• 한국산림과학회지
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• 제104권4호
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• pp.549-557
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• 2015

본 연구에서는 잣나무 엽록체 DNA의 전체 염기서열을 기반으로 엽록체 SSR(chloroplast simple sequence repeat) 영역을 특이적으로 증폭하는 primer를 개발하고 그 특성을 분석하였다. 잣나무 엽록체 DNA에서 총 30개의 SSR 영역을 탐색하였으며, 이들 영역을 증폭하기 위한 30개의 primer를 제작하였다. 모든 primer가 잣나무를 대상으로 PCR 증폭이 가능하였다. 근연종에 대한 primer의 종간 전환률은 잣나무와 동일한 아속(Subgenus Strobus)에 속하는 눈잣나무(100%)와 섬잣나무(97%)에서 가장 높게 나타났다. 반면 소나무아속(Subgenus Pinus)에 속하는 소나무와 구주소나무에서의 종간 전환률은 73%로 비교적 낮게 나타났다. 점봉산 잣나무 집단을 대상으로 조사한 결과 13개의 유전자좌에서 다형성이 관찰되었으며, 평균 haploid 다양도(H)는 0.512로 계산되었다. 다형적 유전자좌로부터 조합된 haplotype의 수(N)는 25개로 확인되었고, haplotype 다양도($H_e$)는 0.992로 매우 높게 나타났다. 집단내 독특하게 관찰되는 haplotype은 22개(88%)로 전체 28개체 중에서 22개체(79%)를 식별하였다. 본 연구에서 개발한 cpSSR primer는 높은 종간 전환률을 나타냄에 따라 소나무속의 근연종, 특히 잣나무아속 수종에 활용 가능성이 높고, 잣나무 유전변이 분석을 위한 충분한 다형성을 제공하는 유용한 표지자로 판단된다.

• Genomics & Informatics
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• 제4권1호
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• pp.1-10
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• 2006

Epigenetic alterations are common features of human solid tumors, though global DNA methylation has been difficult to assess. Restriction Landmark Genomic Scanning (RLGS) is one of technology to examine epigenetic alterations at several thousand Notl sites of promoter regions in tumor genome. To assess sequence information for Notl sequences in RLGS gel, we cloned 1,161 unique Notl-linked clones, compromising about 60% of the spots in the soluble region of RLGS profile, and performed BLAT searches on the UCSC genome server, May 2004 Freeze. 1,023 (88%) unique sequences were matched to the CpG islands of human genome showing a large bias of RLGS toward identifying potential genes or CpG islands. The cloned Notl-loci had a high frequency (71%) of occurrence within CpG islands near the 5' ends of known genes rather than within CpG islands near the 3' ends or intragenic regions, making RLGS a potent tool for the identification of gene-associated methylation events. By mixing RLGS gels with all Notl-linked clones, we addressed 151 Notl sequences onto a standard RLGS gel and compared them with previous reports from several types of tumors. We hope our sequence information will be useful to identify novel epigenetic targets in any types of tumor genome.

• Journal of Species Research
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• 제4권2호
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• pp.152-158
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• 2015

Dendranthema boreale and D. indicum are easily distinguished from other Korean Dendranthema spp. by having yellow flowers. We have found a putative new taxon of Dendranthema having white flowers, except for sharing most characters with Dendranthema boreale. The chloroplast (cp) genome of the putative new taxon of Dendranthema, Dendranthema sp. K247003, registered in National Agro-Biodiversity Center (ABC), was completely characterized as a genetic barcode. The cp-genome of Dendranthema sp. K247003 was 151,175-bp in size: LSC was 82,886-bp, IR 24,971-bp, SSC 18,347-bp. The cp-genome of Dendranthema sp. K247003 contains 113 genes and 21 introns consisted of 79 protein coding genes, 4 RNA genes, and 30 tRNA genes, with 20 group II introns and one group I intron. Some of the genes and there introns were duplicated in IR. The cp-DNA of Dendranthema sp. K247003 is distinguished from that of D. boreale IT121002 by 67 SNPs in genic regions of 24 protein coding genes and by a 9-bp INDEL in ycf1. Further cp-DNA study will give us better information on genetic markers of Dendranthema species.

