Biomedical subjects

Zuhong Lu

Publications and source records attributed to Zuhong Lu.

At least 19 recordsLinked to original sources

PubMed2006

Detection of fetal DNA in maternal plasma by microarray coupled with emulsions PCR.

BACKGROUND: The presence of fetal DNA in maternal plasma made non-invasive prenatal diagnosis possible. Although fetal DNA has been used in several genetic disease diagnoses, many challenges remained in the detection methods. We attempted to develop a sensitive and reliable microarray coupled with emulsions PCR method to detect the fetal DNA in the plasma of pregnant women. METHOD: Fetal DNAs extracted from the plasma of pregnant women were amplified in emulsions, and fluorescence was labeled at the same time. The labeled target DNAs were hybridized and detected by the capturing DNA probes on a modified slide. Six Y chromosome special sequences in gene of SRY, DYS and DYZ as the marker of fetal DNAs were detected simultaneously in this study, and the beta-globin gene was detected as marker of total DNA from maternal plasma. An unrelated sequence was also detected as negative control in this study. 76 pregnant women in the first trimester of gestation joined in this study. Conventional PCR and real time PCR were also carried out for comparison. RESULTS: We could detect the fetal DNAs reliably with this method in early stage of gestation. The 6Y chromosome sequences were detected in 40 of the 42 male fetus carrier samples, and no Y special sequence was detected in the female fetus carrier samples. The earliest plasma sample which we could detect in this study was collected on the 31st day after pregnancy. CONCLUSIONS: The results suggest that the microarray coupled with emulsions PCR method could be used for fetal DNA detections, and emulsions were useful in DNA amplification as reaction media to overcome the primer incompatibility which frequently encounters in multiplex PCR amplification. Our methods have the potential in high-throughput assays and could be widely used in clinical researches and diagnosis.

DNA↗

PubMed2006

Microarray-based molecular margin methylation pattern analysis in colorectal carcinoma.

The positive surgical margins are associated with postsurgical recurrence in colorectal carcinoma patients, and molecular margin analysis is considered to be more sensitive in detecting preneoplastic lesions than is conventional histological margin examination. Here, we developed a microarray and established six calibration curves for hMLH1 gene methylation patterns analysis in 20 colorectal resected margin specimens and corresponding tumor tissue specimens as well as four normal tissue specimens. The results indicated that a moderate methylation level (8-42%) was found in 20 surgical margin tissues, extensive methylation (25-58%) was detected in 20 tumor tissues, and little or no methylation was observed in normal tissues. Of the six paired probes, the average methylation levels in 20 tumor tissues were 60, 35, 43, 53, 38, and 27%, whereas the average methylation levels of the six paired probes in 20 surgical margin tissues were 43, 16, 24, 28, 21, and 11%. Thus, this study demonstrated the feasibility of this assay for molecular assessment use. In addition, it will contribute significant information to our understanding of CpG island methylation for cancer diagnosis and postoperative recurrence.

Adaptor Proteins, Signal Transducing↗

PubMed2006

Exo-Dye-based assay for rapid, inexpensive, and sensitive detection of DNA-binding proteins.

We reported herein a rapid, inexpensive, and sensitive technique for detecting sequence-specific DNA-binding proteins. In this technique, the common exonuclease III (ExoIII) footprinting assay is coupled with simple SYBR Green I staining for monitoring the activities of DNA-binding proteins. We named this technique as ExoIII-Dye-based assay. In this assay, a duplex probe was designed to detect DNA-binding protein. One side of the probe contains one protein-binding site, and another side of it contains five protruding bases at 3' end for protection from ExoIII digestion. If a target protein is present, it will bind to binding sites of probe and produce a physical hindrance to ExoIII, which protects the duplex probe from digestion of ExoIII. SYBR Green I will bind to probe, which results in high fluorescence intensity. On the contrary, in the absence of the target protein, the naked duplex probe will be degraded by ExoIII. SYBR Green I will be released, which results in a low fluorescence intensity. In this study, we employed this technique to successfully detect transcription factor NF-kappaB in crude cell extracts. Moreover, it could also be used to evaluate the binding affinity of NF-kappaB. This technique has therefore wide potential application in research, medical diagnosis, and drug discovery.

Amino Acid Sequence↗

PubMed2006

Support vector machine for classification of meiotic recombination hotspots and coldspots in Saccharomyces cerevisiae based on codon composition.

