痰涂片镜检、基因芯片技术及GeneXpert MTB/RIF对疑似肺结核患者的检测效能分析

目的分析痰涂片镜检、基因芯片及多色巢式荧光定量聚合酶链反应(GeneXpert MTB/RIF)对疑似肺结核患者的检测效能。方法选取2017年1月至2022年12月该院收治的疑似肺结核患者97例作为研究对象,均实施痰涂片镜检、基因芯片、GeneXpert MTB/RIF及痰液罗氏培养检查。以痰液罗氏培养结果为金标准,探究不同检测方式及联合检测对疑似肺结核的诊断效能,采用Kappa值检验与金标准诊断结果的一致性。结果痰液罗氏培养检测结果显示,97例疑似肺结核患者阳性55例,阴性42例,阳性检出率为56.70%(55/97)。痰液罗氏培养检出非结核分枝杆菌18株,包括鸟分枝杆菌4株,胞内分枝杆菌9株,偶发分枝杆菌1株,堪萨斯分枝杆菌3株,海分枝杆菌1株。痰涂片镜检检出阳性34例,真阳性29例,阳性检出率为35.05%(34/97),基因芯片检出阳性41例,真阳性37例,阳性检出率为42.27%(41/97);GeneXpert MTB/RIF检出阳性44例,真阳性37例,阳性检出率为45.36%(44/97)。基因芯片、GeneXpert MTB/RIF灵敏度、准确率高于痰涂片镜检,基因芯片与GeneXpert MTB/RIF敏感度一致,但基因芯片特异度高于GeneXpert MTB/RIF。非结核分枝杆菌中,痰涂片镜检检出鸟分枝杆菌1株、胞内分枝杆菌2株,基因芯片检出胞内分枝杆菌1株,GeneXpert MTB/RIF检出鸟分枝杆菌1株。痰涂片镜检、基因芯片、GeneXpert MTB/RIF三项联合检出阳性55例,真阳性53例,三项联合检测灵敏度为96.36%(53/55)、特异度为95.24%(40/42)、准确率为95.88%(93/97),均高于单一方法检测的灵敏度与准确率,差异均有统计学意义(P<0.05)。痰涂片镜检与痰液罗氏培养一致性为68.04%(Kappa=0.59);基因芯片与痰液罗氏培养一致性为77.32%(Kappa=0.70);GeneXpert MTB/RIF与痰液罗氏培养一致性为74.23%(Kappa=0.66);三项联合与痰液罗氏培养一致性为95.88%(Kappa=0.89)。结论较GeneXpert MTB/RIF、痰涂片镜检技术,基因芯片诊断效能及一致性更高,且3种技术联合诊断效能更高,临床可根据需求选择适宜诊断技术。

Gene Chip Analysis for Rice MicroRNA Response to Low Energy N^+ Beam Radiation

[Objective] The aim of this study was to explore the expression differences of miRNA response to low energy N＋ beam radiation in rice.[Method]Three groups of ion beam irradiation rice seeds and untreated rice seeds were selected respectively,and then the total RNA of seedlings after 96 h of germination was extracted at 30 ℃.Agilent gene chip was used to screen the differentially expressed genes of two groups of rice seedlings.The chip contained 510 miRNA probes;and about two times of expression differences between two samples were considered as the threshold range.[Result]14 miRNA molecules showed significant expression differences between the irradiated group and the control group,and all of them were decreased.[Conclusion]The miRNAs showed expression differences between irradiated group and the control group,which might regulate the expression of certain genes to respond to ion irradiation,thus producing physiological,biochemical and phenotypic differences.

APPLICATION OF GENETIC DEAFNESS GENE CHIP FOR DETECTION OF GENE MUTATION OF DEAFNESS IN PREGNANT WOMEN

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 genom- ic 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 mito- chondrial 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 carri- ers in 24 cases（4.2%）, including 13 cases of the GJB2 heterozygous mutation, 3 cases of SLC26A4 heterozygous mutation, 1 cases 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 muta- tion has a high carrier rate in pregnant women group, 235delC and IVS7-2A〉G heterozygous mutations are common.

