Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target...Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target of this formula on macrophage inflammatory injury at the overall level. Methods: A model of LPS-induced inflammation in RAW264.7 cells was constructed, and the effect of ZGC intervention on the genome-wide expression of inflammatory macrophages 3was examined by gene microarray technology, GO/KEGG enrichment analysis was performed for significantly differentially expressed genes among each group. Results: The results of genome-wide expression profiling microarray analysis showed that the ZGC intervention group upregulated the expression of 5 genes including C4bp and inhibited the expression of 22 genes including Mgat3, Psma6, and Siglecg relative to the LPS model group. KEGG signaling pathway analysis results showed that ZGC mainly acted through cytokine receptor interaction and the C-type lectin receptor signaling pathway. Conclusion: ZGC can interfere with the abnormal expression of 27 genes in inflammatory macrophages, and the related genes may exert corresponding anti-inflammatory effects by affecting cytokine receptor interactions, C-type lectin receptor signaling pathway, and TLR4/ NF-κB signaling pathway.展开更多
The caspase gene family is a crucial gene cluster that regulates apoptosis which contribute to programmed cell death,cell proliferation and differentiation,and several immune responses.In our study,a complete set of 1...The caspase gene family is a crucial gene cluster that regulates apoptosis which contribute to programmed cell death,cell proliferation and differentiation,and several immune responses.In our study,a complete set of 12 caspase genes were identified in spotted sea bass Lateolabrax maculatus.These genes were divided into three subfamilies:2 inflammatory caspases(casp-1 and casp-14-like),5 apoptosis initiators(casp-2,casp-8a,casp-8b,casp-9,and casp-10),and 5 apoptosis executioners(casp-3a,casp-3b,casp-3-like,casp-6,and casp-7).Their phylogenetic relationships,synteny and gene structures were systematically analyzed.Furthermore,the relative expression profiles of the caspase family members in the liver,intestine,head kidney,and spleen were measured by q PCR after infection with Vibrio harveyi.The results showed that the overall mRNA levels of the caspase genes were dramatically increased after V.harveyi infection,and the expression patterns varied among genes and tissues.More caspase genes underwent pronounced expression changes in the head kidney and spleen than in the liver or intestine,mainly after 48 h of the challenge.Specifically,casp-3a,casp-3b,casp-3-like,casp-6,casp-7,casp-8a,casp-8b,casp-10,and casp-14-like in the head kidney,and casp-3-like,casp-6,casp-7,and casp-14-like in the spleen,were the most responsive caspase genes which may contribute significantly to immune regulation in spotted sea bass.Additionally,the apoptosis level in head kidney and spleen after infection were examined using the Caspase assay.Our study provides a systemic overview of the caspase gene family in spotted sea bass after V.harveyi infection and lays a foundation for further deciphering the biological roles of these caspase genes.展开更多
Objective:To clarify the effect of endurance training on the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise.Methods:A total of 45 male C57BL/6 mice were randoml...Objective:To clarify the effect of endurance training on the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise.Methods:A total of 45 male C57BL/6 mice were randomly divided into control(C),low-strength endurance training(LSET)and high-strength endurance training(HSET)groups(n=15).The mice in the control group were not conducted to platform training.The mice in the LSET and HSET groups were conducted to platform training at 30%and 60%of exhaustive exercise once a day for 5 days a week,respectively.The exhaustion exercise was performed after 5 weeks of platform training.Total RNA was extracted from myocardial tissues,and the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues was analyzed using Illimina transcriptome sequencing.Results:The distance and time of exhaustive exercise were longer in the LSET and HSET groups than in the control group,and the distance and time of exhaustive exercise were longer in the HSET group than in the LSET group(P<0.05).A total of 54 differentially expressed circRNAs(28 down-regulated and 26 up-regulated),7 differentially expressed lncRNAs(all down-regulated),3 differentially expressed miRNAs(1 down-regulated and 2 up-regulated)and 99 differentially expressed mRNAs(81 down-regulated and 18 up-regulated)were identified by transcriptome sequencing(P<0.05).Interaction network analysis revealed that ENSMUSG00000113041,MSTRG.79740,mmu-miR-374c-5p,18 down-regulated mRNAs and 3 up-regulated mRNAs formed a regulatory network.GO functional analysis revealed that the differentially expressed mRNAs were mainly enriched in primary metabolic processes and macromolecular synthesis and metabolic processes.KEGG pathway analysis revealed that the differentially expressed mRNAs were mainly enriched in complement and coagulation cascade pathways,estrogen signaling pathway and glucagon signaling pathway.Conclusion:Endurance training could alter the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise,and these differentially expressed RNAs form a regulatory network that affects cardiomyocyte synthesis and metabolism and thus participates in the regulation of myocardial injury.展开更多
CHDTEPDB(URL:http://chdtepdb.com/)is a manually integrated database for congenital heart disease(CHD)that stores the expression profiling data of CHD derived from published papers,aiming to provide rich resources for i...CHDTEPDB(URL:http://chdtepdb.com/)is a manually integrated database for congenital heart disease(CHD)that stores the expression profiling data of CHD derived from published papers,aiming to provide rich resources for investigating a deeper correlation between human CHD and aberrant transcriptome expression.The develop-ment of human diseases involves important regulatory roles of RNAs,and expression profiling data can reflect the underlying etiology of inherited diseases.Hence,collecting and compiling expression profiling data is of critical significance for a comprehensive understanding of the mechanisms and functions that underpin genetic diseases.CHDTEPDB stores the expression profiles of over 200 sets of 7 types of CHD and provides users with more convenient basic analytical functions.Due to the differences in clinical indicators such as disease type and unavoidable detection errors among various datasets,users are able to customize their selection of corresponding data for personalized analysis.Moreover,we provide a submission page for researchers to submit their own data so that increasing expression profiles as well as some other histological data could be supplemented to the database.CHDTEPDB is a user-friendly interface that allows users to quickly browse,retrieve,download,and analyze their target samples.CHDTEPDB will significantly improve the current knowledge of expression profiling data in CHD and has the potential to be exploited as an important tool for future research on the disease.展开更多
[Objectives]In order to clarify the regulatory effects of insect hormones on the expression of BmSuc1 and provide a reference for further analysis of the function and expression regulation mechanism of BmSuc1,this stu...[Objectives]In order to clarify the regulatory effects of insect hormones on the expression of BmSuc1 and provide a reference for further analysis of the function and expression regulation mechanism of BmSuc1,this study explored the expression profiles of BmSuc1 in different tissues and periods of silkworm larvae and the expression changes of BmSuc1 after treatment with exogenous hormones.[Methods]By using the real-time fluorescence quantitative PCR technique,the expression characteristics of BmSuc1 were detected in different periods,different tissues and after treatment with exogenous hormones during the development of silkworm larvae.The expression of BmSuc1 and 20E receptor gene USP was detected after RNA interference with double-stranded RNA(dsRNA)of USP.[Results]The relative expression of BmSuc1 gene in the midgut was the highest,followed by the silk glands,epidermis and hemolymph.However,there was much lower or almost no expression in other tissues.In addition,the BmSuc1 expression profile exhibited a pulse-like pattern in silkworm larvae.The expression level of BmSuc1 was higher at each instar stage before molting,late fifth instar before cocooning and prepupal stage.Silkworm larvae at day 2 of the fifth instar were treated with 20-hydroxyecdysone(20E)and juvenile hormone(JH).It was found that the expression of BmSuc1 was extremely significantly higher at 12 and 18 h after 20E treatment than the control group injected with 0.1%dimethyl sulfoxide(DMSO)(P<0.01,the same below).But there were no significant difference in BmSuc1 expression between the JH treatment and the control group during the measurement time range(P>0.05).The dsRNA of USP was synthesized in vitro and injected into silkworm larvae at day 3 of the fifth instar.It was showed that the USP relative expression was extremely significantly down-regulated at 24 and 36 h after injection,which indicated that dsRNA interference was successful.RNAi of USP would block 20E signal transduction,and the expression of BmSuc1 was inhibited and significantly down-regulated at 24 and 36 h after injection of dsRNA of USP(P<0.05).[Conclusions]The BmSuc1 expression peaks appeared in the molting of silkworm larvae and the metamorphosis of larvae to pupae,which suggests that BmSuc1 may be involved in the metamorphic development process of silkworms.Treatment with exogenous ecdysone 20E can activate the expression of BmSuc1,but blocking the 20E signal transduction pathway may suppress expression of BmSuc1.It indicates that BmSuc1 as a downstream target gene in the 20E signal transduction pathway is directly or indirectly regulated by 20E signals.展开更多
