Identifying disease-relevant genes and functional modules, based on gene expression pro- files and gene functional knowledge, is of high im- portance for studying disease mechanisms and sub- typing disease phenotypes....Identifying disease-relevant genes and functional modules, based on gene expression pro- files and gene functional knowledge, is of high im- portance for studying disease mechanisms and sub- typing disease phenotypes. Using gene categories of biological process and cellular component in Gene Ontology, we propose an approach to selecting func- tional modules enriched with differentially expressed genes, and identifying the feature functional modules of high disease discriminating abilities. Using the differentially expressed genes in each feature module as the feature genes, we reveal the relevance of the modules to the studied diseases. Using three data- sets for prostate cancer, gastric cancer, and leukemia, we have demonstrated that the proposed modular approach is of high power in identifying functionally integrated feature gene subsets that are highly rele- vant to the disease mechanisms. Our analysis has also shown that the critical disease-relevant genes might be better recognized from the gene regulation network, which is constructed using the characterized functional modules, giving important clues to the concerted mechanisms of the modules responding to complex disease states. In addition, the proposed approach to selecting the disease-relevant genes byjointly considering the gene functional knowledge suggests a new way for precisely classifying disease samples with clear biological interpretations, which is critical for the clinical diagnosis and the elucidation of the pathogenic basis of complex diseases.展开更多
AIM： To explore the genetic diversities of UL144 open reading frame （ORF） of cytomegalovirus DNA detected in colon tissue from infants with Hirschsprung＇s disease （HD） by sequencing UL144 DNA in 23 aganglionic c...AIM： To explore the genetic diversities of UL144 open reading frame （ORF） of cytomegalovirus DNA detected in colon tissue from infants with Hirschsprung＇s disease （HD） by sequencing UL144 DNA in 23 aganglionic colon tissue and 4 urine samples from 25 HD infants. METHODS： Nest PCR was performed for amplification of the UL144 gene. The UL144 gene was analyzed with soffwares, such as DNAclub, BioEdit, PROSITE database, and DNAstar. RESULTS： The strains from HD patients were distributed among three genotypes of UL144： group 1A （64%）, group 2 （24%）, and group 3 （12%）. The UL144 genotypes between strains from HD and control group were compared by chi square test （x^2 = 1.870, P = 0.393）. Strains from the colon were sporadically distributed in UL144 genotypes. CONCLUSION： There are genetic diversities of UL144 ORF in colon tissue of infants with HD. However, cytomegalovirus UL144 genotypes are not associated with clinical manifestations of HD.展开更多
Duck enteritis virus(DEV) is a herpesvirus that causes an acute,contagious and fatal disease. In the present article,the DEV UL4 gene was cloned and sequenced from a vaccine virus. A degenerate oligonucleotide primer ...Duck enteritis virus(DEV) is a herpesvirus that causes an acute,contagious and fatal disease. In the present article,the DEV UL4 gene was cloned and sequenced from a vaccine virus. A degenerate oligonucleotide primer for the consensus site of herpesvirus UL3 gene and a specific primer located in UL5 were used in the polymerase chain reaction(PCR) to amplify a DNA product 2 086 bp in size. DNA sequence analysis revealed that a 714 bp open reading frame(ORF) of DEV encoding a 237 amino acid polypeptide is homologous to the family of herpesvirus UL4 proteins and therefore has been characterized as a DEV UL4 gene. Alignment of the DEV UL4 protein sequence with those of other alphaherpesviruses showed that 10 amino acid residues are completely conserved. Phylogenetic tree analysis showed that the seventeen alphaherpesviruses viruses analyzed were classified into four large groups,and the duck enteritis virus branched separately,closely related to the Mardiviruses group comprising Gallid herpesvirus 2(GaHV-2) ,Gallid herpesvirus 3(GaHV-3) and Meleagrid herpesvirus 1(MeHV-1) . The present study showed that the evolutionary relationship of the UL4 protein could be used for classification of alphaherpesviruses.展开更多
Objective To investigate the polymorphism of human cytomegalovirus (HCMV) UL150 open reading frame (ORF) in low-passaged clinical isolates, and to study the relationship between the polymorphism and different pathogen...Objective To investigate the polymorphism of human cytomegalovirus (HCMV) UL150 open reading frame (ORF) in low-passaged clinical isolates, and to study the relationship between the polymorphism and different pathogenesis of congenital HCMV infection. Methods PCR was performed to amplify the entire HCMV UL150 ORF region of 29 clinical isolates, which had been proven containing detectable HCMV-DNA using fluorescence quantitative PCR. PCR amplification products were sequenced directly, and the data were analyzed. Results Totally 25 among 29 isolates were amplified, and 18 isolates were sequenced successfully. HCMV UL150 ORF sequences derived from congenitally infected infants were high variability. The UL150 ORF in all 18 clinical isolates shifted backward by 8 nucleotides leading to frame-shift, and contained a single nucleotide deletion at nucleotide position 226 compared with that of Toledo strain. The nucleotide diversity was 0.1% to 6.8% and the amino acid diversity was 0.2% to 19.2% related to Toledo strain. However, the nucleotide diversity was 0.1% to 6.4% and amino acid diversity was 0.2% to 8.3% by compared with Merlin strain. Compared with Toledo, 4 new cysteine residues and 13 additional posttranslational modification sites were observed in UL150 putative proteins of clinical isolates. Moreover, the UL150 putative protein contained an additional transmembrane helix at position of 4-17 amino acid related to Toledo. Conclusion HCMV UL150 ORF and deduced amino acid sequences of clinical strains are hypervariability. No obvious linkage between the polymorphism and different pathogenesis of congenital HCMV infection is found.展开更多
