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
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
[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 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
Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a v...Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a vital role in the exploration of cancer-related genes. Therefore, the purpose of our study was to identify the progression associated candidate genes of TC by bioinformatics analysis. Five microarray datasets of TC samples were downloaded from the Gene Expression Onmibus （GEO） database and the data of 133 TC patients were screened from The Cancer Genome Atlas （TCGA） head and neck squamous cell carcinoma （HNSC） database. The integrated analysis of five microarray datasets and the RNA sequencing data of TC samples in TCGA-HNSC was performed to obtain 1023 overlapping differentially expressed genes （DEGs） in TC and adjacent normal tissue （ANT） samples. Next, Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis was conducted to enrich the significant pathways of the 1023 DEGs and PI3K- Akt signaling pathway （P=0.011） was selected to be the candidate pathway. A total of 23 DEGs with ｜log2 fold change （FC）｜ ≥1.0 in phosphatidylinositol 3-kinase-serine/threonine kinase （PI3K-Akt） signaling pathway were subjected to survival analysis of 125 eligible TC samples in TCGA database, indicating increased integrin-α3 gene （ITGA3） expression was significantly associated with poorer prognosis. Taken together, our study suggested ITGA3 may facilitate the development of TC via activating PI3K-Akt signaling pathway.展开更多
Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate trau...Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.展开更多
Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking a...Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking and gait. This disease can not be clearly identified through laboratory tests at present, thus application of high-throughput technique in studying the expression profiles of PD helps to find the genetic markers for its early diagnosis. Studies on expression profiles of neurodegenerative diseases have revealed the novel genes and pathways involved in the progress of illness. In this study, the expression profiles of PD in blood were compared, showing that 181 differentially expressed genes （DEG） exhibit a similar expression trend both in patients and in normal controls.展开更多
Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPor...Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPortal databases to analyze the expression and mutation of TOP2αand its co-expressed genes in HCC tissues.GO function and KEGG pathway enrichment of TOP2αand its co-expressed genes were identified.The TIMER database was used to analyze infiltration levels of immune cells in HCC.The impacts of TOP2αand its co-expression genes and the infiltrated immune cells on the survival of HCC patients were assayed by Kaplan-Meier plotter analysis.Results TOP2αand its co-expression genes were highly expressed in HCC(P<0.001)and detrimental to overall survival of HCC patients(P<0.001).TOP2αand its co-expression genes were mainly involved in cell mitosis and proliferation,and cell cycle pathway(ID:hsa04110,P=0.001945).TOP2αand its co-expression genes were mutated in HCC and the mutations were significantly detrimental to overall survival(P=0.0247)and disease-free survival(P=0.0265)of HCC patients.High TOP2αexpression was positively correlated with the infiltration of B cell(r=0.459,P<0.01),CD8^(+)T cell(r=0.312,P<0.01),CD4^(+)T cell(r=0.370,P<0.01),macrophage(r=0.459,P<0.01),neutrophil(r=0.405,P<0.01),and dendritic cell(r=0.473,P<0.01)in HCC.The CD8^(+)T cell infiltration significantly prolonged the 3-and 5-year survival of HCC patients(all P<0.05),and CD4^(+)T cell infiltration significantly shortened the 3-,5-,and 10-year survival of HCC patients(all P<0.05).Conclusion TOP2αmay be an oncogene,which was associated with poor prognosis of HCC patients and could be used as a biomarker for the prognostic prediction of HCC.展开更多
The expression of angiopoietin(ANGPT)1,ANGPT2,vascular endothelial growth factor(VEGF)A,VEGFB,VEGFC,VEGFD,and placental growth factor(PGF)is significantly higher in tumor tissues than in normal tissues in both unpaire...The expression of angiopoietin(ANGPT)1,ANGPT2,vascular endothelial growth factor(VEGF)A,VEGFB,VEGFC,VEGFD,and placental growth factor(PGF)is significantly higher in tumor tissues than in normal tissues in both unpaired and paired hepatocellular carcinoma(HCC)samples.ANGPT2,VEGFB,VEGFC,and PGF are primarily involved in regulating the activation of the epithelialmesenchymal transition pathway;ANGPT1 is primarily involved in regulating the activation of the RAS/mitogen-activated protein kinase and receptor tyrosine kinase(RTK)pathways;VEGFA is engaged in regulating the RTK activation pathway;and VEGFD is mainly involved in regulating the activation of the tuberous sclerosis protein/mammalian target of rapamycin pathway.There is a significant difference in overall survival between HCC patients with high and low expression of ANGPT2,PGF,VEGFA,and VEGFD.Disease free survival(DFS)is significantly shorter in HCC patients with high ANGPT2,PGF,and VEGFA expression than in those with low ANGPT2,PGF,and VEGFA expression.展开更多
