• Title/Summary/Keyword: rDNA ITS region

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Behavior in Solution and Mixing Ratio-Dependent Binding Modes of Carcinogenic Benzo[a]pyrene-7,8-dione to Calf Thymus DNA

  • Jin, Biao;Han, Sung Wook;Lee, Dong Jin
    • Bulletin of the Korean Chemical Society
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    • v.35 no.10
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    • pp.3015-3020
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    • 2014
  • The behavior of benzo[a]pyrene-7,8-dione (BPQ) in aqueous solution and its interaction with native DNA was investigated using conventional absorption and linear dichroism (LD) spectroscopy. The appearance of a broad absorption maximum at long wavelengths and its proportional relationship to solvent polarizability suggested that BPQ adopts a aggregated state for all solutions examined. Disappearance of this absorption band at higher temperatures in aqueous solution also supported BPQ aggregation. When associated with DNA absorption spectral properties were essentially the same as that in aqueous solution. However, two isosbestic wavelengths were found in the concentration-dependent absorption spectrum of the BPQ-DNA complex, suggesting the presence of at least two or more DNA-bound BPQ species. Both species produced $LD^r$ spectra whose magnitude in BPQ absorption region is larger or comparable to that in the DNA absorption region, suggesting that the molecular BPQ plane is near perpendicular relative to the local DNA helical axis. Therefore, BPQ molecules are aligned along the DNA stem in both DNA-aggregated BPQ species.

Leaf variants of Pinus and their ITS DNA sequences (소나무속 잎 변이와 그의 ITS DNA 염기서열)

  • Koo, JaChoon;Whang, Sung Soo
    • Korean Journal of Plant Taxonomy
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    • v.43 no.1
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    • pp.63-68
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    • 2013
  • ITS DNA sequences of two variants of Pinus spp. having single fasciculate leaf or two to three fasciculate leaves within an individual were analysed in order to determine their origin. Also, the same DNA locus of P. densiflora, P. rigida and P. koraiensis, distributed at the same region together with the OTUs having leaf variations, were analysed to compare with each other. Aligned sequences including ITS1, 5.8S and ITS2 were 580~584 bp in length. The 5.8S region was well conserved among all the OTUs we tested except for P. koraiensis, which has two nucleotide substitutions. The partial ITS1 region upstream of the 5.8S region showed relatively high sequence diversity compare to the ITS2 and has 181~185 bp in length. In this region, the sequences of the two variants were identical to that of P. densiflora. The ITS2 has identical for all OTUs in length and the two variants also have same sequences compare to that of P. densiflora. These two variants and samples of P. densiflora were grouped together in the UPGMA tree with 100% similarity level. The result strongly suggest that these two variants were originated from P. densiflora.

Analysis of rDNA ITS Region from Trametes spp. in Kangwon Province, Korea (강원도 지역 구름버섯균의 rDNA의 ITS 부위 염기서열 분석)

  • Lee, Mi-Jeong;Jun, Sang-Cheol;Hwang, Il-Ki;Choi, Han-Ku;Kim, Kyu-Joong
    • The Korean Journal of Mycology
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    • v.33 no.1
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    • pp.1-10
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    • 2005
  • Nineteen strains of Trametes species were collected from the area of Kangwon Province, Korea. They have a variety of color hands and line-up markings on fruit bodies. Most strains were categorized into four types based on color bands, that is, dark brown, light brown, dark gray and light gray. They also have line-up marking shapes from sparse to compact on fruit bodies. In this study, we tried to investigate the relationship between the genetic variation and morphological appearance of these species using the nuclear ribosomal ITS1-5.8S-ITS2 region sequence, we used nineteen strains collected in nature and four species of five standard strains (T. versicolor KCTC16781, KCTC26203, T. villosa KCTC06866, T. suaveolens KCTC26205 and T. hirusta KCTC26200). The data of ITS sequences indicated that nineteen strains of T. versicolor have the difference of $1{\sim}6$ base pairs, comparing with standard strains of T. versicolor KCTC16781, and KCTC26203. Phylogenetic analysis of the Trametes species showed that they grouped into a wide range of single clade. Standard strains except T. versicolor KCTC16781 and KCTC26203, formed separated subgroup.

