Objective Using gene chip technology to explore the molecular mechanism of euphorbiasteroid in the treatment of non-small cell lung cancer(NSCLC).Methods A549 cells were used as the in vitro model,and they were random...Objective Using gene chip technology to explore the molecular mechanism of euphorbiasteroid in the treatment of non-small cell lung cancer(NSCLC).Methods A549 cells were used as the in vitro model,and they were randomly divided into control group and different concentrations of euphorbiasteroid administration groups.Each group had 3 duplicate wells,after the cells were cultured in vitro,the cell viability was evaluated by CCK-8 method.Gene chip technology was used to screen the differentially expressed genes(DEGs)between the control group and the euphorbiasteroid administration group.The differential genes were further analyzed for Gene Ontology(GO)function enrichment and Kyoto Encyclopedia of Genes and Genome(KEGG)pathway enrichment analysis.The STRING online analysis platform combined with Cytoscape software to construct a target protein interaction(PPI)network and perform topological analysis to screen key targets,and use Real-time PCR(RT-PCR)and molecular docking technology to verify key targets.Results According to the analysis of gene chip data,276 differentially expressed genes were screened,including 117 up-regulated genes and 159 down-regulated genes.GO analysis showed that differentially expressed genes were mainly involved in cell division,cell proliferation,cell cycle and other processes,involving protein binding,protein kinase binding and other functions,and were mainly distributed in nucleoplasm,chromosomes and other parts.KEGG signaling pathway analysis showed that differentially expressed genes were involved in cell cycle,pyrimidine metabolism,p53 signaling pathway and other pathways.PPI network analysis showed that CCNA2,TOP2A,CCNB1,CDC20,and RRM2 may be the key targets of euphorbiasteroid in the treatment of NSCLC.RT-PCR results showed that the expressions of CCNA2,TOP2A,CCNB1,CDC20,and RRM2 were significantly down-regulated in the euphorbiasteroid administered group,which was consistent with the gene chip results.Molecular docking results showed that euphorbiasteroid had good affinity with key targets and could bind spontaneously and stably.Conclusion The combination of gene chip,RT-PCR technology and molecular docking technology can find out the differential genes after the intervention of euphorbiasteroid,which can be used to explore the mechanism of euphorbiasteroid in the treatment of NSCLC.展开更多
Based on butterfly microfluidic gene chip technology,a method for rapid,accurate and efficient detection of 19 common pathogenic microorganisms of nosocomial infection was established,and a butterfly microfluidic gene...Based on butterfly microfluidic gene chip technology,a method for rapid,accurate and efficient detection of 19 common pathogenic microorganisms of nosocomial infection was established,and a butterfly microfluidic gene chip with high-throughput detection was designed and fabricated.Using constant temperature amplification technology,using the polymerase with chain replacement function to react at constant temperature(65℃)and combined with microfluidic chip technology,primers were designed according to the target genes of 19 pathogenic microorganisms,and a butterfly microfluidic gene chip which can detect 19 common pathogenic microorganisms of nosocomial infection was made to simplify the inspection operation process and verify the sensitivity of the chip.The butterfly microfluidic gene chip can be used for the rapid and efficient detection of 19 common pathogenic microorganisms of nosocomial infection,and provides a new idea for the detection and auxiliary diagnosis of pathogenic microorganisms of nosocomial infection.展开更多
AIM: In order to obtain lymphogenous metastasisassociated genes, we compared the transcriptional profiles of mouse hepatocarcinoma cell lines Hca-F with highly lymphatic metastasis potential and Hca-P with low lymphat...AIM: In order to obtain lymphogenous metastasisassociated genes, we compared the transcriptional profiles of mouse hepatocarcinoma cell lines Hca-F with highly lymphatic metastasis potential and Hca-P with low lymphatic metastasis potential.METHODS: Total RNA was isolated from Hca-F and Hca-P cells and synthesized into double-stranded cDNA. In vitro transcription double-stranded cDNA was labeled with biotin (i.e. biotin-labeled cRNA, used as the probe). The cRNA probes hybridized with Affymetrix GeneChip() MOE430A (containing 22 690 transcripts, including 14 500 known mouse genes and 4 371 ESTs) respectively and the signals were scanned by the GeneArray Scanner. The results were then analyzed by bioinformatics.RESULTS: Out of the 14 500 known genes investigated,110 (0.8%) were up regulated at least 23 fold. Among the total 4 371 ESTs, 17 ESTs (0.4%) (data were not presented) were up regulated at least 23 fold. According to the Gene Ontology and TreeView analysis, the 110genes were further classified into two groups: differential biological process profile and molecular function profile.CONCLUSION: Using high-throughput gene chip method,a large number of genes and their cellular functions about angiogenesis, cell adhesion, signal transduction, cell motility, transport, microtubule-based process, cytoskeleton organization and biogenesis, cell cycle, transcription,chaperone activity, motor activity, protein kinase activity,receptor binding and protein binding might be involved in the process of lymphatic metastasis and deserve to be used as potential candidates for further investigation.Cyclin D1, Fosl1, Hsp47, EGFR and AR, and Cav-1 are selected as the possible candidate genes of the metastatic phenotype, which need to be validated in later experiments.ESTs (data were not presented) might indicate novel genes associated with lymphatic metastasis. Validating the function of these genes is helpful to identify the key or candidate gene/pathway responsible for lymphatic metastasis, which might be used as the diagnostic markers and the therapeutic targets for lymphatic metastasis.展开更多
