• Korean Journal of Environmental Biology
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• v.39 no.3
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• pp.399-405
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• 2021

Until now, five species (Meghimatium bilineatum, M. fruhstorferi, Limax flavus, L. marginatus, Deroceras reticulatum) in three genera of families Philomycidae and Limacidae have been reported in Korea. Philomycidae is a family of air-breathing land snails. Meghimatium hongdoensis sp. nov. is described based on its middle size (60-80 mm in body length), its body coloration (dark-red yellow), no dorsal with streaks, its genitalia, and 16rDNA sequence analysis. Specimens of this new species were collected from Hongdo island, Sinan-gun, Jeollanam-do, Korea. This species is only known from the type locality at Hongdo to date. It could be found in high-humidity sites. Meghimatium uniforme (Laidlaw 1937) was the first one reported in Korea. It was also collected from Gageodo island, Sinan-gun, Jeollanam-do, Korea. In this study, morphological characteristics including their radula and genital structures of these two species were described. Preliminary results of mitochondrial 16S rDNA sequencing and phylogenetic analyses indicated that these species belonged to the Korean clade.

• Journal of Microbiology and Biotechnology
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• v.21 no.6
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• pp.545-555
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• 2011

The diversity elucidation by amplified ribosomal DNA restriction analysis and 16S rDNA sequencing of 96 associative diazotrophs, isolated from the feeder roots of tea on enriched nitrogen-free semisolid media, revealed the predominance of Gram-positive over Gram-negative bacteria within the Kangra valley in Himachal Pradesh, India. The Gram-positive bacteria observed belong to two taxonomic groupings; Firmicutes, including the genera Bacillus and Paenibacillus; and Actinobacteria, represented by the genus Microbacterium. The Gram-negative bacteria included ${\alpha}$-Proteobacteria genera Brevundimonas, Rhizobium, and Mesorhizobium; ${\gamma}$-Proteobacteria genera Pseudomonas and Stenotrophomonas; and ${\beta}$-Proteobacteria genera Azospira, Burkholderia, Delftia, Herbaspirillum and Ralstonia. The low level of similarity of two isolates, with the type strains Paenibacillus xinjiangensis and Mesorhizobium albiziae, suggests the possibility of raising species novum. The bacterial strains of different phylogenetic groups exhibited distinct carbon-source utilization patterns and fatty acid methyl ester profiles. The strains differed in their nitrogenase activities with relatively high activity seen in the Gramnegative strains exhibiting the highest similarity to Azospira oryzae, Delftia lacustris and Herbaspirillum huttiense.

• Parasites, Hosts and Diseases
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• v.58 no.2
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• pp.191-194
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• 2020

Free-living amoebas (FLAs) can cause severe disease in humans and animals when they become infected. However, there are no accurate survey reports on the prevalence of FLAs in Korea. In this study, we collected 163 tap water samples from buildings, apartments, and restrooms of highway service areas in 7 Korean provinces with high population density. All these buildings and facilities have water storage tanks in common. The survey was separated into categories of buildings, apartments, and highway service areas. Five hundred milliliters of tap water from each building was collected and filtered with 0.2 ㎛ pore filter paper. The filters were incubated in agar plates with heated E. coli at 25℃. After axenization, genomic DNA was collected from each FLA, and species classification was performed using partial 18S-rDNA PCR-sequencing analysis. We found that 12.9% of tap water from buildings with storage tanks in Korea was contaminated with FLAs. The highway service areas had the highest contamination rate at 33.3%. All of the FLAs, except one, were genetically similar to Vermamoeba vermiformis (Hartmannella vermiformis). The remaining FLA (KFA21) was very similar to Acanthamoeba lugdunensis (KA/E26). Although cases of human infection by V. vermiformis are very rare, we must pay attention to the fact that one-third of tap water supplies in highway service areas have been contaminated.

