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Chenghsun Chiu - One of the best experts on this subject based on the ideXlab platform.
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nucleotide and Amino Acid Sequences of orit tram traj tray traa tral regions and mobilization of virulence plasmids of salmonella enterica serovars enteritidis gallinarum pullorum and typhimurium
Journal of Bacteriology, 2002Co-Authors: Chishih Chu, Chenghsun Chiu, Chihong ChuAbstract:The virulence plasmid of Salmonella enterica serovar Gallinarum-Pullorum (pSPV) but not those of Salmonella enterica serovars Enteritidis (pSEV) and Typhimurium (pSTV) can be readily mobilized by an F or F-like conjugative plasmid. To investigate the reason for the difference, the oriT-traM-traJ-traY-traA-traL regions of the three salmonella virulence plasmids (pSVs) were cloned and their nucleotide and deduced Amino Acid Sequences were examined. The cloned fragments were generally mobilized more readily than the corresponding full-length pSVs, but the recombinant plasmid containing the oriT of pSPV was, as expected, more readily mobilized, with up to 100-fold higher frequency than the recombinant plasmids containing the oriT of the other two pSVs. The nucleotide Sequences of the oriT-traM-traJ-traY-traA-traL region of pSEV and pSTV were almost identical (only 4 bp differences), but differed from that of pSPV. Major nucleotide sequence variations were found in traJ, traY, and the Tra protein binding sites sby and sbm. sby of pSPV showed higher similarity than that of pSEV or pSTV to that of the F plasmid. The reverse was true for sbm: similarity was higher with pSEV and pSTV than with pSPV. In the deduced Amino Acid Sequences of the five Tra proteins, major differences were found in TraY: pSEV's TraY was 75 Amino Acids, pSTV's was 106 Amino Acids, and pSPV's was 133 Amino Acids; and there were duplicate consensus betaalphaalpha fragments in the TraY of pSPV and F plasmid, whereas there was only a single betaalphaalpha fragment in that of pSEV and pSTV.
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nucleotide and Amino Acid Sequences of orit tram traj tray traa tral regions and mobilization of virulence plasmids of salmonella enterica serovars enteritidis gallinarum pullorum and typhimurium
Journal of Bacteriology, 2002Co-Authors: Chenghsun Chiu, Jonathan T OuAbstract:The virulence plasmid of Salmonella enterica serovar Gallinarum-Pullorum (pSPV) but not those of Salmonella enterica serovars Enteritidis (pSEV) and Typhimurium (pSTV) can be readily mobilized by an F or F-like conjugative plasmid. To investigate the reason for the difference, the oriT-traM-traJ-traY-traA-traL regions of the three salmonella virulence plasmids (pSVs) were cloned and their nucleotide and deduced Amino Acid Sequences were examined. The cloned fragments were generally mobilized more readily than the corresponding full-length pSVs, but the recombinant plasmid containing the oriT of pSPV was, as expected, more readily mobilized, with up to 100-fold higher frequency than the recombinant plasmids containing the oriT of the other two pSVs. The nucleotide Sequences of the oriT-traM-traJ-traY-traA-traL region of pSEV and pSTV were almost identical (only 4 bp differences), but differed from that of pSPV. Major nucleotide sequence variations were found in traJ, traY, and the Tra protein binding sites sby and sbm. sby of pSPV showed higher similarity than that of pSEV or pSTV to that of the F plasmid. The reverse was true for sbm: similarity was higher with pSEV and pSTV than with pSPV. In the deduced Amino Acid Sequences of the five Tra proteins, major differences were found in TraY: pSEV's TraY was 75 Amino Acids, pSTV's was 106 Amino Acids, and pSPV's was 133 Amino Acids; and there were duplicate consensus βαα fragments in the TraY of pSPV and F plasmid, whereas there was only a single βαα fragment in that of pSEV and pSTV.
Jonathan T Ou - One of the best experts on this subject based on the ideXlab platform.
