Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy.Here,we set the genomic and transcriptomic data as th...Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy.Here,we set the genomic and transcriptomic data as the training population data,using BSLMM,TWAS,and eQTL mapping to prescreen features according to |β_(b)|>0,top 1%of phenotypic variation explained(PVE),expression-associated single nucleotide polymorphisms(eSNPs),and egenes(false discovery rate(FDR)<0.01),where these loci were set as extra fixed effects(named GBLUP-Fix)and random effects(GFBLUP)to improve the prediction accuracy in the validation population,respectively.The results suggested that both GBLUP-Fix and GFBLUP models could improve the accuracy of longissimus dorsi muscle(LDM),water holding capacity(WHC),shear force(SF),and pH in Huaxi cattle on average from 2.14 to 8.69%,especially the improvement of GFBLUP-TWAS over GBLUP was 13.66%for SF.These methods also captured more genetic variance than GBLUP.Our study confirmed that multi-omics-assisted large-effects loci prescreening could improve the accuracyofgenomic prediction.展开更多
Background:Cholangiocarcinoma(CCA)is highly malignant and has a poor prognosis has a high malignant degree and poor prognosis.The purpose of this study is to develop a new prognostic model based on genes related to th...Background:Cholangiocarcinoma(CCA)is highly malignant and has a poor prognosis has a high malignant degree and poor prognosis.The purpose of this study is to develop a new prognostic model based on genes related to the tumor microenvironment(TME).Methods:Derived from the discerned differentially expressed genes within The Cancer Genome Atlas(TCGA)dataset,this investigation employed the methodology of weighted gene co-expression network analysis(WGCNA)to ascertain gene co-expressed modules intricately linked to the Tumor Microenvironment(TME)among Cholangiocarcinoma(CCA)patients.The genes associated with prognosis,as identified through Cox regression analysis,were employed in the formulation of a predictive model.This model underwent validation,leading to the development of a risk score formula and nomogram.Concurrently,we validated the model’s reliability using data from CCA patients in the Gene Expression Omnibus(GEO)database(accession:GSE107943).Results:6139 DEGs were divided into 10 co-expressed gene modules using WGCNA.Among these,two modules(blue module with 832 genes and brown module with 1379 genes)showed high correlation with the TME.Five prognostic genes(BNIP3,COL4A3,SPRED3,CEBPB,PLOD2)were identified through Cox regression analysis,and a prognostic model and risk score formula were developed based on these genes.Risk score formula:Risk score=BNIP3×1.70520-COL4A3×2.39815+SPRED3×1.17936+CEBPB×0.40456+PLOD2×0.24785.Kaplan-Meier survival analysis revealed that the survival probabilities of the low-risk group were significantly higher than those of the high-risk group.Furthermore,the related evaluation indexes suggested that the model exhibited strong predictive ability.Conclusion:The prognostic model,based on five TME-related genes(BNIP3,COL4A3,SPRED3,CEBPB,PLOD2),could accurately assess the prognosis of CCA patients to aid in guiding clinical decisions.展开更多
A novel vacuolar Na+/H+ exchanger, CgNHX1, was cloned from a halophytic species Chenopodium glaucum by using reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) techniq...A novel vacuolar Na+/H+ exchanger, CgNHX1, was cloned from a halophytic species Chenopodium glaucum by using reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) technique. Sequence alignment and phylogenetic analysis of 22 NHX genes from GenBank as well as the new CgNHX1 gene indicate that NHX genes shared a great degree of similarity, regardless of their glycophytic or halophytic origin. Expression of the CgNHX1 gene was induced by NaCl and peaked at 400 mmol/L NaCl. Overexpression of NHX1 genes in rice enhanced their tolerance to salt stress. However, there is no significant difference in salt tolerance among the transgenic rice plants overexpressing the NHX1 genes from either glycophytic or halophytic species. The Na+ content of both the wild type (WT) and transgenic plants increased when exposed to 50 and 100 mmol/L NaCl, and the Na+ concentration in transgenic plants was marginally higher than that of WT. Our data demonstrate that the overexpression of the NHX1 gene from either glycophytic or halophytic species resulted in the enhanced tolerance to salt stress at a similar level, suggesting that NHX gene per se might not be the reason accounting for the difference in salt tolerance between glycophytes and halophytes.展开更多
1Ax1 high molecular weight glutenin subunit(HMW-GS)gene expression cassette(GEC)lacking vector backbone sequences together with selectable marker Bar GEC were co-transformed into Chinese hexaploid cultivars Een 1 and ...1Ax1 high molecular weight glutenin subunit(HMW-GS)gene expression cassette(GEC)lacking vector backbone sequences together with selectable marker Bar GEC were co-transformed into Chinese hexaploid cultivars Een 1 and Emai 12 to test the feasibility and the efficiency of explant regeneration,transformation frequency and transgene expression comparing with whole vector transformation by the approaches of plasmid extraction and excision,immature embryo isolation, particle co-bombardment,tissue culture,DNA extraction,PCR amplification,southern hybridization,leaf-painting test and SDS-PAGE etc.No significant difference was shown in tissue culture response of the proportion of embryogenic calli, somatic embryogenesis and regeneration frequency between GEC and whole plasmid bombarded embryos,but both regenerated less well than non-bombarded control.Total 56 plantlets that survived PPT selection had insertion of at least the Bar gene,18 were from the GEC treatment and 38 from the whole plasmid treatment,the escape ratio averaged 0.23.Six independent transplants f230-f235 with GEC transformation from genotype Emai 12 presented clear PCR amplification bands of Bar and 1Ax1 gene.The transformation and co-transformation frequency were 3.51 and 100%respectively.PCR amplification using a primer-pair specific for ampicillin resistant gene indicated the existence of AmpR gene in whole vectors but the removal in GECs and transplants.Southern blot of total DNA and PCR products from transgenic plants of 1Ax1 GEC confirmed the integration of the transgene 1Ax1 and the absence of the EcoRⅠrecognition site at both ends of the 1Ax1 GEC when integrated.SDS-PAGE showed the expression of 1Ax1 GEC and un-expression of whole plasmid. The length of integrated fragment,the proportion of the gene of interest(GOI)and the selectable marker(MG),bombardment pressure and genotypes are vital for the expression of a transformed GEC.展开更多
