Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca...Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca vulgaris in the Chinese population.This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing.Methods:High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform.The transcriptomes were analyzed using bioinformatics and the differentially expressed genes(DEGs)were verified by immunohistochemistry.Verruca vulgaris exhibited a unique molecular signature.Results:In total,1,643 DEGs were identified in verruca vulgaris compared to normal skin.The functions of the DEGs were studies by Gene Ontology(GO)enrichment,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis,DEGs Reactome analysis,disease annotation function,and STRING protein-protein interaction(PPI)network analysis.The results revealed 595 GO terms associated with the cell cycle,signal transduction,immune system,signaling molecules,and interaction.The Reactome analysis revealed enrichment in reversible hydration of carbon dioxide and BMP signaling,while the disease annotation function revealed that the enriched DEGs are involved in keratosis disorders.The STRING PPI network showed that the edges with the highest density mainly included the 2′-5′oligoadenylate synthase(OAS)family-related proteins.Furthermore,the M-code analysis found ISG15,IRF7,and OASL were scored as significant modules and their high expression compared to the control was verified by immunohistochemistry.Conclusion:These findings contribute to the genetic information of verruca vulgaris in the Chinese population,revealing that interferon-stimulated genes may play essential roles in verruca vulgaris.展开更多
Background:Tuberculosis is a leading cause of death worldwide.BCG is an effective vaccine,but not widely used in many parts of the world due to a variety of issues.Mycobacterium vaccae(M.vaccae)is another vaccine used...Background:Tuberculosis is a leading cause of death worldwide.BCG is an effective vaccine,but not widely used in many parts of the world due to a variety of issues.Mycobacterium vaccae(M.vaccae)is another vaccine used in human subjects to prevent tuberculosis.In the current study,we investigated the potential mechanisms of M.vaccae vaccination by determining differentially expressed genes in mice infected with M.tuberculosis before and after M.vaccae vaccination.Methods:Three days after exposure to M.tuberculosis H37 Rv strain(5×10~5 CFU),adult BALB/c mice randomly received either M.vaccae vaccine(22.5μg)or vehicle via intramuscular injection(n=8).Booster immunization was conducted 14 and 28 days after the primary immunization.Differentially expressed genes were identified by microarray followed by standard bioinformatics analysis.Results:M.vaccae vaccination provided protection against M.tuberculosis infection(most prominent in the lungs).We identified 2,326 upregulated and 2,221 downregulated genes in vaccinated mice.These changes could be mapped to a total of 123 signaling pathways(68 upregulated and 55 downregulated).Further analysis pinpointed to the MyD88-dependent TLR signaling pathway and PI3 K-Akt signaling pathway as most likely to be functional.Conclusions:M.vaccae vaccine provided good protection in mice against M.tuberculosis infection,via a highly complex set of molecular changes.Our findings may provide clue to guide development of more effective vaccine against tuberculosis.展开更多
One of the impediments in the genetic improvement of cotton fiber is the paucity of information about genes associated with fiber development.Availability of chromosome arm substitution line CS-
The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular an...The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular and biological process alterations that occur after SCI for therapy development.The differences between the rostral and caudal regions around an SCI lesion have received little attention.Here,we analyzed the differentially expressed genes between rostral and caudal sites after injury to determine the biological processes in these two segments after SCI.We identified a set of differentially expressed genes,including Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1,between rostral and caudal regions at different time points following SCI.Functional enrichment analysis indicated that these genes were involved in response to mechanical stimulus,blood vessel development,and brain development.We then chose Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1 for quantitative real-time PCR and Fn1 for immunostaining validation.Our results indicate alterations in different biological events enriched in the rostral and caudal lesion areas,providing new insights into the pathology of SCI.展开更多
In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequ...In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequencing and bioinformatics analysis were done. The results show that 34.27 Gb clean data were got by transcriptome sequencing. There are 261 differentially expressed genes among Y_1_vs_G_1, Y_2_vs_G_2 and Y_3_vs_G_3. The pathways contenting most differentially expressed genes are plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway, photosynthesis pathway, starch and sucrose metabolism pathway. 9-cis-epoxycarotenoid dioxygenase(Cla002942), alcohol dehydrogenase(Cla004992), photosystem Ⅰ reaction center subunit Ⅲ, chloroplastic(precursor)(Cla009181), long-chain acyl coenzyme A synthetase(Cla017341), threonine dehydratase biosynthetic(Cla018352) candidates genes were screened out.展开更多
A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/...A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/16-h dark) and long-day(16-h light/8-h dark) conditions.A total of 148 clones were sequenced,representing 76 unique ESTs which corresponded to about 20% of 738 clones from the cDNA library and showed a significant up-regulation of at least three fold verified by dot blot hybridization.The putative functions of ESTs were predicted by Blastn and Blastx.The 43 differentially expressed genes identified by subtractions were classified according to their putative functions generated by Blast analysis.Genetic functional analysis indicated that putative proteins encoded by these genes were related to diverse functions during organism development,which include biological regulation pathways such as transcription,signal transduction and programmed cell death,protein,nucleic acid and carbohydrate macromolecule degradation,the cell wall modification,primary and secondary metabolism and stress response.Two soybean transcription factors enhanced in SD conditions,GAMYB-binding protein and DNA binding protein RAV cDNAs that may be involved in SD soybean photoperiod response,had been isolated using 5'-and 3'-rapid amplification of cDNA ends(RACE)(Genbank Accession numbers DQ112540 and DQ147914).展开更多
Objective:This study aimed to determine the presence of statistically significant relationships between these factors using bioinformatics analysis to identify overlapping differentially expressed genes(DEGs).Methods:...Objective:This study aimed to determine the presence of statistically significant relationships between these factors using bioinformatics analysis to identify overlapping differentially expressed genes(DEGs).Methods:The expression microarray data of GSE19665,GSE65194 and GSE12654 were obtained by GEO2R.Then,the overlapping DEGs of hepatocellular carcinoma(HCC),breast cancer(BC)and depression were analyzed by Gene Ontology,Kyoto Encyclopedia of Genes and Genomes and protein-protein interaction networks.Finally,the protein-protein interaction network was constructed by STRING and DEGs were sorted by Cytoscape.Results:The results indicated that multiple genes,including RNA-binding protein with multiple splicing,GATA binding protein 6,angiotensin II receptor type 1,ETS variant 6,TNF receptor superfamily member 17,aurora kinase A,integrin subunit alpha 6 and fibrinogen-like protein 2 might be common factors related to HCC,BC and depression.Conclusion:These results indicate that the genetic profile of HCC,BC and depression,may yield valuable insights for our understanding of the underlying mechanisms underlying synergistic genetic regulation and may provide novel ideas for developing homeopathic therapies based on bioinformatics data.展开更多
