Comparison of selective genotyping strategies for prediction of breeding values in a population undergoing selection

Genomewide marker information can improve the reliability of breeding value predictions for young selection candidates in genomic selection. However, the cost of genotyping limits its use to elite animals, and how such selective genotyping affects predictive ability of genomic selection models is an open question. We performed a simulation study to evaluate the quality of breeding value predictions for selection candidates based on different selective genotyping strategies in a population undergoing selection. The genome consisted of 10 chromosomes of 100 cM each. After 5,000 generations of random mating with a population size of 100 (50 males and 50 females), generation G(0) (reference population) was produced via a full factorial mating between the 50 males and 50 females from generation 5,000. Different levels of selection intensities (animals with the largest yield deviation value) in G(0) or random sampling (no selection) were used to produce offspring of G(0) generation (G(1)). Five genotyping strategies were used to choose 500 animals in G(0) to be genotyped: 1) Random: randomly selected animals, 2) Top: animals with largest yield deviation values, 3) Bottom: animals with lowest yield deviations values, 4) Extreme: animals with the 250 largest and the 250 lowest yield deviations values, and 5) Less Related: less genetically related animals. The number of individuals in G(0) and G(1) was fixed at 2,500 each, and different levels of heritability were considered (0.10, 0.25, and 0.50). Additionally, all 5 selective genotyping strategies (Random, Top, Bottom, Extreme, and Less Related) were applied to an indicator trait in generation G(0), and the results were evaluated for the target trait in generation G(1), with the genetic correlation between the 2 traits set to 0.50. The 5 genotyping strategies applied to individuals in G(0) (reference population) were compared in terms of their ability to predict the genetic values of the animals in G(1) (selection candidates). Lower correlations between genomic-based estimates of breeding values (GEBV) and true breeding values (TBV) were obtained when using the Bottom strategy. For Random, Extreme, and Less Related strategies, the correlation between GEBV and TBV became slightly larger as selection intensity decreased and was largest when no selection occurred. These 3 strategies were better than the Top approach. In addition, the Extreme, Random, and Less Related strategies had smaller predictive mean squared errors (PMSE) followed by the Top and Bottom methods. Overall, the Extreme genotyping strategy led to the best predictive ability of breeding values, indicating that animals with extreme yield deviations values in a reference population are the most informative when training genomic selection models.

Multi-population genetic algorithm to solve the synchronized and integrated two-level lot sizing and scheduling problem

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pharmaceutical emulsions: a new approach for gene therapy

The concept of gene therapy involves the experimental transfer of a therapeutic gene into an individual's cells and tissues to replace an abnormal gene aiming to treat a disease, or to use the gene to treat a disease just like a medicine, improving the clinical status of a patient. The achievement of a foreigner nucleic acid into a population of cells requires its transfer to the target. Therefore, it is essential to create carriers (vectors) that transfer and protect the nucleic acid until it reaches the target. The obvious disadvantages of the use of viral vectors have directed the research for the development of a nonviral organized system such as emulsions. In fact, recently, there has been an increase of interest in its use in biotechnology as a nonviral vector for gene therapy. This review focuses on the progress of cationic emulsions and the improvement of the formulations, as a potential delivery system for gene therapy.

The sugarcane borer Diatraea saccharalis (Fabr.) (Lep., Crambidae) and its parasitoids: a synchrony approach to spatial and temporal dynamics

A data set on Diatraea saccharalis and its parasitoids, Cotesia flavipes and tachinid flies, was analysed at five spatial scales-sugarcane mill, region, intermediary, farm and zone-to determine the role of spatial scale in synchrony patterns, and on temporal population variability. To analyse synchrony patterns, only the three highest spatial scales were considered, but for temporal population variability, all spatial scales were adopted. The synchrony-distance relationship revealed complex spatial structures depending on both species and spatial scale. Temporal population variability [SD log(x+1)] levels were highest at the smallest spatial scales although, in the majority of the cases, temporal variability was inversely dependent on sample size. All the species studied, with a few exceptions, presented spatial synchrony independent of spatial scale. The tachinid flies exhibited stronger synchrony dynamics than D. saccharalis and C. flavipes in all spatial scales with the latter displaying the weakest synchrony levels, except when mill spatial scales were compared. In some cases spatial synchrony may at first decay and then increase with distance, but the presence of such patterns can change depending on the spatial scale adopted.

How the interplay between individual spatial memory and landscape persistence can generate population distribution patterns

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Frame dependence of the pair contribution to the pion electromagnetic form factor in a light-front approach

The frame dependence of the pair-term contribution to the electromagnetic form factor of the pion is studied within the Light Front approach. A symmetric ansatz for the pion Bethe-Salpeter amplitude with a pseudo scalar coupling of the constituent to the pion field is used. In this model, the pair term vanishes for the Drell-Yan condition, while it is dominant for momentum transfer along the light-front direction.