BACKGROUND: Meiotic double-strand breaks occur at relatively high frequencies in some genomic regions (hotspots) and relatively low frequencies in others (coldspots). Hotspots and coldspots are receiving increasing attention in research into the mechanism of meiotic recombination. However, predicting hotspots and coldspots from DNA sequence information is still a challenging task. RESULTS: We present a novel method for classification of hot and cold ORFs located in hotspots and coldspots respectively in Saccharomyces cerevisiae, using support vector machine (SVM), which relies on codon composition differences. This method has achieved a high classification accuracy of 85.0%. Since codon composition is a fusion of codon usage bias and amino acid composition signals, the ability of these two kinds of sequence attributes to discriminate hot ORFs from cold ORFs was also investigated separately. Our results indicate that neither codon usage bias nor amino acid composition taken separately performed as well as codon composition. Moreover, our SVM based method was applied to the full genome: We predicted the hot/cold ORFs from the yeast genome by using cutoffs of recombination rate. We found that the performance of our method for predicting cold ORFs is not as good as that for predicting hot ORFs. Besides, we also observed a considerable correlation between meiotic recombination rate and amino acid composition of certain residues, which probably reflects the structural and functional dissimilarity between the hot and cold groups. CONCLUSION: We have introduced a SVM-based novel method to discriminate hot ORFs from cold ones. Applying codon composition as sequence attributes, we have achieved a high classification accuracy, which suggests that codon composition has strong potential to be used as sequence attributes in the prediction of hot and cold ORFs.

Algorithms↗

PubMed2006

Expression profilings of 39 genes selected by ANOVA could separate precursors of murine dendritic cells and macrophages.

Dendritic cells (DCs) and macrophages share some stages in the development and function of antigen presentation. But it is difficult to separate them from their precursors. We used one-way ANOVA (analysis of variances) on murine expression profilings of several hematopoietic cells associated with DCs and macrophages to find the genes with great differences across the cell groups. These groups were the DCs from spleen, cultivated DCs, DC precursors, DC progenitors, DC progenitor cell lines, hematopoietic stem cell (HSC), and bone marrow-derived macrophages. The data of expression profilings were all downloaded from GEO and ArrayExpress database. After the normalization of 11 housekeeping genes across 42 arrays, we got 39 genes (44 probesets) by analysis of one-way ANOVA (Bonferroni step-down) with p values cutoff of 0.05. These genes (probesets) could separate the hematopoietic cells well by the methods of unsupervised hierarchical clustering and principal component analysis (PCA). The class prediction also indicated that these genes could separate the precursors of DC and macrophages with 20 arrays composed of 5 cell types with the same normalization. The accuracy rate of class prediction was 90% (18/20). The genes selected by one-way ANOVA included those of MHC (major histocompatibility complex) and defense of immunity, cell adhesion, chemokine or its receptors, and transcription factors. The results indicated that these 39 genes could separate precursors of DC and macrophages very clearly. It was suggested that these genes might represent some important molecules that related with the precursors of DCs and macrophages, and were worthy for further study.

Animals↗

PubMed2006

Quantitative analysis of promoter hypermethylation in multiple genes in osteosarcoma.

BACKGROUND: Osteosarcoma is the most common solid malignant diseases of childhood, occurring in approximately 6 children per million annually; however, to the authors' knowledge to date, the cause of osteosarcoma has remained mostly unknown. Genetic alterations of genes that are specific for osteosarcoma have not been identified. Genetic alternations in the status of DNA methylation, known as epigenetic alterations, are the most common molecular alterations in human neoplasia. Aberrant methylation in the promoter region of tumor-related genes is associated closely with epigenetically mediated gene silencing, which is a common feature in human tumors. METHODS: The authors analyzed CpG islands of 5 different gene loci for aberrant methylation profiles in 30 pairs of osteosarcoma and corresponding normal tissues by using the quantitative methylation-specific polymerase chain reaction method. The objectives of this study were to characterize the methylation changes in osteosarcoma more extensively and to identify epigenetic biomarkers that may be useful in the diagnosis and prevention of osteosarcoma. RESULTS: For the Ras effector homologue (RASSF1A), tissue inhibitor of metalloproteinase 3 (TIMP3), O-6-methylguanine DNA methyltransferase (MGMT), and death-associated protein kinase 1 (DAPK1) genes, significant differences were observed in the degree of hypermethylation between tumors and normal tissues (P < 0.01 and P < 0.001, respectively). Measurement of the cumulative multiple promoter hypermethylation revealed striking differences between tumor specimens and normal tissues (t = 7.31; P < .001). There also was a significant difference in the levels of DNA methylation between the metastatic and nonmetastatic high-grade osteosarcomas (t = 4.57; P < .01). In addition, the methylation levels were associated closely with gender (t = 6.44; P < .001). CONCLUSIONS: The results indicated that tumor tissues from patients with osteosarcoma had a significantly higher incidence of hypermethylation for several genes compared with corresponding normal tissues. The epigenetic changes observed in this study may have prognostic importance for patients with osteosarcoma.