Stripe rust is one of the most important diseases of wheat worldwide.Inheritance of stripe rust resistance and mapping of resistance gene with simple sequence repeat(SSR)markers are studied to formulate efficient stra...Stripe rust is one of the most important diseases of wheat worldwide.Inheritance of stripe rust resistance and mapping of resistance gene with simple sequence repeat(SSR)markers are studied to formulate efficient strategies for breeding cultivars resistant to stripe rust.Zhongliang 88375,a common wheat line,is highly resistant to all three rusts of wheat in China.The gene conferring rust disease was deduced originating from Elytrigia intermedium.Genetic analysis of Zhongliang 88375 indicated that the resistance to PST race CYR31 was controlled by a single dominant gene,temporarily designated as Yr88375.To molecular map Yr88375,a F 2 segregating population consisting of 163 individuals was constructed on the basis of the hybridization between Zhongliang 88375 and a susceptible wheat line Mingxian 169;320 SSR primer pairs were used for analyzing the genetic linkage relation.Six SSR markers,Xgwm335,Xwmc289,Xwmc810, Xgdm116,Xbarc59,and Xwmc783,are linked to Yr88375 as they were all located on chromosome 5BL.Yr88375 was also located on that chromosome arm,closely linked to Xgdm116 and Xwmc810 with genetic distances of 3.1 and 3.9 cM, respectively.The furthest marker Xwmc783 was 13.5 cM to Yr88375.Hence,pedigree analysis of Zhongliang 88375 combined with SSR markers supports the conclusion that the highly resistance gene Yr88375 derived from Elytrigia intermedium is a novel gene for resistance to stripe rust in wheat.It could play an important role in wheat breeding programs for stripe rust resistance.展开更多
106 accessions of Tibetan wild barley, including 50 accessions of the two-rowed wild barley Hordeum vulgare ssp. spontaneum(HS), 27 accessions of the six-rowed bottle-shaped wild barley H. lagunculiforme(HL) and 29 ac...106 accessions of Tibetan wild barley, including 50 accessions of the two-rowed wild barley Hordeum vulgare ssp. spontaneum(HS), 27 accessions of the six-rowed bottle-shaped wild barley H. lagunculiforme(HL) and 29 accessions of the six-rowed wild barley H. agriocrithon(HA) that separately represent different agrigeographical regions of Tibet, were used to study the genetic diversity and genetic differentiation using SSR markers selected from seven barley linkage groups. 229 allelic variants were identified with an average of 7.6 alleles/locus. The average of total number of alleles per locus in HA(6.4) is much higher than that in HS(3.9) and HL(3.4). The genetic diversity and its standard deviation among the three subspecies were in the order of HS>HL>HA. Very significant genetic differentiation was observed among the three subspecies of wild barley. Comparisons of the results from this and previous studies showed a strong Oriental-Occidental differentiation of barley, and that Shannan region of Tibet might be the center of origin of the Tibetan two-rowed wild barley, thus supporting not only the hypothesis of a mono-phyletic origin of cultivated barley but also the proposition that the Tibetan two-rowed wild barley as ultimate progenitor of Chinese cultivated barley.展开更多
Stripe rust is one of the most important wheat diseases worldwide. To identify new resistance genes is significant in wheatbreeding. In this study, stripe rust resistance of a Chinese cultivar Shan 515 was tested with...Stripe rust is one of the most important wheat diseases worldwide. To identify new resistance genes is significant in wheatbreeding. In this study, stripe rust resistance of a Chinese cultivar Shan 515 was tested with Chinese predominant racesof P. striiformis f. sp. tritici in the seedling stage, and genetic analysis and simple sequence repeats (SSR) technique wereused to identify the inheritance model of seedling stripe rust resistance in cultivar Shan 515 and to mark the sites ofresistance gene(s) on chromosome. The genetic analysis indicated that the resistance of Shan 515 against Su11-4 wasconferred by a single dominant gene, which was temporarily designated as YrShan515. Using bulked segregant analysis(BSA) and SSR markers, 12 SSR markers (Xwmc335, Xwmc696, Xwmc476, Xbarc267, Xgwm333, Xwmc653, Xwmc396,Xgwm213, Xgwm112, Xgwm274, Xcfd22, Xgwm131, and Xwmc517) located on wheat chromosome 7BL were linked toYrShan515 with genetic distance ranging from 3 to 24 cM. Based on the previously published genetic map and ChineseSpring nulli-tetrasomic analysis, YrShan515 was located on wheat chromosome 7BL. Polymorphism of wheat cultivarscollected from Huanghuai wheat grown regions were screened with two markers, Xwmc653 and Xbarc267, and all of thesewheat cultivars tested did not present the polymorphic bands as Shan 515 did. Therefore, it suggested that YrShan515might be a allele of the available yellow rust resistance gene. The mapping of the new resistance gene in Shan 515 is usefulfor wheat breeding and diversification of resistance genes against stripe rust in commercial wheat cultivars in China.展开更多
Dear Editor,Reduction in plant height has been associated with yield increases and yield stability in a number of important crop species,such as wheat and rice[1].In these plants,dwarfing is mainly attributed to the i...Dear Editor,Reduction in plant height has been associated with yield increases and yield stability in a number of important crop species,such as wheat and rice[1].In these plants,dwarfing is mainly attributed to the inability to synthesize or respond to certain phytohormones,predominantly gibberellin(GA)[2].Ideal Plant Architecture 1(IPA1),an miR156 target gene,encodes SPL14 and it is able to bind directly to the promoters of multiple GA biosynthetic,signal,and deactivating genes in rice[3].Moreover,IPA1 loss-of-function mutants exhibit dwarf phenotypes[4].展开更多