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nucleotide and Amino Acid Sequences of orit tram traj tray traa tral regions and mobilization of virulence plasmids of salmonella enterica serovars enteritidis gallinarum pullorum and typhimurium
Journal of Bacteriology, 2002Co-Authors: Chenghsun Chiu, Jonathan T OuAbstract:The virulence plasmid of Salmonella enterica serovar Gallinarum-Pullorum (pSPV) but not those of Salmonella enterica serovars Enteritidis (pSEV) and Typhimurium (pSTV) can be readily mobilized by an F or F-like conjugative plasmid. To investigate the reason for the difference, the oriT-traM-traJ-traY-traA-traL regions of the three salmonella virulence plasmids (pSVs) were cloned and their nucleotide and deduced Amino Acid Sequences were examined. The cloned fragments were generally mobilized more readily than the corresponding full-length pSVs, but the recombinant plasmid containing the oriT of pSPV was, as expected, more readily mobilized, with up to 100-fold higher frequency than the recombinant plasmids containing the oriT of the other two pSVs. The nucleotide Sequences of the oriT-traM-traJ-traY-traA-traL region of pSEV and pSTV were almost identical (only 4 bp differences), but differed from that of pSPV. Major nucleotide sequence variations were found in traJ, traY, and the Tra protein binding sites sby and sbm. sby of pSPV showed higher similarity than that of pSEV or pSTV to that of the F plasmid. The reverse was true for sbm: similarity was higher with pSEV and pSTV than with pSPV. In the deduced Amino Acid Sequences of the five Tra proteins, major differences were found in TraY: pSEV's TraY was 75 Amino Acids, pSTV's was 106 Amino Acids, and pSPV's was 133 Amino Acids; and there were duplicate consensus βαα fragments in the TraY of pSPV and F plasmid, whereas there was only a single βαα fragment in that of pSEV and pSTV.
Chihong Chu - One of the best experts on this subject based on the ideXlab platform.
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nucleotide and Amino Acid Sequences of orit tram traj tray traa tral regions and mobilization of virulence plasmids of salmonella enterica serovars enteritidis gallinarum pullorum and typhimurium
Journal of Bacteriology, 2002Co-Authors: Chishih Chu, Chenghsun Chiu, Chihong ChuAbstract:The virulence plasmid of Salmonella enterica serovar Gallinarum-Pullorum (pSPV) but not those of Salmonella enterica serovars Enteritidis (pSEV) and Typhimurium (pSTV) can be readily mobilized by an F or F-like conjugative plasmid. To investigate the reason for the difference, the oriT-traM-traJ-traY-traA-traL regions of the three salmonella virulence plasmids (pSVs) were cloned and their nucleotide and deduced Amino Acid Sequences were examined. The cloned fragments were generally mobilized more readily than the corresponding full-length pSVs, but the recombinant plasmid containing the oriT of pSPV was, as expected, more readily mobilized, with up to 100-fold higher frequency than the recombinant plasmids containing the oriT of the other two pSVs. The nucleotide Sequences of the oriT-traM-traJ-traY-traA-traL region of pSEV and pSTV were almost identical (only 4 bp differences), but differed from that of pSPV. Major nucleotide sequence variations were found in traJ, traY, and the Tra protein binding sites sby and sbm. sby of pSPV showed higher similarity than that of pSEV or pSTV to that of the F plasmid. The reverse was true for sbm: similarity was higher with pSEV and pSTV than with pSPV. In the deduced Amino Acid Sequences of the five Tra proteins, major differences were found in TraY: pSEV's TraY was 75 Amino Acids, pSTV's was 106 Amino Acids, and pSPV's was 133 Amino Acids; and there were duplicate consensus betaalphaalpha fragments in the TraY of pSPV and F plasmid, whereas there was only a single betaalphaalpha fragment in that of pSEV and pSTV.
Chishih Chu - One of the best experts on this subject based on the ideXlab platform.
