• Asian-Australasian Journal of Animal Sciences
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• v.22 no.4
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• pp.465-470
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• 2009

The chicken Mx gene has been regarded as a candidate gene for resistance to avian influenza virus (AIV). In this study, three groups of chickens with homozygotes (AA, GG) and heterozygotes (AG) of the resistant (A) and susceptible alleles (G) to AIV of the Mx gene were constructed from a line of dwarf egg-type chickens. These chickens were not examined for their resistant activities to AIV because the differential resistance had only been detected in vitro. The birds of the three groups were vaccinated with inactivated H5N2 AIV vaccine and the level of hemagglutination inhibition (HI) antibody to AIV was detected. The association between disease resistant activity to AIV and antibody response to AIV vaccination in the three groups was analyzed. The chickens with homozygous resistant allele A showed the lowest antibody levels, whereas the heterozygous chickens (AG) presented the highest antibody level after the boosting vaccination, which indicates that the efficiency of artificial selection on the resistant allele of Mx gene will be compromised since the homozygotes of the allele presented the weakest antibody response to the corresponding vaccine.

• Journal of Life Science
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• v.28 no.4
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• pp.478-482
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• 2018

Human rotavirus is a causative agent of acute diarrhea among children. The artificial gene encoding the truncated $VP8^*$ protein of human rotavirus A (serotype 1 strain WA) was synthesized according to the Escherichia coli codon preference. The synthetic $VP8^*$ gene also possessed the NdeI and HindIII restriction sites for the convenient in-frame cloning for translation and a 6-histidine tag at C-terminus for Ni+ affinity purification. Molecular weight of the truncated $VP8^*$ protein deduced from the nucleotide sequences of the artificial gene was a 19.7-kDa. This synthetic $VP8^*$ DNA fragment was inserted into the pT7-7 expression vector and transformed into E. coli BL21 (DE3). Transformants harboring the synthetic gene encoding the $VP8^*$ protein was induced by supplement of a final concentration of 0.05 mM ITPG at $20^{\circ}C$. Protein crude extract from the E. coli transformants was subjected to Western blotting with the mouse anti-rotavirus capsid antibody, showing ~20-kDa $VP8^*$ protein band. The truncated $VP8^*$ protein band was also observed by Western blotting using the rabbit polyclonal antibody serum made against the truncated $VP8^*$ protein. This study suggested that the synthetic gene could be used as an easy way to produce the antigenic vaccine candidate for control of virus-associated diseases or to develop antibodies for diagnostic purpose.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1994.04a
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• pp.129-130
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• 1994

The science of toxicology is the understanding of the mechanisms by which exogenous agents produce deleterious effects in biological systems. The actions of chemicals such as drugs are ultimately exerted at the cellular and gene levels. Over the past decade. several in vitro alternative methods such as cultured cells for assessing the toxicity of various xenobiotics have been proposed to reduce the use of animals. In this workshop three advanced methods will be presented. These methods are novel important models for toxicologic studies. Dr. Tabuchis group has establishcd two immortalized gastric surface mucosa cell lines from the pminary cultore of gastric fundic mucosal cells of adult transgenic mice harboring a temperature sensitive simian virus 40 large T-anugen gene. As the immortalized cell lines of various tissues possess unique characteristics to maintain their normal functions for several months, these cell lines are extremely useful for not only toxicity testing but also pharmacological screening in new drug development. Professor Funatsu have studied the formation of spherical multicelluar aggregates of adult rat hepatocytes(spheroid) having tissue like structure. The sphcroid shown thre is a prototype module of an artificial liver support system. Thus, the urea synthesis activity of the artificial liver was maintained at least to days in 100％ rat blood plasma. Dr. Takezawa and his coworkers have developed a novel culture system of multicellular spheroids considered 〃organoids〃 by utilizing a thermo-responsive polymer as a substratum of anchorage dependent cells. His final goal is to reconstitute the organoids of various normal organs, e.g., liver, skin etc. and also abnormal deseased organs such as tumor.

