Bioinformatical Analysis on Sequences and Functions of Peroxidase in Arabidopsis

Plant peroxidase （POD） belongs to multigene family, which not is only one of the important enzymes responsible for the removal of active oxygen radicals, but also participates in a variety of physiological and biochemical processes and plays a crucial role in the maintenance of plant growth and development. In this study, the structures and functions of proteins encoded by 73 gene of POD family in Arabidopsis were analyzed with bioinformatics method, including the number of amino acids, isoelectric point, transmemberane domains, signal peptides, secondary structures and phosphorylation sites, and the phylogenic trees with and without signal peptides were constructed by using Mega4.0 software, to investigate the structural characteristics. In addition, the structures of AtPER members were analyzed, to reveal the relationship between the structures and functions, thereby providing theoretical basis for the research of plant oxidative stress resistance.

Identification of Prognostic Related Hub Genes in Clear-Cell Renal Cell Carcinoma via Bioinformatical Analysis

Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma(ccRCC)via bioinformatics analysis.Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were available from the Gene Expression Omnibus database:GSE12606,GSE36895 and GSE66272.The differentially expressed genes were screened with GEO2R and J Venn online tools.Functional annotation including Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)was applied to identify the possible function of the hub genes involved in prognosis of ccRCC.In protein protein interaction network(PPI network),the STRING online tool was used to visualize the network of the differentially expressed genes,and the core gene was selected by MCODE App in Cytoscape software.Finally,GEPIA Survival Plot was performed to assess genes associated with worse survival.Results We totally found 648 diflerentially expressed genes,including 222 up-regulated genes and 426 down-regulated genes.PPI network showed that in 28 up-regulated genes 7(CCNE2,CDK1,CDC6,CCNB2,BUB1,TTK and PTTG1)enriched in cell cycle and 4 genes(CCNE2,CDK1,CCNB2 and RRM2)enriched in p53 signaling pathway.GEPIA Survival Plot assay revealed that ccRCC patients carrying CDK1,CCNB2,RRM2t BUB1,and PTTG1 had a worse survival.GEPIA Box Plot showed that BUB1,CCNB2,PTTG1,and RRM2 were over expressed in the ccRCC tissues in contrast to the normal tissues(P<O.OS).Conclusion ccRCC patients with the four up-regulated differentially expressed genes including BUB1,CCNB2,PTTG1,and RRM2 might manifest a poor prognosis.

Effects of febrile seizures in mesial temporal lobe epilepsy with hippocampal sclerosis on gene expression using bioinformatical analysis

Background:To investigate the effect of long-term febrile convulsions on gene expression in mesial temporal lobe epilepsy with hippocampal sclerosis(MTLE-HS)and explore the molecular mechanism of MTLE-HS.Methods:Microarray data of MTLE-HS were obtained from the Gene Expression Omnibus database.Differentially expressed genes(DEGs)between MTLE-HS with and without febrile seizure history were screened by the GEO2R software.Pathway enrichment and gene ontology of the DEGs were analyzed using the DAVID online database and FunRich software.Protein–protein interaction(PPI)networks among DEGs were constructed using the STRING database and analyzed by Cytoscape.Results:A total of 515 DEGs were identified in MTLE-HS samples with a febrile seizure history compared to MTLEHS samples without febrile seizure,including 25 down-regulated and 490 up-regulated genes.These DEGs were expressed mostly in plasma membrane and synaptic vesicles.The major molecular functions of those genes were voltage-gated ion channel activity,extracellular ligand-gated ion channel activity and calcium ion binding.The DEGs were mainly involved in biological pathways of cell communication signal transduction and transport.Five genes(SNAP25,SLC32A1,SYN1,GRIN1,and GRIA1)were significantly expressed in the MTLE-HS with prolonged febrile seizures.Conclusion:The pathogenesis of MTLE-HS involves multiple genes,and prolonged febrile seizures could cause differential expression of genes.Thus,investigations of those genes may provide a new perspective into the mechanism of MTLE-HS.

