• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.583-590
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• 2018

Genus Typha L. (Typhaceae; Cattail in common) is one of the hydrophytic plants found in semi-aquatic regions. About nine to 18 species of the genus exist all over the world. In Korea, the most commonly found cattail species are T. laxmanni and T. angustifolia. The aim of this study was to prepare a cDNA library and sequences and analyze expressed sequence tags (ESTs) from these species, T. laxmanni and T. angustifolia. In the case of T. laxmanni, we observed that 715 out of 742 ESTs had high quality sequences, whereas the remaining 27 ESTs were low quality sequences. In this study, we identified 77 contigs, 393 unassembled clones and 65.7% singletons. Furthermore, in the case of T. angustifolia, we recorded 992 high quality EST sequences, and by excluding 28 low quality sequences from among them, we retrieved 120 contigs, 348 unassembled clones and 48.9% singletons. The basic local alignment search tool (BLAST) and Kyoto encyclopedia of genes and genomes (KEGG) database results enabled us to identify the functional categories, i.e., molecular function (16.5%), biological process (22.2%) and cellular components (61.3%). In addition, between these two species, the no hits and anonymous genes were 4.2% and 11.7% and 6.2% and 11.2% in T. laxmanni and T. angustifolia, respectively, based on the BLAST results. The study concluded that they have certain species-specific genes. Hence, the results of this study on these two species could be a valuable resource for further studies.

• Journal of Life Science
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• v.28 no.3
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• pp.300-306
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• 2018

Lysozymes are innate immune factors that play a critical role in the defense against pathogens in various invertebrate animals including spoon worms. In this study, an invertebrate-type lysozyme was isolated from the body wall of spoon worm, Urechis unicinctus. The acidified body wall extract was partially separated using a Sep-Pak C18 cartridge. Among the fractions, the materials that were eluted with 60% methanol/0.1% trifluoroacetic acid showed the most potent antimicrobial activity against Bacillus subtilis KCTC 1021. A series of high performance liquid chromatography (HPLC) steps were then utilized to isolate a single antimicrobial absorbance peak. The molecular weight of the antimicrobial peak was approximated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), which was approximately 13 to 14 kDa. The partial primary structure of this antimicrobial protein that was analyzed, using LC-MS/MS, was CTGGRPPTCEDYAK (1611.69 Da). Homology search of these fourteen residues, using the National Center for Biotechnology Information Basic Local Alignment Search Tool (NCBI BLAST), revealed that the isolated protein was similar to the invertebrate-type lysozymes described in other animals. Then, the antimicrobial and lysozyme enzymatic (muramidase) activities of this protein were assessed. The isolated protein possessed antimicrobial activity and potent muramidase activity, which were comparable to those of hen egg white lysozyme. Therefore, the isolated protein was designated as Urechis unicinctus invertebrate-type lysozyme from the body wall, Uu-iLysb.

• Journal of Food Hygiene and Safety
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• v.35 no.3
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• pp.234-242
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• 2020

In this study, we monitored the raw materials in home-meal replacement (HMR) products, which have shown more than 63% growth in market size for two years. A total of 89 HMR products were purchased and the DNA barcodes of 112 raw materials in the product samples were analyzed. In order to identify the raw material species, a primer set specific for the 16S ribosomal RNA region of each raw material species was amplified. The amplicon was purified and sequenced, and then used to perform a BLAST search provided by the National Institutes of Health (NIH). The species of the raw material was determined by comparing the nucleotide sequences of the species registered in GenBank with identity and match score. Twenty-four species and three genera were identified from 112 raw materials. Three genera were identified at the genus level because a large number of species belonging to the same genus exist within 98% of the identity criteria. The results of the determination were compared with the available raw materials suggested in the Korea Food Code to determine the Korean name and availability of the foods. Six non-listed species were determined to be edible according to information provided by influential domestic and foreign organizations.

