Is single-step genomic REML with the algorithm for proven and young more computationally efficient when less generations of data are present?

Efficient computing techniques allow the estimation of variance components for virtually any traditional dataset. When genomic information is available, variance components can be estimated using genomic REML (GREML). If only a portion of the animals have genotypes, single-step GREML (ssGREML) is the method of choice. The genomic relationship matrix (G) used in both cases is dense, limiting computations depending on the number of genotyped animals. The algorithm for proven and young (APY) can be used to create a sparse inverse of G (GAPY~-1) with close to linear memory and computing requirements. In ssGREML, the inverse of the realized relationship matrix (H⁻¹) also includes the inverse of the pedigree relationship matrix, which can be dense with a long pedigree, but sparser with short. The main purpose of this study was to investigate whether costs of ssGREML can be reduced using APY with truncated pedigree and phenotypes. We also investigated the impact of truncation on variance components estimation when different numbers of core animals are used in APY. Simulations included 150K animals from 10 generations, with selection. Phenotypes (h² = 0.3) were available for all animals in generations 1–9. A total of 30K animals in generations 8 and 9, and 15K validation animals in generation 10 were genotyped for 52,890 SNP. Average information REML and ssGREML with G⁻¹ and GAPY~-1 using 1K, 5K, 9K, and 14K core animals were compared. Variance components are impacted when the core group in APY represents the number of eigenvalues explaining a small fraction of the total variation in G. The most time-consuming operation was the inversion of G, with more than 50% of the total time. Next, numerical factorization consumed nearly 30% of the total computing time. On average, a 7% decrease in the computing time for ordering was observed by removing each generation of data. APY can be successfully applied to create the inverse of the genomic relationship matrix used in ssGREML for estimating variance components. To ensure reliable variance component estimation, it is important to use a core size that corresponds to the number of largest eigenvalues explaining around 98% of total variation in G. When APY is used, pedigrees can be truncated to increase the sparsity of H and slightly reduce computing time for ordering and symbolic factorization, with no impact on the estimates.     

Effect of Stocking Density on Growth,Survival, and Condition of the Mexican Cichlid Cichlasoma beani

The Mexican cichlid Cichlasoma beani is currently exploited regionally as food and can be commercialized in the aquarium trade. Natural populations of C. beani may already be negatively affected by anthropogenic alteration of the areas in which it is distributed. The aim of the present study was to examine the effect on growth, survival, and condition of C. beani cultured in three stocking densities: three (D3), six (D6), and nine (D9) fish per each 40 L tank. At the end of a 6‐wk trial the fish cultured in D3 were longer, heavier, and grew faster than the rest of the treatments but their survival was the lowest compared to D6 and D9. The mortalities were caused by a strong aggressive behavior in D3.     

Use of dimethylformamide to cryopreserve alpaca semen previously incubated with collagenase

The objective of this study was to evaluate the effect of collagenase and two final dimethylformamide (DMF) concentrations (4% and 7%) on alpaca frozen-thawed sperm quality. A total of 25 ejaculates from 5 alpaca were obtained using electroejaculation. Each individual ejaculate was evaluated and then diluted 4:1 in a solution of 1 mg/ml collagenase in HEPES-TALP medium and incubated for 4 min at 37°C. Subsequently, samples were diluted in TRIS-fructose-citric acid-egg yolk and cooled to 5°C. Then, each sample was divided in two aliquots and DMF at final concentration of 4% or 7% was added, equilibrated for 1 hr at 5°C and frozen over liquid nitrogen vapours. A Kruskal–Wallis test was used to evaluate the sperm morphometry, and Completely Random Block designs were used to analyse sperm motility, viability, membrane function and acrosome status. After collagenase incubation, none of the samples showed thread formation, and sperm parameters were preserved. Non-progressive motile sperm were higher (p < .05) in equilibrated samples (4% DMF: 31.8 ± 8.3% and 7% DMF: 36.3 ± 11.8%) compared to raw (10.1 ± 4.3%) and frozen-thawed semen (4% DMF: 9.7 ± 1.8% and 7% DMF: 7.5 ± 3.2%). Sperm membrane function, membrane integrity and intact acrosomes were higher (p < .05) in raw semen (40.1 ± 12.2%, 94.6 ± 3.2% and 91.3 ± 8.1%) compared to frozen-thawed samples (4% DMF: 19.8 ± 4.7%, 53.2 ± 2.7%, 65.7 ± 8.7% and 7% DMF: 20.4 ± 4.5%, 54.1 ± 1.4%, 64.6 ± 9.1%). Length of the sperm head was lower in frozen-thawed samples, being statistically different with 4% DMF compared to pre-freezing samples. The ratio between acrosome and head areas was greater (p < .05) in frozen-thawed samples. Incubation of raw alpaca semen with collagenase decreased the thread formation without affecting sperm quality. Frozen of collagenase treated alpaca semen with 4% or 7% DMF did not preserve the sperm parameters in thawed samples.     

