The value of bronchoalveolar lavage fluid genechip analysis for the identification of pathogens in children with refractory pneumonia / 中华实用儿科临床杂志

Objective:To investigate the value of bronchoalveolar lavage fluid (BALF) genechip analysis for the identification of pathogens in children with refractory pneumonia.Methods:A retrospective study of 500 children clinically diagnosed with refractory pneumonia in the Department of Respiratory and Critical Care Medicine, Kunming Children′s Hospital, Kunming Medical University between January 2020 to January 2022 was made.During hospitalization, bronchoscopic examination and bronchoalveolar lavage were performed.BALF was collected and analyzed using genechip technology to detect potential pathogens.At the same time, bacterial culture tests of sputum and BALF samples from the patients were performed. χ2 test was used to compare the positive rates of pathogens detected by different detection methods. Results:Of the 500 children patients, 482 cases (96.4%) were positive of BALF genechip analysis for pathogen identification.There were 71 cases (14.7%) infected with a single pathogen, and 411 cases (85.3%) with 2 or more pathogens.The top 3 bacteria were Streptococcus pneumoniae [117 cases (8.3%)], Haemophilus influenzae [63 cases (4.5%)], and Bordetella pertussis [32 cases (2.3%)]. The patients were mostly infected with respiratory syncytial virus [269 cases (19.1%)], followed by parainfluenza virus [217 cases (15.4%)], and adenovirus [132 cases (9.3%)]. Among the 500 patients, 116 cases (23.2%) were positive of BALF genechip analysis for bacteria identification, 47 cases (9.4%) had a positive BALF culture, 43 cases (8.6%) had a positive sputum culture.The bacterial detection rate of BALF genechip analysis was statistically significantly higher than that of BALF culture and sputum culture tests ( χ2=34.90, 39.85; all P<0.001). Conclusions:Most patients with refractory pneumonia have mixed infections.The genechip technology can rapidly and efficiently identify the pathogens, thus providing clinical guidance for anti-infection treatment.

Analysis of Gene Variation in Thymoma by Microarray / 中国肺癌杂志

BACKGROUND@#Thymoma is the most common malignant tumor in anterior mediastinum, and its specific pathogenesis is still unclear. This limits the study of targeted drugs for thymoma. The aim of the study is to investigate the genes and signal pathways of thymoma, and provide help for the research of thymic tumor pathogenesis using the technology of second-generation genechip to analyze thymoma.@*METHODS@#From January 2015 to December 2017, we analyzed 31 cases of thymoma by CapitaBio mRNA expression profile genechip technology, and then confirmed the genes by reverse transcription-polymerase chain reaction (RT-PCR).@*RESULTS@#We found some genes with different expression levels between thymoma and surrounding thymus tissue. Among them, six driving genes (FANCI, CAPD3, NCAPG, OXCT1, EPHA1 and MCM2) were significantly abnormal in thymoma. Some specific genes affected by copy-number variation were detected: E2F2, EphA1, CCL25 and MCM2 were significantly up-regulated, while IL-6, CD36, FABP4, SH2D1A and MYOC genes were significantly down-regulated. KEGG database analysis showed that the expression of 10 signaling pathway genes was generally up-regulated or down-regulated, such as systemic lupus erythematosus, viral oncogenes, primary immunodeficiency, cell cycle genes and p53 signaling pathway, which may be related to occurrence of thymoma.@*CONCLUSIONS@#We found a variety of genes abnormally expressed in thymoma, which will provide reference for the study of pathogenesis and biomarkers of thymoma in the future.

Analysis of HPV infection types distribution in normal cells and ASC-US in uterine cervix / 国际检验医学杂志