Purpose:To identify the potential target genes of blast lung injury(BLI)for the diagnosis and treatment.Methods:This is an experimental study.The BLI models in rats and goats were established by conducting a fuel-air ...Purpose:To identify the potential target genes of blast lung injury(BLI)for the diagnosis and treatment.Methods:This is an experimental study.The BLI models in rats and goats were established by conducting a fuel-air explosive power test in an unobstructed environment,which was subsequently validated through hematoxylin-eosin staining.Transcriptome sequencing was performed on lung tissues from both goats and rats.Differentially expressed genes were identified using the criteria ofq≤0.05 and|log2 fold change|≥1.Following that,enrichment analyses were conducted for gene ontology and the Kyoto Encyclopedia of Genes and Genomes pathways.The potential target genes were further confirmed through quantitative real-time polymerase chain reaction and enzyme linked immunosorbent assay.Results:Observations through microscopy unveiled the presence of reddish edema fluid,erythrocytes,and instances of focal or patchy bleeding within the alveolar cavity.Transcriptome sequencing analysis identified a total of 83 differentially expressed genes in both rats and goats.Notably,49 genes exhibited a consistent expression pattern,with 38 genes displaying up-regulation and 11 genes demonstrating down-regulation.Enrichment analysis highlighted the potential involvement of the interleukin-17 signaling pathway and vascular smooth muscle contraction pathway in the underlying mechanism of BLI.Furthermore,the experimental findings in both goats and rats demonstrated a strong association between BLI and several key genes,including anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4,which exhibited up-regulation.Conclusions:Anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4 hold potential as target genes for the prognosis,diagnosis,and treatment of BLI.展开更多
BACKGROUND Gastric cancer(GC)has a high mortality rate worldwide.Despite significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains unfavorable.AIM To identify important candi...BACKGROUND Gastric cancer(GC)has a high mortality rate worldwide.Despite significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains unfavorable.AIM To identify important candidate genes related to the development of GC and iden-tify potential pathogenic mechanisms through comprehensive bioinformatics analysis.METHODS The Gene Expression Omnibus database was used to obtain the GSE183136 dataset,which includes a total of 135 GC samples.The limma package in R software was employed to identify differentially expressed genes(DEGs).Thereafter,enrichment analyses of Gene Ontology(GO)terms and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were performed for the gene modules using the clusterProfile package in R software.The protein-protein interaction(PPI)networks of target genes were constructed using STRING and visualized by Cytoscape software.The common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn Diagram.The expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier curves.Moreover,real-time quantitative polymerase chain reaction(RT-qPCR)and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase(GPT)in GC and normal immortalized cell lines.In addition,cell viability,cell cycle distribution,migration and invasion were evaluated by cell counting kit-8,flow cytometry and transwell assays.Furthermore,we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital,Dingli Clinical College of Wenzhou Medical University,The Second Affiliated Hospital of Shanghai University between January 2017 to December 2020.The tumor and adjacent normal samples were collected from the patients to determine the potential association between the expression level of GPT and the clinical as well as pathological features of GC patients.RESULTS We selected 19214 genes from the GSE183136 dataset,among which there were 250 downregulated genes and 401 upregulated genes in the tumor samples of stage III-IV in comparison to those in tumor samples of stage I-II with a P-value<0.05.In addition,GO and KEGG results revealed that the various upregulated DEGs were mainly enriched in plasma membrane and neuroactive ligand-receptor interaction,whereas the downregulated DEGs were primarily enriched in cytosol and pancreatic secretion,vascular smooth muscle contraction and biosynthesis of the different cofactors.Furthermore,PPI networks were constructed based on the various upregulated and downregulated genes,and there were a total 15 upregulated and 10 downregulated hub genes.After a comprehensive analysis,several hub genes,including runt-related transcription factor 2(RUNX2),salmonella pathogenicity island 1(SPI1),lysyl oxidase(LOX),fibrillin 1(FBN1)and GPT,displayed prognostic values.Interestingly,it was observed that GPT was downregulated in GC cells and its upregulation could suppress the malignant phenotypes of GC cells.Furthermore,the expression level of GPT was found to be associated with age,lymph node metastasis,pathological staging and distant metastasis(P<0.05).CONCLUSION RUNX2,SPI1,LOX,FBN1 and GPT were identified key hub genes in GC by bioinformatics analysis.GPT was significantly associated with the prognosis of GC,and its upregulation can effectively inhibit the proliferative,migrative and invasive capabilities of GC cells.展开更多
The term “microgravity” is used to describe the “weightlessness” or “zero-g” circumstances that can only be found in space beyond earth’s atmosphere. Rhodobacter sphaeroides is a gram-negative purple phototroph...The term “microgravity” is used to describe the “weightlessness” or “zero-g” circumstances that can only be found in space beyond earth’s atmosphere. Rhodobacter sphaeroides is a gram-negative purple phototroph, used as a model organism for this study due to its genomic complexity and metabolic versatility. Its genome has been completely sequenced, and profiles of the differential gene expression under aerobic, semi-aerobic, and photosynthetic conditions were examined. In this study, we hypothesized that R. sphaeroides will show altered growth characteristics, morphological properties, and gene expression patterns when grown under simulated microgravity. To test that, we measured the optical density and colony-forming units of cell cultures grown under both microgravity and normal gravity conditions. Differences in the cell morphology were observed using scanning electron microscopy (SEM) images by measuring the length and the surface area of the cells under both conditions. Furthermore, we also identified homologous genes of R. spheroides using the differential gene expression study of Acidovorax under microgravity in our laboratory. Growth kinetics results showed that R. sphaeroides cells grown under microgravity experience a shorter log phase and early stationary phase compared to the cells growing under normal gravity conditions. The length and surface area of the cells under microgravity were significantly higher confirming that bacterial cells experience altered morphological features when grown under microgravity conditions. Differentially expressed homologous gene analysis indicated that genes coding for several COG and GO functions, such as metabolism, signal-transduction, transcription, translation, chemotaxis, and cell motility are differentially expressed to adapt and survive microgravity.展开更多
Detection of the vitality of wounds is essential in forensic practice.The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin.In obtained high quality sequencing...Detection of the vitality of wounds is essential in forensic practice.The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin.In obtained high quality sequencing reads,the reads were mapped onto a reference transcriptome (Mus_musculus.GRCm38.83).The results revealed that there were 659 upregulated and 996 down-regulated differentially expressed genes (DEGs) in contused mouse skin.The DEGs were further analyzed using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases.Genes from different functional categories and signalling pathways were enriched,including the immune system process,immune response,defense response,cytokine-cytokine receptor interaction,complement and coagulation cascades and chemokine signalling pathway.Expression patterns of 11 DEGs were verified by RT-qPCR in mice skins.In addition,alterations of five DEGs were also analyzed in postmortem human wound samples.The results were in concordance with the results of RNA-seq.These findings suggest that RNA-seq is a powerful tool to reveal DEGs as potential markers for vital reaction in terms of forensic practices.展开更多
