A sensitive method to detect the hepatitis B virus mutations by using solid phase PCR on oligonucleotide array

A sensitive method based on solid phase PCR on oligonucleotide array was established to detect two point mutations 1896G-A and 1901G-A in hepatitis B virus (HBV) DNA, in which 6 probes including these two point mutations were immobilized on modified glass slides through 5' terminal linker, while the 3' terminal was made to be free. The mutated loci were designed to locate on the last nucleotides of 3' terminal respectively, and the positive control probes lacked the last nucleotide of 3' terminal in comparison with the probes used for detection. Probes fixed on oligonucleotide array were also the solid phase amplification primers. One pair of liquid primers was used to amplify the short template product from whole HBV DNA. Using target DNA as template, the solid primers were extended under the action of Taq DNA polymerase and incorporated with Cy-3dCTP as marker. During the thermal cycling reaction, probes served as solid phase amplification primers and amplification products bound to the oligonucleotide array, which could be visualized by incorporation with fluorescent dyes. After amplification, the oligonucleotide array was washed, performed with laser scanning, and then used for quantitative analysis to obtain the information for mutations. The hybridization results were compared with DNA sequencing. It was demonstrated that in case of sample A, the ratios of fluorescence intensities in wide type and in the mutated types of 1896G-A and 1901G-A mutations in HBV were 3.81:1 and 1:3.79 respectively, while, in case of sample B, those were 1:2.89 and 1:3.03 respectively, indicating the presence of point mutations in these two loci. These results correlated to those obtained from DNA sequencing analysis in which the fluorescence intensity ratios in wide type and in the mutated types of 1996G-A and 1901D-A mutations in HBV were 1.26:1 and 1.67:1 respectively. From the above observations, it is evident that the method using solid phase PCR based on oligonucleotide array appears to be a sensitive and promising way to detect mutations with low-density.

Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays

AIM： To detect the common intestinal pathogenic bacteria quickly and accurately.METHODS： A rapid （〈3 h） experimental procedure was set up based upon the gene chip technology, Target genes were amplified and hybridized by oligonucleotide microarrays.RESULTS： One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 （96.2%） were identified.CONCLUSION： Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus , Proteus sp., Bacillus cereus, Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range, and discrimination power of this assay can be continually improved by adding further oligonudeotides to the arrays without any significant increase of complexity or cost.

Using oligonucleotide suspension arrays for laboratory identification of bacteria responsible for bacteremia

The aim of this study was to develop and validate an oligonucleotide suspension array for rapid identification of 15 bacterial species responsible for bacteremia, particularly prevalent in Chinese hospitals. The multiplexed array, based on the QIAGEN LiquiChip Workstation, included 15 oligonucleotide probes which were covalently bound to different bead sets. PCR amplicons of a variable region of the bacterial 23S rRNA genes were hybridized to the bead-bound probes. Thirty-eight strains belonging to 15 species were correctly identified on the basis of their corresponding species-specific hybridization profiles. The results show that the suspension array, in a single assay, can differentiate isolates over a wide range of strains and species, and suggest the potential utility of suspension array system to clinical laboratory diagnosis.

Microarray,SAGE and their applications to cardiovascular diseases

The wealth of DNA data generated by the human genome project coupling with recently invented high-throughput gene expression profiling techniques has dramatically sped up the process for biomedical researchers on elucidating the role of genes in human diseases. One powerful method to reveal insight into gene functions is the systematic analysis of gene expression. Two popular high-throughput gene expression technologies, microarray and Serial Analysis of Gene Expression (SAGE) are capable of producing large amounts of gene expression data with the potential of providing novel insights into fundamental disease processes, especially complex syndromes such as cardiovascular disease, whose etiologies are due to multiple genetic factors and their interplay with the environment. Microarray and SAGE have already been used to examine gene expression patterns of cell-culture, animal and human tissues models of cardiovascular diseases. In this review, we will first give a brief introduction of microarray and SAGE technologies and point out their limitations. We will then discuss the major discoveries and the new biological insightsthat have emerged from their applications to cardiovascular diseases. Finally we will touch upon potential challenges and future developments in this area.