Tumor immunotherapy has emerged as a promising method in cancer treatment,but patient responses vary,necessitating personalized strategies and prognostic biomarkers.This study aimed to identify prognostic factors and ...Tumor immunotherapy has emerged as a promising method in cancer treatment,but patient responses vary,necessitating personalized strategies and prognostic biomarkers.This study aimed to identify prognostic factors and construct a predictive model for patient survival outcomes and immunotherapy response.We curated six immunotherapy datasets representing diverse cancer types and treatment regimens.After data preprocessing,patients were stratified based on immunotherapy response.Differential gene expression analysis identified 22 genes consistently dysregulated across multiple datasets.Functional analysis provided critical insights,highlighting the enrichment of these dysregulated genes in immune response pathways and tumor microenvironment-related processes.To create a robust prognostic model,we meticulously employed a multistep approach.Initially,the identified 22 genes underwent rigorous univariate Cox regression analysis to evaluate their individual associations with patient survival outcomes.Genes showing statistical significance(p-values<0.05)at this stage advanced to the subsequent multivariate Cox regression analysis,which aimed to address potential confounding factors and collinearity among genes.From this analysis,we ultimately identified four key genes—ST6GALNAC2,SNORA65,MFAP2,and CDKN2B—that were significantly associated with patient survival outcomes.Incorporating these four key genes along with their corresponding coefficients,we constructed a predictive model.This model’s efficacy was validated through extensive Cox regression analyses,demonstrating its robustness in predicting patient survival outcomes.Furthermore,our model exhibited promising predictive capability for immunotherapy response,providing a potential tool for anticipating treatment efficacy.These findings provide insights into immunotherapy response mechanisms and suggest potential prognostic biomarkers for personalized treatment.Our study contributes to advancing cancer immunotherapy and personalized medicine.展开更多
The biological features of the valvular heart disease with atrial fibrillation(AF-VHD)remain unknown when involving long non-coding RNAs(lncRNAs).This study performed system analysis on lncRNA and messenger RNA(mRNA)e...The biological features of the valvular heart disease with atrial fibrillation(AF-VHD)remain unknown when involving long non-coding RNAs(lncRNAs).This study performed system analysis on lncRNA and messenger RNA(mRNA)expression profiles constructed by using bioinformatics methods and tools for biological features of AF-VHD.Fold change and t-test were used to identify differentially expressed(DE)lncRNAs and mRNAs.The enrichment analysis of DE mRNAs was performed.The subgroups formed by lncRNAs and nearby mRNAs were screened,and a transcriptional regulation network among lncRNAs,mRNAs,and transcription factors(TFs)was constructed.The interactions between mRNAs related to lncRNAs and drugs were predicted.The 620 AF-VHDrelated DE lncRNAs and 452 DE mRNAs were identified.The 3 lncRNA subgroups were screened.The 665 regulations mediated by lncRNAs and TFs were identified.The 9 mRNAs related to lncRNAs had 1 or more potential drug interactions,totaling 37 drugs.Of these,9 drugs targeting 3 genes are already known to be able to control or trigger atrial fibrillation(AF)or other cardiac arrhythmias.The found biological features of AF-VHD provide foundations for further biological experiments to better understand the roles of lncRNAs in development from the valvular heart disease(VHD)to AF-VHD.展开更多
Previous studies on mammals showed that peroxisome proliferator-activated receptor gamma coactivator-1α(PGC-1α)played a prominent role in regulating muscle fiber type transition and composition.However,the role of P...Previous studies on mammals showed that peroxisome proliferator-activated receptor gamma coactivator-1α(PGC-1α)played a prominent role in regulating muscle fiber type transition and composition.However,the role of PGC-1αin chicken muscle has seldom been explored.To investigate the effect of PGC-1αon chicken skeletal muscles in this study,the PGC-1αgene was overexpressed or silenced in chicken primary myoblasts by using lentivirus,and then the effects of the PGC-1αgene overexpression and knockdown on the mRNA expression profile of genes related to myofiber type specificity were examined during fiber formation.The results showed that overexpression of PGC-1αfrom proliferation to differentiation was accompanied by the up-regulated expression of Pax7,MyoD,and CnAα,which was significantly(P<0.01)increased after one day of transfection(1 I).The enhancement of MyoG,MEF2 c,and MyHC SM expression lagged,which was improved significantly(P<0.01)after four days of transfection(1 I3 D).Overexpression of PGC-1αdecreased(P<0.01)the MyHC FWM expression after four days of transfection(1 I3 D),and it had no significant impact(P>0.05)on the expression of CnB1,NFATc3,and MyHC FRM during myofiber formation.The effective silence(P<0.01)of PGC-1αby lentivirus mediating short hairpin RNA(shRNA)was detected after four days of transfection(1 I3 D)in cultures,and the lack of its function in chicken primary myoblasts significantly(P<0.01)down-regulated the expression of Pax7,MyoD,CnAα,MyoG,MEF2 c,and MyHC SM,significantly(P<0.01)up-regulated the expression of MyHC FWM,and had no significant impact(P>0.05)on the expression of CnB1,NFATc3,and MyHC FRM.These results indicated that the role of PGC-1αin regulating the fiber type specificity of chicken skeletal muscles might be similar to that in mammals,which interplayed with key genes related to myocyte differentiation and calcineurin signaling pathway.展开更多
Stress-associated proteins(SAPs)are known as response factors to multiple abiotic and biotic stresses in plants.However,the potential physiological and molecular functions of SAPs remain largely unclear.Castor bean(Ri...Stress-associated proteins(SAPs)are known as response factors to multiple abiotic and biotic stresses in plants.However,the potential physiological and molecular functions of SAPs remain largely unclear.Castor bean(Ricinus communis L.)is one of the most economically valuable non-edible woody oilseed crops,able to be widely cultivated in marginal lands worldwide because of its broad adaptive capacity to soil and climate conditions.Whether SAPs in castor bean plays a key role in adapting diverse soil conditions and stresses remains unknown.In this study,we used the castor bean genome to identify and characterize nine castor bean SAP genes(RcSAP).Structural analysis showed that castor bean SAP gene structures and functional domain types vary greatly,differing in intron number,protein sequence,and functional domain type.Notably,the AN1-C2H2eC2H2 zinc finger domain within RcSAP9 has not been often observed in other plant families.High throughput RNA-seq data showed that castor bean SAP gene profiles varied among different tissues.In addition,castor bean SAP gene expression varied in response to different stresses,including salt,drought,heat,cold and ABA and MeJA,suggesting that the transcriptional regulation of castor bean SAP genes might operate independently of each other,and at least partially independent from ABA and MeJA signal pathways.Cis-element analyses for each castor bean SAP gene showed that no common cis-elements are shared across the nine castor bean SAP genes.Castor bean SAPs were localized to different regions of cells,including the cytoplasm,nucleus,and cytomembrane.This study provides a comprehensive profile of castor bean SAP genes that advances our understanding of their potential physiological and molecular functions in regulating growth and development and their responses to different abiotic stresses.展开更多
CCCH(C3 H) Zinc finger(Znf) transcription factors(TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stre...CCCH(C3 H) Zinc finger(Znf) transcription factors(TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stress resistance.Longan(Dimocarpous longan) is a tropical/subtropical fruit tree of great economic importance in Southeast Asia.However, genomic information on C3 H and their functions in longan are still unknown. In this study, a comprehensive analysis of the longan C3 H(DlC3 H) gene family was carried out. A total of 49 DlC3 H genes in three clades were identified from the longan genome database. Characteristics of the genes were analyzed with respect to gene structure,motif composition, phylogenetic tree and potential functions. The analysis of alternative splicing(AS) events suggested that AS events in DlC3 H genes were related to the transformation from longan non-embryonic to embryonic cultures.Promoter analysis indicated that most of the DlC3 H genes included cis-acting elements associated with hormones and stresses responses. Quantitative real-time PCR(qRT-PCR) analysis indicated that 26 of the 49 DlC3 Hs, which possess methyl jasmonate(MeJA) and abscisic acid(ABA) responsive cis-acting elements, showed differential expression patterns under treatment with ABA, MeJA and their endogenous inhibitors, suggesting that DlC3 Hs might be involved in the ABA and MeJA signaling pathways. The expression profiles of 17 of the 49 DlC3 Hs in non-embryonic callus and three tissues of embryonic cultures showed that only five of the 17 DlC3 Hs had the same expression trends as the FPKM trends in transcriptome data;the expression levels of DlC3 H07/14/16/36/49 in embryogenic callus and DlC3 H04/38 in globular embryos were high, suggesting that they have different functions in embryonic development. Further, we verified that DlC3 H01/03/05/11/19/39 were regulated by sRNAs by a modified 5’ RLM-RACE method. This study provides the first systematic analysis of C3 H genes in longan, and found that C3 H genes may be involved in hormone and stress responses, and somatic embryogenesis. Our preliminary investigation may provide clues to further studies on the characteristics and functions of this family in longan.展开更多