Turbot Scophthalmus maximus is an important mariculture fish species with high economic value.However,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture ...Turbot Scophthalmus maximus is an important mariculture fish species with high economic value.However,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture industry.To understand the immune response of the turbot against V.anguillarum infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after V.anguillarum infection.Differentially expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)enrichment.The gene ontology(GO)classification analysis revealed that V.anguillarum infection had the greatest effect on biological processes and cellular components.Twelve immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat map.The proteinprotein interaction(PPI)networks were constructed to analyze the immune mechanism.The results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against V.anguillarum infection.In the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most significant.Our research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against V.anguillarum infection.展开更多
BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the preval...BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the prevalence of COVID-19 is significantly higher in patients with liver cancer.However,this mechanism of action has not been clarified.Gene sets for COVID-19(GSE180226)and liver cancer(GSE87630)were obtained from the Gene Expression Omnibus database.After identifying the common differentially expressed genes(DEGs)of COVID-19 and liver cancer,functional enrichment analysis,protein-protein interaction network construction and scree-ning and analysis of hub genes were performed.Subsequently,the validation of the differential expression of hub genes in the disease was performed and the regulatory network of transcription factors and hub genes was constructed.RESULTS Of 518 common DEGs were obtained by screening for functional analysis.Fifteen hub genes including aurora kinase B,cyclin B2,cell division cycle 20,cell division cycle associated 8,nucleolar and spindle associated protein 1,etc.,were further identified from DEGs using the“cytoHubba”plugin.Functional enrichment analysis of hub genes showed that these hub genes are associated with P53 signalling pathway regulation,cell cycle and other functions,and they may serve as potential molecular markers for COVID-19 and liver cancer.Finally,we selected 10 of the hub genes for in vitro expression validation in liver cancer cells.CONCLUSION Our study reveals a common pathogenesis of liver cancer and COVID-19.These common pathways and key genes may provide new ideas for further mechanistic studies.展开更多
BACKGROUND Helicobacter pylori(H.pylori)infection is related to various extragastric diseases including type 2 diabetes mellitus(T2DM).However,the possible mechanisms connecting H.pylori infection and T2DM remain unkn...BACKGROUND Helicobacter pylori(H.pylori)infection is related to various extragastric diseases including type 2 diabetes mellitus(T2DM).However,the possible mechanisms connecting H.pylori infection and T2DM remain unknown.AIM To explore potential molecular connections between H.pylori infection and T2DM.METHODS We extracted gene expression arrays from three online datasets(GSE60427,GSE27411 and GSE115601).Differentially expressed genes(DEGs)commonly present in patients with H.pylori infection and T2DM were identified.Hub genes were validated using human gastric biopsy samples.Correlations between hub genes and immune cell infiltration,miRNAs,and transcription factors(TFs)were further analyzed.RESULTS A total of 67 DEGs were commonly presented in patients with H.pylori infection and T2DM.Five significantly upregulated hub genes,including TLR4,ITGAM,C5AR1,FCER1G,and FCGR2A,were finally identified,all of which are closely related to immune cell infiltration.The gene-miRNA analysis detected 13 miRNAs with at least two gene cross-links.TF-gene interaction networks showed that TLR4 was coregulated by 26 TFs,the largest number of TFs among the 5 hub genes.CONCLUSION We identified five hub genes that may have molecular connections between H.pylori infection and T2DM.This study provides new insights into the pathogenesis of H.pylori-induced onset of T2DM.展开更多
Background: Hypertension, also known as increased blood pressure, is a phenomenon in which blood flows in blood vessels and causes persistently higher-than-normal pressure on the vessel wall. The identification of nov...Background: Hypertension, also known as increased blood pressure, is a phenomenon in which blood flows in blood vessels and causes persistently higher-than-normal pressure on the vessel wall. The identification of novel prognostic and pathogenesis biomarkers plays a key role in the management of hypertension. Methods: The GSE7483 and GSE75815 datasets from the gene expression omnibus (GEO) database were used to identify the genes associated with hypertension that were differentially expressed genes (DEGs). The functional role of the DEGs was elucidated by gene body (GO) enrichment analysis. In addition, we performed an immune infiltration assay and GSEA on the DEGs of hypertensive patients and verified the expression of novel DEGs in the blood of hypertensive patients by RT-qPCR. Results: A total of 267 DEGs were identified from the GEO database. GO analysis revealed that these genes were associated mainly with biological processes such as fibroblast proliferation, cell structural organization, extracellular matrix organization, vasculature development regulation, and angiogenesis. We identified five possible biomarkers, Ecm1, Sparc, Sphk1, Thbsl, and Mecp2, which correlate with vascular development and angiogenesis characteristic of hypertension by bioinformatics, and explored the clinical expression levels of these genes by RT-qPCR, and found that Sparc, Sphk1, and Thbs1 showed significant up-regulation, in agreement with the results of the bioinformatics analysis. Conclusion: Our study suggested that Sparc, Sphk1 and Thbs1 may be potential novel biomarkers for the diagnosis, treatment and prognosis of hypertension and that they are involved in the regulation of vascular development and angiogenesis in hypertension.展开更多
Changes in gene expression were examined by microarray analysis during development of the eyed surface dwelling(surface fish)and blind cave-dwelling(cavefish)forms of the teleost Astyanax mexicanus De Filippi,1853.The...Changes in gene expression were examined by microarray analysis during development of the eyed surface dwelling(surface fish)and blind cave-dwelling(cavefish)forms of the teleost Astyanax mexicanus De Filippi,1853.The cross-species microarray used surface and cavefish RNA hybridized to a DNA chip prepared from a closely related species,the zebrafish Danio rerio Hamilton,1822.We identified a total of 67 differentially ex-pressed probe sets at three days post-fertilization:six upregulated and 61 downregulated in cavefish relative to surface fish.Many of these genes function either in eye development and/or maintenance,or in programmed cell death.The upregulated probe set showing the highest mean fold change was similar to the human ubiquitin specific protease 53 gene.The downregulated probe sets showing some of the highest fold changes corresponded to genes with roles in eye development,including those encoding gamma crystallins,the guanine nucleotide binding pro-teins Gnat1 and Gant2,a BarH-like homeodomain transcription factor,and rhodopsin.Downregulation of gam-ma-crystallin and rhodopsin was confirmed by in situ hybridization and immunostaining with specific antibodies.Additional downregulated genes encode molecules that inhibit or activate programmed cell death.The results suggest that cross-species microarray can be used for identifying differentially expressed genes in cavefish,that many of these genes might be involved in eye degeneration via apoptotic processes,and that more genes are downregulated than upregulated in cavefish,consistent with the predominance of morphological losses over gains during regressive evolution.展开更多
Objective:Primordial follicle assembly and the transition from primordial follicle to primary follicle are critical processes in ovarian biology.These processes determine the size of the primordial follicle pool,which...Objective:Primordial follicle assembly and the transition from primordial follicle to primary follicle are critical processes in ovarian biology.These processes determine the size of the primordial follicle pool,which may limit the reproductive lifespan of a female.When the follicle pool is depleted,reproduction ceases and females enter menopause.In this study,we aimed to explore the role of differentially expressed genes(DEGs)in the processes of primordial follicle assembly and the transformation from primordial to primary follicle.Methods:The gene chip GSE9300 was downloaded from the Gene Expression Omnibus database.DEGs between ovaries on postnatal day 0 and ovaries on postnatal day 4,as well as ovaries on postnatal day 4 and ovaries cultured for 7 days from postnatal day 0 were identified.Gene ontology(GO),pathway enrichment analysis,and protein-protein interaction network construction were performed.Results:In total,99 upregulated genes and 123 downregulated genes were identified in the process of primordial follicle assembly,and 101 upregulated genes and 98 downregulated genes were identified in the process of transformation from primordial to primary follicle.The GO analysis showed that response to estradiol was associated with two of the processes of assembly and subsequent development of primordial follicle,but the genes involved in response to estradiol between the two processes were significantly different.Furthermore,the two groups of DEGs were all associated with metabolic pathways.Conclusions:DEGs may provide new insights into the exploration of mechanisms related to primordial follicle assembly and subsequent development.展开更多