Objective To explore the clinical distribution and significant of 23 kinds of human papillomavir-us(HPV)genetypes in normal cells and atypical squamous cells(ASC-US),meanwhile analysis result of cervi-cal histological pathology diagnosis in cases of ASC-US.Methods A total of 1 000 women with normal cells specimens were recruited into control group,and 236 women with ASC-US were selected into the ASC-US group.Polymerase chain reaction(PCR)and gene-chips technology were utilized for the detection of 23 kinds of HPV genetypes,all cases of ASC-US diagnosis of cervical pathological histology.Results A total of 106 ca-ses of HPV infection were detected in the control group,as the total HPV infection rate was 10.6%,in which the single genotypes infection rate was 9.3% and the multiple genotypes infection rate was 1.3%.A total of 139 cases of HPV infection were detected in ASC-US group,as the total HPV infection rate was 58.9%,in which the single genotypes infection rate was 38.1%,and the multiple genotypes infection rate was 20.8%. There were significant differences on the total HPV infection rate,the infection rates of type 1 and multiple geontypes between the control group and ASC-US group(P<0.05).The top six of constituent ratio in the control group were type 43,16,58,33,52,18,42,those in the ASC-US group were type 16,18,52,58,33,51,66.Conclusion PCR combined with the gene-chip technology could be used in the HPV genotypes detection in cervical cells,which has important clinical significance on the further distribution management of ASC-US,and should be draw great attention.

TaqMan Real-time PCR,pyrosequencing and GeneChip microarray using the SNP protocol for rapid determination of ALDH2*2 in a Chinese population / 西安交通大学学报(医学版)

ABSTRACT:Objective To establish a rapid molecular method for the detection of aldehyde dehydrogenase-2 (ALDH2)and investigate the gene polymorphisms of ALDH2?2 and determine whether the polymorphic ALDH2 gene is associated with drinking behavior in a Chinese population.Methods The gene polymorphisms of ALDH2?2 were detected using pyrosequencing,TaqMan Real-time PCR and GeneChip microarray technologies;genotyping of 302 volunteers was performed to assess their genetic associations with alcohol use behavior.Results We developed pyrosequencing,TaqMan Real-time PCR and GeneChip microarray methods to identify ALDH2? 2 polymorphisms.The allele frequency of ALDH2?2 was 20.36% in the Chinese population:16.33% in the alcoholic group and 27.83% in non-drinkers (P=0.001).In contrast,the genotype frequency of heterozygous ALDH2?1/?2 plus homozygous ALDH2?2/?2 was 45.28% in non-drinkers and 32.65% in the alcoholics group (P=0.030). Allele frequency of ALDH2 genotypes differed significantly between our Chinese sample and other ethnic groups in Asia,and it was significantly higher than that in European and American countries.Conclusion The developed pyrosequencing,TaqMan Real-time PCR and GeneChip microarray methods are rapid,accurate,high-throughput, convenient,and reliable for detecting ALDH2 polymorphisms.ALDH2?2 gene can protect against the development of alcoholism.The allele frequency of ALDH2 in this Chinese population differs from that in other ethnic groups.

Clinical application of genechip based detection system in diagnosing mycobacterium infection and TB drug resistance gene mutation / 国际检验医学杂志

Objective To investigate the clinical application value of genechip detection system in the mycobacterial species iden-tification and drug resistance analysis .Methods The specimens of sputum ,punctured pus ,pleural and abdominal ascites ,cerebro-spinal fluid and so on were performed the Mycobacterium DNA detection by using the gene chip technique .Then Mycobacterium tuberculosis positive samples were further performed the drug-resistant analysis .Meanwhile the Ziehl-Neelsen acid-fast staining was adopted to detect the sample .The positive rates were compared between the two groups .And TB-IGRA was used to examine the tubercle bacillus infection in partial patients .Results In 4402 samples ,137 cases (3 .36% ) of M ycobacterium tuberculosis (MTB) and 11 cases(7 .4% ) of non-tuberculosis mycobacterium(NTM) were detected .Puncture solution ,bronchoalveolar lavage fluid and tissue specimen had higher positive rate .In the 137 positive M TB samples by rifampicin-resistant gene rpoB ,isoniazide-re-sistant gene katG and inhA detection ,22 cases of resistance gene mutations were detected ;the positive rate of genechip for detecting sputum ,cerebrospinal fluid ,hydrothorax and ascites was higher than that of acid-fast staining .TB-IGRA detection had higher pos-itive rate of TB infection than genechip .Conclusion The genechip detection system can directly conduct Mycobacterium identifica-tion and drug resistance analysis ,which is especially suitable for sputum ,cerebrospinal fluid ,hydrothorax and ascites samples ,and which is simple and rapid with higher sensitivity and good specificity .