Glucocorticoids Inducing Vascular Repair Disorders under Hypoxia via Inhibiting Cell Migration and Autocrine/paracrine:Bioinformatical Analysis Combined with Cytological Experiment

The exact molecular and cytological mechanism of how glucocorticoids induce vascular repair disorders in glucocorticoid-induced avascular necrosis of the femoral head is still unclear.We used bioinformatical tools for data mining and detected the biological behavior of endothelial cells(ECs)under hypoxia conditions and high dose dexamethasone to reveal the mechanisms above.Six differential expression mi RNAs(DE-miRNAs)were filtered from Gene Expression Omnibus(GEO)database GSE60093 which contained ECs treated with high dose glucocorticoid and control samples.Enrichment and PPI network analyses of the DE-miRNAs target genes showed the most remarkable pathway was HIF-1 signaling pathway and high dose glucocorticoid as a negative regulator of cell differentiation,energy metabolism,migration and cytokines secretion.Glucocorticoids also reduced the activity of autocrine/paracrine via limiting ion channels and transmembrane transporter process.In cytological experiment,HUVECs were divided into four groups:hypoxia group(H),hypoxia+dexamethasone group(HD),dexamethasone group(D),the normal group(N).Cell activity detection and Live/Dead dyeing showed cell activity and the number of live cells in Group H was higher than the other three groups at 24 h after intervention,while cell activity,number and proportion of live cells in HD group were worst.Cytoskeleton staining showed HD group met cytoskeleton form disorders.The scratch assay showed cell migration ability of Group H was strongest while cell migration ability of the HD group was worst.MIF expression in HD group showed a trend of bimodal,the peak of VEGF-A secretion lagged behind the MIF’s.Expression of MIF and VEGF-A in the HD group were low.High dose dexamethasone suppressed the active response of ECs to hypoxia stimulation via directly inhibiting the expression of MIF and interdicting autocrine/paracrine mechanism.We infered that the treatment with high dose glucocorticoid would inhibit neo-angiogenesis under hypoxia followed by aggravating hypoxia/ischemia and osteonecrosis.

Screening biomarkers for spinal cord injury using weighted gene co-expression network analysis and machine learning

Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).

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.

Data driven analysis reveals prognostic genes and immunological targets in human sepsis-associated acute kidney injury

BACKGROUND:The molecular mechanism of sepsis-associated acute kidney injury(SA-AKI)is unclear.We analyzed co-differentially expressed genes(co-DEGs)to elucidate the underlying mechanism and intervention targets of SA-AKI.METHODS:The microarray datasets GSE65682,GSE30718,and GSE174220 were downloaded from the Gene Expression Omnibus(GEO)database.We identified the co-DEGs and constructed a gene co-expression network to screen the hub genes.We analyzed immune correlations and disease correlations and performed functional annotation of the hub genes.We also performed single-cell and microenvironment analyses and investigated the enrichment pathways and the main transcription factors.Finally,we conducted a correlation analysis to evaluate the role of the hub genes.RESULTS:Interleukin 32(IL32)was identified as the hub gene in SA-AKI,and the main enriched signaling pathways were associated with hemopoiesis,cellular response to cytokine stimulus,inflammatory response,and regulation of kidney development.Additionally,IL32 was significantly associated with mortality in SA-AKI patients.Monocytes,macrophages,T cells,and NK cells were closely related to IL32 and were involved in the immune microenvironment in SA-AKI patients.IL32 expression increased significantly in the kidney of septic mouse.Toll-like receptor 2(TLR2)was significantly and negatively correlated with IL32.CONCLUSION:IL32 is the key gene involved in SA-AKI and is significantly associated with prognosis.TLR2 and relevant immune cells are closely related to key genes.

