• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.68-68
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• 2003

HP(2-20) (AKKVFKRLEKLEKLFSKIQNDK) derived from the N-terminus of Helicobacter pylori Ribosomal Protein L1 shows potent antimicrobial activity against bacterial, fungi and cancer cells without cytotoxic effect. In order to investigate the relationships between antimicrobial activity and the structures, several analogues have been designed and synthesized. The structures of these peptides in SDS micelles have been investigated using NMR spectroscopy and they revealed that analogue 3 has the longest, well-defined alpha-helix from Val5 to Trp19. NOESY experiments performed on HP and its analogues in nondeuterated SDS micelles show that protons in the indole ring of Trp16 are in close contact with methylene protons of SDS micelles. In order to probe the position of HP and its analogues relative to the SDS micelles, spin-labeled stearate was added. Large effects are observed for the chemical shifts and the intensities of Phe5, Glu9, Phe12, and Trp16 within the helix region by 16-doxylstearate. This result implies that 16-doxylstearate is located in the center of the micelles and the hydrophobic phase of the amphiphilic ${\alpha}$-helix is located in contact with the acyl chains of the micelles. Also, Lys3 and Lys4 at N-terminus and Lys20 at C-terminus may produce an optimal arrangement for electrostatic interactions between the sulfate head groups of the SDS and the positively charged lysyl N$\sub$3/$\^$+/. Interactions between the indole ring of Trp and the membrane, as well as the amphiphilic ${\alpha}$-helical structure of HP induced by Trp at the C-terminus may allow HP to span the lipid bilayer. These structural features are crucial for their potent antibiotic activities.

• BMB Reports
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• 제52권12호
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• pp.706-711
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• 2019

Cisplatin (Cis-DDP) is one of the most widely used anti-cancer drugs. It is applicable to many types of cancer, including lung, bladder, and breast cancer. However, its use is now limited because of drug resistance. p90 ribosomal S6 kinase (p90RSK) is one of the downstream effectors in the extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) pathway and high expression of p90RSK is observed in human breast cancer tissues. Therefore, we investigated the role of p90RSK in the Cis-DDP resistance-related signaling pathway and epithelial-mesenchymal transition (EMT) in breast cancer cells. First, we discovered that MDA-MB-231 cells exhibited more Cis-DDP resistance than other breast cancer cells, including MCF-7 and BT549 cells. Cis-DDP increased p90RSK activation, whereas the inactivation of p90RSK using a small interfering RNA (siRNA) or dominant-negative kinase mutant plasmid overexpression significantly reduced Cis-DDP-induced cell proliferation and migration via the inhibition of matrix metallopeptidase (MMP)2 and MMP9 in MDA-MB-231 cells. In addition, p90RSK activation was involved in EMT via the upregulation of mRNA expression, including that of Snail, Twist, ZEB1, N-cadherin, and vimentin. We also investigated NF-κB, the upstream regulator of EMT markers, and discovered that Cis-DDP treatment led to NF-κB translocation in the nucleus as well as its promoter activity. Our results suggest that targeting p90RSK would be a good strategy to increase Cis-DDP sensitivity in triple-negative breast cancers.

• 미생물학회지
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• 제53권2호
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• pp.137-140
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• 2017

Caballeronia sordidicola 균주 PAMC 26510은 남극 킹조지섬의 바톤반도에서 채집된 지의류인 Psoroma sp.에서 분리되었다. 균주 PAMC 26510의 초안 유전체 서열은 224개의 콘티그로 이루어졌으며, 총 7,872,143 염기쌍은 59.7% G+C 함량을 나타냈다. 유전체는 7,580개의 단백질 유전자, 6개의 rRNA 유전자와 46개의 tRNA 유전자를 포함하였다. 균주 PAMC 26510는 이전에 연구한 Caballeronia sordidicola에 속하는 북극 균주와 마찬가지로 대사능력에 있어서 광범위한 능력을 가지고 있는 것으로 여겨진다. PAMC 26510의 초안 유전체는 6개의 CRISPR arrays를 각각의 콘티그 상에 가지고 있으며, 이중 두 개의 콘티그 상에 CRISPR-관련 유전자가 연결되어 있었다.