[Objectives]The purpose was to investigate the function and mechanism of exsA gene in type III secretion system of Vibrio alginolyticus.[Methods]The full length of exsA was cloned using molecular biology techniques to...[Objectives]The purpose was to investigate the function and mechanism of exsA gene in type III secretion system of Vibrio alginolyticus.[Methods]The full length of exsA was cloned using molecular biology techniques to analyze its biological information.Fluorescence quantitative PCR technology was used to analyze the expression of exsA after different media stress.[Results]The exsA gene contains an open reading frame(ORF)of 861 bp,encoding 286 amino acids.The physico-chemical analysis shows that the molecular structural formula is C1442H2267N393O441S12,the theoretical molecular weight is 32.549 kD,the theoretical pI value is 6.0,and the protein is non-hydrophilic and unstable.The gene does not contain a transmembrane region,and there is no obvious signal peptide.The prediction result of protein subcellular localization shows that the protein is inside the cell.The deduced amino acid sequence and constructed phylogenetic tree show that V.alginolyticus has a close relationship with Vibrio antiquarius.The qPCR results show that the expression level of exsA in different media is different,highest in TSB medium containing bile salts,followed by DMEM medium,and lowest in ordinary TSB medium.[Conclusions]The gene sequence,molecular structure and isoelectric point of exsA,as well as its expression in three different media were obtained.展开更多
Mast cells are the main effector cells in IgE-associated allergic disorders,and we have reported that mucosal mast cells(MMCs)play a more important role in the development of food allergy(FA).IgE with antigen or calci...Mast cells are the main effector cells in IgE-associated allergic disorders,and we have reported that mucosal mast cells(MMCs)play a more important role in the development of food allergy(FA).IgE with antigen or calcium ionophore stimulation can lead to the activation of MMCs via a calcium-dependent pathway.The purpose of the present study was to identify gene signatures with IgE/antigen(dinitrophenyl-bovine serum albumin,DNP-BSA)or calcium ionophore(A23187)on the activation of MMCs.Differentially expressed genes between the two types of samples were identified with microarray analysis.Gene ontology functional and pathway enrichment analyses of differentially expressed genes were performed using the database for annotation,visualization,and integrated discovery software.The results showed that IgE/antigen and A23187 could induce degranulation,increase vacuoles,and elevate the cytosolic calcium concentration in MMCs.Furthermore,GeneChip analysis showed that the same 134 mRNAs were altered with IgE/DNP-BSA and A23187,suggesting that DNP-BSA/IgE and A23187 affect the same signal pathway partly in degranulation.KEGG analysis showed that the data were enriched in NF-κB,TNF,MAPK,transcription factor activity,DNA binding,and nucleic acid binding,suggesting that activation of MMCs is a complex process.The results provide new insights on MMCs activation.展开更多
In this study, Va 1686 gene was cloned from Vibrio alginolyticus . The total length of the gene is 1 164 bp, and it could encode 387 amino acids. The physicochemical properties, protein structure, genetic evolutionary...In this study, Va 1686 gene was cloned from Vibrio alginolyticus . The total length of the gene is 1 164 bp, and it could encode 387 amino acids. The physicochemical properties, protein structure, genetic evolutionary relationship and antigenic characteristics of the effect protein Va1686 of V. alginolyticus HY9901 type Ⅲ secretion system were studied and analyzed by bioinformatics methods and tools. The results showed that Va1686 is a stable hydrophilic and acidic protein without a transmembrane region and a signal peptide, and secondary structure to α-helix. The evolutionary analysis showed that V. alginolyticus HY9901 and V. harveyi were clustered together, which indicated that the genetic relationship between the two species was the closest. Va1686 contains a Fic superfamily conserved domain associated with cell division. Bioinformatics analysis showed that the B-cell preponderant epitopes of Va1686 might be localized in the regions of 48-49, 82-85, 125-126, 150-153, 185-186, 236-237 and so on. The 3D structure model of Va1686 subunit was simulated by SWISS-MODEL software and it was found that the vopS of V. parahaemolyticus was similar and the similarity was 89.46%. In this study, the feasibility of Va1686 as a common antigen of Vibrio was verified from the perspective of bioinformatics, which laid the foundation for the next step in vaccine development.展开更多
