Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice

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.

Identification of functional genes regulating gastric cancer progression using integrated bioinformatics analysis

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.

Identification of survival-associated biomarkers based on three datasets by bioinformatics analysis in gastric cancer

BACKGROUND Gastric cancer(GC)is one of the most common malignant tumors with poor prognosis in terms of advanced stage.However,the survival-associated biomarkers for GC remains unclear.AIM To investigate the potential biomarkers of the prognosis of patients with GC,so as to provide new methods and strategies for the treatment of GC.METHODS RNA sequencing data from The Cancer Genome Atlas(TCGA)database of STAD tumors,and microarray data from Gene Expression Omnibus(GEO)database(GSE19826,GSE79973 and GSE29998)were obtained.The differentially expressed genes(DEGs)between GC patients and health people were picked out using R software(x644.1.3).The intersections were underwent between the above obtained co-expression of differential genes(co-DEGs)and the DEGs of GC from Gene Expression Profiling Interactive Analysis database,and Gene Ontology(GO)analysis,Kyoto Encyclopedia of Gene and Genome(KEGG)pathway analysis,Gene Set Enrichment Analysis(GSEA),Protein-protein Interaction(PPI)analysis and Kaplan-Meier Plotter survival analysis were performed on these DEGs.Using Immunohistochemistry(IHC)database of Human Protein Atlas(HPA),we verified the candidate Hub genes.RESULTS With DEGs analysis,there were 334 co-DEGs,including 133 up-regulated genes and 201 down-regulated genes.GO enrichment analysis showed that the co-DEGs were involved in biological process,cell composition and molecular function pathways.KEGG enrichment analysis suggested the co-DEGs pathways were mainly enriched in ECM-receptor interaction,protein digestion and absorption pathways,etc.GSEA pathway analysis showed that co-DEGs mainly concentrated in cell cycle progression,mitotic cell cycle and cell cycle pathways,etc.PPI analysis showed 84 nodes and 654 edges for the co-DEGs.The survival analysis illustrated 11 Hub genes with notable significance for prognosis of patients were screened.Furtherly,using IHC database of HPA,we confirmed the above candidate Hub genes,and 10 Hub genes that associated with prognosis of GC were identified,namely BGN,CEP55,COL1A2,COL4A1,FZD2,MAOA,PDGFRB,SPARC,TIMP1 and VCAN.CONCLUSION The 10 Hub genes may be the potential biomarkers for predicting the prognosis of GC,which can provide new strategies and methods for the diagnosis and treatment of GC.

Amplification and Bioinformatics Analysis of h-ns Gene of Vibrio alginolyticus

[Objectives]To amplify the h-ns gene of Vibrio alginolyticus and analyze it by bioinformatics.[Methods]According to the h-ns gene sequence of V.alginolyticus HY9901,a pair of specific primers were designed and amplified by PCR.[Results]The h-ns gene was 408 bp in length and 135 amino acids were encoded.The predicted theoretical protein molecular weight was about 14.98 kD,and the isoelectric point was 4.99.Protein subcellular localization,SignalP 5.0,TMHMM Server 2.0 and SoftBerry-Psite predictions showed that H-NS was located outside the cell membrane,and the protein was unstable and hydrophobic.There was no signal peptide cleavage site,no transmembrane region and no KEGG metabolic pathway.The amino acid sequence contained three phosphorylation sites,one N-terminal myristoylation site and three microsomal C-terminal target signal sites.Using MEGA 5.0,H-NS phylogenetic tree was constructed by ortho-connection method.The results showed that H-NS of V.alginolyticus was closer to H-NS of Vibrio diabolicus.Using SWISS-MODEL,the three-dimensional structure model of H-NS subunit was simulated,which was similar to the crystal structure of Salmonella typhimurium H-NS1-83.[Conclusions]This study lays a foundation for exploring the regulation mechanism of V.alginolyticus H-NS protein on bacterial virulence in the future.