Identify lymphatic metastasis-associated genes in mouse hepatocarcinoma cell lines using gene chip

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.

Gene Chip Technology Used in the Detection of HPV Infection in Esophageal Cancer of Kazakh Chinese in Xinjiang Province

Summary： 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/ll 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.

Gene expression profile differences in gastric cancer, pencancerous epithelium and normal gastric mucosa by gene chip

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.

Hepatitis gene chip in detecting HBV DNA, HCV RNA in serum and liver tissue samples of hepatitis patients

OBJECTIVE: To study the preparation of diagnostic gene chip for detecting hepatitis B virus (HBV) and hepatitis 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, was designed, synthesized and spotted on the modified glass. The probes and some other control probes were assembled on the diagnostic microarray of hepatitis virus. The gene of hepatitis virus, purified from blood or tissue, was labeled with fluorescence and hybridized to the microarray. The hybridized microarry was scanned with microarray scanner and the diagnostic result was analyzed from the scanning data. Fourty patients with hepatitis B virus and 40 healthy people or 40 patients with hepatitis C virus were subjected to detection 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 microparticle quantitation, HBV DNA and HCV RNA in the serum by PCR, and HBcAg in liver tissues by immunocytochemistry or HBV DNA by in situ molecular hybridization. RESULTS: Chip detection of serum specimens showed that 30 patients were HBV DNA positive and 10 HBV DNA negative in the 40 patients with HBV positive, 25 patients were HCV RNA positive and 15 patients were HCV RNA negative in the 40 patients with HCV positive, and all were HBV and HCV negative in the 40 healthy people. In 15 patients with HBV marker positive who were subjected to liver biopsy, 15 patients were detected HBV DNA positive in serum by gene chip, 15 patients HBcAg positive in liver tissues by immunocytochemistry, 14 patients HBV DNA positive in liver tissues by in situ molecular hybridization, and 14 patients HBV DNA positive in liver tissues by gene chip. Paraffin liver tissues specimens from the 99 patients with posthepatitis B cirrhosis showed that 67 patients were detected HBcAg positive by immunocytochemistry, 53 patients HBV DNA positive by in situ molecular hybridization, and 46 patients HBV DNA positive by gene chip. In the 46 patients, 40 patients were detected HBV DNA and HBcAg positive by in situ molecular hybridization and immunocytochemistry, 6 patients only HBcAg positive, and 33 patients HBcAg negative. CONCLUSIONS: The designed diagnostic gene chip can be used to simultaneously detect serum HBV DNA and HCV RNA, but the positive rate of HCV RNA diagnosed by this chip is lower. The gene chip can detect HBV DNA in serum and in liver tissue.

Association between Low-density Lipoprotein Receptor-related Protein 5 Polymorphisms and Type 2 Diabetes Mellitus in Han Chinese:a Case-control Study

Objective To investigate the association between low-density lipoprotein receptor-related protein 5 （LRPS） variants （rs12363572 and rs4930588） and type 2 diabetes mellitus （T2DM） in Han Chinese. Methods A total of 1842 T2DM cases （507 newly diagnosed cases and 1335 previously diagnosed cases） and 7777 controls were included in this case-control study. PCR-RFLP was conducted to detect the genotype of the two single nucleotide polymorphisms （SNPs）. Odds ratios （ORs） and 95% confidence intervals （95% CIs） were calculated to describe the strength of the association by logistic regression. Results In the study subjects, neither rs12363572 nor rs4930588 was significantly associated with T2DM, even after adjusting for relevant covariates. When stratified by body mass index （BMI）, the two SNPs were also not associated with T2DM. Among the 3 common haplotypes, only haplotype ~ was associated with reduced risk of T2DM （OR 0.820, 95% CI 0.732-0.919）. In addition, rs12363572 was associated with BMI （P〈0.001） and rs4930588 was associated with triglyceride levels （P=0.043） in 507 newly diagnosed T2DM cases but not in healthy controls. Conclusion No LRP5 variant was found to be associated with T2DM in Han Chinese, but haplotype TT was found to be associated with T2DM.

Preparation and analysis of cSNP chip on hepatocellular carcinoma-related genes

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.