BACKGROUND Post-traumatic stress disorder(PTSD)is a serious stress-related disorder.AIM To identify the key genes and pathways to uncover the potential mechanisms of PTSD using bioinformatics methods.METHODS Gene expr...BACKGROUND Post-traumatic stress disorder(PTSD)is a serious stress-related disorder.AIM To identify the key genes and pathways to uncover the potential mechanisms of PTSD using bioinformatics methods.METHODS Gene expression profiles were obtained from the Gene Expression Omnibus database.The differentially expressed genes(DEGs)were identified by using GEO2R.Gene functional annotation and pathway enrichment were then conducted.The gene-pathway network was constructed with Cytoscape software.Quantitative real-time polymerase chain reaction(qRT-PCR)analysis was applied for validation,and text mining by Coremine Medical was used to confirm the connections among genes and pathways.RESULTS We identified 973 DEGs including 358 upregulated genes and 615 downregulated genes in PTSD.A group of centrality hub genes and significantly enriched pathways(MAPK,Ras,and ErbB signaling pathways)were identified by using gene functional assignment and enrichment analyses.Six genes(KRAS,EGFR,NFKB1,FGF12,PRKCA,and RAF1)were selected to validate using qRT-PCR.The results of text mining further confirmed the correlation among hub genes and the enriched pathways.It indicated that these altered genes displayed functional roles in PTSD via these pathways,which might serve as key signatures in the pathogenesis of PTSD.CONCLUSION The current study identified a panel of candidate genes and important pathways,which might help us deepen our understanding of the underlying mechanism of PTSD at the molecular level.However,further studies are warranted to discover the critical regulatory mechanism of these genes via relevant pathways in PTSD.展开更多
[Objectives]To clone and analyze the TpiA gene of Vibrio alginolyticus HY9901.[Methods]According to the TpiA gene sequence of V.alginolyticus,a pair of specific primers was designed,and its full length was amplified b...[Objectives]To clone and analyze the TpiA gene of Vibrio alginolyticus HY9901.[Methods]According to the TpiA gene sequence of V.alginolyticus,a pair of specific primers was designed,and its full length was amplified by PCR.[Results]The full length of TpiA gene is 771 bp,encoding 256 amino acid residues in total,and the NCBI accession number is OM906798.According to the deduced amino acid sequence,its molecular weight was predicted to be about 26.97548 kDa,and its isoelectric point was 4.78.The amino acid sequence of the N-terminal signal peptide structure was predicted,and it was found that there was no obvious signal peptide cleavage site,no signal peptide,and no transmembrane region;the amino acid sequence contained 3 N-glycosylation sites,4 protein kinase C phosphorylation sites,2 casein kinase II phosphorylation sites,6 N-myristoylation sites,7 microbody C-terminal target signal site,and 1 triose phosphate isomerase active site.The prediction results of protein subcellular localization showed that TpiA may be located in mitochondria or cytoplasm,with probability of 39.1%and 34.8%,respectively.The amino acid sequence of the TpiA gene of V.alginolyticus shared 98.83%-99.61%homology with other Vibrio species,and it was clustered into the same subfamily with Vibrio parahaemolyticus and had a close relationship.In the secondary structure prediction,the proportions ofα-helix,random coil and extended chain were 44.53%,41.41%and 14.06%,respectively,and the similarity of its tertiary structure model to template 1aw1.1.A was 85.16%.[Conclusions]This study is intended to provide a basis for further research on the role of TpiA gene in the type III secretion system and related research on antibiotic resistance.展开更多
Colorectal cancer(CRC)is one of the most deadly cancers in the world with few reliable biomarkers that have been selected into clinical guidelines for prognosis of CRC patients.In this study,mRNA microarray datasets G...Colorectal cancer(CRC)is one of the most deadly cancers in the world with few reliable biomarkers that have been selected into clinical guidelines for prognosis of CRC patients.In this study,mRNA microarray datasets GSE113513,GSE21510,GSE44076,and GSE32323 were obtained from the Gene Expression Omnibus(GEO)and analyzed with bioinformatics to identify hub genes in CRC development.Differentially expressed genes(DEGs)were analyzed using the GEO2 R tool.Gene ontology(GO)and KEGG analyses were performed through the DAVID database.STRING database and Cytoscape software were used to construct a protein-protein interaction(PPI)network and identify key modules and hub genes.Survival analyses of the DEGs were performed on GEPIA database.The Connectivity Map database was used to screen potential drugs.A total of 865 DEGs were identified,including 374 upregulated and 491 downregulated genes.These DEGs were mainly associated with metabolic pathways,pathways in cancer,cell cycle and so on.The PPI network was identified with 863 nodes and 5817 edges.Survival analysis revealed that HMMR,PAICS,ETFDH,and SCG2 were significantly associated with overall survival of CRC patients.And blebbistatin and sulconazole were identified as candidate drugs.In conclusion,our study found four hub genes involved in CRC,which may provide novel potential biomarkers for CRC prognosis,and two potential candidate drugs for CRC.展开更多
