The Genomes of Oryza sativa: A history of duplications

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.

A comparative approach to somatic cell nuclear transfer in the rhesus monkey

BACKGROUND: Despite the potential utility of primate somatic cell nuclear transfer (SCNT) to biomedical research and to the production of autologous embryonic stem (ES) cells for cell- or tissue-based therapy, a reliable method for SCNT is not yet availab

Reprogramming following somatic cell nuclear transfer in primates is dependent upon nuclear remodeling

BACKGROUND: Somatic cell nuclear transfer (SCNT) requires cytoplast-mediated reprogramming of the donor nucleus. Cytoplast factors such as maturation promoting factor are implicated based on their involvement in nuclear envelope breakdown (NEBD) and prema

Culture potential of Amblypharyngodon mola with carps in polyculture in farmers' pond of northern regions of Bangladesh

To assess the culture potential of mola (Amblypharyngodon mola) along with carps in polyculture systems, an experiment consisted of three treatments each with five replications was conducted for 4 months in two villages of Parbatipur upazilla under Dinajpur district. In the first treatment (SS), catla, rohu, mrigal, grass carp, Thai punti, common carp and a higher density of silver carp (8 per 40m²) were stocked. In the second treatment (SM), stocking density of silver carp was reduced to half and mola was added at a stocking density of 12,500/ha with all other fishes used in SS. In the third treatment (MM), no silver carp was stocked and mola was added at a stocking density of 25,000/ha with all other fishes used in SS. All treatments were subjected to the same regime of feed and fertilizers. The yields of large carps were 2035 kg/ha, 1757 kg/ha and 1326 kg/ha for treatments SS, SM and MM, respectively. Catla, grass carp and carpio showed better growth and production performance in presence of mola at a higher density, while rohu, Thai punti and mrigal showed better performance when stocking density of mola was relatively low. Mola yield was almost two times higher (184 kg/ha) in absence of silver carp (MM) than (62 kg/ha) in presence of silver carp (SM). The result showed that there was a significantly (p<0.01) lower total fish production in treatment MM. But there were no significant difference in total production between treatment SS and SM.

Collapse mechanism maps for the hollow pyramidal core of a sandwich panel under transverse shear

The finite element method has been used to develop collapse mechanism maps for the shear response of sandwich panels with a stainless steel core comprising hollow struts. The core topology comprises either vertical tubes or inclined tubes in a pyramidal arrangement. The dependence of the elastic and plastic buckling modes upon core geometry is determined, and optimal geometric designs are obtained as a function of core density. For the hollow pyramidal core, strength depends primarily upon the relative density ρ̄ of the core with a weak dependence upon tube slenderness. At ρ̄ below about 3%, the tubes of the pyramidal core buckle plastically and the peak shear strength scales linearly with ρ̄. In contrast, at ρ̄ above 3%, the tubes do not buckle and a stable shear response is observed. The predictions of the current study are in excellent agreement with previous measurements on the shear strength of the hollow pyramidal core, and suggest that this core topology is attractive from the perspectives of both core strength and energy absorption. © 2011 Elsevier Ltd. All rights reserved.

Eccentricity effects on acoustic radiation from a spherical source suspended within a thermoviscous fluid sphere.

Acoustic radiation from a spherical source undergoing angularly periodic axisymmetric harmonic surface vibrations while eccentrically suspended within a thermoviscous fluid sphere, which is immersed in a viscous thermally conducting unbounded fluid medium, is analyzed in an exact fashion. The formulation uses the appropriate wave-harmonic field expansions along with the translational addition theorem for spherical wave functions and the relevant boundary conditions to develop a closed-form solution in form of infinite series. The analytical results are illustrated with a numerical example in which the vibrating source is eccentrically positioned within a chemical fluid sphere submerged in water. The modal acoustic radiation impedance load on the source and the radiated far-field pressure are evaluated and discussed for representative values of the parameters characterizing the system. The proposed model can lead to a better understanding of dynamic response of an underwater acoustic lens. It is equally applicable in miniature transducer analysis and design with applications in medical ultrasonics.