The impact of truncating data on the predictive ability for single‐step genomic best linear unbiased prediction

Simulated and swine industry data sets were utilized to assess the impact of removing older data on the predictive ability of selection candidate estimated breeding values (EBV) when using single‐step genomic best linear unbiased prediction (ssGBLUP). Simulated data included thirty replicates designed to mimic the structure of swine data sets. For the simulated data, varying amounts of data were truncated based on the number of ancestral generations back from the selection candidates. The swine data sets consisted of phenotypic and genotypic records for three traits across two breeds on animals born from 2003 to 2017. Phenotypes and genotypes were iteratively removed 1 year at a time based on the year an animal was born. For the swine data sets, correlations between corrected phenotypes (Cp) and EBV were used to evaluate the predictive ability on young animals born in 2016–2017. In the simulated data set, keeping data two generations back or greater resulted in no statistical difference (p‐value > 0.05) in the reduction in the true breeding value at generation 15 compared to utilizing all available data. Across swine data sets, removing phenotypes from animals born prior to 2011 resulted in a negligible or a slight numerical increase in the correlation between Cp and EBV. Truncating data is a method to alleviate computational issues without negatively impacting the predictive ability of selection candidate EBV.     

Growth rates and survival of western rock lobster (Panulirus cygnus) at two temperatures (ambient and 23 °C) and two feeding frequencies

Wild caught post-pueruli, year one and year two post settlement juvenile western rock lobster, Panulirus cygnus, were held at ambient temperatures (15.6 °C to 23.1 °C; mean 19.0 ± 0.07 °C) or at 23 °C, and fed the same ration of a formulated pellet diet either once per night, or 3 times per night, over 12 months, to determine whether elevated temperatures and multiple feeds per night would stimulate growth through increased metabolism and feed utilisation without significant negative impacts on survival. Survival of post-pueruli (mean 63%) did not differ between ambient and 23 °C. Survival of year 1 and 2 juveniles was higher at ambient temperatures (p < 0.01 ambient: year 1 juveniles, 68%; year 2 juveniles, 88%; 23 °C: 57% and 74%, respectively). Feeding frequency did not affect survival of post-pueruli and year 2 juveniles (mean 63%, 81% respectively), but survival was 9% higher for year 1 juveniles fed three times per night (58% versus 67%; p < 0.01). All lobsters grew faster at 23 °C than at ambient temperatures (p < 0.05), with the growth of post-pueruli almost doubled at 23 °C (weight gain at 23 °C versus ambient: post-pueruli, 18 438 % versus 9 915 %; year 1 juveniles 259% versus 165%; year 2 juveniles 23% versus 21%). Feed frequency did not influence the growth of year 1 and 2 juveniles. However, there was an interaction effect of temperature and feed frequency on post-pueruli where weight and carapace length were significantly higher at ambient temperatures when post-pueruli were fed three times a day, whereas at 23 °C weight and carapace length were significantly greater when fed once per day (p < 0.05). Feed intake (g pellet dry matter lobster^− 1 day^− 1) of pellet was higher at 23 °C for all lobsters (p < 0.05), but was the same between lobsters fed 3 times per night versus once per night. This study has shown that increasing temperatures to 23 °C significantly improved the growth of P. cygnus post-pueruli without any adverse effects on survival. The faster growth rates exhibited by year 1 and 2 juveniles at 23 °C may potentially offset their lower survival by significantly reducing culture period. There is no benefit of feeding P. cygnus multiple times at night in terms of growth and survival. The implications for P. cygnus culture are that temperatures should be maintained close to 23 °C during the entire growout period, with due care taken to minimise mortalities through adequate provision of food and shelter. Feeding P. cygnus once daily to excess just prior to dusk to co-incide with nocturnal feeding behaviour is recommended.     

Effect of Stocking Density on the Growth,Survival, and Behavior of Postpuerulus Western Rock Lobster,Panulirus cygnus (George) (Decapoda: Palinuridae)

The effect of four stocking densities (30, 60, 100, and 150 lobsters/m²) on the growth and survival of Panulirus cygnus postpueruli was determined over a 112‐d grow‐out trial. Agonistic behavior at each experimental density was recorded using infrared filming. Survival and growth decreased with increasing density, although this trend was only significant between the lowest (30/m²) and the highest densities (150/m²) (P < 0.05) at the conclusion of the grow‐out trial. Density had no significant effect on apparent feed intake but significantly affected food conversion ratios (FCR) across all four densities, with FCR being best at 30/m² and worst at 150/m². The number and frequency of agonistic encounters per tank differed significantly with density, with agonistic encounters being highest at 150/m² and lowest at 30/m². Agonistic encounters coincided with the crepuscular foraging pattern of postpueruli. The reduction in survival and growth of postpueruli at the highest density (150/m²) can be attributed to the significant increase in the number of agonistic encounters. This study supports that P. cygnus postpueruli should be stocked at densities less than 100/m² in order to minimize the negative effect of density on growth and survival.     