We designed this study to identify potential key protein interaction networks,genes,and correlated pathways in dilated cardiomyopathy(DCM)via bioinformatics methods.We selected the GSE3586 microarray dataset,consistin...We designed this study to identify potential key protein interaction networks,genes,and correlated pathways in dilated cardiomyopathy(DCM)via bioinformatics methods.We selected the GSE3586 microarray dataset,consisting of 15 dilated cardiomyopathic heart biopsy samples and 13 nonfailing heart biopsy samples.Initially,the GSE3586 dataset was downloaded and was analyzed with the limma package to identify differentially expressed genes(DEGs).A total of 172 DEGs consisting of 162 upregulated genes and ten downregulated genes in DCM were selected by the criterion of adjusted P values less than 0.01 and the log2-fold change of 0.6 or greater.Gene Ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis were performed to view the biological processes,cellular components,molecular function,and KEGG pathways of the DEGs.Next,protein-protein interactions were constructed,and the hub protein modules were identifi ed.Then we selected the key genes DLD,UQCRC2,DLAT,SUCLA2,ATP5A1,PRDX3,FH,SDHD,and NDUFV1,which are involved in a wide range of biological activities,such as the citrate cycle,oxidation-reduction processes and cellular respiration,and energy derivation by oxidation of organic compounds in mitochondria.Finally,we found that currently there are no related gene-targeting drugs after exploring the predicted interactions between key genes and drugs,and transcription factors.In conclusion,our study provides greater understanding of the pathogenesis and underlying molecular mechanisms in DCM.This contributes to the exploration of potential gene therapy targets.展开更多
Cytokinin plays a very important role in plants growth and development,and CRE1 has been identified as a cytokinin receptor.However,the biological function of CRE1 in cotton remains unclear.In this paper,GhCRE1 gene w...Cytokinin plays a very important role in plants growth and development,and CRE1 has been identified as a cytokinin receptor.However,the biological function of CRE1 in cotton remains unclear.In this paper,GhCRE1 gene was cloned and its sequence was analyzed by bioinformatics.The results revealed that GhCRE1 had 11 exons and 10 introns,and its molecular weight,theoretical isoelectric point(pI)and number of amino acids differed from those of the homologous gene in Theobroma cacao and Arabidopsis thaliana,with three different protein domains.15 unidentified proteins were found in potential interaction with CRE1 protein and 2 phosphorylation sites on CRE1 protein sequence were predicted by mutiple bioinformatics websites.Additionally,8 cis-acting regulatory elements were detected on CRE1 promoter sequence,and found related to light signal and hormone.These results were conducive to unfolding the function of GhCRE1 in upland cotton.展开更多
BACKGROUND Gastric cancer(GC)is one of the most common cancers and has a poor prognosis.Treatment of GC has remained unchanged over the past few years.AIM To investigate the potential therapeutic targets and related r...BACKGROUND Gastric cancer(GC)is one of the most common cancers and has a poor prognosis.Treatment of GC has remained unchanged over the past few years.AIM To investigate the potential therapeutic targets and related regulatory biomarkers of GC.METHODS We obtained the public GC transcriptome sequencing dataset from the Gene Expression Omnibus database.The datasets contained 348 GC tissues and 141 healthy tissues.In total,251 differentially expressed genes(DEGs)were identified,including 187 down-regulated genes and 64 up-regulated genes.The DEGs’enriched functions and pathways include Progesterone-mediated oocyte maturation,cell cycle,and oocyte meiosis,Hepatitis B,and the Hippo signaling pathway.Survival analysis showed that BUB1,MAD2L1,CCNA2,CCNB1,and BIRC5 may be associated with regulation of the cell cycle phase mitotic spindle checkpoint pathway.We selected 26 regulated genes with the aid of the protein-protein interaction network analyzed by Molecular Complex Detection.RESULTS We focused on three critical genes,which were highly expressed in GC,but negatively related to patient survival.Furthermore,we found that knockdown of Yu K et al.Biochemical analysis in GC WJCC https://www.wjgnet.com 5024 July 26,2023 Volume 11 Issue 21 BIRC5,TRIP13 or UBE2C significantly inhibited cell proliferation and induced cell apoptosis.In addition,knockdown of BIRC5,TRIP13 or UBE2C increased cellular sensitivity to cisplatin.CONCLUSION Our study identified significantly upregulated genes in GC with a poor prognosis using integrated bioinformatics methods.展开更多
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 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.
