Science Foundation of Henan(Grant No.222300420109)。
文摘Potato(Solanum tuberosum)is a globally important staple crop.However,cultivated potato varieties are highly sensitive to low temperatures.The molecular mechanisms underlying freezing resistance in potatoes remain poorly understood.Through comparative metabolome and transcriptome analyses of freezing-tolerant(CM,Solanum commersonii)and freezing-sensitive(DM,DM1-3516R44)varieties,we identified a coldinduced UDP-glycosyltransferase gene,ScUGT73B4,which is associated with the accumulation of glycosylated flavonoids in wild CM varieties.Overexpression of ScUGT73B4 led to increased accumulation of glycosylated flavonoids and enhanced antioxidant capacity,resulting in improved freezing tolerance in potato plantlets.These findings reveal a UDP-glycosyltransferase in the flavonoid pathway and offer a potential valuable genetic resource for breeding potatoes with improved freezing tolerance.
基金supported by the National Key Research and Development Program of China(2023YFF1000100 and 2023YFA0914601)the Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District(PT202101-01).
文摘Increasing number of structural variations(SVs)have been identified as causative mutations for diverse agronomic traits.However,the systematic exploration of SVs quantity,distribution,and contribution in wheat was lacking.Here,we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size,gene number,and TE component,which indicates their representativeness of wheat genetic diversity.Pan-gene analyses uncover 140,261 distinct gene families,of which only 23.2%are shared in all accessions.Moreover,we build a∼16.15 Gb graph pangenome containing 695,897 bubbles,intersecting 5132 genes and 230,307 cis-regulatory regions.Pairwise genome comparisons identify∼1,978,221 non-redundant SVs and 497 SV hotspots.Notably,the density of bubbles as well as SVs show remarkable aggregation in centromeres,which probably play an important role in chromosome plasticity and stability.As for functional SVs exploration,we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups.Additionally,several reported functional genes in wheat display complex structural graphs,for example,PPD-A1,VRT-A2,and TaNAAT2-A.These findings deepen our understanding of wheat genetic diversity,providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.
基金supported by the grants from the National Key Research & Development Plan of China (2022YFF10030022022YFD1200502)+5 种基金the National Natural Science Foundation of China (32372696)the Wuhan Biological Breeding Major Project, China (2022021302024852)the HZAU–AGIS Cooperation Fund, China (SZYJY2023022)the Funds for High Quality Development of Hubei Seed Industry, China (HBZY2023B004)the Hubei Agriculture Research System, China (2024HBSTX4-06)the Funds of National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, China (Horti3Y-2024-008)。
文摘oluble solids content(SSC) plays an important role in determining the flavor of tomato fruits. Tomato fruit SSC is transcriptionally regulated via sugar metabolism. Previous studies have predominantly focused on the role of C2H2-type zinc finger proteins in tomato growth and development. However, the specific regulatory mechanisms of C2H2 in the accumulation of soluble solids in tomato fruits are not fully understood. This study used eight tomato accessions with varying levels of SSC to study the expression of SlC2H2 family genes in red ripe fruits. The levels of SlC2H2-71 expression were found to be significantly reduced in high-SSC accessions compared to low-SSC accessions. Several Slc2h2-71 mutant lines were developed using the CRISPR-Cas9 system, which led to elevated levels of soluble solids, fructose, glucose, malic acid, and citric acid in mature red ripe fruits. However, the sucrose content in the edited Slc2h2-71 mutant lines was generally lower. RNA-seq analysis revealed that fruits from the mutant lines had altered expression of genes related to the sugar and acid metabolic pathways, which was further confirmed by quantitative real-time PCR. Specifically, the expression of SlLIN5 encoding the cell wall invertase(CWIN) was elevated. The yeast one-hybrid(Y1H) assay, 35S::UAS-GUS, dual-luciferase reporter systems and electrophoretic mobility shift assay(EMSA) demonstrated that C2H2-71 regulates tomato sugar metabolism by directly binding to the promoter region of Sl LIN5, culminating in the repression of its transcriptional activity. The activity of acid invertase exhibited a significantly higher level in the SlC2H2-71 knock-out lines compared to the control lines. In summary, the regulation of tomato fruit SSC by C2H2-71 involves the inhibition of SlLIN5 expression.
基金Project supported by the National Natural Science Foundation of China(Grant No.62176217)the Program from the Sichuan Provincial Science and Technology,China(Grant No.2018RZ0081)the Fundamental Research Funds of China West Normal University(Grant No.17E063).
文摘Graph neural networks(GNNs)have demonstrated excellent performance in graph representation learning.However,as the volume of graph data grows,issues related to cost and efficiency become increasingly prominent.Graph distillation methods address this challenge by extracting a smaller,reduced graph,ensuring that GNNs trained on both the original and reduced graphs show similar performance.Existing methods,however,primarily optimize the feature matrix of the reduced graph and rely on correlation information from GNNs,while neglecting the original graph’s structure and redundant nodes.This often results in a loss of critical information within the reduced graph.To overcome this limitation,we propose a graph distillation method guided by network symmetry.Specifically,we identify symmetric nodes with equivalent neighborhood structures and merge them into“super nodes”,thereby simplifying the network structure,reducing redundant parameter optimization and enhancing training efficiency.At the same time,instead of relying on the original node features,we employ gradient descent to match optimal features that align with the original features,thus improving downstream task performance.Theoretically,our method guarantees that the reduced graph retains the key information present in the original graph.Extensive experiments demonstrate that our approach achieves significant improvements in graph distillation,exhibiting strong generalization capability and outperforming existing graph reduction methods.
基金Supported by the Natural Science Foundation of Fujian Province,No.2023J01160Scientific Research Project of Putian University,No.2022059Special Project for Outstanding Young Talents of Putian University,No.2024072.
文摘Gastric cancer(GC),the fifth most common malignancy worldwide,poses a substantial challenge in clinical oncology,particularly in its advanced stages.Despite advancements in immunotherapy,patient prognosis remains poor,underscoring the need for reliable prognostic tools to refine treatment strategies.A study by Yao et al explores the role of the triglyceride-glucose(TyG)index as a prognostic marker for advanced GC patients receiving immunotherapy combined with chemotherapy.The results of the study demonstrate that the TyG index correlates with improved survival outcomes,including better progression-free survival and overall survival.This editorial critically evaluates the significance of these findings,discusses their implications for future research,and highlights innovative directions that could drive further breakthroughs in the application of the TyG index to cancer therapy.This editorial also highlights the potential of TyG in advancing precision oncology and advocates for global validation and mechanistic investigations to further solidify its clinical utility.Future research should focus on validating the TyG index across various malignancies,exploring its potential to influence immunotherapy through metabolic interventions,and developing multi-biomarker models that integrate TyG with immune and genomic profiles.