Effect of the Nixtamalization Process on the Dietary Fiber Content,Starch Digestibility,and Antioxidant Capacity of Blue Maize Tortilla

Nixtamalization is an ancient process developed by the Mesoamerican cultures. Initially, volcanic ashes were used and then calcium hydroxide in commercial production, and more recently nixtamalization with calcium salts (NCS) has been proposed. The aim of this study was to evaluate the effect of NCS on carbohydrate digestibility and antioxidant capacity in the elaboration of blue maize tortillas. NCS in blue tortillas showed a high amount of total dietary fiber (14.27 g/100 g), the main fraction being insoluble dietary fiber. The contents of resistant starch and slowly digestible starch did not change with the nixtamalization process. The predicted glycemic index value was lower in blue tortillas with the NCS process (58) than with the traditional nixtamalization process (71). In general, NCS in blue tortillas presented a higher antioxidant capacity than traditional tortillas (ferric reducing antioxidant power method), indicating that phenolics present in blue maize maintain their activity after cooking. It can be concluded that the nutraceutical features (high dietary fiber content and antioxidant capacity) of blue maize tortillas are enhanced when they are elaborated with the NCS process.     

How much variation can be explained by seasonal,spatial and environmental effects in nekton assemblages of the Terminos Lagoon?

• 1. The coastline is very sensitive to both climatic and human influences but also provides essential goods and services upon which human welfare depends. Species inhabiting these coastal areas provide valuable resources and enhance ecosystem functioning: it is therefore essential to understand the main factors influencing species abundance patterns. The aim of this study is to estimate the amount of variation in nekton coastal assemblages explained by spatial, temporal and environmental variables.
• 2. Nekton sampling was carried out over 17 months in the Terminos Lagoon, a reserve area situated in the Gulf of Mexico, using a shrimp trawl. At each station, 11 environmental variables were recorded. The influence of seasonal, spatial and environmental variables on nekton species abundance was analysed using Partial Canonical Correspondence Analysis (PCCA).
• 3. The explanatory variables explained only 19.7% of the total observed variation in the nekton community for the Terminos Lagoon. The major part of the explained variation was due to the spatial effect (9.2%), while environmental variables and seasonality explained only 3.6% and 0.8%, respectively, suggesting the necessity to consider experimental fishing design in such artisanal fisheries.
• 4. Results also suggest focusing on more integrative indicators of community structure such as measures of taxonomic diversity based on presence/absence or on measures related to functional attributes of communities rather than using species abundance patterns to predict changes in coastal ecosystems.

Copyright © 2007 John Wiley & Sons, Ltd.     