文摘Human tongue cancer （TC） is an aggressive malignancy with a very poor prognosis. There is an urgent need to elucidate the underlying molecular mechanisms involved in TC progression, mRNA expression profiles play a vital role in the exploration of cancer-related genes. Therefore, the purpose of our study was to identify the progression associated candidate genes of TC by bioinformatics analysis. Five microarray datasets of TC samples were downloaded from the Gene Expression Onmibus （GEO） database and the data of 133 TC patients were screened from The Cancer Genome Atlas （TCGA） head and neck squamous cell carcinoma （HNSC） database. The integrated analysis of five microarray datasets and the RNA sequencing data of TC samples in TCGA-HNSC was performed to obtain 1023 overlapping differentially expressed genes （DEGs） in TC and adjacent normal tissue （ANT） samples. Next, Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway analysis was conducted to enrich the significant pathways of the 1023 DEGs and PI3K- Akt signaling pathway （P=0.011） was selected to be the candidate pathway. A total of 23 DEGs with ｜log2 fold change （FC）｜ ≥1.0 in phosphatidylinositol 3-kinase-serine/threonine kinase （PI3K-Akt） signaling pathway were subjected to survival analysis of 125 eligible TC samples in TCGA database, indicating increased integrin-α3 gene （ITGA3） expression was significantly associated with poorer prognosis. Taken together, our study suggested ITGA3 may facilitate the development of TC via activating PI3K-Akt signaling pathway.
基金supported by the National Natural Science Foundation of China,No.81771355the Natural Science Foundation of Chongqing Science and Technology Bureau,Nos.CSTC2015jcyjA10096,cstc2021jcyj-msxmX0262(all to ZL)。
文摘Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway.
基金supported by the National Natural Science Foundation of China(81101302,31270185)SKLID Development Grant(2014,SKLID201)
文摘Parkinson＇s disease （PD） is a typical degenerative disease, which is characterized by the most obvious symptoms of movement dysfunction, including shaking, rigidity, slowness of movement and difficulty in walking and gait. This disease can not be clearly identified through laboratory tests at present, thus application of high-throughput technique in studying the expression profiles of PD helps to find the genetic markers for its early diagnosis. Studies on expression profiles of neurodegenerative diseases have revealed the novel genes and pathways involved in the progress of illness. In this study, the expression profiles of PD in blood were compared, showing that 181 differentially expressed genes （DEG） exhibit a similar expression trend both in patients and in normal controls.
基金This work was partially supported by the Key Project of Natural Science Research of Education Department of Anhui Province(No.KJ2019A0338)Industry-University Cooperation Project of the Ministry of Education(No.202101160001).
文摘Objective To investigate the expression of topoisomeraseⅡα(TOP2α)in hepatocellular carcinoma(HCC)and its role in predicting prognosis of HCC patients.Methods We used HCC-related datasets in UALCAN,HCCDB,and cBioPortal databases to analyze the expression and mutation of TOP2αand its co-expressed genes in HCC tissues.GO function and KEGG pathway enrichment of TOP2αand its co-expressed genes were identified.The TIMER database was used to analyze infiltration levels of immune cells in HCC.The impacts of TOP2αand its co-expression genes and the infiltrated immune cells on the survival of HCC patients were assayed by Kaplan-Meier plotter analysis.Results TOP2αand its co-expression genes were highly expressed in HCC(P<0.001)and detrimental to overall survival of HCC patients(P<0.001).TOP2αand its co-expression genes were mainly involved in cell mitosis and proliferation,and cell cycle pathway(ID:hsa04110,P=0.001945).TOP2αand its co-expression genes were mutated in HCC and the mutations were significantly detrimental to overall survival(P=0.0247)and disease-free survival(P=0.0265)of HCC patients.High TOP2αexpression was positively correlated with the infiltration of B cell(r=0.459,P<0.01),CD8^(+)T cell(r=0.312,P<0.01),CD4^(+)T cell(r=0.370,P<0.01),macrophage(r=0.459,P<0.01),neutrophil(r=0.405,P<0.01),and dendritic cell(r=0.473,P<0.01)in HCC.The CD8^(+)T cell infiltration significantly prolonged the 3-and 5-year survival of HCC patients(all P<0.05),and CD4^(+)T cell infiltration significantly shortened the 3-,5-,and 10-year survival of HCC patients(all P<0.05).Conclusion TOP2αmay be an oncogene,which was associated with poor prognosis of HCC patients and could be used as a biomarker for the prognostic prediction of HCC.
基金Supported by the Special Plan for Condition Construction of Gansu Provincial Scientific Research Institutes,No.20JR10RA432.
文摘The expression of angiopoietin(ANGPT)1,ANGPT2,vascular endothelial growth factor(VEGF)A,VEGFB,VEGFC,VEGFD,and placental growth factor(PGF)is significantly higher in tumor tissues than in normal tissues in both unpaired and paired hepatocellular carcinoma(HCC)samples.ANGPT2,VEGFB,VEGFC,and PGF are primarily involved in regulating the activation of the epithelialmesenchymal transition pathway;ANGPT1 is primarily involved in regulating the activation of the RAS/mitogen-activated protein kinase and receptor tyrosine kinase(RTK)pathways;VEGFA is engaged in regulating the RTK activation pathway;and VEGFD is mainly involved in regulating the activation of the tuberous sclerosis protein/mammalian target of rapamycin pathway.There is a significant difference in overall survival between HCC patients with high and low expression of ANGPT2,PGF,VEGFA,and VEGFD.Disease free survival(DFS)is significantly shorter in HCC patients with high ANGPT2,PGF,and VEGFA expression than in those with low ANGPT2,PGF,and VEGFA expression.
