Classical swine fever virus(CSFV) is the causative agent of classical swine fever, a highly contagious disease of pigs. But there is little information on the recombination in natural populations of CSFVs. Therefore, ...Classical swine fever virus(CSFV) is the causative agent of classical swine fever, a highly contagious disease of pigs. But there is little information on the recombination in natural populations of CSFVs. Therefore, a phylogenetic analysis of 62 fulllength genome CSFV strains, isolated from all over the world, was performed to detect potential recombination events, with the recombinant sequences being analyzed with the SimPlot and RDP programs. The results identified a mosaic virus, Chinese CSFV HCLV(2)(AF091507.1), which is the one naturally emerged recombinant CSFV with two recombination breakpoints at 2 484 and 2 900 bp of the genome alignment. Its two putative parental-like strains were CSFV Shimen(AF092448.2) and CSFV strain C/HVRI(AY805221.1). This work demonstrated that homologous recombination did occur in natural CSFV populations. It had significant implications for understanding the molecular epidemiology of CSFV, and revealed that recombination was an important factor for high genetic diversities of CSFV.展开更多
Porcine epidemic diarrhea(PED)is caused by porcine epidemic diarrhea virus(PEDV),and is characterized by vomiting,diarrhea and dehydration of suckling pigs from 80% to 100% morbidity and 50% to 90% mortality,and resul...Porcine epidemic diarrhea(PED)is caused by porcine epidemic diarrhea virus(PEDV),and is characterized by vomiting,diarrhea and dehydration of suckling pigs from 80% to 100% morbidity and 50% to 90% mortality,and resulted in tremendous economic losses to swine industry.The PEDV mainly infects small intestine of pigs,resulting in vacuolar degeneration and necrosis of mucosal epithelium.The IPEC-J2 is a pig intestine epithelial cell line,which is similar to the intestinal environment of piglets,can be used to isolate and identify the PEDV field isolates.In this study,it appeared the PEDV typical postmortem changes and histopathological lesion of degeneration and destruction of small intestine in infected piglets,and IHC identified that the PEDV distributed in the mucosa and submucosa of small intestine mostly.Furthermore,the PEDV HLJ strain was successfully isolated and characterized in the IPEC-J2 cells,and indicated that the IPEC-J2 cell line was sensitive to isolate and adapt the PEDV field strain,and could be utilized to multiply the PEDV rapidly.The S gene analysis indicated that the PEDV HLJ strain was the prevailed virus,belonged to Group 1 with attenuated virulent DR13,SC1402 and J-S2/2015 strains isolated in South Korea and China from 2014 to 2015.This study had important theoretical and practical significances on analyzing genetic variation of the PEDV,understanding the pathogenic characteristics of the virus and developing new vaccines for the PED.展开更多
Encephalomyocarditis virus(EMCV)is a positive single-stranded small RNA virus without envelope,which can infect a variety of mammals.Swines are the most susceptible animals,which can cause acute myocarditis and respir...Encephalomyocarditis virus(EMCV)is a positive single-stranded small RNA virus without envelope,which can infect a variety of mammals.Swines are the most susceptible animals,which can cause acute myocarditis and respiratory failure in piglets and reproductive failure in pregnant sows.Diseases caused by EMCV have a wide range of effects on the global swine industry.In this study,a strain of EMCV was isolated from a swine aborted fetus in northeast China.It was identified by reverse transcriptase polymerase chain reaction(RT-PCR),electron microscopic observation and indirect immunofluorescence assay.The subsequent results showed that the virus titer of HLJ strain grew to 8.3 lgTCID50 on baby hamster kidney 21(BHK-21)cells.And HLJ strain caused the specific cytopathic effect(CPE)on BHK-21 cells and severe pathological changes in mice.Complete genome sequencing and multiple sequence alignment showed that the homology between HLJ strain and other isolates worldwide was 71.5%-99.7%.Phylogenetic analysis showed that EMCV isolates fell into five clusters:lineageⅠ,Ⅱ,Ⅲ,ⅣandⅤ,based on the nucleotide sequences of the entire open reading frame(ORF)and VP1 gene.HLJ isolate was grouped into lineage I.The analyses of amino acid mutation sites of VP1 protein showed that the amino acids at positions 20 and 54 in VP1 junction were unique to HLJ strain.The isolation of HLJ strain enriched the epidemiological database of EMCV.展开更多
