• 한국물환경학회지
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• 제24권6호
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• pp.817-822
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• 2008

In order to identify various Cryptosporidium species in environment, nested PCR-RFLP and DNA sequencing method were used. The sensitivity of nested PCR-RFLP based on 18s rRNA gene was shown to 1 oocyst. Therefore, we applied nested PCR-RFLP method to environmental samples. As a result, only 4 samples out of 8 samples confirmed as Cryptosporidium parvum by standard method of Cryptosporidium were identified as Cryptosporidium parvum by nested PCR-RFLP and DNA sequencing method. The rest of 4 samples among 8 samples were identified as Cryptosporidium muris, Cryptosporidium bailey. Therefore, in addition to standard method of Cryptosporidium, supplementary verification through nested PCR-RFLP and DNA sequencing should be needed to give more accurate information about risk of Cryptosporidium.

• Tuberculosis and Respiratory Diseases
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• 제84권1호
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• pp.55-66
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• 2021

Background: Particulate matter 10 (PM₁₀; airborne particles <10 ㎛) inhalation has been demonstrated to induce airway and lung diseases. In this study, we investigate the effects of PM₁₀ inhalation on RNA expression in lung tissues using a murine model. Methods: Female BALB/c mice were affected with PM₁₀, ovalbumin (OVA), or both OVA and PM₁₀. PM₁₀ was administered intranasally while OVA was both intraperitoneally injected and intranasally administered. Treatments occurred 4 times over a 2-week period. Two days after the final challenges, mice were sacrificed. Full RNA sequencing using lung homogenates was conducted. Results: While PM₁₀ did not induce cell proliferation in bronchoalveolar fluid or lead to airway hyper-responsiveness, it did cause airway inflammation and lung fibrosis. Levels of interleukin 1β, tumor necrosis factor-α, and transforming growth factor-β in lung homogenates were significantly elevated in the PM₁₀-treated group, compared to the control group. The PM₁₀ group also showed increased RNA expression of Rn45a, Snord22, Atp6v0c-ps2, Snora28, Snord15b, Snora70, and Mmp12. Generally, genes associated with RNA splicing, DNA repair, the inflammatory response, the immune response, cell death, and apoptotic processes were highly expressed in the PM₁₀-treated group. The OVA/PM₁₀ treatment did not produce greater effects than OVA alone. However, the OVA/PM₁₀-treated group did show increased RNA expression of Clca1, Snord22, Retnla, Prg2, Tff2, Atp6v0c-ps2, and Fcgbp when compared to the control groups. These genes are associated with RNA splicing, DNA repair, the inflammatory response, and the immune response. Conclusion: Inhalation of PM₁₀ extensively altered RNA expression while also inducing cellular inflammation, fibrosis, and increased inflammatory cytokines in this murine mouse model.

• Journal of Microbiology and Biotechnology
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• 제32권11호
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• pp.1485-1495
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• 2022

The development of a yeast strain capable of fermenting mixed sugars efficiently is crucial for producing biofuels and value-added materials from cellulosic biomass. Previously, a mutant Pichia stipitis YN14 strain capable of co-fermenting xylose and cellobiose was developed through evolutionary engineering of the wild-type P. stipitis CBS6054 strain, which was incapable of co-fermenting xylose and cellobiose. In this study, through genomic and transcriptomic analyses, we sought to investigate the reasons for the improved sugar metabolic performance of the mutant YN14 strain in comparison with the parental CBS6054 strain. Unfortunately, comparative whole-genome sequencing (WGS) showed no mutation in any of the genes involved in the cellobiose metabolism between the two strains. However, comparative RNA sequencing (RNA-seq) revealed that the YN14 strain had 101.2 times and 5.9 times higher expression levels of HXT2.3 and BGL2 genes involved in cellobiose metabolism, and 6.9 times and 75.9 times lower expression levels of COX17 and SOD2.2 genes involved in respiration, respectively, compared with the CBS6054 strain. This may explain how the YN14 strain enhanced cellobiose metabolic performance and shifted the direction of cellobiose metabolic flux from respiration to fermentation in the presence of cellobiose compared with the CBS6054 strain.

• Journal of Plant Biology
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• 제38권2호
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• pp.129-136
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• 1995

Complementary DNA of the genomic RNA of odontoglossum ringspot virus Cymbidium strain (ORSV-Cy) was synthesized from polyadenylated viral RNA and cloned. Selected clones containing the viral RNA-dependent RNA polymerase gene of the virus has been sequenced by automated sequencing system. The complete nucleotide sequence of an open reading frame is 1377 base pairs in length, and encodes a protein of 458 amino acids about 52, 334 D. The 52 kD protein of ORSV shares four sequence motifs characteristic of viral RNA-dependent RNA polymerase. Comparison of the ORSV 52 kD protein sequence with that of other five viruses in tobamovirus group showed 76.0 to 60.7% homologies at the amino acid level and the conservation of the four motifs betwen the viruses.