• Computers and Concrete
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• v.32 no.1
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• pp.1-13
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• 2023

This paper discusses a framework for predicting the flexural strength of prestressed and non-prestressed FRP reinforced T-shaped concrete beams using soft computing techniques. An analysis of 83 tests performed on T-beams of varying widths has been conducted for this purpose with different widths of compressive face, beam depth, compressive strength of concrete, area of prestressed and non-prestressed FRP bars, elasticity modulus of prestressed and non-prestressed FRP bars, and the ultimate tensile strength of prestressed and non-prestressed FRP bars. By analyzing the data using two soft computing techniques, named artificial neural networks (ANN) and gene expression programming (GEP), the fundamental parameters affecting the flexural performance of prestressed and non-prestressed FRP reinforced T-shaped beams were identified. The results showed that although the proposed ANN model outperformed the GEP model with higher values of R and lower error values, the closed-form equation of the GEP model can provide a simple way to predict the effect of input parameters on flexural strength as the output. The sensitivity analysis results revealed the most influential input parameters in ANN and GEP models are respectively the beam depth and elasticity modulus of FRP bars.

• Genomics & Informatics
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• v.19 no.3
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• pp.22.1-22.5
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• 2021

Automatic document classification for highly interrelated classes is a demanding task that becomes more challenging when there is little labeled data for training. Such is the case of the coronavirus disease 2019 (COVID-19) clinical repository-a repository of classified and translated academic articles related to COVID-19 and relevant to the clinical practice-where a 3-way classification scheme is being applied to COVID-19 literature. During the 7th Biomedical Linked Annotation Hackathon (BLAH7) hackathon, we performed experiments to explore the use of named-entity-recognition (NER) to improve the classification. We processed the literature with OntoGene's Biomedical Entity Recogniser (OGER) and used the resulting identified Named Entities (NE) and their links to major biological databases as extra input features for the classifier. We compared the results with a baseline model without the OGER extracted features. In these proof-of-concept experiments, we observed a clear gain on COVID-19 literature classification. In particular, NE's origin was useful to classify document types and NE's type for clinical specialties. Due to the limitations of the small dataset, we can only conclude that our results suggests that NER would benefit this classification task. In order to accurately estimate this benefit, further experiments with a larger dataset would be needed.

• Journal of Microbiology and Biotechnology
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• v.30 no.6
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• pp.804-810
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• 2020

The profitability of the dairy and beef industries is largely affected by the actually achieved reproductive efficiency. Although a large proportion of cows worldwide are bred by artificial insemination (AI) services, many potential factors affecting the outcome of pregnancy by AI remain to be addressed. In the present study, we investigated the vaginal microbiota by high-throughput sequencing of 16S rRNA gene and analyzed their association with differential pregnancy outcomes (i.e., pregnant vs. nonpregnant) of multiple AI services in dairy cows. Sequencing of the V3-V4 region totally produced 512,046 high-quality sequences that were computationally clustered into 2,584 operational taxonomic units (OTUs). All OTUs were taxonomically assigned to 10 bacterial phyla. There were statistically significant differences among the three AI service times (T1, T2 and T3) with respect to the Shannon index and number of observed OTUs (p < 0.05). Bray-Curtis distance-based PCoA analysis also revealed that T2 group could be significantly distinguished from T1 and T3. However, no significant difference between the pregnant and nonpregnant cows was found in confidence regarding both alpha diversity and beta diversity. These results could help us better understand the possible influence of vaginal microbial community on pregnancy outcomes of AI service in cows.

• The Korean Journal of Zoology
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• v.26 no.2
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• pp.95-106
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• 1983

Selections for rapid and slow walking behavior were carried out with the populations, drived from Oregon-R and lethal free strain of Drosophila melanogaster. The behavior was measured by means of connected test-tube apparatus. The populations responded effectively to the artificial selection, and it reached the selection plateau after 7 generations. The realized heritability for the first 10 generations was estimated to be about $9\\sim14%$ for the rapid walking behavior, and those for slow walking behavior was about $11\\sim16%$. The results of hybridization analysis between selected populations at generations 8 and 10 indicated that some polygenes showing a slow walking behavior were partially dominant over polygenes controlled rapid trait. The populations selected for rapid and slow walking behavior were relaxed after 10 generations of selection. The response to natural selection of rapid population was completely returned to their neutral states after only 5 generations. Such phenomena would be explained by the genetic homeostasis resulted from an action of natural selection. However, the slow population did not make any difference from walking scores of their original artificial selection. It seems reasonable to assume that the slow walking behavior was possibly controlled by a major gene.