Adolescent↗

PubMed2006

Bisulfite-modified target DNA array for aberrant methylation analysis.

Aberrant DNA methylation of CpG islands is among the earliest and most frequent alterations in cancer. It is of great importance to develop simple and high-throughput methods of methylation analysis for earlier cancer diagnosis or the detection of recurrence. In this study, bisulfite-modified target DNA arrays were prepared on positively charged nylon membrane with two different procedures: fixing PCR products and fixing genomic DNA. First, a bisulfite PCR product array was prepared through fixing PCR products amplified in bisulfite sequencing primers from the bisulfite-modified genomic DNA of different clinical samples on membrane. Furthermore, bisulfite-modified genomic DNA of the different samples was directly fixed on membrane to fabricate bisulfite genomic DNA arrays. The two kinds of arrays were hybridized by probes labeled with digoxigenin, and the hybridization signals were obtained through chemiluminescent detection. The methylation statuses of the IGFBP7 gene for breast tumor and normal tissue samples and for normal human blood cell samples were detected successfully by the two procedures. It was shown that the methods are reliable and sensitive and that they have high potential in screening molecular methylation markers from a large number of clinical samples.

Base Sequence↗

PubMed2006

Microarray-based methylation analysis using dual-color fluorescence hybridization.

BACKGROUND: Aberrant DNA methylation of CpG sites is among the earliest and most frequent alterations in cancer. It is of great importance to develop simple, high-throughput and quantitative methods for methylation detection. METHODS: A high-throughput methylation analysis method has been developed based on microarray and dual-color fluorescence hybridization. The genomic DNA was treated with bisulfite, resulting in conversion of non-methylated cytosine, but not methylated cytosine, into uracil within CpG islands of interest. PCR products of the treated genomic templates were spotted and immobilized onto a poly-l-lysine coated glass slide to fabricate a microarray and then interrogated by hybridization with dual-color probes to determine the methylation status. The hybridized signals were obtained with a scanner and the results were analyzed with the software Genepix Pro 3.0. RESULTS: The methylation status of the CpG islands of IGFBP7 gene has been successfully evaluated by the microarray method for twenty-seven samples. All the investigated samples, including twenty human breast tumor tissues, six corresponding normal human breast tissues and one liver cell line, all CpG sites were found completely methylated. CONCLUSIONS: The microarray technology has been proven to have potential for high-throughput detection of the methylation status for a given gene in multi-genomic samples, which could be a novel approach for rapidly screening DNA methylation marker for early stage cancer diagnosis.

Base Sequence↗

PubMed2006

Analysis of fluorescence from algae fossils of the Neoproterozoic Doushantuo formation of China by confocal laser scanning microscope.

Chinese algae fossils can provide unique information about the evolution of the early life. Thin sections of Neoproterozoic algae fossils, from Guizhou, China, were studied by confocal laser scanning microscopy, and algae fossils were fluorescenced at different wavelengths when excited by laser light of 488 nm, 476 nm, and 568 nm wavelength. When illuminated by 488 nm laser light, images of the algae fossils were sharper and better defined than when illuminated by 476 nm and 568 nm laser light. The algae fossils fluoresce at a wide range of emission wavelengths. The three-dimensional images of the fluorescent algae fossils were compared with the transmission images taken by light microscope. We found that the fluorescence image of the confocal laser scanning microscope in a single optical section could pass for the transmission image taken by a light microscope. We collected images at different sample depths and made a three-dimensional reconstruction of the algae fossils. And on the basis of the reconstruction of the three-dimensional fluorescent images, we conclude that the two algae fossils in our present study are red algae.

Cell Wall↗

PubMed2006

Evaluating the binding affinities of NF-kappaB protein to the single-nucleotide mismatch DNA binding sites by using double-stranded DNA microarray.

Protein-DNA sequence-specific interaction plays an essential role in many biological processes. Here we immobilized a series of double-stranded DNA probes on an agarose coated slide to investigate the binding affinity of NF-kappaB p50 homodimer to the single-nucleotide mismatches (G<-->A or T<-->C) of the 10 base pair (bp) protein binding sites. The results demonstrated that the nucleotides at different positions contribute differently to the p50p50/DNA binding interaction. Within the 10 bp binding sites, the 5tG or 6cA mismatch has less effect on the protein-DNA binding affinity. Even the 5tG mismatch may have the ability to enhance the protein-DNA interaction (5t/w = 1.07). On the other hand, the 7cA or 10tG mismatch blocked the protein-DNA interaction more significantly than other six single-nucleotide mismatches. (7c/W = 0.37, 10t/W = 0.35). It also indicated that the duplex DNA probes immobilized on the agarose-coated surface were apt to be recognized by DNA-binding proteins, and this method would provide a reliable method for exploring the binding affinities of DNA-binding proteins with a larger number of DNA targets.