The p65 protein is a functional subunit of NF-κB family and exhibits a crucial role in host immune and inflammatory responses,apoptosis and tumor proliferation if improperly-regulated.Given its ubiquitous association...The p65 protein is a functional subunit of NF-κB family and exhibits a crucial role in host immune and inflammatory responses,apoptosis and tumor proliferation if improperly-regulated.Given its ubiquitous association with nearly all the animal cells and its pleotropic functions,the gene encoding NF-κB p65 subunit was cloned and sequenced from porcine kidney(PK-15)cells.The gene was 1662 bp in length,encoded a 553-amino acid protein and contained the prototypical NF-κB functional domains.Real-time quantitative RT-PCR and Western blot were used to characterize the transcription and expression levels of the p65 in different pig tissues.The results indicated that the p65 gene and protein were both broadly expressed in pig tissues,but most highly expressed in the intestine-associated lymph nodes and the lungs.To localize the recombinant protein in intestinal porcine epithelial cells(IPEC-J2),the gene was subcloned into the vector pEGFP(pEGFP-p65).Using fluorescence microscopy,the protein was found confined to the cytoplasm in normal cells;however,during porcine epidemic diarrhea virus(PEDV)infection,mRNA and protein expression were significantly up-regulated and the protein exhibited an overt tendency for nuclear translocalization consistent with a regulatory role in antiviral innate immunity.展开更多
Japanese encephalitis virus（JEV） is a significant causative agent of arthropod-borne encephalitis and what is less clear that the factors cause the virus wide spread. The objective was to confirm whether the homolog...Japanese encephalitis virus（JEV） is a significant causative agent of arthropod-borne encephalitis and what is less clear that the factors cause the virus wide spread. The objective was to confirm whether the homologous recombination imposed on JEV. The phylogenetic and homologous recombination analyses were performed based on 163 complete JEV genomes which were recently isolated. They were still separated into five genotypes（GI-GV） and the most of recently isolated JEVs were GI rather than GIII in Asian areas including China's Mainland. Two recombinant events were identified in JEV and the evidence of the recombination was observed between China and Japan isolates that partitioned into two distinct subclades, but still the same genotype（GIII）. Our data further suggested that most of the nucleotides in JEV genome were under negative selection; however, changes within codon 2 316（amino acid NS4b-44） showed an evidence of the positive selection.展开更多
目的使用高斯核函数和欧式距离函数改进微阵列显著分析法(significance analysis of microarray,SAM)得到MSAM1法(modified significance analysis of microarray-1,MSAM1)和MSAM2法(modified significance analysis of microarray-2,MS...目的使用高斯核函数和欧式距离函数改进微阵列显著分析法(significance analysis of microarray,SAM)得到MSAM1法(modified significance analysis of microarray-1,MSAM1)和MSAM2法(modified significance analysis of microarray-2,MSAM2),与SAM法、Relief法、支持向量机递归特征消除法(support vector machine recursive feature elimination, SVM-RFE)进行对比,评价在基因表达数据中MSAM1法、MSAM2法的基因选择和分类预测能力。方法从Bioconductor中的golubEsets包获得leukemia数据集(Golub等人给出了该数据集所包含的50个差异基因),运用R软件实现5种算法,分别用正确率和ROC曲线下面积即AUC值评价基因选择能力和分类预测能力,用Kruskal-Wallis H检验比较5种方法的正确率和AUC值的组间差异,进一步的两两比较采用SNK-q检验。结果正确率和AUC值均表现为MSAM1和MSAM2最优,SAM和SVM-RFE法次之,Relief法排在最后;5种方法的组间差异有统计学意义(H=150.333,P<0.0001和H=293.2579,P<0.0001),两两比较结果显示虽然MSAM1和MSAM2之间差异无统计学意义(P>0.05),但两种方法与其他3种方法之间差异均有统计学意义(P<0.05)。结论用高斯核函数和欧式距离函数改进的加权SAM法提高了SAM法的基因选择和分类预测能力,在实际基因表达数据的应用中可以得到更为稳定的分析结果。展开更多
基金Supported by the National Natural Science Foundation of China(31370140 31372438)
文摘Classical swine fever virus(CSFV) is the causative agent of classical swine fever, a highly contagious disease of pigs. But there is little information on the recombination in natural populations of CSFVs. Therefore, a phylogenetic analysis of 62 fulllength genome CSFV strains, isolated from all over the world, was performed to detect potential recombination events, with the recombinant sequences being analyzed with the SimPlot and RDP programs. The results identified a mosaic virus, Chinese CSFV HCLV(2)(AF091507.1), which is the one naturally emerged recombinant CSFV with two recombination breakpoints at 2 484 and 2 900 bp of the genome alignment. Its two putative parental-like strains were CSFV Shimen(AF092448.2) and CSFV strain C/HVRI(AY805221.1). This work demonstrated that homologous recombination did occur in natural CSFV populations. It had significant implications for understanding the molecular epidemiology of CSFV, and revealed that recombination was an important factor for high genetic diversities of CSFV.