Piwi-interacting RNAs(piRNAs)is a novel class of non-coding RNAs.However,changes in piRNA expression profiles in recurrent spontaneous abortion(RSA)have not yet been investigated.The aim of this study was to identify ...Piwi-interacting RNAs(piRNAs)is a novel class of non-coding RNAs.However,changes in piRNA expression profiles in recurrent spontaneous abortion(RSA)have not yet been investigated.The aim of this study was to identify differentially expressed piRNAs in deciduas of RSA patients.Decidua tissues were collected by curettage from recruited RSA patients and normal early pregnant(NEP)women with their informed consent.Small RNA sequencing was used to evaluate the differences in piRNA expression profiles between RSA and NEP.The present results demonstrated that the counts of total piRNA reads in RSA samples were increased compared with those in NEP samples(0.21%vs.0.11%).Differential expression analysis identified 29 upregulated piRNAs and 18 downregulated piRNAs in RSA samples.RT-qPCR further confirmed that the expression levels of uniq-109625,uniq-89328,uniq-50651 and uniq-4569 were decreased in 8 RSA tissues,compared with 13 NEP tissues.Otherwise,pi-22628 and uniq-173406 were increased in 8 RSA tissues.Based on GO term and KEGG pathway analysis,we speculate that these piRNAs regulate RSA by targeting extracellular matrix component pathway,cell adhesion pathway and focal adhesion pathway.PiRNAs may be involved in RSA pathogenesis by target genes function on adhesion and extracellular matrix component.展开更多
Metformin is a first-line drug in the fight against type 2 diabetes.In recent years,studies have shown that metformin has some preventive and therapeutic effects on liver cancer,but the effects of metformin on the gen...Metformin is a first-line drug in the fight against type 2 diabetes.In recent years,studies have shown that metformin has some preventive and therapeutic effects on liver cancer,but the effects of metformin on the gene expression of liver cancer cells are not fully known.This study focused on the differences in the gene expression profiles in liver cancer cells treated with or without metformin.A total of 153 differentially expressed genes(DEGs)(FC>2 and q-values<0.001)were found,including 77 upregulated genes and 76 downregulated genes.These DEGs are involved in mitogen-activated protein kinase(MAPK),nuclear factor-kappa B(NF-κB),cell adhesion molecules(CAMs),and leukocyte transendothelial migration signaling pathways.These findings reveal the effects of metformin treatment on gene expression profiles in liver cancer cells and provide new clues for unveiling the mechanism of the antitumor effects of metformin.展开更多
Objective:To study the effect of Baiban Ointment on gene expression profile of vulvar lichen sclerosus before and after treatment,and to provide theoretical basis for the early diagnosis and clinical treatment of vulv...Objective:To study the effect of Baiban Ointment on gene expression profile of vulvar lichen sclerosus before and after treatment,and to provide theoretical basis for the early diagnosis and clinical treatment of vulvar lichen sclerosus.Methods:Nine patients with vulvar lichen sclerosus diagnosed pathologically were selected as the study object,and the Baiban ointment was applied locally for 3 months.Gene chip technology was used to detect the vulva skin tissue in the same area before and after treatment,and the peripheral normal skin was used as the normal control group to analyze the change of gene expression profile.FC and P values were used as research indicators,and the standard of differential expression was FC value≥1.5,P value<0.05.The differentially expressed genes were screened,and GO analysis and KEGG database gene pathway analysis were carried out.Results:Compared with the normal control group,there were 22 differentially expressed genes in Group A before treatment,of which 21 were up-regulated and 1 was down regulated;compared with Group B before treatment,there were 23 differentially expressed genes,all of which were up regulated.The differentially expressed genes related to Baiban ointment treatment included TBK1、STAT1、ITGAM、VCAN、PRKACB、PROM1、PLAT、SERPINA1.Go analysis showed that the up-regulated differential genes were mainly concentrated in the extracellular exosome,cytosol,extracellular space,Golgi apparatus and other cellular component,using the biological process such as positive regulation of cell metabolism,signal transduction regulation,cell adhesion,etc.,to play a role in protein binding,enzyme activity regulation and other molecular functions.KEGG signaling pathway showed that the differentially expressed genes were significantly enriched in Toll like receptor signaling pathway,Nod like receptor signaling pathway and Fc RI signaling pathway,all of which were up-regulated signaling pathways.Among them,Toll like receptor signaling pathway and Nod like receptor signaling pathway are most closely related to the disease.Conclusion:Baiban ointment may play a role in regulating metabolism,inflammation and immune response by regulating the expression of related genes,affecting the signal transduction such as Toll like receptor signal pathway.The pathway and the genes screened in this study will provide a direction for the future study of this disease.展开更多
Cotton(Gossypium hirsutum L.) is the leading fiber crop and one of the mainstays of the economy in the world.Cotton fibers,as the main product of cotton plants,are unicellular,linear
Objective:Long noncoding RNAs(lncRNAs)play an important role in regulating the occurrence and development of cardiovascular diseases.However,the role of lncRNAs in heart aging remains poorly understood.The objective o...Objective:Long noncoding RNAs(lncRNAs)play an important role in regulating the occurrence and development of cardiovascular diseases.However,the role of lncRNAs in heart aging remains poorly understood.The objective of this study was to identify differentially expressed lncRNAs in the heart of aging mice and elucidate the relevant regulatory pathways of cardiac aging.Materials and methods:Echocardiography was used to detect the cardiac function of 18-months(aged)and 3-months(young)old C57BL/6 mice.Microarray analysis was performed to unravel the expression profiles of lncRNAs and mRNAs,and qRT-PCR to verify the highly dysregulated lncRNAs.Results:Our results demonstrated that the heart function in aged mice was impaired relative to young ones.Microarray results showed that 155 lncRNAs were upregulated and 37 were downregulated,and 170 mRNAs were significantly upregulated and 44 were remarkably downregulated in aging hearts.Gene ontology analysis indicated that differentially expressed genes are mainly related to immune function,cell proliferation,copper ion response,and cellular cation homeostasis.KEGG pathway analysis showed that the differentially expressed mRNAs are related to cytokine-cytokine receptor interaction,inflammatory mediator regulation of TRP channels,and the NF-kappa B signaling pathway.Conclusion:These results imply that the differentially expressed lncRNAs may regulate the development of heart aging.This study provides a new perspective on the potential effects and mechanisms of lncRNAs in heart aging.展开更多