• 한국자기공명학회논문지
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• 제22권4호
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• pp.119-124
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• 2018

Although the transcription factor CP2c has been recently validated as a promising target for development of novel anticancer therapy, its structure has not been solved yet. In the present study, the purified recombinant protein corresponding to the tetramerization domain of CP2c appeared to be well folded, whereas the Elf-1 domain showed a largely unfolded conformation. Particularly, the Elf-1 domain, which contains the putative DNA-binding region, showed a conformational equilibrium between relatively less-ordered and well-ordered conformers. Interestingly, addition of zinc shifted the equilibrium to the relatively more structured conformer, whereas zinc binding decreased the overall stability of the protein, leading to a promoted precipitation. Likewise, a dodecapeptide that has been suggested to bind to the Elf-1 domain also appeared to shift the conformational equilibrium and to destabilize the protein. These results constitute the first structural characterization of the CP2c domains and newly suggest that zinc ion might be involved in the conformational regulation of the protein.

• 한국어병학회지
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• 제6권1호
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• pp.57-64
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• 1993

어병 세균으로부터 분리된 R-plasmid의 특성과 그 DNA 구조는 Aeromonas hydrophila, A. salmonicida, Edwardsiella tarda, Enterococcus seriolicida, Pasteurella piscicida, Vibrio onguillarum등 세균의 종류에 따라 다르다. 그러나 A. hydrophila와 E. tarda로부터 그리고 A. hydrophila와 A. salmonicida로부터 분리된 몇몇 R-plasmid는 같은 내성형을 가지면서 유사한 DNA 구조를 보였다, V. anguillarum에서 분리된 R-plasmid는 1977년 이전, 1980년과 1983년 사이 그리고 1989년과 1991년 사이에 분리된 것이 그 DNA 구조에 차이를 보여 각각 그룹 1, 2, 3으로 구분되어졌다. P. piscicida의 경우에는 연도와 지역에 관계없이 동일한 DNA 구조를 갖는 R-plasmid가 분리되었다. Macrolide계 항생제(MLs), lincomycin(LM), tetracycline(TC) 그리고 MLs, LIM, chloramphenicol(CP) 내성을 나타내는 R-plasmid를 갖는 E. seriolicida가 각 지역의 Yellowtail 어장에 분포되어 있었다. P. piscicida의 R-plasmid에는 type I의 chloramphenicol acetyltransferase(CAT)에 의하여 CP 내성을 나타내는 유전자(cat)가, 그리고 E. tarda, A. salmonicida와 1980년 이후에 분리된 V. anguillarum의 R-plasmid에는 CAT type II에 해당하는 car 유전자가 분포되어 있었다. TC 내성 유전자(tet)의 경우에는 1977년 이전과 1980년 이후에 분리된 V. anguillarum으로부터 class B, G의 tet 유전자가 확인되었으나, E. tarda, P. piscicida, A. hydrophila 그리고 1989년 이후에 분리된 V. anguillarum등 어병세균의 R-plasmid에는 class D의 tet 유전자가 널리 분포하고 있는 것으로 나타났다.

• Journal of Plant Biotechnology
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• 제47권1호
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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.

• 식물분류학회지
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• 제46권2호
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• pp.247-255
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• 2016

천주교 대구교구청에 심어져 있는 오래된 왕벚나무의 기원을 추적하기 위하여 제주도에 자생하는 야생 왕벚나무와 재배 왕벚나무(Somei-yoshino cherry)의 계통분류학적 유연관계를 알아보았다. 한국과 일본에서 채집한 야생 왕벚나무, 재배 왕벚나무 및 근연종인 올벚나무, 총 25 개체에 대하여 cpDNA 두 구간(rpl16 유전자, trnS-trnG intergenic spacer)의 염기서열을 사용하여 계통수와 반수체형(haplotype) 네트워크를 작성하여 두 분류군을 비교하였다. 야생 왕벚나무와 재배 왕벚나무는 서로 구별되는 분류군으로 드러났으며, 비록 적은 샘플을 대상으로 비교적 짧은 유전자위가 사용되었지만 야생 왕벚나무는 재배 왕벚나무보다 반수체형 다양성이 높은 것으로 나타났다. 이는 야생 왕벚나무의 교배 기원에 모계쪽으로 기여한 것으로 알려진 올벚나무의 유전적 다양성에서 기인하는 것으로 추정된다. 따라서, 야생 왕벚나무와 재배 왕벚나무의 계통분류학적 관계를 보다 명확하게 파악하기 위하여 올벚나무를 한국과 일본의 다양한 분포 지역에서 넓게 채집하여 추가 연구를 실시할 필요가 있다고 생각된다. Taquet 신부가 제주에서 채집하여 대구에 옮겨 심었다고 추정되었던 천주교 대구교구청의 오래된 왕벚나무는 야생 왕벚나무가 아닌 재배 왕벚나무로 보는 것이 타당하다.