Genotype of ethanol metabolizing enzyme genes by oligonucleotide microarray in alcoholic liver disease in Chinese people

OBJECTIVE: To explore the relationship between genetic polymorphisms of the ethanol metabolizing enzymes and the occurrence of alcoholic liver disease (ALD). METHODS: Sixty-five healthy male controls and 165 alcoholisms (including 122 ALD patients and 43 male alcohol abusers without liver complications defined as alcohol-dependent) were analyzed by polymerase chain reaction and hybridized with oligonucleotide microarray to detect the polymorphisms of the ethanol metabolizing enzymes genes. RESULTS: The frequencies of alcohol dehydrogenase gene 2 * 1 ( ADH2 * 1 ) allele were shown as 37.69%, 46.51% and 59.02% in control, alcohol-dependent and ALD groups respectively; while those of ADH2 * 2 allele were shown as 62.31 %, 53.49% and 40.98% respectively. No ADH2 * 3 was detected in any of the subjects. The frequency of ADH2 * 1 was significantly higher in alcoholisms (ALD group and alcohol-dependent group) than in healthy controls ( P

Differential gene expression during capillary morphogenesis in a microcarrier-based three-dimensional in vitro model of angiogenesis with focus on chemokines and chemokine receptors

AIM:To globally compare the gene expression profiles during the capillary morphogenesis of human microvascular endothelial cells (HMVECs) in an in vitro angiogeness system with affymetrix oligonucleotide array. METHODS: A microcarrier-based in vitro angiogenesis system was developed, in which ECs migrated into the matrix, proliferated, and formed capillary sprouts. The sprouts elongated, branched and formed networks. The total RNA samples from the HMVECs at the selected time points (0.5, 24, and 72 h) during the capillary morphogenesis were used for microarray analyses, and the data were processed with the softwares provided by the manufacturers. The expression patterns of some genes were validated and confirmed by semi-quantitative RT-PCR. The regulated genes were grouped based on their molecular functions and expression patterns, and among them the expression of chemokines and chemokine receptors was specially examined and their functional implications were analyzed. RESULTS: A total of 1 961 genes were up- or downreg-ulated two-folds or above, and among them, 468 genes were up- or down-regulated three-folds or above. The regulated genes could be grouped into categories based on their molecular functions, and were also clustered into six groups based on their patterns of expression. As for chemokines and chemokine receptors, CXCL1/GRO-α, CXCL2/GRO-β, CXCL5/ENA-78, CXCL6/GCP2, IL-8/CXCL8, CXCL12/SDF-1, CXCL9/Mig, CXC11/ITAC, OOCL1/fractalkine, CCL2/MCP-1, CCL3, CCL5/RANTES, CCL7, CCL15, CCL21, CCL23, CCL28, and CCR1, CCR9, CXCR4 were identified. Moreover, these genes demonstrated different changing patterns during the capillary morphogenesis, which implied that they might have different roles in the sequential process. Among the chemokines identified, CCL2/MCP-1, CCL5/RANTES and CX3CL1 were specially up-regulated at the 24-h time point when the sprouting characterized the morphological change. It was thus suggested that they might exert crucial roles at the early stage of angiogenesis. CONCLUSION: The present study demonstrates a global profile of gene expression during endothelial capillary morphogenesis, and the results provide us much information about the molecular mechanisms of angiogenesis, with which further evaluation of individual genes can be conducted.