基金National Natural Science Foundation of China(32073015).
文摘[Objectives]The purpose was to investigate the function and mechanism of exsA gene in type III secretion system of Vibrio alginolyticus.[Methods]The full length of exsA was cloned using molecular biology techniques to analyze its biological information.Fluorescence quantitative PCR technology was used to analyze the expression of exsA after different media stress.[Results]The exsA gene contains an open reading frame(ORF)of 861 bp,encoding 286 amino acids.The physico-chemical analysis shows that the molecular structural formula is C1442H2267N393O441S12,the theoretical molecular weight is 32.549 kD,the theoretical pI value is 6.0,and the protein is non-hydrophilic and unstable.The gene does not contain a transmembrane region,and there is no obvious signal peptide.The prediction result of protein subcellular localization shows that the protein is inside the cell.The deduced amino acid sequence and constructed phylogenetic tree show that V.alginolyticus has a close relationship with Vibrio antiquarius.The qPCR results show that the expression level of exsA in different media is different,highest in TSB medium containing bile salts,followed by DMEM medium,and lowest in ordinary TSB medium.[Conclusions]The gene sequence,molecular structure and isoelectric point of exsA,as well as its expression in three different media were obtained.
基金This work was supported by the“Xinlin Young Talent Program”(A1-U1820502040237)from Shanghai University of Traditional Chinese Medicine“Sasakawa Scientific Research Grant”(23-401)from the Japan Science Society.
文摘Mast cells are the main effector cells in IgE-associated allergic disorders,and we have reported that mucosal mast cells(MMCs)play a more important role in the development of food allergy(FA).IgE with antigen or calcium ionophore stimulation can lead to the activation of MMCs via a calcium-dependent pathway.The purpose of the present study was to identify gene signatures with IgE/antigen(dinitrophenyl-bovine serum albumin,DNP-BSA)or calcium ionophore(A23187)on the activation of MMCs.Differentially expressed genes between the two types of samples were identified with microarray analysis.Gene ontology functional and pathway enrichment analyses of differentially expressed genes were performed using the database for annotation,visualization,and integrated discovery software.The results showed that IgE/antigen and A23187 could induce degranulation,increase vacuoles,and elevate the cytosolic calcium concentration in MMCs.Furthermore,GeneChip analysis showed that the same 134 mRNAs were altered with IgE/DNP-BSA and A23187,suggesting that DNP-BSA/IgE and A23187 affect the same signal pathway partly in degranulation.KEGG analysis showed that the data were enriched in NF-κB,TNF,MAPK,transcription factor activity,DNA binding,and nucleic acid binding,suggesting that activation of MMCs is a complex process.The results provide new insights on MMCs activation.
基金Supported by Shenzhen Science and Technology Project(JCYJ20170818111629778,JCYJ20170306161613251)National Natural Science Foundation of Guangdong Province(2017A030313174)+2 种基金Natural Science Foundation of Guangdong Ocean University(C17379)Undergraduate Innovative and Entrepreneurial Team Project(CCTD201802)Science and Technology Program of Guangdong Province(2015A020209163)
文摘In this study, Va 1686 gene was cloned from Vibrio alginolyticus . The total length of the gene is 1 164 bp, and it could encode 387 amino acids. The physicochemical properties, protein structure, genetic evolutionary relationship and antigenic characteristics of the effect protein Va1686 of V. alginolyticus HY9901 type Ⅲ secretion system were studied and analyzed by bioinformatics methods and tools. The results showed that Va1686 is a stable hydrophilic and acidic protein without a transmembrane region and a signal peptide, and secondary structure to α-helix. The evolutionary analysis showed that V. alginolyticus HY9901 and V. harveyi were clustered together, which indicated that the genetic relationship between the two species was the closest. Va1686 contains a Fic superfamily conserved domain associated with cell division. Bioinformatics analysis showed that the B-cell preponderant epitopes of Va1686 might be localized in the regions of 48-49, 82-85, 125-126, 150-153, 185-186, 236-237 and so on. The 3D structure model of Va1686 subunit was simulated by SWISS-MODEL software and it was found that the vopS of V. parahaemolyticus was similar and the similarity was 89.46%. In this study, the feasibility of Va1686 as a common antigen of Vibrio was verified from the perspective of bioinformatics, which laid the foundation for the next step in vaccine development.
