Plant peroxidase （POD） belongs to multigene family, which not is only one of the important enzymes responsible for the removal of active oxygen radicals, but also participates in a variety of physiological and bioch...Plant peroxidase （POD） belongs to multigene family, which not is only one of the important enzymes responsible for the removal of active oxygen radicals, but also participates in a variety of physiological and biochemical processes and plays a crucial role in the maintenance of plant growth and development. In this study, the structures and functions of proteins encoded by 73 gene of POD family in Arabidopsis were analyzed with bioinformatics method, including the number of amino acids, isoelectric point, transmemberane domains, signal peptides, secondary structures and phosphorylation sites, and the phylogenic trees with and without signal peptides were constructed by using Mega4.0 software, to investigate the structural characteristics. In addition, the structures of AtPER members were analyzed, to reveal the relationship between the structures and functions, thereby providing theoretical basis for the research of plant oxidative stress resistance.展开更多
Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma(ccRCC)via bioinformatics analysis.Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were ava...Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma(ccRCC)via bioinformatics analysis.Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were available from the Gene Expression Omnibus database:GSE12606,GSE36895 and GSE66272.The differentially expressed genes were screened with GEO2R and J Venn online tools.Functional annotation including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)was applied to identify the possible function of the hub genes involved in prognosis of ccRCC.In protein protein interaction network(PPI network),the STRING online tool was used to visualize the network of the differentially expressed genes,and the core gene was selected by MCODE App in Cytoscape software.Finally,GEPIA Survival Plot was performed to assess genes associated with worse survival.Results We totally found 648 diflerentially expressed genes,including 222 up-regulated genes and 426 down-regulated genes.PPI network showed that in 28 up-regulated genes 7(CCNE2,CDK1,CDC6,CCNB2,BUB1,TTK and PTTG1)enriched in cell cycle and 4 genes(CCNE2,CDK1,CCNB2 and RRM2)enriched in p53 signaling pathway.GEPIA Survival Plot assay revealed that ccRCC patients carrying CDK1,CCNB2,RRM2t BUB1,and PTTG1 had a worse survival.GEPIA Box Plot showed that BUB1,CCNB2,PTTG1,and RRM2 were over expressed in the ccRCC tissues in contrast to the normal tissues(P<O.OS).Conclusion ccRCC patients with the four up-regulated differentially expressed genes including BUB1,CCNB2,PTTG1,and RRM2 might manifest a poor prognosis.展开更多
Background:To investigate the effect of long-term febrile convulsions on gene expression in mesial temporal lobe epilepsy with hippocampal sclerosis(MTLE-HS)and explore the molecular mechanism of MTLE-HS.Methods:Micro...Background:To investigate the effect of long-term febrile convulsions on gene expression in mesial temporal lobe epilepsy with hippocampal sclerosis(MTLE-HS)and explore the molecular mechanism of MTLE-HS.Methods:Microarray data of MTLE-HS were obtained from the Gene Expression Omnibus database.Differentially expressed genes(DEGs)between MTLE-HS with and without febrile seizure history were screened by the GEO2R software.Pathway enrichment and gene ontology of the DEGs were analyzed using the DAVID online database and FunRich software.Protein–protein interaction(PPI)networks among DEGs were constructed using the STRING database and analyzed by Cytoscape.Results:A total of 515 DEGs were identified in MTLE-HS samples with a febrile seizure history compared to MTLEHS samples without febrile seizure,including 25 down-regulated and 490 up-regulated genes.These DEGs were expressed mostly in plasma membrane and synaptic vesicles.The major molecular functions of those genes were voltage-gated ion channel activity,extracellular ligand-gated ion channel activity and calcium ion binding.The DEGs were mainly involved in biological pathways of cell communication signal transduction and transport.Five genes(SNAP25,SLC32A1,SYN1,GRIN1,and GRIA1)were significantly expressed in the MTLE-HS with prolonged febrile seizures.Conclusion:The pathogenesis of MTLE-HS involves multiple genes,and prolonged febrile seizures could cause differential expression of genes.Thus,investigations of those genes may provide a new perspective into the mechanism of MTLE-HS.展开更多
The exact molecular and cytological mechanism of how glucocorticoids induce vascular repair disorders in glucocorticoid-induced avascular necrosis of the femoral head is still unclear.We used bioinformatical tools for...The exact molecular and cytological mechanism of how glucocorticoids induce vascular repair disorders in glucocorticoid-induced avascular necrosis of the femoral head is still unclear.We used bioinformatical tools for data mining and detected the biological behavior of endothelial cells(ECs)under hypoxia conditions and high dose dexamethasone to reveal the mechanisms above.Six differential expression mi RNAs(DE-miRNAs)were filtered from Gene Expression Omnibus(GEO)database GSE60093 which contained ECs treated with high dose glucocorticoid and control samples.Enrichment and PPI network analyses of the DE-miRNAs target genes showed the most remarkable pathway was HIF-1 signaling pathway and high dose glucocorticoid as a negative regulator of cell differentiation,energy metabolism,migration and cytokines secretion.Glucocorticoids also reduced the activity of autocrine/paracrine via limiting ion channels and transmembrane transporter process.In cytological experiment,HUVECs were divided into four groups:hypoxia group(H),hypoxia+dexamethasone group(HD),dexamethasone group(D),the normal group(N).Cell activity detection and Live/Dead dyeing showed cell activity and the number of live cells in Group H was higher than the other three groups at 24 h after intervention,while cell activity,number and proportion of live cells in HD group were worst.Cytoskeleton staining showed HD group met cytoskeleton form disorders.The scratch assay showed cell migration ability of Group H was strongest while cell migration ability of the HD group was worst.MIF expression in HD group showed a trend of bimodal,the peak of VEGF-A secretion lagged behind the MIF’s.Expression of MIF and VEGF-A in the HD group were low.High dose dexamethasone suppressed the active response of ECs to hypoxia stimulation via directly inhibiting the expression of MIF and interdicting autocrine/paracrine mechanism.We infered that the treatment with high dose glucocorticoid would inhibit neo-angiogenesis under hypoxia followed by aggravating hypoxia/ischemia and osteonecrosis.展开更多
Wax gourd(Benincasa hispida)is an important cucurbit crop with economic and medicinal value.The myeloblastosis(MYB)gene family is one of the largest gene families in plants and regulates various biological processes,w...Wax gourd(Benincasa hispida)is an important cucurbit crop with economic and medicinal value.The myeloblastosis(MYB)gene family is one of the largest gene families in plants and regulates various biological processes,whereas the MYB gene family has not been systematically studied in wax gourd.In this study,we performed genome-wide identification of the MYB gene family in wax gourd and analyzed their phylogenetic relationship,MYB DNA-binding domain(MYB DBD),gene structure,protein motif,synteny,duplication mode and expression pattern.As a result,a total of 215 BhMYB genes(BhMYBs)were identified,belonging to four subfamilies:1R-,2R-,3R-and 4R-MYB subfamilies.Genes of 1R-MYB subfamily and 2R-MYB subfamily were subdivided into different subgroups respectively.The analysis of MYB DBD,gene structure and protein motif showed that the most genes in the same subgroup had similar characteristics and the 2R-MYB genes were more conserved than the 1R-MYB genes.Interestingly,the long terminal retrotransposons(LTR-RTs)were found in the long introns of several BhMYBs.The results of synteny analysis showed that there were more syntenic gene pairs between wax gourd and other cucurbit crops,while the least number of syntenic gene pairs existed between wax gourd and rice.Gene duplication was the main reason for the expansion of the MYB gene family in wax gourd,with the transposed duplication(TRD)mode contributing more.All duplication BhMYB genes were under purifying selection pressure.Further expression analysis showed that many BhMYBs exhibited obvious tissue-specific expression and several BhMYBs were significantly induced by one or more abiotic stresses.BhMYB79 was particularly expressed in roots and significantly induced by salt,drought,cold and heat stresses,overexpression of which led to reduced tolerance to salt stress in Arabidopsis.In conclusion,our results provide a systematic analysis of wax gourd MYB gene family and facilitate the biological role study of BhMYB79 during wax gourd salt stress response process.展开更多
BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alte...BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain unclear.CASE SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and V.Targeted gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder NEC.Twelve mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and pathways.The results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder carcinoma.CONCLUSION Gallbladder NEC requires standardized treatment.Comparisons with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways.展开更多
Background:Small ubiquitin-like modifier(SUMO)-specific proteases(SENPs)cleave the isopeptidic bond between SUMO1/2/3 and protein substrates,thus regulating the structure,activity,and lifetime of a variety of proteins...Background:Small ubiquitin-like modifier(SUMO)-specific proteases(SENPs)cleave the isopeptidic bond between SUMO1/2/3 and protein substrates,thus regulating the structure,activity,and lifetime of a variety of proteins.Recently,accumulating evidence has suggested that SENPs play a role in the initiation and progression of human cancers.Nevertheless,the potential role of the SENP family of proteins in liver cancer has yet to be fully elucidated.Methods:This study conducted a comprehensive bioinformatics analysis of the SENP family in liver cancer,including differential expression profiling,survival analysis,mutation and copy number variations(CNVs)assessment,immune infiltration and drug sensitivity correlation,functional enrichment analyses using data from The Cancer Genome Atlas(TCGA),Clinical Proteomic Tumor Analysis Consortium(CPTAC),LinkedOmics,and other public databases.Furthermore,we performed in vitro experiments using Huh-7 and Hep-3B cell lines to investigate the functional roles of SENP1 and SENP3 in hepatocellular carcinoma cell proliferation,colony formation,and migration.Results:Our results indicated that SENP1,3,and 7 were significantly overexpressed in liver hepatocellular carcinoma(LIHC).Elevated expressions of SENP1,3,and 7 are positively correlated with poor overall survival(OS)in LIHC patients.In addition,SENP1,3,and 7 expressions are related to immune infiltration and drug sensitivity.SENP1,3,and 7 co-expressed genes were enriched in mitochondrial function,ribosomal translation,and cell cycle control.Conclusion:SENP1,3,and 7 are prognostic biomarkers and potential therapeutic targets for LIHC.Knockdown of SENP1 and SENP3 inhibited the proliferation,clonogenicity,and migration of hepatocellular carcinoma cells.展开更多
Dear Editor,We extend our academic appreciation to the contributors of this pioneering study,1 which leverages Mendelian Randomization(MR)to investigate the causal relationship between immune cell phenotypes and intra...Dear Editor,We extend our academic appreciation to the contributors of this pioneering study,1 which leverages Mendelian Randomization(MR)to investigate the causal relationship between immune cell phenotypes and intracranial aneurysms(IAs),demonstrating a certain level of innovation.By extracting 731 immunophenotypes from publicly available genetic databases and conducting large-scale analyses,the study comprehensively evaluates the impact of immune cell traits on IAs.Moreover,multivariable MR analysis was employed to adjust for interactions between different immune phenotypes,providing a novel perspective on the interplay between the immune system and IAs.展开更多
Kinesins are a superfamily of proteins widely present in eukaryotes,playing crucial roles in plant cell wall assembly,cell elongation regulation,gravity sensing,and fertility control.In this study,bioinformatics analy...Kinesins are a superfamily of proteins widely present in eukaryotes,playing crucial roles in plant cell wall assembly,cell elongation regulation,gravity sensing,and fertility control.In this study,bioinformatics analysis of the OsKMP2 gene(LOC_Os02g28850)was performed using online tools such as ExPASy-ProtParam,ProtScale,CD-search,and DNAMAN software.Additionally,qRT-PCR was employed to analyze the tissue expression pattern of OsKMP2.The results showed that the molecular weight of the OsKMP2 is 118.39728 kDa,and it is a hydrophilic and unstable acidic protein.Secondary structure prediction revealed that it primarily consists ofα-helices(69.45%),random coils(25.19%),and extended strands(5.36%).The gene was expressed in various rice tissues,with the highest expression level observed in leaves.These results indicate that the OsKMP2 gene exhibits high evolutionary conservation and functional diversity in rice.展开更多
[Objectives]To develop a pair of specific primers for the PCR amplification of the full-length relA gene from Vibrio alginolyticus strain HY9901,as well as to conduct bioinformatics analysis.[Methods]The relA gene was...[Objectives]To develop a pair of specific primers for the PCR amplification of the full-length relA gene from Vibrio alginolyticus strain HY9901,as well as to conduct bioinformatics analysis.[Methods]The relA gene was amplified through PCR,and the resulting gene sequence was subsequently analyzed using bioinformatics tools,including amino acid sequence prediction,functional site analysis,subcellular localization prediction,and homology comparison.[Results]The relA gene had a total length of 2220 bp and encoded 739 amino acid residues.The molecular weight was approximately 84.1261 kDa,and its isoelectric point was 5.95.The protein lacked a signal peptide and transmembrane regions,while exhibiting multiple phosphorylation sites.Predictions regarding its subcellular localization suggested that it was predominantly situated in the cytoplasm.The amino acid sequence demonstrated a homology of 97%to 99%with other species within the genus Vibrio,and it clustered within the same subfamily as V.antiquarius and V.diabolicus.In the prediction of secondary structure,the proportions ofα-helix,extended strand,random coil,andβ-sheet were 54.13%,12.04%,28.15%and 5.68%,respectively.The similarity between the tertiary structure model and template 5kpw.1.w was 66%.[Conclusions]In this study,the relA gene of V.alginolyticus strain HY9901 has been successfully amplified and analyzed.The structural characteristics and potential functions of the encoded protein have been elucidated,thereby providing foundational data for understanding the role of this gene in V.alginolyticus.展开更多
Background:The nuclear receptor coactivator(NCOA)family,including NCOA1,NCOA2,and NCOA3,is critical in regulating gene expression through interactions with nuclear receptors and other transcription factors.These coact...Background:The nuclear receptor coactivator(NCOA)family,including NCOA1,NCOA2,and NCOA3,is critical in regulating gene expression through interactions with nuclear receptors and other transcription factors.These coactivators are implicated in various cancers,but their comprehensive roles across different cancer types remain poorly understood.Methods:We performed a pan-cancer bioinformatics analysis using data from The Cancer Genome Atlas and the Genotype-Tissue Expression project.We assessed the differential expression,copy number variations,mutations,methylation status,tumor mutation burden,microsatellite instability,and immune cell infiltration associated with NCOA family members across various cancers.Differential expression analysis was conducted using the DESeq2 package.Methylation data were analyzed using the ChAMP package,and immune cell infiltration was estimated using the CIBERSORT algorithm.Results:NCOA1 and NCOA2 were predominantly downregulated in multiple cancers,suggesting potential tumor suppressor roles,whereas NCOA3 was largely upregulated,indicating a consistent oncogenic function.These expression patterns significantly correlated with patient prognosis.Frequent copy number variations,particularly gains,and high mutation rates were observed in NCOA2.NCOA3 demonstrated consistent hypomethylation in tumors,which was associated with increased gene expression.Significant correlations were found between NCOA expression and tumor mutation burden,microsatellite instability,and immune cell infiltration,indicating their involvement in genomic instability and immune modulation.Conclusion:This comprehensive analysis reveals significant alterations in the expression,genomic,and epigenetic profiles of NCOA family members across various cancers.The findings highlight the multifaceted roles of NCOA1,NCOA2,and NCOA3 in tumorigenesis and their potential as biomarkers and therapeutic targets.Future research should focus on elucidating the mechanisms underlying the associations between NCOA expression,genomic alterations,and immune modulation to develop targeted cancer therapies.展开更多