Identification and Validation of SLC9A2 as A Potential Tumor Suppressor in Colorectal Cancer:Integrating Bioinformatics Analysis with Experimental Confirmation

Objective To uncover the mechanisms underlying the development of colorectal cancer(CRC),we applied bioinformatic analyses to identify key genes and experimentally validated their possible roles in CRC onset and progression.Methods We performed Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis on differentially expressed genes(DEGs),constructed a protein-protein interaction(PPI)network to find the top 10 hub genes,and analyzed their expression in colon adenocarcinoma(COAD)and rectum adenocarcinoma(READ).We also studied the correlation between these genes and immune cell infiltration and prognosis and validated the expression of SLC9A2 in CRC tissues and cell lines using qRT-PCR and Western blotting.Functional experiments were conducted in vitro to investigate the effects of SLC9A2 on tumor growth and metastasis.Results We found 130 DEGs,with 45 up-regulated and 85 down-regulated in CRC.GO analysis indicated that these DEGs were primarily enriched in functions related to the regulation of cellular pH,zymogen granules,and transmembrane transporter activity.KEGG pathway analysis revealed that the DEGs played pivotal roles in pancreatic secretion,rheumatoid arthritis,and the IL-17 signaling pathway.We identified 10 hub genes:CXCL1,SLC26A3,CXCL2,MMP7,MMP1,SLC9A2,SLC4A4,CLCA1,CLCA4,and ZG16.GO enrichment analysis showed that these hub genes were predominantly involved in the positive regulation of transcription.Gene expression analysis revealed that CXCL1,CXCL2,MMP1,and MMP7 were highly expressed in CRC,whereas CLCA1,CLCA4,SLC4A4,SLC9A2,SLC26A3,and ZG16 were expressed at lower levels.Survival analysis revealed that 5 key genes were significantly associated with the prognosis of CRC.Both mRNA and protein expression levels of SLC9A2 were markedly reduced in CRC tissues and cell lines.Importantly,SLC9A2 overexpression in SW480 cells led to a notable inhibition of cell proliferation,migration,and invasion.Western blotting analysis revealed that the expression levels of phosphorylated ERK(p-ERK)and phosphorylated JNK(p-JNK)proteins were significantly increased,whereas there were no significant changes in the expression levels of ERK and JNK following SLC9A2 overexpression.Correlation analysis indicated a potential link between SLC9A2 expression and the MAPK signaling pathway.Conclusion Our study suggests that SLC9A2 acts as a tumor suppressor through the MAPK pathway and could be a potential target for CRC diagnosis and therapy.

RNA-sequencing expression profile and functional analysis of retinal pigment epithelium in atrophic age-related macular degeneration

The retinal pigment epithelium(RPE)is fundamental to sustaining retinal homeostasis.RPE abnormality leads to visual defects and blindness,including age-related macular degeneration(AMD).Although breakthroughs have been made in the treatment of neovascular AMD,effective intervention for atrophic AMD is largely absent.The adequate knowledge of RPE pathology is hindered by a lack of the patients'RPE datasets,especially at the single-cell resolution.In the current study,we delved into a large-scale single-cell resource of AMD donors,in which RPE cells were occupied in a substantial proportion.Bulk RNA-seq datasets of atrophic AMD were integrated to extract molecular characteristics of RPE in the pathogenesis of atrophic AMD.Both in vivo and in vitro models revealed that carboxypeptidase X,M14 family member 2(CPXM2),was specifically expressed in the RPE cells of atrophic AMD,which might be induced by oxidative stress and involved in the epithelial-mesenchymal transition of RPE cells.Additionally,silencing of CPXM2 inhibited the mesenchymal phenotype of RPE cells in an oxidative stress cell model.Thus,our results demonstrated that CPXM2 played a crucial role in regulating atrophic AMD and might serve as a potential therapeutic target for atrophic AMD.

Cloning and Bioinformatics Analysis of CsFK111 Gene from Cucumbers

At the early stage,the transcriptome sequencing technique was used to detect the differentially expressed gene CsFK111 between vine cucumber and dwarf cucumber D0462.The gene was cloned,and bioinformatics software tools were used to analyze and predict the gene family and this gene.There were 30 members of the cucumber F-box gene family.The coding region of the cucumber CsFK111 gene was full-length 1314 bp,which encoded 437 amino acids and was predicted to be located in the nucleus.The protein encoded by this gene was a non-transmembrane protein,and the prediction of the secondary structure showed thatβ-lamellar structure and irregular crimp were dominant.A comparison of the phylogenetic tree showed that it was closest to cantaloupe and belonged to the same branch.The results provided a basis for future study on the regulation mechanism of the CsFK111 gene on cucumber dwarfing and also laid a foundation for further study of FBK family proteins.