Microarray analysis of extracellular matrix genes expression in myocardium of mouse with Coxsackie virus B_3 myocarditis

Background Extracellular matrix (ECM) orchestrates cell behaviour including growth, death, apoptosis, adhesion, migration, and invasion by activating several signalling pathways Certain components of ECM, such as integrins, may act as receptors or co-receptors of enterovirus ECM-activated gene expressions in myocardium of viral heart disease including myocarditis and partial cardiomyopathy remain elusive This study was to investigate the expression of ECM-activated genes in myocardium of mouse with viral myocarditis Methods BALB/c mice were infected with Coxsackie virus B 3 (CVB 3) to establish an animal model of myocarditis Uninfected mice were also prepared and served as controls Specific mRNA expression pattern in myocarditic mouse heart was analysed by an in-house cDNA microarray containing 8192 genes Overexpressed ECM genes were selected and subsequently confirmed by Northern blot analysis Results Nine ECM genes were isolated, from the array of 8192 genes, as overexpressed genes in hearts of myocarditic mice in comparison with controls Subsequent Northern blot analysis confirmed that four of the nine genes were highly expressed Expression of these four genes, Fin15, ILk, Lamr1 and ADAMTS-1, has not been reported previously to be induced by Coxsackie virus Conclusion CVB 3-induced myocarditis is associated with gene expression profiles of certain ECM components

Effect of acupuncture at Renying(ST 9) on gene expression profile of hypothalamus in spontaneously hypertensive rats

OBJECTIVE: To investigate changes in gene expression profiles in the hypothalamus related to the effects of acupuncture at the Renying(ST 9) acupoint in spontaneously hypertensive(SH) rats.METHODS: We randomly divided 18 SH rats into Renying(ST 9) group and model control group, 9 body weight-matched Wistar-Kyoto rats were used as blank controls. Acupuncture was performed manually for 20-min daily over 28 d in the Renying(ST 9) group. Rat Gene 2.0 array technology was used for the determination of gene expression profiles and the screened key genes were verified by real-time quantitative polymerase chain reaction(RT-PCR) analyses.RESULTS: The different groups exhibited differential gene expression: compared with the blank control group, 48 genes were up-regulated and 91 genes were down-regulated in the model group;compared with the model group, 79 genes were up-regulated and 80 genes were down-regulated in Renying(ST 9) group. The RT-PCR results of the key genes including Chi3 l1, Ephx2, Klk1, 5-HT1 A and Cbs were consistent with that of gene chip analysis.CONCLUTION: Acupuncture at Renying(ST 9)could significantly lower the blood pressure of SH rats and affect their hypothalamic gene expression profile. Genes associated with the contraction of vascular smooth muscle and the regulation of inflammation, neurotransmitters may be involved in acupuncture's antihypertensive mechanism.

Pallister-Killian syndrome： meiosis Ⅱ non-disjunction may be the first step in the formation of isochromosome 12p

Pallister-Killian syndrome （PKS） is a rare and sporadic genetic disorder due to tissue-limited mosaicism for supernumerary isochromosome 12p（i（12p））, which is usually absent or at low-level mosaicism in cultured lymphocytes but present in fibroblasts. PKS was first described in adults by Pallister in 19771 and later in children by Killian and Teschler-Nicola in 1981.2 An accurate incidence is unknown. It is clinically characterized by profound mental retardation, seizures,hypotonia, supernumerary nipples, pigmentary dysplasia,diaphragmatic hernia, ＂coarse＂ face, including prominent forehead with sparse anterior scalp hair, hypertelorism,short nose with anteverted nares, flat nasal bridge, long philtrum, cleft palate and short neck. Here we report a patient with PKS, who is the first confirmed case with PKS in China's Mainland. Molecular analysis was performed to explore the formation mechanism of i（12p）.The results suggest that the maternal meiosis Ⅱ sister chromatid non-disjunction was likely the first step in the formation of i（12p）, followed by postzygotic mitotic centromeric misdivision.

Polymorphisms of GSTM1 and CYP1A1 genes and their genetic susceptibility to prostate cancer in Chinese men

