• Animal Bioscience
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• v.37 no.3
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• pp.428-436
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• 2024

Objective: This study compared five distinct sets of biological pathways and associated genes related to semen volume (VOL), number of sperm (NS), and sperm motility (MOT) in the Thai multibreed dairy population. Methods: The phenotypic data included 13,533 VOL records, 12,773 NS records, and 12,660 MOT records from 131 bulls. The genotypic data consisted of 76,519 imputed and actual single nucleotide polymorphisms (SNPs) from 72 animals. The SNP additive genetic variances for VOL, NS, and MOT were estimated for SNP windows of one SNP (SW1), ten SNP (SW10), 30 SNP (SW30), 50 SNP (SW50), and 100 SNP (SW100) using a single-step genomic best linear unbiased prediction approach. The fixed effects in the model were contemporary group, ejaculate order, bull age, ambient temperature, and heterosis. The random effects accounted for animal additive genetic effects, permanent environment effects, and residual. The SNPs explaining at least 0.001% of the additive genetic variance in SW1, 0.01% in SW10, 0.03% in SW30, 0.05% in SW50, and 0.1% in SW100 were selected for gene identification through the NCBI database. The pathway analysis utilized genes associated with the identified SNP windows. Results: Comparison of overlapping and non-overlapping SNP windows revealed notable differences among the identified pathways and genes associated with the studied traits. Overlapping windows consistently yielded a larger number of shared biological pathways and genes than non-overlapping windows. In particular, overlapping SW30 and SW50 identified the largest number of shared pathways and genes in the Thai multibreed dairy population. Conclusion: This study yielded valuable insights into the genetic architecture of VOL, NS, and MOT. It also highlighted the importance of assessing overlapping and non-overlapping SNP windows of various sizes for their effectiveness to identify shared pathways and genes influencing multiple traits.

• Asian-Australasian Journal of Animal Sciences
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• v.9 no.4
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• pp.363-370
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• 1996

The effect of breeding length of sire on genetic progress was examined in the Holstein dairy cattle population in Japan. Genetic progress was extimated by gene flow method. Breeding length of sires directly influences the replacement rates of sires and the selection intensity of sires because there are a fixed number of progeny tested young bulls per year. As breeding length of sires increased, rate of gene flow decreased and average proportions of genes deriving from selected animals had lower asymptotic values. When breeding length was short, average proportions of genes required a longer period to converge to asymptotic values. Changes of Rcow-sire's(sire to breed recorded cows) and Ncow-sire's(sire to breed non recorded cows) breeding length influenced not only transmission of their genes but also that of genes derived from all other selected animals. Irrespective of whether the discount rate was assumed to be 0 or 6%, longer term (${\geq}$ 20 years) expected total genetic improvement was maximized by a sire breeding length of five years. For shorter term assessment(10 years), genetic improvement was maximized by a sire breeding length of three years. There was a linear increase in the contribution of the sire to bulls pathway to the total genetic improvement, with increase in the term of assessment.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.351-355
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• 2005

In the storage roots of sweetpotato (Ipomoea batatas (L.) Lam. cv. Kokei 14), 10 to 20% of starch is essentially unbranched linear amylose and the other major component is branched amylopectin. Amylose is produced by the enzyme GBSSI (granule bound starch synthase I), whereas amylopectin is produced by a concerted action of soluble starch synthase and starch branching enzymes (SBEI and SBEII). We constructed double-stranded RNA (dsRNA) interference vectors of GBSSI and IbSBEII and introduced them into sweetpotato genome via Agrobacterium-mediated gene transformation. The endogenous GBSSI expression was inhibited by dsRNA of GBSSI in 73 % of transgenic plants giving rise to the storage tubers containing amylopectin but not amylose. On the other hand, all sweetpotato plants transformed with dsRNA of IbSBEII contained a larger amount of amylose than the non-transgenic control (up to 25% compared to 10% in the controls). The RNA interference (RNAi) is effectively inhibited the gene expression in thestarch metabolic pathway and modified the characteristics of starch in sweetpotato.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.28 no.3C
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• pp.159-166
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• 2008

The stress-strain behavior of soils can usually be regarded as non-linear, while it is also known that the soil exhibits the linear-elastic behavior at pre-failure state (very small strain range, $<10^{-3}%$). This study aims to analyze the variation of anisotropic elastic shear moduli of granular soils in various stress conditions. The stress probe experiments with the triaxial testing device equipped with local strain gages and multi-directional bender elements were conducted. When the stress ratio exceeds the range between -0.5 and 1.5, the elastic shear stiffness in the axial direction deviates from the empirical correlation with current stresses, which indicates that the yielding of soils alters the internal pathway through which the elastic shear wave propagates. The experimental results show that the variation of elastic shear moduli in the horizontal direction closely relates to the volume change of soils.

