• Molecules and Cells
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• 제40권11호
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• pp.823-827
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• 2017

Genome editing using programmable nucleases such as CRISPR/Cas9 or Cpf1 has emerged as powerful tools for gene knock-out or knock-in in various organisms. While most genetic diseases are caused by point mutations, these genome-editing approaches are inefficient in inducing single-nucleotide substitutions. Recently, Cas9-linked cytidine deaminases, named base editors (BEs), have been shown to convert cytidine to uridine efficiently, leading to targeted single-base pair substitutions in human cells and organisms. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. Injection of base editor 3 (BE3) ribonucleoprotein targeting the tyrosinase (tyr) gene in early embryos can induce site-specific base conversions with the rates of up to 20.5%, resulting in oculocutaneous albinism phenotypes without off-target mutations. We further test this base-editing system by targeting the tp53 gene with the result that the expected single-base pair substitutions are observed at the target site. Collectively, these data establish that the programmable deaminases are efficient tools for creating targeted point mutations for human disease modeling in Xenopus.

• Genomics & Informatics
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• 제5권3호
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• pp.102-106
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• 2007

Radiofrequency (RF) radiation at the frequency of mobile phones has been not reported to induce cellular responses in in vitro and in vivo models. We exposed HEI-OC1, conditionally-immortalized mouse auditory cells, to RF radiation to characterize cellular responses to 1763 MHz RF radiation. While we could not detect any differences upon RF exposure, whole-genome expression profiling might provide the most sensitive method to find the molecular responses to RF radiation. HEI-OC1 cells were exposed to 1763 MHz RF radiation at an average specific absorption rate (SAR) of 20 W/kg for 24 hr and harvested after 5 hr of recovery (R5), alongside sham-exposed samples (S5). From the whole-genome profiles of mouse neurons, we selected 9 differentially-expressed genes between the S5 and R5 groups using information gain-based recursive feature elimination procedure. Based on support vector machine (SVM), we designed a prediction model using the 9 genes to discriminate the two groups. Our prediction model could predict the target class without any error. From these results, we developed a prediction model using biomarkers to determine the RF radiation exposure in mouse auditory cells with perfect accuracy, which may need validation in in vivo RF-exposure models.

• 생명과학회지
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• 제23권4호
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• pp.595-601
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• 2013

생물들에서 생명의 본질적 기능을 수행하는 단백질들의 종류와 보존성을 밝히기 위해 COG (Clusters of Orthologous Groups of proteins) 알고리즘을 이용하였다. 66종의 미생물에서 보존적인 63개의 ortholog 그룹들은 진핵생물 7종에서 104개의 ortholog들로 확산되었으며, 7종 모두의 핵에 보존적인 KOG (euKaryotic Orthologous Group)은 71개였다. 71개 중 단백질 합성에 관여하는 유전자들이 총 54개로 생명현상에서의 단백질의 중요성을 확인할 수 있었다. Distance value로 보존적 유전자가 생물종 사이에 나타내는 유전자 변이의 정도를 파악하니 'Translation initiation factor'인 KOG3403과 KOG3271 그리고 'Prolyl-tRNA synthetase' (KOG4163) 등이 높은 보존성을 보였다. 보존적 KOG들의 평균과 분산으로 유전체 분석을 수행하여 꼬마선충이 KOG 평균사이의 편차가 제일 커 유전자의 변이가 다양한 것을 알 수 있었다. 본 연구결과는 기초연구와 항생제 개발 등에 이용될 수 있을 것이다.