Objective:To use the gene chip of pseudomonas aeruginosa as a research sample and to explore it at an omics level,aiming at elucidating the co-expression network characteristics of the virulence genes exoS and exoU of...Objective:To use the gene chip of pseudomonas aeruginosa as a research sample and to explore it at an omics level,aiming at elucidating the co-expression network characteristics of the virulence genes exoS and exoU of pseudomonas aeruginosa in the lower respiratory tract from the perspective of molecular biology and identifying its key regulatory genes.Methods:From March 2016 to May 2018,312 patients infected with pseudomonas aeruginosa in the lower respiratory tract who were admitted to Department of Respiratory Medicine of Baogang Hospital and given follow-up treatments in the hospital were selected as subjects by use of cluster sampling.Alveolar lavage fluid and sputum collected from those patients were used as biological specimens.The genes of pseudomonas aeruginosa were detected with the help of oligonucleotide probes to make a pre-processing of chip data.A total of 8 common antibiotics(ceftazidime,gentamicin,piperacillin,amikacin,ciprofloxacin,levofloxacin,doripenem and ticarcillin)against Gram-negative bacteria were selected to determine the drug resistance of biological specimens.MCODE algorithm was used to construct a co-expression network model of the drug-resistance genes focused on exoS/exoU.Results:The expression level of exoS/exoU in the drug-resistance group was significantly higher than that in the non-resistance group(p<0.05).The top 5 differentially expressed genes in the alveolar lavage fluid specimens from the drug-resistance group were RAC1,ITGB1,ITGB5,CRK and IGF1R in the order from high to low.In the sputum specimens,the top 5 differentially expressed genes were RAC1,CRK,IGF1R,ITGB1 and ITGB5.In the alveolar lavage fluid specimens,only RAC1 had a positive correlation with the expression of exoS and exoU(p<0.05).In the sputum specimens,RAC1,ITGB1,ITGB5,CRK and IGF1R were positively correlated with the expression of exoS and exoU(p<0.05).The genes included in the co-expression network contained exoS,exoU,RAC1,ITGB1,ITGB5,CRK,CAMK2D,RHOA,FLNA,IGF1R,TGFBR2 and FOS.Among them,RAC1 had a highest score in the aspect of regulatory ability(72.00)and the largest number of regulatory genes(6);followed by ITGB1,ITGB5 and CRK genes.Conclusions:The high expression of exoS and exoU in the sputum specimens suggests that pseudomonas aeruginosa has a higher probability to get resistant to antibiotics;RAC1,ITGB1,ITGB5 and CRK genes may be the key genes that can regulate the expression of exoS and exoU.展开更多
Background:The aim of this work is to detect and compare the peripheral blood mi RNA expression profiles in patients with severe traumatic brain injury(s TBI)2,12,24,48,and 72 h after injury at high altitude and to pr...Background:The aim of this work is to detect and compare the peripheral blood mi RNA expression profiles in patients with severe traumatic brain injury(s TBI)2,12,24,48,and 72 h after injury at high altitude and to predict the target genes of differential expressed mi RNAs.Methods:Twenty s TBI patients from high-altitude areas were randomly selected according to the inclusion and exclusion criteria and were divided into five groups:the 2-h group,12-h group,24-h group,48-h group,and 72-h group.Peripheral blood mi RNA expression profiles were detected using real-time quantitative PCR(q RT-PCR).Results:The expression levels of mi R-18 a,mi R-203,mi R-146 a,mi R-149,mi R-23 b,and mi R-let-7 b in peripheral blood showed significant differences between the 2-h group and the 12-h group.The expression levels of mi R-203,mi R-146 a,mi R-149,mi R-23 b,and mi R-let-7 f in peripheral blood were up-regulated in the 24-h group.In the 48-h group,the expression levels of mi R-181 d,mi R-29 a,and mi R-18 b were upregulated.In the 72-h group,the expression levels of mi R-203,mi R-146 a,mi R-149,mi R-23 b,and mi R-let-7 f changed.The main target genes of the differentiation expressed mi RNAs were genes that regulate inflammatory responses,apoptosis,and DNA damage/repair.Conclusions:mi RNAs may be involved in the pathogenesis of s TBI by dynamically regulating the target genes that regulate inflammatory responses,apoptosis,and DNA damage/repair pathways.展开更多
OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarrayand detect target genes for further study.METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 ...OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarrayand detect target genes for further study.METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases ofmoderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of18 000 genes.RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively.We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0%genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normalsamples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes,transcription factor genes were identified.CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate geneexpression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism wouldplay an important role in the pathogenesis of pancreatic carcinoma.展开更多
CBF/DREB proteins play a critical role in abiotic stress-mediated gene expression and represent attractive regulons for plant breeding programs.However,no study has been conducted for CBF/DREB protein-related genes in...CBF/DREB proteins play a critical role in abiotic stress-mediated gene expression and represent attractive regulons for plant breeding programs.However,no study has been conducted for CBF/DREB protein-related genes in jujube(Ziziphus jujuba Mill.).In this study,twenty-five ZjDREB genes were identified and annotated from the jujube(Z.jujuba‘Dongzao’)genome.Detailed analysis,including gene classification,annotation,phylogenetic evaluation,conserved motif determination and expression profiling were performed on all genes.Phylogenetic analysis showed that ZjDREB proteins were divided into five subgroups(A1–A5),but lacking a subgroup A6 corresponding to AtDREBs.The ZjDREB genes were distributed in nine of twelve chromosomes in the genome.Additionally,the expression patterns of the DREB genes under different abiotic stresses were investigated using q RT-PCR.Nineteen ZjDREB genes were down-regulated under low temperature,in contrast six ZjDREB genes(01,03,05,11,23 and 24)were up-regulated.Under drought,salinity and high temperature conditions,expression of ZjDREB03,09,10,14,15,17 and 20 genes were induced and showed similar expression patterns,suggesting that various stress conditions share common elements in the signaling pathway.The results suggest that the family of DREB genes play an important role in abiotic stresses in jujube,and provide a foundation for further functional studies of this important class of transcriptional regulators.展开更多
AIM:Optimal molecular markers for detecting colorectal cancer(CRC)in a blood-based assay were evaluated.METHODS:A matched(by variables of age and sex)case-control design(111 CRC and 227 non-cancer samples)was applied....AIM:Optimal molecular markers for detecting colorectal cancer(CRC)in a blood-based assay were evaluated.METHODS:A matched(by variables of age and sex)case-control design(111 CRC and 227 non-cancer samples)was applied.Total RNAs isolated from the338 blood samples were reverse-transcribed,and the relative transcript levels of candidate genes were analyzed.The training set was made of 162 random samples of the total 338 samples.A logistic regression analysis was performed,and odds ratios for each gene were determined between CRC and non-cancer.The samples(n=176)in the testing set were used to validate the logistic model,and an inferred performance(generality)was verified.By pooling 12 public microarray datasets(GSE 4107,4183,8671,9348,10961,13067,13294,13471,14333,15960,17538,and 18105),which included 519 cases of adenocarcinoma and 88 controls of normal mucosa,we were able to verify the selected genes from logistic models and estimate their external generality.RESULTS:The logistic regression analysis resulted in the selection of five significant genes(P<0.05;MDM2,DUSP6,CPEB4,MMD,and EIF2S3),with odds ratios of 2.978,6.029,3.776,0.538 and 0.138,respectively.The five-gene model performed stably for the discrimination of CRC cases from controls in the training set,with accuracies ranging from 73.9%to 87.0%,a sensitivity of 95%and a specificity of 95%.In addition,a good performance in the test set was obtained using the discrimination model,providing 83.5%ac-curacy,66.0%sensitivity,92.0%specificity,a positive predictive value of 89.2%and a negative predictive value of 73.0%.Multivariate logistic regressions analyzed 12 pooled public microarray data sets as an external validation.Models that provided similar expected and observed event rates in subgroups were termed well calibrated.A model in which MDM2,DUSP6,CPEB4,MMD,and EIF2S3 were selected showed the result in logistic regression analysis(H-L P=0.460,R2=0.853,AUC=0.978,accuracy=0.949,specificity=0.818 and sensitivity=0.971).CONCLUSION:A novel gene expression profile was associated with CRC and can potentially be applied to blood-based detection assays.展开更多
基金Chinese Academy of Traditional Chinese Medicine Autonomous Topic Selection Project(No.ZZ2018017)Research Development Fund Project of the Medical Experimental Center of the Chinese Academy of Traditional Chinese Medicine(No.FZ2023003)。
文摘Objective: The effect of Chuanzhi Fang (ZGC) on the whole genome expression profile of RAW264.7 cells activated by lipopolysaccharide (LPS) was analyzed, and to explore the possible mechanism of action and core target of this formula on macrophage inflammatory injury at the overall level. Methods: A model of LPS-induced inflammation in RAW264.7 cells was constructed, and the effect of ZGC intervention on the genome-wide expression of inflammatory macrophages 3was examined by gene microarray technology, GO/KEGG enrichment analysis was performed for significantly differentially expressed genes among each group. Results: The results of genome-wide expression profiling microarray analysis showed that the ZGC intervention group upregulated the expression of 5 genes including C4bp and inhibited the expression of 22 genes including Mgat3, Psma6, and Siglecg relative to the LPS model group. KEGG signaling pathway analysis results showed that ZGC mainly acted through cytokine receptor interaction and the C-type lectin receptor signaling pathway. Conclusion: ZGC can interfere with the abnormal expression of 27 genes in inflammatory macrophages, and the related genes may exert corresponding anti-inflammatory effects by affecting cytokine receptor interactions, C-type lectin receptor signaling pathway, and TLR4/ NF-κB signaling pathway.
