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.     

Biological characteristics and pathogenicity of avian Escherichia coli strains.

Fifty avian (chicken) pathogenic Escherichia coli strains (APEC) isolated from individuals suffering from omphalitis, septicaemia and swollen head syndrome, and 30 strains isolated from healthy chickens were studied regarding their biological characteristics such as serogroups, haemolysin, colicin, cytotoxin, toxin and siderophore production, adhesion capacity to in vitro cultivated cells, and absorption of Congo red dye. Serotyping demonstrated that most of the omphalitis and normal strains were untypable, whereas most of the septicaemic strains were either untypable or rough. There was no prevalent serogroup among the pathogenic strains studied. The capacity for adhesion and invasion of in vitro cultured cells (HeLa, HEp-2, KPCC), as well as the agglutination of different types of red blood cells and the LD50 of each strain were also evaluated. No correlation was observed between the biological characteristics and pathogenicity, except that colicin was characteristically produced by swollen head syndrome E. coli strains. No correlation was found between adhesion or haemagglutination patterns and pathogenicity. Only six of the 50 strains revealed invasive capacity and the strain that best invaded the cell lines was the one with the lowest LD50.     

A high-resolution radiation hybrid map of the human genome draft sequence

We have constructed a physical map of the human genome by using a panel of 90 whole-genome radiation hybrids (the TNG panel) in conjunction with 40,322 sequence-tagged sites (STSs) derived from random genomic sequences as well as expressed sequences. Of 36,678 STSs on the TNG radiation hybrid map, only 3604 (9.8%) were absent from the unassembled draft sequence of the human genome. Of 20,030 STSs ordered on the TNG map as well as the assembled human genome draft sequence and the Celera assembled human genome sequence, 36% of the STSs had a discrepant order between the working draft sequence and the Celera sequence. The TNG map order was identical to one of the two sequence orders in 60% of these discrepant cases.     

Comparison of the Reproductive Performance of Similarly-Sized Wild and Captive Farfantepenaeus paulensis

The reproduction of wild-caught Farfantepenaeus paulensis in captivity has been successfully achieved since 1983. However, year-round supply of wild broodstock is costly and unpredictable. This study compares the reproductive performance of animals of similar size (females from 32–33 g and males from 19–21 g) but from different sources: estuary-caught juveniles reared indoors for 9 mo and wild-caught adults from shallow coastal waters. Groups of 20 males and 30 unilaterally eyestalk-ablated females were maintained for 60 d in four maturation tanks under controlled environmental conditions. A higher number of eggs per spawning event (78,414 ± 34,491) and total egg production (4,469,600) were observed for the wild females. Nevertheless, captive females produced a higher number of nauplii (1,788,259) due to their higher percentage of fertilized spawns. Therefore, within the size range of this study, the reproductive performance of estuary-caught F. paulensis juveniles over-wintered indoors was found to be equivalent to that of wild-caught females from shallow coastal waters.     

Modelling soil-water-plant relationships in the Cerrado soils of Brazil: The case of maize (Zea mays L.)

A soil-water balance simulation model developed for the Cerrado soils of central Brazil is presented. The model calculates daily soil water evaporation, plant transpiration and soil-water balance for fourteen soil layers of 15 mm each. The model includes a subroutine to calculate capillary water movement. Computer simulations of daily soil water levels at five soil depths (15, 30, 45, 60 and 90 cm) for a field of maize are compared with actual field measurements over an 80-day period. Results indicated that the developed model can, in general, estimate the soil-water balance of the various depths within ± 10% of actual measurements.     

Use of two fungal species to induce agarwood resin formation in Gyrinops walla

Gyrinops walla Gaertn. is the only species growing in Sri Lanka that belongs to the agarwood family,Thymelaeaceae. Although agarwood resin induction and extraction from Aquilaria species of the same family have been practised for many decades in Southeast Asian region,the ability of producing agarwood resins in G. walla was discovered recently. Since previous studies were on agarwood resins formed due to natural causes, the present study was conducted to identify the potential fungal species that are capable of artificially inducing agarwood resin formation in G. walla. Since this is the first ever study conducted on artificial inducement of agarwood resin formation in G.walla, Aspergillus niger and Fusarium solani were selected owing to their high abundance in the naturally formed agarwood resinous tissues collected from 25 G. walla trees.Both fungal species were separately grown in yeast extract glucose agar and used to inoculate healthy G. walla trees under aseptic conditions. Three holes were made for each tree and 2 g of fungal culture including the medium were placed in each hole. Tissue discoloration, characteristic aroma, resin content and resin constituents were checked at10 cm intervals above and below the inoculation points for a period of 1 year. Results revealed that tissue discoloration and resin content were higher in the trees inoculated with A. niger. Other than at 10 cm above and below the inoculation points, samples collected at all locations had significantly higher resin contents when inoculated with A. niger compared to F. solani. Sixteen agarwood resin constituents, which were also recorded in Aquilaria species, were identified from the discolored tissues using GC–MS analysis. Jinkohol, agarospirol and 2(2-phenyl)chromone derivatives were found in all discolored tissues collected at 10-cm intervals of the trees inoculated with both fungi. b-Seline, c-eudesmol and valerenal were found in nine of 10 sample points on the stem. c-Elemene was recorded only in one sample. The characteristic aroma during burning was stronger for dark-colored tissues than the light-colored ones. The present study confirmed the potential use of certain fungal species to induce agarwood resin in G. walla and that A. niger is more effective than F.solani.     

Benchmarking Local Potato Processing in Developing Countries: The Case of French Fries in Lima,Peru

Declining tariffs and exchange rate appreciation have raised concerns about the competitive position of local potato processors in developing countries. Yet, relatively little is known about these processors, their competitiveness under current market conditions, how that might change with future tariff reductions or shifts in exchange rates, or what might be done to improve their efficiency over time. This study focuses on the market for French fries in Lima, Peru. Estimates based on field work carried out among local, small-scale processors indicate that locally made, peeled and cut fresh potatoes cost considerably less than imported, industrial-scale, frozen French fries under various tariff and exchange rate scenarios. A series of recommendations are put forward to continue to improve the efficiency of local processors and the quality of their finished product as well as some topics for future research.