• The Plant Pathology Journal
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• 제31권4호
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• pp.388-401
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• 2015

Sweet potatoes (Ipomea batatas L.) are grown extensively, in tropical and temperate regions, and are important food crops worldwide. In Korea, potyviruses, including Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG), Sweet potato virus 2 (SPV2), and Sweet potato latent virus (SPLV), have been detected in sweet potato fields at a high (~95%) incidence. In the present work, complete genome sequences of 18 isolates, representing the five potyviruses mentioned above, were compared with previously reported genome sequences. The complete genomes consisted of 10,081 to 10,830 nucleotides, excluding the poly-A tails. Their genomic organizations were typical of the Potyvirus genus, including one target open reading frame coding for a putative polyprotein. Based on phylogenetic analyses and sequence comparisons, the Korean SPFMV isolates belonged to the strains RC and O with >98% nucleotide sequence identity. Korean SPVC isolates had 99% identity to the Japanese isolate SPVC-Bungo and 70% identity to the SPFMV isolates. The Korean SPVG isolates showed 99% identity to the three previously reported SPVG isolates. Korean SPV2 isolates had 97% identity to the SPV2 GWB-2 isolate from the USA. Korean SPLV isolates had a relatively low (88%) nucleotide sequence identity with the Taiwanese SPLV-TW isolates, and they were phylogenetically distantly related to SPFMV isolates. Recombination analysis revealed that possible recombination events occurred in the P1, HC-Pro and NIa-NIb regions of SPFMV and SPLV isolates and these regions were identified as hotspots for recombination in the sweet potato potyviruses.

• Biotechnology and Bioprocess Engineering:BBE
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• 제11권4호
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• pp.319-324
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• 2006

Although the sera used in animal cell culture media provide the macromolecules, nutrients, hormones, and growth factors necessary to support cell growth, it could also be an obstacle to the production of recombinant proteins in animal cell culture systems used in many sectors of the biotechnology industry. For this reason, many research groups, including our laboratory, have been trying to develop serum-free media (SFM) or serum-supplemented media (SSM) for special or multi-purpose cell lines. The Chinese hamster ovary (CHO) cell, for example, is frequently used to produce proteins and is especially valuable in the large-scale production of pharmaceutically important proteins, yet information about its genome is lacking. Also, SFMs have only been evaluated by comparing growth patterns for cells grown in SFMs with those grown in SSM or by measuring the titer of the target protein obtained from cells grown in each type of medium. These are not reliable methods of obtaining the type of information needed to determine whether an SFM should be replaced with an SSM. We carried out a cDNA microarray analysis to evaluate MED-3, an SFM developed in our laboratory, as a CHO culture medium When CHO cells were cultured in MED-3 instead of an SSM, several genes associated with cell growth were down-regulated, although this change diminished over time. We found that the insulin-like growth factor (IGF) gene was representative of the proteins that were down-regulated in cells cultured in MED-3. When several key supplements - including insulin, transferrin, ethanolamine, and selenium - were removed from MED-3, the IGF expression was consistently down- regulated and cell growth decreased proportionately. Based on these results, we concluded that when an SFM is used as a culture medium, it is important to supplement it with substances that can help the cells maintain a high level of IGF expression. The data presented in this study, therefore, might provide useful information for the design and development of SFM or SSM, as well as for the design of genome-based studies of CHO cells to determine how they can be used optimally for protein production in pharmaceutical and biomedical research.

• 미생물학회지
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• 제26권4호
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• pp.305-311
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• 1988

Slow growing R. japonicum R-l68 균주로부터 spectinomycin 내성 균주를 선발하고 이 Rhizobium내에 Tn-5를 도입시키기 위하여 Tn5가 함유된 E. coli WA 803/pGS9과의 conjugation을 통한 transposon mutagenesis를 실시하였다. 이때 C conjugation을 통한 Tn5 전이 빈도는 $1.0\times 10^{-5}-5.0\times 10^{-7}$ 범위 이였으며, 얻어진 transconjugant들은 spectinomycin (($100{\mu}$g/ml)과 kanamycin ($50{\mu}$g/ml)을 함유한 yeast extract-mannitol 배지에서 8-10일 배양후 colony를 형성하였다. 또한 transconjugant들은 genome상에 Tn-5를 함유하고 있음을 hybridization-을 통하여 확인하였다. 한편 nodule은 형성 하나 질소고정 활성이 없는 돌연변이주 R. japonicum RMa 75 $nod^{+}fix^{-}$ 균주를 선발하였는데 이 균주는 nodule내에 leghemoglobin이 결핍되어 있음이 확인되었다.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2005년도 생물공학의 동향(XVII)
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• pp.634-634
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• 2005