基金the National Key R&D Program of China(No.2020YFD0900204)the National Natural Science Foundation of China(No.32072947)+1 种基金the China Agriculture Research System of MOF and MARA(No.CARS-47)the KU-OUC Dual Master’s Program and Ocean University of China Scholarship Council。
文摘The caspase gene family is a crucial gene cluster that regulates apoptosis which contribute to programmed cell death,cell proliferation and differentiation,and several immune responses.In our study,a complete set of 12 caspase genes were identified in spotted sea bass Lateolabrax maculatus.These genes were divided into three subfamilies:2 inflammatory caspases(casp-1 and casp-14-like),5 apoptosis initiators(casp-2,casp-8a,casp-8b,casp-9,and casp-10),and 5 apoptosis executioners(casp-3a,casp-3b,casp-3-like,casp-6,and casp-7).Their phylogenetic relationships,synteny and gene structures were systematically analyzed.Furthermore,the relative expression profiles of the caspase family members in the liver,intestine,head kidney,and spleen were measured by q PCR after infection with Vibrio harveyi.The results showed that the overall mRNA levels of the caspase genes were dramatically increased after V.harveyi infection,and the expression patterns varied among genes and tissues.More caspase genes underwent pronounced expression changes in the head kidney and spleen than in the liver or intestine,mainly after 48 h of the challenge.Specifically,casp-3a,casp-3b,casp-3-like,casp-6,casp-7,casp-8a,casp-8b,casp-10,and casp-14-like in the head kidney,and casp-3-like,casp-6,casp-7,and casp-14-like in the spleen,were the most responsive caspase genes which may contribute significantly to immune regulation in spotted sea bass.Additionally,the apoptosis level in head kidney and spleen after infection were examined using the Caspase assay.Our study provides a systemic overview of the caspase gene family in spotted sea bass after V.harveyi infection and lays a foundation for further deciphering the biological roles of these caspase genes.
基金The Medical and Health Science and Technology Development Planning Project of Shandong Province(202103011061)。
文摘Objective:To clarify the effect of endurance training on the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise.Methods:A total of 45 male C57BL/6 mice were randomly divided into control(C),low-strength endurance training(LSET)and high-strength endurance training(HSET)groups(n=15).The mice in the control group were not conducted to platform training.The mice in the LSET and HSET groups were conducted to platform training at 30%and 60%of exhaustive exercise once a day for 5 days a week,respectively.The exhaustion exercise was performed after 5 weeks of platform training.Total RNA was extracted from myocardial tissues,and the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues was analyzed using Illimina transcriptome sequencing.Results:The distance and time of exhaustive exercise were longer in the LSET and HSET groups than in the control group,and the distance and time of exhaustive exercise were longer in the HSET group than in the LSET group(P<0.05).A total of 54 differentially expressed circRNAs(28 down-regulated and 26 up-regulated),7 differentially expressed lncRNAs(all down-regulated),3 differentially expressed miRNAs(1 down-regulated and 2 up-regulated)and 99 differentially expressed mRNAs(81 down-regulated and 18 up-regulated)were identified by transcriptome sequencing(P<0.05).Interaction network analysis revealed that ENSMUSG00000113041,MSTRG.79740,mmu-miR-374c-5p,18 down-regulated mRNAs and 3 up-regulated mRNAs formed a regulatory network.GO functional analysis revealed that the differentially expressed mRNAs were mainly enriched in primary metabolic processes and macromolecular synthesis and metabolic processes.KEGG pathway analysis revealed that the differentially expressed mRNAs were mainly enriched in complement and coagulation cascade pathways,estrogen signaling pathway and glucagon signaling pathway.Conclusion:Endurance training could alter the expression profile of circRNA-lncRNA-miRNA-mRNA in myocardial tissues of mice after exhaustive exercise,and these differentially expressed RNAs form a regulatory network that affects cardiomyocyte synthesis and metabolism and thus participates in the regulation of myocardial injury.
文摘CHDTEPDB(URL:http://chdtepdb.com/)is a manually integrated database for congenital heart disease(CHD)that stores the expression profiling data of CHD derived from published papers,aiming to provide rich resources for investigating a deeper correlation between human CHD and aberrant transcriptome expression.The develop-ment of human diseases involves important regulatory roles of RNAs,and expression profiling data can reflect the underlying etiology of inherited diseases.Hence,collecting and compiling expression profiling data is of critical significance for a comprehensive understanding of the mechanisms and functions that underpin genetic diseases.CHDTEPDB stores the expression profiles of over 200 sets of 7 types of CHD and provides users with more convenient basic analytical functions.Due to the differences in clinical indicators such as disease type and unavoidable detection errors among various datasets,users are able to customize their selection of corresponding data for personalized analysis.Moreover,we provide a submission page for researchers to submit their own data so that increasing expression profiles as well as some other histological data could be supplemented to the database.CHDTEPDB is a user-friendly interface that allows users to quickly browse,retrieve,download,and analyze their target samples.CHDTEPDB will significantly improve the current knowledge of expression profiling data in CHD and has the potential to be exploited as an important tool for future research on the disease.
基金Supported by The Special Agricultural Basic Cooperative Research Program of Yunnan Province(202301BD070001-229)Yunnan Fundamental Research Projects(202201AT070226)The Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities Association(2021BA070001-070).
文摘[Objectives]In order to clarify the regulatory effects of insect hormones on the expression of BmSuc1 and provide a reference for further analysis of the function and expression regulation mechanism of BmSuc1,this study explored the expression profiles of BmSuc1 in different tissues and periods of silkworm larvae and the expression changes of BmSuc1 after treatment with exogenous hormones.[Methods]By using the real-time fluorescence quantitative PCR technique,the expression characteristics of BmSuc1 were detected in different periods,different tissues and after treatment with exogenous hormones during the development of silkworm larvae.The expression of BmSuc1 and 20E receptor gene USP was detected after RNA interference with double-stranded RNA(dsRNA)of USP.[Results]The relative expression of BmSuc1 gene in the midgut was the highest,followed by the silk glands,epidermis and hemolymph.However,there was much lower or almost no expression in other tissues.In addition,the BmSuc1 expression profile exhibited a pulse-like pattern in silkworm larvae.The expression level of BmSuc1 was higher at each instar stage before molting,late fifth instar before cocooning and prepupal stage.Silkworm larvae at day 2 of the fifth instar were treated with 20-hydroxyecdysone(20E)and juvenile hormone(JH).It was found that the expression of BmSuc1 was extremely significantly higher at 12 and 18 h after 20E treatment than the control group injected with 0.1%dimethyl sulfoxide(DMSO)(P<0.01,the same below).But there were no significant difference in BmSuc1 expression between the JH treatment and the control group during the measurement time range(P>0.05).The dsRNA of USP was synthesized in vitro and injected into silkworm larvae at day 3 of the fifth instar.It was showed that the USP relative expression was extremely significantly down-regulated at 24 and 36 h after injection,which indicated that dsRNA interference was successful.RNAi of USP would block 20E signal transduction,and the expression of BmSuc1 was inhibited and significantly down-regulated at 24 and 36 h after injection of dsRNA of USP(P<0.05).[Conclusions]The BmSuc1 expression peaks appeared in the molting of silkworm larvae and the metamorphosis of larvae to pupae,which suggests that BmSuc1 may be involved in the metamorphic development process of silkworms.Treatment with exogenous ecdysone 20E can activate the expression of BmSuc1,but blocking the 20E signal transduction pathway may suppress expression of BmSuc1.It indicates that BmSuc1 as a downstream target gene in the 20E signal transduction pathway is directly or indirectly regulated by 20E signals.