A 3-year-old boy presented with bluish patch and scattered blue spots on the left side of his face.After several sessions of laser treatment,the azury patch in the periorbital area became even darker.Histopathology sh...A 3-year-old boy presented with bluish patch and scattered blue spots on the left side of his face.After several sessions of laser treatment,the azury patch in the periorbital area became even darker.Histopathology showed many bipolar,pigment-laden dendritic cells scattered in the papillary and upper reticular dermis.Immunohistochemically,these cells were positive for S100,SOX-10,melan-A,P16,and HMB-45.The positive rate of Ki-67 was less than 5%.Finally,the lesion was diagnosed with nevus of Ota concurrent with common blue nevus.Therefore,for cases of the nevus of Ota with poor response to laser treatment,the possible coexisting diseases should be suspected.展开更多
Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic...Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic acid on the proliferation of cutaneous T-cell lymphoma(CTCL)cells.We aimed to further investigate the underlying mechanism of the proliferation inhibition induced by ursolic acid in CTCL cells using transcriptome sequencing.Methods:Cell counting kit-8 assays were used to observe the effects of six traditional medicine monomers on the proliferation of CTCL cells.Transcriptome sequencing was used to identify differentially expressed genes after ursolic acid treatment.Bioinformatics analysis was performed to determine the potential mechanism.Real-time quantitative PCR and western blotting analyses were performed to confirm the sequencing results and verify the possible mechanisms of ursolic acid-mediated proliferation inhibition in CTCL cells.Results:Ursolic acid exhibited the strongest inhibitory effect on the proliferation of CTCL cells among the six traditional medicine monomers.Transcriptome sequencing analysis showed that 2,466 genes were significantly altered.Combined with Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction network analysis,the interaction of various pathways and signaling molecules,such as tumor necrosis factor-α,NLR family pyrin domain containing 1,c-Jun N-terminal kinase,and melanoma differentiation-associated gene 5,accounted for the anti-tumor effects of ursolic acid in CTCL cells.Conclusion:Ursolic acid significantly inhibited the proliferation of CTCL cells,and our study laid a theoretical foundation for the future treatment of CTCL using ursolic acid.展开更多
Objective:To study the effect of plumbagin(PL)on the migration and invasion of human hepatocellular carcinoma(HCC)cells and its possible mechanism.Methods:The cell counting kit(CCK-8)was used to detect the effects of ...Objective:To study the effect of plumbagin(PL)on the migration and invasion of human hepatocellular carcinoma(HCC)cells and its possible mechanism.Methods:The cell counting kit(CCK-8)was used to detect the effects of different concentrations of plumbagin on the proliferation of human hepatocellular carcinoma Huh-7 and LM3 cells.The effect of plumbagin on the migration ability of Huh-7 and LM3 cells was detected by scratch test and Transwell migration test,and the effect of on the invasion ability of Huh-7 and LM3 cells was detected by Transwell invasion test.Western Blot was used to detect the expression of E-cadherin,N-cadherin,matrix metalloproteinase-2 and related proteins in JAK2/STAT3 signaling pathway in Huh-7 and LM3 cells.Results:Plumbagin could inhibit the proliferation of Huh-7 and LM3 cells in a time-and concentration-dependent manner.Plumbagin inhibited the migration and invasion of Huh-7 and LM3 cells in a concentration dependent manner,and it can down-regulate the expression of N-cadherin and MMP-2 protein,up-regulate the expression of E-cadherin protein,and inhibit the activation of JAK2/STAT3 signaling pathway.Conclusion:Plumbagin can inhibit the migration and invasion of human hepatocellular carcinoma Huh-7 and LM3 cells,and the molecular mechanism of this process may be related to the inhibition of JAK2/STAT3 signaling pathway activation.展开更多
Innovations in sequencing technology and the development of bioinformatics have allowed for studies of the genomics of many rice pests.At present,draft genomes of rice pests including Nilaparvata lugens,Sogatella furc...Innovations in sequencing technology and the development of bioinformatics have allowed for studies of the genomics of many rice pests.At present,draft genomes of rice pests including Nilaparvata lugens,Sogatella furcifera,Laodelphax striatellus,Sesamia inferens,Chilo suppressalis,Scirpophaga incertulas.展开更多
Tbx18,Wt1,and Tcf21 have been identified as epicardial markers during the early embryonic stage.However,the gene markers of mature epicardial cells remain unclear.Single-cell transcriptomic analysis was performed with...Tbx18,Wt1,and Tcf21 have been identified as epicardial markers during the early embryonic stage.However,the gene markers of mature epicardial cells remain unclear.Single-cell transcriptomic analysis was performed with the Seurat,Monocle,and CellphoneDB packages in R software with standard procedures.Spatial transcriptomics was performed on chilled Visium Tissue Optimization Slides(10x Genomics)and Visium Spatial Gene Expression Slides(10x Genomics).Spatial transcriptomics analysis was performed with Space Ranger software and R software.Immunofluorescence,whole-mount RNA in situ hybridization and X-gal staining were performed to validate the analysis results.Spatial transcriptomics analysis revealed distinct transcriptional profiles and functions between epicardial tissue and non-epicardial tissue.Several gene markers specific to postnatal epicardial tissue were identified,including Msln,C3,Efemp1,and Upk3b.Single-cell transcriptomic analysis revealed that cardiac cells from wildtype mouse hearts(from embryonic day 9.5 to postnatal day 9)could be categorized into six major cell types,which included epicardial cells.Throughout epicardial development,Wt1,Tbx18,and Upk3b were consistently expressed,whereas genes including Msln,C3,and Efemp1 exhibited increased expression during the mature stages of development.Pseudotime analysis further revealed two epicardial cell fates during maturation.Moreover,Upk3b,Msln,Efemp1,and C3 positive epicardial cells were enriched in extracellular matrix signaling.Our results suggested Upk3b,Efemp1,Msln,C3,and other genes were mature epicardium markers.Extracellular matrix signaling was found to play a critical role in the mature epicardium,thus suggesting potential therapeutic targets for heart regeneration in future clinical practice.展开更多
