Biomedical subjects

Yao Li

Publications and source records attributed to Yao Li.

At least 55 records · Page 3Linked to original sources

PubMed2004

[Cluster analysis and identify significance of novel genes related to glioma in molecule classification].

OBJECTIVE: To screen differentially expressed genes in the development of human glioma and establish molecular classification of glioma preliminary based on gene expression using cDNA microarray. METHODS: Brain specimens were obtained from 18 patients with glioma, 10 males and 8 females, aged 14 approximately 62 with an average age of 44.4. The total RNAs of these glioma specimens and 2 specimens of donated brain of normal adults were extracted. BioStarH140S microarray (including 8347 old genes and 5592 novel genes) were adopted and hybridized with probes which were prepared from the total RNAs. Differentially expressed genes between the normal tissues and glioma tissues were assayed after scanning cDNA microarray with ScanArray 4000. Northern hybridization, and in situ hybridization (ISH) were used to identify the functions of novel genes. Those differentially expressed genes were studied with Hierarchical method and molecular classification of glioma was preliminarily carried out. RESULTS: Among the 13 939 target genes, there were 1200 (8.61%) differentially expressed genes and 395 (2.83%) novel genes. 348 genes were up-regulated and 852 genes were down-regulated in glioma. The results of bioinformatical analysis, Northern hybridization and ISH revealed that those novel genes were highly associated with glioma. There were multiple genes which were relevance to classification by Hierarchical method, such as MAP gene, cytoskeleton and matrix motility genes, etc. Molecular classification of glioma with Hierarchical cluster was in accordance with pathology and revealed internal essence in tumorigenesis and development. CONCLUSION: Multiple genes play important roles in development of glioma. cDNA microarray technology is a powerful technique in screening for differentially expressed genes between two different kinds of tissues.

Adolescent↗

PubMed2004

Effects of vitamin E succinate on the expression of Fas and PCNA proteins in human gastric carcinoma cells and its clinical significance.

AIM: To investigate the effects of vitamin E succinate (VES) on the expression of Fas and PCNA proteins as well as its clinical significance in human gastric carcinoma, and to explore the mechanism of VES-induced inhibition of gastric carcinoma cell growth. METHODS: Immunohistochemical methods were used to detect Fas and PCNA expression both in human gastric cancer SGC-7901 cells treated with VES at different doses and in human gastric carcinoma tissues. RESULTS: After the SGC-7901 cells were treated with VES at 5, 10, 20 mg/L for 48 h, the positive rates of Fas expression were 16%, 27% and 48%, respectively, significantly increased compared to that of control group (P< 0.05); while the positive rates of PCNA expression in groups treated with different doses of VES were 20%, 18% and 7%, respectively, which were significantly decreased compared to that of the control group (P<0.05). In human gastric carcinoma tissues, the Fas positive expression rate was 42.4%(25/59), which declined with the decrease in the degree of tumor differentiation (P<0.05) and with the existence of lymph node metastasis (P<0.001). While the PCNA positive expression rate was 91.5%(54/59), no relationship was observed between PCNA expression and clinicopathologic parameters. CONCLUSION: VES inhibited the growth of gastric cancer cells by inducing Fas expression and inhibiting PCNA expression. It is, therefore, considered that the expression of Fas and PCNA genes, through tumor cell apoptosis and proliferation, respectively, may be useful as a clinical predictive index in the application of VES to gastric carcinoma therapy, where as Fas may be of more value than PCNA.

Carcinoma↗

PubMed2004

Systematic comparison of the fidelity of aRNA, mRNA and T-RNA on gene expression profiling using cDNA microarray.

In cDNA microarray technology, there are three main reverse transcription based RNA labeling methods, using total RNA (T-RNA), mRNA, and amplified antisense RNA (aRNA), respectively. However, despite the common use of the three types of RNAs, limited data are available regarding their differences and concordances. In this report, we compared the three methods through two sets of self-comparison experiments using the same RNA sample in all cases. Within each method, duplicate hybridizations are highly reproducible with low biases, which are randomly produced. When combining different RNAs within a single array, correlation coefficients between the two channels are rather low, while the discrepancies are persistent. Furthermore, the fidelity of aRNA and mRNA microarrays in the expression profile study shows no significant difference with standard T-RNA based labeling methods. These results suggest that some RNA abundance are selectively changed during aRNA amplification/mRNA purification processes, but it will not affect the gene expression ratio of the two samples if the same type RNA are used. Therefore all three types of RNAs can be used in expression profiling analysis as long as the test and reference samples are generated by identical method within single study.