Analysis on the feasibility of genechip method in detecting Mycobacterium tuberculosis drug resistance / 国际检验医学杂志

Objective To analyse the sensitivity ,specificity and coincidence rate of genechip method in the detection of resistance to antibacterial agents in Mycobacterium tuberculosis(MTB) ,in order to provide a convenient ,accurate and rapid method for detec‐ting antibacterial resistance in MTB .Methods The DNA sequencing was taken as gold standard ,and antibacterial resistance of the strains of MTB isolated from sputum specimens of 250 cases of patients with tuberculosis from August to December 2014 were de‐tected by using the genechip method and proportion method for susceptibility testing at the same time .Efficacies of the two methods in detecting MTB resistance to rifarnpin and isoniazid were compared .Results The MTB resistance rate to rifarnpin detected by u‐sing the genechip method and proportion method for susceptibility testing was 3 .0% and 3 .5% respectively ;that to isoniazid was 6 .7% and 8 .2% respectively .For detecting M TB resistance to rifarnpin and isoniazid ,the DNA sequencing was taken as gold standard ,the sensitivity ,specificity and coincidence rate of genechip method was higher than those of proportion method for suscep‐tibility testing ,and the test time of genechip method was shorter than that of proportion method for susceptibility testing ,there were statistically significant differences(P<0 .05) .Conclusion Using the genechip method to detecting MTB resistance to rifampin and isoniazid has high sensitivity ,specificity and coincidence rate ,which could replace the proportion method for susceptibility tes‐ting and become an effective method .

Study of the distribution of HPV infective genotypes in healthy women and cervical carcinoma patients / 国际检验医学杂志

Objective To compare the genotype distribution of HPV in cervical cells of natural crowd and tissues of cervical in‐traepithelial neoplasia(CINⅢ grade) and cervical carcinomas patients .Methods PCR and gene‐chip technology were utilized for the genotype detection of 23 kinds of HPV in cell specimens from 1 047 women of natural crowd (normal group) and tissue specimens from 173 cases of cervical intraepithelial neoplasia(precancerosis group) and 133 cases of patients with cervical carcinoma (cervical carcinoma group) .Results There were 109 ,159 and 121 cases of HPV positive specimens respectively in normal group ,precancer‐osis group and cervical carcinoma group ,and the HPV infection rates were 10 .41% (109/1 047) ,91 .91% (159/173) and 90 .98%(121/133) ,respectively .Conclusion PCR and gene‐chip technology can be used to detect HPV genotypes in cervical cells and cer‐vical tissues specimens .

Gene screening of Buyang Huanwu Decoction used for delaying denervated tibial muscle atrophy of rats / 中草药

Objective: To screen the target gene of Buyang Huanwu Decoction (BHD) used for delaying denervated tibial muscle atrophy of rats by genechip technique and to verify the differentially expressed gene PI3K. Methods: After 20 Sprague-Dawley (SD) rats were subjected to common peroneal nerve crush model of 5 mm injury, they were randomly divided into BHD and model groups, for daily ig administration of drugs after operation. The drug administration lasted for 18 d, the genechip analysis was performed to screen the differentially expressed gene. Then, RT-PCR and Western-blotting were used to detect the differential expression of PI3K and protein. Results: Compared with the model group, there was a significant difference of gene expression profile in BHD group. Among them, the expression of 14 genes had up-regulation and 10 genes had down-regulation. In the differential expression genes, Angptl4 and Pik3c2g had the more obvious change (up-regulation for 5-fold). Simultaneously, the validation tests showed: Compared with the model group, the PI3K mRNA and protein expression in the BHD mid- and high-dose (crude drug 12.96 and 25.92 g/kg) groups increased significantly (P < 0.05, 0.01). Conclusion: The preventive and therapeutic effects of BHD on denervated tibial muscle atrophy of rats are relevant with the regulation of many related genes. The mechanism may be as follows: promoting energy synthesis and blood neogenesis, neuroprotection, anti-apoptosis, and inhibition of collage synthesis; BHD could delay the denervated tibial muscle atrophy of rats by increasing the expression of PI3K and protein; The activation of PI3K/Akt signal transduction pathway probably play an important role in delaying the denervated muscle atropy by BHD.

Transcriptome response to nitrogen starvation in rice.