Dear Editor,Autophagy is an evolutionarily conserved catabolic process that involves the sequestration and transport of organelles,macromolecules,or invading microorganisms to lysosomes for degradation[1].Sequestosome...Dear Editor,Autophagy is an evolutionarily conserved catabolic process that involves the sequestration and transport of organelles,macromolecules,or invading microorganisms to lysosomes for degradation[1].Sequestosome 1(p62/SQSTM1)was the first protein shown to bind target-associated ubiquitin(Ub)and LC3 conjugated to the phagophore membrane,thus,acting as an important autophagy receptor for ubiquitinated targets[2].展开更多
Background:The Qingjiehuagong decoction(QJHGD),which has been used in clinical trials to treat acute pancreatitis(AP),has demonstrated encouraging results.Methods:In this particular investigation,we used both metabolo...Background:The Qingjiehuagong decoction(QJHGD),which has been used in clinical trials to treat acute pancreatitis(AP),has demonstrated encouraging results.Methods:In this particular investigation,we used both metabolomics and network pharmacology to investigate the fundamental processes and targets that QJHGFD employs to cure AP.Results:Using a cerulein-induced rat model of AP,we showed that QJHGD effectively improved pancreatic tissue damage and reduced serum levels of AMY,LPS,IL-1β,IL-6,IL-8 and TNF-α.In total,28 blood entry compounds derived from QJHGD were identified by ultra-performance liquid chromatography-high resolution mass spectrometry technology.The intersecting target genes of 108 genes associated with identified compounds in QJHGD and AP disease genes were identified using a network pharmacology approach.The protein interaction network revealed AKT1,TNF-α,IL-6,VEGFA,and TP53 as important targets.Gene ontology analysis showed that response to stimulus,molecular function regulator and organelle part were the main functions,and Kyoto Encyclopedia of Genes and Genomes analysis showed that 20 pathways such as AGE-RAGE signaling pathway in diabetic complications and the IL-17 signaling pathway were the main pathways involved in the anti-AP effects of QJHGD.Thirty-two potential metabolic markers and 13 possible metabolic pathways were identified by metabolomics analysis.Combined network pharmacological analysis revealed that QJHGD affects four metabolic pathways(tryptophan metabolism;glycolysis and gluconeogenesis metabolism;valine,leucine and isoleucine degradation metabolism;the urea cycle and metabolism of arginine,proline,glutamate,aspartate and asparagine),five metabolites(indole-3-acetate,pyruvate,methylmalonate,L-citrulline,N-acetyl-l-glutamate)and four related targets(AKT1,ALDH2,NOS2,NOS3)to combat inflammation.The strong affinity of QJHGD’s interactions with its primary targets was established by molecular docking and molecular dynamics simulations.Conclusion:This research investigate the critical targets and mechanisms of QJHGFD for treating AP.The results of this investigation provide novel tactics and complementary techniques for the clinical treatment of AP.展开更多
Objective:To investigate the mechanism of action and material basis of AiTongXiao granule in the treatment of hepatocellular carcinoma(HCC)based on network pharmacology and transplanted liver cancer rat model.Methods:...Objective:To investigate the mechanism of action and material basis of AiTongXiao granule in the treatment of hepatocellular carcinoma(HCC)based on network pharmacology and transplanted liver cancer rat model.Methods:TCMSP database was used to screen out effective components and its corresponding potential pharmaceutical targets,and databases including Gene Cards,OMIM,Drugbank and TTD were further used to collect HCC-related drug targets.The intersecting targets were obtained by mapping the drug and disease targets.The component-targets network was constructed and visualized by Cytoscape 3.8.2 software.Protein-protein interaction(PPI)network was built by STRING online platform,and the topological relationship and core targets was analyzed and screened by using CytoNCA software.In addition,Metascape database was used to perform gene ontology(GO)enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis of the core targets.At last,rat liver transplanted liver cancer model was established by using Walker-256 cell line and treated by AiTongXiao granule for 15 days.Western blot was used to further compare the expression levels of AKT,pAKT,p53,p-p53,ERK1/2 and ERK1/2 in the tumor between treatment group and the control group.Results:257 active components were obtained from AiTongXiao granule,corresponding to 294 drug targets.Meanwhile,233 of the 7993 HCC disease targets were screened out between AiTongXiao granule drug and HCC disease targets.11 core targets including AKT1,IL6,TP53,MAPK3,TNF,JUN,CASP3,MAPK1,MYC,PTGS2,MMP9 were further obtained by median screening.GO and KEGG analysis results showed that these core targets enriched to HBV,TNF and cancer related pathways.The rat transplanted liver cancer model results indicated significant down regulation for AKT,p-AKT,pERK1/2,and significant up regulation of p-p53 after AiTongXiao granule treatment(P<0.05).Conclusion:AiTongXiao granule could act to multiple cancer related pathways,and AKT,p53 and ERK1/2 were validated to be regulated by ATXF in rat model.The mechanism may be through the regulation of the above signaling pathways to exert anti-liver cancer effect.展开更多
Tissue engineering is an interdisciplinary field of bioengineering,cell biology,and biomaterials that seeks to create functional tissues for therapeutic purposes.It is a rapidly growing field of regenerative medicine ...Tissue engineering is an interdisciplinary field of bioengineering,cell biology,and biomaterials that seeks to create functional tissues for therapeutic purposes.It is a rapidly growing field of regenerative medicine that has the potential to revolutionize the treatment for many diseases and injuries.General research areas mainly include the engineering of the cardiovascular system,bone and cartilage,oral cavity and skin,and other tissues[1].Skin tissue engineering is one of the earliest clinically applied,most mature and widely used products in the field of tissue engineering[2].展开更多
基金This research was supported by the National Natural Science Foundations of China(31872975)the Science and Technology Project of Inner Mongolia Autonomous Region,China(2020GG0210)the Program of National Beef Cattle and Yak Industrial Technology System,China(CARS-37).