[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers w...[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers were designed based on the sequence of the V.alginolyticus cobQ gene and used to amplify the full-length gene by PCR.[Results] The PCR amplification results indicated that the cobQ gene has a full length of 780 bp,encoding 259 amino acid residues.The deduced amino acid sequence predicts a molecular weight of approximately 28.83 kD and an isoelectric point of 9.21.Sequence analysis revealed no N-terminal signal peptide cleavage site,suggesting the absence of both a signal peptide and transmembrane regions in this protein.The amino acid sequence contains 2 N-terminal myristoylation sites,1 N-glycosylation site,1 glycosaminoglycan attachment site,4 microbody C-terminal targeting signal sites,3 casein kinase II phosphorylation sites,and 4 protein kinase C phosphorylation sites.Subcellular localization prediction showed that the CobQ protein is primarily localized in the cytoplasm(65.2%probability).Homology analysis demonstrated that the amino acid sequence of the cobQ gene from V.alginolyticus shares up to 99%homology with other Vibrio species,clustering within the same subclade as Vibrio parahaemolyticus,indicating close phylogenetic relationships.Secondary structure prediction revealed proportions ofα-helices,random coils,and extended strands as 44.40%,36.68%,and 18.92%,respectively.The tertiary structure model exhibited 87.62%similarity to the template A0A165XBE1.1.[Conclusions] In this study,the V.alginolyticus cobq gene was successfully cloned and its sequence was analyzed by bioinformatics.It is expected to lay a foundation for the subsequent study of the regulatory mechanism of its protein on the virulence of V.alginolyticus.展开更多
[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginol...[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginolyticus for PCR cloning of its full-length sequence.Systematic bioinformatics analyses were conducted to predict the physicochemical properties,secondary structure,and tertiary structure of the encoded protein.[Results]The trxB gene is 960 bp in length,encoding 319 amino acid residues.The deduced protein has a predicted molecular weight of 34.32 kDa and an isoelectric point(pI)of 4.77.Analysis of the amino acid sequence revealed a distinct signal peptide cleavage site at the N-terminus,with no transmembrane domains.The functional sites are as follows:1 N-glycosylation site,1 cAMP-and cGMP-dependent protein kinase phosphorylation site,4 protein kinase C phosphorylation sites,7 casein kinase II phosphorylation sites,1 tyrosine kinase phosphorylation site,11 N-myristoylation sites,1 prenyl group binding site,3 microbody C-terminal targeting signal sites,and 1 xanthine nucleotide-disulfide oxidoreductase class II active site.Subcellular localization prediction indicated the highest probability(44.4%)for endoplasmic reticulum localization.The TrxB amino acid sequence of V.alginolyticus shares 97.2%-98.4%homology with other Vibrio species,and they were clustered within the same subgroup.Secondary structure prediction showed proportions of random coils(31.97%),alpha-helices(31.66%),extended strands(25.08%),and beta turns(11.29%).The tertiary structure model exhibited 88.68%similarity to template 5vt3.1.A.[Conclusions]This study elucidated the characterization of the TrxB protein in V.alginolyticus,laying a theoretical foundation for the development of outer membrane protein subunit vaccines against this pathogen.展开更多
[Objective] The aim was to clone the cDNA and DNA sequences of the CCR （Cinnamoyl-CoA reductase） gene which involves in lignin biosynthesis, from Pennisetum purpureum, and to make comprehensive analysis on these seq...[Objective] The aim was to clone the cDNA and DNA sequences of the CCR （Cinnamoyl-CoA reductase） gene which involves in lignin biosynthesis, from Pennisetum purpureum, and to make comprehensive analysis on these sequences. [Method] CCR sequences were cloned from P. purpureum by using conventional RT-PCR and RACE （Rapid Amplification of cDNA Ends） methods; and the bioinformatic analyses of the CCR were conducted by means of NCBI, ProtParam ProtScale, TMHMM, TargetP, SignalP, Pfam20.0, Prosite, Swiss-Model, ClustalW2, DNAman, DNAstar and MEGA5. [Result] The cloned PpCCR （P. purpureum CCR） cDNA sequence was 1 316 bp, including a 1 110 bp ORF and 206 bp 3’-UTR. The cloned DNA sequence from PpCCR was 6 133 bp in full-length, containing five exons and four introns. Bioinformatic analysis indicated that PpCCR encoded a polypeptide of 369 amino acids, the secondary structure of which was primarily composed of random coil and α-helix, belonging to NAD-dependent epimerase/dehydratase family, and its co-factor binding sites and substrate binding sites were highly conserved. [Conclusion] DNA and cDNA sequences of CCR gene were obtained from P. purpureum, which had the typical characteristics of other homologous genes. The obtained bioinformatic data provided theoretical references for the further analysis of CCR and better application of P. purpureum in the future.展开更多
BACKGROUND Liver fibrosis and hepatocellular carcinoma(HCC)are common adverse consequences of chronic liver injury.The interaction of various risk factors may cause them to happen.Identification of specific biomarkers...BACKGROUND Liver fibrosis and hepatocellular carcinoma(HCC)are common adverse consequences of chronic liver injury.The interaction of various risk factors may cause them to happen.Identification of specific biomarkers is of great significance for understanding the occurrence,development mechanisms,and determining the novel tools for diagnosis and treatment of both liver fibrosis and HCC.AIM To identify liver fibrosis-related core genes,we analyzed the differential expression pattern of core genes in liver fibrosis and HCC.METHODS Gene expression profiles of three datasets,GSE14323,GSE36411,and GSE89377,obtained from the Gene Expression Omnibus(GEO)database,were analyzed,and differentially expressed genes(DEGs)between patients with liver cirrhosis and healthy controls were identified by screening via R software packages and online tool for Venn diagrams.The WebGestalt online tool was used to identify DEGs enriched in biological processes,molecular functions,cellular components,and Kyoto Encyclopedia of Genes and Genomes pathways.The protein–protein interactions of DEGs were visualized using Cytoscape with STRING.Next,the expression pattern of core genes was analyzed using Western blot and immunohistochemistry in a carbon tetrachloride(CCl_(4))-induced liver cirrhosis mouse model and in patient liver samples.Finally,Kaplan-Meier curves were constructed using the Kaplan-Meier plotter online server.RESULTS Forty-five DEGs(43 upregulated and 2 downregulated genes)associated with liver cirrhosis were identified from three GEO datasets.Ten hub genes were identified,which were upregulated in liver cirrhosis.Western blot and immunohistochemical analyses of the three core genes,decorin(DCN),dermatopontin(DPT),and SRY-box transcription factor 9(SOX9),revealed that they were highly expressed in the CCl4-induced liver cirrhosis mouse model.The expression levels of DCN and SOX 9 were positively correlated with the degree of fibrosis,and SOX 9 level in HCC patients was significantly higher than that in fibrosis patients.However,high expression of DPT was observed only in patients with liver fibrosis,and its expression in HCC was low.The gene expression profiling interactive analysis server(GEPIA)showed that SOX9 was significantly upregulated whereas DCN and DPT were significantly downregulated in patients with HCC.In addition,the Kaplan-Meier curves showed that HCC patients with higher SOX9 expression had significantly lower 5-year survival rate,while patients with higher expression of DCN or DPT had significantly higher 5-year survival rates.CONCLUSION The expression levels of DCN,DPT,and SOX9 were positively correlated with the degree of liver fibrosis but showed different correlations with the 5-year survival rates of HCC patients.展开更多
