• 한국미생물·생명공학회지
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• 제18권3호
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• pp.309-316
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• 1990

Bacillus circulans F-2의 생산하는 NaCl 의존성 amylase(NaCl-dependent amylase) 유전자를 함유하는 1795bp의 DNA 염기배열을 결정하였다. 본 유전자의 ORF는 총염기수 1005bp(335 아미노산)로 구성되며, 분자량 38,006의 amylase의 분자량 약 35,000과 일치하였다. 본 유전자의 상류영역(upstream region)에는 고초균(Bacillus subtiis)의 전형적인 전사발현영역(transcriptional region)과 상보적인 DNA역역이 존재하였다. 성숙단백질의 N-말단측 아미노산 배열은 Ala-Ser-Lys-Val-Gly이며, 분비에 필요한 20개의 signal 아미노산 배열을 갖는 전형적인 분비 단백질임이 확인 되었다. 한편 다른 amylase들과 비교결과, smylase 활성발현과 밀접히 관련되 있는 4개 부위의 상보성영역(homologous region)을 가지고 있었다.

• Mycobiology
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• 제38권2호
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• pp.89-96
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• 2010

This study evaluated the optimal vegetative growth conditions and molecular phylogenetic relationships of eleven strains of Agrocybe cylindracea collected from different ecological regions of Korea, China and Taiwan. The optimal temperature and pH for mycelial growth were observed at $25^{\circ}C$ and 6. Potato dextrose agar and Hennerberg were the favorable media for vegetative growth, whereas glucose tryptone was unfavorable. Dextrin, maltose, and fructose were the most effective carbon sources. The most suitable nitrogen sources were arginine and glycine, whereas methionine, alanine, histidine, and urea were least effective for the mycelial propagation of A. cylindracea. The internal transcribed spacer (ITS) regions of rDNA were amplified using PCR. The sequence of ITS2 was more variable than that of ITS1, while the 5.8S sequences were identical. The reciprocal homologies of the ITS sequences ranged from 98 to 100%. The strains were also analyzed by random amplification of polymorphic DNA (RAPD) using 20 arbitrary primers. Fifteen primers efficiently amplified the genomic DNA. The average number of polymorphic bands observed per primer was 3.8. The numbers of amplified bands varied based on the primers and strains, with polymorphic fragments ranging from 0.1 to 2.9 kb. The results of RAPD analysis were similar to the ITS region sequences. The results revealed that RAPD and ITS techniques were well suited for detecting the genetic diversity of all A. cylindracea strains tested.

• ALGAE
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• 제22권3호
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• pp.221-228
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• 2007

Frequent occurrences of green tides caused by Ulva species (Ulvales, Ulvophyceae) associated with eutrophication along enclosed coasts are currently causing environmental problems in coastal ecosystems. In addition, increasing intercontinental introductions of coastal marine organisms, including Ulva, are also a serious issue. However, due to the considerable morphological plasticity of this genus, the taxonomy of Ulva species based on morphological studies is problematic. Therefore, in order to elucidate the species diversity and seasonal changes of the dominant Ulva species in Mikawa Bay, central Honshu, Japan, we made seasonal collections of Ulva species at seven localities, and identified the dominant species using the ITS2 rDNA region sequences. We identified the following nine taxa as common Ulva species in the area: 1) Ulva pertusa Kjellman; 2) U. ohnoi Hiraoka et Shimada; 3) U. linza L.; 4) U. californica Wille; 5) U. flexuosa Wulfen; 6) U. fasciata Delile; 7) U. compressa L.; 8) U. armoricana Dion et al.; 9) U. scandinavica Bliding. Among the species, U. pertusa was most common and dominant from spring to summer, and U. ohnoi from autumn to winter. Ulva californica and U. scandinavica have not been reported before from Japan.

• Journal of Microbiology
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• 제38권2호
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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.

• 한국식물병리학회지
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• 제14권4호
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• pp.350-357
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• 1998

A total of 12 strains of fluorescent Pseudomonas isolated from the cultivated mushrooms such as Agaricus bisporus and Pleurotus ostreatus were collected. They consisted of pathogenic Pseudomonas spp. and epiphytic Pseudomonas spp. of the cultivated mushroom. To analyze the phylogenetic relationship of these strains, ITS I region, the 16S-23S intergenic spacer region in the ribosomal RNA (rRNA) operon, was cloned and sequenced. The spacer regions of these strains were 495∼527 nucleotides in length and contained the genes encoding isoleucine-tRNA (tRNAIle) and alanine-tRNA (tRNAAla). The reciprocal homologies of each ITS I sequence among these strains were in the range of 84.2%∼98.8%. According to the analysis of ITS I sequences, the fluorescent Pseudomonas spp. were phylogenetically classified into three clusters. Cluster I consisted of Pseudomonas fluorescens, P. tolaasii, P. gingeri’, and P.‘reactans’(WLRO). Cluster II comprised Pseudomonas fluorescens biovar C and F. Cluster III composed P. agarici. Cluster I and II could be classified into P. fluorescens complex. P. agarici formed an independent taxon clearly separable from P. florescens complex.