Orthogonal projections and bootstrap resampling procedures in the study of infraspecific variation

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Correlation between the mobility of spin-labeled peptide chains and resin solvation: An approach to optimize the synthesis of aggregating sequences

Resin solvation properties affect the efficiency of the coupling reactions in solid-phase peptide synthesis. Here we report a novel approach to evaluate resin solvation properties, making use of spin label electron paramagnetic resonance (EPR) spectroscopy. The aggregating VVLGAAIV and ING sequences were assembled in benzhydrylamine-resin with different amino group contents (up to 2.6 mmol/g) to examine the extent of chain association within the beads. These model peptidyl-resins were first labeled at their N-terminus with the amino acid spin label 2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid (Toac). Their solvation properties in different solvents were estimated, either by bead swelling measurement or by assessing the dynamics of their polymeric matrixes through the analysis of Toac EPR spectra, and were correlated with the yield of the acylation reaction. In most cases the coupling rate was found to depend on bead swelling. Comparatively, the EPR approach was more effective. Line shape analysis allowed the detection of more than one peptide chain population, which influenced the reaction. The results demonstrated the unique potential of EPR spectroscopy not only for improving the yield of peptide synthesis, even in challenging conditions, but also for other relevant polymer-supported methodologies in chemistry and biology.

Heat transfer in fixed bed: a model non-linearity approach

Studies have been carried out on the heat transfer in a packed bed of glass beads percolated by air at moderate flow rates. Rigorous statistic analysis of the experimental data was carried out and the traditional two parameter model was used to represent them. The parameters estimated were the effective radial thermal conductivity, k, and the wall coefficient, h, through the least squares method. The results were evaluated as to the boundary bed inlet temperature, T-o, number of terms of the solution series and number of experimental points used in the estimate. Results indicated that a small difference in T-o was sufficient to promote great modifications in the estimated parameters and in the statistical properties of the model. The use of replicas at points of high parametric information of the model improved the results, although analysis of the residuals has resulted in the rejection of this alternative. In order to evaluate cion-linearity of the model, Bates and Watts (1988) curvature measurements and the Box (1971) biases of the coefficients were calculated. The intrinsic curvatures of the model (IN) tend to be concentrated at low bed heights and those due to parameter effects (PE) are spread all over the bed. The Box biases indicated both parameters as responsible for the curvatures PE, h being somewhat more problematic. (C) 2000 Elsevier B.V. Ltd. All rights reserved.

Pb1-xCaxTiO3 solid solution (x=0.0, 0.25, 0.50, and 0.75): A theoretical and experimental approach

In this paper we report an experimental and theoretical study based on a periodic density functional investigation into selected compositions of Pb1-xCaxTiO3 (x=0.0, 0.25, 0.50, and 0.75). Based on our findings, we propose that the pseudocubic structure of these perovskites presents a long-range tendency for cubic symmetry, while the short-range displacements bring the solid solution to a tetragonal symmetry. The results are discussed in terms of x-ray diffraction, structural optimized parameters, Raman spectroscopy, band structure, density of states, Mulliken charge, and overlap population.

Population genetic structure and dispersal in white-lipped peccaries (Tayassu pecari) from the Brazilian Pantanal

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Evaluating genetic algorithms with different population structures on a lot sizing and scheduling problem

This paper studies the use of different population structures in a Genetic Algorithm (GA) applied to lot sizing and scheduling problems. The population approaches are divided into two types: single-population and multi-population. The first type has a non-structured single population. The multi-population type presents non-structured and structured populations organized in binary and ternary trees. Each population approach is tested on lot sizing and scheduling problems found in soft drink companies. These problems have two interdependent levels with decisions concerning raw material storage and soft drink bottling. The challenge is to simultaneously determine the lot sizing and scheduling of raw materials in tanks and products in lines. Computational results are reported allowing determining the better population structure for the set of problem instances evaluated. Copyright 2008 ACM.

A Bayesian approach to estimate the accuracy of in-house ELISA assay to measure rabies antibodies from compulsory vaccinated dogs and cattle

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Inclusive Social Protection in Latin America: a comprehensive, rights-based approach

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Proposed regional agenda on population and development for Latin America and the Caribbean beyond 2014

The document revisits, broadens and updates the discussions contained in ECLAC documents Input for the preparation of a regional agenda for the Programme of Action of the International Conference on Population and Development: towards 2014 and beyond (LC/L.3219(CEP.2010/4)), of 2010, and Reflections on the population and development agenda for Latin America and the Caribbean beyond 2014 (LC/L.3481(CEP.2/5)), of 2012..