文摘Presently,integrating multi-omics information into a prediction model has become a ameliorate strategy for genomic selection to improve genomic prediction accuracy.Here,we set the genomic and transcriptomic data as the training population data,using BSLMM,TWAS,and eQTL mapping to prescreen features according to |β_(b)|>0,top 1%of phenotypic variation explained(PVE),expression-associated single nucleotide polymorphisms(eSNPs),and egenes(false discovery rate(FDR)<0.01),where these loci were set as extra fixed effects(named GBLUP-Fix)and random effects(GFBLUP)to improve the prediction accuracy in the validation population,respectively.The results suggested that both GBLUP-Fix and GFBLUP models could improve the accuracy of longissimus dorsi muscle(LDM),water holding capacity(WHC),shear force(SF),and pH in Huaxi cattle on average from 2.14 to 8.69%,especially the improvement of GFBLUP-TWAS over GBLUP was 13.66%for SF.These methods also captured more genetic variance than GBLUP.Our study confirmed that multi-omics-assisted large-effects loci prescreening could improve the accuracyofgenomic prediction.
基金supported by Medical Scientific Research Foundation of Chongqing of China(2022MSXM048).
文摘Background:Cholangiocarcinoma(CCA)is highly malignant and has a poor prognosis has a high malignant degree and poor prognosis.The purpose of this study is to develop a new prognostic model based on genes related to the tumor microenvironment(TME).Methods:Derived from the discerned differentially expressed genes within The Cancer Genome Atlas(TCGA)dataset,this investigation employed the methodology of weighted gene co-expression network analysis(WGCNA)to ascertain gene co-expressed modules intricately linked to the Tumor Microenvironment(TME)among Cholangiocarcinoma(CCA)patients.The genes associated with prognosis,as identified through Cox regression analysis,were employed in the formulation of a predictive model.This model underwent validation,leading to the development of a risk score formula and nomogram.Concurrently,we validated the model’s reliability using data from CCA patients in the Gene Expression Omnibus(GEO)database(accession:GSE107943).Results:6139 DEGs were divided into 10 co-expressed gene modules using WGCNA.Among these,two modules(blue module with 832 genes and brown module with 1379 genes)showed high correlation with the TME.Five prognostic genes(BNIP3,COL4A3,SPRED3,CEBPB,PLOD2)were identified through Cox regression analysis,and a prognostic model and risk score formula were developed based on these genes.Risk score formula:Risk score=BNIP3×1.70520-COL4A3×2.39815+SPRED3×1.17936+CEBPB×0.40456+PLOD2×0.24785.Kaplan-Meier survival analysis revealed that the survival probabilities of the low-risk group were significantly higher than those of the high-risk group.Furthermore,the related evaluation indexes suggested that the model exhibited strong predictive ability.Conclusion:The prognostic model,based on five TME-related genes(BNIP3,COL4A3,SPRED3,CEBPB,PLOD2),could accurately assess the prognosis of CCA patients to aid in guiding clinical decisions.
基金Project supported by the National Natural Science Foundation of China (Nos. 30471118 and 30460015)the Key Project of Educa-tion Ministry of China (No. 205178)
文摘A novel vacuolar Na+/H+ exchanger, CgNHX1, was cloned from a halophytic species Chenopodium glaucum by using reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) technique. Sequence alignment and phylogenetic analysis of 22 NHX genes from GenBank as well as the new CgNHX1 gene indicate that NHX genes shared a great degree of similarity, regardless of their glycophytic or halophytic origin. Expression of the CgNHX1 gene was induced by NaCl and peaked at 400 mmol/L NaCl. Overexpression of NHX1 genes in rice enhanced their tolerance to salt stress. However, there is no significant difference in salt tolerance among the transgenic rice plants overexpressing the NHX1 genes from either glycophytic or halophytic species. The Na+ content of both the wild type (WT) and transgenic plants increased when exposed to 50 and 100 mmol/L NaCl, and the Na+ concentration in transgenic plants was marginally higher than that of WT. Our data demonstrate that the overexpression of the NHX1 gene from either glycophytic or halophytic species resulted in the enhanced tolerance to salt stress at a similar level, suggesting that NHX gene per se might not be the reason accounting for the difference in salt tolerance between glycophytes and halophytes.
基金supported by China Post-Doctorial Foundation(2002031255)Rothamsted International Foundation(2002)of the UKNatural Science Foundation of Zhejiang Province,China(M303081).
文摘1Ax1 high molecular weight glutenin subunit(HMW-GS)gene expression cassette(GEC)lacking vector backbone sequences together with selectable marker Bar GEC were co-transformed into Chinese hexaploid cultivars Een 1 and Emai 12 to test the feasibility and the efficiency of explant regeneration,transformation frequency and transgene expression comparing with whole vector transformation by the approaches of plasmid extraction and excision,immature embryo isolation, particle co-bombardment,tissue culture,DNA extraction,PCR amplification,southern hybridization,leaf-painting test and SDS-PAGE etc.No significant difference was shown in tissue culture response of the proportion of embryogenic calli, somatic embryogenesis and regeneration frequency between GEC and whole plasmid bombarded embryos,but both regenerated less well than non-bombarded control.Total 56 plantlets that survived PPT selection had insertion of at least the Bar gene,18 were from the GEC treatment and 38 from the whole plasmid treatment,the escape ratio averaged 0.23.Six independent transplants f230-f235 with GEC transformation from genotype Emai 12 presented clear PCR amplification bands of Bar and 1Ax1 gene.The transformation and co-transformation frequency were 3.51 and 100%respectively.PCR amplification using a primer-pair specific for ampicillin resistant gene indicated the existence of AmpR gene in whole vectors but the removal in GECs and transplants.Southern blot of total DNA and PCR products from transgenic plants of 1Ax1 GEC confirmed the integration of the transgene 1Ax1 and the absence of the EcoRⅠrecognition site at both ends of the 1Ax1 GEC when integrated.SDS-PAGE showed the expression of 1Ax1 GEC and un-expression of whole plasmid. The length of integrated fragment,the proportion of the gene of interest(GOI)and the selectable marker(MG),bombardment pressure and genotypes are vital for the expression of a transformed GEC.