Molecular Cloning and Bioinformatics Analysis of msrA Gene from Vibrio alginolyticus Strain HY9901

[Objectives]This study was conducted to understand the structure and function of MsrA protein.[Methods]With Vibrio alginolyticus HY9901 as the object of study,primers were designed to amplify the full-length gene of msrA,and its bioinformatics analysis was carried out.[Results]The full length of msrA gene was 639 bp,encoding 212 amino acids,and its theoretical molecular weight was about 23729.60 Da.The protein had a stable structure,and it was hydrophobic overall.The structure of signal peptides at the N terminal of the amino acid sequence was predicted,and it was found that there was no signal peptide cleavage site and no transmembrane region.The amino acid sequence of MsrA contained multiple signal binding sites.Protein subcellular localization showed that MsrA protein was most likely located in the cytoplasm.Homology analysis showed that MsrA of V.alginolyticus had high homology with other Vibrio species,and the highest homology with V.alginolyticus.In the prediction of functional domains,MsrA had the function of methionine sulfoxide reduction.In secondary structure prediction,MsrA contained random coils at a proportion of 46.70%,which was the highest.The similarity between the tertiary structure model of MsrA and template Q87SW6.1.A was 89.15%.PTM analysis showed that MsrA protein had many PTM modification sites such as phosphorylation and glycosylation sites.[Conclusions]This study provides some reference value for further study on the role of MsrA in bacterial antioxidant stress.

Molecular Cloning of sodB Gene from Vibrio alginolyticus HY9901 and Its Bioinformatics Analysis

Vibrio alginolyticus is a zoonotic bacterium.A pair of specific primers was designed using the sodB gene sequence of Vibrio alginolyticus HY9901 in order to amplify the full length of the gene by PCR.The results indicated that the total length of the sodB gene was 585 bp and that it could encode 194 amino acids.The predicted amino acid sequence derivation indicated that the molecular weight of the protein was approximately 21.56 kDa,with an isoelectric point of 4.95.Upon prediction of the N-terminal signal peptide structure of the protein,no significant signal peptide cleavage site was observed,indicating that the protein lacked both a signal peptide and a transmembrane region.The amino acid sequence contained an N-glycosylation site,a casein kinase II phosphorylation site,a microsomal C-terminal target signal site,and a manganese and iron superoxide dismutase signal site.The probability of intracytoplasmic localization of the SodB protein was 56.5%,which was analyzed according to the subcellular localization of the protein.The amino acid sequence of the sodB gene of V.alginolyticus exhibited 98%-100%homology to other Vibrio species,clustering into the same subfamily with V.parahaem,indicating a relatively close relationship between them.In the prediction of protein structure,the proportions ofα-helix,random coil,β-sheet,and extended strand were 48.45%,30.41%,5.67%,and 15.46%,respectively.The similarity to template 1dt0.1.A reached 71.58%.A PTM site analysis revealed the presence of phosphorylation,glycosylation,ubiquitination,sumoylation,acetylation,and methylation modification sites,as well as the absence of lactylation modification sites.

Molecular Cloning and Bioinformatics Analysis of cyaA Gene of Vibrio alginolyticus Strain HY9901