BACKGROUND Gastric signet ring cell carcinoma(GSRCC)is one of the most malignant tumors.It has the features of high invasiveness,rapid progression,and resistance to chemotherapy.However,systematic analyses of mRNAs ha...BACKGROUND Gastric signet ring cell carcinoma(GSRCC)is one of the most malignant tumors.It has the features of high invasiveness,rapid progression,and resistance to chemotherapy.However,systematic analyses of mRNAs have not yet been performed for GSRCC.AIM To identify key mRNAs and signaling pathways in GSRCC.METHODS A transcriptome analysis of two GSRCC and two non-GSRCC samples was performed in this study.Differentially expressed mRNAs and pathways were identified based on the KEGG and PANTHER pathway annotations.The interactive relationships among the differential genes were mapped with the STRING database.Quantitative real-time polymerase chain reaction was used to validate the key gene expression in GSRCC.RESULTS About 1162 differential genes(using a 2-fold cutoff,P<0.05)were identified in GSRCC compared with non-GSRCC.The enriched KEGG and PANTHER pathways for the differential genes included immune response pathways,metabolic pathways,and metastasis-associated pathways.Ten genes(MAGEA2,MAGEA2B,MAGEA3,MAGEA4,MAGEA6,MUC13,GUCA2A,FFAR4,REG1A,and REG1B)were identified as hub genes in the protein-protein interaction network.The expression levels of five genes(MAGEA2,MAGEA3,MAGEA4,MAGEA6,and REG1B)showed potential clinical value.CONCLUSION We have identified the potential key genes and pathways in GSRCC,and these hub genes and pathways could be diagnostic markers and therapeutic targets for GSRCC.展开更多
Jumonji, AT-rich interactive domain 1C （JARID1C） protein belongs to the highly conserved ARID protein family, which is involved in chromatin remodeling and transcriptional regulation during cell growth, differentiat...Jumonji, AT-rich interactive domain 1C （JARID1C） protein belongs to the highly conserved ARID protein family, which is involved in chromatin remodeling and transcriptional regulation during cell growth, differentiation, and development. In humans, this gene plays a vital role in normal brain development and function. Using an in silico approach in combination with 5＇ rapid amplification of cDNA ends （5＇ RACE）, the full-length cDNA of JARIDIC （GenBank accession No. EF139241） from porcine ovary, which contains 5,908 bp nucleotides, with an open reading frame （ORF） of 4,548 bp, has been cloned. The putative porcine JARID 1C protein, which is located in the nucleus, encodes 1,516 amino acids with a molecular weight of 170 kDa and a pI of 5.44. Bioinformatic prediction indicates that the protein contains several conserved domains： a JmjN domain, an ARID domain, a JmjC domain, a C5HC2 zinc finger domain, and a PHD zinc finger domain. Similarity comparisons for nucleic and amino acid sequences reveal that the porcine JARID1C protein shares a high identity with its dog, mouse, rat, and human counterparts. The phylogenetic tree of the JARID1 subfamily proteins has been constructed to reveal the evolutionary relationship of various species. Real-time PCR analysis shows that the JARIDIC gene is expressed in various tissues, but at different levels. The expression levels of this gene are higher in the brain and gonad than in other tissues, suggesting that the JARID1C protein plays a role in porcine brain and gonad functions.展开更多
Studies have shown that microRNAs(miRNAs) mediate posttranscriptional regulation of target genes and participate in various physiological and pathological processes, including peripheral nerve injury. However, it is h...Studies have shown that microRNAs(miRNAs) mediate posttranscriptional regulation of target genes and participate in various physiological and pathological processes, including peripheral nerve injury. However, it is hard to select key miRNAs with essential biological functions among a large number of differentially expressed miRNAs. Previously, we collected injured sciatic nerve stumps at multiple time points after nerve crush injury, examined gene changes at different stages(acute, sub-acute, and post-acute), and obtained mRNA expression profiles. Here, we jointly analyzed mRNAs and miRNAs, and investigated upstream miRNAs of differentially expressed mRNAs using Ingenuity Pathway Analysis bioinformatic software. A total of 31, 42, 30, and 23 upstream miRNAs were identified at 1, 4, 7, and 14 days after rat sciatic nerve injury, respectively. Temporal expression patterns and biological involvement of commonly involved upstream miRNAs(miR-21, let-7, miR-223, miR-10 b, miR-132, miR-15 b, miR-127, miR-29 a, miR-29 b, and miR-9) were then determined at multiple time points. Expression levels of miR-21, miR-132, miR-29 a, and miR-29 b were robustly increased after sciatic nerve injury. Biological processes involving these miRNAs include multicellular organismal response to stress, positive regulation of the epidermal growth factor receptor signaling pathway, negative regulation of epithelial cell differentiation, and regulation of myocardial tissue growth. Moreover, we constructed mechanistic networks of let-7, miR-21, and miR-223, the most significantly involved upstream miRNAs. Our findings reveal that multiple upstream miRNAs(i.e., let-7, miR-21, and miR-223) were associated with gene expression changes in rat sciatic nerve stumps after nerve injury, and these miRNAs play an important role in peripheral nerve regeneration. This study was approved by the Experimental Animal Ethics Committee of Jiangsu Province of China(approval No. 20190303-18) on March 3, 2019.展开更多
Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is s...Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).展开更多
Objective Gastric cancer(GC)is a deadly cancer and a challenging public health problem globally.This study aimed to analyze potential genes associated with pathogenesis and prognosis of gastric cancer.Methods This wor...Objective Gastric cancer(GC)is a deadly cancer and a challenging public health problem globally.This study aimed to analyze potential genes associated with pathogenesis and prognosis of gastric cancer.Methods This work selected the overlapping differentially expressed genes(DEGs)in GC from four datasets,the GSE29272,GSE29998,GSE54129 and GSE118916 Gene Expression Omnibus databases.These DEGs were used to carry out comprehensive bioinformatic analysis to analyze the related functions and pathways enriched,the relative expression levels and immune infiltrates,the prognostic characteristics and the interaction network.Results In total,55 DEGs increased while 98 decreased in their expression levels.For those DEGs with increased expression,they were mostly concentrated on“focal adhesion”and“ECM-receptor interaction”,whereas DEGs with decreased expression were mostly associated with“gastric acid secretion”and“drug metabolism cytochrome P450”.MCODE and ClueGO results were then integrated to screen 10 hub genes,which were FN1,COL1A1,COL3A1,BGN,TIMP1,COL1A2,LUM,VCAN,COL5A2 and SPP1.Survival analysis revealed that higher expression of the ten hub genes significantly predicted lower overall survival of GC patients.TIMP1 was most significantly related to neutrophils,CD8+T cells,as well as dendritic cells,while LUM was most significantly related to macrophages.Conclusion Immunohistochemistry results and functional testing showed that the expression of COL5A2 was elevated in GC and that it might be a key gene in GC tumorigenesis.展开更多
基金Supported by National Natural Science Foundation of China(31070361)the Fundamental Research Funds for the Central Universities(0910KYZY43,1112KYQN31)+1 种基金"985 Project"from Minzu University of China(MUC98504-14)Scientific Research Project from State Ethnic Affairs Commission(10ZY01)~~
文摘Plant peroxidase （POD） belongs to multigene family, which not is only one of the important enzymes responsible for the removal of active oxygen radicals, but also participates in a variety of physiological and biochemical processes and plays a crucial role in the maintenance of plant growth and development. In this study, the structures and functions of proteins encoded by 73 gene of POD family in Arabidopsis were analyzed with bioinformatics method, including the number of amino acids, isoelectric point, transmemberane domains, signal peptides, secondary structures and phosphorylation sites, and the phylogenic trees with and without signal peptides were constructed by using Mega4.0 software, to investigate the structural characteristics. In addition, the structures of AtPER members were analyzed, to reveal the relationship between the structures and functions, thereby providing theoretical basis for the research of plant oxidative stress resistance.
