• Food Science and Biotechnology
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• v.14 no.1
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• pp.49-57
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• 2005

Enterococcus faecium MJ-14, having strong antilisterial activity, was isolated from Korean fermented food, Meju. MJ-14 showed the same phenotypic characteristics, but different sugar utilization, as reference strain, E. faecium KCCM12118. It could utilize D-xylose, amygdaline, and gluconate, whereas E. faecium KCCM12118 could not. Optimal condition for bacteriocin production by E. faecium MJ-14 was at $37^{\circ}C$ and pH 7.0. Bacteriocin activity appeared in mid exponential phase and increased rapidly up to stationary phase. Activity was significantly promoted in MRS broth containing 3.0% glucose, 1.5% lactose, 2.0% peptone, or 1.5% tryptone. Bacteriocins effectively inhibited Enterococcus faecalis and Listeria spp. of Gram-positive bacteria, and Helicobacter pylori of Gram-negative bacteria, but did not inhibit yeasts and molds. They were stable against heat (for 30 min at $100^{\circ}C$), pH (3.0-9.0), long-term storage (for 60 days at 4 or $-20^{\circ}C$), and enzymatic digestion by catalase, proteinase K, papain, lysozyme, trypsin, chymotrypsin, and lipase, etc. Bacteriocin activity was completely inhibited by protease and pepsin, and 50% by ${\alpha}$-amylase. Studies on PCR detection of enterocin structural genes revealed bacteriocins are identical to enterocins A and B.

• Korean Journal of Veterinary Service
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• v.33 no.2
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• pp.143-149
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• 2010

BIn the present study, Enterococcus isolates originating from livestock were studied for the phenotypic and genotypic assessment of tetracycline resistance. A total of 74 isolates encompassing the species Enterococcus faecalis (n=12) and E. faecium (n=62) displayed phenotypic resistance to tetracycline. Tetracycline resistance gene [tet (M), 1,886bp] were sequenced by dye terminator cycle sequencing method and compared with tet (M) sequences available from the GenBank database. Sequencing analysis of PCR amplicons showed high homology to the reference strains ranging 97.2~100%. The tet (M) genes were divided into three major subgroups according to phylogenetic analysis. The genetic information obtained from this study could be useful for the molecular study of enterococci.

• Korean Journal of Clinical Laboratory Science
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• v.38 no.3
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• pp.158-165
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• 2006

Although Mycobacterium tuberculosis complex strains remain responsible for the majority of diseases caused by mycobacterial infections worldwide, the increase in HIV infections has allowed for the emergence of other non-tuberculous mycobacteria as clinically significant pathogens. However, Mycobacterium species has a long period of incubation, and requires serious biochemical tests such as niacin, catalase, and nitrate test that are often tedious. The development of rapid and accurate diagnostics can aid in the early diagnosis of disease caused by Mycobacterium. The current DNA amplification and hybridization methods that have been developed target several genes for the detection of mycobacterial species such as hps65, 16S rDNA, rpoB, and dnaj. These methods produce rapid and accurate results. In this study, PCR-restriction fragment length polymorphism analysis(PCR-RFLP) based on the region of the rpoB gene was used to verify the identification of non-tuburculosis Mycobacterium species. A total of 8 mycobacterial reference strains and 13 clinical isolates were digested with restriction enzymes such as Msp I in this study. The results of using this process clearly demonstrated that all 13 specimens were identified by rpoB gene PRA method. The PCR-RFLP method based on the rpoB gene is a simple, rapid, and accurate test for the identification of Mycobacterium.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.8_spc
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• pp.1275-1283
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• 2019

Goats (Capra hircus) were domesticated during the late Neolithic, approximately 10,500 years ago, and humans exerted minor selection pressure until fairly recently. Probably the largest genetic change occurring over the millennia happened via natural selection and random genetic drift, the latter causing genes to be fixed in small and isolated populations. Recent human-influenced genetic changes have occurred through biometrics and genomics. For the most part, biometrics has concentrated upon the refining of estimates of heritabilities and genetic correlations. Heritabilities are instrumental in the calculation of estimated breeding values and genetic correlations are necessary in the construction of selection indices that account for changes in multiple traits under selection at one time. Early genomic studies focused upon microsatellite markers, which are short tandem repeats of nucleic acids and which are detected using polymerase chain reaction primers flanking the microsatellite. Microsatellite markers have been very important in parentage verification, which can impact genetic progress. Additionally, microsatellite markers have been a useful tool in assessing genetic diversity between and among breeds, which is important in the conservation of minor breeds. Single nucleotide polymorphisms are a new genomic tool that have refined classical BLUP methodology (biometric) to provide more accurate genomic estimated breeding values, provided a large reference population is available.

• Animal Bioscience
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• v.36 no.5
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• pp.679-691
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• 2023

The fat deposition is an important factor affecting chicken meat quality, which is closely related to lipid metabolism of chickens. Therefore, it is important to regulate the lipid metabolism of chickens to improve the chicken meat quality. Plant extracts have special regulatory effects on animal's growth and health and have been widely used in chicken breeding. Some plant extracts have been reported to have functions of changing the fatty acid composition, reducing abdominal fat percentage, and enhancing the intramuscular fat content of chickens by improving the antioxidant capacity, regulating the expression of genes, enzymes, and signaling pathways related to lipid metabolism, modulating intestinal microbiota, affecting hormones level, and regulating DNA methylation. This paper reviewed the application and mechanism of plant extracts on regulating lipid metabolism of chickens to provide a reference for the further application of plant extracts in chicken breeding.