Objective The study is to identify the carrier rate of common deafness mutation in Chinese pregnant women via detecting deafness gene mutations with gene chip.Methods The pregnant women in obstetric clinic without hea...Objective The study is to identify the carrier rate of common deafness mutation in Chinese pregnant women via detecting deafness gene mutations with gene chip.Methods The pregnant women in obstetric clinic without hearing impairment and hearing disorders family history were selected.The informed consent was signed.Peripheral blood was taken to extract genomic DNA.Application of genetic deafness gene chip for detecting 9 mutational hot spot of the most common 4 Chinese deafness genes,namely GJB2(35delG,176del16bp,235delC,299delAT),GJB3(C538T),SLC26A4(IVS72A>G,A2168G)and mitochondrial DNA 12S rRNA(A1555G,C1494T).Further genetic testing were provided to the spouses and newborns of the screened carriers.Results Peripheral blood of 430 pregnant women were detected,detection of deafness gene mutation carriers in 24 cases(4.2%),including 13 cases of the GJB2 heterozygous mutation,3 cases of SLC26A4 heterozygous mutation,1cases of GJB3 heterozygous mutation,and 1 case of mitochondrial 12S rRNA mutation.18 spouses and 17 newborns took further genetic tests,and 6 newborns inherited the mutation from their mother.Conclusion The common deafness genes mutation has a high carrier rate in pregnant women group,235delC and IVS7-2A>G heterozygous mutations are common.展开更多
This study was aimed to screen human papillomavirus(HPV) types associated with esophageal squamous cell carcinoma of Kazakh in Xinjiang using the gene chip technique and study the clinical significance of this applica...This study was aimed to screen human papillomavirus(HPV) types associated with esophageal squamous cell carcinoma of Kazakh in Xinjiang using the gene chip technique and study the clinical significance of this application. The DNAs were collected from esophageal squamous cell carcinoma tissues and healthy esophageal mucosa of Kazakh adults in Xinjiang, and amplified firstly using HPV MY09/11 and then using HPV G5+/6+ to screen positive HPV specimens. These positive specimens were further detected by the gene chip technique to screen highly pathogenic HPV types. After determination with nested PCR amplification with HPV MY09/11 and G5+/6+, the infection rate of HPV was 66.67% in the esophageal squamous cell carcinoma group and 12.12% in the healthy control group. By testing the positive HPV specimens from the esophageal squamous cell carcinoma group, the infection rate of HPV16 was 97.72% and the co-infection rate of HPV16 and HPV18 was 2.27%. HPV16 infection may be involved in the development of esophageal squamous cell carcinoma in Xinjiang Hazakh adults.展开更多
AIM: To study the difference of gene expression in gastric cancer (T), pericancerous epithelium (P) and normal tissue of gastric mucosa (C), and to screen an associated novel gene in early gastric carcinogenesis by ol...AIM: To study the difference of gene expression in gastric cancer (T), pericancerous epithelium (P) and normal tissue of gastric mucosa (C), and to screen an associated novel gene in early gastric carcinogenesis by oligonudeotide microarray.METHODS: U133A (Affymetrix, Santa Clara, CA) gene chip was used to detect the gene expression profile difference in T, P and C, respectively. Bioinformatics was used to analyze the detected results.RESULTS: When gastric cancer was compared with normal gastric mucosa, 766 genes were found, with a difference of more than four times in expression levels. Of the 766 genes,530 were up-regulated (Signal Log Ratio [SLR]＞2), and 236 were down-regulated (SLR＜-2). When pericancerous epithelium was compared with normal gastric mucosa, 64genes were found, with a difference of more than four times in expression levels. Of the 64 genes, 50 were up-regulated (SLR＞2), and 14 were down-regulated (SLR＜-2). Compared with normal gastric mucosa, a total of 143 genes with a difference in expression levels (more than four times, either in cancer or in pericancerous epithelium) were found in gastric cancer (T) and pericancerous epithelium (P). Of the 143 genes, 108 were up-regulated (SLR＞2), and 35were down-regulated (SLR＜-2).CONCLUSION: To apply a gene chip could find 143 genes associated with the genes of gastric cancer in pericancerous epithelium, although there were no pathological changes in the tissue slices. More interesting, six genes of pericancerous epithelium were up-regulated in comparison with genes of gastric cancer and three genes were down-regulated in comparison with genes of gastric cancer. It is suggested that these genes may be related to the carcinogenesis and development of early gastric cancer.展开更多
OBJECTIVE: To study the preparation of diagnostic gene chip for detecting hepatitis B virus (HBV) andhepatitis C virus (HCV) and its accuracy in detecting HBV DNA and HCV RNA in serum and liver tissues.METHODS: The pr...OBJECTIVE: To study the preparation of diagnostic gene chip for detecting hepatitis B virus (HBV) andhepatitis C virus (HCV) and its accuracy in detecting HBV DNA and HCV RNA in serum and liver tissues.METHODS: The probes, which depend on the conservative gene fragment of hepatitis virus, wasdesigned, synthesized and spotted on the modified glass. The probes and some other control probes wereassembled on the diagnostic microarray of hepatitis virus. The gene of hepatitis virus, purified from bloodor tissue, was labeled with fluorescence and hybridized to the microarray. The hybridized microarry wasscanned with microarray scanner and the diagnostic result was analyzed from the scanning data. Fourtypatients with hepatitis B virus and 40 healthy people or 40 patients with hepatitis C virus were subjected todetection of HBV DNA and HCV RNA with the hepatitis virus gene chip by the double-blind method.Paraffin liver specimens obtained from 99 cases of posthepatitic cirrhosis were used to detect HBV DNA.The liver tissues and serum from 15 cases of chronic hepatitis B were used to detect HBV DNA.Simultaneously, HBsAg and HBcAg were detected in the serum by fluorescence