• 한국균학회지
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• 제50권4호
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• pp.373-381
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• 2022

Strain E4, an unrecorded species of dimorphic fungi, was isolated from the gut of earthworms collected in Gyeonggi Province, South Korea. Nucleotide sequence analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region revealed that this species is a member of the genus Blastobotrys, Blastobotrys illinoisensis. Strain E4 differed from its closest known species, B. mokoenaii and B. malaysiensis, by harboring 3-5 and 12-14 nucleotide substitutions in the D1/D2 and ITS regions, respectively. Phylogenetic analysis based on concatenated sequences of the D1/D2 region of the LSU rRNA gene and the ITS region also indicated that strain E4 belongs to the Blastobotrys clade and is distinct from other related species in the clade. The previously unreported isolate could be distinguished from closely related species by its inability to ferment carbon sources. To our knowledge, this is the first report on the isolation of Blastobotrys species from the gut of earthworms in Korea. The strain used was E4 (=KCTC 27831=JCM 33428).

• Asian-Australasian Journal of Animal Sciences
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• 제31권3호
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• pp.449-456
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• 2018

Objective: Nanog, a homeodomain protein, has been investigated in humans and mice using embryonic stem cells (ESCs). Because of the limited availability of ESCs, few studies have reported the function and role of Nanog in porcine ESCs. Therefore, in this study, we investigated the location of the porcine Nanog chromosome and its basal promoter activity, which might have potential applications in development of ESCs specific marker as well as understanding its operating systems in the porcine. Methods: To characterize the porcine Nanog promoter, the 5'-flanking region of Nanog was isolated from cells of mini-pig ears. BLAST database search showed that there are two porcine Nanog genomic loci, chromosome 1 and 5, both of which contain an exon with a start codon. Deletion mutants from the 5'-flanking region of both loci were measured using the Dual-Luciferase Reporter Assay System, and a fluorescence marker, green fluorescence protein. Results: Promoter activity was detected in the sequences of chromosome 5, but not in those of chromosome 1. We identified the sequences from -99 to +194 that possessed promoter activity and contained transcription factor binding sites from deletion fragment analysis. Among the transcription factor binding sites, a Sp1 was found to play a crucial role in basal promoter activity, and point mutation of this site abolished its activity, confirming its role in promoter activity. Furthermore, gel shift analysis and chromatin immunoprecipitation analysis confirmed that Sp1 transcription factor binds to the Sp1 binding site in the porcine Nanog promoter. Taken together, these results show that Sp1 transcription factor is an essential element for porcine Nanog basal activity the same as in human and mouse. Conclusion: We showed that the porcine Nanog gene is located on porcine chromosome 5 and its basal transcriptional activity is controlled by Sp1 transcription factor.

• Archives of Pharmacal Research
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• 제21권1호
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• pp.35-40
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• 1998

Human cytochrome P450 4F2 shows high regioselectivity in hydroxylation of stearic acid and leukotriene $ B_4.$ As a first step of its regulation study, human cytochrome P450 4F2 genomic DNA was isolated from liver of a person who was administered clofibrate for 10 years. From Southern hybridization, restriction enzyme digestion and sequencing experiments, isolated genomic DNA fragment was found to contain around 32 Kb DNA and more than 20 Kb of $5^I$ end regulatory region. Sequences of the structural gene region revealed exon 1 and exon 2. Further regulation studies would elucidate the feedback mechanisms of the oxidative degradation of fatty acids, inflammatory response and the clearance of leukotriene B4 in the liver. Furthermore, regulation study of this gene could explain the species difference in responses to peroxisome proliferator and help in the safety evaluation of peroxisome proliferating chemicals to human being.

• 한국자원식물학회지
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• 제25권6호
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• pp.753-761
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• 2012

We performed phylogenetic analyses of a total of 21 acessions covering 5 species in the Korean Trigonotis and one outgroup species using nuclear ribosomal ITS and chloroplast rbcL, matK, ndhF sequences. Outgroup were chosen from the closely related genus Lithospermum zollingeri. Both parsimony and Bayesian Inference methods were used to reconstruct the evolutionary history of the group. The evidence collected indicated that phylogenetic relationships among Korean Trigonotis species are unresolved based on nuclear marker (ITS), as the same as based on separated chloroplast sequences. While the phylogenetic relationships of Korean Trigonotis species almost clearly were resolved in combined chloroplast sequences. Thus, the members of Trigonotis coreana can be distinguished to the members of Trigonotis peduncularis in combined cpDNA sequences and Trigonotis nakaii was treated as a synonymed to Trigonotis radicans var. sericea. In addition, the MP and BI analysis showed Trigonotis icumae as sister of the remained Korean Trigonotis species based on combined molecular markers (BI: PP = 1).

• 한국균학회소식:학술대회논문집
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• 한국균학회 2014년도 춘계학술대회 및 임시총회
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• pp.45-45
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• 2014

Individualities of precious health mushroom called Zhenghonggu@ from respective protections scattered among all main mountains of Fujian China were collected and recognized locally, then compared with Russula griseocarnosa. Their internal transcribed spacer (ITS) region (ITS1, ITS2 and 5.8S rDNA) of the nuclear rDNA were amplified, AMOVA analyzed, nested clade analyzed and then compared with the ITS sequences of relative Russula species from other regions of China to confirm the taxonomic status of Zhenghonggu$^@$ and its population structure. Total 23 haplotypes from different protections of Fujian can be clustered into three clades similar to the three lineages of Dahongjun$^@$ from southeastern China reported by Li et al. The geographic distribution characteristic of these three phylogeny clades may be closely coupled with the vegetation regionalization and/or the differences of coenosium construction of Fagaceae that is the host of Russula griseocarnosa. The correlation of taxonomy, phylogeny and geographical distribution of Russula are discussed.