Carcinoma, Hepatocellular↗

PubMed2004

Molecular cloning and characterization of a novel dual-specificity phosphatase 23 gene from human fetal brain.

Most of dual-specificity protein phosphatases (DSPs) play an important role in the regulation of mitogenic signal transduction and controlling the cell cycle in response to extracellular stimuli. In this study, a novel human dual-specificity protein phosphatases gene named dual-specificity phosphatase 23 (DUSP23) was isolated by large-scale sequencing analysis of a human fetal brain cDNA library. Its cDNA was 726 bp in length, encoding a 150-amino acid polypeptide which contained a dual-specificity phosphatase catalytic (DSPc) domain but not a CDC25 homology (CH2) domain. Reverse transcription-PCR (RT-PCR) revealed that the DUSP23 was expressed in most fetal tissues and two adult tissues: testis and colon. Transient transfection experiment suggested that DUSP23 was localized in the cytoplasm of HEK293 cells. DUSP23 showed distinctive phosphatase activity toward p-nitrophenyl phosphate (pNPP), as well as oligopeptides containing phospho-tyrosine and phospho-threonine residues. Furthermore, DUSP23 could dephosphorylate p44ERK1 but not p38 and p54SAPKbeta in vitro. All the results indicated that DUSP23 was a novel protein phosphatase with dual substrate specificity.

Adult↗

PubMed2004

Detection of rifampin-resistant Mycobacterium tuberculosis strains by using a specialized oligonucleotide microarray.

DNA microarray represents one of the major advances in diagnostic sequencing of polymerase chain reaction (PCR) products. Until now, arrays have been relatively expensive, complex to perform, and difficult to interpret, limiting their wide application in the clinical laboratory. A moderate-density oligonucleotide microarray that can rapidly identify Mycobacterium tuberculosis rifampin-resistant strains was developed. The method is based on the detection of point mutations and other rearrangements in the rpoB gene region determining rifampin resistance. Rifampin resistance was determined by hybridizing fluorescently labeled, amplified genetic material generated from bacterial colonies to the array. Fifty-three rifampin-resistant M. tuberculosis and 15 rifampin-susceptible M. tuberculosis were tested and results were concordant with those based on culture drug susceptibility testing and sequencing. Rifampin-resistant clinical isolates were detected in as little as 1.5 hours after PCR amplification with visual results. It is demonstrated that oligonucleotide microarray is an efficient, specialized technique to implement and can be used as a rapid method for detecting rifampin resistance to complement standard culture-based method.

Antibiotics, Antitubercular↗

PubMed2004

cDNA cloning and expression analysis of a novel human F-box domain containing gene.

F-box proteins are a large family of eukaryotic proteins that are characterized by an approximately 40 amino acid motif. Some F-box proteins are critical for the controlled degradation of cellular regulatory proteins. Here we report that a novel member of F-box proteins, FBXO35 gene, was cloned and identified during the large-scale sequencing analysis from a human fetal brain cDNA library. FBXO35 gene shares amino acid similarity with several putative mouse genes not only in F-box domain but also in the rest of the sequence, which indicates that FBXO35 might also contain some other unknown conserved domain. RT-PCR analysis indicated that FBXO35 gene had a ubiquitously low expression pattern in most human adult tissues. According to bioinformatics analysis, the FBXO35 gene was found located in chromosome 3p21.

Amino Acid Sequence↗

PubMed2004

Characterization of a cDNA encoding a protein with limited similarity to beta1, 3-N-acetylglucosaminyltransferase.