文摘Tumor immunotherapy has emerged as a promising method in cancer treatment,but patient responses vary,necessitating personalized strategies and prognostic biomarkers.This study aimed to identify prognostic factors and construct a predictive model for patient survival outcomes and immunotherapy response.We curated six immunotherapy datasets representing diverse cancer types and treatment regimens.After data preprocessing,patients were stratified based on immunotherapy response.Differential gene expression analysis identified 22 genes consistently dysregulated across multiple datasets.Functional analysis provided critical insights,highlighting the enrichment of these dysregulated genes in immune response pathways and tumor microenvironment-related processes.To create a robust prognostic model,we meticulously employed a multistep approach.Initially,the identified 22 genes underwent rigorous univariate Cox regression analysis to evaluate their individual associations with patient survival outcomes.Genes showing statistical significance(p-values<0.05)at this stage advanced to the subsequent multivariate Cox regression analysis,which aimed to address potential confounding factors and collinearity among genes.From this analysis,we ultimately identified four key genes—ST6GALNAC2,SNORA65,MFAP2,and CDKN2B—that were significantly associated with patient survival outcomes.Incorporating these four key genes along with their corresponding coefficients,we constructed a predictive model.This model’s efficacy was validated through extensive Cox regression analyses,demonstrating its robustness in predicting patient survival outcomes.Furthermore,our model exhibited promising predictive capability for immunotherapy response,providing a potential tool for anticipating treatment efficacy.These findings provide insights into immunotherapy response mechanisms and suggest potential prognostic biomarkers for personalized treatment.Our study contributes to advancing cancer immunotherapy and personalized medicine.
基金the National Natural Science Foundation of China under Grants No.61872405 and No.61720106004the Key Project of Natural Science Foundation of Guangdong Province under Grant No.2016A030311040.
文摘The biological features of the valvular heart disease with atrial fibrillation(AF-VHD)remain unknown when involving long non-coding RNAs(lncRNAs).This study performed system analysis on lncRNA and messenger RNA(mRNA)expression profiles constructed by using bioinformatics methods and tools for biological features of AF-VHD.Fold change and t-test were used to identify differentially expressed(DE)lncRNAs and mRNAs.The enrichment analysis of DE mRNAs was performed.The subgroups formed by lncRNAs and nearby mRNAs were screened,and a transcriptional regulation network among lncRNAs,mRNAs,and transcription factors(TFs)was constructed.The interactions between mRNAs related to lncRNAs and drugs were predicted.The 620 AF-VHDrelated DE lncRNAs and 452 DE mRNAs were identified.The 3 lncRNA subgroups were screened.The 665 regulations mediated by lncRNAs and TFs were identified.The 9 mRNAs related to lncRNAs had 1 or more potential drug interactions,totaling 37 drugs.Of these,9 drugs targeting 3 genes are already known to be able to control or trigger atrial fibrillation(AF)or other cardiac arrhythmias.The found biological features of AF-VHD provide foundations for further biological experiments to better understand the roles of lncRNAs in development from the valvular heart disease(VHD)to AF-VHD.
基金supported by the National Natural Science Foundation of China(31301967)the Natural Science Foundation of Jiangsu Province,China(BK20161322)+4 种基金the projects of Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province(JQLAB-ZZ-201703)the Major Breeding Programs in Jiangsu Province,China(PZCZ201728)the earmarked fund for China Agriculture Research System(CARS-41)the Independent Scientific Foundation of Public Welfare Scientific Institutes in Jiangsu Province,China(BM2018026)the Open Projects of Key Laboratory of Chicken Genetics and Breeding,Ministry of Agriculture and Rural Affairs of China(CGB-201704)。
文摘Previous studies on mammals showed that peroxisome proliferator-activated receptor gamma coactivator-1α(PGC-1α)played a prominent role in regulating muscle fiber type transition and composition.However,the role of PGC-1αin chicken muscle has seldom been explored.To investigate the effect of PGC-1αon chicken skeletal muscles in this study,the PGC-1αgene was overexpressed or silenced in chicken primary myoblasts by using lentivirus,and then the effects of the PGC-1αgene overexpression and knockdown on the mRNA expression profile of genes related to myofiber type specificity were examined during fiber formation.The results showed that overexpression of PGC-1αfrom proliferation to differentiation was accompanied by the up-regulated expression of Pax7,MyoD,and CnAα,which was significantly(P<0.01)increased after one day of transfection(1 I).The enhancement of MyoG,MEF2 c,and MyHC SM expression lagged,which was improved significantly(P<0.01)after four days of transfection(1 I3 D).Overexpression of PGC-1αdecreased(P<0.01)the MyHC FWM expression after four days of transfection(1 I3 D),and it had no significant impact(P>0.05)on the expression of CnB1,NFATc3,and MyHC FRM during myofiber formation.The effective silence(P<0.01)of PGC-1αby lentivirus mediating short hairpin RNA(shRNA)was detected after four days of transfection(1 I3 D)in cultures,and the lack of its function in chicken primary myoblasts significantly(P<0.01)down-regulated the expression of Pax7,MyoD,CnAα,MyoG,MEF2 c,and MyHC SM,significantly(P<0.01)up-regulated the expression of MyHC FWM,and had no significant impact(P>0.05)on the expression of CnB1,NFATc3,and MyHC FRM.These results indicated that the role of PGC-1αin regulating the fiber type specificity of chicken skeletal muscles might be similar to that in mammals,which interplayed with key genes related to myocyte differentiation and calcineurin signaling pathway.
基金This research was funded by National Natural Science Foundation of China(31661143002,31771839,31701123and 31501034)Yunnan Applied Basic Research Projects(2016FB060 and 2016FB040).
文摘Stress-associated proteins(SAPs)are known as response factors to multiple abiotic and biotic stresses in plants.However,the potential physiological and molecular functions of SAPs remain largely unclear.Castor bean(Ricinus communis L.)is one of the most economically valuable non-edible woody oilseed crops,able to be widely cultivated in marginal lands worldwide because of its broad adaptive capacity to soil and climate conditions.Whether SAPs in castor bean plays a key role in adapting diverse soil conditions and stresses remains unknown.In this study,we used the castor bean genome to identify and characterize nine castor bean SAP genes(RcSAP).Structural analysis showed that castor bean SAP gene structures and functional domain types vary greatly,differing in intron number,protein sequence,and functional domain type.Notably,the AN1-C2H2eC2H2 zinc finger domain within RcSAP9 has not been often observed in other plant families.High throughput RNA-seq data showed that castor bean SAP gene profiles varied among different tissues.In addition,castor bean SAP gene expression varied in response to different stresses,including salt,drought,heat,cold and ABA and MeJA,suggesting that the transcriptional regulation of castor bean SAP genes might operate independently of each other,and at least partially independent from ABA and MeJA signal pathways.Cis-element analyses for each castor bean SAP gene showed that no common cis-elements are shared across the nine castor bean SAP genes.Castor bean SAPs were localized to different regions of cells,including the cytoplasm,nucleus,and cytomembrane.This study provides a comprehensive profile of castor bean SAP genes that advances our understanding of their potential physiological and molecular functions in regulating growth and development and their responses to different abiotic stresses.
基金funded by the National Natural Science Foundation of China(31672127 and 31572088)the Scientific Research Foundation of Horticulture College of Fujian Agriculture and Forestry University,China(2018S02)+1 种基金the Construction of Plateau Discipline of Fujian Province,China(102/71201801101)the Project of Fujian Academy of Agricultural Sciences,China(AB2017-4)。
文摘CCCH(C3 H) Zinc finger(Znf) transcription factors(TFs), as a novel type of Znf gene, regulate the expression of genes by binding to their mRNAs and play important roles in plant growth and development and abiotic stress resistance.Longan(Dimocarpous longan) is a tropical/subtropical fruit tree of great economic importance in Southeast Asia.However, genomic information on C3 H and their functions in longan are still unknown. In this study, a comprehensive analysis of the longan C3 H(DlC3 H) gene family was carried out. A total of 49 DlC3 H genes in three clades were identified from the longan genome database. Characteristics of the genes were analyzed with respect to gene structure,motif composition, phylogenetic tree and potential functions. The analysis of alternative splicing(AS) events suggested that AS events in DlC3 H genes were related to the transformation from longan non-embryonic to embryonic cultures.Promoter analysis indicated that most of the DlC3 H genes included cis-acting elements associated with hormones and stresses responses. Quantitative real-time PCR(qRT-PCR) analysis indicated that 26 of the 49 DlC3 Hs, which possess methyl jasmonate(MeJA) and abscisic acid(ABA) responsive cis-acting elements, showed differential expression patterns under treatment with ABA, MeJA and their endogenous inhibitors, suggesting that DlC3 Hs might be involved in the ABA and MeJA signaling pathways. The expression profiles of 17 of the 49 DlC3 Hs in non-embryonic callus and three tissues of embryonic cultures showed that only five of the 17 DlC3 Hs had the same expression trends as the FPKM trends in transcriptome data;the expression levels of DlC3 H07/14/16/36/49 in embryogenic callus and DlC3 H04/38 in globular embryos were high, suggesting that they have different functions in embryonic development. Further, we verified that DlC3 H01/03/05/11/19/39 were regulated by sRNAs by a modified 5’ RLM-RACE method. This study provides the first systematic analysis of C3 H genes in longan, and found that C3 H genes may be involved in hormone and stress responses, and somatic embryogenesis. Our preliminary investigation may provide clues to further studies on the characteristics and functions of this family in longan.