• Research in Plant Disease
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• v.22 no.2
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• pp.122-126
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• 2016

In June 2015, an exhibited typical signs and symptoms of brown rot was observed on fruit of Apricot cvs. Modern and Alexander at an incidence of 5% of fruit in Jeonju, Korea. Early symptoms on fruit showed small, circular, light brown spots that eventually destroyed the entire fruit. Small sporodochia appeared on the fruit surface. Fruit susceptibility to brown rot increases during the 1 to 2 weeks period prior to harvest. The conidia were one-celled, hyaline, lemon-shaped, $14.6-18.0{\times}8.5-11{\mu}m$, and borne in branched monilioid chains. Based on the morphological characteristics and phylogenetic analysis of internal transcribed spacer (ITS), the fungus was identified as Monilinia fructicola. A BLAST search revealed that sequences of the fungus shared 100% identity to those of M. fructicola. Pathogenicity of a representative isolate was proved by artificial inoculation, fulfilling Koch's postulates. To our knowledge, this is the first confirmed report on the occurrence of M. fructicola on apricot in Korea.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.9
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• pp.1334-1341
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• 2007

This study identified hepatic differentially expressed genes (DEGs) affecting the marbling of muscle. Most dietary nutrients bypass the liver and produce plasma lipoproteins. These plasma lipoproteins transport free fatty acids to the target tissue, adipose tissue and muscle. We examined hepatic genes differentially expressed in a differential-display reverse transcription-polymerase chain reaction (ddRT-PCR) analysis comparing high- and low-marbled Hanwoo steers. Using 60 arbitrary primers, we found 13 candidate genes that were upregulated and five candidate genes that were downregulated in the livers of high-marbled Hanwoo steers compared to low-marbled individuals. A BLAST search for the 18 DEGs revealed that 14 were well characterized, while four were not annotated. We examined four DEGs: ATP synthase F0, complement component CD, insulin-like growth factor binding protein-3 (IGFBP3) and phosphatidylethanolamine binding protein (PEBP). Of these, only two genes (complement component CD and IGFBP3) were differentially expressed at p<0.05 between the livers of high- and low-marbled individuals. The mean mRNA levels of the PEBP and ATP synthase F0 genes did not differ significantly between the livers of high- and low-marbled individuals. Moreover, these DEGs showed very high inter-individual variation in expression. These informative DEGs were assigned to the bovine chromosome in a BLAST search of MS marker subsets and the bovine genome sequence. Genes related to energy metabolism (ATP synthase F0, ketohexokinase, electron-transfer flavoprotein-ubiquinone oxidoreductase and NADH hydrogenase) were assigned to BTA 1, 11, 17, and 22, respectively. Syntaxin, IGFBP3, decorin, the bax inhibitor gene and the PEBP gene were assigned to BTA 3, 4, 5, 5, and 17, respectively. In this study, the in silico physical maps provided information on the specific location of candidate genes associated with economic traits in cattle.

• Journal of the Korean Applied Science and Technology
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• v.39 no.5
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• pp.605-613
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• 2022

The genus Flavobacterium, type genus of the family Flavobacteriaceae and a member of the phylum Bacteriodetes includes gram-negative and yellow-pigmented rods. Those bacteria have been isolated from various environments of the earth. A yellow-pigmented, gram-negative rod was isolated from a pond in the campus of the Changwon University, Changwon, Kyeongnam and designated as strain B1. Strain B1 was further analyzed physiologically, biochemically and phylogenetically, and concluded to be a member of genus Flavobacterium. BLAST search of the 16S rRNA gene sequence of strain B1 shows homology no higher than 99.0% with those sequences of other bacteria. The major fatty acids of strain B1 are iso-C_15:0 (19.6%), summed feature 3(C_16:1 ω7c and/or C_16:1 ω6c, 16.1%), iso-C_17:0 3OH(10.2%), iso-C_15:0 3OH(8.4%) and iso-C_15:1 G(6.6%) showing significant differences in fatty acid compositions between strain B1 and the other known Flavobacterium species. DNA sequence of 16S rRNA gene of strain B1 was deposited in genbank under accession number OP060681.