microparticlequantitation, HBV DNA and HCV RNA in the serum by PCR, and HBcAg in liver tissues byimmunocytochemistry or HBV DNA by in situ molecular hybridization.RESULTS: Chip detection of serum specimens showed that 30 patients were HBV DNA positive and 10HBV DNA negative in the 40 patients with HBV positive, 25 patients were HCV RNA positive and 15patients were HCV RNA negative in the 40 patients with HCV positive, and all were HBV and HCVnegative in the 40 healthy people. In 15 patients with HBV marker positive who were subjected to liverbiopsy, 15 patients were detected HBV DNA positive in serum by gene chip, 15 patients HBcAg positivein liver tissues by immunocytochemistry, 14 patients HBV DNA positive in liver tissues by in situmolecular hybridization, and 14 patients HBV DNA positive in liver tissues by gene chip. Paraffin livertissues specimens from the 99 patients with posthepatitis B cirrhosis showed that 67 patients were detectedHBcAg positive by immunocytochemistry, 53 patients HBV DNA positive by in situ molecularhybridization, and 46 patients HBV DNA positive by gene chip. In the 46 patients, 40 patients weredetected HBV DNA and HBcAg positive by in situ molecular hybridization and immunocytochemistry, 6patients only HBcAg positive, and 33 patients HBcAg negative.CONCLUSIONS: The designed diagnostic gene chip can be used to simultaneously detect serum HBVDNA and HCV RNA, but the positive rate of HCV RNA diagnosed by this chip is lower. The gene chipcan detect HBV DNA in serum and in liver tissue.展开更多
The purified terephthalic acid (PTA) petrochemical wastewater molecula r toxicity detected by use of Mouse Genome 430A 2.0 GeneChip was conducted in th is research. The toxic dose to male mice was 0.03 g/(kg·d) o...The purified terephthalic acid (PTA) petrochemical wastewater molecula r toxicity detected by use of Mouse Genome 430A 2.0 GeneChip was conducted in th is research. The toxic dose to male mice was 0.03 g/(kg·d) of PTA in the wa stewater. The mice liver total RNA was isolated as the temple for synthesis of cDNA and then the cDNA as the temple for synthesis of cRNA. Hybridizing the cRN A with the target genes on the gene chip, there were 232 genes expression levels up-regulated and 74 genes down-regulated discovered obviously. The foremost 40 genes for both the highest and the lowest expression levels involved endogenetic steroid and hormone metabolism, immune system, the leukocyte activity and infla mmation, detoxification in liver, reproduction and growth hormone, regulation im mune factors of anti-tumor and anti-infection and cancer to the mice sampled. Th e data suggest the PTA wastewater contained over 5 aromatics and their toxicitie s integrated were much higher than the pure chemical PTA. And the pure chemical PTA toxicities data cannot be used to evaluate the toxicity of the PTA wastewate r instead.展开更多
Objective:To investigate the pharmacological action and mechanism of cholic acid derivatives in traditional Chinese medicine(TCM)based on the regulation of gene expression.Methods:Genome-wide gene expression profiles ...Objective:To investigate the pharmacological action and mechanism of cholic acid derivatives in traditional Chinese medicine(TCM)based on the regulation of gene expression.Methods:Genome-wide gene expression profiles of Michigan Cancer Foundation-7(MCF-7)cells treated with or without 4 cholic acid derivatives were detected by gene chip technology.Similarities in upregulated and downregulated genes were analyzed using the Connectivity Map(CMap)database.The affinity between cholic acid derivatives and the potential target was confirmed by molecular docking.The cholic acid derivative-regulated pathway enrichment analysis was performed by the STRING database,and the potential pathway was confirmed by in vitro experiments on MD Anderson-Metastatic Breast-231(MDA-MB-231)cells.Results:Compared with the reference genome in the CMap database,the gene expression profiles of cholic acid derivatives were similar to those of antipsychotic,anticancer,anti-inflammatory,and antiinfective drugs.Among them,4 derivatives were associated with antianxiety drugs,and molecular docking results showed that these compounds may act by binding to the ligand-binding site of gammaaminobutyric acid(GABA)receptors.Moreover,the cytoskeletal pathway is one of the pathways enriched in the derivatives.Of them,ursodeoxycholic acid showed significant inhibitory activity on the cytoskeleton formation of MDA-MB-231 cells.Conclusion:The gene expression detection method,combined with CMap and pathway enrichment analysis,could be used to study the mechanism of the active ingredients of TCM.In addition,our research showed that cholic acid derivatives have a potential affinity for membrane receptors,where they can exert anxiolytic activity by modulating opioid receptor,GABA receptor,and dopamine receptor.Moreover,ursodeoxycholic and chenodeoxycholic acid inhibit cytoskeleton formation,probably by acting on membrane proteins to activate the corresponding cytoskeletal pathways.展开更多
OBJECTIVE:To determine the mechanisms by which Kangxianling(KXL) treats renal interstitial fibrosis using a customized gene chip.METHODS:Twelve out of 18 specific pathogen-free sprague dawley(SPF SD) rats underwent a ...OBJECTIVE:To determine the mechanisms by which Kangxianling(KXL) treats renal interstitial fibrosis using a customized gene chip.METHODS:Twelve out of 18 specific pathogen-free sprague dawley(SPF SD) rats underwent a unilateral ureteral occlusion.These rats were then randomly assigned into either the model unilateral ureteral obstruction(UUO) or Kangxianling(KXL) group.The other six rats were assigned to the sham-operated group.The UUO and sham-operated groups were given normal saline via intragastric administration,whereas the KXL group was given KXL via intragastric administration.All rats were sacrificed for renal tissue collection(i.e.left nephridial tissue),and the detection of genetic changes with the customized chip.RESULTS:Compared to the sham-operated group,transforming growth factor-β1(TGF-β1),Smad2,and Smad3 genes were significantly up-regulated in the UUO group,with >1.5-fold rise(P<0.01).The Smad7 gene was significantly reduced in the UUO versus sham-operated group,with a down-regulation of >1.5-fold(P<0.01).In the KXL group,TGF-β1,Smad2,and Smad3 genes were significantly reduced compared to the UUO group,with a down-regulation of >1.5-fold(P<0.01),whereas the Smad7 gene was significantly increased compared to the UUO group,with an up-regulation of >1.5-fold(P<0.01).CONCLUSION:It was found that KXL can significantly reduce the gene levels of TGF-β1,Smad2,and Smad3.Immunohistochemistry findings also revealed significantly lower TGF-β1/Smads-mediated gene transcription activity.These findings suggest that KXL may negatively regulate the TGF-β1/Smads signal pathway to inhibit the occurrence of renal fibrosis.展开更多