Analysis of hippocampal gene expression profile of Alzheimer's disease model rats using genome chip bioinformatics

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.

PM2.5-induced Alterations of Gene Expression in HBE Cells Revealed by Gene Chip Analysis

PM2.5 are fine inhalable particles with diameters that are generally 2.5 micrometers and smaller and are characterized by a small particle size,a large surface area,and a strong toxin absorption ability[1-3].PM2.5 contains heavy metals and organic pollutants that are harmful to human health and exert carcinogenic,teratogenic,and mutagenic effects[4-7].PM2.5 has been classified as a human carcinogen by the International Agency for Research on Cancer(IARC)[2].The economy has developed rapidly making air pollution a serious environmental health problem in China.The purpose of this study was to explore the differentially expressed genes and pathways after a PM2.5 exposure in the human bronchial epithelial(HBE)cells via gene chip technology and bioinformatics analysis.

PTA wastewater molecular toxicity detected with gene chip

The purified terephthalic acid （PTA） petrochemical wastewater molecular toxicity detected by use of Mouse Genome 430A 2.0 GeneChip was conducted in this research. The toxic dose to male mice was 0.03 g/（kg, d） of PTA in the wastewater. The mice liver total RNA was isolated as the temple for synthesis of eDNA and then the cDNA as the temple for synthesis of cRNA. Hybridizing the cRNA 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 inflammation, detoxification in liver, reproduction and growth hormone, regulation immune factors of anti-tumor and anti-infection and cancer to the mice sampled. The data suggest the PTA wastewater contained over 5 aromatics and their toxicities 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 wastewater instead.

Fast species identification of mycobacterium by rpoB gene chip technology

Based on rpoB gene micro array as target gene, we are going to use gene chip technology to test 24 mycobacterium standard specimens, 8 non-mycobacterium specimens and 86 mycobacterium clinical isolated specimens. As a result, after mycobacterium and non-mycobacterium standard specimens were duplicated by PCR, mycobacterium standard specimens reproduced 360bp DNA fragments; on the other hand, non-mycobacterium specimens did not reproduce any fragments except for hemolytic streptococcus and corynebacterium pseudodiphtheriticum which had the same results as mycobacterium standard specimens. Sensitive test is able to detect lpg tuberculosis mycobacterium DNA. The probe test showed that, among 21 oligonucleotide probes, probe-M. fortuitum and M. marinum were cross-hybrid; the other probes were specific. We used the new method to identify 126 mycobacterium clinical isolated specimens. The test results of this new method matched with conventional method. In conclusion, compared to the traditional method, the use of rpob gene chip technology to identify mycobacterium species will be faster, more accurate and higher value in application.

Screening differentially expressed genes from cyclin B1 down-regulated by high-throughput gene chip

Objective: To study differentially expressed genes by silencing cyclin B1, and to sift out autophagy-related genes. Methods: Double thymidine deoxyribonucleoside blocking was used to synchronize nasopharyngeal carcinoma cell (CNE-2) to S phase, then flow cytometry was applied to test transfection efficiency. The mRNA and protein expression level of cyclin B1 was assessed by q-PCR and western blot, respectively. Differentially expressed genes were screened by high-throughput gene chip. Results: Double thymidine deoxyribonucleoside (2.5 mmol/L) blocking was used to synchronize the cell cycle to S phase. The transfection efficiency of CNE-2 cells was 85.6%. Compared with negative group,cyclin B1-siRNA treated group significantly down-regulated mRNA expression of cyclin B1 (80%) and protein level (75.3%). Totally, 2408 differentially expressed genes were found in CNE-2, including 1245 up-regulated genes and 1163 down-regulated genes. Moreover, PTEN, an autophagy-related gene, was preliminarily sifted out. Conclusions: Cyclin B1-siRNA significantly down-regulated the expression of cyclin B1 and yielded a total of 2408 differentially expressed genes, including PETN (an autophagy-related gene).

Effects of Euphorbiasteroid on gene expression in lung cancer cells based on gene chip

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.

Optimization of Multiplex PCR Systems for Gene-chip Detection of Mutations in Exons in cTnI Gene Associated with FHCM

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.

