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Nonparallel genome changes within subpopulations over time contributed to genetic diversity within the US Holstein population
Get PDFjournal articleMaintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. The 20,990 genotyped animals, representing the breeding animals in the year 2014, were identified as the sires of animals born after 2010 with at least 25 progenies, and females measured for type traits within the last 2 yr of data. K-means clustering with 5 clusters (C1, C2, C3, C4, and C5) was applied to the genomic relationship matrix based on 58,990 SNP markers to stratify the selected candidates into subpopulations. The general higher inbreeding resulting from within-cluster mating than across-cluster mating suggests the successful stratification into genetically different groups. The largest cluster (C4) contained animals that were less related to each animal within and across clusters. The average fixation index was 0.03, indicating that the populations were differentiated, and allele differences across the subpopulations were not due to drift alone. Starting with the selected candidates within each cluster, a family unit was identified by tracing back through the pedigree, identifying the genotyped ancestors, and assigning them to a pseudogeneration. Each of the 5 families (F1, F2, F3, F4, and F5) was traced back for 10 generations, allowing for changes in frequency of individual SNPs over time to be observed, which we call allele frequencies change. Alternative procedures were used to identify SNPs changing in a parallel or nonparallel way across families. For example, markers that have changed the most in the whole population, markers that have changed differently across families, and genes previously identified as those that have changed in allele frequency. The genomic trajectory taken by each family involves selective sweeps, polygenic changes, hitchhiking, and epistasis. The replicate frequency spectrum was used to measure the similarity of change across families and showed that populations have changed differently. The proportion of markers that reversed direction in allele frequency change varied from 0.00 to 0.02 if the rate of change was greater than 0.02 per generation, or from 0.14 to 0.24 if the rate of change was greater than 0.005 per generation within each family. Cluster-specific SNP effects for stature were estimated using only females and applied to obtain indirect genomic predictions for males. Reranking occurs depending on SNP effects used. Additive genetic correlations between clusters show possible differences in populations. Further research is required to determine how this knowledge can be applied to maintain diversity and optimize selection decisions in the future.journal articl
Juvenile hormone identification in the cabbage bug Eurydema rugosa
Get PDFjournal articleJuvenile hormone (JH) plays a pivotal role in almost every aspect of insect development and reproduction. The chemical structure of the JH in heteropteran species has long remained elusive until methyl (2R,3S,10R)-2,3;10,11-bisepoxyfarnesoate, commonly named as juvenile hormone III skipped bisepoxide (JHSB3), was isolated from Plautia stali (Hemiptera: Heteroptera: Pentatomidae). Recently, several groups reported the presence of JHSB3 in other heteropteran species. However, most of the studies paid no attention to the determination of the relative and absolute structure of the JH. In this study, we investigated the JH of the cabbage bug Eurydema rugosa (Hemiptera: Heteroptera: Pentatomidae), known as a pest for wild and cultivated crucifers. JHSB3 was detected in the hexane extract from the corpus allatum (CA) product using a chiral ultraperformance liquid chromatography-tandem mass spectrometer (UPLC-MS/MS) which can inform the absolute stereochemistry of the JH. Its stereoisomers were not detected. Topical application of the synthetic JHSB3 to the last instar nymphs inhibited their metamorphosis and induced nymphal-type colouration of the dorsal abdomen in a dose-dependent manner. Additionally, the topical application of JHSB3 effectively terminated summer and winter diapauses in females. These results indicate that the JH of E. rugosa is JHSB3. Although individuals in summer and winter diapauses are physiologically distinct in E. rugosa, the results suggest that the physiological differences between these diapauses are based, not on the responsiveness to JH, but on the processes governing activation of the CA or on its upstream cascades.journal articl
Production profile of lipid mediators in conjunctival lavage fluid in allergic and infectious conjunctivitis in guinea pigs
Get PDFjournal articleIntroduction: Conjunctivitis is a major ocular disease classified into allergic or infectious. The pathological features of conjunctivitis are not fully understood despite its high morbidity rate; thus, its differentiation can be difficult. Materials and methods: We used ovalbumin-induced allergic conjunctivitis and lipopolysaccharide-induced infectious conjunctivitis models of guinea pigs. Both models showed conjunctival swelling. Histological studies revealed that numerous eosinophils infiltrated the conjunctiva in the allergic model, whereas neutrophils infiltrated the conjunctiva in the infectious model. We collected conjunctival lavage fluid (COLF) and comprehensively analyzed lipid production using liquid chromatography-tandem mass spectrometry. Results: COLF showed increase of 20 and 12 lipid species levels in the allergic and infectious models, respectively. Specifically, the levels of a major allergic mediator, prostaglandin D2 and its three metabolites and several cytochrome P450-catalyzed lipids increased in the allergic model. In the infectious model, the levels of prostaglandin E2 and 8-iso-prostaglandin E2 increased, indicating tissue inflammation. Moreover, the level of 12-oxo-eicosatetraenoic acid, a lipoxygenase metabolite, increased in the infectious model. Conclusion: These differences in lipid production in the COLF reflected the pathological features of allergic and infectious conjunctivitis.journal articl
Exploring Appropriate Strategies for Vaccination against Classical Swine Fever under a Dynamic Change in Antibody Titer in Sows after Starting Vaccination in a Japanese Farm Setting
Get PDFjournal articleAfter 26 years of absence in Japan, a classical swine fever (CSF) outbreak occurred at a domestic pig farm in 2018. Vaccination against the CSF virus with a live attenuated vaccine at pig farms was restarted in October 2019, which was 13 years after the 2006 ban on vaccination. An individual-based simulation model for CSF antibody dynamics was developed to determine an effective CSF vaccination strategy for pig populations. In creating a simulated pig herd, the optimal vaccination age of piglets and the effect of vaccinating piglets twice were evaluated. Additionally, the herd immunity was monitored every 6 months for 4 years after the start of vaccination, and the effects of intensive sow replacement policies were assessed. The simulation results indicated that the vaccination age should be delayed relative to the age used before the 2006 ban on vaccination and shifted earlier, from 8 weeks to 6 weeks, as time elapses. The simulations indicated a tradeoff in protection between the weaning period (i.e., maternally derived antibodies) and the fattening period (i.e., by vaccine-induced antibodies). Mixing sows with high and low antibody titers, particularly sows that received the first vaccination and those born after the start of vaccination, resulted in a high variation in antibody titer among pigs on the farm. This study also clarified the positive effect of intensive sow replacement strategies on shortening the period in which sows show diverse titers. Differences in sow replacement rates among farms and/or the time lag in starting vaccination in different prefectures result in heterogeneity in herd immunity in Japan; thus, herd immunity status should be examined at every farm using this simulation model.journal articl