Objective: To study the changes of the gene expression pattern of spinal cord tissues in the early stage after injury by DNA microarray (gene chip). Methods: The contusion model of rat spinal cord was established acco...Objective: To study the changes of the gene expression pattern of spinal cord tissues in the early stage after injury by DNA microarray (gene chip). Methods: The contusion model of rat spinal cord was established according to Allen’s falling strike method and the gene expression patterns of normal and injured spinal cord tissues were studied by gene chip. Results: The expression of 45 genes was significantly changed in the early stage after spinal cord injury, in which 22 genes up regulated and 23 genes down regulated. Conclusions: The expression of some genes changes significantly in the early stage after spinal cord injury, which indicates the complexity of secondary spinal cord injury.展开更多
The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of c...The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of cancer susceptibility. In preparing a gene chip for detecting polymorphisms on coding region of genes in hepatocellular carcinoma tissues, some cSNPs are of interest for their potential links with phenotype. METHODS: The genes harboring in loss regions with high frequency of hepatocellular carcinoma (HCC) were selected, the related information of cSNP sequences was obtained from the SNP database (dbSNP) of the National Center for Biotechnology Information (NCBI). Then appropriate primers and oligonucleotide probes were designed according to the SNP sites, and a gene chip for the detection of SNPs was constructed. The chip included 48 cSNPs of 25 hepatocellular carcinoma-related genes. The PCR products labeled by Dig-dUTP were hybridized with the cSNP chip. RESULTS:The sensitivity, influence by probe concentration, and reiteration of the chip were detected, with a high sensitivity of 6 × 10-3 ng/μl. The signal of hybridization was reduced with a lower concentration of probe. Seven polymorphisms of caspase 9 (rs2308941) C →T and DOK2 (rs2242241) T→G, 6 of polymorphisms of EGFL3 (rs947345) A→G, caspase 9 (rs2308938) C→G and PHGDH (rs1801955)T→A, 5 of polymorphisms of E2F2(rs3218170) G→A,4 of polymorphisms of MUTYH( rs1140507) T→C and BNIP3L(rs1055806)G→T, and 1 of polymorphism of TNFRSF1B (rs1061622)T→G were detected by the chip in the tissues of 10 HCC. Samples of caspase 9 (rs2308941G) and (rs2308941A) were verified by PCR-SSCP and sequencing. CONCLUSION:The cSNP chip of hepatocellular carcinoma-related genes can accelerate the discovery of polymorphic markers on hepatocellular carcinoma.展开更多
In this study,an Alzheimer's disease model was established in rats through stereotactic injection of condensed amyloid beta 1-40 into the bilateral hippocampus,and the changes of gene expression profile in the hip...In this study,an Alzheimer's disease model was established in rats through stereotactic injection of condensed amyloid beta 1-40 into the bilateral hippocampus,and the changes of gene expression profile in the hippocampus of rat models and sham-operated rats were compared by genome expression profiling analysis.Results showed that the expression of 50 genes was significantly up-regulated(fold change ≥ 2),while 21 genes were significantly down-regulated in the hippocampus of Alzheimer's disease model rats(fold change ≤ 0.5) compared with the sham-operation group.The differentially expressed genes are involved in many functions,such as brain nerve system development,neuronal differentiation and functional regulation,cellular growth,differentiation and apoptosis,synaptogenesis and plasticity,inflammatory and immune responses,ion channels/transporters,signal transduction,cell material/energy metabolism.Our findings indicate that several genes were abnormally expressed in the metabolic and signal transduction pathways in the hippocampus of amyloid beta 1-40-induced rat model of Alzheimer's disease,thereby affecting the hippocampal and brain functions.展开更多
Hypertrophic cardiomyopathy (HCM) is one of the diseases damaging people health most badly and some mutations of exons in cardiac troponin I (cTnI) gene are closely associated with family hypertrophic cardiomyopathy (...Hypertrophic cardiomyopathy (HCM) is one of the diseases damaging people health most badly and some mutations of exons in cardiac troponin I (cTnI) gene are closely associated with family hypertrophic cardiomyopathy (FHCM).A microarray was fabricated to screen mutations in exons 3,5,7,and 8 in cTnI gene.Primers were designed for the PCR (polymerase chain reaction) to amplify the target DNA fragments from fresh blood samples.In order to simplify the PCR process,multiplex PCR technology was investigated in detail.The concentration of Mg^(2+) played an important role in multiplex PCR process,a properly low concentration of Mg^(2+) submitted a better speciality of PCR products.The speciality was also favored when the annealing temperature was reasonably enhanced and 64℃is the optimal annealing temperature for the multiplex PCR systems.When applying the fabricated gene-chip to detect the target fragments from PCR mixture,the signal intensity sequence is in accordance with that from theoretic estimate.展开更多
基金This study was supported by the National Key Research and Development Program of China(Grant No.2018YFE0197900).