• Journal of Life Science
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• v.20 no.5
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• pp.789-793
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• 2010

Artificial chromosome manipulation and amplification of single-copy yeast artificial chromosome (YAC) are usually required in order to use YACs for applications such as physical mapping and functional analysis in eukaryotes. We designed and implemented a Simultaneous YAC Manipulation-Amplification (SYMA) system that combines the copy number amplification system of YAC with a convenient YAC manipulation system. To achieve the desired split and to amplify a YAC clone-harboring plant chromosome, a pBGTK plasmid containing a conditional centromere and thymidine kinase (TK) gene was constructed as a template to amplify the splitting fragment via PCR. By splitting, new 490-kb and 100-kb split YACs containing the elements for copy number amplification were simultaneously generated from a 590-kb YAC clone. The 100-kb split YAC was then successfully amplified 14.4-fold by adding 3 mg/ml sulfanilamide and $50\;{\mu}g/ml$ methotrexate (S3/M50) as inducing substances.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.843-853
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• 2014

In the context of artificial groundwater recharge, a reactive soil column at pilot-scale (4.5 m depth and 3 m in diameter) fed by treated wastewater was designed to evaluate soil filtration ability. Here, as a part of this project, the impact of treated wastewater filtration on soil bacterial communities and the soil's biological ability for wastewater treatment as well as the relevance of the use of multi-bioindicators were studied as a function of depth and time. Biomass; bacterial 16S rRNA gene diversity fingerprints; potential nitrifying, denitrifying, and sulfate-reducing activities; and functional gene (amo, nir, nar, and dsr) detection were analyzed to highlight the real and potential microbial activity and diversity within the soil column. These bioindicators show that topsoil (0 to 20 cm depth) was the more active and the more impacted by treated wastewater filtration. Nitrification was the main activity in the pilot. No sulfate-reducing activity or dsr genes were detected during the first 6 months of wastewater application. Denitrification was also absent, but genes of denitrifying bacteria were detected, suggesting that the denitrifying process may occur rapidly if adequate chemical conditions are favored within the soil column. Results also underline that a dry period (20 days without any wastewater supply) significantly impacted soil bacterial diversity, leading to a decrease of enzyme activities and biomass. Finally, our work shows that treated wastewater filtration leads to a modification of the bacterial genetic and functional structures in topsoil.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.214-214
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• 2022

Soluble starch synthases (SSs) elongate α-glucans from ADP-Glc to the glucan nonreducing ends and play a critical role in synthesizing resistant starch in the rice. A total of 10 SSs isoforms were reported in rice, including granules-bound starch synthase I (GBSSI), GBSSII, starch synthase I (SSI), SSIIa (SSII-3), SSIIb (SSII-2), SSIIc (SSII-1), SSIIIa (SSIII-2), SSIIIb (SSIII-1), SSIVa (SSIV-1), and SSIVb (SSIV-2). SSIII proteins are involved in forming the B chain and elongating cluster filling chains in amylopectin metabolism. The functions of SSIIIb (SSIII-1) are less clear as compared to SSs. Here, we sought to shed light on the genetic diversity profiling of the SSIII-1 gene in 374 rice accessions composed of 54 wild-type accessions and 320 bred cultivars (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture). In total, 17 haplotypes were identified in the SSIII-1 coding region of 320 bred cultivars, while 44 haplotypes were detected from 54 wild-type accessions. The genetic diversity indices revealed the most negative Tajima's D value in the temperate-japonica, followed by the wild type, while Tajima's D values in other ecotypes were positive, indicating balancing selection. Nucleotide diversity in the SSIII-1 region was highest in the wild group (0.0047) while lowest in temperate-japonica. Lower nucleotide diversity in the temperate-japonica is evidenced by the negative Tajima's D and suggested purifying selection. The fixation index (F_ST) revealed a very high level of gene flow (low F_ST) between the tropical-japonica and admixture groups (F_ST=-0.21) followed by admixture and wild groups (-0.04), indica and admixture groups (0.02), while low gene flow with higher F_ST estimates between the temperate-japonica and aus groups (0.72), tropical-japonica and aromatic groups (0.71), and temperate-japonica and admixture groups (0.52). Taken together, our study offers insights into haplotype diversity and evolutionary fingerprints of SSIII-1. It provides genomic information to increase the resistant starch content of cooked rice.