Base Pair Mismatch↗

PubMed2005

Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae.

Publication of the complete genome sequence for the Acanthamoeba sp. endosymbiont UWE25 has illuminated the evolution history of chlamydiae. In this study, the codon usage bias in UWE25 and five other species of pathogenic chlamydiae was calculated. It was found that genomic composition constraints are the major source of codon usage variation in UWE25. This result is different from the former observation in pathogenic chlamydiae, whose genomic base composition is more unbiased. Four other factors, such as strand-specific mutational bias, natural selection acting at the level of translation, hydropathy level of each protein and the conservation level of amino acids also have influence in shaping the codon usage in these six species to some extent. Further analysis suggests that the high stability of the UWE25 genome partially account for the difference in codon usage pattern between environmental and pathogenic chlamydiae. Moreover, our results imply that the replicational selection pressure in pathogenic chlamydiae is stronger than that in UWE25. Analyzing the codon usage pattern in the environmental chlamydia and comparing it with that of the pathogenic chlamydiae may provide clues how the chlamydiae have evolved from their common ancestor.

Amino Acids↗

PubMed2005

Reaction of porous silicon with both end-functionalized organic compounds bearing alpha-bromo and omega-carboxy groups for immobilization of biomolecules.

Both end-functionalized (alpha-bromo and omega-carboxy) compounds were first tested for the radical reaction on the silicon-hydride (Si-H) terminated porous silicon (PSi) with/without the presence of diacyl peroxide initiator under microwave irradiation. Then the carboxylic acid monolayers (CAMs) assembled on PSi through the robust Si-C bonds were converted to amino-reactive linker, N-hydroxysuccinimide (NHS)-ester, terminated monolayers. And finally two proteins of bovine serum albumin (BSA) and lysozyme (Lys) were immobilized through amide bonds. The optimum PSi membrane for protein immobilization without collapse, with parameters of porous radii 4-10 nm and depth 0.2-4.6 mum, was prepared from the (100)-oriented p-type silicon wafer. The chemically converted surface products were monitored with Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and field emission scanning electron microscopy (FESEM).

Animals↗

PubMed2005

Expression profiles of mouse dendritic cell sarcoma are similar to those of hematopoietic stem cells or progenitors by clustering and principal component analyses.

We isolated and screened two tumor cell clones DD1 and DG6 with different capacity of metastasis from the same parent cell line, a mouse dendritic cell (DC) sarcoma, using limited dilution method. The genome-wide expressions of DD1 and DG6 cells were detected by Affymetrix's MOE-430A microarray. The expression profiles related with mouse DC development were downloaded from GEO at NCBI and ArrayExpress at EBI database. In order to compare the expression of DC sarcoma and DC developmental arrays which was performed by MG-U74av2, we had screened the best matched probesets between MOE-430A and MG-U74av2 according to the probe identities from Affymetrix technical annotation. After the normalization of 11 housekeeping genes across the 34 arrays (2 DC sarcoma and 32 DC developmental arrays), all these expression profiles were analyzed by the methods of hierarchical clustering, principal component analysis, nearest-neighborhood, and self-organizing maps. The results indicate that expression profiles of DC sarcoma are closer to those of the DC progenitors and hematopoietic stem cells from bone marrow compared with the sorted DCs from spleen. The results support the hypothesis that cancers (tumors or sarcomas) arise from stem cells. It is suggested that the DC sarcomas are more similar to the DC progenitors and hematopoietic stem cells than the relative mature DCs in gene expressions on the large-scale.

Animals↗

PubMed2005

Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses.

In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes.

Base Composition↗

PubMed2005

Optimization of on-chip elongation for fabricating double-stranded DNA microarrays.