• BMB Reports
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• v.39 no.4
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• pp.361-370
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• 2006

Genetic variation and molecular phylogeny of 22 taxa representing 14 extant species and 3 unidentified taxa of Boesenbergia in Thailand and four outgroup species (Cornukaempferia aurantiflora, Hedychium biflorum, Kaempferia parviflora, and Scaphochlamys rubescens) were examined by sequencing of 3 chloroplast (cp) DNA regions (matK, psbA-trnH and petA-psbJ). Low interspecific genetic divergence (0.25-1.74%) were observed in these investigated taxa. The 50% majority-rule consensus tree constructed from combined chloroplast DNA sequences allocated Boesenbergia in this study into 3 different groups. Using psbA-1F/psbA-3R primers, an insertion of 491 bp was observed in B. petiolata. Restriction analysis of the amplicon (380-410 bp) from the remaining species with Rsa I further differentiated Boesenbergia to 2 groupings; I (B. basispicata, B. longiflora, B. longipes, B. plicata, B. pulcherrima, B. tenuispicata, B. thorelii, B. xiphostachya, Boesenbergia sp.1 and Boesenbergia sp.3; phylogenetic clade A) that possesses a Rsa I restriction site and II (B. curtisii, B. regalis, B. rotunda and Boesenbergia sp.2; phylogenetic clade B and B. siamensis; phylogenetic clade C) that lacks a restriction site of Rsa I. Single nucleotide polymorphism (SNP) and indels found can be unambiguously applied to authenticate specie-origin of all investigated samples and revealed that Boesenbergia sp.1, Boesenbergia sp.2 and B. pulcherrima (Mahidol University, Kanchanaburi), B. cf. pulcherrima1 (Prachuap Khiri Khan) and B. cf. pulcherrima2 (Thong Pha Phum, Kanchanaburi) are B. plicata, B. rotunda and B. pulcherrima, respectively. In addition, molecular data also suggested that Boesenbergia sp.3 should be further differentiated from B. longiflora and regarded as a newly unidentified Boesenbergia species.

• Genomics & Informatics
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• v.7 no.2
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• pp.65-84
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• 2009

Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomics related studies, genome annotation and SNP discovery. We analyzed 7,392 high-quality chromatograms (Phred value ${\geq}$30) obtained from sequencing the 5' ends of clones derived from full-length enriched cDNA libraries of Korean native pigs including brainstem, liver, cerebellum, neocortex and spleen libraries. In addition, 50,000 EST sequence trace files obtained from GenBank were combined with our sequences to identify cSNPs in silico. The process generated 11,324 contigs, of which 2,895 contigs contained at least one SNP and among them 610 contigs had a minimum of one sequence from Korean native pigs. Of 610 contigs, we randomly selected 262 contigs and performed in silico analysis for the identification of cSNPs. From the results, we identified 1,531 putative coding single nucleotide polymorphisms (cSNPs) and the SNP detection frequency was one SNP per 465 bp. A large-scale sequencing result of clones from full-length enriched cDNA libraries and identified cSNPs will serve as a useful resource to functional genomics related projects such as a pig HapMap project in the near future.

• ALGAE
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• v.35 no.3
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• pp.293-301
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• 2020

The applications of DNA barcoding have a wide range of uses, such as in taxonomic studies to help elucidate cryptic species and phylogenetic relationships and analyzing environmental samples for biodiversity monitoring and conservation assessments of species. After obtaining the DNA barcode sequences, sequence similarity-based homology analysis is commonly used. This means that the obtained barcode sequences are compared to the DNA barcode reference databases. This bioinformatic analysis necessarily implies that the overall quantity and quality of the reference databases must be stringently monitored to not have an adverse impact on the accuracy of species identification. With the development of next-generation sequencing techniques, a noticeably large number of DNA barcode sequences have been produced and are stored in online databases, but their degree of validity, accuracy, and reliability have not been extensively investigated. In this study, we investigated the extent to which the amount and types of erroneous barcode sequences were deposited in publicly accessible databases. Over 4.1 million sequences were investigated in three largescale DNA barcode databases (NCBI GenBank, Barcode of Life Data System [BOLD], and Protist Ribosomal Reference database [PR2]) for four major DNA barcodes (cytochrome c oxidase subunit 1 [COI], internal transcribed spacer [ITS], ribulose bisphosphate carboxylase large chain [rbcL], and 18S ribosomal RNA [18S rRNA]); approximately 2% of erroneous barcode sequences were found and their taxonomic distributions were uneven. Consequently, our present findings provide compelling evidence of data quality problems along with insufficient and unreliable annotation of taxonomic data in DNA barcode databases. Therefore, we suggest that if ambiguous taxa are presented during barcoding analysis, further validation with other DNA barcode loci or morphological characters should be mandated.

