Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals ...Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.展开更多
Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different specie...Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.展开更多
Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstl...Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.展开更多
Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational proper...Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.展开更多
[Objective] The research aimed to construct the discriminant classification model of DNA sequence by combining with the biology knowledge and the mathematical method.[Method] According to the polarity nature of side c...[Objective] The research aimed to construct the discriminant classification model of DNA sequence by combining with the biology knowledge and the mathematical method.[Method] According to the polarity nature of side chain radical in the amino acid,the classification information of amino acid which represented the sequence characteristic from the content and array situation of base was extracted from the different sequences that the amino acid content was different.The four-dimension vector was used to represent.Mahalanobis distance and Fisher discriminant methods were used to classify the given sequence.[Result] In the model,the back substitution rates of sample obtained by two kinds of classification methods were both 100%,and the consistent rate of classification was 90%.[Conclusion] In the model,the calculation method was simple,and the accuracy of classification result was higher.It was superior to the discriminant classification model which was only based on the base content.展开更多
The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.T...The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.The results indicate that most minor codons for these coronaviruses are preferentially used in the initial and terminal region.The minor codons preferentially used in the initial region are thought to have a negative effect on gene expression,which can be explained by the minor codon modulator hypothesis.It also indicates that the minor codons preferentially used in the terminal region may regulate the level of gene expression.The proposed results strongly imply that the minor codon modulator hypothesis can be applied to both some bacteria and some viruses.展开更多
基金funded by the grant National Key R&D Program of China(2017ZX10103011-004 and 2018YFC1603804)the Science and Technology Program of Guangdong Province(2018B020207013 and 2019B030316013).
文摘Objective This study aimed to understand the epidemic status and phylogenetic relationships of rotavirus group A(RVA)in the Pearl River Delta region of Guangdong Province,China.Methods This study included individuals aged 28 days–85 years.A total of 706 stool samples from patients with acute gastroenteritis collected between January 2019 and January 2020 were analyzed for 17 causative pathogens,including RVA,using a Gastrointestinal Pathogen Panel,followed by genotyping,virus isolation,and complete sequencing to assess the genetic diversity of RVA.Results The overall RVA infection rate was 14.59%(103/706),with an irregular epidemiological pattern.The proportion of co-infection with RVA and other pathogens was 39.81%(41/103).Acute gastroenteritis is highly prevalent in young children aged 0–1 year,and RVA is the key pathogen circulating in patients 6–10 months of age with diarrhea.G9P[8](58.25%,60/103)was found to be the predominant genotype in the RVA strains,and the 41 RVA-positive strains that were successfully sequenced belonged to three different RVA genotypes in the phylogenetic analysis.Recombination analysis showed that gene reassortment events,selection pressure,codon usage bias,gene polymorphism,and post-translational modifications(PTMs)occurred in the G9P[8]and G3P[8]strains.Conclusion This study provides molecular evidence of RVA prevalence in the Pearl River Delta region of China,further enriching the existing information on its genetics and evolutionary characteristics and suggesting the emergence of genetic diversity.Strengthening the surveillance of genotypic changes and gene reassortment in RVA strains is essential for further research and a better understanding of strain variations for further vaccine development.
基金This work was supported by the National Major Basic Research and Development Program(No.TG1999016004)Jiangsu Provincial Natural Science Foundation(No.BK2003213).
文摘Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.
文摘Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as ＇optimal codons＇ might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.
文摘Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.
基金Supported by Science Research Project of Ningbo Dahongying University in2011(CF102601)~~
文摘[Objective] The research aimed to construct the discriminant classification model of DNA sequence by combining with the biology knowledge and the mathematical method.[Method] According to the polarity nature of side chain radical in the amino acid,the classification information of amino acid which represented the sequence characteristic from the content and array situation of base was extracted from the different sequences that the amino acid content was different.The four-dimension vector was used to represent.Mahalanobis distance and Fisher discriminant methods were used to classify the given sequence.[Result] In the model,the back substitution rates of sample obtained by two kinds of classification methods were both 100%,and the consistent rate of classification was 90%.[Conclusion] In the model,the calculation method was simple,and the accuracy of classification result was higher.It was superior to the discriminant classification model which was only based on the base content.
文摘The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.The results indicate that most minor codons for these coronaviruses are preferentially used in the initial and terminal region.The minor codons preferentially used in the initial region are thought to have a negative effect on gene expression,which can be explained by the minor codon modulator hypothesis.It also indicates that the minor codons preferentially used in the terminal region may regulate the level of gene expression.The proposed results strongly imply that the minor codon modulator hypothesis can be applied to both some bacteria and some viruses.