Objective: To explore the effect of curcumin on the proliferation of renal cell carcinoma and analyze its regulation mechanism. Methods: In RCC cell lines of A498 and 786-O, the effects of curcumin(2.5, 5, 10 μmo/L) ...Objective: To explore the effect of curcumin on the proliferation of renal cell carcinoma and analyze its regulation mechanism. Methods: In RCC cell lines of A498 and 786-O, the effects of curcumin(2.5, 5, 10 μmo/L) on the proliferation were analyzed by Annexin V+PI staining. Besides, A498 was inoculated into nude mice to establish tumorigenic models, and the model mice were treated with different concentrations of curcumin(100, 200, and 400 mg/kg), once daily for 30 days. Then the tumor diameter was measured, the tumor cells were observed by hematoxylin-eosin staining, and the protein expressions of miR-148 and ADAMTS18were detected by immunohistochemistry. In vitro, after transfection of miR-148 mimics, miR-148 inhibitor or si-ADAMTS18 in cell lines, the expression of ADAMTS18 was examined by Western blotting and the cell survival rate was analyzed using MTT. Subsequently, Western blot analysis was again used to examine the autophagy phenomenon by measuring the relative expression level of LC3-Ⅱ/LC3-Ⅰ;autophagy-associated genes,including those of Beclin-1 and ATG5, were also examined when miR-148 was silenced in both cell lines with curcumin treatment. Results: Curcumin could inhibit the proliferation of RCC in cell lines and nude mice. The expressions of miR-148 and ADAMTS18 were upregulated after curcumin treatment both in vitro and in vivo(P<0.05). The cell survival rate was dramatically declined upon miR-148 or ADAMTS18 upregulated. However,si-ADAMTS18 treatment or miR-148 inhibitor reversed these results, that is, both of them promoted the cell survival rate. Conclusion: Curcumin can inhibit the proliferation of renal cell carcinoma by regulating the miR-148/ADAMTS18 axis through the suppression of autophagy in vitro and in vivo. There may exist a positive feedback loop between mi R-148 and ADAMTS18 gene in RCC.展开更多
基金supported in part by the National Natural Science Foundation of China(Grant Nos.30170515,30370388,30370798,30570424&30571034)the National High Tech Development Project of China(Grant Nos.2003AA2Z2051&2002AA2Z2052)+3 种基金Heilongjiang Science&Technology Key Project(Grant No.GB03C602-4)Harbin(City)Science&Technology Key Project(Grant No.2003AA3CS113)the Natural Science Foundation of Heilongjiang Province(Grant No.F0177)0utstanding 0verseas Scientist Foundation of Education Department of Heilongjiang Province(Grant No.1055HG009).
文摘Identifying disease-relevant genes and functional modules, based on gene expression pro- files and gene functional knowledge, is of high im- portance for studying disease mechanisms and sub- typing disease phenotypes. Using gene categories of biological process and cellular component in Gene Ontology, we propose an approach to selecting func- tional modules enriched with differentially expressed genes, and identifying the feature functional modules of high disease discriminating abilities. Using the differentially expressed genes in each feature module as the feature genes, we reveal the relevance of the modules to the studied diseases. Using three data- sets for prostate cancer, gastric cancer, and leukemia, we have demonstrated that the proposed modular approach is of high power in identifying functionally integrated feature gene subsets that are highly rele- vant to the disease mechanisms. Our analysis has also shown that the critical disease-relevant genes might be better recognized from the gene regulation network, which is constructed using the characterized functional modules, giving important clues to the concerted mechanisms of the modules responding to complex disease states. In addition, the proposed approach to selecting the disease-relevant genes byjointly considering the gene functional knowledge suggests a new way for precisely classifying disease samples with clear biological interpretations, which is critical for the clinical diagnosis and the elucidation of the pathogenic basis of complex diseases.
基金Supported by the National Natural Science Foundation of China, No.30170986
文摘AIM： To explore the genetic diversities of UL144 open reading frame （ORF） of cytomegalovirus DNA detected in colon tissue from infants with Hirschsprung＇s disease （HD） by sequencing UL144 DNA in 23 aganglionic colon tissue and 4 urine samples from 25 HD infants. METHODS： Nest PCR was performed for amplification of the UL144 gene. The UL144 gene was analyzed with soffwares, such as DNAclub, BioEdit, PROSITE database, and DNAstar. RESULTS： The strains from HD patients were distributed among three genotypes of UL144： group 1A （64%）, group 2 （24%）, and group 3 （12%）. The UL144 genotypes between strains from HD and control group were compared by chi square test （x^2 = 1.870, P = 0.393）. Strains from the colon were sporadically distributed in UL144 genotypes. CONCLUSION： There are genetic diversities of UL144 ORF in colon tissue of infants with HD. However, cytomegalovirus UL144 genotypes are not associated with clinical manifestations of HD.