Objective:To search the the differentially expressed genes between breast cell carcinoma tissues and normal tissues by using bioinformatics technology,and the potential therapeutic drugs for breast cancer were identif...Objective:To search the the differentially expressed genes between breast cell carcinoma tissues and normal tissues by using bioinformatics technology,and the potential therapeutic drugs for breast cancer were identified,which can provide reference for clinical immune targeted therapy and drug therapy of breast cancer in the future.Methods:"Breast cancer"was searched by using Gene Expression Omnibus(GEO),and GSE79586 chip data was downloaded.The differentially expressed genes in the control group and the breast cancer model group were screened by using bio-communication technology and subjected to GO function analysis,KEGG pathway analysis,differential gene characteristic expression analysis and protein-protein interaction network(PPI)analysis,and the analysis results were further visualized.Prognosis analysis,related function prediction and immune infiltration analysis were performed using the GEPIA,GeneMANIA,and Timer2.0 databases,respectively.Finally,the compounds with potential therapeutic effects on breast cancer are identified through Connectivity Map(CMap).Western blotting and real-time PCR(RT-PCR)were used to verify the core genes and potential therapeutic agents with the highest correlation in vitro.Results:A total of 3916 differentially expressed genes including 1786 up-regulated genes and 2130 down-regulated genes were screened.GO analysis showed that the differential genes were mainly involved in the positive regulation of phosphorylation,secretory vesicles,racemase and epimerase activities.KEGG analysis showed that differential genes were involved in systemic lupus erythematosus,alcoholism,sticky spots,amoebic dysentery Ras signal pathways and other disease pathways.The characteristic expression analysis of differential genes showed that MEK inhibitors,HSP90 inhibitors and signal transduction pathway kinase inhibitors were drugs similar to the differential genes.PPI results showed that H2AFJ,TFF1,GATA3,FOXA1,and CDH1 were core genes related to breast cancer.Two core genes of H2AFJ and TFF1 with the highest correlation were further selected for GEPIA analysis.The results of the analysis showed that the mRNA expression levels of H2AFJ and TFF1 in breast cancer cells were significantly higher than those in normal tissues,and there was a significant correlation with the pathological staging,overall survival rate and disease-free survival rate of breast cancer patients.H2AFJ and TFF1 may be potential prognostic biomarkers for survival of breast cancer patients.The functions of differentially expressed H2AFJ and TFF1 are mainly related to hormone receptor binding,epithelial structure maintenance and epigenetic negative regulation of genes,chromatin tissue involved in negative regulation of transcription,etc.The results of immune infiltration showed that the expressions of H2AFJ and TFF1 had a significant correlation with the infiltration of macrophages,neutrophils,monocytes,CD4+T,CD8+T,B lymphocytes and other immune cells.CMap results showed that compounds such as Gefitinib,Alpelisib,Sorafenib,and Sunitinib had potential therapeutic effects on breast cancer.Western blot and RT-PCR results showed that H2AFJ and TFF1 were significantly overexpressed in breast cancer cells.Gefitinib significantly inhibited the expression of H2AFJ and TFF1 in breast cancer cells(P<0.05,P<0.01).Conclusion:In this study,differentially expressed genes between breast cell carcinoma tissues and normal tissues were screened out by bioinformatics means to further identify key genes and compounds with potential therapeutic effects in the onset process of breast cancer and to further verify the effectiveness of the screened drugs on breast cancer through experiments.It will provide reference for clinical research and development of new drugs against breast cancer in the future in order to develop more effective treatment options.展开更多
High Feed efficiency (FE) in growing heifers has economic importance in dairy, but remains less understood in buffaloes. Feed conversion efficiency is defined as dry matter intake (DMI) per unit body weight gain and i...High Feed efficiency (FE) in growing heifers has economic importance in dairy, but remains less understood in buffaloes. Feed conversion efficiency is defined as dry matter intake (DMI) per unit body weight gain and is determined as residual feed intake (RFI), i.e., the difference between actual and predicted feed intake to gain unit body weight during a feed trial run for 78 days under control feeding. A large variation was identified ranging between -0.42 to 0.35 in growing buffalo heifers (n = 40) of age between 11 to 15 months. An average daily weight gain (ADG) varied between 382.0 and 807.6 g/day when compared with the control-fed heifers at an organized buffalo farm. The whole blood transcriptome data obtained from the selected growing heifers from extremes of estimated high and low RFI efficiency were compared with the reference assembly generated from the transcriptome of multiparous buffaloes (n = 16) of diverse age of maturity, period of regaining post partum cyclicity and level of milk production. Differentially expressed genes (DEGs) were identified using the reference genome of Mediterranean water buffalo. GO: terms (Padj 0.05, FDR 0.05) enriched by annotated DEGs and biological pathways in gene network for RFI efficiency trait were identified. GO: terms specific to pre-transcriptional regulation of nucleus and Chromatin organization under Nucleoplasm, Energy balancing, Immunity, Cell signaling, ROS optimization, ATP generation through the Electron Transport chain and cell proliferation were determined. The study reveals the indicators targeting the actual metabolic changes and molecular functions underlying the feed utilization capacity of buffaloes. Estimated RFI efficiency revealed a large variation over heifers which may lower the DMI even up to 13.6% thus, enabling an increase in ADG up to 16% by involving efficient heifers in breeding plan. The study revealed a scope of high gain by selective breeding for FE in heifers. FE variants catalogued in the study are useful breed-specific RFI markers for future reference. The study contributes to the understanding of feed efficiency in buffaloes and its association with key interactive traits such as reproduction and growth. This knowledge can be utilized to develop more effective breeding programs.展开更多
Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identi...Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identified and described.Nonetheless,the molecular mechanism of height regulation in high-culm rice mutants has not been well studied.By using transcriptome and weighted gene co-expression network analysis(WGCNA),we identified the differentially expressed genes(DEGs)between high-culm rice mutants(MUT)and wild-type(WT)and explored the key pathways and potential candidate genes involved in PH regulation.Transcriptome analysis identified a total of 2,184 DEGs,of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage.Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction,ABC transportation,and steroid hormone biosynthesis.Among these metabolic pathways,LOC_Os05g43910 and LOC_Os01g35030 were auxin(IAA)-related genes,up-regulated in MUT and LOC_Os02g08500(LEPTO1),LOC_Os11g04720,and LOC_Os12g04500 were cytokinin(CK)-related genes,downregulated in MUT.The WGCNA identified four modules(light cyan,dark grey,grey,and pale turquoise)closely related to PH,and seven key genes were screened from these modules,of which two were up-regulated cell wallrelated genes(LOC_Os01g26174(OsWAK5),LOC_Os06g05050)in MUT,and one gibberellic acid(GA)gene(LOC_Os06g37364,OsKO2)was also up-regulated.These genes might be closely related to PH regulation.These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.展开更多
基金The National Natural Science Foundation of China(Grant No.81903227)supported our study.
