We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilities for each base. Clone-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4

The migratory locust is one of the most notorious agricultural pests that undergo a well known reversible, density-dependent phase transition from the solitary to the gregarious. To demonstrate the underlying molecular mechanisms of the phase change, we generated 76,012 ESTs from the whole body and dissected organs in the two phases. Comparing 12,161 unigene clusters, we identified 532 genes as phase-related (P<0.01). Comprehensive assessment of the phase-related expression revealed that, whereas most of the genes in various categories from hind legs and the midgut are down-regulated in the gregarious phase, several gene classes in the head are impressively up-regulated, including those with peptidase, receptor, and oxygen-binding activities and those related to development, cell growth, and responses to external stimuli. Among them, a superfamily of proteins, the JHPH superfamily, which includes juvenile hormone-binding protein, hexamerins, prophenoloxidase, and hemocyanins, were highly expressed in the heads of the gregarious hoppers and hind legs of the solitary hoppers. Quantitative PCR experiments confirmed in part the EST results. These differentially regulated genes have strong functional implications that numerous molecular activities are involved in phase plasticity. This study provides ample molecular markers and genomic information on hemimetabolous insects and insights into the genetic and molecular mechanisms of phase changes in locusts.

An experimental system was set up to generate the impact force, measure the response wave signal, and analyse the frequency spectrum for physical property detection of biological product. The egg dynamic resonance frequency was obtained through the analysis of the dynamically measured frequency response of an egg excited by pendulum. The effects of excitation point, detected point, impact intensity, excitation material, egg mass, egg density, shell stiffness and shell crack on the dominant frequency were analysed. The results showed that the dominant frequency was significantly affected by the shell crack, shell stiffness, egg mass and egg density, and not significantly affected by excitation point, detected point, excitation velocity and impacting material. The dominant frequency increased with increasing of shell stiffness or egg density, and decreased with increase of the egg mass. The coefficient of determination (R2) of the quadratic relationship between the dominant frequency and the three egg physical properties was 0.62-0.68.