Nitrogen is an essential mineral nutrient required for plant growth and development. Insufficient nitrogen (N) supply triggers extensive physiological and biochemical changes in plants. In this study, we used Affymetrix GeneChip rice genome arrays to analyse the dynamics of rice transcriptome under N starvation. N starvation induced or suppressed transcription of 3518 genes, representing 10.88% of the genome. These changes, mostly transient, affected various cellular metabolic pathways, including stress response, primary and secondary metabolism, molecular transport, regulatory process and organismal development. 462 or 13.1% transcripts for N starvation expressed similarly in root and shoot. Comparative analysis between rice and Arabidopsis identified 73 orthologous groups that responded to N starvation, demonstrated the existence of conserved N stress coupling mechanism among plants. Additional analysis of transcription profiles of microRNAs revealed differential expression of miR399 and miR530 under N starvation, suggesting their potential roles in plant nutrient homeostasis.

The expression of interferon associated genes mRNA in patients with pulmonary embolism / 中华内科杂志

Objective To investigate the gene expression difference of IFN and their receptors in peripheral blood mononuclear cells (PBMC) of pulmonary embolism (PE) patients.Methods Twenty cases of PE patients and twenty sex and age matched controls were recruited into the study.Human cDNA microarray analysis was used to detect the gene expression difference of IFN associated genes between the two groups,and random variance model corrected t test was used to analyze the statistical data.Results In comparison with the control group, mRNA expression of type Ⅰ IFN, including IFNα5 mRNA,IFNα6 mRNA,IFNα8 mRNA,IFNα14 mRNA,IFNκ mRNA,IFNω1 mRNA,IFNε1 mRNA in PBMC of PE patients Were down-regulated (P ＜ 0.05 ).There was no significant difference in gene expression of type Ⅰ IFN receptors IFNαR1 and IFNαR2 between the PE and control groups (P ＞ 0.05 ).In comparison with the control group,mRNA expression of IFNγ gene was down-regulated ( P ＜ 0.05 ).The mRNA expression of IFNγR1 and IFNγR2 genes were upregulated compared with the control (P ＞ 0.05 ).Conclusion mRNA expression of type Ⅰ and type Ⅱ IFN in PE are significantly down-regulated,but not the IFN receptors.Reduced immune function may play an important role in the PE patients who are susceptible to virus,intracellular bacteria and parasites.

Differential expression profile in the progeny of normal human liver cells irradiated by 60Co γ-rays / 中华放射医学与防护杂志

Objective To investigate the differential expression profile in the progeny of human liver cells surviving from ionizing radiation.Methods Complemental DNA gene chip was used to measure the transcriptional profile in progeny of HL-7702 cells exposed to 0, 2, 4, and 6 Gy of 60Co γ-rays, and the differentially expressed genes HAVCR2 and RAN were further identified by real-time PCR.Results The transcription level of 262 genes, 2746 genes and 3406 genes changed in the progeny of survival cells at 2, 4 and 6 Gy, respectively.A total of 71 common differentially expressed genes were screened, most of which were associated with transduction, cell cycle regulation, cellular immunity, cytoskeleton and movement, cell replication and repair mechanism.Conclusions Ionizing radiation could induce the expression changes of many genes, which might reveal the molecular mechanisms of gene expression in radiation induced genomic instability.

Preliminary study on gene expression profiles of sporadic parathyroid adenoma with application of gene-chip technology / 中华内分泌外科杂志

Objective To investigate the differentially expressed genes in sporadic parathyroid adenomas using genechip and provide basis for further studying the mechanism and diagnosis of sporadic parathyroid adeno-mas. Methods Total RNA was extracted from normal parathyroid tissues and adenomas tissues. The mRNA was used to prepare probes. The mixed probes were hybridized to the cDNA microarray. After washing, the DNA chips were scanned by laser scanner. The acquired image was analyzed. Results Among the 47 000 target genes, 2302 genes were identified in sporadic parathyroid adenomas tissues that had at least two-fold changes compared to normal parathyroid tissues, and 1012 genes up-regulated and 1290 down-regulated were found in this study. Of 10 genes up-regulated and 27 down-regulated, the changes were over five-fold. The function of these changed genes was involved in transport, cell adhesion, signal transduetion, transcription, ion binding and so on. Conclusions Many parathyroid adenomas associated genes have been screened by high-throughout gene chip method, Which may help to identify the mechanism and diagnosis of sporadic parathyroid adenomas.