• Journal of Mushroom
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• v.20 no.1
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• pp.7-12
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• 2022

The ascomycete fungus Cordyceps militaris infects lepidopteran insect pupae, forming characteristic fruiting bodies called "Dong Chung Ha Cho" in Korean. They have been used as medicines owing to their anti-allergic, anti-inflammatory, and immune-enhancing effects. This fungus can be grown on the geminated soybeans Rhynchosia nulubilis, which also contains several novel isoflavones. We performed a comparative transcriptome analysis to determine core gene sets or pathways contributing to biologically active products such as isoflavone. Initially, we sequenced 2-week-old fungal cultures on different soybean agar media, where different amounts of water agar were implemented to show different surface topology. We selected 830 upregulated and 188 downregulated genes by comparing linear models of the samples (two-fold change threshold). Gene ontology analysis identified that the "IMP biosynthesis" term was significantly found in the upregulated gene sets. The pathway is involved in the synthesis of cordycepin, the reference chemical for C. militaris. This finding in the transcriptome data is consistent with the previous observation: increased cordycepin concentrations in the C. militaris cultured on germinated soybean.

• Genomics & Informatics
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• v.21 no.2
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• pp.24.1-24.7
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• 2023

Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.

• Journal of Genetic Medicine
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• v.20 no.2
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• pp.39-45
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• 2023

As advanced sequencing technologies continue to uncover an increasing number of variants in genes associated with human genetic diseases, there is a growing demand for systematic approaches to assess the impact of these variants on human development, health, and disease. While in silico analyses have provided valuable insights, it is essential to complement these findings with model organism studies to determine the functional consequences of genetic variants in vivo. Drosophila melanogaster is an excellent genetic model for such functional studies due to its efficient genetic technologies, high gene conservation with humans, accessibility to mutant fly resources, short life cycles, and cost-effectiveness. The traditional GAL4-UAS system, allowing precise control of gene expression through binary regulation, is frequently employed to assess the effects of monoallelic variants. Recombinase medicated cassette exchange or CRISPR-Cas9-mediated GAL4 insertion within coding introns or substitution of gene body with Kozak-Gal4 result in the loss-of-function of the target gene. This GAL4 insertion strategy also enables the expression of reference complementary DNA (cDNA) or cDNA carrying genetic variants under the control of endogenous regulatory cis elements. Furthermore, the CRISPR-Cas9-directed tissue-specific knockout and cDNA rescue system provides the flexibility to investigate candidate variants in a tissue-specific and/or developmental-timing dependent manner. In this review, we will delve into the diverse genetic techniques available in Drosophila and their applications in diagnosing and studying numerous undiagnosed diseases over the past decade.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.326-335
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• 2015

Citrus is an economically important fruit tree with the largest amount of fruit production in the world. It provides important nutrition such as vitamin C and other health-promoting compounds including its unique flavonoids for human health. However, it is classified into the most difficult crops to develop new cultivars through conventional breeding approaches due to its long juvenility and some unique reproductive biological features such as gamete sterility, nucellar embryony, and high level of heterozygosity. Due to global warming and changes in consumer trends, establishing a systematic and efficient breeding programs is highly required for sustainable production of high quality fruits and diversification of cultivars. Recently, reference genome sequences of sweet orange and clementine mandarin have been released. Based on the reference whole-genome sequences, comparative genomics, reference-guided resequencing, and genotyping-by-sequencing for various citrus cultivars and crosses could be performed for the advance of functional genomics and development of traits-related molecular markers. In addition, a full understanding of gene function and gene co-expression networks can be provided through combined analysis of various transcriptome data. Analytic information on whole-genome and transcriptome will provide massive data on polymorphic molecular markers such as SNP, INDEL, and SSR, suggesting that it is possible to construct integrated maps and high-density genetic maps as well as physical maps. In the near future, integrated maps will be useful for map-based precise cloning of genes that are specific to citrus with major agronomic traits to facilitate rapid and efficient marker-assisted selection.

• Journal of fish pathology
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• v.19 no.2
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• pp.127-139
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• 2006

From 2002 to 2004, various vibrios were isolated from the olive flounder, Paralichthys olivaceus of culturing size with disease signs. During this survey, it was known that the high proportion of Vibrio ichthyoenteri was occupied among the isolated vibrios. Generally, V. ichthyoenteri is well known as the pathogen of bacterial enteritis of olive flounder larvae. The aim of the present study was the compare the characteristics of two groups of V. ichthyoenteri, culturing sized olive flounder, and larvae of olive flounder showing the intestinal necrosis. The research was focused on the physiology, biochemistry, genetics in the two bacterial groups. The physiological and biochemical characteristics of the tested strains were very similar. The intergenic spacer (IGS) region between the 16S and 23S rRNA genes of 21 isolated strains and 3 reference strains, V. ichthyoenteri, were investigated by PCR fragment length typing and DNA sequencing. After the isolated strains were identified as V. ichthyoenteri, not only phenotypic characteristics of the isolated and reference strains but also homology of 16S-23S IGS of all isolated strains and reference strains as 99.1~100%. The V. ichthyoenteri showed 4 specific 16S-23S patterns and contained no-tRNA, tRNAGlu(TTC) , tRNAIle(GAT) tRNAAla(TGC) type .