Contributions and perspectives of chicken genomics in Brazil: from biological model to export commodity

Chicken is one of the most important sources of animal protein for human consumption, and breeding programmes have been responsible for constant improvements in production efficiency and product quality. Furthermore, chicken has largely contributed to fundamental discoveries in biology for the last 100 years. In this article we review recent developments in poultry genomics and their contribution to adding functional information to the already existing structural genomics, including the availability of the complete genome sequence, a comprehensive collection of mRNA sequences ( ESTs), microarray platforms, and their use to complement QTL mapping strategies in the identification of genes that underlie complex traits. Efforts of the Brazilian Poultry Genomics Programme in this area resulted in generation of a resource population, which was used for identification of Quantitative Trait Loci ( QTL) regions, generation of ESTs and candidate gene studies that contributed to furthering our understanding of the complex biological processes involved in growth and muscular development in chicken.

A kinetic model of phosphorus metabolism in growing goats

The effect of increasing phosphorus (P) intake on P utilization was investigated in balance experiments using 12 Saanen goats, 4 to 5 mo of age and weighing 20 to 30 kg. The goats were given similar diets with various concentrations of P, and 32P was injected to trace the movement of P in the body. A P metabolism model with four pools was developed to compute P exchanges in the system. The results showed that P absorption, bone resorption, and excretion of urinary P and endogenous and fecal P all play a part in the homeostatic control of P. Endogenous fecal output was positively correlated to P intake (P < .01). Bone resorption of P was not influenced by intake of P, and P recycling from tissues to the blood pool was lesser for low P intake. Endogenous P loss occurred even in animals fed an inadequate P diet, resulting in a negative P balance. The extrapolated minimum endogenous loss in feces was .067 g of P/d. The minimum P intake for maintenance in Saanen goats was calculated to be .61 g of P/ d or .055 g of P/(kg.75·d) at 25 kg BW. Model outputs indicate greater P flow from the blood pool to the gut and vice versa as P intake increased. Intake of P did not significantly affect P flow from bone and soft tissue to blood. The kinetic model and regressions could be used to estimate P requirement and the fate of P in goats and could also be extrapolated to both sheep and cattle.

Heteropicnotic chromatin and nucleolar activity in meiosis and spermiogenesis of Limnogonus aduncus (Heteroptera, Gerridae): a stained nucleolar organizing region that can serve as a model for studying chromosome behavior.

Males of Limnogonus aduncus were found to have the sex chromosome system X0 and chromosome number 2n = 23 (22A + X0). Testis cells were stained with lacto-acetic orcein and silver nitrate so that changes in the morphology and degree of staining of the heteropicnotic chromatin and the nucleolar material could be observed during meiosis and spermiogenesis. These structures share the same nuclear position and could be seen until almost the end of spermiogenesis. A chromosome region stained with silver nitrate was indicative of a nucleolar organizing region (NOR), which is rarely detected in Heteroptera with this technique. The NOR is located at one end of a single member of an autosome pair. The finding of this stained region enabled us to observe that the telomeric association of sister chromatids that characterizes the Heteroptera does not include the chromosome ends, where NORs are located; we also observed in anaphase that the chromosome end through which it is pulled to the pole is the one containing the NOR. Another observation was that the single nucleolar body present in the cells at anaphase never goes to the cell pole that does not receive the NOR. We conclude that L. aduncus is a good model for cytogenetic studies involving nucleolar activity and also may be useful for studying the mechanisms of activation and inactivation of kinetic activity at the chromosome ends. Although the chromosomes of Heteroptera are known to be holocentric, whether kinetic activity is restricted to one or involves both chromosome ends is still not well understood.