基金Supported by the National Natural Science Foundation of China(31201911 31372438)
文摘Porcine epidemic diarrhea(PED)is caused by porcine epidemic diarrhea virus(PEDV),and is characterized by vomiting,diarrhea and dehydration of suckling pigs from 80% to 100% morbidity and 50% to 90% mortality,and resulted in tremendous economic losses to swine industry.The PEDV mainly infects small intestine of pigs,resulting in vacuolar degeneration and necrosis of mucosal epithelium.The IPEC-J2 is a pig intestine epithelial cell line,which is similar to the intestinal environment of piglets,can be used to isolate and identify the PEDV field isolates.In this study,it appeared the PEDV typical postmortem changes and histopathological lesion of degeneration and destruction of small intestine in infected piglets,and IHC identified that the PEDV distributed in the mucosa and submucosa of small intestine mostly.Furthermore,the PEDV HLJ strain was successfully isolated and characterized in the IPEC-J2 cells,and indicated that the IPEC-J2 cell line was sensitive to isolate and adapt the PEDV field strain,and could be utilized to multiply the PEDV rapidly.The S gene analysis indicated that the PEDV HLJ strain was the prevailed virus,belonged to Group 1 with attenuated virulent DR13,SC1402 and J-S2/2015 strains isolated in South Korea and China from 2014 to 2015.This study had important theoretical and practical significances on analyzing genetic variation of the PEDV,understanding the pathogenic characteristics of the virus and developing new vaccines for the PED.
基金Supported by the National Natural Science Foundation of China(31372438)。
文摘Encephalomyocarditis virus(EMCV)is a positive single-stranded small RNA virus without envelope,which can infect a variety of mammals.Swines are the most susceptible animals,which can cause acute myocarditis and respiratory failure in piglets and reproductive failure in pregnant sows.Diseases caused by EMCV have a wide range of effects on the global swine industry.In this study,a strain of EMCV was isolated from a swine aborted fetus in northeast China.It was identified by reverse transcriptase polymerase chain reaction(RT-PCR),electron microscopic observation and indirect immunofluorescence assay.The subsequent results showed that the virus titer of HLJ strain grew to 8.3 lgTCID50 on baby hamster kidney 21(BHK-21)cells.And HLJ strain caused the specific cytopathic effect(CPE)on BHK-21 cells and severe pathological changes in mice.Complete genome sequencing and multiple sequence alignment showed that the homology between HLJ strain and other isolates worldwide was 71.5%-99.7%.Phylogenetic analysis showed that EMCV isolates fell into five clusters:lineageⅠ,Ⅱ,Ⅲ,ⅣandⅤ,based on the nucleotide sequences of the entire open reading frame(ORF)and VP1 gene.HLJ isolate was grouped into lineage I.The analyses of amino acid mutation sites of VP1 protein showed that the amino acids at positions 20 and 54 in VP1 junction were unique to HLJ strain.The isolation of HLJ strain enriched the epidemiological database of EMCV.
基金Supported by the National Natural Science Foundation of China(31370140,31372438)。
文摘The p65 protein is a functional subunit of NF-κB family and exhibits a crucial role in host immune and inflammatory responses,apoptosis and tumor proliferation if improperly-regulated.Given its ubiquitous association with nearly all the animal cells and its pleotropic functions,the gene encoding NF-κB p65 subunit was cloned and sequenced from porcine kidney(PK-15)cells.The gene was 1662 bp in length,encoded a 553-amino acid protein and contained the prototypical NF-κB functional domains.Real-time quantitative RT-PCR and Western blot were used to characterize the transcription and expression levels of the p65 in different pig tissues.The results indicated that the p65 gene and protein were both broadly expressed in pig tissues,but most highly expressed in the intestine-associated lymph nodes and the lungs.To localize the recombinant protein in intestinal porcine epithelial cells(IPEC-J2),the gene was subcloned into the vector pEGFP(pEGFP-p65).Using fluorescence microscopy,the protein was found confined to the cytoplasm in normal cells;however,during porcine epidemic diarrhea virus(PEDV)infection,mRNA and protein expression were significantly up-regulated and the protein exhibited an overt tendency for nuclear translocalization consistent with a regulatory role in antiviral innate immunity.
基金Supported by the National Natural Science Foundation of China(31272569,31270187)Projects in the National Science&Technology Pillar Program during 12th Five-year Plan Period(2013BAD12B04)Harbin Science and Technology Bureau(RC2012XK002003)
文摘Japanese encephalitis virus（JEV） is a significant causative agent of arthropod-borne encephalitis and what is less clear that the factors cause the virus wide spread. The objective was to confirm whether the homologous recombination imposed on JEV. The phylogenetic and homologous recombination analyses were performed based on 163 complete JEV genomes which were recently isolated. They were still separated into five genotypes（GI-GV） and the most of recently isolated JEVs were GI rather than GIII in Asian areas including China's Mainland. Two recombinant events were identified in JEV and the evidence of the recombination was observed between China and Japan isolates that partitioned into two distinct subclades, but still the same genotype（GIII）. Our data further suggested that most of the nucleotides in JEV genome were under negative selection; however, changes within codon 2 316（amino acid NS4b-44） showed an evidence of the positive selection.