Phylogeny of Korean Rhus spp. Based on ITS and rbcL Sequences (ITS 및 rbcL 염기서열에 근거한 한국 자생 옻나무속의 계통분류)

  • Lee, Won-Kyung;Kim, Myong-Jo;Heo, Kweon
    • Korean Journal of Medicinal Crop Science
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    • v.12 no.1
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    • pp.60-66
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    • 2004
  • This study was carried out to confirm the phylogenetic relationships in Korean Rhus species. Sequences from internal transcribed spacers (ITS) of nuclear ribosomal DNA and rbcL gene of chloroplast DNA were determined. Cotinus coggygria was selected as outgroup because it is closest allied with Rhus in Anacardiaceae. Also, ingroup was limited as six Korean Rhus species. ITS 1 sequences in six species of Rhus and one species of Cotinus ranged from 246 to 253 bp and ITS 2 sequences from 234 to 244 bp. Concerning the G+C content of the studied taxa, ITS 1 sequences ranged from 58.0 to 68.13% and ITS 2 from 59.75 to 68.46%. On the other hand, rbcL sequences were same size in the all species examined by 1,428 bp. G+C contents of rbcL sequences were ranged from 43.56 to 43.77% which means there are nearly no different from interspecies each other. Phylogenetic tree strongly supports the colse relationships between R. succedanea and R. sylvestris. Rhus javanica and Cotinus coggygria were also closely allied with each other in ITS and rbcL trees. Therefore, R. javanica was regarded as most primitive species among the Korean Rhus species. ITS 1 region of nuclear ribosomal DNA was suggested as very useful taxonomical marker for genus Rhus.

Phylogenetic Analysis of Agaricus blazei and Related Taxa by Comparing the Sequences of Internal Transcribed Spacers and 5.8S rDNA (Internal Transcribed Spacer와 5.8S ribosomal DNA의 염기서열 분석에 의한 Agaricus blazei와 근연종에 대한 계통분류학적인 연구)

  • 김기영;하명규;이태호;이재동
    • Korean Journal of Microbiology
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    • v.35 no.3
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    • pp.180-184
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    • 1999
  • Molecular spslemaucs of Agaricus species was investigated on the base of the sequences of the internal transcribed spaceriITS) regions in ribosomal DNA (rDNA). The sequences of the ITS region in 5 species and two group of Agaricus genus were resolved. In the phylogenetic trees. the species generally divided inlo two subclusters, refered to here as the group I and group 11. The group I consisted of Agaricus blazei ATCC 76739, Agarictrs blazei species cultivated in Korean hmings. Ago/-icus anmensis IMSNU 32049 and Agaricus can~pestris VPI-OKM 25665. Between Agaricus blazei NCC 76739 and the Agaricus blazei species cultivated in Korean farmings had the variation in lhe 5 nucleotide on the ITS regions. These varieties were presumed the variation by the geographic and cultivated conditions. In addition the subgroup of group I was formed by Agaricus arvensis LMSNU 32049 and Agaricus carnpests VPI-OKM 25665. The group IT included Agnrictrs bispoms CH 3004 and Agaricus pocillotor DUKE-J 173.

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miR-7b Promoter Contains Negative Gene Elements (네거티브 유전자 조절인자를 포함하는 마이크로RNA, miR-7b의 프로모터)

  • Choi, Ji-Woong;Lee, Heon-Jin
    • Journal of Life Science
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    • v.21 no.12
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    • pp.1784-1788
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    • 2011
  • The typical miRNA and its nearby host gene are co-expressed by sharing the same promoter. We assumed that miR-7b and its host gene FICT might use an identical promoter for their brain specific gene expression. Sequence comparison of the genomic DNA of mouse miR-7b, human miR-7-3 and their host genes by using the bioinformatic tools revealed high sequence homology and several putative transcription factor-binding sites on the promoter region. In order to probe the hypothesis we used a luciferase vector system into which we cloned the 5' upstream conserved region of miR-7b and FICT. The putative promoter region showed decreased luciferase activity, suggesting that the 5' upstream of miR-7b and FICT contain a negative regulator for gene expression.

Sequence Analysis of Nuclear 18S rDNA from Porphya tenera (Rhodophyta) in Korea (한국산 참김 (Porphya tenera)의 핵 18S rDNA염기서열 분석)

  • JIN Long-Guo;KIM Myung-Sook;CHOI Jae-Suk;CHO Ji-Young;JIN Duck-Hee;HONG Yong-Ki
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.36 no.1
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    • pp.35-38
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    • 2003
  • Nuclear 18S ribosomal RNA gene (185 rDNA) from the aquaculturable seaweed Porphya tenera (Bangiales, Rhodophyta) was amplified using the polymerase chain reaction and its sequence was analysed. Complete 185 rDNA has an 1,822 bp exon and a 510 bp intron. The G+C contents of exon and intron were $48.68\%\;and\;54,90\%,$ respectively. The exon sequence showed $99.6\%$ homology to the GebBank accession number AB029880 of the Japanese P. tenera. The intron region that is inserted upstream between 568 and 1,079 showed $43.6\%$ homology to the AB029880.