文摘Introduction:Verruca vulgaris is one of the most common low-risk HPV infections and is characterized by excessive proliferation of keratinocytes.Currently,very little genetic information is available regarding verruca vulgaris in the Chinese population.This study aimed to obtain comprehensive transcript information of verruca vulgaris by RNA sequencing.Methods:High-throughput sequencing was performed on three fresh verruca vulgaris samples and adjacent normal skin on the Illumina sequencing platform.The transcriptomes were analyzed using bioinformatics and the differentially expressed genes(DEGs)were verified by immunohistochemistry.Verruca vulgaris exhibited a unique molecular signature.Results:In total,1,643 DEGs were identified in verruca vulgaris compared to normal skin.The functions of the DEGs were studies by Gene Ontology(GO)enrichment,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis,DEGs Reactome analysis,disease annotation function,and STRING protein-protein interaction(PPI)network analysis.The results revealed 595 GO terms associated with the cell cycle,signal transduction,immune system,signaling molecules,and interaction.The Reactome analysis revealed enrichment in reversible hydration of carbon dioxide and BMP signaling,while the disease annotation function revealed that the enriched DEGs are involved in keratosis disorders.The STRING PPI network showed that the edges with the highest density mainly included the 2′-5′oligoadenylate synthase(OAS)family-related proteins.Furthermore,the M-code analysis found ISG15,IRF7,and OASL were scored as significant modules and their high expression compared to the control was verified by immunohistochemistry.Conclusion:These findings contribute to the genetic information of verruca vulgaris in the Chinese population,revealing that interferon-stimulated genes may play essential roles in verruca vulgaris.
基金supported by Grants from the National Natural Science Foundation of China(81801643)the National Key Program for Infectious Disease of China(2018ZX10731301–005)+1 种基金Beijing Municipal Science&Technology Commission(Z181100001718005)the Medical Science and Technology Youth Cultivation Program of PLA(16QNP075)。
文摘Background:Tuberculosis is a leading cause of death worldwide.BCG is an effective vaccine,but not widely used in many parts of the world due to a variety of issues.Mycobacterium vaccae(M.vaccae)is another vaccine used in human subjects to prevent tuberculosis.In the current study,we investigated the potential mechanisms of M.vaccae vaccination by determining differentially expressed genes in mice infected with M.tuberculosis before and after M.vaccae vaccination.Methods:Three days after exposure to M.tuberculosis H37 Rv strain(5×10~5 CFU),adult BALB/c mice randomly received either M.vaccae vaccine(22.5μg)or vehicle via intramuscular injection(n=8).Booster immunization was conducted 14 and 28 days after the primary immunization.Differentially expressed genes were identified by microarray followed by standard bioinformatics analysis.Results:M.vaccae vaccination provided protection against M.tuberculosis infection(most prominent in the lungs).We identified 2,326 upregulated and 2,221 downregulated genes in vaccinated mice.These changes could be mapped to a total of 123 signaling pathways(68 upregulated and 55 downregulated).Further analysis pinpointed to the MyD88-dependent TLR signaling pathway and PI3 K-Akt signaling pathway as most likely to be functional.Conclusions:M.vaccae vaccine provided good protection in mice against M.tuberculosis infection,via a highly complex set of molecular changes.Our findings may provide clue to guide development of more effective vaccine against tuberculosis.
文摘One of the impediments in the genetic improvement of cotton fiber is the paucity of information about genes associated with fiber development.Availability of chromosome arm substitution line CS-
基金supported by Postgraduate Research&Practice Innovation Program of Jiangsu Province,No.KYCX-2065(to XMC).
文摘The initial mechanical damage of a spinal cord injury(SCI)triggers a progressive secondary injury cascade,which is a complicated process integrating multiple systems and cells.It is crucial to explore the molecular and biological process alterations that occur after SCI for therapy development.The differences between the rostral and caudal regions around an SCI lesion have received little attention.Here,we analyzed the differentially expressed genes between rostral and caudal sites after injury to determine the biological processes in these two segments after SCI.We identified a set of differentially expressed genes,including Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1,between rostral and caudal regions at different time points following SCI.Functional enrichment analysis indicated that these genes were involved in response to mechanical stimulus,blood vessel development,and brain development.We then chose Col3a1,Col1a1,Dcn,Fn1,Kcnk3,and Nrg1 for quantitative real-time PCR and Fn1 for immunostaining validation.Our results indicate alterations in different biological events enriched in the rostral and caudal lesion areas,providing new insights into the pathology of SCI.
基金Project(31260476)supported by the National Natural Science Foundation of China
文摘In order to screen the genes controlling watermelon rind color and luster, the experiment was carried out with yellow watermelon skin mutants as tester and green wild type watermelon as control, and transcriptome sequencing and bioinformatics analysis were done. The results show that 34.27 Gb clean data were got by transcriptome sequencing. There are 261 differentially expressed genes among Y_1_vs_G_1, Y_2_vs_G_2 and Y_3_vs_G_3. The pathways contenting most differentially expressed genes are plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway, photosynthesis pathway, starch and sucrose metabolism pathway. 9-cis-epoxycarotenoid dioxygenase(Cla002942), alcohol dehydrogenase(Cla004992), photosystem Ⅰ reaction center subunit Ⅲ, chloroplastic(precursor)(Cla009181), long-chain acyl coenzyme A synthetase(Cla017341), threonine dehydratase biosynthetic(Cla018352) candidates genes were screened out.
文摘A cDNA subtractive library enriched for dark-induced up-regulated ESTs was constructed by suppression subtractive hybridization(SSH) from leaf tissues of soybean cultivar DongNong L13 treated with short-day(8-h light/16-h dark) and long-day(16-h light/8-h dark) conditions.A total of 148 clones were sequenced,representing 76 unique ESTs which corresponded to about 20% of 738 clones from the cDNA library and showed a significant up-regulation of at least three fold verified by dot blot hybridization.The putative functions of ESTs were predicted by Blastn and Blastx.The 43 differentially expressed genes identified by subtractions were classified according to their putative functions generated by Blast analysis.Genetic functional analysis indicated that putative proteins encoded by these genes were related to diverse functions during organism development,which include biological regulation pathways such as transcription,signal transduction and programmed cell death,protein,nucleic acid and carbohydrate macromolecule degradation,the cell wall modification,primary and secondary metabolism and stress response.Two soybean transcription factors enhanced in SD conditions,GAMYB-binding protein and DNA binding protein RAV cDNAs that may be involved in SD soybean photoperiod response,had been isolated using 5'-and 3'-rapid amplification of cDNA ends(RACE)(Genbank Accession numbers DQ112540 and DQ147914).
文摘Objective:This study aimed to determine the presence of statistically significant relationships between these factors using bioinformatics analysis to identify overlapping differentially expressed genes(DEGs).Methods:The expression microarray data of GSE19665,GSE65194 and GSE12654 were obtained by GEO2R.Then,the overlapping DEGs of hepatocellular carcinoma(HCC),breast cancer(BC)and depression were analyzed by Gene Ontology,Kyoto Encyclopedia of Genes and Genomes and protein-protein interaction networks.Finally,the protein-protein interaction network was constructed by STRING and DEGs were sorted by Cytoscape.Results:The results indicated that multiple genes,including RNA-binding protein with multiple splicing,GATA binding protein 6,angiotensin II receptor type 1,ETS variant 6,TNF receptor superfamily member 17,aurora kinase A,integrin subunit alpha 6 and fibrinogen-like protein 2 might be common factors related to HCC,BC and depression.Conclusion:These results indicate that the genetic profile of HCC,BC and depression,may yield valuable insights for our understanding of the underlying mechanisms underlying synergistic genetic regulation and may provide novel ideas for developing homeopathic therapies based on bioinformatics data.
基金Natural Science Basis Research Plan in Shaanxi Province of China(Program No.2023-JC-YB-684).