Phenotypic plasticity of composite beef cattle performance using reaction norms model with unknown covariate

The objective of the present study was to determine the presence of genotype by environment interaction (G × E) and to characterize the phenotypic plasticity of birth weight (BW), weaning weight (WW), postweaning weight gain (PWG) and yearling scrotal circumference (SC) in composite beef cattle using the reaction norms model with unknown covariate. The animals were born between 1995 and 2008 on 33 farms located throughout all Brazilian biomes between latitude -7 and -31, longitude -40 and -63. The contemporary group was chosen as the environmental descriptor, that is, the environmental covariate of the reaction norms. In general, higher estimates of direct heritability were observed in extreme favorable environments. The mean of direct heritability across the environmental gradient ranged from 0.05 to 0.51, 0.09 to 0.43, 0.01 to 0.43 and from 0.12 to 0.26 for BW, WW, PWG and SC, respectively. The variation in direct heritability observed indicates a different response to selection according to the environment in which the animals of the population are evaluated. The correlation between the level and slope of the reaction norm for BW and PWG was high, indicating that animals with higher average breeding values responded better to improvement in environmental conditions, a fact characterizing a scale of G × E. Low correlation between the intercept and slope was obtained for WW and SC, implying re-ranking of animals in different environments. Genetic variation exists in the sensitivity of animals to the environment, a fact that permits the selection of more plastic or robust genotypes in the population studied. Thus, the G × E is an important factor that should be considered in the genetic evaluation of the present population of composite beef cattle. © The Animal Consortium 2012.

Characterization of the variable cow's age at last calving as a measurement of longevity by using the Kaplan-Meier estimator and the Cox model

In most studies on beef cattle longevity, only the cows reaching a given number of calvings by a specific age are considered in the analyses. With the aim of evaluating all cows with productive life in herds, taking into consideration the different forms of management on each farm, it was proposed to measure cow longevity from age at last calving (ALC), that is, the most recent calving registered in the files. The objective was to characterize this trait in order to study the longevity of Nellore cattle, using the Kaplan-Meier estimators and the Cox model. The covariables and class effects considered in the models were age at first calving (AFC), year and season of birth of the cow and farm. The variable studied (ALC) was classified as presenting complete information (uncensored = 1) or incomplete information (censored = 0), using the criterion of the difference between the date of each cow's last calving and the date of the latest calving at each farm. If this difference was >36 months, the cow was considered to have failed. If not, this cow was censored, thus indicating that future calving remained possible for this cow. The records of 11 791 animals from 22 farms within the Nellore Breed Genetic Improvement Program ('Nellore Brazil') were used. In the estimation process using the Kaplan-Meier model, the variable of AFC was classified into three age groups. In individual analyses, the log-rank test and the Wilcoxon test in the Kaplan-Meier model showed that all covariables and class effects had significant effects (P < 0.05) on ALC. In the analysis considering all covariables and class effects, using the Wald test in the Cox model, only the season of birth of the cow was not significant for ALC (P > 0.05). This analysis indicated that each month added to AFC diminished the risk of the cow's failure in the herd by 2%. Nonetheless, this does not imply that animals with younger AFC had less profitability. Cows with greater numbers of calvings were more precocious than those with fewer calvings. Copyright © The Animal Consortium 2012.

Estimating abundance and spatial distribution patterns of the bubble crab Dotilla fenestrata (Crustacea : Brachyura)

The bubble crab Dotilla fenestrata forms very dense populations on the sand flats of the eastern coast of Inhaca Island, Mozambique, making it an interesting biological model to examine spatial distribution patterns and test the relative efficiency of common sampling methods. Due to its apparent ecological importance within the sandy intertidal community, understanding the factors ruling the dynamics of Dotilla populations is also a key issue. In this study, different techniques of estimating crab density are described, and the trends of spatial distribution of the different population categories are shown. The studied populations are arranged in discrete patches located at the well-drained crests of nearly parallel mega sand ripples. For a given sample size, there was an obvious gain in precision by using a stratified random sampling technique, considering discrete patches as strata, compared to the simple random design. Density average and variance differed considerably among patches since juveniles and ovigerous females were found clumped, with higher densities at the lower and upper shore levels, respectively. Burrow counting was found to be an adequate method for large-scale sampling, although consistently underestimating actual crab density by nearly half. Regression analyses suggested that crabs smaller than 2.9 mm carapace width tend to be undetected in visual burrow counts. A visual survey of sampling plots over several patches of a large Dotilla population showed that crab density varied in an interesting oscillating pattern, apparently following the topography of the sand flat. Patches extending to the lower shore contained higher densities than those mostly covering the higher shore. Within-patch density variability also pointed to the same trend, but the density increment towards the lowest shore level varied greatly among the patches compared.