• Journal of the Korean Applied Science and Technology
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• v.40 no.4
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• pp.881-889
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• 2023

The genus Hymenobacter, type genus of the family Hymenobacteraceae and a member of the phylum Bacteroidota includes gram-negative and red-pigmented rods. Those bacteria have been isolated from various environments of the earth. I isolated a red-pigmented, gram-negative rod from a pond in the campus of the Changwon University, Changwon, Kyeongnam and designated this bacterium as strain B2. Strain B2 was further analyzed phylogenetically and biochemically, and concluded as a member of genus Hymenobacter. BLAST search of the 16S rRNA gene sequence of strain B2 showed its homology lower than 98.7% with those sequences of the other bacteria whose 16S rRNA gene sequences have been reported. Fatty acid composition of the strain B2 was analyzed and its major fatty acids are summed feature 3(C_16:1 ω7c and/or C_16:1 ω6c, 22.8%), iso-C_15:0 (16.2%), anteiso-C_15:0(12.9%), C_16:1ω5c(12.4%) and summed feature 4 (iso-C_17:1 I/anteiso-C_17:1)(9.5%) showing significant differences in fatty acid compositions between strain B2 and the other known Hymenobacter species. DNA sequence of 16S rRNA gene of strain B2 was deposited in genbank under accession number OQ318247.

• Molecules and Cells
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• v.25 no.1
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• pp.78-85
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• 2008

In a search for new molecular pathways associated with asthma, we performed an mRNA differential display analysis using total RNA extracted from the tracheal tissues of ovalbumin (OVA)-challenged mice and sham controls. cDNAs corresponding to mRNAs for which expression levels were altered by OVA-challenge were isolate and sequenced. Twenty-eight genes differentially expressed in sham and OVA challenged mice were identified. A GenBank BLAST homology search revealed that they were related to cytoskeleton remodeling, transcription, protein synthesis and modification, energy production, and cell growth and differentiation. Two were selected for further characterization. Up-regulation of both the perinatal skeletal myosin heavy chain (skMHC) and fast skeletal muscle myosin light chain (skMLC) genes was confirmed by RT-PCR of trachea tissue from OVA challenged mice. Overexpression of skMLC protein was observed in the smooth muscle layers of OVA-challenged mice by immunohistochemistry, and the surface areas stained with skMLC antibody increased in the OVA-challenged mice. The overexpression of skMLC in murine asthma may be associated with the changes of bronchial smooth muscle.

• Tuberculosis and Respiratory Diseases
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• v.69 no.5
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• pp.331-336
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• 2010

Background: Recently, the rate of infections with non-tuberculous mycobacteria (NTM) has been increasing in Korea. Precise identification of NTM is critical to determination of the pathogen and to target treatment of NTM patients. Methods: Sixty-eight unclassified mycobacteria isolates by rpoB PCR-RFLP assay (PRA) collected in 2008 were analyzed by National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) search after sequencing of 16S rRNA, hsp65, rpoB genes. Results: Nineteen strains of 68 isolates were specified as species after sequencing analysis of 3 gene types. We found 3 M. lentifulavum, 5 M. arupense, 4 M. triviale, 4 M. parascrofulaceum, and one M. obuense. One M. tuberculosis and another M. peregrinum were mutated at the Msp I recognition site needed for rpoB PRA. The remaining 49 isolates did not coincide with identical species at the 3 kinds genes. Conclusion: Sequencing analysis of 16S rRNA, hsp65, rpoB was useful for identification of NTM unclassified by rpoB PRA.

• Animal cells and systems
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• v.14 no.1
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• pp.25-30
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• 2010

We employed a new and improved differential display reverse transcription-polymerase chain reaction (DDRT-PCR) method, which involves annealing control primers (ACPs), to identify the genes that are specifically or prominently expressed in olive flounder (Paralichthys olivaceus) juveniles (35 days post-hatch; dph) compared to larval-stage (dph 21) flounder. Using 60 ACPs, we identified eight differentially expressed genes (DEGs) and basic local alignment search tool (BLAST) searches revealed eight known genes. Gene expression levels were confirmed by RT-PCR. Phosphoglucose isomerase (PGI) was highly expressed at 21 dph, while nephrosin, myosin light chain (MLC), myosin heavy chain (MHC), carboxypeptidase A, chymotrypsin B, fish-egg protein, and matrix protein were expressed at 35 dph. PGI, MLC, and MHC expression was further analyzed by RT-PCR. The differentially expressed genes identified in this study may provide insights into the molecular basis of development in olive flounder.