The sequence-specific recognitions between DNA and proteins are playing important roles in many biological functions. The double-stranded DNA microarrays (dsDNA microarrays) can be used to study the sequence-specific recognitions between DNAs and proteins in highly parallel way. In this paper, two different elongation processes in forming dsDNA from the immobilized oligonucleotides have been compared in order to optimize the fabrication of dsDNA microarrays: (1) elongation from the hairpins formed by the self-hybridized oligonucleatides spotted on a glass; (2) elongation from the complementary primers hybridized on the spotted oligonucleatides. The results suggested that the dsDNA probes density produced by the hybridized-primer extension was about four times lower than those by the self-hybridized hairpins. Meanwhile, in order to reduce the cost of dsDNA microarrays, we have replaced the Klenow DNA polymerase with Taq DNA polymerase, and optimized the reaction conditions of on-chip elongation. Our experiments showed that the elongation temperature of 50 degrees C and the Mg(2+) concentration of 2.5 mM are the optimized conditions in elongation with Taq DNA polymerase. A dsDNA microarray has been successfully constructed with the above method to detect NF-kB protein.

Carbocyanines↗

PubMed2005

Exonuclease III protection assay with FRET probe for detecting DNA-binding proteins.

We describe a new method for the assay of sequence-specific DNA-binding proteins in this paper. In this method, the sensitive fluorescence resonance energy transfer (FRET) technology is combined with the common DNA footprinting assay in order to develop a simple, rapid and high-throughput approach for quantitatively detecting the sequence-specific DNA-binding proteins. We named this method as exonuclease III (ExoIII) protection assay with FRET probe. The FRET probe used in this assay was a duplex DNA which was designed to contain one FRET pair in the center and two flanking protein-binding sites. During protein detection, if a target protein exists, it will bind to the two protein-binding sites of the FRET probe and thus protect the FRET pair from ExoIII digestion, resulting in high FRET. However, if the target protein does not exist, the FRET pair on the naked FRET probe will be degraded by ExoIII, resulting in low FRET. Three kinds of recombinant transcription factors including NF-kappaB, SP1 and p50, and the target protein of NF-kappaB in HeLa cell nuclear extracts, were successfully detected by the assay. This assay can be extensively used in biomedical research targeted at DNA-binding proteins.

Cell Nucleus↗

PubMed2005

A semi-quantitative microarray method to detect fetal RNAs in maternal plasma.

OBJECTIVES: To set up a semi-quantitative microarray method for the detection of fetal RNAs in maternal plasma. METHODS: We developed a semi-quantitative microarray method for the detection of placental RNA in maternal plasma. Firstly, the selected fetal RNAs were linearly amplified from the maternal plasma and then fluorescently labeled as the target DNAs. Finally, the targets were hybridized and detected by capturing DNA probes on a microarray slide. Two genes of beta subunit of human chorionic gonadotrophin (beta-hCG) and zinc finger gene on the Y chromosome (ZFY) were assayed with the microarray, and beta actin gene was used as an internal standard. Eighty-five pregnant women in the first trimester and the third trimester of gestation joined in this experiment, 14 of them also sampling in 36 h after delivery for the same assay. Real-time quantitative PCR was performed for comparison. RESULTS: It was found that the mRNA level of beta-hCG decreased with the increasing of gestation age, and it was much higher in the carriers of the female fetus than in the carriers of the male fetus in the first trimester of gestation, which was consistent with the real-time quantitative PCR results. The results also reveal that delivery would result in the clearance of fetal mRNA in maternal plasma. CONCLUSIONS: The results suggest that the semi-quantitative microarray method has great potential as a high-throughput assay in prenatal diagnosis and clinical laboratory.

Chorionic Gonadotropin, beta Subunit, Human↗

PubMed2005

Polyacrylamide gel film immobilized molecular beacon array for single nucleotide mismatch detection.

We reported polyacrylamide gel immobilized molecular beacon array for single nucleotide mismatch detection in this paper. Molecular beacons are oligonucleotide probes fluorescing upon hybridization to their complementary DNA/RNA targets with excellent sensitivity and high selectivity. The specially designed molecular beacon for immobilization contains a 15 base loop sequence with a 5 base pair stem, a polyT (20 bases) spacer, a 5'-end amino group for immobilization, a fluorescein in the middle of the sequence as the fluorophore, and a 3'-end DABCYL as the quencher. Between the 5'-end amino group and the stem, the polyT is used to minimize disability caused by 5'-end immobilization. The molecular beacon microarray was fabricated by a pin-based spotting robot and the hybridization was investigated by confocal microscope. A real-time hybridization process at room temperature was registered every minute for 20 min after the target solution was pumped into the hybridization cell. The result indicates that a polyacrylamide film coated glass slide provides an ideal solution-like environment for molecular beacon probes. The potential applications of this kind of molecular beacon array are mutation detection, disease mechanisms, disease diagnostics, etc. in a parallel, cost saving, and label-free detection way.

Acrylic Resins↗