Background Variation in prostate cancer incidence between different racial groups has been well documented, for which genetic polymorphisms are hypothesized to be an explanation. We evaluated the association between polymorphisms in the cytochrome P-450 CYP1A1 （CYP1A1） and glutathione S-transferase M1 （GSTM1） genes and genetic susceptibility to prostate cancer in Chinese men.Methods TWO hundred and eight prostate cancer patients and 230 age matched controls were enrolled in this study. All DNA samples from peripheral blood lymphocytes were genotyped for common genetic polymorphisms of the CYP1A1 and GSTM1 genes using the oligonucleotide microarray （DNA chip） technique and the polymorphism results confirmed by sequencing. The different polymorphisms in prostate cancer patients were also analyzed according to age at diagnosis, prostate specific antigen level, cancer stage and grade （Gleason score）.Results The prevalence of the GSTM1 （0/0） genotype was significantly higher in prostate cancer patients （58.2%） than in controls （41.7%, P〈0.05）. Further analysis demonstrated that the prostate cancer patients with a GSTM1 （0/0） genotype were younger than those with the GSTM1 （＋/＋） genotype （P=-0.024）. No significant differences in the frequency distributions of CYP1A1 polymorphisms were observed between prostate cancer patients and controls.Conclusion GSTM1 （0/0）-gene polymorphism may be linked to prostate cancer risk and early age of Onset in Chinese.

Analysis of differentially expressed genes in fetal skin of scarless and scar-forming periods of gestational rats

Objective ：To study the differences of gene expression between earlier gestational skin and later gestational skin of rats with the aids of single primer amplification （SPA） and high-density oligonucleotide DNA array to understand the molecular mechanism of scarless healing. Methods： Total RNAs were isolated from fetal rat skin of the scarless（E15） and scar-forming （ E18 ） periods of gestation （term = 21.5 days）. The RNAs from earlier gestational skin （ EGS ） and later gestational skin （ LGS ） were both reversely transcribed to cDNAs, then labeled with the incorporation of fluorescent dCTP for preparing the hybridization probes by SPA method. The mixed probes were then hybridized to the oligonucleotide DNA arrays which contained 5 705 probes representing 5 705 rat genes. After highly stringent washing, these DNA arrays were scanned for fluorescent signals to display the differentially expressed genes between the 2 groups of skin. Results. Among 5 705 rat genes, there were 53 genes （0.93%） with differentially expressed levels between EGS and LGS groups, 27 genes, including fibroblast growth factor 2 （ FGF2 ） and follistatin were up-regulated （0.47%） and 26 genes were down-regulated （0.46%） in fetal skin during scarless period versus scar-forming period. Higher expressions of FGF2 and follistatin in EGS than those in LGS were also revealed by RT-PCR method. Conclusions： High-density oligonucleotide DNA array provided a powerful tool for investigating differential gene expression in earlier and later gestational fetal skins. This technology validates that the mechanism of fetal scarless healing is very complicate and the change of many gene expressions is associated with fetal scarless healing.

Study on Effects of Acupuncture at the Heart Meridian on Gene Expression Pattern of Hypothalamus in Rats with Acute Myocardial Ischemia

Objective： To discovery the central mechanism of acupuncture Heart Meridian precondition myocardial ischemia in gene expression pattern, the authors applied gene chip tech to filter variably expressed genes in hypothalamus. Methods： Rats were seperated into normal, model, acupuncture Heart Meridian group and acup Lung Meridian group randomly. Acute myocardial ischemia rat model was made with ligation left anterior descending branch of the coronary artery. After model succeed, select hypothalamus seperately and mixed the same group together of 3 rats. Then applied Rats U230A genechip refered by Affymetrix Co. to compare the variations between these groups. Results： To compare with normal group, differential expression genes and expression sequence tags （ESTs） in model group were 73 with signal log ratio ≥ 1 and 92 with signal log ratio ≤-1 , mainly included ion channel, calcium/ calmodulin-dependent protein kinase Ⅱ inhibitor, antigen and so on. Similarly, compared with model group, differential expression genes and expression sequence tags （ESTs） were 190 with signal log ratio ≥ 1 and 34 with signal log ratio ≤-1 in acupuncture Heart Meridian group, mainly included 5-hydroxytryptamine receptor, cellular metabolism, fatty, immuno reaction, G-protein coupled receptors, ion transport, signal transductions and so on, while in acupucnturc Lung Meridian, the number is 57 and 26 correspondly. Conclusion： There were exactly variations in hypothalamus mechanism that relate to acupuncture Heart and Lung Meridians.