Glycosyltransferases constitute a large group of enzymes that are involved in a wide range of functions in all living organisms. By large-scale sequencing analysis of a human fetal brain cDNA library, we isolated a novel human putative glycosyltransferase gene named beta3GnTL1. Its cDNA is 1372 base pair in length, encoding a predicted protein with 361 amino acid residues. The human beta3GnTL1 is located to chromosome 17q25.3 by comparison of its cDNA with human gemome database. RT-PCR result shows the beta3GnTL1 is expressed at various levels in most of tissues examined.

Amino Acid Sequence↗

PubMed2004

Cloning and identification of a novel human gene PDLIM5, a homolog of AD-associated neuronal thread protein (AD7c-NTP).

A novel human gene cDNA was successfully cloned from the human fetal brain cDNA library constructed by our lab, and this gene was termed PDLIM5 after acquiring the agreement of HUGO. BLASTX searching revealed that the hypothetical protein is a homolog of AD-associated neuronal thread protein (AD7c-NTP), which is over-expressed in Alzheimer disease (AD) beginning early in the course of disease, and over-expression of the AD7c-NTP gene would cause neuritic sprouting and cell death. SMART analysis showed that both our predicted protein and AD7c-NTP comprise BCL domain (only contains BH1 and BH2 regions). RT-PCR experiment revealed that the expression level of PDLIM5 in brain, skeletal muscle, prostate, colon and leukocyte is obviously higher than that in other tissues.

Amino Acid Sequence↗

PubMed2004

Cloning and expression of human GTDC1 gene (glycosyltransferase-like domain containing 1) from human fetal library.

The glycosyltransferases (GTs) catalyze the synthesis of the carbohydrate portions of glycoproteins, glycolipids, and proteoglycans. Here we report the cloning and characterization of a novel human GTDC1 (glycosyltransferase-like domain containing 1) gene, which locates on human chromosome 2q22. The GTDC1 cDNA is 2954 bp in length, encoding a putative protein of 458 amino acids. At protein level human GTDC1 has 75 and 37% identity with its homologous counterparts in the mouse and fruitfly, respectively. RT-PCR analysis revealed its relatively high expression level in the adult lung, spleen, testis, and peripheral blood leukocyte.

Amino Acid Sequence↗

PubMed2004

Modulation of the gene expression in the protective effects of electroacupuncture against cerebral ischemia: a cDNA microarray study.

In the present study, a cDNA microarray technology was used to analyze the gene expression profile in ischemia and in electroacupuncture (EA)-treated ischemia. A focal cerebral ischemia/reperfusion model on Macaca mulatta was performed with a modified middle cerebral artery occlusion method. Among the nearly 8000 genes, approximately 8% of the total number of genes examined were affected after ischemia/reperfusion injury. Major altered genes were downregulated. In EA-treated monkeys, approximately 10% of the total number of genes examined were affected. Major altered genes were upregulated, including signal transduction-, cell-cycle-, metabolism-, stress response-, DNA repair-related genes. One of the representative upregulated genes encodes insulin-like growth factor-1 (IGF-1) was confirmed using in situ hybridization. Results showed that after ischemia/reperfusion injury, IGF-1 mRNA expression decreased in ipsilateral striatum, whereas increased in ipsilateral hippocampus. No expression changes were observed in cortex. EA treatment could obviously upregulate the IGF-1 mRNA expression in striatum, and further enhance its expression in hippocampus. Therefore, the data presented suggest a possible mediator underlying the mechanisms of anti-ischemic effect of acupuncture. In conclusion, the protective mechanisms of EA against stroke include several related pathways and gene expressions. Microarray analysis may provide a framework for understanding these complicated mechanisms and yield valuable, clinically relevant insights and potentially therapeutic targets of stroke.

Animals↗

PubMed2004

[Differential expression of apoptosis-related gene induced by clinical and laboratory Mycobacterium tuberculosis strain in macrophages U937 revealed by oligonucleotide microarray].