文摘Objective Using gene chip technology to explore the molecular mechanism of euphorbiasteroid in the treatment of non-small cell lung cancer(NSCLC).Methods A549 cells were used as the in vitro model,and they were randomly divided into control group and different concentrations of euphorbiasteroid administration groups.Each group had 3 duplicate wells,after the cells were cultured in vitro,the cell viability was evaluated by CCK-8 method.Gene chip technology was used to screen the differentially expressed genes(DEGs)between the control group and the euphorbiasteroid administration group.The differential genes were further analyzed for Gene Ontology(GO)function enrichment and Kyoto Encyclopedia of Genes and Genome(KEGG)pathway enrichment analysis.The STRING online analysis platform combined with Cytoscape software to construct a target protein interaction(PPI)network and perform topological analysis to screen key targets,and use Real-time PCR(RT-PCR)and molecular docking technology to verify key targets.Results According to the analysis of gene chip data,276 differentially expressed genes were screened,including 117 up-regulated genes and 159 down-regulated genes.GO analysis showed that differentially expressed genes were mainly involved in cell division,cell proliferation,cell cycle and other processes,involving protein binding,protein kinase binding and other functions,and were mainly distributed in nucleoplasm,chromosomes and other parts.KEGG signaling pathway analysis showed that differentially expressed genes were involved in cell cycle,pyrimidine metabolism,p53 signaling pathway and other pathways.PPI network analysis showed that CCNA2,TOP2A,CCNB1,CDC20,and RRM2 may be the key targets of euphorbiasteroid in the treatment of NSCLC.RT-PCR results showed that the expressions of CCNA2,TOP2A,CCNB1,CDC20,and RRM2 were significantly down-regulated in the euphorbiasteroid administered group,which was consistent with the gene chip results.Molecular docking results showed that euphorbiasteroid had good affinity with key targets and could bind spontaneously and stably.Conclusion The combination of gene chip,RT-PCR technology and molecular docking technology can find out the differential genes after the intervention of euphorbiasteroid,which can be used to explore the mechanism of euphorbiasteroid in the treatment of NSCLC.
基金Key Research and Development Plan Project of Ningxia Hui Autonomous Region(Project No.:2019BEG03026)Ningxia Overseas Returnees Innovation and Entrepreneurship Project(Project No.:2017-659)+2 种基金Ningxia Key Research and Development Plan Project(Project No.2018BFG02017)Ningxia Medical University Young Backbone Talents Training Program School-level Academic Technology Leader Reserve Cultivation ObjectFirst-Class Discipline Construction Founded Project of Ningxia Medical University and the School of Clinical Medicine(No.NXYLXK2017A05).
文摘Based on butterfly microfluidic gene chip technology,a method for rapid,accurate and efficient detection of 19 common pathogenic microorganisms of nosocomial infection was established,and a butterfly microfluidic gene chip with high-throughput detection was designed and fabricated.Using constant temperature amplification technology,using the polymerase with chain replacement function to react at constant temperature(65℃)and combined with microfluidic chip technology,primers were designed according to the target genes of 19 pathogenic microorganisms,and a butterfly microfluidic gene chip which can detect 19 common pathogenic microorganisms of nosocomial infection was made to simplify the inspection operation process and verify the sensitivity of the chip.The butterfly microfluidic gene chip can be used for the rapid and efficient detection of 19 common pathogenic microorganisms of nosocomial infection,and provides a new idea for the detection and auxiliary diagnosis of pathogenic microorganisms of nosocomial infection.
基金Supported by the National Natural Science Foundation of China,No. 30371583
文摘AIM: In order to obtain lymphogenous metastasisassociated genes, we compared the transcriptional profiles of mouse hepatocarcinoma cell lines Hca-F with highly lymphatic metastasis potential and Hca-P with low lymphatic metastasis potential.METHODS: Total RNA was isolated from Hca-F and Hca-P cells and synthesized into double-stranded cDNA. In vitro transcription double-stranded cDNA was labeled with biotin (i.e. biotin-labeled cRNA, used as the probe). The cRNA probes hybridized with Affymetrix GeneChip() MOE430A (containing 22 690 transcripts, including 14 500 known mouse genes and 4 371 ESTs) respectively and the signals were scanned by the GeneArray Scanner. The results were then analyzed by bioinformatics.RESULTS: Out of the 14 500 known genes investigated,110 (0.8%) were up regulated at least 23 fold. Among the total 4 371 ESTs, 17 ESTs (0.4%) (data were not presented) were up regulated at least 23 fold. According to the Gene Ontology and TreeView analysis, the 110genes were further classified into two groups: differential biological process profile and molecular function profile.CONCLUSION: Using high-throughput gene chip method,a large number of genes and their cellular functions about angiogenesis, cell adhesion, signal transduction, cell motility, transport, microtubule-based process, cytoskeleton organization and biogenesis, cell cycle, transcription,chaperone activity, motor activity, protein kinase activity,receptor binding and protein binding might be involved in the process of lymphatic metastasis and deserve to be used as potential candidates for further investigation.Cyclin D1, Fosl1, Hsp47, EGFR and AR, and Cav-1 are selected as the possible candidate genes of the metastatic phenotype, which need to be validated in later experiments.ESTs (data were not presented) might indicate novel genes associated with lymphatic metastasis. Validating the function of these genes is helpful to identify the key or candidate gene/pathway responsible for lymphatic metastasis, which might be used as the diagnostic markers and the therapeutic targets for lymphatic metastasis.