Study on the mechanism of cholic acid derivatives in traditional Chinese medicine based on the regulation of gene expression

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.

Research and Development of Butterfly Microfluidic Gene Chip for 19 Common Pathogenic Microorganisms of Nosocomial Infection

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.

基于Goldengate高通量耳聋基因芯片分析听力筛查未通过新生儿的耳聋基因突变类型

目的利用Goldengate高通量耳聋基因芯片技术,对听力筛查未通过新生儿的耳聋基因突变类型进行研究。方法选择2020年2月至2022年2月邢台医学高等专科学校第二附属医院284例听力筛查未通过新生儿,其中男性154例,女性130例;年龄3~10 d,平均年龄6.46 d(标准差1.57 d);体质量2.5~4.1 kg,平均体质量3.26 kg(标准差0.34 kg);家族史10例,用药史15例。采用Goldengate高通量耳聋基因芯片筛查耳聋基因。分析耳聋基因突变位点和类型,研究基因突变患儿与听力损失程度的关系。结果284例听力筛查未通过新生儿中耳聋基因突变32例(11.27%),其中SLC26A4突变18例(6.34%),GJB2突变9例(3.17%),GJB3突变3例(1.06%),TMC1突变1例(0.35%),MYO6突变1例(0.35%)。SLC26A4基因突变频率最高的2个位点分别为IVS7-2A>G(5例)、697G>C(4例),GJB2基因突变频率最高的2个位点分别为299_300delAT(4例)、235deIC(3例),GJB3、TMC1各突变位点仅有1例。18例SLC26A4突变新生儿的Goldengate高通量芯片与Sanger测序法检测结果基本一致。SLC26A4突变新生儿听力损失程度以轻中度为主,而GJB2突变新生儿听力损失程度以中重度为主,SLC26A4、GJB2突变新生儿的听力损失程度分布差异有统计学意义(χ^(2)=7.481,P=0.024)。结论Goldengate高通量耳聋基因芯片分析可准确检测听力筛查未通过新生儿的耳聋基因突变类型,其中聋病易感型基因主要为SLC26A4、GJB2。

基于网络药理学与GEO差异基因芯片数据探讨芦丁治疗脊髓损伤的作用机制

为了探究芦丁治疗脊髓损伤的作用机制,基于网络药理学和GEO差异基因芯片数据分析,结合体内实验,筛选芦丁对脊髓损伤的作用靶点.首先通过TCMSP、Swiss Target Prediction和SuperPred数据库获得芦丁的作用靶点,同时采用GEO差异基因、CTD、OMIM、PharmGkb疾病数据库获取脊髓损伤的疾病靶点;然后应用Cytoscape软件采用蛋白互作的方式筛选芦丁治疗脊髓损伤的核心靶点,并采用R语言对核心靶点进行GO功能及KEGG通路富集分析;最后采用Rutgers MASCIS脊髓损伤撞击器建立大鼠急性脊髓损伤模型,芦丁干预3 d后采用BBB运动评分法对大鼠后肢运动功能进行评价,采用酶联免疫吸附测定法检测脊髓中炎症因子TNF-α、IL-6、IL-1β和NF-κB的表达水平以及ROS和MDA含量.结果发现:(1)芦丁共有56个对应的蛋白靶点,脊髓损伤筛选到4 624个疾病靶点,合并后得到5个核心靶点,即CASP3、ESR1、GSK3B、IL-6、MTOR;(2) GO功能主要集中在对氧化应激的反应、活性氧代谢过程、NF-κB结合等,KEGG通路分析显示,芦丁治疗脊髓损伤相关的通路包括PI3K-Akt信号通路、AMPK信号通路、HIF-1信号通路等;(3)分子对接实验和分子动力学模拟表明,芦丁与5个核心靶点均有良好且稳定的结合;(4)体内实验结果显示,脊髓损伤后使用芦丁进行药物干预处理可以降低脊髓的含水量,减少炎性因子和氧化应激因子的产生.上述结果证实,芦丁可以通过多个靶点以及多条通路在治疗脊髓损伤中发挥抗炎和抗氧化作用.