The complete genomic sequence of foot-and-mouth disease virus (FMDV) Chinese strain OH/CHA/99 was determined. The 8040 nt sequence and the deduced amino acid sequence werecompared with FMDV sequences published. The re...The complete genomic sequence of foot-and-mouth disease virus (FMDV) Chinese strain OH/CHA/99 was determined. The 8040 nt sequence and the deduced amino acid sequence werecompared with FMDV sequences published. The results showed that OH/CHA/99 shared highersequence homology with OTYTW/97, indicating their close genetic relationship. However,the strain had lower sequence identity with O1/Kaufbeuren/66 strain. Besides, largedeletions in 3A coding region were observed in OH/CHA/99. It was shown that the poly (A)tail of OH/CHA/99 had 56 As at least.展开更多
The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of c...The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of cancer susceptibility. In preparing a gene chip for detecting polymorphisms on coding region of genes in hepatocellular carcinoma tissues, some cSNPs are of interest for their potential links with phenotype. METHODS: The genes harboring in loss regions with high frequency of hepatocellular carcinoma (HCC) were selected, the related information of cSNP sequences was obtained from the SNP database (dbSNP) of the National Center for Biotechnology Information (NCBI). Then appropriate primers and oligonucleotide probes were designed according to the SNP sites, and a gene chip for the detection of SNPs was constructed. The chip included 48 cSNPs of 25 hepatocellular carcinoma-related genes. The PCR products labeled by Dig-dUTP were hybridized with the cSNP chip. RESULTS:The sensitivity, influence by probe concentration, and reiteration of the chip were detected, with a high sensitivity of 6 × 10-3 ng/μl. The signal of hybridization was reduced with a lower concentration of probe. Seven polymorphisms of caspase 9 (rs2308941) C →T and DOK2 (rs2242241) T→G, 6 of polymorphisms of EGFL3 (rs947345) A→G, caspase 9 (rs2308938) C→G and PHGDH (rs1801955)T→A, 5 of polymorphisms of E2F2(rs3218170) G→A,4 of polymorphisms of MUTYH( rs1140507) T→C and BNIP3L(rs1055806)G→T, and 1 of polymorphism of TNFRSF1B (rs1061622)T→G were detected by the chip in the tissues of 10 HCC. Samples of caspase 9 (rs2308941G) and (rs2308941A) were verified by PCR-SSCP and sequencing. CONCLUSION:The cSNP chip of hepatocellular carcinoma-related genes can accelerate the discovery of polymorphic markers on hepatocellular carcinoma.展开更多
A new way of indexing and processing twig patterns in an XML documents is proposed in this paper. Every path in XML document can be transformed into a sequence of labels by Structure-Encoded that constructs a one-to-o...A new way of indexing and processing twig patterns in an XML documents is proposed in this paper. Every path in XML document can be transformed into a sequence of labels by Structure-Encoded that constructs a one-to-one correspondence between XML tree and sequence. Base on identifying characteristics of nodes in XML tree, the elements are classified and clustered. During query proceeding, the twig pattern is also transformed into its Structure-Encoded. By performing subsequence matching on the set of sequences in XML documents, all the occurrences of path in the XML documents are refined. Using the index, the numbers of elements retrieved are minimized. The search results with pertinent format provide more structure information without any false dismissals or false alarms. The index also supports keyword search Experiment results indicate the index has significantly efficiency with high precision.展开更多
The majority of single nucleotide polymorphisms(SNPs)found in the coding region(cSNPs)are single base substitutions that may or may not lead to amino acid substitutions,most of which are related to diseases.Some cSNPs...The majority of single nucleotide polymorphisms(SNPs)found in the coding region(cSNPs)are single base substitutions that may or may not lead to amino acid substitutions,most of which are related to diseases.Some cSNPs may prove useful for their potential links to functional cSNPs via linkage disequilibrium mapping.We have selected 48 cSNPs located in the coding regions of 25 genes to construct the cSNP chip.These genes are harbored in the high frequency loss regions of the chromosome 1p and 8p and related with apoptosis,cell cycles,signal transduction,oncogene,tumor suppressor genes and so on.All of the cSNPs can lead to amino acid substitutions except TP73(rs1801174).The PCR products amplified from 31 hepatocellular carcinoma(HCC)specimens were labeled with Dig-dUTP and then hybridized with the cSNP chips.The results showed that there was no hybridization signal when there was more than one site of mutation in the amplification sequence,indicating that the cSNP chip had a high sensitivity.The statistic data of the SNP(MT,homozygous and HT,heterozygous)in the HCC patients with different phenotypes(HBV+/-,differentiation stage,family history positive or negative,tumor size)indicated that the number of MT was distinctly different between patients with positive HBV and negative HBV.The MT and HT numbers of all the 48 cSNPs were significantly different between low differentiation and high differentiation HCC patients.The numbers of MT and HT were not different between positived and negative family history groups and between tumor size>3 cm and≤3 cm groups.The study results provided useful information for understanding the molecular mechanisms of HCC development.展开更多
文摘The complete genomic sequence of foot-and-mouth disease virus (FMDV) Chinese strain OH/CHA/99 was determined. The 8040 nt sequence and the deduced amino acid sequence werecompared with FMDV sequences published. The results showed that OH/CHA/99 shared highersequence homology with OTYTW/97, indicating their close genetic relationship. However,the strain had lower sequence identity with O1/Kaufbeuren/66 strain. Besides, largedeletions in 3A coding region were observed in OH/CHA/99. It was shown that the poly (A)tail of OH/CHA/99 had 56 As at least.