Analysis of deafness gene mutations by gene chip and its clinical significance / 临床耳鼻咽喉头颈外科杂志

Objective:To analyze deafness gene mutations by genechip. Method,The peripheral blood samples were obtained and DNA templates were extracted by extraction kits. The deafness gene mutations were distinguished by genechip. Resalt:Among 42 patients with non-syndromic hearing loss, GJB2 235de1C was found in 11cases (7 cases were homozygosis, 4 eases were heterozygosis);4 eases were shown to carry the PDS IVS7-2A＞G mutation. Conclusion: The incidence of GJB2 gene and PDS IVS7-2A＞G mutations among the deaf-mute children in Guiyang city is 38. 10%. Mole-cular genetic screening for these mutations and genetic counseling are effective methods to prevent the occurrence of hereditary heating loss.

A study on surface plasmon resonance-based gene chip system for rapid pathogen detection / 中华检验医学杂志

Objective To study application of surface plasmon resonance(SIR)system in detection of clinical pathogen with a gene chip.Methods 27 clinical samples were detected by SPR-based gene chip system.These samples were composed by 8 positive blood samples,3 positive pyoid samples,9 positive leucorrhea samples and positive reproductive tract pyoid samples,1 positive biopsy sample and 6 negative biopsy samples.Specific primers and probes for target pathogens were designed by bioinformatics methods and validated by PCR and enzyme-labelled chemiluminescence,respectively.SPR-based gene chip was prepared and utilized to detect clinical samples by SPR system.Results The primers and probes showed good specificity and accuracy,which can be applied to perform PCR and application of the gene chip.Compared with the clinical analysis,gene chip analysis of 26 clinical samples showed the consistent results.Conclusions SPR detection system proved to be accurate and reliable.The chip will have a promising prospect in application.

Identification of Nodal-regulated Genes in Zebrafish Embryos / 生物化学与生物物理进展

Nodal signals play important roles in mesendoderm induction, establishment of left-right asymmetry and anteroposterior patterning of the neuroectoderm during vertebrate embryogenesis. It is aimed at identifying Nodal-regulated genes in zebrafish embryos, particularly those encoding transcription factors. A (Affymetrix) genechip analysis was performed using RNAs derived from embryos injected with squint mRNA, MZoep mutant embryos that are deficient in Nodal signaling, and wildtype embryos at the 30% epiboly stage. Transcripts (genes) with at least two-fold changes in expression level between wildtype and the other samples were identified. In squint mRNA-injected embryos, 265 transcripts show an increased expression level and 111 have a decreased expression level; in MZoep embryos, the expression of 1 495 transcripts increases while 550 transcripts express at a decreased level. Furthermore, overexpression of squint causes increased expression of 26 and decreased expression of 11 annotated transcription factor genes; in MZoep embryos, the number of transcription factor genes showing an increase and decrease of expression are 69 and 30, respectively. These results would provide useful information for further studying mechanisms and biological functions of Nodal signal transduction.

The Influence of Peptidoglycan of Lactobacillus on Immune Function of Mouse / 中国生物工程杂志

Mice was stimulated by peptidoglycan from Lactobacillus sp and detect cytokines production。It was found that PG induced the production of inflammatory cytokines (IL-1,TNF-? in peritoneal macrophages,IFN-? in spleen cell)and did not induce the IL-2 production in spleen cell. Affymetrix MOE430A genechip was used to analyze changed gene expression of immune cells. It was found that expression of cytokines and related genes were changed under peptidoglycan administration. This might induced by activation of TLR-NF-?B signal pathway.