• BMB Reports
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• 제44권6호
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• pp.393-398
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• 2011

Polydnaviruses are a group of double-stranded DNA viruses and are symbiotically associated with some ichneumonoid wasps. As proviruses, the replication of polydnaviruses occurs in the female reproductive organ at the pupal stage. This study analyzed the effects of two developmental hormones, juvenile hormone (JH) and ecdysteroid, on the viral replication of Cotesia plutellae bracovirus (CpBV). All 23 CpBV segments identified contained a conserved excision/rejoining site ('AGCTTT') from their proviral segments. Using quantitative real-time PCR based on this excision/rejoining site marker, initiation of CpBV replication was determined to have occurred on day 4 on the pupal stage. Pyriproxyfen, a JH agonist, significantly inhibited adult emergence of C. plutellae, whereas RH5992, an ecdysteroid agonist, had no inhibitory effect. Although RH5992 had no effect dose on adult development, it significantly accelerated viral replication. The results of immunoblotting assays against viral coat proteins support the effects of the hormone agonists on viral replication.

• Biomolecules & Therapeutics
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• 제23권2호
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• pp.180-188
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• 2015

This study investigated the possible effects and molecular mechanisms of diallyl disulfide (DADS) against cyclophosphamide (CP)-induced hemorrhagic cystitis (HC) in rats. Inflammation response was assessed by histopathology and serum cytokines levels. We determined the protein expressions of nuclear transcription factor kappa-B (NF-${\kappa}B$), inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), and tumor necrosis factor-${\alpha}$ (TNF-${\alpha}$), oxidative stress, urinary nitrite-nitrate, malondialdehyde (MDA), and 8-hydroxy-2'-deoxyguanosine (8-OHdG). Finally, we studied the involvement of mitogen-activated protein kinases (MAPKs) signaling in the protective effects of DADS against CP-induced HC. CP treatment caused a HC which was evidenced by an increase in histopathological changes, proinflammatory cytokines levels, urinary nitrite-nitrate level, and the protein expression of NF-${\kappa}B$, COX-2, iNOS, TNF-${\alpha}$, p-c-Jun N-terminal kinase (JNK), and p-extracellular signal regulated kinase (ERK). The significant decreases in glutathione content and glutathione-S-transferase and glutathione reductase activities, and the significant increase in MDA content and urinary MDA and 8-OHdG levels indicated that CP-induced bladder injury was mediated through oxidative DNA damage. In contrast, DADS pretreatment attenuated CP-induced HC, including histopathological lesion, serum cytokines levels, oxidative damage, and urinary oxidative DNA damage. DADS also caused significantly decreased the protein expressions of NF-${\kappa}B$, COX-2, iNOS, TNF-${\alpha}$, p-JNK, and p-ERK. These results indicate that DADS prevents CP-induced HC and that the protective effects of DADS may be due to its ability to regulate proinflammatory cytokines production by inhibition of NF-${\kappa}B$ and MAPKs expressions, and its potent anti-oxidative capability through reduction of oxidative DNA damage in the bladder.

• The Plant Pathology Journal
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• 제24권3호
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• pp.361-364
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• 2008

The complete nucleotide sequences of a Korean isolate of Potato virus X(PVX-Kr) has been determined. Full-length cDNA of PVX-Kr has been directly amplified by long template reverse transcription and polymerase chain reaction(RT-PCR) using virus specific 5'-end primer and 3'-end primer, and then constructed in a plasmid vector. Consecutive subclones of a full-length cDNA clone were constructed to identify whole genome sequence of the virus. Total nucleotide sequences of genome of PVX-Kr were 6,435 excluding one adenine at poly A tail, and genome organization was identical with that of typical PVX species. Comparison of whole genome sequence of PVX-Kr with those of European and South American isolates showed 95.4-96.8% and 77.4-77.9%, in nucleotide similarity, respectively. Sequenced PVX-Kr in this study and twelve isolates already reported could be divided into two subgroups in phylogeny based on their complete nucleotide sequences. Phylogenetic tree analysis demonstrated that PVX-Kr was clustered with European and Asian isolates(Taiwan, os, bs, Kr, S, X3, UK3, ROTH1, Tula) in the same subgroup and South American isolates(CP, CP2, CP4, HB) were clustered in the other subgroup.