• Journal of Korean Society of Environmental Engineers
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• v.31 no.2
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• pp.125-131
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• 2009

Reductive dechlorination of polychlorinated dibenzo-p-dioxins (PCDDs) and its toxicity change were predicted by the linear free energy relationship (LFER) model to assess the zero-valent iron (ZVI) and anaerobic dechlorinating bacteria (ADB) as electron donors in PCDDs dechlorination. Reductive dechlorination of PCDDs involves 256 reactions linking 76 congeners with highly variable toxicities, so is challenging to assess the overall effect of this process on the environmental impact of PCDD contamination. The Gibbs free energies of PCDDs in aqueous solution were updated to density functional theory (DFT) calculation level from thermodynamic results of literatures. All of dechlorination kinetics of PCDDs was evaluated from the linear correlation between the experimental dechlorination kinetics of PCDDs and the calculated thermodynamics of PCDDs. As a result, it was predicted that over 100 years would be taken for the complete dechlorination of octachlorinated dibenzo-p-dioxin (OCDD) to non-chlorinated compound (dibenzo-p-dioxin, DD), and the toxic equivalent quantity (TEQ) of PCDDs could increase to 10 times larger from initial TEQ with the dechlorination process. The results imply that the single reductive dechlorination using ZVI or ADB is not suitable for the treatment strategy of PCDDs contaminated soil, sediment and fly ash. This LFER approach is applicable for the prediction of dechlorination process for organohalogen compounds and for the assessment of electron donating system for treatment strategies.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.2
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• pp.157-162
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• 2018

Objective: The aim of this study is to identify single nucleotide polymorphisms (SNPs) and genes related to pig IMF and estimate the heritability of intramuscular fat content (IMF). Methods: Genome-wide association study (GWAS) on 704 inbred Berkshires was performed for IMF. To consider the inbreeding among samples, associations of the SNPs with IMF were tested as random effects in a mixed linear model using the genetic relationship matrix by GEMMA. Significant genes were compared with reported pig IMF quantitative trait loci (QTL) regions and functional classification of the identified genes were also performed. Heritability of IMF was estimated by GCTA tool. Results: Total 365 SNPs were found to be significant from a cutoff of p-value <0.01 and the 365 significant SNPs were annotated across 120 genes. Twenty five genes were on pig IMF QTL regions. Bone morphogenetic protein-binding endothelial cell precursor-derived regulator, forkhead box protein O1, ectodysplasin A receptor, ring finger protein 149, cluster of differentiation, tyrosine-protein phosphatase non-receptor type 1, SRY (sex determining region Y)-box 9 (SOX9), MYC proto-oncogene, and macrophage migration inhibitory factor were related to mitogen-activated protein kinase pathway, which regulates the differentiation to adipocytes. These genes and the genes mapped on QTLs could be the candidate genes affecting IMF. Heritability of IMF was estimated as 0.52, which was relatively high, suggesting that a considerable portion of the total variance of IMF is explained by the SNP information. Conclusion: Our results can contribute to breeding pigs with better IMF and therefore, producing pork with better sensory qualities.

• Economic and Environmental Geology
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• v.23 no.4
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• pp.425-452
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• 1990

A tentative hydrogeologic and hydrodispersive study was carried out to evaluate the groundwater pollution potential at a selected site by utilizing empirical assessment methodologies in an advanced stage of quantitative computer aided assessment. The upper most aquifer is defind as saturated overburden and weathered zone including the upper part of highly fractured rock. Representative hydraulic conductivity and storativity of the uppermost aquifer are estimated at 2.88 E-6 m/s and 0.09, respectively. Also calculated Darcian and average linear velocity of groundwater along the major pathway are 0.011 m/d and 0.12 m/d with average hydraulic gradient of 4.6% in the site. The results of empirical assessment methodologies indicate that 1) DRASTIC depicts that the site is situated on non-sensitive and non-vulnerable area. 2) Legrand numerical rating system shows that the probability of contamination and degree of acceptability are classed to "Maybe-Improbable, and Probable Acceptable and Marginally Unacceptable" with situation grade of "B". 3)Waste soil-site interaction matrix assessment categorizes that the study site is located on "Class-8 Site".

• Journal of Microbiology and Biotechnology
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• v.33 no.4
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• pp.552-558
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• 2023

Levulinic acid (LA) is a valuable chemical used in fuel additives, fragrances, and polymers. In this study, we proposed possible biosynthetic pathways for LA production from lignin and poly(ethylene terephthalate). We also created a genetically encoded biosensor responsive to LA, which can be used for screening and evolving the LA biosynthesis pathway genes, by employing an LvaR transcriptional regulator of Pseudomonas putida KT2440 to express a fluorescent reporter gene. The LvaR regulator senses LA as a cognate ligand. The LA biosensor was first examined in an Escherichia coli strain and was found to be non-functional. When the host of the LA biosensor was switched from E. coli to P. putida KT2440, the LA biosensor showed a linear correlation between fluorescence intensity and LA concentration in the range of 0.156-10 mM LA. In addition, we determined that 0.156 mM LA was the limit of LA detection in P. putida KT2440 harboring an LA-responsive biosensor. The maximal fluorescence increase was 12.3-fold in the presence of 10 mM LA compared to that in the absence of LA. The individual cell responses to LA concentrations reflected the population-averaged responses, which enabled high-throughput screening of enzymes and metabolic pathways involved in LA biosynthesis and sustainable production of LA in engineered microbes.