Apoptosis-Induced Gene Profiles of a Myeloma Cell P3-X63-Ag8.653

BACKGROUND: Apoptosis is a physiologic phenomenon involved in development, elimination of damaged cells, and maintenance of cell homeostasis. Deregulation of apoptosis may cause diseases, such as cancers, immune diseases, and neurodegenerative disorders. The mouse myeloma cell P3-X63-Ag8.653 (v653) is an HGPRT deficient (HGPRT) mutant strain. High dependency on de novo transcription and translation of aminopterin induced apoptosis of this cell seems to be an ideal experimental system for searching apoptosis-induced genes. METHODS & RESULTS: For searching apoptosis-related genes we carried out GE-array (dot blot), Affymetrix GeneChip analysis, Northern analysis and differential display-PCR techniques. The chip data were analyzed with three different programs. 66 genes were selected through Affymetrix GeneChip analyses. All genes selected were classified into 8 groups according to their known functions. They were Genes of 1) Cell growth/maintenance/death/ enzyme, 2) Cell cycle, 3) Chaperone, 4) Cancer/disease-related genes, 5) Mitochondria, 6) Membrane protein/signal transduction, 7) Nuclear protein/nucleic acid binding/ transcription binding and 8) Translation factor. Among these groups number of genes were the largest in the genes of cell growth/maintenance/death/enzyme. Expression signals of most of all groups were peaked at 3 hour of apoptosis except genes of Nuclear protein/nucleic acid binding/ transcription factor which showed maximum signal at 1 hour. CONCLUSION: This study showed induction of wide range of proapoptotic factors which accelerate cell death at various stage of cell death. In addition apoptosis studied in this research can be classified as a type 2 which involves cytochrome c and caspase 9 especially in early stages of death. But It also has progressed to type 1 in late stage of the death process.

Identification of Candidate Diagnostic Tumor Markers for Human Hepatocellular Carcinoma Using Genechip Technology / 中国普外基础与临床杂志

Objective To identify genes associated with hepatocellular carcinoma (HCC) as candidate diagnostic markers in a genome-wide scale. Methods The gene expression profiles of 40 pairs of HCC tumor tissue and peripheral non-tumorous liver tissue were analyzed by using gene chip technology.The gene chips were fabricated at the National Cancer Institute (NCI). Each gene chip contained 9 180 genes. The fluorescent targets were prepared by a direct labeling approach using two kinds of fluorescences as following: 100 ?g of total RNA from non-cancerous liver tissue was labeled with Cy3-dUTP and 200 ?g of total RNA from HCC was labeled with Cy5-dUTP. The targets were mixed together and hybridized with genes on the gene chips. Unsupervised hierarchical clustering analysis was done by CLUSTER and TREEVIEW software using median centered correlation and complete linkage. Results A total of 10 genes were found up-regulated in over 80% of primary tumors comparing with that of their corresponding non-tumorous liver tissues at a two-fold filter with an unsupervised hierarchical clustering algorithm, including protocadherin-alpha 9, ESTs, Homo sapiens cDNA FLJ, KPNA2, RPS20, SNRPE, CDKN2A, UBD, MDK and ANXA2. Conclusion These genes are supposed to be candidates for the diagnosis of HCC. Further investigation of these genes in a large scale of patients with HCC and patients with non-malignant hepatic diseases will be needed to disclose whether they could be used clinically as novel diagnostic tumor markers for HCC.

HLA-DQB1 gene polymorphisms in Guangdong province detected by genechip / 第三军医大学学报

*0603.Conclusion The GF data of Chinese in Southern China are useful to correlation of diseases and anthropologic research.

Effect of ischemic preconditioning on gene expression profile in small intestinal allografts in rats / 中国普通外科杂志

Objective To determine the changes of gene expression profile in small intestinal allograft in rats after ischemic preconditioning(IPC),and to study the mechanism of graft protection of IPC.Methods Rats are randomly divided into 3 groups:sham operation(S group),small bowel transplant(SBT group)and IPC small bowel transplant group(ISBT group).Total RNAs was extracted from intestine of the 3 groups 1h after the intestine remored and cold preservation/reperfusion,and then purified to mRNA.mRNAs was then reversely transcribed to cDNA and to prepare hybridization probes.The mixed probes were hybridized to the cDNA microarray.After high-stringent washing,the fluorescent signals on cDNA microarray were scanned and analyzed.Results Among the 4 096 target genes,297 differentially expressed genes were identified between normal intestine and intestinal allograft in ISBT group;among those 84 genes which have been reported,including 18 genes expressing down and 66 genes expressing up regulation.Differentially expressing genes could be related to the protective effect of IPC.Conclusions The mechanisms of protective effect of IPC on cells of the graft are by modulation of genes related to cell adhesion,related to cellular energy and metabolism,and related to the signal transmission of the cells.