文摘Objective The study is to identify the carrier rate of common deafness mutation in Chinese pregnant women via detecting deafness gene mutations with gene chip.Methods The pregnant women in obstetric clinic without hearing impairment and hearing disorders family history were selected.The informed consent was signed.Peripheral blood was taken to extract genomic DNA.Application of genetic deafness gene chip for detecting 9 mutational hot spot of the most common 4 Chinese deafness genes,namely GJB2(35delG,176del16bp,235delC,299delAT),GJB3(C538T),SLC26A4(IVS72A>G,A2168G)and mitochondrial DNA 12S rRNA(A1555G,C1494T).Further genetic testing were provided to the spouses and newborns of the screened carriers.Results Peripheral blood of 430 pregnant women were detected,detection of deafness gene mutation carriers in 24 cases(4.2%),including 13 cases of the GJB2 heterozygous mutation,3 cases of SLC26A4 heterozygous mutation,1cases of GJB3 heterozygous mutation,and 1 case of mitochondrial 12S rRNA mutation.18 spouses and 17 newborns took further genetic tests,and 6 newborns inherited the mutation from their mother.Conclusion The common deafness genes mutation has a high carrier rate in pregnant women group,235delC and IVS7-2A>G heterozygous mutations are common.
文摘This study was aimed to screen human papillomavirus(HPV) types associated with esophageal squamous cell carcinoma of Kazakh in Xinjiang using the gene chip technique and study the clinical significance of this application. The DNAs were collected from esophageal squamous cell carcinoma tissues and healthy esophageal mucosa of Kazakh adults in Xinjiang, and amplified firstly using HPV MY09/11 and then using HPV G5+/6+ to screen positive HPV specimens. These positive specimens were further detected by the gene chip technique to screen highly pathogenic HPV types. After determination with nested PCR amplification with HPV MY09/11 and G5+/6+, the infection rate of HPV was 66.67% in the esophageal squamous cell carcinoma group and 12.12% in the healthy control group. By testing the positive HPV specimens from the esophageal squamous cell carcinoma group, the infection rate of HPV16 was 97.72% and the co-infection rate of HPV16 and HPV18 was 2.27%. HPV16 infection may be involved in the development of esophageal squamous cell carcinoma in Xinjiang Hazakh adults.
文摘AIM: To study the difference of gene expression in gastric cancer (T), pericancerous epithelium (P) and normal tissue of gastric mucosa (C), and to screen an associated novel gene in early gastric carcinogenesis by oligonudeotide microarray.METHODS: U133A (Affymetrix, Santa Clara, CA) gene chip was used to detect the gene expression profile difference in T, P and C, respectively. Bioinformatics was used to analyze the detected results.RESULTS: When gastric cancer was compared with normal gastric mucosa, 766 genes were found, with a difference of more than four times in expression levels. Of the 766 genes,530 were up-regulated (Signal Log Ratio [SLR]＞2), and 236 were down-regulated (SLR＜-2). When pericancerous epithelium was compared with normal gastric mucosa, 64genes were found, with a difference of more than four times in expression levels. Of the 64 genes, 50 were up-regulated (SLR＞2), and 14 were down-regulated (SLR＜-2). Compared with normal gastric mucosa, a total of 143 genes with a difference in expression levels (more than four times, either in cancer or in pericancerous epithelium) were found in gastric cancer (T) and pericancerous epithelium (P). Of the 143 genes, 108 were up-regulated (SLR＞2), and 35were down-regulated (SLR＜-2).CONCLUSION: To apply a gene chip could find 143 genes associated with the genes of gastric cancer in pericancerous epithelium, although there were no pathological changes in the tissue slices. More interesting, six genes of pericancerous epithelium were up-regulated in comparison with genes of gastric cancer and three genes were down-regulated in comparison with genes of gastric cancer. It is suggested that these genes may be related to the carcinogenesis and development of early gastric cancer.