Cloning and Bioinformatics Analysis of vscB Gene of T3SS Chaperone of Vibrio alginolyticus

[Objectives]To clone and analyze the vscB gene of Vibrio alginolyticus HY9901 by bioinformatics.[Methods]A pair of specific primers were designed according to the vscB gene sequence of Vibrio alginolyticus HY9901.The full length of the primers was cloned by PCR and analyzed by bioinformatics.[Results]The vscB gene was 429 bp long,encoding 142 amino acids,with a theoretical molecular weight of 16.4 kDa and a pI value of 5.48.Amino acid sequence analysis of VscB showed that VscB was not a secretory protein,without signal peptide and transmembrane region,and there were protein kinase C phosphorylation site and casein kinase II phosphorylation site in the sequence.Homologous comparison of amino acid sequences showed that VscB of V.alginolyticus had the highest protein similarity with Vibrio Parahaemolyticus,reaching 91%.Phylogenetic tree analysis showed that the corresponding proteins of V.alginolyticus VscB,Vibrio Parahaemolyticus and Vibrio diabolicus were clustered in the same subfamily.Functional domain analysis showed that it had CesT family domain.Tertiary structure prediction showed that there were 3α-helices and 5β-turns in VscB protein.[Conclusions]This study provided a theoretical basis for further study on the function of chaperone of V.alginolyticus.

Cloing and Bioinformatics Analysis of ndk Gene from Vibrio alginolyticus

[Objectives]The paper was to clone and analyze bioinformatics of ndk gene from Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the ndk gene sequence of V.alginolyticus HY9901.The full length of ndk gene was amplified by PCR and bioinformatics analysis was performed.MEGA 5.0 software was used to construct NDK phylogenetic tree by neighbor-joining method.SWISS-MODEL program was used to obtain the three-dimensional structural model of single subunit from NDK protein.[Results]The ndk gene,molecular structural formula C702H1094N192O214S7,was 426 bp in total,encoding 141 amino acids,with the theoretical molecular weight of 15.87199 kD and the theoretical pI value of 5.13.The prediction results of protein subcellular localization,SignalP 5.0,TMHMM Server 2.0 and SoftBerry-Psite showed that NDK mainly existed in the cytoplasm,and the protein was unstable and hydrophobic.There was neither signal peptide cleavage site,nor transmembrane region and KEGG metabolic pathway.The amino acid sequence had two protein kinase C phosphorylation sites,a casein kinaseⅡphosphorylation site,a N-myristoylation site,three microbody C-terminal target signal sites,and a nucleoside diphosphate kinase active site.Homology analysis showed that the NDK of V.alginolyticus had high homology with that of V.diabolicus,with a similarity of 98.58%.Analysis of the structural functional domain revealed that the protein had one NDK structural functional domain.The prediction results of secondary structure showed that theα-helix,random coil,β-sheet and extended strand accounted for 53.19%,28.37%,7.09%and 11.35%,respectively.Analysis of NDK protein via STRING database demonstrated that the proteins interacting with NDK protein were NrdA,NrdB,GmK,CmK,TmK,PyrG,PyrH,RelA,FolE and SpoT.[Conclusions]The study plays a positive role in the prevention and control of vibriosis and the improvement of the current aquaculture environment.

Amplification and Bioinformatics Analysis of vscN Gene from Vibrio alginolyticus

[Objectives]The paper was to clone and analyze bioinformatics of vscN gene from Vibrio alginolyticus.[Methods]A pair of specific primers was designed based on the vscN gene sequence of V.alginolyticus HY9901.The full length of vscN gene was amplified by PCR and bioinformatics analysis was performed.[Results]The vscN gene was 1323 bp in total,encoding 440 amino acids,with the theoretical molecular weight of 47.86 kD and the theoretical pI value of 5.89.The online prediction showed that there was no signal peptide and no transmembrane region in VscN.The amino acid sequence had 10 N-myristoylation sites,8 phosphorylation sites(2 protein kinase C phosphorylation sites,6 casein kinase II phosphorylation sites),1 amidation site,11 microbody C-terminal target signal sites,1 ATP/GTP binding site motif A(P ring),and 1 ATPaseαandβsubunit specific site.Homology analysis showed that the VscN protein of V.alginolyticus had high homology with that of V.antiquarius,with a similarity of 95.14%.Phylogenetic tree analysis showed that the VscN of V.alginolyticus was clustered into the same subgroup as that of V.diabolicus and V.antiquarius.Functional domain analysis of VscN protein showed that it had Pfam and AAA domains,and involved in the regulation of bacterial virulence.The three-dimensional structure model of VscN simulated by SWISS-MODEL software was similar to the structure of flagellate-specific ATPase FliH-FliI complex.[Conclusions]The results lay a foundation for further study on the regulatory mechanism of VscN protein on bacterial virulence.

Bioinformatics Analysis Raises Candidate Genes in Blood for Early Screening of Parkinson's Disease

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.