Tuberculosis(TB) remains one of the major problems in global health. Macrophage (MPhi) apoptosis, induced by Mycobacterium tuberculosis (Mtb), is a cornerstone of effective innate microbial defense mechanism. Elucidation of the complex apoptosis-related gene expression may facilitate understanding the mechanism and regulation of macrophage apoptosis in response to Mtb, and contribute to developing novel measures to counter TB. DNA microarray containing 19,200 gene or gene fragments was used to compare the macrophage cell line U937 gene expression response to the clinical and laboratory Mtb infection. Northern blotting and RT-PCR were used to confirm the microarray results. Mtb H37Rv infection were found to downregulate the bcl-2, vitamin D receptor, interferon regulatory factor 3, cytochrome c oxidase, gene expression by 2-, 3-, 3-, 2.5-fold, respectively, while the clinical strain infection leads to upregulate the SOD2, SOD3, serine protease, toll-like receptor 2, signal transducer and activator (STAT1), hypoxia-inducible factor 22, 2.9-, 2.5-, 2.5-, 2.2-, 2.4-, 5.9-fold respectively. The findings suggest that the clinical strain infection tends to override the macrophage apoptosis by which the host attempt to limit the growth of the invader. The research on the complex factors network involved in the interaction will benefit the vaccine and novel drug target development.

Apoptosis↗

PubMed2004

[Detecting genetic polymorphisms of CYP1 A1 and GSTM1 simultaneously with oligonucleotide microarray].

Cytochrome P4501A1 plays a major role in the bioactivation of a number of tobacco procarcinogens. Glutathione S-transferase( GSTM1), a member of the class of GST gene family, has been shown to be polymorphic because of gene deletion resulting in a failure to express the GSTM1 gene in 50% approximately 60% of individuals. Some CYP1 A1/GSTM1 null genotype combinations seem to predispose the lung, esophagus, and oral cavity of smokers to an even higher risk for cancer or DNA damage, requiring, however, confirmation. An easy and reliable oligonuleotide microarray approach validated through direct sequencing method is developed in order to accurately detect single nucleotide polymorphisms of CYP1 A1 gene and discriminate the presence and absence of GSTM1 gene. The m1 (Msp I) and m2 (Ile462Val) polymorphisms of CYP1 A1 gene and GSTM1 null genotype were also determined in a random population of 84 healthy, unrelated volunteers with developed microarray-based method. Of 84 cases, 47.6% were calssified as GSTM1 null, close to the published data. It's interesting that there lack three genotypes of m1 -m2 locus in the population: TT-AG, TT-GG and TC-GG. However, according to the data of the genotype frequencies independently happened at both m1 and m2 site, the combination frequencies of above three genotypes are 11.4%, 2.6%, and 3.1% respectively. Therefore we assume that the haplotypes of m1 -m2 are only T-A, C-A and C-G, but not T-G, as it were,there is no recombination happened between m1 site and m2 site. The frequencies of three haplotypes of T-A, C-A and C-G, calculated through corresponding genotypes, are 69.6%, 7.7% and 22.6% respectively.

Base Sequence↗

PubMed2004

[Molecular mutations of rpoB gene of multidrug resistant Mycobacterium tuberculosis isolates from China].

To characterize rpoB mutations of multidrug resistant Mycobacterium tuberculosis clinical isolates from China, mutations in the 81 bp rifampin resistance determining region (RRDR) and mutation V176F locating in the beginning of the rpoB gene were analyzed by DNA sequencing. Eighty six Mycobacterium tuberculosis clinical isolates, including 72 rifampin resistant strains and 14 rifampin sensitive strains were sequenced. Six five mutations of 22 distinct kinds, 21 point mutations and one insertion, were observed in 65 of 72 resistant isolates. The most frequent mutations were in codon 531 (41%), 526 (40%), and 516 (4%). Mutations were not found in seven (10%) of the resistant isolates. Six new alleles within the RRDR, along with five novel mutations outside the RRDR, are reported. None of isolates contained the V176 mutation.

Bacterial Proteins↗

PubMed2004

[ABO genotyping by duplex amplification and oligonucleotide arrays assay].