• Journal of Mushroom
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• v.8 no.1
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• pp.27-32
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• 2010

This study was carried out to analyze the genetic relationships among 22 strains of Sparassis crispa, which were collected from various regions of worldwide. The cleaved amplified polymorphic sequence were obtained from the ribosomal DNA ITS regions of each strain. Based on the sequence analysis, the presence of five different groups were observed. Most strains shared the high nucleotide sequence similarity (about 90%) to each other, except only one strain, KACC50866. Nucleotide sequence similarity of KACC50866 was below 10% to other strains, indicating the genetic relatedness of strain KACC50866 was low compared to other strains. More works such as mitochondria genome analysis should help to determine the precise genetic diversity of S. crispa strains.

• Food Science and Preservation
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• v.30 no.3
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• pp.483-491
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• 2023

This study aimed to compare the bioactive compounds in Centella asiatica (C. asiatica) cultivated in a smart farm and a field and their effects on human keratinocyte cells. C. asiatica was collected in Jeju-do, Korea, and cultured in a smart farm and a field. The main bioactive compounds in the two differentially cultured C. asiatica were identified, and their activation in keratinocytes were assessed. Amplification and sequencing of the internal transcribed spacer (ITS) DNA in the nucleus and psbA-H DNA in the chloroplast were performed for species analysis. A comparison of DNA of plants reported in the NCBI GenBank was performed. The ITS DNA and psbA-H DNA sequences of C. asiatica cultivated in a smart farm and a field were consistent with No. MH768338.1 and No. JQ425422.1, respectively. Analysis of the triterpenes was performed using high performance liquid chromatography (HPLC) and as a result, C. asiatica cultured in a smart farm had more triterpenes than those cultured in a field. The effects of C. asiatica grown in a smart farm on cell proliferation and scratch recovery in HaCaT cells were greater than those grown in a field. These results suggest that C. asiatica cultivated in a smart farm can be effectively utilized as a health functional food.

• Journal of Microbiology and Biotechnology
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• v.10 no.6
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• pp.881-884
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• 2000

A polymerase chain reaction (PCR) was performed to rapidly identify Lactobacillus plantarum from type strains and kimchi samples. The PCR experiments were carried out using specific oligonucleotide primer sets based on the 16S rRNA gene sequences of L. plantarum. The expected DNA amplificate of 419 bp was obtained when either purified DNA or whole cells of L. plantarum strains reacted with LP primers, yet not with any of the other strains. The PCR product was confirmed by DNA sequencing. Accordingly, since the PCR method used is simple, specific, and rapid, it will be useful for monitoring and evaluation L. plantarum in the mixed microbial population found in kimchi.

• Korean Journal of Food Science and Technology
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• v.40 no.6
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• pp.656-660
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• 2008

Fermented soybean foods are an important component of the Korean diet. Eoyukjang is a type of traditional fermented soybean source. Microbial analysis of eoyukjang was conducted during the fermentation period in this study. Microorganisms isolated from eoyukjang were identified by biochemical tests and 16S rDNA sequencing. 17 different microorganisms, including bacteria, yeast, and fungi were detected in eoyukjang during the fermentation period. Even though Aspergillus participated in the early stage of fermentation of eoyukjang, Bacillus species and Saccharomyces cerevisiae were the major microzymes in eoyukjang throughout the maturation period. Eoyukjang is generally consumed after the boiling of the final sample. Therefore, the final sample of eoyukjang was boiled and analyzed. Our results showed that no vegetative microorganisms survived under the boiling conditions for eoyukjang. Fermented soybean products in the domestic market were also assessed for comparison with the results from eoyukjang. The total cell number of kanjang (soy sauce) samples was between 0 to 42 CFU/mL. The isolated microorganisms were identified as Bacillus species. All Bacillus isolates were not found to harbor the three enterotoxin-producing and emetic toxin-producing genes.