文摘Purpose:To identify the potential target genes of blast lung injury(BLI)for the diagnosis and treatment.Methods:This is an experimental study.The BLI models in rats and goats were established by conducting a fuel-air explosive power test in an unobstructed environment,which was subsequently validated through hematoxylin-eosin staining.Transcriptome sequencing was performed on lung tissues from both goats and rats.Differentially expressed genes were identified using the criteria ofq≤0.05 and|log2 fold change|≥1.Following that,enrichment analyses were conducted for gene ontology and the Kyoto Encyclopedia of Genes and Genomes pathways.The potential target genes were further confirmed through quantitative real-time polymerase chain reaction and enzyme linked immunosorbent assay.Results:Observations through microscopy unveiled the presence of reddish edema fluid,erythrocytes,and instances of focal or patchy bleeding within the alveolar cavity.Transcriptome sequencing analysis identified a total of 83 differentially expressed genes in both rats and goats.Notably,49 genes exhibited a consistent expression pattern,with 38 genes displaying up-regulation and 11 genes demonstrating down-regulation.Enrichment analysis highlighted the potential involvement of the interleukin-17 signaling pathway and vascular smooth muscle contraction pathway in the underlying mechanism of BLI.Furthermore,the experimental findings in both goats and rats demonstrated a strong association between BLI and several key genes,including anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4,which exhibited up-regulation.Conclusions:Anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4 hold potential as target genes for the prognosis,diagnosis,and treatment of BLI.
文摘BACKGROUND Gastric cancer(GC)has a high mortality rate worldwide.Despite significant progress in GC diagnosis and treatment,the prognosis for affected patients still remains unfavorable.AIM To identify important candidate genes related to the development of GC and iden-tify potential pathogenic mechanisms through comprehensive bioinformatics analysis.METHODS The Gene Expression Omnibus database was used to obtain the GSE183136 dataset,which includes a total of 135 GC samples.The limma package in R software was employed to identify differentially expressed genes(DEGs).Thereafter,enrichment analyses of Gene Ontology(GO)terms and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways were performed for the gene modules using the clusterProfile package in R software.The protein-protein interaction(PPI)networks of target genes were constructed using STRING and visualized by Cytoscape software.The common hub genes that emerged in the cohort of DEGs that was retrieved from the GEPIA database were then screened using a Venn Diagram.The expression levels of these overlapping genes in stomach adenocarcinoma samples and non-tumor samples and their association with prognosis in GC patients were also obtained from the GEPIA database and Kaplan-Meier curves.Moreover,real-time quantitative polymerase chain reaction(RT-qPCR)and western blotting were performed to determine the mRNA and protein levels of glutamic-pyruvic transaminase(GPT)in GC and normal immortalized cell lines.In addition,cell viability,cell cycle distribution,migration and invasion were evaluated by cell counting kit-8,flow cytometry and transwell assays.Furthermore,we also conducted a retrospective analysis on 70 GC patients diagnosed and surgically treated in Wenzhou Central Hospital,Dingli Clinical College of Wenzhou Medical University,The Second Affiliated Hospital of Shanghai University between January 2017 to December 2020.The tumor and adjacent normal samples were collected from the patients to determine the potential association between the expression level of GPT and the clinical as well as pathological features of GC patients.RESULTS We selected 19214 genes from the GSE183136 dataset,among which there were 250 downregulated genes and 401 upregulated genes in the tumor samples of stage III-IV in comparison to those in tumor samples of stage I-II with a P-value<0.05.In addition,GO and KEGG results revealed that the various upregulated DEGs were mainly enriched in plasma membrane and neuroactive ligand-receptor interaction,whereas the downregulated DEGs were primarily enriched in cytosol and pancreatic secretion,vascular smooth muscle contraction and biosynthesis of the different cofactors.Furthermore,PPI networks were constructed based on the various upregulated and downregulated genes,and there were a total 15 upregulated and 10 downregulated hub genes.After a comprehensive analysis,several hub genes,including runt-related transcription factor 2(RUNX2),salmonella pathogenicity island 1(SPI1),lysyl oxidase(LOX),fibrillin 1(FBN1)and GPT,displayed prognostic values.Interestingly,it was observed that GPT was downregulated in GC cells and its upregulation could suppress the malignant phenotypes of GC cells.Furthermore,the expression level of GPT was found to be associated with age,lymph node metastasis,pathological staging and distant metastasis(P<0.05).CONCLUSION RUNX2,SPI1,LOX,FBN1 and GPT were identified key hub genes in GC by bioinformatics analysis.GPT was significantly associated with the prognosis of GC,and its upregulation can effectively inhibit the proliferative,migrative and invasive capabilities of GC cells.
文摘The term “microgravity” is used to describe the “weightlessness” or “zero-g” circumstances that can only be found in space beyond earth’s atmosphere. Rhodobacter sphaeroides is a gram-negative purple phototroph, used as a model organism for this study due to its genomic complexity and metabolic versatility. Its genome has been completely sequenced, and profiles of the differential gene expression under aerobic, semi-aerobic, and photosynthetic conditions were examined. In this study, we hypothesized that R. sphaeroides will show altered growth characteristics, morphological properties, and gene expression patterns when grown under simulated microgravity. To test that, we measured the optical density and colony-forming units of cell cultures grown under both microgravity and normal gravity conditions. Differences in the cell morphology were observed using scanning electron microscopy (SEM) images by measuring the length and the surface area of the cells under both conditions. Furthermore, we also identified homologous genes of R. spheroides using the differential gene expression study of Acidovorax under microgravity in our laboratory. Growth kinetics results showed that R. sphaeroides cells grown under microgravity experience a shorter log phase and early stationary phase compared to the cells growing under normal gravity conditions. The length and surface area of the cells under microgravity were significantly higher confirming that bacterial cells experience altered morphological features when grown under microgravity conditions. Differentially expressed homologous gene analysis indicated that genes coding for several COG and GO functions, such as metabolism, signal-transduction, transcription, translation, chemotaxis, and cell motility are differentially expressed to adapt and survive microgravity.
基金National Natural Science Foundation of China[grant num-bers 81430045 and 81401556]Natural Science Foundation of Guangdong Province[grant number 2014A030310293].
文摘Detection of the vitality of wounds is essential in forensic practice.The present study used Illumina RNA-seq technology to determine gene expression profiles in contused mouse skin.In obtained high quality sequencing reads,the reads were mapped onto a reference transcriptome (Mus_musculus.GRCm38.83).The results revealed that there were 659 upregulated and 996 down-regulated differentially expressed genes (DEGs) in contused mouse skin.The DEGs were further analyzed using the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases.Genes from different functional categories and signalling pathways were enriched,including the immune system process,immune response,defense response,cytokine-cytokine receptor interaction,complement and coagulation cascades and chemokine signalling pathway.Expression patterns of 11 DEGs were verified by RT-qPCR in mice skins.In addition,alterations of five DEGs were also analyzed in postmortem human wound samples.The results were in concordance with the results of RNA-seq.These findings suggest that RNA-seq is a powerful tool to reveal DEGs as potential markers for vital reaction in terms of forensic practices.