• 미생물학회지
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• 제53권2호
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• pp.141-143
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• 2017

Caballeronia sordidicola 균주 PAMC 26577은 다산 기지 근처에서 채집된 지의류인 Cladonia 종에서 분리되었다. Illumina 방식으로 분석한 균주 PAMC 26577의 초안 유전체 서열은 182개의 콘티그로 이루어졌으며, N50값은 159,226 염기쌍 길이에 해당하였다. 초안 유전체로 총 8,334,211 염기쌍을 확인하였으며, 59.4% G+C 함량을 나타냈다. 유전체는 단백질을 코드하지 않는 8개의 rRNA 유전자와 51개의 tRNA 유전자를 포함하였다. 8,065개의 단백질 유전자는 기본 대사 과정뿐 아니라 부탄올/부티르산 생합성, 폴리하이드록시부티르산 대사, serine cycle methylotrophy 및 글라이코겐 대사 유전자들을 가지고 있었다. 2백개 이상의 막 전달 단백질은, 인산화 전달 시스템과 TRAP 전달시스템이 부재하였다. PAMC 26577은 CRISPR 관련 서열 및 단백질이 없었으며, 파아지 유전자의 감염흔적으로 인한 11개의 파아지 관련 유전자를 찾아낼 수 있었다.

• Parasites, Hosts and Diseases
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• 제54권5호
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• pp.631-636
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• 2016

This study aimed to develop a multiplex-touchdown PCR method to simultaneously detect 3 species of protozoan parasites, i.e., Cryptosporidium parvum, Giardia lamblia, and Cyclospora cayetanensis, the major causes of traveler's diarrhea and are resistant to standard antimicrobial treatments. The target genes included the Cryptosporidium oocyst wall protein for C. parvum, Glutamate dehydrogenase for G. lamblia, and 18S ribosomal RNA (18S rRNA) for C. cayetanensis. The sizes of the amplified fragments were 555, 188, and 400 bps, respectively. The multiplex-touchdown PCR protocol using a primer mixture simultaneously detected protozoa in human stools, and the amplified gene was detected in > $1{\times}10^3$ oocysts for C. parvum, > $1{\times}10^4$ cysts for G. lamblia, and > 1 copy of the 18S rRNA gene for C. cayetanensis. Taken together, our protocol convincingly demonstrated the ability to simultaneously detect C. parvum, G. lamblia, and C. cayetanenesis in stool samples.

• Bulletin of the Korean Chemical Society
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• 제22권12호
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• pp.1361-1365
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• 2001

Recombinant immunotoxins are hybrid cytotoxic proteins designed to selectively kill cancer cells. A divalent immunotoxins, [B3(FabH1)-PE38]2, was constructed by recombining Fab domain of B3 antibody as a cell-targeting domain and Pseudo monas exotoxin A (PE) as a cytotoxic domain. Monoclonal antibody, B3, is the murine antibody (IgG1k) directed against Lewis Y-related carbohydrate antigens, which are abundant on the surface of many carcinomas. Fab fragment of this antibody was used in this study with the modified hinge sequence where last two cysteines out of three were mutated to serine. PE is a 66 kDa bacterial toxin that kills eukaryotic cells by inhibiting protein synthesis with ADP ribosylation of ribosomal elongation factor 2 (EF2). Fc region of B3 antibody was substituted with the truncated form of PE (38 kDa, PE38) on DNA level. [B3(FabH1)-PE38]2 was formed by disulfide bond between cysteines in the modified hinge region of B3(FabH1)-PE38. Each polypeptide for recombinant immunotoxins was overexpressed in Escherichia coli and collected as inclusion bodies. Each inclusion body was solubilized and refolded, and cytotoxic effects were measured. Divalent immunotoxins, [B3(FabH1)-PE38]2, had ID50 values of about 10 ng/mL on A431 cell lines and about 4 ng/mL on CRL1739 cell lines. Control immunotoxins, B3(scFv)-PE40, had ID50 values of about 28 ng/mL on A431 cell lines and about 41 ng/mL on CRL1739 cell lines. Divalent immunotoxins, [B3(FabH1)-PE38]2, had higher cytotoxic effects than B3(scFv)-PE40 control immunotoxins.

• 미생물학회지
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• 제55권2호
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• pp.171-173
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• 2019

Paenibacillaceae계의 Cohnella 속은 다양한 환경 속에서 서식한다. 여기에 우리는 한국 한라산 꼭대기의 구상나무(Abies koreana) 근권 토양으로부터 분리된 Cohnella sp. HS21의 전체 게놈 서열을 보고한다. 균주 HS21은 원형 염색체 7,059,027 bp와 44.8%의 GC 함량을 가지고 있다. 5,939개의 단백질 코딩 유전자와 78개의 트랜스퍼 (tRNA) 유전자, 27개의 리보솜 RNA (rRNA) 유전자, 4개의 비 코딩 RNA 유전자(ncRNA), 90개의 위 유전자가 존재했다. 박테리아는 항생제 관련 유전자 클러스터와 식물 세포벽 분해 효소를 코딩하는 유전자를 포함하고 있다.

