• Journal of Microbiology
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• v.38 no.2
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• pp.66-73
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• 2000

To investigate the genetic relationship among 12 species belonging to the Fusarium section Martiella, Dlaminia, Gibbosum, Arthrosporiella, Liseola and Elegans, the internal transcribed spacer(ITS) regions of ribosomal DNA (rDNA) were amplified with primer pITS1 and pITS4 using the polymerase chain reaction(PCR). After the amplified products were digested with 7 restriction enzymes, restriction fragment length polymorphism (RFLP) patterns were analyzed. The partial nucleotide sequences of the ITS region were determined and compared. Little variation was observed in the size of the amplified product having sizes of 550bp or 570bp. Based on the RFLP analysis, the 12 species studied were divided into 5 RFLP types. In particular, strains belonging to the section Martiella were separated into three RFLP types. Interestingly, the RFLP type of F. solani f. sp. piperis was identical with that of isolates belonging to the section Elegans. In the dendrogram derived from RFLP analysis of the ITS region, the Fusarium spp. examined were divided into two major groups. In general, section Martiella excluding F. solani f. sp. piperis showed relatively low similarity with the other section. The dendrogram based on the sequencing analysis of the ITS2 region also gave the same results as that of the RFLP analysis. As expected, 5.8S, a coding region, was highly conserved, whereas the ITS2 region was more variable and informative. The difference in the ITS2 region between the length of F. solani and its formae speciales excluding F. solani f. sp. piperis and that of other species was caused by the insertion/deletion of nucleotides in positions 143-148 and 179-192.

• KSBB Journal
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• v.18 no.1
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• pp.39-44
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• 2003

A Gene content phylogenetic tree and a 16s rRNA based phylogenetic tree were compared for 33 whole-genome sequenced procaryotes, neighbor joining and bootstrap methods (n=1,000). Ratio of conserved COG (clusters of orthologous groups of proteins) to orthologs revealed that they were within the range of 4.60% (Mezorhizobium loti) or 56.57% (Mycopiasma genitalium). This meant that the ratio was diverse among analyzed procaryotes and indicated the possibility of searching for useful genes. Over 20% of orthologs were independent among the same species. The gene content tree and the 16s rDNA tree showed coincidence and discordance in Archaeabacteria, Proteobacteria and Firmicutes. This might have resulted from non-conservative genes in the gene content phylogenetic tree and horizontal gene transfer. The COG based gene content tree could be regarded as a midway phylogeny based on biochemical tests and nucleotide sequences.

• Environmental Analysis Health and Toxicology
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• v.26
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• pp.5.1-5.11
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• 2011

Objectives: In order to identify the possibility of slender bitterling (SB) (Acheilognathus yamatsutae) being used as a test species for estrogenic endocrine disrupting chemicals (EEDCs), we carried out the cloning and sequence characterization of the estrogen receptor (ER). Methods: The ER from a slender bitterling was obtained by reverse transcriptase-polymerase chain reaction (RT-PCR), 5'- and 3'-rapid amplification of cDNA ends (5'-RACE and 3'-RACE) and T-vector cloning. The expression of ER mRNA was also analyzed in six tissues (brain, liver, kidney, gill, gonad, and intestines) by real-time PCR. Results: We obtained an ER from the slender bitterling. The SB ER cDNA was 2189 base pairs (bp) in length and contained a 1707 bp open reading frame that encoded 568 amino acid residues. The SB ER amino acid sequence clustered in a monophyletic group with the $ER{\alpha}$ of other fish, and was more closely related to zebrafish $ER{\alpha}$(88% identity) than to the $ER{\alpha}$ of other fish. The SB ER cDNA was divided into A/B, C, D, E and F domains. The SB ER has conserved important sequences for ER functions, such as the DNA binding domain (D domain), which are consistent with those of other teleosts. Conclusions: The ER of the slender bitterling could provide basic information in toxicological studies of EEDCs in the slender bitterling.