基金the National 973 Programof China(G2000016200)Program for Changjiang Scholars and Innovative Research Teamin University from Ministry of Education of China(200558)
文摘Stripe rust is one of the most important diseases of wheat worldwide.Inheritance of stripe rust resistance and mapping of resistance gene with simple sequence repeat(SSR)markers are studied to formulate efficient strategies for breeding cultivars resistant to stripe rust.Zhongliang 88375,a common wheat line,is highly resistant to all three rusts of wheat in China.The gene conferring rust disease was deduced originating from Elytrigia intermedium.Genetic analysis of Zhongliang 88375 indicated that the resistance to PST race CYR31 was controlled by a single dominant gene,temporarily designated as Yr88375.To molecular map Yr88375,a F 2 segregating population consisting of 163 individuals was constructed on the basis of the hybridization between Zhongliang 88375 and a susceptible wheat line Mingxian 169;320 SSR primer pairs were used for analyzing the genetic linkage relation.Six SSR markers,Xgwm335,Xwmc289,Xwmc810, Xgdm116,Xbarc59,and Xwmc783,are linked to Yr88375 as they were all located on chromosome 5BL.Yr88375 was also located on that chromosome arm,closely linked to Xgdm116 and Xwmc810 with genetic distances of 3.1 and 3.9 cM, respectively.The furthest marker Xwmc783 was 13.5 cM to Yr88375.Hence,pedigree analysis of Zhongliang 88375 combined with SSR markers supports the conclusion that the highly resistance gene Yr88375 derived from Elytrigia intermedium is a novel gene for resistance to stripe rust in wheat.It could play an important role in wheat breeding programs for stripe rust resistance.
文摘106 accessions of Tibetan wild barley, including 50 accessions of the two-rowed wild barley Hordeum vulgare ssp. spontaneum(HS), 27 accessions of the six-rowed bottle-shaped wild barley H. lagunculiforme(HL) and 29 accessions of the six-rowed wild barley H. agriocrithon(HA) that separately represent different agrigeographical regions of Tibet, were used to study the genetic diversity and genetic differentiation using SSR markers selected from seven barley linkage groups. 229 allelic variants were identified with an average of 7.6 alleles/locus. The average of total number of alleles per locus in HA(6.4) is much higher than that in HS(3.9) and HL(3.4). The genetic diversity and its standard deviation among the three subspecies were in the order of HS>HL>HA. Very significant genetic differentiation was observed among the three subspecies of wild barley. Comparisons of the results from this and previous studies showed a strong Oriental-Occidental differentiation of barley, and that Shannan region of Tibet might be the center of origin of the Tibetan two-rowed wild barley, thus supporting not only the hypothesis of a mono-phyletic origin of cultivated barley but also the proposition that the Tibetan two-rowed wild barley as ultimate progenitor of Chinese cultivated barley.
基金We thank Dr Qiang Liu for giving some advice and polishing the writing and thank Dr Yu-Chuan Zhou for fruitful discussions. We are also grateful to Ai- H ua Liu fur technical assistance in immunohistochemistry assay. This work was supported by grants from the National Natural Science Foundation of China (No. 30930053) and the Chinese Academy of Sciences Knowledge Innovation Program (No. KSCX2-EW-R-07).
基金funded by the Colleges and Universities Planto Subsidize Innovation and "Bring Wisdom", Min-istry of Education, China (B07049)the "Technology of Prevention and Control of Major Pests and Diseasesof Wheat"of the Key Technologies R&D Program of China during the 11th Five-Year Plan Period(2006BAD08A05)the Toxicity Variation of Wheat Stripe Rust Pathotypes and Comprehensive Research and Demonstration Projects of Stripe Rust Pathogen,China (200903035-02)
文摘Stripe rust is one of the most important wheat diseases worldwide. To identify new resistance genes is significant in wheatbreeding. In this study, stripe rust resistance of a Chinese cultivar Shan 515 was tested with Chinese predominant racesof P. striiformis f. sp. tritici in the seedling stage, and genetic analysis and simple sequence repeats (SSR) technique wereused to identify the inheritance model of seedling stripe rust resistance in cultivar Shan 515 and to mark the sites ofresistance gene(s) on chromosome. The genetic analysis indicated that the resistance of Shan 515 against Su11-4 wasconferred by a single dominant gene, which was temporarily designated as YrShan515. Using bulked segregant analysis(BSA) and SSR markers, 12 SSR markers (Xwmc335, Xwmc696, Xwmc476, Xbarc267, Xgwm333, Xwmc653, Xwmc396,Xgwm213, Xgwm112, Xgwm274, Xcfd22, Xgwm131, and Xwmc517) located on wheat chromosome 7BL were linked toYrShan515 with genetic distance ranging from 3 to 24 cM. Based on the previously published genetic map and ChineseSpring nulli-tetrasomic analysis, YrShan515 was located on wheat chromosome 7BL. Polymorphism of wheat cultivarscollected from Huanghuai wheat grown regions were screened with two markers, Xwmc653 and Xbarc267, and all of thesewheat cultivars tested did not present the polymorphic bands as Shan 515 did. Therefore, it suggested that YrShan515might be a allele of the available yellow rust resistance gene. The mapping of the new resistance gene in Shan 515 is usefulfor wheat breeding and diversification of resistance genes against stripe rust in commercial wheat cultivars in China.
基金Thisworkwas funded by the National Natural Science Foundation of China(grants 31960433 and 31860562)Natural Science Foundation of Jiangxi Province(grant 20171ACB20001).
文摘Dear Editor,Reduction in plant height has been associated with yield increases and yield stability in a number of important crop species,such as wheat and rice[1].In these plants,dwarfing is mainly attributed to the inability to synthesize or respond to certain phytohormones,predominantly gibberellin(GA)[2].Ideal Plant Architecture 1(IPA1),an miR156 target gene,encodes SPL14 and it is able to bind directly to the promoters of multiple GA biosynthetic,signal,and deactivating genes in rice[3].Moreover,IPA1 loss-of-function mutants exhibit dwarf phenotypes[4].
基金This study was funded by the CAMS Innovation Fund for Medical Sciences(CIFMS-2021-I2M-1-001)National Natural Science Foundation of China(82103705).