文摘OBJECTIVE: To study the preparation of diagnostic gene chip for detecting hepatitis B virus (HBV) andhepatitis C virus (HCV) and its accuracy in detecting HBV DNA and HCV RNA in serum and liver tissues.METHODS: The probes, which depend on the conservative gene fragment of hepatitis virus, wasdesigned, synthesized and spotted on the modified glass. The probes and some other control probes wereassembled on the diagnostic microarray of hepatitis virus. The gene of hepatitis virus, purified from bloodor tissue, was labeled with fluorescence and hybridized to the microarray. The hybridized microarry wasscanned with microarray scanner and the diagnostic result was analyzed from the scanning data. Fourtypatients with hepatitis B virus and 40 healthy people or 40 patients with hepatitis C virus were subjected todetection of HBV DNA and HCV RNA with the hepatitis virus gene chip by the double-blind method.Paraffin liver specimens obtained from 99 cases of posthepatitic cirrhosis were used to detect HBV DNA.The liver tissues and serum from 15 cases of chronic hepatitis B were used to detect HBV DNA.Simultaneously, HBsAg and HBcAg were detected in the serum by fluorescence microparticlequantitation, HBV DNA and HCV RNA in the serum by PCR, and HBcAg in liver tissues byimmunocytochemistry or HBV DNA by in situ molecular hybridization.RESULTS: Chip detection of serum specimens showed that 30 patients were HBV DNA positive and 10HBV DNA negative in the 40 patients with HBV positive, 25 patients were HCV RNA positive and 15patients were HCV RNA negative in the 40 patients with HCV positive, and all were HBV and HCVnegative in the 40 healthy people. In 15 patients with HBV marker positive who were subjected to liverbiopsy, 15 patients were detected HBV DNA positive in serum by gene chip, 15 patients HBcAg positivein liver tissues by immunocytochemistry, 14 patients HBV DNA positive in liver tissues by in situmolecular hybridization, and 14 patients HBV DNA positive in liver tissues by gene chip. Paraffin livertissues specimens from the 99 patients with posthepatitis B cirrhosis showed that 67 patients were detectedHBcAg positive by immunocytochemistry, 53 patients HBV DNA positive by in situ molecularhybridization, and 46 patients HBV DNA positive by gene chip. In the 46 patients, 40 patients weredetected HBV DNA and HBcAg positive by in situ molecular hybridization and immunocytochemistry, 6patients only HBcAg positive, and 33 patients HBcAg negative.CONCLUSIONS: The designed diagnostic gene chip can be used to simultaneously detect serum HBVDNA and HCV RNA, but the positive rate of HCV RNA diagnosed by this chip is lower. The gene chipcan detect HBV DNA in serum and in liver tissue.
基金The Ph. D Fund of the National Education Ministry of China (No. 20030284038) and the Hi-Tech Research and DevelopmentProgram(863) of China(No. 2001AA214191)
文摘The purified terephthalic acid (PTA) petrochemical wastewater molecula r toxicity detected by use of Mouse Genome 430A 2.0 GeneChip was conducted in th is research. The toxic dose to male mice was 0.03 g/(kg·d) of PTA in the wa stewater. The mice liver total RNA was isolated as the temple for synthesis of cDNA and then the cDNA as the temple for synthesis of cRNA. Hybridizing the cRN A with the target genes on the gene chip, there were 232 genes expression levels up-regulated and 74 genes down-regulated discovered obviously. The foremost 40 genes for both the highest and the lowest expression levels involved endogenetic steroid and hormone metabolism, immune system, the leukocyte activity and infla mmation, detoxification in liver, reproduction and growth hormone, regulation im mune factors of anti-tumor and anti-infection and cancer to the mice sampled. Th e data suggest the PTA wastewater contained over 5 aromatics and their toxicitie s integrated were much higher than the pure chemical PTA. And the pure chemical PTA toxicities data cannot be used to evaluate the toxicity of the PTA wastewate r instead.
基金supported by the National Natural Science Foundation of China(22067016).
文摘Objective:To investigate the pharmacological action and mechanism of cholic acid derivatives in traditional Chinese medicine(TCM)based on the regulation of gene expression.Methods:Genome-wide gene expression profiles of Michigan Cancer Foundation-7(MCF-7)cells treated with or without 4 cholic acid derivatives were detected by gene chip technology.Similarities in upregulated and downregulated genes were analyzed using the Connectivity Map(CMap)database.The affinity between cholic acid derivatives and the potential target was confirmed by molecular docking.The cholic acid derivative-regulated pathway enrichment analysis was performed by the STRING database,and the potential pathway was confirmed by in vitro experiments on MD Anderson-Metastatic Breast-231(MDA-MB-231)cells.Results:Compared with the reference genome in the CMap database,the gene expression profiles of cholic acid derivatives were similar to those of antipsychotic,anticancer,anti-inflammatory,and antiinfective drugs.Among them,4 derivatives were associated with antianxiety drugs,and molecular docking results showed that these compounds may act by binding to the ligand-binding site of gammaaminobutyric acid(GABA)receptors.Moreover,the cytoskeletal pathway is one of the pathways enriched in the derivatives.Of them,ursodeoxycholic acid showed significant inhibitory activity on the cytoskeleton formation of MDA-MB-231 cells.Conclusion:The gene expression detection method,combined with CMap and pathway enrichment analysis,could be used to study the mechanism of the active ingredients of TCM.In addition,our research showed that cholic acid derivatives have a potential affinity for membrane receptors,where they can exert anxiolytic activity by modulating opioid receptor,GABA receptor,and dopamine receptor.Moreover,ursodeoxycholic and chenodeoxycholic acid inhibit cytoskeleton formation,probably by acting on membrane proteins to activate the corresponding cytoskeletal pathways.
