• Food Science of Animal Resources
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• v.43 no.4
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• pp.685-702
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• 2023

Lactic acid bacteria (LAB) are commonly used as probiotics; however, not all LAB strains have the same beneficial effects. To successfully use LAB as probiotics in canines, LAB species should originate from the canine intestinal tract as they display host specificity. The objective of this study was to investigate the phenotypic and genomic traits of potential probiotic LAB isolated from canine fecal samples. Twenty LAB samples were evaluated for their potential probiotic characteristics including resistance to low pH, bile salts, hydrophobicity, auto-aggregation, co-aggregation, adhesion to epithelia or mucosa, and production of inhibitory compounds. Additionally, we evaluated their safety and other beneficial effects on canine health, such as DPPH free radical scavenging, and β-galactosidase. Four strains demonstrated potential probiotic characteristics and were selected: Enterococcus hirae Pom4, Limosilactobacillus fermentum Pom5, Pediococcus pentosaceus Chi8, and Ligilactobacillus animalis FB2. Safety evaluations showed that all strains lacked hemolytic activity, could not produce biogenic amines, and did not carry any pathogenic genes. In addition, L. fermentum Pom5 and P. pentosaceus Chi8 displayed susceptibility to all antibiotics and concordant with the absence of antibiotic resistance genes. Based on their phenotypic and genomic characteristics, L. fermentum Pom5 and P. pentosaceus Chi8 were identified as potential probiotic candidates for canines.

• Animal Bioscience
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• v.37 no.8
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• pp.1355-1366
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• 2024

Objective: The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens. Methods: The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures. Results: A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients (F_ROH) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable (r = 0.18-1). Five ROH islands harbouring important quantitative trait loci were identified. Conclusion: This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions.

• Advances in Traditional Medicine
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• v.5 no.2
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• pp.117-123
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• 2005

Dyers woad leaf (Daqingye) is a traditional Chinese medicine commonly used as anti-pyretic, anti-bacterial and anti-viral agent against infectious diseases. The Chinese Pharmacopoeia (2005) records that Dyers woad leaf should be derived from the leaves of Isatis indigotica Fort., but the leaves of Polygonum tinctorium Ait., Baphicacanthus cusia (Nees) Bremek. and Clerodendron cyrtophyllum Turcz. have also been used as substitutes of Dyers woad leaf in different regions of China. The leaf morphologies of these four species show a close resemblance, and based on their morphological appearance, it is difficult to identify them. Here, molecular genetic methods were developed as a target to identify different members of Dyers woad leaf. The 5S-rRNA spacer domain was amplified by polymerase chain reaction from genomic DNAs isolated from I. indigotica, P. tinctorium, B. cusia and C. cyrtophyllum, and the nucleotide sequences showed a great diversity. In addition, random amplification of polymorphic DNA analysis was also used to distinguish the members of Dyers woad leaf. These molecular methods could be used as a tool in authentic identification of Dyers woad leaf.

• Advances in Traditional Medicine
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• v.7 no.1
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• pp.26-33
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• 2007

Genetic polymorphism and molecular authentication were investigated with the commercial medicinal herb, Peony (Paeonia spp.), using random amplified polymorphic DNA (RAPD) markers. To identify the polymorphism of the RAPD patterns among plant origins, 20 different random primers were applied to the genomic DNA extracted from Paeonia spp. plants such as Paeonia (P.) lactiflora, P. officinale and P. japonica. Ten primers out of 20 primers could be used to discriminate the plant species in the same genus and 72 out of 81 scored DNA fragments (88.9%) generated with these primers were polymorphic. Especially, four primers, such as OPA1, OPA3, OP9, and OPA13, were useful to discriminate the plant origins among the species of Peony. In the results of cluster analysis using RAPD data obtained from the 10 primers, Peony (Paeonia spp.) plants used in this study were grouped into the two distinctive clusters, genetically. Herb medicine, especially P. lactiflora, were easily identified, when species-specific primers were applied to the investigation for discriminating herb medicine currently traded in domestic herb market, Kyungdongmart. Consequently, RAPD analysis was useful method to discriminate plant origins and the commercial medicinal herbs, Paeonia spp..

• Ocean and Polar Research
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• v.31 no.2
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• pp.213-218
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• 2009

We examined the intracellular antioxidative effects of 20 Arctic seaweed extracts in Raw 264.7 cells. Each seaweed species was subjected to extraction using acetone/dichloromethane and methanol, respectively, after which the extracts were combined and used as the test sample. The antioxidant ability of all 20 seaweeds extracts was evaluated using four different activity tests, including the degree of occurrence of intracellular reactive oxygen species (ROS), $ONOO^-$, and lipid peroxidation in Raw 264.7 cells, as well as the extent of oxidative damage of genomic DNA purified from Raw 264.7 cells. Crude extracts from Monostroma obscurum, Alaria esculnta, Laminaria digitata, Desmarestia aculeata, Chorda filum, Ptilota seriata, Phycidrys rubens, Devaleraea ramentacea and Palmaria palmata exhibited significant scavenging effects on the generation of intracellular ROS. Among them, Monostroma obscurum and Phycidrys rubens significantly inhibited membrane lipid peroxidation and DNA oxidation. Moreover, Phycidrys rubens exhibited scavenging effects on peroxynitrite generated from SIN-1.