Subcellular localization of proteins labeled with GFP in Xanthomonas citri ssp citri: targeting the division septum

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

Quantitative aspects of the migration and evolutive asynchronism of Schistosoma mansoni in mice

Two groups of white mice (Mus musculus) were infected with 65 and 440 cercariae transcutaneously. Migration of Schistosoma mansoni from skin to the lungs and to the portal system thereafter was studied through fitting mathematical equations. Six evolutive stages previously defined were used to determine the asynchronic development of parasites in the portal system. Equations the moment of maximum schistosomula recovery in skin and lungs. In the portal system the equations lead to different days of maximum recovery according to each stage. These differences measure quantitatively the asynchronism of S. mansoni.

Endogenous corticosteroids and insulin in acute inflammation

Carrageenin-induced inflammatory responses in the hindpaws of rats were quantitated by measuring: (1) alterations in volumes of the paws; and (2) alterations in concentration of dye, previously injected intravenously, which was recovered in perfusates from the paws. The inflammatory response in one paw was attenuated by previously inducing an inflammatory response in the contralateral paw. The effect was abolished by pretreatment with insulin. Indexes of adrenal activity were increased after the induction of the inflammatory response and they were not attenuated by pretreatment with insulin. Adrenal hyperactivity was characterized by increased serum corticosterone concentration, decreased adrenal ascorbic acid content, and reduced number of circulating eosinophils. It is concluded that inflammatory stimuli which lead to alterations in microvessels depend on a facilitatory effect of insulin. This effect is antagonized by glucocorticoids released in enhanced concentrations after the application of noxious stimuli. Therefore, endogenous insulin and glucocorticoids act as modulators of inflammatory responses.

An objective reconstruction of the chain of contagion

North's clustering method, which is based on a much used ecological model, the nearest neighbor distance, was applied to the objective reconstruction of the chain of household-to-household transmission of variola minor (the mild form of smallpox). The discrete within-household outbreaks were considered as points which were ordered in a time sequence using a 10-40 day interval between introduction of the disease into a source household and a receptor household. The closer points in the plane were assumed to have a larger probability of being links of a chain of household-to-household spread of the disease. The five defining distances (Manhattan or city-block distance between presumptive source and receptor dwellings) were 100, 200, 300, 400 and 500 m. The subchain sets obtained with the five defining distances were compared with the subchains empirically reconstructed during the field study of the epidemic through direct investigation of personal contacts of the introductory cases with either introductory or subsequent cases from previously affected households. The criteria of fit of theoretical to empirical clusters were: (a) the number of clustered dwellings and subchains, (b) number of dwellings in a subchain and (c) position of dwellings in a subchain. The defining distance closet to the empirical findings was 200 m, which fully agrees with the travelling habits of the study population. Less close but acceptable approximations were obtained with 100, 300, 400 and 500 m. The latter two distances gave identical results, as if a clustering ceiling had been reached. It seems that North's clustering model may be used for an objective reconstruction of the chain of contagious whose links are discrete within-household outbreaks. © 1984.

Theoretical Dynamics of Experimental Populations of Introduced and Native Blowflies (Diptera: Calliphoridae)

Equilibrium dynamics in experimental populations of Chrysomya megacephala (F.) and C. putoria (Wiedemann), which have recently invaded the Americas, and the native species Cochliomyia macellaria (F.), were investigated using nonlinear difference equations. A theoretical analysis of the mathematical model using bifurcation theory established the combination of demographic parameters responsible for producing shifts in blowfly population dynamics from stable equilibria to bounded cycles and aperiodic behavior. Mathematical modeling shows that the populations of the 2 introduced Chrysomya species will form stable oscillations with numbers fluctuating 3-4 times in successive generations. However, in the native species C. macellaria, the dynamics is characterized by damping oscillations in population size, leading to a stable population level.