• The Plant Pathology Journal
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• 제38권4호
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• pp.287-295
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• 2022

Citrus tristeza virus (CTV) is efficiently transmitted in a semi-persistent manner by the brown citrus aphid (Toxoptera citricida (Kirkaldy)). Currently, the most sensitive method for detecting plant viruses in insect vectors is reverse-transcription quantitative polymerase chain reaction (RT-qPCR). In this study, the elongation factor-1 alpha (EF-1α) gene and acidic p0 ribosomal protein (RPAP0) gene were confirmed to be suitable reference genes for RT-qPCR normalization in viruliferous T. citricida aphids using the geNorm, NormFinder, and BestKeeper tools. Then the relative CTV titer in aphids (T. citricida) at different post-acquisition feeding times on healthy plants was quantified by RT-qPCR using EF-1α and RPAP0 as reference genes. The relative CTV titer retained in the aphids gradually decreased with increasing feeding time. During the first 0.5 h of feeding time on healthy plants, the remaining CTV titer in aphids showed about 80% rapid loss for the highly transmissible isolate CT11A and 40% loss for the poorly transmissible isolate CTLJ. The relative CTV titer in aphids during more than 12 h post-acquisition times for CT11A was significantly lower than at the other feeding times, which is similar to the trend found for CTLJ. To our knowledge, this is the first report about the relative titer variation of CTV remaining in T. citricida at different post-acquisition feeding times on healthy plants.

• Genomics & Informatics
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• 제20권1호
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• pp.12.1-12.7
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• 2022

The two complete mitochondrial genomes (mitogenomes) of Paedocypris progenetica, the smallest fish in the world which belonged to the Cyprinidae family, were sequenced and assembled. The circular DNA molecules of mitogenomes P1-P. progenetica and S3-P. progenetica were 16,827 and 16,616 bp in length, respectively, and encoded 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The gene arrangements of P. progenetica were identical to those of other Paedocypris species. BLAST and phylogenetic analyses revealed variations in the mitogenome sequences of two Paedocypris species from Perak and Selangor. The circular DNA molecule of P. progenetica yield a standard vertebrate gene arrangement and an overall nucleotide composition of A 33.0%, T 27.2%, C 23.5%, and G 15.5%. The overall AT content of this species was consistent with that of other species in other genera. The negative GC-skew and positive AT-skew of the control region in P. progenetica indicated rich genetic variability and AT nucleotide bias, respectively. The results of this study provide genomic variation information and enhance the understanding of the mitogenome of P. progenetica. They could later deliver highly valuable new insight into data for phylogenetic analysis and population genetics.

• 식물병연구
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• 제29권1호
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• pp.94-99
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• 2023

Blueberry red ringspot virus (BRRSV) and blueberry scorch virus (BlScV) are included in the quarantine virus list managed by the Korean Animal and Plant Quarantine Agency. A multiplex polymerase chain reaction (PCR) assay with an internal control was developed for the simultaneous detection of both viruses. The specific primers used here were designed based on the highly conserved regions of the genomic sequences of each virus, obtained from the National Center for Biotechnology Information nucleotide databases. The primers were designed to amplify a partial sequence within coat protein (CP) for detecting BRRSV and a partial sequence within the CP-16 kDa for detecting BlScV. 18S ribosomal RNA (rRNA) was used as internal control, and the primer set used in a previous study was modified in this study for detecting 18S rRNA. Each conventional PCR using the BRRSV, BlScV, and 18S rRNA primers exhibited a sensitivity of approximately 1 fg plasmid DNA. The multiplex PCR assay using the BRRSV, BlScV, and 18S rRNA primers was effective in simultaneously detecting the two viruses and 18S rRNA with a sensitivity of 1 fg plasmid DNA, similar to that of conventional PCR assays. The multiplex PCR assay developed in this study was performed using 14 blueberry cultivars grown in South Korea. BRRSV and BlScV were not detected, but 18S rRNA was all detected in all the plants tested. Therefore, our optimized multiplex PCR assay could simultaneously detect the two viruses and 18S rRNA in field samples collected from South Korea in a time-efficient manner. This approach could be valuable in crop protection and plant quarantine management.