Effect of Modification of the NI Artificial Diet on the Biological Fitness Parameters of Mass Reared Western Tarnished Plant Bug, Lygus hesperus

The NI artificial diet is the only known successful diet for mass rearing the western tarnished plant bug, Lygus hesperus Knight (Hemiptera: Miridae). This diet has been used for more than a decade. However, because it contains cooked chicken egg, and thus requires laborious preparation (Cohen 2000), this diet is difficult to use. Three modifications (D1, D2, D3) of the NI diet were investigated in hopes of developing a more easily prepared diet that avoids the cooked egg and improves mass fitness parameters of L. hesperus. The modified D3 diet, containing autoclaved chicken egg yolk based component, had the highest egg/cage/day production (13120 ± 812 SE). This was significantly greater than diets D1, containing autoclaved dry chicken egg yolk based component (9027 ± 811 SE), D2, containing autoclaved chicken egg white based component (8311 ± 628 SE), and NI, which contained autoclaved chicken egg yolk + cooked egg diet (7890 ± 761 SE). Significant differences were observed in the weights of all developmental stages except for eggs and first instar nymphs. Higher rates of fertility, hatchability, and low mortality in nymphs during the first instar were also obtained in the modified D3 diet. The results clearly indicated that the D3 diet provided an opportunity to significantly reduce rearing cost by avoiding time-consuming issues with preparation of a cooked egg diet. This should result in an increase in production capacity and a reduction in production costs

Stage-Specific Effects of Population Density on the Development and Fertility of the Western Tarnished Plant Bug, Lygus hesperus

The western tarnished plant bug Lygus hesperus Knight (Heteroptera: Miridae), a major pest of cotton and other key economic crops, was tested for its sensitivity to population density during nymph and adult stages. Nymphs reared to adulthood under increasing densities in laboratory conditions exhibited incremental delays in maturation, heightened mortality rates, and reductions in body mass and various size parameters. In contrast, gonadal activity in both males and females rose with initial density increases. Supplemental nutrients provided to the nymphs failed to offset the negative effects of high density, suggesting that contact frequency, rather than resource partitioning, may be the primary stress. Unlike nymphs, newly eclosed adults exposed to increasing population densities did not suffer negative physiological effects; body mass, mortality rates and patterns of ovipositional activity were unchanged. Collectively, these results indicate that population density can dramatically influence Lygus development, but the specific effects are stage-dependent

From Isotropic to Anisotropic Side Chain Representations: Comparison of Three Models for Residue Contact Estimation

The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the -to- atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. The AES model eliminates about 95% of the incorrectly counted contact-pairs in the ISS model. Algorithm analysis shows that AES model is the most computational intensive while ADC model has moderate computational cost. We derived a dataset of the mis-estimated contact pairs by AES model. The most misjudged pairs are Arg-Glu, Arg-Asp and Arg-Tyr. Such a dataset can be useful for developing the improved AES model by incorporating the pair-specific information for the cutoff distance

Genome-wide identification of SNPs and copy number variation in common bean (Phaseolus vulgaris L.) using genotyping-by-sequencing (GBS)

Next-generation sequencing technologies have increased markedly the throughput of genetic studies, allowing the identification of several thousands of SNPs within a single experiment. Even though sequencing cost is rapidly decreasing, the price for whole-genome re-sequencing of a large number of individuals is still costly, especially in plants with a large and highly redundant genome. In recent years, several reduced representation library approaches have been developed for reducing the sequencing cost per individual. Among them, genotyping-by-sequencing (GBS) represents a simple, cost-effective, and highly multiplexed alternative for species with or without an available reference genome. However, this technology requires specific optimization for each species, especially for the restriction enzyme (RE) used. Here we report on the application of GBS in a test experiment with 18 genotypes of wild and domesticated Phaseolus vulgaris. After an in silico digestion with different RE of the P. vulgaris genome reference sequence, we selected CviAII as the most suitable RE for GBS in common bean based on the high frequency and even distribution of restriction sites. A total of 44,875 SNPs, 1940 deletions, and 1693 insertions were identified, with 50 % of the variants located in genic sequences and tagging 11,027 genes. SNP and InDel distributions were positively correlated with gene density across the genome. In addition, we were able to also identify putative copy number variations of genomic segments between different genotypes. In conclusion, GBS with the CviAII enzyme results in thousands of evenly spaced markers and provides a reliable, high-throughput, and cost-effective approach for genotyping both wild and domesticated common beans