We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, bo... more 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 superscaffolds 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. Citation: Yu J, Wang J, Lin W, Li S, Li H, et al. (2005) The genomes of Oryza sativa: A history of duplications. PLoS Biol 3(2): e38.
Background and purpose: As a molecular chaperone, acetylcholinesterase (AChE; EC 3.1.1.7) plays a... more Background and purpose: As a molecular chaperone, acetylcholinesterase (AChE; EC 3.1.1.7) plays a critical role in the pathogenesis of Alzheimer's disease (AD). The peripheral anionic site (PAS) of AChE has been indicated as the amyloid-b (Ab) binding domain. The goal of this study was to determine other motifs in AChE involved in Ab aggregation and deposition. Methods and results: The b-hairpin in monomeric Ab is the key motif of nucleation-dependent Ab self-aggregation. As AChE could induce Ab aggregation and deposition, we searched AChE for b-hairpin structures. In A11-specific dot blot assay, AChE was detected by an oligomer-specific antibody A11, implying the existence of b-hairpin structures in AChE as b-hairpin was the core motif of oligomers. A molecular superimposing approach further revealed that the N-terminal region, from Glu7 to Ile20, in AChE (AChE 7-20) was similar to the b-hairpin domain in Ab. The results of further dot blot assays, thioflavin T fluorescence assays, and electron microscopy imaging experiments, indicated that the N-terminal synthetic peptide AChE 7-20 had nearly the same ability as AChE with regard to triggering Ab aggregation and deposition. Conclusions: AChE 7-20, a b-hairpin region in AChE, might be a new motif in AChE capable of triggering Ab aggregation and deposition. This finding will be helpful to design new and more effective Ab aggregation inhibitors for AD treatment.
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, bo... more 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 superscaffolds 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. Citation: Yu J, Wang J, Lin W, Li S, Li H, et al. (2005) The genomes of Oryza sativa: A history of duplications. PLoS Biol 3(2): e38.
Background and purpose: As a molecular chaperone, acetylcholinesterase (AChE; EC 3.1.1.7) plays a... more Background and purpose: As a molecular chaperone, acetylcholinesterase (AChE; EC 3.1.1.7) plays a critical role in the pathogenesis of Alzheimer's disease (AD). The peripheral anionic site (PAS) of AChE has been indicated as the amyloid-b (Ab) binding domain. The goal of this study was to determine other motifs in AChE involved in Ab aggregation and deposition. Methods and results: The b-hairpin in monomeric Ab is the key motif of nucleation-dependent Ab self-aggregation. As AChE could induce Ab aggregation and deposition, we searched AChE for b-hairpin structures. In A11-specific dot blot assay, AChE was detected by an oligomer-specific antibody A11, implying the existence of b-hairpin structures in AChE as b-hairpin was the core motif of oligomers. A molecular superimposing approach further revealed that the N-terminal region, from Glu7 to Ile20, in AChE (AChE 7-20) was similar to the b-hairpin domain in Ab. The results of further dot blot assays, thioflavin T fluorescence assays, and electron microscopy imaging experiments, indicated that the N-terminal synthetic peptide AChE 7-20 had nearly the same ability as AChE with regard to triggering Ab aggregation and deposition. Conclusions: AChE 7-20, a b-hairpin region in AChE, might be a new motif in AChE capable of triggering Ab aggregation and deposition. This finding will be helpful to design new and more effective Ab aggregation inhibitors for AD treatment.
Uploads
Papers by feng zhang