OBJECTIVE: ABO genotyping for forensic identification by oligonucleotide chip. METHODS: Oligonucleotide microarrays which could detect 3 different SNPs in exon 6 and exon 7 for ABO genotyping were used. Population studies on ABO was carried out in a sample of 115 unrelated Chinese Han individuals. The method was also applied to cases. RESULTS: The technique could identify 6 genotypes of ABO system. According to the results of population studies, no significant deviations from Hardy-Weinberg equilibrium could be found. The observed and expected heterozygosities were 0.591 and 0.616 respectively. The polymorphic information content was 0.544. The average exclusion probabilities in buos and trios was 0.188 and 0.344 respectively. The discrimination power is 0.777. CONCLUSION: The data and case application demonstrated that ABO typing by oligonucleotide probe arrays was a useful technique for paternity testing and individual identification.

ABO Blood-Group System↗

PubMed2003

Determining a detectable threshold of signal intensity in cDNA microarray based on accumulated distribution.

In microarray data mining, one of the key problems is how to handle weak signals. Based on a bent piecewise linear accumulated distribution generally found in the microarray data, a new detectable threshold finding method is proposed to filter genes with unreliable information in this paper. More reliable and reproducible data is produced for the subsequent data mining.

DNA, Complementary↗

PubMed2003

Identification of a novel human doublecortin-domain-containing gene (DCDC1) expressed mainly in testis.

Mutations in the X-linked gene doublecortex (DCX) result in lissencephaly in males or subcortical laminar heterotopia (double cortex) in females. Recently, an evolutionarily conserved doublecortin (DC) domain important for microtubule binding and microtubule polymerization was defined according to detailed sequence analysis of DCX and DCX-like proteins. Subsequently we cloned a novel human cDNA that contained a DC domain during large-scale DNA sequencing of the human fetal brain cDNA library, and termed it doublecortin-domain-containing 1 (DCDC1). According to a search against the human genome database, DCDC1 was mapped to 11p13. Expression analysis showed that DCDC1 was mainly expressed in adult testis. Furthermore, the expression level of DCDC1 in fetal brain was much higher than in adult brain.

Amino Acid Sequence↗

PubMed2003

[Genotyping of HLA-DRB by oligonucleotide arrays in Han populations in southern China].

OBJECTIVE: To develop an oligoneucleotide array for HLA-DRB typing and evaluate its function in comparison with that of PCR-SSP typing. METHODS: According to the specific allele sequences of HLA-DRB loci in Han populations in Southern China, 44 synthesized typing probes were immobilized on a glass supports. A pair of group-specific primers was designed according to the sequence of HLA-DRB exon2, then the primers and Cy5-dCTP were used in PCR, thus the PCR products were labeled with Cy5. The labeled PCR products were hybridized with the probes in the array, and the signals were scanned by scanner and then analyzed by Image software.110 samples of DNA of the lymphocytes from the spleens or peripheral blood of kidney recipients and unrelated donors were typed by this array and the results were compared with those of PCR-SSP typing. RESULTS: All the samples except for one without PCR product had been genotyped by HLA array successfully. Ten samples were identified differently by these 2 methods. PCR-SSO verified the correctness of the array in 7 samples among which 6 samples were identified as homozygous by PCR-SSP and heterozygous by array and 1 sample was identified as heterozygous by PCR-SSP and homozygous by the array; and proved that among the remaining 3 samples the results of 2 samples identified by PCR-SSP and 1 sample identified by the array were wrong. CONCLUSION: The HLA-DRB oligoneucleotide array technique is a precise, rapid molecular method for HLA-DRB genotyping. Compared with PCR-SSP method, the genotyping chip is more sensitive and specific and can test several samples at a time.

Alleles↗

PubMed2003

[Effects of Mycobacterium tuberculosis infection on the transcriptional expression of human macrophage gene encoding ion channels and related regulatory elements].

Expression microarray was employed in this study to investigate whether the ion channels and their regulatory elements encoding genes participate in the immune response to Mycobacterium tuberculosis infection. The results of a virulent strain were compared with those of the clinically isolated strains. The data demonstrate that K(+), Na(+), Ca(2+) and Cl(-) channels and their regulatory elements, such as the G protein, receptor and second messenger, protein kinase and protein phosphatase were involved in the immune reaction. The clinical strain affected more types of ion channels and respective regulatory elements. The data provides clues for further scrutiny into the role of ion channels and related elements in the interaction between Mycobacterium tuberculosis and host macrophage.

Gene Expression Regulation↗