文摘Duck enteritis virus(DEV) is a herpesvirus that causes an acute,contagious and fatal disease. In the present article,the DEV UL4 gene was cloned and sequenced from a vaccine virus. A degenerate oligonucleotide primer for the consensus site of herpesvirus UL3 gene and a specific primer located in UL5 were used in the polymerase chain reaction(PCR) to amplify a DNA product 2 086 bp in size. DNA sequence analysis revealed that a 714 bp open reading frame(ORF) of DEV encoding a 237 amino acid polypeptide is homologous to the family of herpesvirus UL4 proteins and therefore has been characterized as a DEV UL4 gene. Alignment of the DEV UL4 protein sequence with those of other alphaherpesviruses showed that 10 amino acid residues are completely conserved. Phylogenetic tree analysis showed that the seventeen alphaherpesviruses viruses analyzed were classified into four large groups,and the duck enteritis virus branched separately,closely related to the Mardiviruses group comprising Gallid herpesvirus 2(GaHV-2) ,Gallid herpesvirus 3(GaHV-3) and Meleagrid herpesvirus 1(MeHV-1) . The present study showed that the evolutionary relationship of the UL4 protein could be used for classification of alphaherpesviruses.
基金Supported by the National Natural Science Foundation of China(30170986,30371492).
文摘Objective To investigate the polymorphism of human cytomegalovirus (HCMV) UL150 open reading frame (ORF) in low-passaged clinical isolates, and to study the relationship between the polymorphism and different pathogenesis of congenital HCMV infection. Methods PCR was performed to amplify the entire HCMV UL150 ORF region of 29 clinical isolates, which had been proven containing detectable HCMV-DNA using fluorescence quantitative PCR. PCR amplification products were sequenced directly, and the data were analyzed. Results Totally 25 among 29 isolates were amplified, and 18 isolates were sequenced successfully. HCMV UL150 ORF sequences derived from congenitally infected infants were high variability. The UL150 ORF in all 18 clinical isolates shifted backward by 8 nucleotides leading to frame-shift, and contained a single nucleotide deletion at nucleotide position 226 compared with that of Toledo strain. The nucleotide diversity was 0.1% to 6.8% and the amino acid diversity was 0.2% to 19.2% related to Toledo strain. However, the nucleotide diversity was 0.1% to 6.4% and amino acid diversity was 0.2% to 8.3% by compared with Merlin strain. Compared with Toledo, 4 new cysteine residues and 13 additional posttranslational modification sites were observed in UL150 putative proteins of clinical isolates. Moreover, the UL150 putative protein contained an additional transmembrane helix at position of 4-17 amino acid related to Toledo. Conclusion HCMV UL150 ORF and deduced amino acid sequences of clinical strains are hypervariability. No obvious linkage between the polymorphism and different pathogenesis of congenital HCMV infection is found.
基金Beijing Traditional Chinese Medicine Development Fundation(No.QN-2020-03)。
文摘Objective: To explore the effect of curcumin on the proliferation of renal cell carcinoma and analyze its regulation mechanism. Methods: In RCC cell lines of A498 and 786-O, the effects of curcumin(2.5, 5, 10 μmo/L) on the proliferation were analyzed by Annexin V+PI staining. Besides, A498 was inoculated into nude mice to establish tumorigenic models, and the model mice were treated with different concentrations of curcumin(100, 200, and 400 mg/kg), once daily for 30 days. Then the tumor diameter was measured, the tumor cells were observed by hematoxylin-eosin staining, and the protein expressions of miR-148 and ADAMTS18were detected by immunohistochemistry. In vitro, after transfection of miR-148 mimics, miR-148 inhibitor or si-ADAMTS18 in cell lines, the expression of ADAMTS18 was examined by Western blotting and the cell survival rate was analyzed using MTT. Subsequently, Western blot analysis was again used to examine the autophagy phenomenon by measuring the relative expression level of LC3-Ⅱ/LC3-Ⅰ;autophagy-associated genes,including those of Beclin-1 and ATG5, were also examined when miR-148 was silenced in both cell lines with curcumin treatment. Results: Curcumin could inhibit the proliferation of RCC in cell lines and nude mice. The expressions of miR-148 and ADAMTS18 were upregulated after curcumin treatment both in vitro and in vivo(P<0.05). The cell survival rate was dramatically declined upon miR-148 or ADAMTS18 upregulated. However,si-ADAMTS18 treatment or miR-148 inhibitor reversed these results, that is, both of them promoted the cell survival rate. Conclusion: Curcumin can inhibit the proliferation of renal cell carcinoma by regulating the miR-148/ADAMTS18 axis through the suppression of autophagy in vitro and in vivo. There may exist a positive feedback loop between mi R-148 and ADAMTS18 gene in RCC.