Prevalence of Rickettsia species antibodies and Rickettsia species DNA in the blood of cats with and without fever

Rickettsia species antibodies have been detected in some cats but it is unknown whether infected cats develop clinical signs. The prevalence of Rickettsia species deoxyribonucleic acid (DNA) in blood from clinically ill cats has not been determined. The objective of this study was to determine if cats with fever (body temperature >or=102.5 degrees F [39.2 degrees C]) were more likely to have evidence of rickettsial infection than healthy, age-matched, control cats with a body temperature<102.5 degrees F. Rickettsia species polymerase chain reaction (PCR) assays were performed to detect rickettsial DNA extracted from blood (71 paired samples), indirect immunofluorescence assays (IFA) were performed to detect serum antibodies against Rickettsia felis (90 paired samples) and Rickettsia rickettsii (91 paired samples), and the results between pairs were compared. All samples were negative for Rickettsia species DNA. More cats with fever were seropositive for R felis or R rickettsii than control cats, but results were not statistically significant. Results of this pilot study failed to show an association between Rickettsia species DNA or Rickettsia species antibodies and fever.     

Sorption of pesticides in tropical and temperate soils from Australia and the Philippines

The sorption behavior of diuron, imidacloprid, and thiacloprid was investigated using 22 soils collected in triplicate from temperate environments in Australia and tropical environments in Australia and the Philippines. Within the temperate environment in Australia, the soils were selected from a range of land uses. The average KOC values (L/kg) for imidacloprid were 326, 322, and 336; for thiacloprid, the values were 915, 743, and 842; and for diuron, the values were 579, 536, and 618 for the Ord (tropical), Mt. Lofty (temperate), and Philippines (tropical) soils, respectively. For all soils, the sorption coefficients decreased in the following order: thiacloprid > diuron > imidacloprid. There were no significant differences in sorption behavior between the tropical soils from the Philippines and the temperate soils from Australia. Sorption was also not significantly related with soil characteristics, namely, organic carbon (OC) content, clay content, and pH, for any of the three chemicals studied. When the data were sorted into separate land uses, the sorption of all three chemicals was highly correlated (P < 0.001) with OC for the rice soils from the Philippines. Sorption coefficients for all three chemicals were highly correlated with OC in temperate, native soils only when one extreme value was removed. The relationships between sorption of all three chemicals and OC in temperate, pasture soils were best described by a polynomial. Sorption coefficients for imidacloprid and thiacloprid determined in the temperate pasture soils remained fairly consistent as the OC content increased from 3.3 to 5.3%, indicating that, although the total OC in the pasture soils was increasing, the component of OC involved with sorption of these two compounds may have been remaining constant. This study demonstrated that the origin of the soils (i.e., temperate vs tropical) had no significant effect on the sorption behavior, but in some cases, land use significantly affected the sorption behavior of the three pesticides studied. The impact of land use on the nature of soil OC will be further investigated by NMR analysis.     

Effect of Albizia julibrissin water extracts on low-density lipoprotein oxidization

High-value phytochemicals could be extracted from biomass prior to the current cellulosic pretreatment technologies (i.e., lime, ammonia, dilute acid, or pressurized hot water treatments) provided that the extraction is performed with a solvent that is compatible with the pretreatment. This work reports on the extraction of flavonoids from Albizia julibrissin biomass. While extracting A. julibrissin foliage with 50 degrees C water, 2.227 mg/g of hyperoside and 8.134 mg/g quercitrin were obtained, which is in the realm of what was obtained with 60% methanol. A. julibrissin foliage, flower, and whole plant extracts were tested in terms of their potential to inhibit low-density lipoprotein (LDL) oxidization. The highest inhibition was obtained with foliage water extracts, which were standardized at 2.5 microM of flavonoids. Also, the 2.5 microM foliage water extract resulted in a reduction from 43% to only 1% of the observed monocyte adherence. To have commercial application, A. julibrissin water extracts should be devoid of toxicity. The A. julibrissin foliage, flower, and whole plant water extracts were not toxic to Vero 76 cells. In summary, A. julibrissin biomass can be extracted with 50 degrees C water to yield an antioxidant stream, showing that it may be possible to couple extraction of valuable phytochemicals to the cellulosic pretreatment step.     

Genetic mapping provides evidence for the role of additive and non-additive QTLs in the response of inter-specific hybrids of <Emphasis Type="Italic">Eucalyptus</Emphasis> to <Emphasis Type="Italic">Puccinia psidii</Emphasis> rust infection

Eucalypts are susceptible to a wide range of diseases. One of the most important diseases that affect Eucalyptus plantations worldwide is caused by the rust fungus Puccinia psidii. Here, we provide evidence on the complex genetic control of rust resistance in Eucalyptus inter-specific hybrids, by analyzing a number of full-sib families that display different patterns of segregation for rust resistance. These families are totally unrelated to those previously used in other inheritance studies of rust resistance. By using a full genome scan with 114 genetic markers (microsatellites and expressed sequence tag derived microsatellites) we also corroborated the existence and segregation of a resistance locus, explaining 11.5% of the phenotypic variation, on linkage group 3, corresponding to Ppr1. This find represents an additional validation of this locus in totally unrelated pedigree. We have also detected significant additive × additive digenic interactions with LOD >10.0 on several linkage groups. The additive and epistatic QTLs identified explain between 29.8 and 44.8% of the phenotypic variability for rust resistance. The recognition that both additive and non-additive genetic variation (epistasis) are important contributors to rust resistance in eucalypts reveals the complexity of this host-pathogen interaction and helps explain the success that breeding has achieved by selecting rust-resistant clones, where all the additive and non-additive effects are readily captured. The positioning of epistatic QTLs also provides starting points to look for the underlying genes or genomic regions controlling this phenotype on the upcoming E. grandis genome sequence.