基金the National Technical system of Chinese Medicinal Materials Industry(No.CARS-21)the Key Natural Science Projects of West Anhui University in China(No.WXZR201932)+4 种基金the Training Program of Innovate and Entrepreneurship of National College students in China(No.201810376058,201810376061)Anhui Provincial Natural Science Foundation in China(No.2017A030311022)Anhui Provincial University Natural Science Project in China(No.KJ2018A0413,KJ2017a407)Anhui Provincial Quality of Undergraduate project in China(No.2018zygc075,2018jyxm1153,2018jyxm1155)the Teaching and Research Projects of West Anhui University in China(No.wxxy2018026).
文摘Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma(ccRCC)via bioinformatics analysis.Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were available from the Gene Expression Omnibus database:GSE12606,GSE36895 and GSE66272.The differentially expressed genes were screened with GEO2R and J Venn online tools.Functional annotation including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)was applied to identify the possible function of the hub genes involved in prognosis of ccRCC.In protein protein interaction network(PPI network),the STRING online tool was used to visualize the network of the differentially expressed genes,and the core gene was selected by MCODE App in Cytoscape software.Finally,GEPIA Survival Plot was performed to assess genes associated with worse survival.Results We totally found 648 diflerentially expressed genes,including 222 up-regulated genes and 426 down-regulated genes.PPI network showed that in 28 up-regulated genes 7(CCNE2,CDK1,CDC6,CCNB2,BUB1,TTK and PTTG1)enriched in cell cycle and 4 genes(CCNE2,CDK1,CCNB2 and RRM2)enriched in p53 signaling pathway.GEPIA Survival Plot assay revealed that ccRCC patients carrying CDK1,CCNB2,RRM2t BUB1,and PTTG1 had a worse survival.GEPIA Box Plot showed that BUB1,CCNB2,PTTG1,and RRM2 were over expressed in the ccRCC tissues in contrast to the normal tissues(P<O.OS).Conclusion ccRCC patients with the four up-regulated differentially expressed genes including BUB1,CCNB2,PTTG1,and RRM2 might manifest a poor prognosis.
基金the Sanming Project of Medicine in Shenzhen(No.SZSM201911003)National Natural Science Foundation of China(No.81571266,81771405).
文摘Background:To investigate the effect of long-term febrile convulsions on gene expression in mesial temporal lobe epilepsy with hippocampal sclerosis(MTLE-HS)and explore the molecular mechanism of MTLE-HS.Methods:Microarray data of MTLE-HS were obtained from the Gene Expression Omnibus database.Differentially expressed genes(DEGs)between MTLE-HS with and without febrile seizure history were screened by the GEO2R software.Pathway enrichment and gene ontology of the DEGs were analyzed using the DAVID online database and FunRich software.Protein–protein interaction(PPI)networks among DEGs were constructed using the STRING database and analyzed by Cytoscape.Results:A total of 515 DEGs were identified in MTLE-HS samples with a febrile seizure history compared to MTLEHS samples without febrile seizure,including 25 down-regulated and 490 up-regulated genes.These DEGs were expressed mostly in plasma membrane and synaptic vesicles.The major molecular functions of those genes were voltage-gated ion channel activity,extracellular ligand-gated ion channel activity and calcium ion binding.The DEGs were mainly involved in biological pathways of cell communication signal transduction and transport.Five genes(SNAP25,SLC32A1,SYN1,GRIN1,and GRIA1)were significantly expressed in the MTLE-HS with prolonged febrile seizures.Conclusion:The pathogenesis of MTLE-HS involves multiple genes,and prolonged febrile seizures could cause differential expression of genes.Thus,investigations of those genes may provide a new perspective into the mechanism of MTLE-HS.
基金the National Natural Science Foundation of Chinagrant number:81301562 and 81572147。
文摘The exact molecular and cytological mechanism of how glucocorticoids induce vascular repair disorders in glucocorticoid-induced avascular necrosis of the femoral head is still unclear.We used bioinformatical tools for data mining and detected the biological behavior of endothelial cells(ECs)under hypoxia conditions and high dose dexamethasone to reveal the mechanisms above.Six differential expression mi RNAs(DE-miRNAs)were filtered from Gene Expression Omnibus(GEO)database GSE60093 which contained ECs treated with high dose glucocorticoid and control samples.Enrichment and PPI network analyses of the DE-miRNAs target genes showed the most remarkable pathway was HIF-1 signaling pathway and high dose glucocorticoid as a negative regulator of cell differentiation,energy metabolism,migration and cytokines secretion.Glucocorticoids also reduced the activity of autocrine/paracrine via limiting ion channels and transmembrane transporter process.In cytological experiment,HUVECs were divided into four groups:hypoxia group(H),hypoxia+dexamethasone group(HD),dexamethasone group(D),the normal group(N).Cell activity detection and Live/Dead dyeing showed cell activity and the number of live cells in Group H was higher than the other three groups at 24 h after intervention,while cell activity,number and proportion of live cells in HD group were worst.Cytoskeleton staining showed HD group met cytoskeleton form disorders.The scratch assay showed cell migration ability of Group H was strongest while cell migration ability of the HD group was worst.MIF expression in HD group showed a trend of bimodal,the peak of VEGF-A secretion lagged behind the MIF’s.Expression of MIF and VEGF-A in the HD group were low.High dose dexamethasone suppressed the active response of ECs to hypoxia stimulation via directly inhibiting the expression of MIF and interdicting autocrine/paracrine mechanism.We infered that the treatment with high dose glucocorticoid would inhibit neo-angiogenesis under hypoxia followed by aggravating hypoxia/ischemia and osteonecrosis.
基金supported by the Key-Area Research and Development Program of Guangdong Province(Grant No.2020B020220003)National Natural Science Foundation of China(32202504)+2 种基金Guangdong Basic and Applied Basic Research Foundation(Grant No.2023A1515030049)Guangdong Rural Revitalization Strategy Special Project(Grant No.2023-NJS-00-003)Special fund for scientific and technological talents introduction of Guangdong Academy of Agricultural Sciences(Grant No.R2021YJ-YB2004)。
文摘Wax gourd(Benincasa hispida)is an important cucurbit crop with economic and medicinal value.The myeloblastosis(MYB)gene family is one of the largest gene families in plants and regulates various biological processes,whereas the MYB gene family has not been systematically studied in wax gourd.In this study,we performed genome-wide identification of the MYB gene family in wax gourd and analyzed their phylogenetic relationship,MYB DNA-binding domain(MYB DBD),gene structure,protein motif,synteny,duplication mode and expression pattern.As a result,a total of 215 BhMYB genes(BhMYBs)were identified,belonging to four subfamilies:1R-,2R-,3R-and 4R-MYB subfamilies.Genes of 1R-MYB subfamily and 2R-MYB subfamily were subdivided into different subgroups respectively.The analysis of MYB DBD,gene structure and protein motif showed that the most genes in the same subgroup had similar characteristics and the 2R-MYB genes were more conserved than the 1R-MYB genes.Interestingly,the long terminal retrotransposons(LTR-RTs)were found in the long introns of several BhMYBs.The results of synteny analysis showed that there were more syntenic gene pairs between wax gourd and other cucurbit crops,while the least number of syntenic gene pairs existed between wax gourd and rice.Gene duplication was the main reason for the expansion of the MYB gene family in wax gourd,with the transposed duplication(TRD)mode contributing more.All duplication BhMYB genes were under purifying selection pressure.Further expression analysis showed that many BhMYBs exhibited obvious tissue-specific expression and several BhMYBs were significantly induced by one or more abiotic stresses.BhMYB79 was particularly expressed in roots and significantly induced by salt,drought,cold and heat stresses,overexpression of which led to reduced tolerance to salt stress in Arabidopsis.In conclusion,our results provide a systematic analysis of wax gourd MYB gene family and facilitate the biological role study of BhMYB79 during wax gourd salt stress response process.