• Mycobiology
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• v.48 no.5
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• pp.351-363
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• 2020

Here, we investigated fungal microbiota in the understory root layer of representative well-conserved geographically segregated natural wetlands in the Korean Peninsula. We obtained 574,143 quality fungal sequences in total from soil samples in three wetlands, which were classified into 563 operational taxonomic units (OTU), 5 phyla, 84 genera. Soil texture, total nitrogen, organic carbon, pH, and electrical conductivity of soil were variable between geographical sites. We found significant differences in fungal phyla distribution and ratio, as well as genera variation and richness between the wetlands. Diversity was greater in the Jangdo islands wetland than in the other sites (Chao richness/Shannon/Simpson's for wetland of the Jangdo islands: 283/6.45/0.97 > wetland of the Mt. Gariwang primeval forest: 169/1.17/0.22 > wetland of the Hanbando geology: 145/4.85/0.91), and this variance corresponded to the confirmed number of fungal genera or OTUs (wetlands of Jangdo islands: 42/283> of Mt. Gariwang primeval forest: 32/169> of the Hanbando geology: 25/145). To assess the uniqueness of the understory root layer fungus taxa, we analyzed fungal genera distribution. We found that the percentage of fungal genera common to two or three wetland sites was relatively low at 32.3%, while fungal genera unique to each wetland site was 67.7% of the total number of identified fungal species. The Jangdo island wetland had higher fungal diversity than did the other sites and showed the highest level of uniqueness among fungal genera (Is. Jangdo wetland: 34.5% > wetland of Mt. Gariwang primeval forest: 28.6% > wetland of the Hanbando geology: 16.7%).

• Mycobiology
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• v.36 no.3
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• pp.161-166
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• 2008

The retrotransposon marY1 is a gypsy family retroelement, which is detected ubiquitously within the fungal taxonomic groups in which mushrooms are included. To utilize marY1 as a molecular marker for the DNA fingerprinting of mushrooms, oligonucleotides marY1-LTR-L and marY1-LTR-R were designed on the basis of highly conserved regions from the multiple sequence alignment of 30 marY1 sequences retrieved from a nucleotide sequence database. In accordance with $\underline{Re}trotransposon$ $\underline{M}icrosatellite$ $\underline{A}mplified$ $\underline{P}olymorphism$ (REMAP) fingerprinting methodology, the two oligonucleotides were utilized together with the short sequence repeat primers UBC807 and UBC818 for polymerase chain reaction using templates from different mushroom genomic DNAs. Among the tested oligonucleotides, the marY1-LTR-L and UBC807 primer set yielded the greatest amount of abundance and variation in terms of DNA band numbers and patterns. This method was successfully applied to 10 mushroom species, and the primer set successfully discriminated between different commercial mushroom cultivars of the same strains of 14 Pleurotus ostreatus and 16 P. eryngii. REMAP reproducibility was superior to other popular DNA fingerprinting methodologies including the random amplified polymorphic DNA method.

• Journal of Plant Biotechnology
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• v.47 no.1
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• pp.15-25
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• 2020

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima's D and -1.19 for Fu's Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

• Journal of fish pathology
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• v.23 no.2
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• pp.177-187
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• 2010

The Interferon stimulated gene 15 (ISG15) is strongly induced in many cell types by IFNs, viral infections, and double-stranded RNA (poly I:C). The ISG15 homologue cDNA was isolated from the rock bream LPS stimulated leukocyte cDNA library. The rock bream ISG15 homologue was found to consist of 833 bp encoding 157 amino acid residues. Compared with other known ISG15 peptide sequences, the most conserved regions of the rock bream ISG15 peptide were found to be the tandem ubiquitin-like domains and a C-terminal LRLRGG conjugating motif, characteristic of mammalian and non-mammalian ISG15 proteins. Phylogenetic analysis based on the deduced amino acid sequence revealed a homologous relationship between the ISG15 sequence of rock bream and that of Atlantic salmon, Atlantic cod, northern snake head, black rockfish and olive flounder. The expression of the rock bream ISG15 molecule was induced in the peripheral blood leukocytes (PBLs) from 1 to 24 h following poly I:C stimulation, with a peak at 3 h post-stimulation. The rock bream ISG15 gene was predominantly expressed in the PBLs, spleen and gill.