[Objectives]This study was conducted to explore the biological functions of cyaA gene of Vibrio alginolyticus.[Methods]With DNA of V.alginolyticus HY 9901 as a template,primers were designed according to the sequence of cyaA gene,and the cyaA gene was amplified by PCR.Bioinformatics analysis was performed.[Results]The cyaA gene of V.alginolyticus HY9901 was 2529 bp in size,and encoded 842 amino acids.The molecular structure of CyaA protein was C_(4358)H_(6745)N_(1171)O_(1286)S_(35).Its theoretical molecular weight was 97.24167 kDa and the theoretical pI value was 5.56.It had no signal peptide and transmembrane domain.CyaA protein had three N-terminal glycosylation sites,one cAMP and cGMP-dependent protein kinase phosphorylation site,nine protein kinase C phosphorylation sites,nine casein kinase II phosphorylation sites,one tyrosine kinase phosphorylation site,seven N-terminal myristoylation sites,one pentenyl binding site and ten microbody C-terminal localization signal sites.Subcellular localization prediction showed that CyaA protein was mainly located in the nucleus and cytoplasm.Through multi-sequence alignment and phylogenetic tree construction,it was concluded that V.alginolyticus had high CyaA homology with other Vibrio species.cyaA of V.alginolyticus was clustered with Vibrio fluminensis and Vibrio marinisedimini,and they were closely related.The secondary structure of CyaA protein consisted ofα-helixes(43.11%),random coils(38.00%)and extended strands(14.49%).In protein network interaction,it was found that the proteins adjacent to CyaA protein were Crp-2,CpdA,Crr,PtsG-2,ANP67209.1,Crp-1,PykF,Pyk,RelA and Ndk.[Conclusions]This study provides a new idea for formulating strategies for the prevention and control of vibriosis.

Bioinformatics Analysis of the Association between Ewing’s Sarcoma and Tuberculosis Comorbidity

Objective To screen and analyze the differentially expressed genes of Ewing’s sarcoma (ES) and Tuberculosis (TB) by bioinformatics. Methods GEO gene chip public database in NCBI was used for data retrieval, and chip data GSE17674 and GSE57736 were selected as analysis objects. The R language limma toolkit was used to screen DEmRNAs, and the data were standardized, and the common differentially expressed genes were screened by Venn diagram. The GO function and KEGG pathway enrichment of common differentially expressed genes were analyzed by using the R cluster Profiler package. String database was selected for PPI analysis, and the results were imported into Cytoscape software to obtain PPI interaction map, core module and Hub gene. Import Hub gene into BioGPS database. Results: A total of 3 Hub genes were screened, namely CD3D, LCK, KLRB1;The genes were imported into BioGPS database to obtain the specific genes. Conclusion The selected differential genes and related signaling pathways are helpful to understand the molecular mechanism of ES and TB, and can provide the basis for early diagnosis of ES complicated with TB. It also provides new ideas for clinical treatment and diagnosis.

Bioinformatics Analysis of the Association between Osteosarcoma and Ewing Sarcoma Comorbidity

Purpose: This paper aims to explore the genetic correlation between osteosarcoma (OS) and Ewing’s sarcoma (EWS) by bioinformatics, and to find the common differentially expressed genes between the two in order to provide reference for early clinical diagnosis. Method: The GEO gene chip public database in NCBI was used for data retrieval, and the chip data GSE17674 and GSE16088 were selected as the analysis objects. DEmRNAs were screened by R language limma kit, and the data were standardized. The common differentially expressed genes were screened by Venn diagram. The R language clusterProfiler package was used to perform GO function and KEGG pathway enrichment analysis on the common differentially expressed genes. The String database was used for PPI analysis, and the results were imported into Cytoscape software to obtain PPI interaction map, core module and Hub gene. Result: In this study, 1482 differentially expressed genes were screened from GSE17674 and 933 differentially expressed genes were screened from GSE16088. The Wayne diagram analyzed 335 common differentially expressed genes. GO/KEGG analysis suggested that the above common differentially expressed genes were mainly involved in cell cycle, ECM receptor interaction, sister chromatid separation, ossification, etc. Five core genes NCAPG, MAD2L1, CDK1, RRM2 and RFC4 were screened from the PPI network. The five genes were highly expressed in sarcoma. Conclusion: The five core common differentially expressed genes and related signaling pathways screened by bioinformatics analysis are helpful to understand the molecular mechanism of OS and ES pathogenesis, and are related to the prognosis of patients. They may become potential biomarkers for future research on OS comorbid ES, provide a basis for early diagnosis of OS combined with ES, and provide new ideas for clinical drug treatment research.

