• BMB Reports
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• 제52권3호
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• pp.196-201
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• 2019

The Alu element, the most abundant transposable element, is transcribed to Alu RNA. We hypothesized that the PIWI protein regulates the expression of Alu RNA in retinal pigment epithelial (RPE) cells, where accumulated Alu RNA leads to macular degeneration. Alu transcription was induced in RPE cells treated with $H_2O_2$. At an early stage of oxidative stress, PIWIL4 was translocated into the nucleus; however, subsequently it was sequestered into cytoplasmic stress granules, resulting in the accumulation of Alu RNA. An elevated amount of Alu RNA was positively correlated with the disruption of the epithelial features of RPE via induction of mesenchymal transition. Therefore, we suggest that oxidative stress causes Alu RNA accumulation via PIWIL4 sequestration into the cytoplasmic stress granules.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.77-85
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• 2004

A significant portion (about 8% in human genome) of mammalian mRNA sequences contains AU(Adenine and Uracil) rich elements or AREs at their 3' untranslated regions (UTR). These mRNA sequences are usually stable. ARE motifs are assorted into three classes. The importance of AREs in biology is that they make certain mRNA unstable. We analyzed the occurrences of AREs and Alu, and propose a possible mechanism on how human mRNA could acquire and keep A REs at its 3' UTR originated from Alu repeats. Interspersed in the human genome, Alu repeats occupy 5% of the 3' UTR of mRNA sequences. Alu has poly-adenine (poly-A) regions at the end that lead to poly -thymine (poly-T) regions at the end of its complementary Alu. It has been discovered that AREs are present at the poly -T regions. In the all ARE's classes, 27-40% of ARE repeats were found in the poly -T region of Alu with mismatch allowed within 10% of ARE's length from the 3' UTRs of the NCBI's reference m RNA sequence database. We report that Alu, which has been reported as a junk DNA element, is a source of AREs. We found that one third of AREs were derived from the poly -T regions of the complementary Alu.

• 생명과학회지
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• 제14권6호
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• pp.1028-1039
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• 2004

6500만년동안, Alu 서열은 RNA-중합효소 III에 의한 전사체를 통해 증폭해왔고, 영장류 게놈 내에 약 140만 복사의 수에 도달되었다. 그들은 가동성 인자 중에서 가장 큰 집단이며, 인간 게놈의 $10\%$를 구성한다. Alu 서열이 유전적으로 기능이 없다고 생각되었지만, 최근 많은 연구자들이 새로운 기능 및 질병과의 관련성을 증명해왔다 이들 Alu 서열은 삽입돌연변이, Alu-매개 재조합, 유전자 발현에 대해 유전자 전환 그리고 스플라이싱 사이트를 유발하고, 유전자 구조, 단백질 서열, 스플라이싱 모티프와 발현 양상에 영향을 준다. 우리는 Alu의 구조와 기원, 그들 패밀리의 컨센서스 서열, Alu의 진화와 분포 그리고 그들의 기능에 대하여 요약 정리하였다. 또한 영장류의 진화과정에 있어 질병과 관련하여 Alu 패밀리의 새로운 연구방향을 제시하였다.

• BMB Reports
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• 제53권2호
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• pp.94-99
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• 2020

Brain cytoplasmic 200 RNA (BC200 RNA) is proposed to act as a local translational modulator by inhibiting translation after being targeted to neuronal dendrites. However, the mechanism by which BC200 RNA inhibits translation is not fully understood. Although a detailed functional analysis of RNA motifs is essential for understanding the BC200 RNA-mediated translation-inhibition mechanism, there is little relevant research on the subject. Here, we performed a systematic domain-dissection analysis of BC200 RNA to identify functional RNA motifs responsible for its translational-inhibition activity. Various RNA variants were assayed for their ability to inhibit translation of luciferase mRNA in vitro. We found that the 111-200-nucleotide region consisting of part of the Alu domain as well as the A/C-rich domain (consisting of both the A-rich and C-rich domains) is most effective for translation inhibition. Surprisingly, we also found that individual A-rich, A/C-rich, and Alu domains can enhance translation but at different levels for each domain, and that these enhancing effects manifest as cap-dependent translation.

• 생명과학회지
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• 제8권2호
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• pp.126-130
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• 1998

Vibrio unlnificus ATCC 27562의 16S rRNA 유전자를 PCR법과 제한효소절단법으로 분석 하여 얻은 결과는 다음과 같다. 1. 고안된 한쌍의 primer로 PCR을 시행하여 얻은 산물은 약 1.3Kb 였다. 2. PCR산물을 여섯가지의 제한 효소로 절단하여 얻은 단편들은 아래와 같다. BamH I: 어떤 restriction fragment도 만들지 않았다. Alu I : 약 400bp와 200bp의 두가지 fragment를 생산하였다. Sau3A I : 약 70bp에서 450bp 사이에 세가지 fragment를 생산하였다. Hind III : 약 800bp와 500bp의 약간 큰 두가지 fragment를 생산하였다. Sal I : 약 500bp와 750bp의 두가지 fragment를 생산하였다. Sma I : 약 800bp와 470bp의 두가지 fragment를 생산하였다.

• Genomics & Informatics
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• 제2권2호
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• pp.86-91
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• 2004

Even though it represents $6-13\%$ of human genomic DNA, Alu sequences are rarely found in coding regions. When in exon region, over $80\%$ of them are found in 3' untranslated region (UTR). Pseudogenes are an important component of human genome. Their functions are not clearly known and the mechanism of how they are generated is still debatable. Both the Alu and Pseudogenes are important research problems in molecular biology. mRNA is thought to be a prime source of pseudogene and active research is going on its molecular mechanism. We report, for the first time, that mRNAs containing Alu repeats at 3' UTR has a significantly high correlation with processed pseudogenes, suggesting a possibility that Alu containing mRNAs have a high tendency to become processed pseudogenes. It is known that about $10\%$ of all human genes have been transposed. Transposed genes at 3' UTR without Alu repeat have about two processed pseudogenes per gene on average while we found with statistical significance that a transposed gene with Alu had over three processed Pseudogenes on average. Therefore, we propose Alu repeats as a new and important factor in the generation of pseudogenes.