文摘The understanding of cSNPs of cancer-related genes harboring in high frequency loss regions of tumor chromosomes can advance the disclosure of genetic and variant mechanisms of tumorigenesis,and the investigation of cancer susceptibility. In preparing a gene chip for detecting polymorphisms on coding region of genes in hepatocellular carcinoma tissues, some cSNPs are of interest for their potential links with phenotype. METHODS: The genes harboring in loss regions with high frequency of hepatocellular carcinoma (HCC) were selected, the related information of cSNP sequences was obtained from the SNP database (dbSNP) of the National Center for Biotechnology Information (NCBI). Then appropriate primers and oligonucleotide probes were designed according to the SNP sites, and a gene chip for the detection of SNPs was constructed. The chip included 48 cSNPs of 25 hepatocellular carcinoma-related genes. The PCR products labeled by Dig-dUTP were hybridized with the cSNP chip. RESULTS:The sensitivity, influence by probe concentration, and reiteration of the chip were detected, with a high sensitivity of 6 × 10-3 ng/μl. The signal of hybridization was reduced with a lower concentration of probe. Seven polymorphisms of caspase 9 (rs2308941) C →T and DOK2 (rs2242241) T→G, 6 of polymorphisms of EGFL3 (rs947345) A→G, caspase 9 (rs2308938) C→G and PHGDH (rs1801955)T→A, 5 of polymorphisms of E2F2(rs3218170) G→A,4 of polymorphisms of MUTYH( rs1140507) T→C and BNIP3L(rs1055806)G→T, and 1 of polymorphism of TNFRSF1B (rs1061622)T→G were detected by the chip in the tissues of 10 HCC. Samples of caspase 9 (rs2308941G) and (rs2308941A) were verified by PCR-SSCP and sequencing. CONCLUSION:The cSNP chip of hepatocellular carcinoma-related genes can accelerate the discovery of polymorphic markers on hepatocellular carcinoma.
基金Supported by the National Natural Science Foundation of China (60473085)
文摘A new way of indexing and processing twig patterns in an XML documents is proposed in this paper. Every path in XML document can be transformed into a sequence of labels by Structure-Encoded that constructs a one-to-one correspondence between XML tree and sequence. Base on identifying characteristics of nodes in XML tree, the elements are classified and clustered. During query proceeding, the twig pattern is also transformed into its Structure-Encoded. By performing subsequence matching on the set of sequences in XML documents, all the occurrences of path in the XML documents are refined. Using the index, the numbers of elements retrieved are minimized. The search results with pertinent format provide more structure information without any false dismissals or false alarms. The index also supports keyword search Experiment results indicate the index has significantly efficiency with high precision.
文摘The majority of single nucleotide polymorphisms(SNPs)found in the coding region(cSNPs)are single base substitutions that may or may not lead to amino acid substitutions,most of which are related to diseases.Some cSNPs may prove useful for their potential links to functional cSNPs via linkage disequilibrium mapping.We have selected 48 cSNPs located in the coding regions of 25 genes to construct the cSNP chip.These genes are harbored in the high frequency loss regions of the chromosome 1p and 8p and related with apoptosis,cell cycles,signal transduction,oncogene,tumor suppressor genes and so on.All of the cSNPs can lead to amino acid substitutions except TP73(rs1801174).The PCR products amplified from 31 hepatocellular carcinoma(HCC)specimens were labeled with Dig-dUTP and then hybridized with the cSNP chips.The results showed that there was no hybridization signal when there was more than one site of mutation in the amplification sequence,indicating that the cSNP chip had a high sensitivity.The statistic data of the SNP(MT,homozygous and HT,heterozygous)in the HCC patients with different phenotypes(HBV+/-,differentiation stage,family history positive or negative,tumor size)indicated that the number of MT was distinctly different between patients with positive HBV and negative HBV.The MT and HT numbers of all the 48 cSNPs were significantly different between low differentiation and high differentiation HCC patients.The numbers of MT and HT were not different between positived and negative family history groups and between tumor size>3 cm and≤3 cm groups.The study results provided useful information for understanding the molecular mechanisms of HCC development.