基金the National Key Research and Development Program of the Ministry of Science and Technology(CN)(No.2022YFD2400401)the Key Research and Development Plan of Shandong Province(CN)(for Academician Team in Shandong)(No.2023ZLYS02)+1 种基金the Fundamental Research Funds for the Central Universities(No.202261029)the Enterprise Authorized Project(No.20200025)。
文摘Turbot Scophthalmus maximus is an important mariculture fish species with high economic value.However,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture industry.To understand the immune response of the turbot against V.anguillarum infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after V.anguillarum infection.Differentially expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)enrichment.The gene ontology(GO)classification analysis revealed that V.anguillarum infection had the greatest effect on biological processes and cellular components.Twelve immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat map.The proteinprotein interaction(PPI)networks were constructed to analyze the immune mechanism.The results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against V.anguillarum infection.In the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most significant.Our research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against V.anguillarum infection.
文摘BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the prevalence of COVID-19 is significantly higher in patients with liver cancer.However,this mechanism of action has not been clarified.Gene sets for COVID-19(GSE180226)and liver cancer(GSE87630)were obtained from the Gene Expression Omnibus database.After identifying the common differentially expressed genes(DEGs)of COVID-19 and liver cancer,functional enrichment analysis,protein-protein interaction network construction and scree-ning and analysis of hub genes were performed.Subsequently,the validation of the differential expression of hub genes in the disease was performed and the regulatory network of transcription factors and hub genes was constructed.RESULTS Of 518 common DEGs were obtained by screening for functional analysis.Fifteen hub genes including aurora kinase B,cyclin B2,cell division cycle 20,cell division cycle associated 8,nucleolar and spindle associated protein 1,etc.,were further identified from DEGs using the“cytoHubba”plugin.Functional enrichment analysis of hub genes showed that these hub genes are associated with P53 signalling pathway regulation,cell cycle and other functions,and they may serve as potential molecular markers for COVID-19 and liver cancer.Finally,we selected 10 of the hub genes for in vitro expression validation in liver cancer cells.CONCLUSION Our study reveals a common pathogenesis of liver cancer and COVID-19.These common pathways and key genes may provide new ideas for further mechanistic studies.
基金Supported by National Natural Science Foundation of China,No.82100594.
文摘BACKGROUND Helicobacter pylori(H.pylori)infection is related to various extragastric diseases including type 2 diabetes mellitus(T2DM).However,the possible mechanisms connecting H.pylori infection and T2DM remain unknown.AIM To explore potential molecular connections between H.pylori infection and T2DM.METHODS We extracted gene expression arrays from three online datasets(GSE60427,GSE27411 and GSE115601).Differentially expressed genes(DEGs)commonly present in patients with H.pylori infection and T2DM were identified.Hub genes were validated using human gastric biopsy samples.Correlations between hub genes and immune cell infiltration,miRNAs,and transcription factors(TFs)were further analyzed.RESULTS A total of 67 DEGs were commonly presented in patients with H.pylori infection and T2DM.Five significantly upregulated hub genes,including TLR4,ITGAM,C5AR1,FCER1G,and FCGR2A,were finally identified,all of which are closely related to immune cell infiltration.The gene-miRNA analysis detected 13 miRNAs with at least two gene cross-links.TF-gene interaction networks showed that TLR4 was coregulated by 26 TFs,the largest number of TFs among the 5 hub genes.CONCLUSION We identified five hub genes that may have molecular connections between H.pylori infection and T2DM.This study provides new insights into the pathogenesis of H.pylori-induced onset of T2DM.
文摘Background: Hypertension, also known as increased blood pressure, is a phenomenon in which blood flows in blood vessels and causes persistently higher-than-normal pressure on the vessel wall. The identification of novel prognostic and pathogenesis biomarkers plays a key role in the management of hypertension. Methods: The GSE7483 and GSE75815 datasets from the gene expression omnibus (GEO) database were used to identify the genes associated with hypertension that were differentially expressed genes (DEGs). The functional role of the DEGs was elucidated by gene body (GO) enrichment analysis. In addition, we performed an immune infiltration assay and GSEA on the DEGs of hypertensive patients and verified the expression of novel DEGs in the blood of hypertensive patients by RT-qPCR. Results: A total of 267 DEGs were identified from the GEO database. GO analysis revealed that these genes were associated mainly with biological processes such as fibroblast proliferation, cell structural organization, extracellular matrix organization, vasculature development regulation, and angiogenesis. We identified five possible biomarkers, Ecm1, Sparc, Sphk1, Thbsl, and Mecp2, which correlate with vascular development and angiogenesis characteristic of hypertension by bioinformatics, and explored the clinical expression levels of these genes by RT-qPCR, and found that Sparc, Sphk1, and Thbs1 showed significant up-regulation, in agreement with the results of the bioinformatics analysis. Conclusion: Our study suggested that Sparc, Sphk1 and Thbs1 may be potential novel biomarkers for the diagnosis, treatment and prognosis of hypertension and that they are involved in the regulation of vascular development and angiogenesis in hypertension.
基金supported by grants from the National Insitute of Health(EY-014619)the National Science Foun-dation(IBN-052384).
文摘Changes in gene expression were examined by microarray analysis during development of the eyed surface dwelling(surface fish)and blind cave-dwelling(cavefish)forms of the teleost Astyanax mexicanus De Filippi,1853.The cross-species microarray used surface and cavefish RNA hybridized to a DNA chip prepared from a closely related species,the zebrafish Danio rerio Hamilton,1822.We identified a total of 67 differentially ex-pressed probe sets at three days post-fertilization:six upregulated and 61 downregulated in cavefish relative to surface fish.Many of these genes function either in eye development and/or maintenance,or in programmed cell death.The upregulated probe set showing the highest mean fold change was similar to the human ubiquitin specific protease 53 gene.The downregulated probe sets showing some of the highest fold changes corresponded to genes with roles in eye development,including those encoding gamma crystallins,the guanine nucleotide binding pro-teins Gnat1 and Gant2,a BarH-like homeodomain transcription factor,and rhodopsin.Downregulation of gam-ma-crystallin and rhodopsin was confirmed by in situ hybridization and immunostaining with specific antibodies.Additional downregulated genes encode molecules that inhibit or activate programmed cell death.The results suggest that cross-species microarray can be used for identifying differentially expressed genes in cavefish,that many of these genes might be involved in eye degeneration via apoptotic processes,and that more genes are downregulated than upregulated in cavefish,consistent with the predominance of morphological losses over gains during regressive evolution.
基金funded by the National Natural Science Foundation of China(No.21577119).
文摘Objective:Primordial follicle assembly and the transition from primordial follicle to primary follicle are critical processes in ovarian biology.These processes determine the size of the primordial follicle pool,which may limit the reproductive lifespan of a female.When the follicle pool is depleted,reproduction ceases and females enter menopause.In this study,we aimed to explore the role of differentially expressed genes(DEGs)in the processes of primordial follicle assembly and the transformation from primordial to primary follicle.Methods:The gene chip GSE9300 was downloaded from the Gene Expression Omnibus database.DEGs between ovaries on postnatal day 0 and ovaries on postnatal day 4,as well as ovaries on postnatal day 4 and ovaries cultured for 7 days from postnatal day 0 were identified.Gene ontology(GO),pathway enrichment analysis,and protein-protein interaction network construction were performed.Results:In total,99 upregulated genes and 123 downregulated genes were identified in the process of primordial follicle assembly,and 101 upregulated genes and 98 downregulated genes were identified in the process of transformation from primordial to primary follicle.The GO analysis showed that response to estradiol was associated with two of the processes of assembly and subsequent development of primordial follicle,but the genes involved in response to estradiol between the two processes were significantly different.Furthermore,the two groups of DEGs were all associated with metabolic pathways.Conclusions:DEGs may provide new insights into the exploration of mechanisms related to primordial follicle assembly and subsequent development.