文摘A 3-year-old boy presented with bluish patch and scattered blue spots on the left side of his face.After several sessions of laser treatment,the azury patch in the periorbital area became even darker.Histopathology showed many bipolar,pigment-laden dendritic cells scattered in the papillary and upper reticular dermis.Immunohistochemically,these cells were positive for S100,SOX-10,melan-A,P16,and HMB-45.The positive rate of Ki-67 was less than 5%.Finally,the lesion was diagnosed with nevus of Ota concurrent with common blue nevus.Therefore,for cases of the nevus of Ota with poor response to laser treatment,the possible coexisting diseases should be suspected.
基金This work was supported by the National Natural Science Foundation of China(No.82003808).
文摘Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer cells.Our study is the first to demonstrate the strong inhibitory effects of ursolic acid on the proliferation of cutaneous T-cell lymphoma(CTCL)cells.We aimed to further investigate the underlying mechanism of the proliferation inhibition induced by ursolic acid in CTCL cells using transcriptome sequencing.Methods:Cell counting kit-8 assays were used to observe the effects of six traditional medicine monomers on the proliferation of CTCL cells.Transcriptome sequencing was used to identify differentially expressed genes after ursolic acid treatment.Bioinformatics analysis was performed to determine the potential mechanism.Real-time quantitative PCR and western blotting analyses were performed to confirm the sequencing results and verify the possible mechanisms of ursolic acid-mediated proliferation inhibition in CTCL cells.Results:Ursolic acid exhibited the strongest inhibitory effect on the proliferation of CTCL cells among the six traditional medicine monomers.Transcriptome sequencing analysis showed that 2,466 genes were significantly altered.Combined with Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction network analysis,the interaction of various pathways and signaling molecules,such as tumor necrosis factor-α,NLR family pyrin domain containing 1,c-Jun N-terminal kinase,and melanoma differentiation-associated gene 5,accounted for the anti-tumor effects of ursolic acid in CTCL cells.Conclusion:Ursolic acid significantly inhibited the proliferation of CTCL cells,and our study laid a theoretical foundation for the future treatment of CTCL using ursolic acid.
基金Program of Guangxi Natural Science Foundation(No.2019GXNSDA 245003)The second batch of"Qihuang Project"high-level talent team cultivation project of Guangxi University of Traditional Chinese Medicine(No.2021001)+1 种基金Doctoral Research Initiation Fund of Guangxi University of Traditional Chinese Medicine(2020BS027)2021 Guangxi Postgraduate Innovation Project(No.YCXJ2021007)。
文摘Objective:To study the effect of plumbagin(PL)on the migration and invasion of human hepatocellular carcinoma(HCC)cells and its possible mechanism.Methods:The cell counting kit(CCK-8)was used to detect the effects of different concentrations of plumbagin on the proliferation of human hepatocellular carcinoma Huh-7 and LM3 cells.The effect of plumbagin on the migration ability of Huh-7 and LM3 cells was detected by scratch test and Transwell migration test,and the effect of on the invasion ability of Huh-7 and LM3 cells was detected by Transwell invasion test.Western Blot was used to detect the expression of E-cadherin,N-cadherin,matrix metalloproteinase-2 and related proteins in JAK2/STAT3 signaling pathway in Huh-7 and LM3 cells.Results:Plumbagin could inhibit the proliferation of Huh-7 and LM3 cells in a time-and concentration-dependent manner.Plumbagin inhibited the migration and invasion of Huh-7 and LM3 cells in a concentration dependent manner,and it can down-regulate the expression of N-cadherin and MMP-2 protein,up-regulate the expression of E-cadherin protein,and inhibit the activation of JAK2/STAT3 signaling pathway.Conclusion:Plumbagin can inhibit the migration and invasion of human hepatocellular carcinoma Huh-7 and LM3 cells,and the molecular mechanism of this process may be related to the inhibition of JAK2/STAT3 signaling pathway activation.
基金supported by the Zhejiang Provincial Key Research and Development Plan, China(Grant Nos.2020C02001 and 2022C02034)the National Natural Science Foundation of China(Grant No.31672022)。
文摘Innovations in sequencing technology and the development of bioinformatics have allowed for studies of the genomics of many rice pests.At present,draft genomes of rice pests including Nilaparvata lugens,Sogatella furcifera,Laodelphax striatellus,Sesamia inferens,Chilo suppressalis,Scirpophaga incertulas.
基金supported by grants from the National Natural Science Foundation of China(Grant No.:82270281)Chongqing Medical University Program for Youth Innovation in Future Medicine(Grant No.:W0133)+2 种基金Senior Medical Talents Program of Chongqing for Young and Middle-aged,China(Program No.:JianlinDu[2022])Postdoctoral Research Funding of the Second Affiliated Hospital of Chongqing Medical University,China(Grant No.:rsc-postdoctor114)and Kuanren Talents Program of the Second Affiliated Hospital of Chongqing Medical University,China(Program No.:kryc-gg-2102).
文摘Tbx18,Wt1,and Tcf21 have been identified as epicardial markers during the early embryonic stage.However,the gene markers of mature epicardial cells remain unclear.Single-cell transcriptomic analysis was performed with the Seurat,Monocle,and CellphoneDB packages in R software with standard procedures.Spatial transcriptomics was performed on chilled Visium Tissue Optimization Slides(10x Genomics)and Visium Spatial Gene Expression Slides(10x Genomics).Spatial transcriptomics analysis was performed with Space Ranger software and R software.Immunofluorescence,whole-mount RNA in situ hybridization and X-gal staining were performed to validate the analysis results.Spatial transcriptomics analysis revealed distinct transcriptional profiles and functions between epicardial tissue and non-epicardial tissue.Several gene markers specific to postnatal epicardial tissue were identified,including Msln,C3,Efemp1,and Upk3b.Single-cell transcriptomic analysis revealed that cardiac cells from wildtype mouse hearts(from embryonic day 9.5 to postnatal day 9)could be categorized into six major cell types,which included epicardial cells.Throughout epicardial development,Wt1,Tbx18,and Upk3b were consistently expressed,whereas genes including Msln,C3,and Efemp1 exhibited increased expression during the mature stages of development.Pseudotime analysis further revealed two epicardial cell fates during maturation.Moreover,Upk3b,Msln,Efemp1,and C3 positive epicardial cells were enriched in extracellular matrix signaling.Our results suggested Upk3b,Efemp1,Msln,C3,and other genes were mature epicardium markers.Extracellular matrix signaling was found to play a critical role in the mature epicardium,thus suggesting potential therapeutic targets for heart regeneration in future clinical practice.