Bioinformatics Analysis of the Biological Properties of Ewing Sarcoma

Purpose: Bioinformatics-based approach to screen and analyze differentially expressed genes associated with the biological characteristics of Ewing sarcoma. Means: The GSE17674 dataset was selected for analysis, obtained by data retrieval based on the GEO public database. The R language limma toolkit was used to screen DEmRNAs. After the data were normalized, the Metascape online analysis software and the R language clusterProfiler package were used to analyze the GO function and KEGG pathway enrichment of DEmRNAs lines, respectively. The string database was selected for PPI analysis, and the results were imported into Cytoscape software to derive the core modules and predicted core genes. The genes selected above were analyzed for tissue localization specificity. Results: Through the analysis of GSE17674, differentially expressed genes were screened out, and GO and KEGG analyses were performed on the differentially expressed genes. The GO functional enrichment analysis was mainly enriched in the process of muscle system, muscle contraction, myocyte development, contractile fibers, myogenic fibers, myofibers, myofibrillar segments, actin binding, structural composition of muscle, and actin filament binding. KEGG pathway analysis showed that the core pathways associated with the development of ES were the core genes for myocardial contraction, congestive cardiomyopathy, and hypertrophic cardiomyopathy. Five Hub genes were obtained based on Cytoscape prediction. Tissue localization specificity analysis of Hub genes was performed, and a total of 2 Hub genes with tissue specificity were screened;MYH6 was specifically expressed in cardiac cells and MYL1 was specifically expressed in skeletal muscle cells. Conclusions: The differential genes screened will help to understand the molecular mechanisms underlying the highly invasive and metastasis-prone biological characteristics of ES, as well as provide new ideas for clinical drug-targeted treatment of ES.

Bioinformatics Analysis of the Relationship between Dilated Cardiomyopathy and Chronic Heart Failure

Objective: To screen and analyze the differentially expressed genes between dilated cardiomyopathy (DCM) and chronic heart failure (CHF) based on bioinformatics methods. Methods: The Gene Expression Omnibus (GEO) database was used for data retrieval, and the chip data GSE3585 was downloaded, which was the original data of DCM and normal control group. At the same time, the chip data GSE76701 was downloaded, which was the original data of CHF and control group. Differentially expressed mRNAs (DEmRNAs) were screened by R language limma package, the data were standardized, and the common differentially expressed genes were screened. GO function and KEGG pathway enrichment analysis were performed on the common differentially expressed genes. String11.0 online tool was used for data analysis to obtain differentially expressed genes, and the results were imported into Cytoscape 3.9.1 software. The results were imported into Cytoscape 3.9.1 software, and the common expression gene module was obtained by MOCDE algorithm. Nine Hub genes were obtained by 10 algorithms such as MCC. Results: A total of 248 differentially expressed genes were screened. GO analysis showed that differentially expressed genes were mainly concentrated in 9 different physiological and pathological processes. KEGG analysis showed that the main signaling pathways involved in differentially expressed genes were 2, and 9 key differentially expressed genes were predicted: NPPB, NPPA, MYH6, FRZB, ASPN, SFRP4, RPS4Y1, DDX3Y. Conclusion: This study preliminarily explored the molecular mechanism of DCM and CHF, and obtained the common differentially expressed genes of the two diseases. Further experimental studies are needed to verify the correlation between gene expression and clinicopathological features. Provide new ideas for clinical drug treatment research.