• Korean Journal of Plant Resources
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• v.14 no.3
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• pp.235-240
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• 2001

Polymerase chain reaction (PCR) is used in a wide array of researches in plant molecular genetics and breeding. However, considerable time and cost are still required for the preparation of DNA suitable for reliable PCR results, especially in plant species containing high amounts of polyphenols. To reduce time and effort for PCR-based analysis, a simplified but reliable method was developed by a combinational employment of a simple and fast DNA extraction procedure and BLOTTO (Bovine Lacto Transfer Technique Optimizer) in reaction mixture. Genomic DNAs prepared by one-step extraction method from recalcitrant plant species such as Rubus coreanus, apple, grape and lettuce were successfully amplified by random primers in the reaction mixture containing 2 to 4% BLOTTO. Successful amplification of ${\gamma}$-TMT transgene in lettuce transformants by the specific primers was also achieved in the same condition, making rapid screening of positive transformants possible. Our results suggest that use of a simple DNA extraction procedure and incorporation of BLOTTO in reaction mixture in combination can reduce time and effort required for the analyses of a large number of germplasms and transformants by PCR-based techniques.

• International Journal of Industrial Entomology and Biomaterials
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• v.44 no.2
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• pp.55-64
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• 2022

Bombyx shini Park & Sohn, 2002 (Lepidoptera: Bombycidae), which was listed as an endemic species in South Korea has recently been renamed as the East Asian silk moth Rotunda rotundapex Miyata & Kishida, 1990 (Lepidoptera: Bombycidae). In this study, we sequenced the complete mitochondrial genome (mitogenome) of the R. rotundapex to announce genomic characteristics and to clarify its validity with a new name. The 15,294-bp long complete mitogenome comprises a typical set of genes [13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes] and one major noncoding, A + T-rich region, with an arrangement identical to that observed in most lepidopteran mitogenomes. The A/T content of the whole mitogenome was 79.22%; however, it varied among the regions/genes as follows: A + T-rich region, 91.62%; srRNA, 84.67%; lrRNA, 83.01%; tRNAs, 81.43%; and PCGs, 77.46%. Phylogenetic analyses of 35 species in the Bombycoidea superfamily showed the sister relationship between the families Sphingidae and Bombycidae s. str., with the higher nodal support [bootstrap support (BS) = 78%]. The Saturniidae was placed as the sister to the two families, but the nodal support for this relationship was low (BS = 53%). Current R. rotundapex was placed together with previously reported con-species with the highest nodal support, forming a separate clade from Bombyx, validating that B. shini can have a new genus name, Rotunda. However, the Korean R. rotundapex showed a substantial sequence divergence at 5.28% to that originated from an individual of type locality Taiwan in 1,459-bp of COI sequences. Considering such a high sequence divergence an additional study, which includes morphological and DNA barcoding data from further extensive distributional range maybe is needed for further robust taxonomic conclusion.

• Journal of Plant Biotechnology
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• v.48 no.4
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• pp.223-227
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• 2021

Several hypotheses for the origin of cultivated sweetpotato [Ipomoea batatas L. (Lam)] have been suggested but the exact progenitor is still unknown. Based on the results of RFLP patterns, microsatellite markers, SNP markers, FISH analyses, and genome analyses of haplotypes, wild species belonging to batatas group, I. trifida, I. leucantha, I. littoralis, I. tabascana, I. tenuissima, I. tiliacea, and I. triloba have been suggested as a progenitor. However, recently, advanced genomic technologies and characterization of the inserted T-DNA fragments of Agrobacterium in the genome of cultivated sweetpotato and wild species through horizontal gene transfer suggest that there may be an older progenitor than the wild species suggested so far.

• Journal of Microbiology and Biotechnology
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• v.32 no.12
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• pp.1553-1560
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• 2022

A Gram-stain-negative, rod-shaped bacterial strain, JC4^T, was isolated from a freshwater sample and determined the taxonomic position. Initial identification based on 16S rRNA gene sequences revealed that strain JC4^T is affiliated to the genus Mucilaginibacter with a sequence similarity of 97.97% to Mucilaginibacter rigui WPCB133^T. The average nucleotide identity and digital DNA-DNA hybridization values between strain JC4^T and Mucilaginibacter species were estimated below 80.92% and 23.9%, respectively. Strain JC4^T contained summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and iso-C_15:0 as predominant cellular fatty acids. The dominant polar lipids were identified as phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was MK-7. The genomic DNA G+C content of strain JC4^T was determined to be 42.44%. The above polyphasic evidences support that strain JC4^T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter aquariorum sp. nov. is proposed. The type strain is JC4^T (= KCTC 92230^T = LMG 32715^T).