基金Supported by School-Level Key Projects at Bengbu Medical College,No.2021byzd109.
文摘BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain unclear.CASE SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and V.Targeted gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder NEC.Twelve mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and pathways.The results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder carcinoma.CONCLUSION Gallbladder NEC requires standardized treatment.Comparisons with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways.
基金supported by grants from the National Natural Science Foundation of China(Grant Nos.32070616 and 82170794).
文摘Background:Small ubiquitin-like modifier(SUMO)-specific proteases(SENPs)cleave the isopeptidic bond between SUMO1/2/3 and protein substrates,thus regulating the structure,activity,and lifetime of a variety of proteins.Recently,accumulating evidence has suggested that SENPs play a role in the initiation and progression of human cancers.Nevertheless,the potential role of the SENP family of proteins in liver cancer has yet to be fully elucidated.Methods:This study conducted a comprehensive bioinformatics analysis of the SENP family in liver cancer,including differential expression profiling,survival analysis,mutation and copy number variations(CNVs)assessment,immune infiltration and drug sensitivity correlation,functional enrichment analyses using data from The Cancer Genome Atlas(TCGA),Clinical Proteomic Tumor Analysis Consortium(CPTAC),LinkedOmics,and other public databases.Furthermore,we performed in vitro experiments using Huh-7 and Hep-3B cell lines to investigate the functional roles of SENP1 and SENP3 in hepatocellular carcinoma cell proliferation,colony formation,and migration.Results:Our results indicated that SENP1,3,and 7 were significantly overexpressed in liver hepatocellular carcinoma(LIHC).Elevated expressions of SENP1,3,and 7 are positively correlated with poor overall survival(OS)in LIHC patients.In addition,SENP1,3,and 7 expressions are related to immune infiltration and drug sensitivity.SENP1,3,and 7 co-expressed genes were enriched in mitochondrial function,ribosomal translation,and cell cycle control.Conclusion:SENP1,3,and 7 are prognostic biomarkers and potential therapeutic targets for LIHC.Knockdown of SENP1 and SENP3 inhibited the proliferation,clonogenicity,and migration of hepatocellular carcinoma cells.
文摘Dear Editor,We extend our academic appreciation to the contributors of this pioneering study,1 which leverages Mendelian Randomization(MR)to investigate the causal relationship between immune cell phenotypes and intracranial aneurysms(IAs),demonstrating a certain level of innovation.By extracting 731 immunophenotypes from publicly available genetic databases and conducting large-scale analyses,the study comprehensively evaluates the impact of immune cell traits on IAs.Moreover,multivariable MR analysis was employed to adjust for interactions between different immune phenotypes,providing a novel perspective on the interplay between the immune system and IAs.
基金Supported by College Student Innovation and Entrepreneurship Training Program(S202210553003)Hunan Provincial Education Department Outstanding Youth Research Project(23B0820).
文摘Kinesins are a superfamily of proteins widely present in eukaryotes,playing crucial roles in plant cell wall assembly,cell elongation regulation,gravity sensing,and fertility control.In this study,bioinformatics analysis of the OsKMP2 gene(LOC_Os02g28850)was performed using online tools such as ExPASy-ProtParam,ProtScale,CD-search,and DNAMAN software.Additionally,qRT-PCR was employed to analyze the tissue expression pattern of OsKMP2.The results showed that the molecular weight of the OsKMP2 is 118.39728 kDa,and it is a hydrophilic and unstable acidic protein.Secondary structure prediction revealed that it primarily consists ofα-helices(69.45%),random coils(25.19%),and extended strands(5.36%).The gene was expressed in various rice tissues,with the highest expression level observed in leaves.These results indicate that the OsKMP2 gene exhibits high evolutionary conservation and functional diversity in rice.
基金Supported by Natural Science Foundation of Guangdong Province(2025A1515011061)Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean University+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘[Objectives]To develop a pair of specific primers for the PCR amplification of the full-length relA gene from Vibrio alginolyticus strain HY9901,as well as to conduct bioinformatics analysis.[Methods]The relA gene was amplified through PCR,and the resulting gene sequence was subsequently analyzed using bioinformatics tools,including amino acid sequence prediction,functional site analysis,subcellular localization prediction,and homology comparison.[Results]The relA gene had a total length of 2220 bp and encoded 739 amino acid residues.The molecular weight was approximately 84.1261 kDa,and its isoelectric point was 5.95.The protein lacked a signal peptide and transmembrane regions,while exhibiting multiple phosphorylation sites.Predictions regarding its subcellular localization suggested that it was predominantly situated in the cytoplasm.The amino acid sequence demonstrated a homology of 97%to 99%with other species within the genus Vibrio,and it clustered within the same subfamily as V.antiquarius and V.diabolicus.In the prediction of secondary structure,the proportions ofα-helix,extended strand,random coil,andβ-sheet were 54.13%,12.04%,28.15%and 5.68%,respectively.The similarity between the tertiary structure model and template 5kpw.1.w was 66%.[Conclusions]In this study,the relA gene of V.alginolyticus strain HY9901 has been successfully amplified and analyzed.The structural characteristics and potential functions of the encoded protein have been elucidated,thereby providing foundational data for understanding the role of this gene in V.alginolyticus.
基金supported by grants from the Tianjin Health Technology Project(Grant No.2022QN106).
文摘Background:The nuclear receptor coactivator(NCOA)family,including NCOA1,NCOA2,and NCOA3,is critical in regulating gene expression through interactions with nuclear receptors and other transcription factors.These coactivators are implicated in various cancers,but their comprehensive roles across different cancer types remain poorly understood.Methods:We performed a pan-cancer bioinformatics analysis using data from The Cancer Genome Atlas and the Genotype-Tissue Expression project.We assessed the differential expression,copy number variations,mutations,methylation status,tumor mutation burden,microsatellite instability,and immune cell infiltration associated with NCOA family members across various cancers.Differential expression analysis was conducted using the DESeq2 package.Methylation data were analyzed using the ChAMP package,and immune cell infiltration was estimated using the CIBERSORT algorithm.Results:NCOA1 and NCOA2 were predominantly downregulated in multiple cancers,suggesting potential tumor suppressor roles,whereas NCOA3 was largely upregulated,indicating a consistent oncogenic function.These expression patterns significantly correlated with patient prognosis.Frequent copy number variations,particularly gains,and high mutation rates were observed in NCOA2.NCOA3 demonstrated consistent hypomethylation in tumors,which was associated with increased gene expression.Significant correlations were found between NCOA expression and tumor mutation burden,microsatellite instability,and immune cell infiltration,indicating their involvement in genomic instability and immune modulation.Conclusion:This comprehensive analysis reveals significant alterations in the expression,genomic,and epigenetic profiles of NCOA family members across various cancers.The findings highlight the multifaceted roles of NCOA1,NCOA2,and NCOA3 in tumorigenesis and their potential as biomarkers and therapeutic targets.Future research should focus on elucidating the mechanisms underlying the associations between NCOA expression,genomic alterations,and immune modulation to develop targeted cancer therapies.