Network pharmacology and bioinformatics analysis identify potential therapeutic effects of berberine on colon cancer complicated with radiation enteritis

Objective:Patients with colon adenocarcinoma(COAD)who undergo radiation therapy develop radiation enteritis(RE).The predictive value of RE in COAD is yet to be established.Berberine,an active compound derived from the traditional Chinese medicinal plant,Coptis chinensis,has notable anti-inflammatory properties and offers protection to the intestinal mucosa.This study aimed to evaluate the possible therapeutic effect and mechanism of berberine as a treatment for COAD complicated with RE(COAD&RE).Methods:Relevant genetic features of diverse COAD&RE populations were analyzed using bioinformatics and the Cox proportional hazards regression model.The therapeutic targets of berberine were predicted using network pharmacology and molecular docking.In vivo and in vitro experiments were conducted to validate the core genes identified using molecular docking.Results:RE has a certain impact on the prognosis of COAD and berberine may play an important role in the treatment of COAD&RE.In addition,we identified five core therapeutic targets of berberine by network pharmacology and molecular docking:CCND1,MYC,AR,LEP,and CYP19A1.In vivo experiments showed that berberine increased short-term survival rate,body weight,and intestinal epithelial cell recovery in mice after radiation.In an in vitro study,berberine promoted the proliferation of human intestinal epithelial cells and enhanced the radiosensitivity of HT29 cells after radiation,and the relative mRNA expression levels of CCND1 and MYC closely correlated with these effects.Conclusions:This study predicted the potential therapeutic effects of berberine on COAD&RE and verified the relevant mechanisms,which may provide insights and suggestions for the clinical treatment of COAD&RE.

A Bioinformatics Analysis of FAM3A to Identify its Potential Role as a Biomarker in Liver Hepatocellular Cancer

Liver hepatocellular cancer(LIHC)is positioned as the third cancer with the highest mortalities worldwide,and high mortalities are associated with late diagnosis and recurrence.This study advances bioinformatics analysis of FAM3A expression in LIHC to evaluate its potential as a prognostic,diagnostic and therapeutic biomarker.Bioinformatics tools such as UALCAN,GEPIA2,KM plotter,TIMER2 and cBioPortal are employed to conduct analysis.Initially,the expression analysis revealed up-regulation of FAM3A in LIHC based on various variables.Further,the study observed that FAM3A methylation regulates expression as variation in methylation level of FAM3A was assessed in LIHC.Moreover,this over-expression of FAM3A results in poor overall survival(OS)in LIHC patients.All of these proposed that FAM3A has a role in the progression and development of LIHC.While examined association of FAM3A expression and infiltration level of CD8+T cells in LIHC patients using TIMER2 revealed that FAM3A has a positive correlation with purity in LIHC that highlights the molecular landscape.Analysis of genetic alteration revealed minute role of FAM3A in LIHC still provides valuable insight.Overall,our findings reveal that FAM3A has potential as diagnostic,therapeutic and prognostic biomarkers in LIHC.

Cloning and Bioinformatic Analysis of Cinnamoyl-CoA Reductase Gene (CCR) from Pennisetum purpureum

[Objective] The aim was to clone the cDNA and DNA sequences of the CCR （Cinnamoyl-CoA reductase） gene which involves in lignin biosynthesis, from Pennisetum purpureum, and to make comprehensive analysis on these sequences. [Method] CCR sequences were cloned from P. purpureum by using conventional RT-PCR and RACE （Rapid Amplification of cDNA Ends） methods; and the bioinformatic analyses of the CCR were conducted by means of NCBI, ProtParam ProtScale, TMHMM, TargetP, SignalP, Pfam20.0, Prosite, Swiss-Model, ClustalW2, DNAman, DNAstar and MEGA5. [Result] The cloned PpCCR （P. purpureum CCR） cDNA sequence was 1 316 bp, including a 1 110 bp ORF and 206 bp 3’-UTR. The cloned DNA sequence from PpCCR was 6 133 bp in full-length, containing five exons and four introns. Bioinformatic analysis indicated that PpCCR encoded a polypeptide of 369 amino acids, the secondary structure of which was primarily composed of random coil and α-helix, belonging to NAD-dependent epimerase/dehydratase family, and its co-factor binding sites and substrate binding sites were highly conserved. [Conclusion] DNA and cDNA sequences of CCR gene were obtained from P. purpureum, which had the typical characteristics of other homologous genes. The obtained bioinformatic data provided theoretical references for the further analysis of CCR and better application of P. purpureum in the future.