• International Journal of Industrial Entomology and Biomaterials
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• v.11 no.1
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• pp.57-61
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• 2005

A strain of Bacillus thuringiensis that showed signifi­cantly high toxicity to Plutella xylostella was isolated from a dust sample collected from Chinese tobacco warehouse and characterized. The isolate named B. thuringiensis LY-99 was determined to belong to subsp. alesti (H3a3c) by an H antisera agglutination test and produced bipyramidal inclusions. Plasmid and crystal protein patterns of the LY-99 were different from those of the reference strain, subsp. alesti. PCR analysis with specific primers revealed that this isolate contained abundant cry genes including crylAa, crylAc, crylB, crylD, crylE, crylF and cry2 genes, which was absolutely different from cry gene profile of the subsp. alesti. In addition, insecticidal activity of the LY-99 against P. xylostella larvae was about 44 times higher than that of the subsp. alesti.

• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1240-1249
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• 2005

Saccharomyces cerevisiae KNU5377 has potential as an industrial strain that can ferment wasted paper for fuel ethanol at $40^{\circ}C$ [15, 16]. To understand the characteristics of the strain, genome-wide expression was performed using DNA microarray technology. We compared the homology of the DNA microarray between genomic DNAs of S. cerevisiae KNU5377 and a control strain, S. cerevisiae S288C. Approximately $97\%$ of the genes in S. cerevisiae KNU5377 were identified with those of the reference strain. YHR053c (CUP1), YLR155c (ASP3), and YDR038c (ENA5) showed lower homology than those of S. cerevisiae S288C. In particular, the differences in the regions of YHR053c and YLR155c were confirmed by Southern hybridization, but did not with that of the region of YDR038c. The expression level of mRNA in S. cerevisiae KNU5377 and S288C was also compared: the 550 ORFs of S. cerevisiae KNU5377 showed more than two-fold higher intensity than those of S. cerevisiae S288C. Among the 550 ORFs, 59 ORFs belonged to the groups of ribosomal proteins and mitochondrial ribosomal proteins, and 200 ORFs belonged to the group of cellular organization. DIP5 and GAP1 were the most highly expressed genes. These results suggest that upregulated DIP5 and GAP 1 might take the place of ASP3 and, additionally, the sensitivity against copper might be contributable to the lowest expression level of copper-binding metallothioneins encoded by CUP 1a (YHR053c) and CUP1b (YHR055c) in S. cerevisiae KNU5377.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.2
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• pp.155-160
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• 2008

Several studies have reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2 (http://www.animalgenome.org/QTLdb/pig.html). For application of the molecular genetic information to the pig industry through marker-assisted selection, single nucleotide polymorphism (SNP) markers were analyzed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes with DNA from commercial pig breeds such as Berkshire, Yorkshire, Landrace, Duroc and Korean Native pig. A total of 34 SNPs were identified in 15 PCR products producing an average of one SNP in every 253 bp. PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to investigate allele frequencies in five commercial pig breeds in Korea. Eight of the SNPs appear to be fixed in at least one of the five pig breeds, which indicates that different selection among pig breeds might be applied to these SNPs. Polymorphisms detected in the PTH, CSF2 and FOLR genes were chosen to genotype a Berkshire-Yorkshire pig breed reference family for linkage and association analyses. Using linkage analysis, PTH and CSF2 loci were mapped to pig chromosome 2, while FOLR was mapped to pig chromosome 9. Association analyses between SNPs in the PTH, CSF2 and FOLR suggested that the CSF2 MboII polymorphism was significantly associated with several pork quality traits in the Berkshire and Yorkshire crossed F2 pigs. Our current findings provide useful SNP marker information to fine map QTL regions on pig chromosome 2 and to clarify the relevance of SNP and quantitative traits in commercial pig populations.