基金Natural Science Foundation of Guangdong Province(2025A1515011061)Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean University+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘[Objectives] To analyze the function of cobQ gene from Vibrio alginolyticus strain HY9901,and to provide a reference for exploring the possible mechanism of cobQ gene from V.alginolyticus.[Methods] A pair of primers were designed based on the sequence of the V.alginolyticus cobQ gene and used to amplify the full-length gene by PCR.[Results] The PCR amplification results indicated that the cobQ gene has a full length of 780 bp,encoding 259 amino acid residues.The deduced amino acid sequence predicts a molecular weight of approximately 28.83 kD and an isoelectric point of 9.21.Sequence analysis revealed no N-terminal signal peptide cleavage site,suggesting the absence of both a signal peptide and transmembrane regions in this protein.The amino acid sequence contains 2 N-terminal myristoylation sites,1 N-glycosylation site,1 glycosaminoglycan attachment site,4 microbody C-terminal targeting signal sites,3 casein kinase II phosphorylation sites,and 4 protein kinase C phosphorylation sites.Subcellular localization prediction showed that the CobQ protein is primarily localized in the cytoplasm(65.2%probability).Homology analysis demonstrated that the amino acid sequence of the cobQ gene from V.alginolyticus shares up to 99%homology with other Vibrio species,clustering within the same subclade as Vibrio parahaemolyticus,indicating close phylogenetic relationships.Secondary structure prediction revealed proportions ofα-helices,random coils,and extended strands as 44.40%,36.68%,and 18.92%,respectively.The tertiary structure model exhibited 87.62%similarity to the template A0A165XBE1.1.[Conclusions] In this study,the V.alginolyticus cobq gene was successfully cloned and its sequence was analyzed by bioinformatics.It is expected to lay a foundation for the subsequent study of the regulatory mechanism of its protein on the virulence of V.alginolyticus.
基金Supported by Natural Science Foundation of Guangdong Province(2025A1515011061)Outstanding Graduate Entering Laboratory Project of College of Fisheries,Guangdong Ocean University+1 种基金Undergraduate Innovation and Entrepreneurship Training Program of Guangdong Ocean University(CXXL2024007)Undergraduate Innovation Team of Guangdong Ocean University(CCTD201802).
文摘[Objectives]This study was conducted to investigate the functional characteristics of the trxB gene in Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the trxB gene sequence of V.alginolyticus for PCR cloning of its full-length sequence.Systematic bioinformatics analyses were conducted to predict the physicochemical properties,secondary structure,and tertiary structure of the encoded protein.[Results]The trxB gene is 960 bp in length,encoding 319 amino acid residues.The deduced protein has a predicted molecular weight of 34.32 kDa and an isoelectric point(pI)of 4.77.Analysis of the amino acid sequence revealed a distinct signal peptide cleavage site at the N-terminus,with no transmembrane domains.The functional sites are as follows:1 N-glycosylation site,1 cAMP-and cGMP-dependent protein kinase phosphorylation site,4 protein kinase C phosphorylation sites,7 casein kinase II phosphorylation sites,1 tyrosine kinase phosphorylation site,11 N-myristoylation sites,1 prenyl group binding site,3 microbody C-terminal targeting signal sites,and 1 xanthine nucleotide-disulfide oxidoreductase class II active site.Subcellular localization prediction indicated the highest probability(44.4%)for endoplasmic reticulum localization.The TrxB amino acid sequence of V.alginolyticus shares 97.2%-98.4%homology with other Vibrio species,and they were clustered within the same subgroup.Secondary structure prediction showed proportions of random coils(31.97%),alpha-helices(31.66%),extended strands(25.08%),and beta turns(11.29%).The tertiary structure model exhibited 88.68%similarity to template 5vt3.1.A.[Conclusions]This study elucidated the characterization of the TrxB protein in V.alginolyticus,laying a theoretical foundation for the development of outer membrane protein subunit vaccines against this pathogen.
基金Supported by the National Natural Science Foundation of China(30972138)the Guangdong Natural Science Foundation(9451064201003804)~~
文摘[Objective] The aim was to clone the cDNA and DNA sequences of the CCR （Cinnamoyl-CoA reductase） gene which involves in lignin biosynthesis, from Pennisetum purpureum, and to make comprehensive analysis on these sequences. [Method] CCR sequences were cloned from P. purpureum by using conventional RT-PCR and RACE （Rapid Amplification of cDNA Ends） methods; and the bioinformatic analyses of the CCR were conducted by means of NCBI, ProtParam ProtScale, TMHMM, TargetP, SignalP, Pfam20.0, Prosite, Swiss-Model, ClustalW2, DNAman, DNAstar and MEGA5. [Result] The cloned PpCCR （P. purpureum CCR） cDNA sequence was 1 316 bp, including a 1 110 bp ORF and 206 bp 3’-UTR. The cloned DNA sequence from PpCCR was 6 133 bp in full-length, containing five exons and four introns. Bioinformatic analysis indicated that PpCCR encoded a polypeptide of 369 amino acids, the secondary structure of which was primarily composed of random coil and α-helix, belonging to NAD-dependent epimerase/dehydratase family, and its co-factor binding sites and substrate binding sites were highly conserved. [Conclusion] DNA and cDNA sequences of CCR gene were obtained from P. purpureum, which had the typical characteristics of other homologous genes. The obtained bioinformatic data provided theoretical references for the further analysis of CCR and better application of P. purpureum in the future.
基金Supported by the Beijing Natural Science Foundation,No.7222097Beijing Hospitals Authority the Digestive Medical Coordinated Development Center,No.XXZ0401+1 种基金National Natural Science Foundation of China,No.82000555 and No.81900547Beijing Municipal Science and Technology Commission,No.D171100003117005.
文摘BACKGROUND Liver fibrosis and hepatocellular carcinoma(HCC)are common adverse consequences of chronic liver injury.The interaction of various risk factors may cause them to happen.Identification of specific biomarkers is of great significance for understanding the occurrence,development mechanisms,and determining the novel tools for diagnosis and treatment of both liver fibrosis and HCC.AIM To identify liver fibrosis-related core genes,we analyzed the differential expression pattern of core genes in liver fibrosis and HCC.METHODS Gene expression profiles of three datasets,GSE14323,GSE36411,and GSE89377,obtained from the Gene Expression Omnibus(GEO)database,were analyzed,and differentially expressed genes(DEGs)between patients with liver cirrhosis and healthy controls were identified by screening via R software packages and online tool for Venn diagrams.The WebGestalt online tool was used to identify DEGs enriched in biological processes,molecular functions,cellular components,and Kyoto Encyclopedia of Genes and Genomes pathways.The protein–protein interactions of DEGs were visualized using Cytoscape with STRING.Next,the expression pattern of core genes was analyzed using Western blot and immunohistochemistry in a carbon tetrachloride(CCl_(4))-induced liver cirrhosis mouse model and in patient liver samples.Finally,Kaplan-Meier curves were constructed using the Kaplan-Meier plotter online server.RESULTS Forty-five DEGs(43 upregulated and 2 downregulated genes)associated with liver cirrhosis were identified from three GEO datasets.Ten hub genes were identified,which were upregulated in liver cirrhosis.Western blot and immunohistochemical analyses of the three core genes,decorin(DCN),dermatopontin(DPT),and SRY-box transcription factor 9(SOX9),revealed that they were highly expressed in the CCl4-induced liver cirrhosis mouse model.The expression levels of DCN and SOX 9 were positively correlated with the degree of fibrosis,and SOX 9 level in HCC patients was significantly higher than that in fibrosis patients.However,high expression of DPT was observed only in patients with liver fibrosis,and its expression in HCC was low.The gene expression profiling interactive analysis server(GEPIA)showed that SOX9 was significantly upregulated whereas DCN and DPT were significantly downregulated in patients with HCC.In addition,the Kaplan-Meier curves showed that HCC patients with higher SOX9 expression had significantly lower 5-year survival rate,while patients with higher expression of DCN or DPT had significantly higher 5-year survival rates.CONCLUSION The expression levels of DCN,DPT,and SOX9 were positively correlated with the degree of liver fibrosis but showed different correlations with the 5-year survival rates of HCC patients.