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nucleotide and Amino Acid Sequences of orit tram traj tray traa tral regions and mobilization of virulence plasmids of salmonella enterica serovars enteritidis gallinarum pullorum and typhimurium
Journal of Bacteriology, 2002Co-Authors: Chishih Chu, Chenghsun Chiu, Chihong ChuAbstract:The virulence plasmid of Salmonella enterica serovar Gallinarum-Pullorum (pSPV) but not those of Salmonella enterica serovars Enteritidis (pSEV) and Typhimurium (pSTV) can be readily mobilized by an F or F-like conjugative plasmid. To investigate the reason for the difference, the oriT-traM-traJ-traY-traA-traL regions of the three salmonella virulence plasmids (pSVs) were cloned and their nucleotide and deduced Amino Acid Sequences were examined. The cloned fragments were generally mobilized more readily than the corresponding full-length pSVs, but the recombinant plasmid containing the oriT of pSPV was, as expected, more readily mobilized, with up to 100-fold higher frequency than the recombinant plasmids containing the oriT of the other two pSVs. The nucleotide Sequences of the oriT-traM-traJ-traY-traA-traL region of pSEV and pSTV were almost identical (only 4 bp differences), but differed from that of pSPV. Major nucleotide sequence variations were found in traJ, traY, and the Tra protein binding sites sby and sbm. sby of pSPV showed higher similarity than that of pSEV or pSTV to that of the F plasmid. The reverse was true for sbm: similarity was higher with pSEV and pSTV than with pSPV. In the deduced Amino Acid Sequences of the five Tra proteins, major differences were found in TraY: pSEV's TraY was 75 Amino Acids, pSTV's was 106 Amino Acids, and pSPV's was 133 Amino Acids; and there were duplicate consensus betaalphaalpha fragments in the TraY of pSPV and F plasmid, whereas there was only a single betaalphaalpha fragment in that of pSEV and pSTV.
Masatoshi Nei - One of the best experts on this subject based on the ideXlab platform.
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accuracies of ancestral Amino Acid Sequences inferred by the parsimony likelihood and distance methods
Journal of Molecular Evolution, 1997Co-Authors: Jianzhi Zhang, Masatoshi NeiAbstract:Information about protein Sequences of ancestral organisms is important for identifying critical Amino Acid substitutions that have caused the functional change of proteins in evolution. Using computer simulation, we studied the accuracy of ancestral Amino Acids inferred by two currently available methods (maximum-parsimony [MP] and maximum-likelihood [ML] methods) in addition to a distance method, which was newly developed in this paper. All three methods give reliable inference when the divergence of Amino Acid Sequences is low. When the extent of sequence divergence is high, however, the ML and distance methods give more accurate results than the MP method, particularly when the phylogenetic tree includes long branches. The accuracy of inferred ancestral Amino Acids does not change very much when a few present-day Sequences are added or eliminated. When an incorrect model of Amino Acid substitution is used for the ML and distance methods, the accuracy decreases, but it is still higher than that for the MP method. When the tree topology used is partially incorrect, the accuracy in the correct part of the tree is virtually unaffected. The posterior probability of inferred ancestral Amino Acids computed by the ML and distance methods is an unbiased estimate of the true probability when a correct substitution model is used but may become an overestimate when a simpler model is used.
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a new method of inference of ancestral nucleotide and Amino Acid Sequences
Genetics, 1995Co-Authors: Ziheng Yang, Sudhir Kumar, Masatoshi NeiAbstract:A statistical method was developed for reconstructing the nucleotide or Amino Acid Sequences of extinct ancestors, given the phylogeny and Sequences of the extant species. A model of nucleotide or Amino Acid substitution was employed to analyze data of the present-day Sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or Amino Acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozyme c Sequences of six mammals were analyzed by using the likelihood and parsimony methods. The new likelihood-based method was found to be superior to the parsimony method. The probability that the Amino Acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an Amino Acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral Sequences.