基金supported by Supported by the National Natural Science Foundation of China(81603418,82074271)Scientific Research Project of"Outstanding Innovative Talents Support Plan"of Heilongjiang University of Chinese Medicine(2020YQ05)。
文摘Objective:To search the the differentially expressed genes between breast cell carcinoma tissues and normal tissues by using bioinformatics technology,and the potential therapeutic drugs for breast cancer were identified,which can provide reference for clinical immune targeted therapy and drug therapy of breast cancer in the future.Methods:"Breast cancer"was searched by using Gene Expression Omnibus(GEO),and GSE79586 chip data was downloaded.The differentially expressed genes in the control group and the breast cancer model group were screened by using bio-communication technology and subjected to GO function analysis,KEGG pathway analysis,differential gene characteristic expression analysis and protein-protein interaction network(PPI)analysis,and the analysis results were further visualized.Prognosis analysis,related function prediction and immune infiltration analysis were performed using the GEPIA,GeneMANIA,and Timer2.0 databases,respectively.Finally,the compounds with potential therapeutic effects on breast cancer are identified through Connectivity Map(CMap).Western blotting and real-time PCR(RT-PCR)were used to verify the core genes and potential therapeutic agents with the highest correlation in vitro.Results:A total of 3916 differentially expressed genes including 1786 up-regulated genes and 2130 down-regulated genes were screened.GO analysis showed that the differential genes were mainly involved in the positive regulation of phosphorylation,secretory vesicles,racemase and epimerase activities.KEGG analysis showed that differential genes were involved in systemic lupus erythematosus,alcoholism,sticky spots,amoebic dysentery Ras signal pathways and other disease pathways.The characteristic expression analysis of differential genes showed that MEK inhibitors,HSP90 inhibitors and signal transduction pathway kinase inhibitors were drugs similar to the differential genes.PPI results showed that H2AFJ,TFF1,GATA3,FOXA1,and CDH1 were core genes related to breast cancer.Two core genes of H2AFJ and TFF1 with the highest correlation were further selected for GEPIA analysis.The results of the analysis showed that the mRNA expression levels of H2AFJ and TFF1 in breast cancer cells were significantly higher than those in normal tissues,and there was a significant correlation with the pathological staging,overall survival rate and disease-free survival rate of breast cancer patients.H2AFJ and TFF1 may be potential prognostic biomarkers for survival of breast cancer patients.The functions of differentially expressed H2AFJ and TFF1 are mainly related to hormone receptor binding,epithelial structure maintenance and epigenetic negative regulation of genes,chromatin tissue involved in negative regulation of transcription,etc.The results of immune infiltration showed that the expressions of H2AFJ and TFF1 had a significant correlation with the infiltration of macrophages,neutrophils,monocytes,CD4+T,CD8+T,B lymphocytes and other immune cells.CMap results showed that compounds such as Gefitinib,Alpelisib,Sorafenib,and Sunitinib had potential therapeutic effects on breast cancer.Western blot and RT-PCR results showed that H2AFJ and TFF1 were significantly overexpressed in breast cancer cells.Gefitinib significantly inhibited the expression of H2AFJ and TFF1 in breast cancer cells(P<0.05,P<0.01).Conclusion:In this study,differentially expressed genes between breast cell carcinoma tissues and normal tissues were screened out by bioinformatics means to further identify key genes and compounds with potential therapeutic effects in the onset process of breast cancer and to further verify the effectiveness of the screened drugs on breast cancer through experiments.It will provide reference for clinical research and development of new drugs against breast cancer in the future in order to develop more effective treatment options.
文摘High Feed efficiency (FE) in growing heifers has economic importance in dairy, but remains less understood in buffaloes. Feed conversion efficiency is defined as dry matter intake (DMI) per unit body weight gain and is determined as residual feed intake (RFI), i.e., the difference between actual and predicted feed intake to gain unit body weight during a feed trial run for 78 days under control feeding. A large variation was identified ranging between -0.42 to 0.35 in growing buffalo heifers (n = 40) of age between 11 to 15 months. An average daily weight gain (ADG) varied between 382.0 and 807.6 g/day when compared with the control-fed heifers at an organized buffalo farm. The whole blood transcriptome data obtained from the selected growing heifers from extremes of estimated high and low RFI efficiency were compared with the reference assembly generated from the transcriptome of multiparous buffaloes (n = 16) of diverse age of maturity, period of regaining post partum cyclicity and level of milk production. Differentially expressed genes (DEGs) were identified using the reference genome of Mediterranean water buffalo. GO: terms (Padj 0.05, FDR 0.05) enriched by annotated DEGs and biological pathways in gene network for RFI efficiency trait were identified. GO: terms specific to pre-transcriptional regulation of nucleus and Chromatin organization under Nucleoplasm, Energy balancing, Immunity, Cell signaling, ROS optimization, ATP generation through the Electron Transport chain and cell proliferation were determined. The study reveals the indicators targeting the actual metabolic changes and molecular functions underlying the feed utilization capacity of buffaloes. Estimated RFI efficiency revealed a large variation over heifers which may lower the DMI even up to 13.6% thus, enabling an increase in ADG up to 16% by involving efficient heifers in breeding plan. The study revealed a scope of high gain by selective breeding for FE in heifers. FE variants catalogued in the study are useful breed-specific RFI markers for future reference. The study contributes to the understanding of feed efficiency in buffaloes and its association with key interactive traits such as reproduction and growth. This knowledge can be utilized to develop more effective breeding programs.
基金supported by the National Natural Science Foundation of China(31760428,31860371,and 32060476)Guangxi Natural Science Foundation of China(2020GXNSFAA259041)+1 种基金Guangxi Science and Technology Project(Guike AB21238009)Guangxi Academy of Agricultural Sciences Foundation(2021JM04,JM49,YT030,QN-11,14,20,29,and 35).
文摘Plant height(PH)is a complex trait regulated by the environment and multiple genes.PH directly affects crop yield,harvest index,and lodging resistance.From plant dwarf mutants,many genes related to PH have been identified and described.Nonetheless,the molecular mechanism of height regulation in high-culm rice mutants has not been well studied.By using transcriptome and weighted gene co-expression network analysis(WGCNA),we identified the differentially expressed genes(DEGs)between high-culm rice mutants(MUT)and wild-type(WT)and explored the key pathways and potential candidate genes involved in PH regulation.Transcriptome analysis identified a total of 2,184 DEGs,of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage.Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction,ABC transportation,and steroid hormone biosynthesis.Among these metabolic pathways,LOC_Os05g43910 and LOC_Os01g35030 were auxin(IAA)-related genes,up-regulated in MUT and LOC_Os02g08500(LEPTO1),LOC_Os11g04720,and LOC_Os12g04500 were cytokinin(CK)-related genes,downregulated in MUT.The WGCNA identified four modules(light cyan,dark grey,grey,and pale turquoise)closely related to PH,and seven key genes were screened from these modules,of which two were up-regulated cell wallrelated genes(LOC_Os01g26174(OsWAK5),LOC_Os06g05050)in MUT,and one gibberellic acid(GA)gene(LOC_Os06g37364,OsKO2)was also up-regulated.These genes might be closely related to PH regulation.These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.