• 한국식물병리학회지
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• 제12권2호
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• pp.191-196
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• 1996

위축, 황화, 총생 증상 등 전형적인 병징을 나타내는 phytoplasma에 감염된 식물에서 phytoplasma만을 특이적으로 검출하기 위하여 polymerase chain reaction(PCR) 방법을 이용하였다. Phytoplasma의 16S rRNA gence의 DNA 단편을 증폭하기 위하여 1.4 kb primers (forward, 5` -GTTGATCCTGGCTCAGGATT-3` 와 reverse, 5` -AACCCCGAGAACGTATTCACC -3`)를 사용하여 증폭한 결과, phytoplasma에 이병된 오동나무, 라일락 및 미역취에서는 약 1.4 kbp의 위치에서 특이 band가 검출되었으나 control로 사용한 건전주에서는 어떠한 band 검출되지 않았다. 위의 결과를 재확인 하기 위하여 약 0.5 kb의 primers(forward, 5` -ACGAAAGCGTGGGGAGCAAA-3` 와 reverse, 5` -GAAGTCGAGTTGCAGACTTC-3`)를 사용하여 증폭한 결과, 0.5 kb의 위치에서 특이 band가 검출되었으나 control로 사용한 건전주에서는 어떠한 band도 검출되지 않았다. Phytoplasma에 이병된 식물의 PCR 반응산물을 제한효소인 AluI으로 처리하 sruf과, 오동나무와 라일락에서는 동일한 band pattern을 나타내어 서로 유연관계가 가까운 phytoplasma인 것으로 생각되며, 미역취에서는 이들과는 다른 band pattern을 나타내어 오동나무와 라일락의 phytoplasma와는 유연관계가 먼 것으로 추측된다.

• Genomics & Informatics
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• 제5권2호
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• pp.68-76
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• 2007

Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.

• 생명과학회지
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• 제31권8호
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• pp.710-718
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• 2021

태반유래 중간엽줄기세포(PD-MSCs)는 재생의학에서 세포기반치료제로 잘 알려진 세포군이다. PD-MSCs의 손상된 부위로의 이동과 호밍 기능은 MSC 생착의 중요한 특성이다. miRNA는 최근 MSC의 증식, 생존 이동과 같은 중요한 기능을 조절하는 것으로 알려져 있다. 본 연구의 목적은 담관결찰(BDL) 쥐 모델에서 PD-MSCs 호밍에 관련된 miRNA 및 표적 유전자를 동정하는 것으로, 마이크로어레이 분석을 이용하여 PD-MSCs 호밍에 관여하는 유전자 표적 miRNA를 선별하였다. BDL 쥐모델에 PD-MSCs을 이식한 일주일 후 간 조직에서 PD-MSCs 생착여 부는 면역형광분석법과 qRT-PCR에 의한 인간 Alu유전자 발현으로 확인되었다. 저산소 및 정상조건(Hyp/Nor)에서 이동한 PD-MSC에 비하여, PD-MSCs 이식한 BDL군 간 조직에서 miRNAs 발현의 차이가 크게 나타났으며, PD-MSCs 호밍 관련 miRNA와 표적유전자를 검증하였다. miR199a-5p 및 miR-148a-3p에 대한 표적 유전자 인테그린 α4 (ITGA4)와 α5 (ITGA5)의 발현은 이식(Tx)그룹에서(p<0.05) 유의하게 상향 조절되었다. 또한 인테그린 β1 (ITGB1)과 β8 (ITGB8)의 발현은 miR-183-5p 및 miR-145-5p억제에 의하여 크게 증가되었다. 따라서 이러한 결과는 BDL에 의해 손상된 쥐간에서 PD-MSCs가 호밍효과을 위해 인테그린 그룹과 관련된 miRNA 발현 조절에 관여함을 나타내었다. 본 연구결과는 miRNA에 의한 인테그린 그룹 조절기능이 BDL에 의해 유도된 간섬유증 쥐모델에서 PD-MSCs의 치료효과에 기여할 수 있음을 시사한다.

• 한국미생물·생명공학회지
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• 제48권2호
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• pp.193-204
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• 2020

Sixteen acetic acid bacteria (AAB) were isolated from blueberries and citric fruits of the Salto Grande region (Concordia, Entre Rios, Argentina) using enrichment techniques and plate isolation. Enrichment broths containing ethanol and acetic acid enabled maximum AAB recovery, since these components promote their growth. Biochemical tests allowed classification of the bacteria at genus level. PCR-RFLP of the 16S rRNA and PCR-RFLP of the 16S-23S rRNA intergenic spacer allowed further classification at the species level; this required treatment of the amplified products of 16S and 16S-23S ITS ribosomal genes with the following restriction enzymes: AluI, RsaI, HaeIII, MspI, TaqI, CfoI, and Tru9I. C7, C8, A80, A160, and A180 isolates were identified as Gluconobacter frateurii; C1, C2, C3, C4, C5, C6, A70, and A210 isolates as Acetobacter pasteurianus; A50 and A140 isolates as Acetobacter tropicalis; and C9 isolate as Acetobacter syzygii. The bacteria identified by 16S rRNA PCR-RFLP were validated by 16S-23S PCR-RFLP; however, the C1 isolate showed different restriction patterns during identification and validation. Partial sequencing of the 16S gene resolved the discrepancy.