• Korean Journal of Plant Resources
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• v.31 no.5
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• pp.522-530
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• 2018

Brachypodium distachyon has been developed as a monocot model plant for temperate grasses and bioenergy crops. Although B. distachyon research is moving forward rapidly, the study of photoresponses has not been explored. To extend our knowledge of responses to light in monocots, we performed photoresponse analysis of B. distachyon using two inbred lines, Bd21 and Bd21-3. In this study, we first compared growing phenotypes between the two lines and investigated coleoptile and primary leaf growths under dark, far-red, red, and white light conditions. The results showed that the growth of the two lines were similar until tillering stage, but other developmental stages from heading to senescence were much delayed in Bd21-3, which resulted in increased height and tiller numbers. Under different light conditions, primary leaf lengths were kept increasing during the growth period, whereas the coleoptile extension was inhibited 4 to 7 days after growth depending on the light conditions applied. These results suggest that the responses to light in B. distachyon can be examined by measuring coleoptile lengths approximately 7 days after seedling growth. Moreover, we selected light-responsive genes known in Arabidopsis thaliana, such as chlorophyll A/B binding protein (CAB), light-harvesting chlorophyll binding protein (Lhcb) and chalcone synthase (CHS), and confirmed their light-induced gene expression in B. distachyon. Therefore, the present study suggests that the inhibition of coleoptile growth can be used as the parameter to analyze photoresponses in the monocot model plant, and also provide the reference genes whose expression is induced by far-red and red light treatment.

• Korean Journal of Veterinary Research
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• v.42 no.2
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• pp.225-229
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• 2002

We report that mycoplasma organisms from lung tissues of slaughter pigs were identified to genes fragments with references use of nested-PCR technique(nPCR). Seven strains of mycoplasma species were isolated from 70 lung tissues. The organisms were detected by in vitro amplification of 16S rRNA and 23S rRNA genes. Nucleotide sequences of the spacer between 16S and 23S in the ribosomal RNA operons of mycoplasma were identified by the analysis of products from the nested PCR. Four common PCR primers, MhF1, MhF2 MhR1 and MhR2, were designed by analysis between these sequences by first amplified with F1, R1 and second with F2, R2, respectively. Specific amplification of the spacer region for reference strains of M. hyopneumoniae, M. hyorhinis, M. flocculare were confirmed by first round of PCR in which the traduced fragments of 690bp, 460bp, 630bp. But amplications of second round was changed to 240bp, 210bp, 230bp, respectively. Three different strains (M. hyopneumoniae:4, M. hyorhinis:2, M. flocculare:1) were detected by the nested-PCR technique. The results suggest that the detection of swine mycoplasma by n-PCR can be analyzed the nucleotide sequences between rRNA operons and homology study.

• Genomics & Informatics
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• v.8 no.2
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• pp.76-80
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• 2010

Although autism spectrum disorder (ASD) has been thought to have a substantial genetic background, major contributing genes have yet to be identified or successfully replicated. Immunological dysfunction has been suggested to be associated with ASD, and T cell-mediated immunity was considered important for the development of ASD. In this study, we analyzed 163 ASD subjects and 97 normal controls by genomic quantitative PCR to evaluate the association between the copy number variation of the 7q34 locus, harboring the TCRB gene, and ASDs. As a result, there was no significant difference of the frequency distribution of TCRB copy numbers between ASD cases and normal controls. TCRB gene copy numbers ranged from 0 to 5 copies, and the frequency distribution of each copy number was similar between the two groups. The proportion of the individuals with <2 copies of TCRB was 52.8% (86/163) in ASD cases and 57.1% (52/91) in the control group (p=0.44). The proportion of individuals with >2 copies of TCRB was 11.7% (19/163) in ASD cases and 12.1% (11/91) in the control group (p=0.68). After the effects of sex were adjusted by logistic regression, ORs for individuals with <2 copies or >2 copies showed no significant difference compared with the diploid copy number as reference (n=2). Although we could not see the positive association, our results will be valuable information for mining ASD-associated genes and for exploring the role of T cell immunity further in the pathogenesis of ASD.

• Journal of fish pathology
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• v.34 no.1
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• pp.23-29
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• 2021

Interferon regulatory factors (IRFs) are a family of transcription factors essential to the control of antiviral immune response, cell growth, differentiation and apoptosis. IRF10 of zebrafish (Danio rerio) was negative regulation of the interferonΦ1 and 3 response in vitro. In this study, we analyze the induction of in vivo immune response activation from the IRF10 gene of zebrafish and the protective effect against VHSV. As the results, the group inoculated with IRF10 expression vectors, there was no expression of IFNΦ1, suggestion that IRF10 may function as a negative regulator of IRF3, which binds to the IFNΦ1 promoter. And other types of interferon genes (IFNΦ2-4) are thought to have been activated, inducing to the expression of pro-inflammatory cytokine and Mx genes. As the results of challenge test performed at 14 days after inoculation of the expression vectors, the maximum survival rate [50% (1㎍ DNA) and 42.5% (10㎍ DNA)] for IRF10 group were recorded. Meanwhile, the survival rates of pcDNA3.1 and PBS as the control groups were 10% and 15%, respectively. This study suggests that the possibility that activation of IRF10 molecule could be exploited as a VHS control method.