基金Supported by National Key R&D Program of China,No.2018YFC1313101Wu Jieping Medical Foundation,No.320.6750.15276
文摘BACKGROUND Gastric signet ring cell carcinoma(GSRCC)is one of the most malignant tumors.It has the features of high invasiveness,rapid progression,and resistance to chemotherapy.However,systematic analyses of mRNAs have not yet been performed for GSRCC.AIM To identify key mRNAs and signaling pathways in GSRCC.METHODS A transcriptome analysis of two GSRCC and two non-GSRCC samples was performed in this study.Differentially expressed mRNAs and pathways were identified based on the KEGG and PANTHER pathway annotations.The interactive relationships among the differential genes were mapped with the STRING database.Quantitative real-time polymerase chain reaction was used to validate the key gene expression in GSRCC.RESULTS About 1162 differential genes(using a 2-fold cutoff,P<0.05)were identified in GSRCC compared with non-GSRCC.The enriched KEGG and PANTHER pathways for the differential genes included immune response pathways,metabolic pathways,and metastasis-associated pathways.Ten genes(MAGEA2,MAGEA2B,MAGEA3,MAGEA4,MAGEA6,MUC13,GUCA2A,FFAR4,REG1A,and REG1B)were identified as hub genes in the protein-protein interaction network.The expression levels of five genes(MAGEA2,MAGEA3,MAGEA4,MAGEA6,and REG1B)showed potential clinical value.CONCLUSION We have identified the potential key genes and pathways in GSRCC,and these hub genes and pathways could be diagnostic markers and therapeutic targets for GSRCC.
基金the National High Technology Development Program of China (No. 2006AA10Z136).
文摘Jumonji, AT-rich interactive domain 1C （JARID1C） protein belongs to the highly conserved ARID protein family, which is involved in chromatin remodeling and transcriptional regulation during cell growth, differentiation, and development. In humans, this gene plays a vital role in normal brain development and function. Using an in silico approach in combination with 5＇ rapid amplification of cDNA ends （5＇ RACE）, the full-length cDNA of JARIDIC （GenBank accession No. EF139241） from porcine ovary, which contains 5,908 bp nucleotides, with an open reading frame （ORF） of 4,548 bp, has been cloned. The putative porcine JARID 1C protein, which is located in the nucleus, encodes 1,516 amino acids with a molecular weight of 170 kDa and a pI of 5.44. Bioinformatic prediction indicates that the protein contains several conserved domains： a JmjN domain, an ARID domain, a JmjC domain, a C5HC2 zinc finger domain, and a PHD zinc finger domain. Similarity comparisons for nucleic and amino acid sequences reveal that the porcine JARID1C protein shares a high identity with its dog, mouse, rat, and human counterparts. The phylogenetic tree of the JARID1 subfamily proteins has been constructed to reveal the evolutionary relationship of various species. Real-time PCR analysis shows that the JARIDIC gene is expressed in various tissues, but at different levels. The expression levels of this gene are higher in the brain and gonad than in other tissues, suggesting that the JARID1C protein plays a role in porcine brain and gonad functions.
基金supported by the National Natural Science Foundation of China,No.31971276(to JHH)the Natural Science Foundation of Jiangsu Higher Education Institutions of China(Major Program),No.19KJA320005(to JHH)。
文摘Studies have shown that microRNAs(miRNAs) mediate posttranscriptional regulation of target genes and participate in various physiological and pathological processes, including peripheral nerve injury. However, it is hard to select key miRNAs with essential biological functions among a large number of differentially expressed miRNAs. Previously, we collected injured sciatic nerve stumps at multiple time points after nerve crush injury, examined gene changes at different stages(acute, sub-acute, and post-acute), and obtained mRNA expression profiles. Here, we jointly analyzed mRNAs and miRNAs, and investigated upstream miRNAs of differentially expressed mRNAs using Ingenuity Pathway Analysis bioinformatic software. A total of 31, 42, 30, and 23 upstream miRNAs were identified at 1, 4, 7, and 14 days after rat sciatic nerve injury, respectively. Temporal expression patterns and biological involvement of commonly involved upstream miRNAs(miR-21, let-7, miR-223, miR-10 b, miR-132, miR-15 b, miR-127, miR-29 a, miR-29 b, and miR-9) were then determined at multiple time points. Expression levels of miR-21, miR-132, miR-29 a, and miR-29 b were robustly increased after sciatic nerve injury. Biological processes involving these miRNAs include multicellular organismal response to stress, positive regulation of the epidermal growth factor receptor signaling pathway, negative regulation of epithelial cell differentiation, and regulation of myocardial tissue growth. Moreover, we constructed mechanistic networks of let-7, miR-21, and miR-223, the most significantly involved upstream miRNAs. Our findings reveal that multiple upstream miRNAs(i.e., let-7, miR-21, and miR-223) were associated with gene expression changes in rat sciatic nerve stumps after nerve injury, and these miRNAs play an important role in peripheral nerve regeneration. This study was approved by the Experimental Animal Ethics Committee of Jiangsu Province of China(approval No. 20190303-18) on March 3, 2019.
基金supported by the Notional Natural Science Foundation of China,No.81960417 (to JX)Guangxi Key Research and Development Program,No.GuiKeA B20159027 (to JX)the Natural Science Foundation of Guangxi Zhuang Autonomous Region,No.2022GXNSFBA035545 (to YG)。
文摘Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).
基金The authors declare that there is no conflict of interest with any financial organization or corporation or individual that can inappropriately influence this work.
文摘Objective Gastric cancer(GC)is a deadly cancer and a challenging public health problem globally.This study aimed to analyze potential genes associated with pathogenesis and prognosis of gastric cancer.Methods This work selected the overlapping differentially expressed genes(DEGs)in GC from four datasets,the GSE29272,GSE29998,GSE54129 and GSE118916 Gene Expression Omnibus databases.These DEGs were used to carry out comprehensive bioinformatic analysis to analyze the related functions and pathways enriched,the relative expression levels and immune infiltrates,the prognostic characteristics and the interaction network.Results In total,55 DEGs increased while 98 decreased in their expression levels.For those DEGs with increased expression,they were mostly concentrated on“focal adhesion”and“ECM-receptor interaction”,whereas DEGs with decreased expression were mostly associated with“gastric acid secretion”and“drug metabolism cytochrome P450”.MCODE and ClueGO results were then integrated to screen 10 hub genes,which were FN1,COL1A1,COL3A1,BGN,TIMP1,COL1A2,LUM,VCAN,COL5A2 and SPP1.Survival analysis revealed that higher expression of the ten hub genes significantly predicted lower overall survival of GC patients.TIMP1 was most significantly related to neutrophils,CD8+T cells,as well as dendritic cells,while LUM was most significantly related to macrophages.Conclusion Immunohistochemistry results and functional testing showed that the expression of COL5A2 was elevated in GC and that it might be a key gene in GC tumorigenesis.
