ABSTRACT: The genome sequence of the Severe Acute Respiratory Syndrome (SARS)-associated virus provides essential information for the
identification of pathogen(s), exploration of etiology and evolution, interpretation of transmission and pathogenesis, development
of diagnostics, prevention by future vaccination, and treatment by developing new drugs. We report the complete genome sequence
and comparative analysis of an isolate (BJ01) of the coronavirus that has been recognized as a pathogen for SARS. The genome
is 29725 nt in size and has 11 ORFs (Open Reading Frames). It is composed of a stable region encoding an RNA-dependent RNA
polymerase (composed of 2 ORFs) and a variable region representing 4 CDSs (coding sequences) for viral structural genes (the
S, E, M, N proteins) and 5 PUPs (putative uncharacterized proteins). Its gene order is identical to that of other known coronaviruses.
The sequence alignment with all known RNA viruses places this virus as a member in the family of Coronaviridae. Thirty putative
substitutions have been identified by comparative analysis of the 5 SARS-associated virus genome sequences in GenBank. Fifteen
of them lead to possible amino acid changes (non-synonymous mutations) in the proteins. Three amino acid changes, with predicted
alteration of physical and chemical features, have been detected in the S protein that is postulated to be involved in the
immunoreactions between the virus and its host. Two amino acid changes have been detected in the M protein, which could be
related to viral envelope formation. Phylogenetic analysis suggests the possibility of non-human origin of the SARS-associated
viruses but provides no evidence that they are man-made. Further efforts should focus on identifying the etiology of the SARS-associated
virus and ruling out conclusively the existence of other possible SARS-related pathogen(s).
KeywordsSevere Acute Respiratory Syndrome (SARS)-coronavirus-genome-phylogeny
Chinese Science Bulletin 04/2012; 48(10):941-948. · 1.32 Impact Factor
ABSTRACT: Streptococcus equi subsp. zooepidemicus is an opportunistic pathogen. It has caused a very large economic loss in the swine industry of China and has become a threat to human health. We announce the complete genome sequence of S. equi subsp. zooepidemicus strain ATCC 35246, which provides opportunities to understand its pathogenesis mechanism and genetic basis.
Journal of bacteriology 10/2011; 193(19):5583-4. · 3.94 Impact Factor
ABSTRACT: The direct asymmetric aldol reactions of equivalent molar amounts of aldehydes and ketones were carried out at -20 degrees C over alkaline Al(2)O(3) with 20 mol % of Pro-Trp as catalyst and 20 mol % of N-methylmorpholine or 1,4-diazabicyclo[2.2.2]octane as additive. After simple and environmentally friendly work-up, moderate to high isolated yields (up to 95%), good diastereoselectivities (>99:1), and enantioselectivities (up to 98% ee) have been achieved for the reactions of different kinds of ketones with various aldehydes. The catalytic system could be reused without decrease of activity by addition of 10 mol % catalyst and base in the catalytic system.
Chirality 11/2009; 22(6):580-6. · 2.35 Impact Factor
ABSTRACT: We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000-40,000. Only 2%-3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
PLoS Biology 03/2005; 3(2):e38. · 11.45 Impact Factor
ABSTRACT: We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.
Genomics Proteomics & Bioinformatics 06/2003; 1(2):101-7.