• Journal of Life Science
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• v.26 no.8
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• pp.904-910
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• 2016

Complex traits are determined by the combined effects of many loci and are affected by gene networks or biological pathways. Systems biology approaches have an important role in the identification of candidate genes related to complex diseases or traits at the system level. The gene network analysis has been performed by diverse types of methods such as gene co-expression, gene regulatory relationships, protein-protein interaction (PPI) and genetic networks. Moreover, the network-based methods were described for predicting gene functions such as graph theoretic method, neighborhood counting based methods and weighted function. However, there are a limited number of researches in livestock. The present study systemically analyzed genes associated with 102 types of economic traits based on the Animal Trait Ontology (ATO) and identified their relationships based on the gene co-expression network and PPI network in cattle. Then, we constructed the two types of gene network databases and network visualization system (http://www.nabc.go.kr/cg). We used a gene co-expression network analysis from the bovine expression value of bovine genes to generate gene co-expression network. PPI network was constructed from Human protein reference database based on the orthologous relationship between human and cattle. Finally, candidate genes and their network relationships were identified in each trait. They were typologically centered with large degree and betweenness centrality (BC) value in the gene network. The ontle program was applied to generate the database and to visualize the gene network results. This information would serve as valuable resources for exploiting genomic functions that influence economically and agriculturally important traits in cattle.

• Korean Journal of Veterinary Research
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• v.43 no.2
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• pp.247-253
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• 2003

Actinobacillus pleuropneumoniae causes a highly contagious pleuropneumoniae in swine. The bacterium produces several virulence factors such as exotoxin, LPS, capsular polysaccharide, etc. Among them, the exotoxin, called Apx, has been focused as the major virulence factor, and the toxin consists of 4 gene cluster. apx CABD. apxA is the structural gene of toxin and has four different types, I, II, III, and IV. As the first step of development of a new subunit vaccine, the three different types of apxA gene were amplified from A. pleuropneumoniae isolated from Korea by PCR with primer designed based on the N- and C-terminal of the toxin. The sizes of apxIA, IIA and IIIA were 3,073, 2,971 and 3,159bps, respectively. The comparison of whole DNA sequences of apxIA, IIA and IIIA genes with those of the reference strain demonstrated 98%, 99% and 98% homology, respectively. In addition, the phylogenetic analysis was performed based on the amino acid sequences compared with 12 different RTX toxin family using the neighbor-joining method. ApxA proteins of Korean isolates were identical with reference strains in this study. All ApxA proteins were expressed in E. coli with pQE expression vector and identified using Western blot with polyclonal antibodies against culture supernatants of A. pleuropneumoniae serotype 2 or 5. The sizes of each expressed ApxA protein were about 120, 110, 125 kDa (M.W.), respectively. The results obtained in this study could be used for the future study to develop a new vaccine to porcine pleuropneumoniae.

• Journal of Veterinary Clinics
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• v.23 no.4
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• pp.405-410
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• 2006

Using internal transcribed spacer 1 (ITS1) region ribosomal DNA sequences from 9 strains of Microsporum canis and 5 strains of Microsporum gypseum isolated from dogs and a cat with dermatophytosis, we demonstrated the mutual phylogenetic relationship of these strains. Nucleotide sequence analysis of the ITS 1 gene fragments from the 9 strains of M canis had the 100% nucleotide sequence similarities and the 5 strains of M gypseum also had the 100% nucleotide sequence similarities. The phylogenetic analysis of the nucleotide sequences of the 9 strains of M canis formed a nested cluster with the reference strains of M canis originating from USA, Australia, Japan, and Europe. M canis were genetically distinct from the other reference strains of Microsporum spp, but M distortum, M equinum, and M. ferrugineum were genetically very close to M canis. M gypseum from a cluster in the phylogenetic tree with M canis as an outgroup. The molecular analysis of ITS 1 genes provided the useful information for the identification of these microsporum species and the understanding of their relationship.