• 한국동물학회:학술대회논문집
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• 한국동물학회 1995년도 한국생물과학협회 학술발표대회
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• pp.312.1-312
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• 1995

• 생명과학회지
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• 제27권12호
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• pp.1494-1499
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• 2017

Candida albicans에 의한 구강 감염(캔디다증)은 구강 점막에 빈번하게 발생하며 잘 알려진 질병이다. 구강 캔디다증은 생명을 위협하는 정도의 곰팡이 감염증은 아니나, 특정상황에서 개인에게 심각한 위험을 초래할 수도 있다. 마이크로 RNA는 세포 내에서 다른 타겟 유전자를 저해하는 작은 크기의 RNA 분자이며 단백질을 코딩하지는 않고 번역과정을 억제하는 조절자로서의 역할을 하고 있다. 본 연구는 C. albicans의 마이크로RNA를 처음으로 동정하고 그러한 마이크로RNA가 지닌 기능을 조사하기 위함이다. 이를 위하여 C. albicans의 small RNA를 차세대 염기분석법을 통하여 분석하고 그러한 RNA들의 2차 구조를 생물정보학적 방법으로 조사하였다. 분석한 small RNA들은 마이크로 RNA라고 불리울 수 있는 특징들을 가지고 있었으며, 특별히 높게 발현되고 있는 두개의 마이크로 RNA 정도 크기의 RNA가 CBP1 유전자의 3' 말단 비번역구역(UTR)에서 반대방향으로 발현하는 것을 밝혀 내었다. 우리는 이러한 C. albicans의 RNA가 CBP1 유전자를 타겟으로 하여 조절하는지 알아보기 위해 RNA를 인위적으로 합성한 후 세포 내로 주입하고, 형광형미경으로 도입 사실을 확인하였다. 하지만 4시간과 8시간 후에 CBP1의 발현 변화는 관찰되지 않았다. 따라서, 이러한 결과는 C. albicans가 마이크로RNA에 의한 RNA 간섭(RNAi) 작용이 다른 진핵세포와는 다르게 작용하는 것을 알 수 있다.

• Journal of Plant Biology
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• 제37권3호
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• pp.349-355
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• 1994

Viral RNA was extracted from a purified orchid strain of tobacco mosaic virus (TMV-O) from Cymbidium "Grace Kelly". Polyadenylated viral RNAs were primed with Not I-oligo (dT) primer-adapter. First-strand cDNAs were reversely transcribed by Moloney murine leukaemia virus reverse transcriptase (RNAse H-), and then second-strand cDNAs were synthesized by RNase H and DNA polymerase I. The resulting double-stranded cDNAs were ligated into pSPORT1 vector and transformed into competent E. coli strain JM109 cells. The size of cDNAs within the recombinant plasmids was ranging from 0.9 to 3.9 kb. Among the selected clones, pTMO-0205 and -0210 covered the 3' half and the 5' half of the viral genomic RNA, respectively, which were covering more than 99% of the viral genemo size based on sequencing analysis. Two cDNA fragments which were 3.1 kb BamHI and NotI fragement released from pTMO-0.205 and 3.3 kb SalI and BamHI fragment released from pTMO-0210 were ligated with T4 DNA ligase. The clone was almost entire length, lacking only 31 nucleotides from the 5' terminus based on the sequencing result. This method was shown to be efficiently applicable to other plant viral gnomic RNA for the construction of cDNA.n of cDNA.

• 한국치위생학회지
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• 제13권5호
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• pp.889-900
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• 2013

Objectives : Molecular biology techniques were employed to assess diversity of bacterial in children's dental caries. Methods : DNA of germs was extracted and the diversity of the 16S rRNA clones was analyzed by amplified rDNA restriction analysis and sequencing. The experimental samples were pit and fissure caries (PC), deep dentinal caries (DC), smooth surface caries (SC), and supragingival plaque (PQ) from 50 children of age less than 12 years old. The control group was healthy teeth supragingival plaque (HT). Thirty clones from each 16S rRNA clone library of 5 samples were randomly selected, thus a total of 150 clones were analyzed. Results : Amplified rDNA restriction analysis uncovered 18, 20, 11, 17, and 22 phylotypes from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and supragingival plaque, respectively. Sequencing analysis found the dominance of Actinomycs naeslundii and Fusobacterium nucleatum in the healthy teeth; Leptotrichia sp. in the pit and fissure caries; Actinomyces sp., Streptococcus mutans, and Rahnella aquatilis in the deep dentinal caries; Streptococcus mutans and Actinomyces sp. in the smooth surface caries; Enterobacter hormaechei and Streptococcus sanguinis in the supragingival plaque. Conclusions : Clonal analysis identified 6 phyla, 20 genera, and 51 species.

• 환경생물
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• 제41권3호
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• pp.308-324
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• 2023

This study investigated unrecorded freshwater bacterial species in Korea. Water and sediment samples were collected from the Nakdong River basin from 2020-2022. Bacterial isolates obtained through the conventional culture method with commercial media were subjected to 16S rRNA gene sequencing to identify unrecorded bacterial species. Results of 16S rRNA gene sequencing of the bacterial isolates revealed that a total of 44 bacterial isolates shared 16S rRNA gene sequence similarities of more than 98.65%, with validly published bacterial species not reported in Korea yet. These isolates were phylogenetically assigned to 4 phyla, 7 classes, 21 orders, 33 families, and 42 genera. A total of 2, 6, 12, and 24 species belonged to phyla Bacillota, Bacteroidota, Actinomycetota, and Pseudomonadota, respectively. Here, we provide details of these 44 unrecorded bacterial species, including Gram staining, colony and cellular morphologies, biochemical properties, and phylogenetic position.