基金Supported by the National Natural Science Foundation of China Grants(No.81801523)the Natural Science Foundation of Guangdong Province(Nos.2017A030313789,2018A030313528,2019A1515011984)+3 种基金the Science and Technology Planning Foundation of Guangzhou City(201904010017,202102080102)Guangdong Province Medical Research Funding(No.A2021269)the Family Planning Research Institute Innovation Team of Guangdong Province grants(C-03)the Family Planning Research Institute of Guangdong Province Grants(S2018010).
文摘Piwi-interacting RNAs(piRNAs)is a novel class of non-coding RNAs.However,changes in piRNA expression profiles in recurrent spontaneous abortion(RSA)have not yet been investigated.The aim of this study was to identify differentially expressed piRNAs in deciduas of RSA patients.Decidua tissues were collected by curettage from recruited RSA patients and normal early pregnant(NEP)women with their informed consent.Small RNA sequencing was used to evaluate the differences in piRNA expression profiles between RSA and NEP.The present results demonstrated that the counts of total piRNA reads in RSA samples were increased compared with those in NEP samples(0.21%vs.0.11%).Differential expression analysis identified 29 upregulated piRNAs and 18 downregulated piRNAs in RSA samples.RT-qPCR further confirmed that the expression levels of uniq-109625,uniq-89328,uniq-50651 and uniq-4569 were decreased in 8 RSA tissues,compared with 13 NEP tissues.Otherwise,pi-22628 and uniq-173406 were increased in 8 RSA tissues.Based on GO term and KEGG pathway analysis,we speculate that these piRNAs regulate RSA by targeting extracellular matrix component pathway,cell adhesion pathway and focal adhesion pathway.PiRNAs may be involved in RSA pathogenesis by target genes function on adhesion and extracellular matrix component.
基金supported by the National Natural Science Foundation of China(81773013)the National Key Research and Development Program in China(2016YFC1303604)the Priority Academic Program Development of Jiangsu Higher Education Institutions(Animal Science and Veterinary Medicine)and Special Subject of Youth Science and Technology of Suzhou Vocational Health College(szwzy201910).
文摘Metformin is a first-line drug in the fight against type 2 diabetes.In recent years,studies have shown that metformin has some preventive and therapeutic effects on liver cancer,but the effects of metformin on the gene expression of liver cancer cells are not fully known.This study focused on the differences in the gene expression profiles in liver cancer cells treated with or without metformin.A total of 153 differentially expressed genes(DEGs)(FC>2 and q-values<0.001)were found,including 77 upregulated genes and 76 downregulated genes.These DEGs are involved in mitogen-activated protein kinase(MAPK),nuclear factor-kappa B(NF-κB),cell adhesion molecules(CAMs),and leukocyte transendothelial migration signaling pathways.These findings reveal the effects of metformin treatment on gene expression profiles in liver cancer cells and provide new clues for unveiling the mechanism of the antitumor effects of metformin.
基金Harbin Science and technology plan project(NO.2016RAXJ060)
文摘Objective:To study the effect of Baiban Ointment on gene expression profile of vulvar lichen sclerosus before and after treatment,and to provide theoretical basis for the early diagnosis and clinical treatment of vulvar lichen sclerosus.Methods:Nine patients with vulvar lichen sclerosus diagnosed pathologically were selected as the study object,and the Baiban ointment was applied locally for 3 months.Gene chip technology was used to detect the vulva skin tissue in the same area before and after treatment,and the peripheral normal skin was used as the normal control group to analyze the change of gene expression profile.FC and P values were used as research indicators,and the standard of differential expression was FC value≥1.5,P value<0.05.The differentially expressed genes were screened,and GO analysis and KEGG database gene pathway analysis were carried out.Results:Compared with the normal control group,there were 22 differentially expressed genes in Group A before treatment,of which 21 were up-regulated and 1 was down regulated;compared with Group B before treatment,there were 23 differentially expressed genes,all of which were up regulated.The differentially expressed genes related to Baiban ointment treatment included TBK1、STAT1、ITGAM、VCAN、PRKACB、PROM1、PLAT、SERPINA1.Go analysis showed that the up-regulated differential genes were mainly concentrated in the extracellular exosome,cytosol,extracellular space,Golgi apparatus and other cellular component,using the biological process such as positive regulation of cell metabolism,signal transduction regulation,cell adhesion,etc.,to play a role in protein binding,enzyme activity regulation and other molecular functions.KEGG signaling pathway showed that the differentially expressed genes were significantly enriched in Toll like receptor signaling pathway,Nod like receptor signaling pathway and Fc RI signaling pathway,all of which were up-regulated signaling pathways.Among them,Toll like receptor signaling pathway and Nod like receptor signaling pathway are most closely related to the disease.Conclusion:Baiban ointment may play a role in regulating metabolism,inflammation and immune response by regulating the expression of related genes,affecting the signal transduction such as Toll like receptor signal pathway.The pathway and the genes screened in this study will provide a direction for the future study of this disease.
基金This work was supported by the National Natural Science Foundation of China (No 30370904and No 30671258)the National High Technology Research and Development Program(863 project)of China (No 2006AA10Z121)the Program for New Century Excellent Talents in University(No NCET-07-0712)
文摘Cotton(Gossypium hirsutum L.) is the leading fiber crop and one of the mainstays of the economy in the world.Cotton fibers,as the main product of cotton plants,are unicellular,linear
基金This work was supported by the National Natural Science Fund of China(81573434/81872857)the Program for New Century Excellent Talents in Heilongjiang Provincial University(grant number 1252-NCET-013).
文摘Objective:Long noncoding RNAs(lncRNAs)play an important role in regulating the occurrence and development of cardiovascular diseases.However,the role of lncRNAs in heart aging remains poorly understood.The objective of this study was to identify differentially expressed lncRNAs in the heart of aging mice and elucidate the relevant regulatory pathways of cardiac aging.Materials and methods:Echocardiography was used to detect the cardiac function of 18-months(aged)and 3-months(young)old C57BL/6 mice.Microarray analysis was performed to unravel the expression profiles of lncRNAs and mRNAs,and qRT-PCR to verify the highly dysregulated lncRNAs.Results:Our results demonstrated that the heart function in aged mice was impaired relative to young ones.Microarray results showed that 155 lncRNAs were upregulated and 37 were downregulated,and 170 mRNAs were significantly upregulated and 44 were remarkably downregulated in aging hearts.Gene ontology analysis indicated that differentially expressed genes are mainly related to immune function,cell proliferation,copper ion response,and cellular cation homeostasis.KEGG pathway analysis showed that the differentially expressed mRNAs are related to cytokine-cytokine receptor interaction,inflammatory mediator regulation of TRP channels,and the NF-kappa B signaling pathway.Conclusion:These results imply that the differentially expressed lncRNAs may regulate the development of heart aging.This study provides a new perspective on the potential effects and mechanisms of lncRNAs in heart aging.