基金supported by the Ministry of Science and Technology of China (2019YFA0802103)the National Natural Science Foundation of China (31900804, 31960179)+1 种基金the Department of Science and Technology of Zhejiang Province (2021C03104)the Science and Technology Commission of Shanghai Municipality (19140903500)
文摘Dear Editor,Autophagy is an evolutionarily conserved catabolic process that involves the sequestration and transport of organelles,macromolecules,or invading microorganisms to lysosomes for degradation[1].Sequestosome 1(p62/SQSTM1)was the first protein shown to bind target-associated ubiquitin(Ub)and LC3 conjugated to the phagophore membrane,thus,acting as an important autophagy receptor for ubiquitinated targets[2].
文摘Background:The Qingjiehuagong decoction(QJHGD),which has been used in clinical trials to treat acute pancreatitis(AP),has demonstrated encouraging results.Methods:In this particular investigation,we used both metabolomics and network pharmacology to investigate the fundamental processes and targets that QJHGFD employs to cure AP.Results:Using a cerulein-induced rat model of AP,we showed that QJHGD effectively improved pancreatic tissue damage and reduced serum levels of AMY,LPS,IL-1β,IL-6,IL-8 and TNF-α.In total,28 blood entry compounds derived from QJHGD were identified by ultra-performance liquid chromatography-high resolution mass spectrometry technology.The intersecting target genes of 108 genes associated with identified compounds in QJHGD and AP disease genes were identified using a network pharmacology approach.The protein interaction network revealed AKT1,TNF-α,IL-6,VEGFA,and TP53 as important targets.Gene ontology analysis showed that response to stimulus,molecular function regulator and organelle part were the main functions,and Kyoto Encyclopedia of Genes and Genomes analysis showed that 20 pathways such as AGE-RAGE signaling pathway in diabetic complications and the IL-17 signaling pathway were the main pathways involved in the anti-AP effects of QJHGD.Thirty-two potential metabolic markers and 13 possible metabolic pathways were identified by metabolomics analysis.Combined network pharmacological analysis revealed that QJHGD affects four metabolic pathways(tryptophan metabolism;glycolysis and gluconeogenesis metabolism;valine,leucine and isoleucine degradation metabolism;the urea cycle and metabolism of arginine,proline,glutamate,aspartate and asparagine),five metabolites(indole-3-acetate,pyruvate,methylmalonate,L-citrulline,N-acetyl-l-glutamate)and four related targets(AKT1,ALDH2,NOS2,NOS3)to combat inflammation.The strong affinity of QJHGD’s interactions with its primary targets was established by molecular docking and molecular dynamics simulations.Conclusion:This research investigate the critical targets and mechanisms of QJHGFD for treating AP.The results of this investigation provide novel tactics and complementary techniques for the clinical treatment of AP.
基金Guangxi Science and Technology Base and Talent Project (Guike AD20297013)Guangxi Natural Science Foundat ion Project (2021GXNSFBA220036)The second batch of"Qihuang Project"High-Level Talent Team Cultivation Project of Guangxi University of Traditional Chinese Medicine (2021001)。
文摘Objective:To investigate the mechanism of action and material basis of AiTongXiao granule in the treatment of hepatocellular carcinoma(HCC)based on network pharmacology and transplanted liver cancer rat model.Methods:TCMSP database was used to screen out effective components and its corresponding potential pharmaceutical targets,and databases including Gene Cards,OMIM,Drugbank and TTD were further used to collect HCC-related drug targets.The intersecting targets were obtained by mapping the drug and disease targets.The component-targets network was constructed and visualized by Cytoscape 3.8.2 software.Protein-protein interaction(PPI)network was built by STRING online platform,and the topological relationship and core targets was analyzed and screened by using CytoNCA software.In addition,Metascape database was used to perform gene ontology(GO)enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis of the core targets.At last,rat liver transplanted liver cancer model was established by using Walker-256 cell line and treated by AiTongXiao granule for 15 days.Western blot was used to further compare the expression levels of AKT,pAKT,p53,p-p53,ERK1/2 and ERK1/2 in the tumor between treatment group and the control group.Results:257 active components were obtained from AiTongXiao granule,corresponding to 294 drug targets.Meanwhile,233 of the 7993 HCC disease targets were screened out between AiTongXiao granule drug and HCC disease targets.11 core targets including AKT1,IL6,TP53,MAPK3,TNF,JUN,CASP3,MAPK1,MYC,PTGS2,MMP9 were further obtained by median screening.GO and KEGG analysis results showed that these core targets enriched to HBV,TNF and cancer related pathways.The rat transplanted liver cancer model results indicated significant down regulation for AKT,p-AKT,pERK1/2,and significant up regulation of p-p53 after AiTongXiao granule treatment(P<0.05).Conclusion:AiTongXiao granule could act to multiple cancer related pathways,and AKT,p53 and ERK1/2 were validated to be regulated by ATXF in rat model.The mechanism may be through the regulation of the above signaling pathways to exert anti-liver cancer effect.
基金the National Natural Science Foundation of China(82003808)the The Open Project of Jiangsu Provincial Science and Technology Resources(Clinical Resources)Coordination Service Platform(No.TC2022B015).
文摘Tissue engineering is an interdisciplinary field of bioengineering,cell biology,and biomaterials that seeks to create functional tissues for therapeutic purposes.It is a rapidly growing field of regenerative medicine that has the potential to revolutionize the treatment for many diseases and injuries.General research areas mainly include the engineering of the cardiovascular system,bone and cartilage,oral cavity and skin,and other tissues[1].Skin tissue engineering is one of the earliest clinically applied,most mature and widely used products in the field of tissue engineering[2].