• Molecules and Cells
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• 제38권9호
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• pp.781-788
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• 2015

Mutations of MYO15A are generally known to cause severe to profound hearing loss throughout all frequencies. Here, we found two novel MYO15A mutations, c.3871C>T (p.L1291F) and c.5835T>G (p.Y1945X) in an affected individual carrying congenital profound sensorineural hearing loss (SNHL) through targeted resequencing of 134 known deafness genes. The variant, p.L1291F and p.Y1945X, resided in the myosin motor and IQ2 domains, respectively. The p.L1291F variant was predicted to affect the structure of the actin-binding site from three-dimensional protein modeling, thereby interfering with the correct interaction between actin and myosin. From the literature analysis, mutations in the N-terminal domain were more frequently associated with residual hearing at low frequencies than mutations in the other regions of this gene. Therefore we suggest a hypothetical genotype-phenotype correlation whereby MYO15A mutations that affect domains other than the N-terminal domain, lead to profound SNHL throughout all frequencies and mutations that affect the N-terminal domain, result in residual hearing at low frequencies. This genotype-phenotype correlation suggests that preservation of residual hearing during auditory rehabilitation like cochlear implantation should be intended for those who carry mutations in the N-terminal domain and that individuals with mutations elsewhere in MYO15A require early cochlear implantation to timely initiate speech development.

• 한국산학기술학회논문지
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• 제21권1호
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• pp.656-664
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• 2020

본 연구는 일개 대학교에 재학 중인 학생들의 창의융합역량 수준을 분석하여 창의융합역량을 갖춘 인재 양성을 위한 기초자료를 마련하고자 진행되었다. 본 연구는 2018년 10월 1일부터 11월 10일까지 물리치료학과, 치위생학과, 제약공학과, 컴퓨터공학과에 재학 중인 1학년과 4학년을 대상으로 자기기입식설문을 진행하였다. 총 296명의 자료를 분석에 이용 하였으며 IBM SPSS/Win statistics 23.0 program을 사용하였다. 분석결과, 일반적 특성인 졸업 고등학교 지역이 수도권인 경우와 학과만족도가 높은 경우 창의융합역량이 높게 나타났으며 통계적으로 유의한 결과를 보였다(p<0.05). 또한, 비교과프로그램인 교내/외 경진대회, 글로벌 직무역량교육/해외연수 프로그램, 캡스톤디자인 및 팀 프로젝트 기반수업을 경험한 경우에서 통계적으로 유의미하게 높은 창의융합역량 수준을 확인할 수 있었다(p<0.05). 이에 창의융합역량을 증진 시킬 수 있는 대학 차원의 다양한 비교과목의 개발 및 운영이 이루어져야 할 필요성을 확인하였다. 본 연구결과를 바탕으로 창의융합역량 수준의 차이를 보인 다양한 변인을 확인함으로써 체계적인 교육을 통한 학생들의 창의융합역량 확장을 도모하고 새로운 가치를 창출할 수 있는 인재를 양성하기 위한 구체적 방안을 마련해야 할 것이다.

• ETRI Journal
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• 제37권2호
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• pp.212-221
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• 2015

As the amount of re-sequencing genome data grows, minimizing the execution time of an analysis is required. For this purpose, recent computing systems have been adopting both high-performance coprocessors and host processors. However, there are few applications that efficiently utilize these heterogeneous computing resources. This problem equally refers to the work of single nucleotide polymorphism (SNP) detection, which is one of the bottlenecks in genome data processing. In this paper, we propose a method for speeding up an SNP detection by enhancing the utilization of heterogeneous computing resources often used in recent high-performance computing systems. Through the measurement of workload in the detection procedure, we divide the SNP detection into several task groups suitable for each computing resource. These task groups are scheduled using a window overlapping method. As a result, we improved upon the speedup achieved by previous open source applications by a magnitude of 10.