Analysis of Morphological and Genetic Relationships amomg Isolates of the Artificially Cultivated Mushroom, Hypsizygusmarmoreus (느티만가닥버섯 균주의 형태 및 유전적 유연관계 분석)

  • Kim, Min-Kyung
    • The Korean Journal of Mycology
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    • v.48 no.3
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    • pp.313-323
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    • 2020
  • To investigate the morphological characteristics and genetic relationships among isolate of the artificially cultivated mushroom Hypsizygus marmoreus, 111 isolates were collected from Korea and other countries. Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) and ITS rDNA sequencing were used to confirm the genetic relationships among the collected H. marmoreus isolates. As a result of RAPD analysis using universal rice primer (URP)-PCR, all isolates of H. marmoreus clustered into three groups, which showed high sequence similarity (>90%). In addition, isolates with morphological and geographical differences formed independent clusters. However, it was impossible to distinguish between brown and white strains. Sixteen strains showing morphological and geographic differences were selected, and their ITS region sequences (640 bp) were aligned and compared. The ITS region sequences belonging to these isolates showed 94.8-99.1% similarities to those of publicly available H. marmoreus strains in GenBank. In conclusion, there were differences among isolates in terms of morphology and the area from which they were collected, but all the isolates used in the experiment were classified as H. marmoreus.

Phylogenetic relationships of genera Grifola on the basis of ITS region sequences (rDNA의 ITS 부위 염기서열 분석에 의한 잎새버섯(Grifola)속 균주의 유전적인 유연관계 분석)

  • Lee, Chan-Jung;Jhune, Chang-Sung;Cheong, Jong-Chun;Kong, Won-Sik;Suh, Jang-Sun
    • Journal of Mushroom
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    • v.10 no.2
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    • pp.93-99
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    • 2012
  • This study was carried to identify a correct species and asses genetic diversity within the same species of Grifola spp. preserved in Division of applied Microbiology. Contaminated isolates showed different growth rates, morphology and color of hyphae. We have reconstructed the phylogenetic tree of a select group of Grifola spp. using nucleotide sequences of the internal transcribed spacer region(ITS) region. The phylogenetic tree was constructed by using the neighbor-joining method. PELF primers of 20-mer were used to assess genetic diversity of preserved isolates. Sequence analysis showed that four strains were identified completely different nomenclature. According to the analysis of ITS sequences, the genus Grifola clustered into one group, most of which correlated with species-groups identified by RAPD method. Eight isolates included strain GM01 showed high similarity with Grifola frondosa. All isolates were collected in the Japan(GM01, GM02, GM03) was identified as Grifola frondosa and isolates of the China(GM05, GM06, GM08) was identified as Bjerkandera fumosa, Grifola frondosa and Dichomitus squalens, respectively. RAPD analysis of genetic polymorphisms of genus Grifola showed a very different band patterns on the isolat. As the result of RAPD and ITS region sequences analysis for preserved isolates, it seems likely that 4 isolates of Grifola spp. may be need to reclassify or eliminate from preserved catalogue.

Phylogenetic relationships of genera Trametes on the basis of ITS region sequences (rDNA의 ITS 부위 염기서열 분석에 의한 구름버섯 균주의 유전적인 유연관계 분석)

  • Lee, Chan-Jung;Jhune, Chang-Sung;Cheong, Jong-Chun;Oh, Jin-A;Han, Hye-Su;Um, Na-Na
    • Journal of Mushroom
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    • v.9 no.1
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    • pp.27-33
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    • 2011
  • This study was carried to identify a correct species and asses genetic diversity within the same species of Trametes spp. preserved in Division of applied Microbiology The morphological and cultural characteristics of preserved strains were observed through microscope and investigated on PDA, respectively. Contaminated isolates showed different growth rates, morphology and color of hyphae. We have reconstructed the phylogenetic tree of a select group of Trametes spp. using nucleotide sequences of the internal transcribed spacer region(ITS) region. The phylogenetic tree was constructed by using the neighbor-joining method. PELF primers of 20-mer were used to assess genetic diversity of preserved isolates. Sequence analysis showed that five strains were different species and six strains were identified completely different nomenclature. According to the analysis of ITS sequences, the genus Trametes clustered into four distinct group, most of which correlated with species-groups identified by RAPD method. Seven isolates included TM 01 strain showed high similarity with Trametes versicolr, TM 07 and TM 10 high similarity with Trametes gibbosa, and TM 05 high similarity with Trametes elegans. But isolates collected in the United States was identified as T. junipericola. T. gibbosa and T. versicolor by RAPD analysis of genetic polymorphisms showed a very different band patterns and these strains showed different band patterns on areas. As the result of RAPD and ITS region sequences analysis for preserved isolates, it seems likely that 11 isolates of Trametes spp. may be need to reclassify or eliminate from preserved catalogue.