文摘Objective:To use the gene chip of pseudomonas aeruginosa as a research sample and to explore it at an omics level,aiming at elucidating the co-expression network characteristics of the virulence genes exoS and exoU of pseudomonas aeruginosa in the lower respiratory tract from the perspective of molecular biology and identifying its key regulatory genes.Methods:From March 2016 to May 2018,312 patients infected with pseudomonas aeruginosa in the lower respiratory tract who were admitted to Department of Respiratory Medicine of Baogang Hospital and given follow-up treatments in the hospital were selected as subjects by use of cluster sampling.Alveolar lavage fluid and sputum collected from those patients were used as biological specimens.The genes of pseudomonas aeruginosa were detected with the help of oligonucleotide probes to make a pre-processing of chip data.A total of 8 common antibiotics(ceftazidime,gentamicin,piperacillin,amikacin,ciprofloxacin,levofloxacin,doripenem and ticarcillin)against Gram-negative bacteria were selected to determine the drug resistance of biological specimens.MCODE algorithm was used to construct a co-expression network model of the drug-resistance genes focused on exoS/exoU.Results:The expression level of exoS/exoU in the drug-resistance group was significantly higher than that in the non-resistance group(p<0.05).The top 5 differentially expressed genes in the alveolar lavage fluid specimens from the drug-resistance group were RAC1,ITGB1,ITGB5,CRK and IGF1R in the order from high to low.In the sputum specimens,the top 5 differentially expressed genes were RAC1,CRK,IGF1R,ITGB1 and ITGB5.In the alveolar lavage fluid specimens,only RAC1 had a positive correlation with the expression of exoS and exoU(p<0.05).In the sputum specimens,RAC1,ITGB1,ITGB5,CRK and IGF1R were positively correlated with the expression of exoS and exoU(p<0.05).The genes included in the co-expression network contained exoS,exoU,RAC1,ITGB1,ITGB5,CRK,CAMK2D,RHOA,FLNA,IGF1R,TGFBR2 and FOS.Among them,RAC1 had a highest score in the aspect of regulatory ability(72.00)and the largest number of regulatory genes(6);followed by ITGB1,ITGB5 and CRK genes.Conclusions:The high expression of exoS and exoU in the sputum specimens suggests that pseudomonas aeruginosa has a higher probability to get resistant to antibiotics;RAC1,ITGB1,ITGB5 and CRK genes may be the key genes that can regulate the expression of exoS and exoU.
基金Qinghai Provincial Agricultural Science and Technology Achievements Transformation and Extension Project(2013-N-531).
文摘Background:The aim of this work is to detect and compare the peripheral blood mi RNA expression profiles in patients with severe traumatic brain injury(s TBI)2,12,24,48,and 72 h after injury at high altitude and to predict the target genes of differential expressed mi RNAs.Methods:Twenty s TBI patients from high-altitude areas were randomly selected according to the inclusion and exclusion criteria and were divided into five groups:the 2-h group,12-h group,24-h group,48-h group,and 72-h group.Peripheral blood mi RNA expression profiles were detected using real-time quantitative PCR(q RT-PCR).Results:The expression levels of mi R-18 a,mi R-203,mi R-146 a,mi R-149,mi R-23 b,and mi R-let-7 b in peripheral blood showed significant differences between the 2-h group and the 12-h group.The expression levels of mi R-203,mi R-146 a,mi R-149,mi R-23 b,and mi R-let-7 f in peripheral blood were up-regulated in the 24-h group.In the 48-h group,the expression levels of mi R-181 d,mi R-29 a,and mi R-18 b were upregulated.In the 72-h group,the expression levels of mi R-203,mi R-146 a,mi R-149,mi R-23 b,and mi R-let-7 f changed.The main target genes of the differentiation expressed mi RNAs were genes that regulate inflammatory responses,apoptosis,and DNA damage/repair.Conclusions:mi RNAs may be involved in the pathogenesis of s TBI by dynamically regulating the target genes that regulate inflammatory responses,apoptosis,and DNA damage/repair pathways.
文摘OBJECTIVES: To survey the gene expression profiles in pancreatic carcinoma by using cDNA microarrayand detect target genes for further study.METHODS: Three mixed samples from 2 cases of normal pancreatic tissue and 4 cases ofmoderate-differentiated pancreatic carcinoma were studied by means of cDNA microarray consisting of18 000 genes.RESULTS: 1484 and 1353 different expressed genes were observed in two cancer samples respectively.We identified 455 genes altered with the same tendency in both samples, including 102 up-regulated and353 down-regulated genes. There were 274 known genes and 181 unknown genes; 27.8% and 52.0%genes respectively had an expression level in cancer that was 2-fold higher or lower than that in normalsamples. Tumor suppressor genes, growth factors and receptor genes, signal conduction genes,transcription factor genes were identified.CONCLUSIONS: cDNA microarray is an efficient and high-throughout method to investigate geneexpression profiles in pancreatic carcinoma. MBD1, EDG1 and gene hypermethylation mechanism wouldplay an important role in the pathogenesis of pancreatic carcinoma.
基金funded by the National Natural Science Foundation of China(31372019)Key Laboratory of Urban Agriculture(North China)Ministry of Agriculture,P.R.China(kf2017015)the Beijing Municipal Education Commission(CEFF-PXM2017_014207_000043)
文摘CBF/DREB proteins play a critical role in abiotic stress-mediated gene expression and represent attractive regulons for plant breeding programs.However,no study has been conducted for CBF/DREB protein-related genes in jujube(Ziziphus jujuba Mill.).In this study,twenty-five ZjDREB genes were identified and annotated from the jujube(Z.jujuba‘Dongzao’)genome.Detailed analysis,including gene classification,annotation,phylogenetic evaluation,conserved motif determination and expression profiling were performed on all genes.Phylogenetic analysis showed that ZjDREB proteins were divided into five subgroups(A1–A5),but lacking a subgroup A6 corresponding to AtDREBs.The ZjDREB genes were distributed in nine of twelve chromosomes in the genome.Additionally,the expression patterns of the DREB genes under different abiotic stresses were investigated using q RT-PCR.Nineteen ZjDREB genes were down-regulated under low temperature,in contrast six ZjDREB genes(01,03,05,11,23 and 24)were up-regulated.Under drought,salinity and high temperature conditions,expression of ZjDREB03,09,10,14,15,17 and 20 genes were induced and showed similar expression patterns,suggesting that various stress conditions share common elements in the signaling pathway.The results suggest that the family of DREB genes play an important role in abiotic stresses in jujube,and provide a foundation for further functional studies of this important class of transcriptional regulators.
基金Supported by Taiwan’s SBIR promoting program from the De-partment of Industrial Technology of the Ministry of Economic Affairs,Advpharma,Incthe National Defense Medical Cen-ter(NDMC),Bureau of Military Medicine,Ministry of Defense,Taiwan
文摘AIM:Optimal molecular markers for detecting colorectal cancer(CRC)in a blood-based assay were evaluated.METHODS:A matched(by variables of age and sex)case-control design(111 CRC and 227 non-cancer samples)was applied.Total RNAs isolated from the338 blood samples were reverse-transcribed,and the relative transcript levels of candidate genes were analyzed.The training set was made of 162 random samples of the total 338 samples.A logistic regression analysis was performed,and odds ratios for each gene were determined between CRC and non-cancer.The samples(n=176)in the testing set were used to validate the logistic model,and an inferred performance(generality)was verified.By pooling 12 public microarray datasets(GSE 4107,4183,8671,9348,10961,13067,13294,13471,14333,15960,17538,and 18105),which included 519 cases of adenocarcinoma and 88 controls of normal mucosa,we were able to verify the selected genes from logistic models and estimate their external generality.RESULTS:The logistic regression analysis resulted in the selection of five significant genes(P<0.05;MDM2,DUSP6,CPEB4,MMD,and EIF2S3),with odds ratios of 2.978,6.029,3.776,0.538 and 0.138,respectively.The five-gene model performed stably for the discrimination of CRC cases from controls in the training set,with accuracies ranging from 73.9%to 87.0%,a sensitivity of 95%and a specificity of 95%.In addition,a good performance in the test set was obtained using the discrimination model,providing 83.5%ac-curacy,66.0%sensitivity,92.0%specificity,a positive predictive value of 89.2%and a negative predictive value of 73.0%.Multivariate logistic regressions analyzed 12 pooled public microarray data sets as an external validation.Models that provided similar expected and observed event rates in subgroups were termed well calibrated.A model in which MDM2,DUSP6,CPEB4,MMD,and EIF2S3 were selected showed the result in logistic regression analysis(H-L P=0.460,R2=0.853,AUC=0.978,accuracy=0.949,specificity=0.818 and sensitivity=0.971).CONCLUSION:A novel gene expression profile was associated with CRC and can potentially be applied to blood-based detection assays.