Two-Way Selection for Daily Gain and Feed Conversion in a Composite Rabbit Population

We conducted a two-way selection experiment in a composite rabbit population to investigate the responses to selection for postweaning ADG and feed conversion (FC). Two generations of crossing, followed by four generations of random pair matings, preceded three generations of selection. Selection was practiced within four lines: high-feed conversion (HFC), low-feed conversion (LFC), high gain (HG), and low gain (LG). Data on 1,446 rabbits from the random mating and selection generations were fitted to an animal model to estimate heritabilities of and the genetic correlation between ADG and FC. The two-trait model included rabbit and common litter random effects and line, generation, and sex fixed effects. Estimates of heritability of ADG and FC were .48 and .29, respectively, and the genetic correlation between them was -.82. Common litter environmental effects accounted for a proportion of .11 and . 13 of the phenotypic variation of the two traits, respectively. For ADG (in g/d) the regressions of mean breeding values on generation number during the selection period were 1.23 ± .12 (P < .01) in the HG line and -.86 ± .12 (P < .01) in the LG line; the regressions for FC (in g feed/g gain) were -.07 ± .01 (P < .01) in the HFC line and .03 ± .01 (P < .05) in the LFC line. Selection for ADG was effective in improving ADG and FC.

A comparative evaluation of open loop and closed loop drug administration strategies in the treatment of AIDS.

In recent years, many researchers in the field of biomedical sciences have made successful use of mathematical models to study, in a quantitative way, a multitude of phenomena such as those found in disease dynamics, control of physiological systems, optimization of drug therapy, economics of the preventive medicine and many other applications. The availability of good dynamic models have been providing means for simulation and design of novel control strategies in the context of biological events. This work concerns a particular model related to HIV infection dynamics which is used to allow a comparative evaluation of schemes for treatment of AIDS patients. The mathematical model adopted in this work was proposed by Nowak & Bangham, 1996 and describes the dynamics of viral concentration in terms of interaction with CD4 cells and the cytotoxic T lymphocytes, which are responsible for the defense of the organism. Two conceptually distinct techniques for drug therapy are analyzed: Open Loop Treatment, where a priori fixed dosage is prescribed and Closed Loop Treatment, where the doses are adjusted according to results obtained by laboratory analysis. Simulation results show that the Closed Loop Scheme can achieve improved quality of the treatment in terms of reduction in the viral load and quantity of administered drugs, but with the inconvenience related to the necessity of frequent and periodic laboratory analysis.

Biophysical Characterization of Interactions Involving Importin-α during Nuclear Import

Proteins containing the classical nuclear localization sequences (NLSs) are imported into the nucleus by the importin-α/β heterodimer. Importin-α contains the NLS binding site, whereas importin-β mediates the translocation through the nuclear pore. We characterized the interactions involving importin-α during nuclear import using a combination of biophysical techniques (biosensor, crystallography, sedimentation equilibrium, electrophoresis, and circular dichroism). Importin-α is shown to exist in a monomeric autoinhibited state (association with NLSs undetectable by biosensor). Association with importin-β (stoichiometry, 1:1; K D = 1.1 × 10 -8 M) increases the affinity for NLSs; the importin-α/β complex binds representative monopartite NLS (simian virus 40 large T-antigen) and bipartite NLS (nucleoplasmin) with affinities (K D = 3.5 × 10 -8 M and 4.8 × 10 -8 M, respectively) comparable with those of a truncated importin-α lacking the autoinhibitory domain (T-antigen NLS, K D = 1.7 × 10 -8 M; nucleoplasmin NLS, K D = 1.4 × 10 -8 M). The autoinhibitory domain (as a separate peptide) binds the truncated importin-α, and the crystal structure of the complex resembles the structure of full-length importin-α. Our results support the model of regulation of nuclear import mediated by the intrasteric autoregulatory sequence of importin-α and provide a quantitative description of the binding and regulatory steps during nuclear import.