• Journal of fish pathology
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• v.23 no.3
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• pp.323-334
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• 2010

Bactericidal/permeability-increasing protein (BPI) and lipopolysaccharide-binding protein (LBP) are important components of the mammalian innate defence system against Gram-negative infections. The BPI/LBP cDNA was identified from the black rockfish ConA/PMA or LPS stimulated leukocyte cDNA library. The full-length BR-BPI/LBP cDNA was 2118 bp long and contained an open reading frame (ORF) of 1422 bp that encoded 473 amino-acid residues. The 5' UTR had a length of 57 bp, and the 3' UTR 639 bp. The molecular weight and theoretical isoelectric point (pI) values were calculated 51.4 kDa and 9.72, respectively. Compared with other known BPI or BPI/LBP peptide sequences, the most conserved regions of the black rockfish BPI/LBP peptide were found to be the BPI1 N-terminal, BPI2 C-terminal domains and a LPS binding domain. Phylogenetic analysis based on the deduced amino acid sequence revealed a homologous relationship between the BPI/LBP sequence of black rockfish and that of other teleosts. The black rockfish BPI/LBP gene was predominantly expressed in the PBLs, head kidney, trunk kidney and spleen. The expression of the black rockfish BPI/LBP molecule was induced in the peripheral blood leukocytes (PBLs) from 1 to 24 h following LPS stimulation, with a peak at 12 h post-stimulation.

• BMB Reports
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• v.52 no.11
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• pp.653-658
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• 2019

MYB-type transcription factors (TFs) play important roles in plant growth and development, and in the rapid responses to unfavorable environmental conditions. We recently reported the isolation and characterization of a rice (Oryza sativa) MYB TF, OsMYB102, which is involved in the regulation of leaf senescence by downregulating abscisic acid (ABA) biosynthesis and the downstream signaling response. Based on the similarities of their sequences and expression patterns, OsMYB102 appears to be a homolog of the Arabidopsis thaliana AtMYB44 TF. Since AtMYB44 is a key regulator of leaf senescence and abiotic stress responses, it is important to examine whether AtMYB44 homologs in other plants also act similarly. Here, we generated transgenic Arabidopsis plants expressing OsMYB102 (OsMYB102-OX). The OsMYB102-OX plants showed a delayed senescence phenotype during dark incubation and were more susceptible to salt and drought stresses, considerably similar to Arabidopsis plants overexpressing AtMYB44. Real-time quantitative PCR (RT-qPCR) revealed that, in addition to known senescence-associated genes, genes encoding the ABA catabolic enzymes AtCYP707A3 and AtCYP707A4 were also significantly upregulated in OsMYB102-OX, leading to a significant decrease in ABA accumulation. Furthermore, protoplast transient expression and chromatin immunoprecipitation assays revealed that OsMYB102 directly activated AtCYP707A3 expression. Based on our findings, it is probable that the regulatory functions of AtMYB44 homologs in plants are highly conserved and they have vital roles in leaf senescence and the abiotic stress responses.

• Molecules and Cells
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• v.44 no.9
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• pp.637-646
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• 2021

Free fatty acids are converted to acyl-CoA by long-chain acyl-CoA synthetases (ACSLs) before entering into metabolic pathways for lipid biosynthesis or degradation. ACSL family members have highly conserved amino acid sequences except for their N-terminal regions. Several reports have shown that ACSL1, among the ACSLs, is located in mitochondria and mainly leads fatty acids to the β-oxidation pathway in various cell types. In this study, we investigated how ACSL1 was localized in mitochondria and whether ACSL1 overexpression affected fatty acid oxidation (FAO) rates in C2C12 myotubes. We generated an ACSL1 mutant in which the N-terminal 100 amino acids were deleted and compared its localization and function with those of the ACSL1 wild type. We found that ACSL1 adjoined the outer membrane of mitochondria through interaction of its N-terminal region with carnitine palmitoyltransferase-1b (CPT1b) in C2C12 myotubes. In addition, overexpressed ACSL1, but not the ACSL1 mutant, increased FAO, and ameliorated palmitate-induced insulin resistance in C2C12 myotubes. These results suggested that targeting of ACSL1 to mitochondria is essential in increasing FAO in myotubes, which can reduce insulin resistance in obesity and related metabolic disorders.