基金Supported by the National Natural Science Foundation of China,No.81603529,81673982,and 81704084the Natural Science Foundation of the Jiangsu Higher Education Institutions,No.16KJB360002+3 种基金the Advantages of the Nursing Discipline Project of Jiangsu Province,No.2019YSHL005China Scholarship Council,No.201908320373the Jiangsu Government Scholarship for Overseas Studiesand the Qing Lan Project,No.014000773/2018-00376.
文摘BACKGROUND Post-traumatic stress disorder(PTSD)is a serious stress-related disorder.AIM To identify the key genes and pathways to uncover the potential mechanisms of PTSD using bioinformatics methods.METHODS Gene expression profiles were obtained from the Gene Expression Omnibus database.The differentially expressed genes(DEGs)were identified by using GEO2R.Gene functional annotation and pathway enrichment were then conducted.The gene-pathway network was constructed with Cytoscape software.Quantitative real-time polymerase chain reaction(qRT-PCR)analysis was applied for validation,and text mining by Coremine Medical was used to confirm the connections among genes and pathways.RESULTS We identified 973 DEGs including 358 upregulated genes and 615 downregulated genes in PTSD.A group of centrality hub genes and significantly enriched pathways(MAPK,Ras,and ErbB signaling pathways)were identified by using gene functional assignment and enrichment analyses.Six genes(KRAS,EGFR,NFKB1,FGF12,PRKCA,and RAF1)were selected to validate using qRT-PCR.The results of text mining further confirmed the correlation among hub genes and the enriched pathways.It indicated that these altered genes displayed functional roles in PTSD via these pathways,which might serve as key signatures in the pathogenesis of PTSD.CONCLUSION The current study identified a panel of candidate genes and important pathways,which might help us deepen our understanding of the underlying mechanism of PTSD at the molecular level.However,further studies are warranted to discover the critical regulatory mechanism of these genes via relevant pathways in PTSD.
基金Project for Outstanding Undergraduates Entering the Laboratory in Fisheries College of Guangdong Ocean UniversityNational Natural Science Foundation of China (32073015)+3 种基金Natural Science Foundation of Guangdong Province (2021A1515011078)Special Fund for Science and Technology Innovation Strategy of Guangdong Province(Scientific and Technological Innovation Cultivation of College Students)(pdjh2021b0239)Students’Platform for Innovation and Entrepreneurship Training Program of Guangdong Ocean University (CXXL2021122)Undergraduate Innovation Team Project of Guangdong Ocean University(CCTD201802)。
文摘[Objectives]To clone and analyze the TpiA gene of Vibrio alginolyticus HY9901.[Methods]According to the TpiA gene sequence of V.alginolyticus,a pair of specific primers was designed,and its full length was amplified by PCR.[Results]The full length of TpiA gene is 771 bp,encoding 256 amino acid residues in total,and the NCBI accession number is OM906798.According to the deduced amino acid sequence,its molecular weight was predicted to be about 26.97548 kDa,and its isoelectric point was 4.78.The amino acid sequence of the N-terminal signal peptide structure was predicted,and it was found that there was no obvious signal peptide cleavage site,no signal peptide,and no transmembrane region;the amino acid sequence contained 3 N-glycosylation sites,4 protein kinase C phosphorylation sites,2 casein kinase II phosphorylation sites,6 N-myristoylation sites,7 microbody C-terminal target signal site,and 1 triose phosphate isomerase active site.The prediction results of protein subcellular localization showed that TpiA may be located in mitochondria or cytoplasm,with probability of 39.1%and 34.8%,respectively.The amino acid sequence of the TpiA gene of V.alginolyticus shared 98.83%-99.61%homology with other Vibrio species,and it was clustered into the same subfamily with Vibrio parahaemolyticus and had a close relationship.In the secondary structure prediction,the proportions ofα-helix,random coil and extended chain were 44.53%,41.41%and 14.06%,respectively,and the similarity of its tertiary structure model to template 1aw1.1.A was 85.16%.[Conclusions]This study is intended to provide a basis for further research on the role of TpiA gene in the type III secretion system and related research on antibiotic resistance.