Effects of Pre-Stratification Storage Conditions on Black Walnut Seed Post-Stratification Germination Capacity

The objective of this work was to quantify changes in the germination capacity of Juglans nigra seeds following storage and then artificial stratification. Seeds were stored at 5 and –20 °C under 5% and 14% internal moisture content (IMC) for 0, 8, 10, and 12 months under conditions with oxygen or under vacuum. Germination percentage (GP) was affected by storage temperature, IMC, and storage period. Seeds stored with 5% IMC succeeded in germinating regardless of the temperature. Seeds stored with 14% IMC did not germinate (–20 °C) or germinated during storage (5 °C). The GP was reduced with the time of storage in seeds at –20 °C and 5% IMC and this effect was avoided in storage under vacuum. In conclusion, the germination capacity of black walnut seeds did not change for up to 12 months at low above-zero temperature and low IMC (5 °C, 5% IMC), being the most cost-effective alternative for long-term storage of black walnut seeds in commercial nurseries. Vacuum storage avoided the decrease of around 50% in average germination capacity of seeds stored for a year at –20 °C.     

Is Discrimination of 13C in Potato Leaflets and Tubers an Appropriate Trait to Describe Genotype Responses to Restrictive and Well‐Watered Conditions?

Selection for drought tolerance entails prioritizing plant traits that integrate critical physiological processes occurring during crop growth. Discrimination against ¹³C (?) in leaflets (?_leaflet) and tubers (?_tuber) was compared under two water regimes in two potato‐improved varieties selected to maintain yield under drought conditions (Unica and Sarnav) and one drought susceptible European cultivar (Désirée). In the control treatment, soil water content was kept at field capacity over the whole growth cycle, while in the drought treatment water supply was restricted after tuber initiation (50 % of field capacity). Gas exchange and N content per unit leaf area (N_area) as well as ? were assessed at different stages. Sarnav showed the highest tuber yield in both water conditions, suggesting that yield in the water restriction treatment was largely driven by yield potential in this genotype. Higher stomatal conductance (g_s) and N_area and lower ?_leaflet in well‐watered Sarnav suggested higher photosynthetic capacity. Under water restriction, Sarnav maintained higher g_s indicating that carbon diffusion was a key factor for biomass accumulation under water restriction. Our results suggest the use of ? determined after tuber initiation as an indirect selection indicator for tuber yield under both well‐watered and restricted soil water availability conditions.     

Morphological and quantitative study of the Leydig cells of pigs fed with anabolic doses of clenbuterol

The effects of clenbuterol administered at anabolic doses on the testicular interstitium were studied in 30 pigs allocated to three experimental groups. The diet of two groups was supplemented with clenbuterol (Clb) (1 ppm), but whereas in the Clb+ group the treatment was given until slaughter (treatment period: 3 months), in the Clb- group the clenbuterol was withdrawn 2 weeks before slaughter (treatment period: 2-5 months); in the control group, the pigs were fed without clenbuterol. For histological procedures, a fractional sampling scheme was applied and routine techniques for light and transmission electron microscopy were used. The results of subjective morphology and morphometrics showed slight differences between the treated and the control groups. Conversely, the stereological results identified a prominent hyperplasia of the Leydig cells and ultrastructural analysis of these cells revealed a conspicuous increase in the organelles related to testosterone production, suggesting a functional activation of the interstitial cells in response to the clenbuterol treatment.     

Effects of anabolic implants of oestradiol alone or in combination with trenbolone acetate on the ultrastructure of mammary glands in female lambs regarding their interference in prolactin secretion

The side-effects of anabolic steroid implants on mammary gland ultrastructure were evaluated in female lambs treated with oestradiol (n = 10) and with oestradiol plus trenbolone acetate (n = 10). Ten non-implanted lambs were used as controls. Apart from the ultrastructural study of the mammary gland, an assessment of the prolactin pituitary cell population was carried out by immunological methods. Our results showed that oestrogenic implants exert stimulating effects on mammary gland development, both by activating the synthesis process at mammary gland cell levels and by increasing prolactin pituitary production. Nevertheless, there was no evidence of secretory products in the lumen of the gland. Implants containing trenbolone acetate counteracted the mammary stimulus of oestrogens showing ultrastructural images of cell autolysis and necrosis.