基金Supported by National Natural Science Foundation of China Grant(30873259)/(81173219)Ministry of Science and Technology in the pharmaceutical industry,scientific research and special(201007005)+7 种基金Shanghai Science and Technology Innovation Plan of Action(11DZ1973100)Shanghai Excellent academic leaders Project Grant(08XD14039)E-institute of TCM Internal Medicine of Shanghai Municipal Education Commission Grant(E03008)Innovative Research Team in Universities,Shanghai Municipal Education Commission of GrantWenzhou Science & Technology Bureau of Grant(Y20070049)Wenzhou Municipal Health Bureau of Grant(2010A012)Wenzhou Center of Traditional Chinese Medicine Laboratory GrantZhejiang Province 151 and Wenzhou Municipal 551 Talented Grant
文摘OBJECTIVE:To determine the mechanisms by which Kangxianling(KXL) treats renal interstitial fibrosis using a customized gene chip.METHODS:Twelve out of 18 specific pathogen-free sprague dawley(SPF SD) rats underwent a unilateral ureteral occlusion.These rats were then randomly assigned into either the model unilateral ureteral obstruction(UUO) or Kangxianling(KXL) group.The other six rats were assigned to the sham-operated group.The UUO and sham-operated groups were given normal saline via intragastric administration,whereas the KXL group was given KXL via intragastric administration.All rats were sacrificed for renal tissue collection(i.e.left nephridial tissue),and the detection of genetic changes with the customized chip.RESULTS:Compared to the sham-operated group,transforming growth factor-β1(TGF-β1),Smad2,and Smad3 genes were significantly up-regulated in the UUO group,with >1.5-fold rise(P<0.01).The Smad7 gene was significantly reduced in the UUO versus sham-operated group,with a down-regulation of >1.5-fold(P<0.01).In the KXL group,TGF-β1,Smad2,and Smad3 genes were significantly reduced compared to the UUO group,with a down-regulation of >1.5-fold(P<0.01),whereas the Smad7 gene was significantly increased compared to the UUO group,with an up-regulation of >1.5-fold(P<0.01).CONCLUSION:It was found that KXL can significantly reduce the gene levels of TGF-β1,Smad2,and Smad3.Immunohistochemistry findings also revealed significantly lower TGF-β1/Smads-mediated gene transcription activity.These findings suggest that KXL may negatively regulate the TGF-β1/Smads signal pathway to inhibit the occurrence of renal fibrosis.
文摘Objective: To study the changes of the gene expression pattern of spinal cord tissues in the early stage after injury by DNA microarray (gene chip). Methods: The contusion model of rat spinal cord was established according to Allen’s falling strike method and the gene expression patterns of normal and injured spinal cord tissues were studied by gene chip. Results: The expression of 45 genes was significantly changed in the early stage after spinal cord injury, in which 22 genes up regulated and 23 genes down regulated. Conclusions: The expression of some genes changes significantly in the early stage after spinal cord injury, which indicates the complexity of secondary spinal cord injury.
文摘The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of cancer susceptibility. In preparing a gene chip for detecting polymorphisms on coding region of genes in hepatocellular carcinoma tissues, some cSNPs are of interest for their potential links with phenotype. METHODS: The genes harboring in loss regions with high frequency of hepatocellular carcinoma (HCC) were selected, the related information of cSNP sequences was obtained from the SNP database (dbSNP) of the National Center for Biotechnology Information (NCBI). Then appropriate primers and oligonucleotide probes were designed according to the SNP sites, and a gene chip for the detection of SNPs was constructed. The chip included 48 cSNPs of 25 hepatocellular carcinoma-related genes. The PCR products labeled by Dig-dUTP were hybridized with the cSNP chip. RESULTS:The sensitivity, influence by probe concentration, and reiteration of the chip were detected, with a high sensitivity of 6 × 10-3 ng/μl. The signal of hybridization was reduced with a lower concentration of probe. Seven polymorphisms of caspase 9 (rs2308941) C →T and DOK2 (rs2242241) T→G, 6 of polymorphisms of EGFL3 (rs947345) A→G, caspase 9 (rs2308938) C→G and PHGDH (rs1801955)T→A, 5 of polymorphisms of E2F2(rs3218170) G→A,4 of polymorphisms of MUTYH( rs1140507) T→C and BNIP3L(rs1055806)G→T, and 1 of polymorphism of TNFRSF1B (rs1061622)T→G were detected by the chip in the tissues of 10 HCC. Samples of caspase 9 (rs2308941G) and (rs2308941A) were verified by PCR-SSCP and sequencing. CONCLUSION:The cSNP chip of hepatocellular carcinoma-related genes can accelerate the discovery of polymorphic markers on hepatocellular carcinoma.
基金sponsored by the National Natural Science Foundation of China,No. 30973779
文摘In this study,an Alzheimer's disease model was established in rats through stereotactic injection of condensed amyloid beta 1-40 into the bilateral hippocampus,and the changes of gene expression profile in the hippocampus of rat models and sham-operated rats were compared by genome expression profiling analysis.Results showed that the expression of 50 genes was significantly up-regulated(fold change ≥ 2),while 21 genes were significantly down-regulated in the hippocampus of Alzheimer's disease model rats(fold change ≤ 0.5) compared with the sham-operation group.The differentially expressed genes are involved in many functions,such as brain nerve system development,neuronal differentiation and functional regulation,cellular growth,differentiation and apoptosis,synaptogenesis and plasticity,inflammatory and immune responses,ion channels/transporters,signal transduction,cell material/energy metabolism.Our findings indicate that several genes were abnormally expressed in the metabolic and signal transduction pathways in the hippocampus of amyloid beta 1-40-induced rat model of Alzheimer's disease,thereby affecting the hippocampal and brain functions.
文摘Hypertrophic cardiomyopathy (HCM) is one of the diseases damaging people health most badly and some mutations of exons in cardiac troponin I (cTnI) gene are closely associated with family hypertrophic cardiomyopathy (FHCM).A microarray was fabricated to screen mutations in exons 3,5,7,and 8 in cTnI gene.Primers were designed for the PCR (polymerase chain reaction) to amplify the target DNA fragments from fresh blood samples.In order to simplify the PCR process,multiplex PCR technology was investigated in detail.The concentration of Mg^(2+) played an important role in multiplex PCR process,a properly low concentration of Mg^(2+) submitted a better speciality of PCR products.The speciality was also favored when the annealing temperature was reasonably enhanced and 64℃is the optimal annealing temperature for the multiplex PCR systems.When applying the fabricated gene-chip to detect the target fragments from PCR mixture,the signal intensity sequence is in accordance with that from theoretic estimate.