基金supported by grants from the National Natural Science Foundation of China(No.81672748 and No.81871936)。
文摘Colorectal cancer(CRC)is one of the most deadly cancers in the world with few reliable biomarkers that have been selected into clinical guidelines for prognosis of CRC patients.In this study,mRNA microarray datasets GSE113513,GSE21510,GSE44076,and GSE32323 were obtained from the Gene Expression Omnibus(GEO)and analyzed with bioinformatics to identify hub genes in CRC development.Differentially expressed genes(DEGs)were analyzed using the GEO2 R tool.Gene ontology(GO)and KEGG analyses were performed through the DAVID database.STRING database and Cytoscape software were used to construct a protein-protein interaction(PPI)network and identify key modules and hub genes.Survival analyses of the DEGs were performed on GEPIA database.The Connectivity Map database was used to screen potential drugs.A total of 865 DEGs were identified,including 374 upregulated and 491 downregulated genes.These DEGs were mainly associated with metabolic pathways,pathways in cancer,cell cycle and so on.The PPI network was identified with 863 nodes and 5817 edges.Survival analysis revealed that HMMR,PAICS,ETFDH,and SCG2 were significantly associated with overall survival of CRC patients.And blebbistatin and sulconazole were identified as candidate drugs.In conclusion,our study found four hub genes involved in CRC,which may provide novel potential biomarkers for CRC prognosis,and two potential candidate drugs for CRC.
文摘We designed this study to identify potential key protein interaction networks,genes,and correlated pathways in dilated cardiomyopathy(DCM)via bioinformatics methods.We selected the GSE3586 microarray dataset,consisting of 15 dilated cardiomyopathic heart biopsy samples and 13 nonfailing heart biopsy samples.Initially,the GSE3586 dataset was downloaded and was analyzed with the limma package to identify differentially expressed genes(DEGs).A total of 172 DEGs consisting of 162 upregulated genes and ten downregulated genes in DCM were selected by the criterion of adjusted P values less than 0.01 and the log2-fold change of 0.6 or greater.Gene Ontology functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis were performed to view the biological processes,cellular components,molecular function,and KEGG pathways of the DEGs.Next,protein-protein interactions were constructed,and the hub protein modules were identifi ed.Then we selected the key genes DLD,UQCRC2,DLAT,SUCLA2,ATP5A1,PRDX3,FH,SDHD,and NDUFV1,which are involved in a wide range of biological activities,such as the citrate cycle,oxidation-reduction processes and cellular respiration,and energy derivation by oxidation of organic compounds in mitochondria.Finally,we found that currently there are no related gene-targeting drugs after exploring the predicted interactions between key genes and drugs,and transcription factors.In conclusion,our study provides greater understanding of the pathogenesis and underlying molecular mechanisms in DCM.This contributes to the exploration of potential gene therapy targets.
文摘Cytokinin plays a very important role in plants growth and development,and CRE1 has been identified as a cytokinin receptor.However,the biological function of CRE1 in cotton remains unclear.In this paper,GhCRE1 gene was cloned and its sequence was analyzed by bioinformatics.The results revealed that GhCRE1 had 11 exons and 10 introns,and its molecular weight,theoretical isoelectric point(pI)and number of amino acids differed from those of the homologous gene in Theobroma cacao and Arabidopsis thaliana,with three different protein domains.15 unidentified proteins were found in potential interaction with CRE1 protein and 2 phosphorylation sites on CRE1 protein sequence were predicted by mutiple bioinformatics websites.Additionally,8 cis-acting regulatory elements were detected on CRE1 promoter sequence,and found related to light signal and hormone.These results were conducive to unfolding the function of GhCRE1 in upland cotton.
文摘BACKGROUND Gastric cancer(GC)is one of the most common cancers and has a poor prognosis.Treatment of GC has remained unchanged over the past few years.AIM To investigate the potential therapeutic targets and related regulatory biomarkers of GC.METHODS We obtained the public GC transcriptome sequencing dataset from the Gene Expression Omnibus database.The datasets contained 348 GC tissues and 141 healthy tissues.In total,251 differentially expressed genes(DEGs)were identified,including 187 down-regulated genes and 64 up-regulated genes.The DEGs’enriched functions and pathways include Progesterone-mediated oocyte maturation,cell cycle,and oocyte meiosis,Hepatitis B,and the Hippo signaling pathway.Survival analysis showed that BUB1,MAD2L1,CCNA2,CCNB1,and BIRC5 may be associated with regulation of the cell cycle phase mitotic spindle checkpoint pathway.We selected 26 regulated genes with the aid of the protein-protein interaction network analyzed by Molecular Complex Detection.RESULTS We focused on three critical genes,which were highly expressed in GC,but negatively related to patient survival.Furthermore,we found that knockdown of Yu K et al.Biochemical analysis in GC WJCC https://www.wjgnet.com 5024 July 26,2023 Volume 11 Issue 21 BIRC5,TRIP13 or UBE2C significantly inhibited cell proliferation and induced cell apoptosis.In addition,knockdown of BIRC5,TRIP13 or UBE2C increased cellular sensitivity to cisplatin.CONCLUSION Our study identified significantly upregulated genes in GC with a poor prognosis using integrated bioinformatics methods.