Molecular Cloning,Bioinformatics Analysis and Transcriptional Expression of Virulence-related Gene(exsA)of Vibrio alginolyticus

[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.

Bioinformatics Analysis and Identification of Potential Genes Associated with Pathogenesis and Prognosis of Gastric Cancer

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.

Identification of key pathways and gene expression in the activation of mast cells via calcium flux using bioinformatics analysis

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.

Molecular Cloning and Bioinformatics Analysis of TypeⅢSecretion System Effector Protein Va1686 Gene of Vibrio alginolyticus

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.

TopoisomeraseⅡαGene as a Marker for Prognostic Prediction of Hepatocellular Carcinoma:A Bioinformatics Analysis

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.

Prognostic role of expression of angiogenesis markers in hepatocellular carcinoma:A bioinformatics analysis

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.

Identification of ITGA3 as an Oncogene in Human Tongue Cancer via Integrated Bioinformatics Analysis

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.

Identification of four novel prognosis biomarkers and potential therapeutic drugs for human colorectal cancer by bioinformatics analysis

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.

Identification of key genes involved in post-traumatic stress disorder:Evidence from bioinformatics analysis

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.

Importance of Mitochondrial-Related Genes in Dilated Cardiomyopathy Based on Bioinformatics Analysis

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.

Molecular Cloning and Bioinformatics Analysis of araC Gene of Vibrio alginolyticus

[Objective]To clone araC gene of Vibrio alginolyticus HY9901 strain,and analyze bioinformatics.[Methods]the whole genome sequence of Vibrio alginolyticus on GenBank was used to design specific primers.According to the principle of PCR amplification sequence,the target gene araC was amplified,and then the sequence was further analyzed by bioinformatics method to establish the phylogenetic tree of araC gene and its corresponding subunit three-dimensional structure model.[Results]Sequence analysis revealed araC gene is 711 bp and encodes a putative protein of 236 amino acids.The predicted molecular mass of AraC was 26.92 ku.Using Signal P 4.0 and TMHMM Server 2.0 software for analysis,it was predicted that the AraC protein did not contain a signal peptide or a transmembranous region.The AraC protein had two cAMP and cGMP dependent protein kinase phosphorylation site,five protein kinase C phosphorylation sites,three casein kinase II phosphorylation sites,one prenyl group binding site(CAAX box)and five microbodies C-terminal targeting signal.The predicted results of protein subcellular localization showed that AraC was located in the mitochondria,nucleus and cytoplasm.Its protein is unstable and hydrophilic.The AraC protein is a transcriptional regulatory protein which belongs to HTH_18 superfamily.According to the prediction,secondary structure:a-helix(Alpha helix)accounted for 52.12%,random coil(31.78%),extended strand(11.02%),b-fold(Beta turn)accounted for 5.08%.V.alginolyticus,Vibrio parahaemolyticus and Vibrio palustris were clustered together,which implies that the genetic relationship between these three species was the closest.

Cloning and Bioinformatics Analysis of pepck Gene in Vibrio alginolyticus

[Objectives]To clone the pepck gene of Vibrio alginolyticus strain HY9901 and analyze its sequence by bioinformatics.[Methods]According to the complete gene sequence of V.alginolyticus on GenBank,specific primers were designed to amplify the target gene pepck by PCR.The sequence of the pepck gene was analyzed using bioinformatics.The phylogenic tree of pepck gene and the corresponding single-subunit three-dimensional structure were constructed.[Results]The pepck gene of V.alginolyticus strain HY9901 has a full length of 1629 bp,with theoretical molecular weight of 60.12 kD.The prediction results show that there is no signal peptide or transmembrane region at the N-terminus of the sequence,the amino acid sequence contains 11 phosphorylation sites of casein kinase II.The prediction results of protein subcellular localization indicate that PEPEK protein is localized in the cytoplasm.The protein is stable and hydrophobic.The tertiary structure of the PEPCK protein of V.alginolyticus is similar to that of Vibrio parahaemolyticus.It is predicted that PEPCK has a major functional domain PEPCK_ATP.In the secondary structure,alpha helix,random coil,and extended strand accounted for 21.96%,52.03%and 26.01%,respectively.The PEPCK homology between V.alginolyticus and Vibrio diabolicus is as high as 99%.[Conclusions]This study lays the foundation for further understanding the function of pepck gene in V.alginolyticus.