• Title/Summary/Keyword: Editing

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Evolution of CRISPR towards accurate and efficient mammal genome engineering

  • Ryu, Seuk-Min;Hur, Junseok W;Kim, Kyoungmi
    • BMB Reports
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    • v.52 no.8
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    • pp.475-481
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    • 2019
  • The evolution of genome editing technology based on CRISPR (clustered regularly interspaced short palindromic repeats) system has led to a paradigm shift in biological research. CRISPR/Cas9-guide RNA complexes enable rapid and efficient genome editing in mammalian cells. This system induces double-stranded DNA breaks (DSBs) at target sites and most DNA breakages induce mutations as small insertions or deletions (indels) by non-homologous end joining (NHEJ) repair pathway. However, for more precise correction as knock-in or replacement of DNA base pairs, using the homology-directed repair (HDR) pathway is essential. Until now, many trials have greatly enhanced knock-in or substitution efficiency by increasing HDR efficiency, or newly developed methods such as Base Editors (BEs). However, accuracy remains unsatisfactory. In this review, we summarize studies to overcome the limitations of HDR using the CRISPR system and discuss future direction.

DNA Barcoding for the Hydrothermal Vent Crab Austinograea Species (Crustacea: Bythograeidae) from the North Fiji Basin, Southwestern Pacific Ocean

  • Lee, Won-Kyung;Ju, Se-Jong;Hou, Bo Kyeng;Kim, Se-Joo
    • Animal Systematics, Evolution and Diversity
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    • v.35 no.1
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    • pp.30-32
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    • 2019
  • The brachyuran crab Bythograeidae Williams, 1980 is common in hydrothermal vent fields worldwide and has recorded to sixteen species of six genera. In this study, we firstly determined the cytochrome c oxidase subunit 1 (CO1) DNA barcodes for the fifth species of Austinograea, A. hourdezi, from hydrothermal vent regions of the North Fiji Basin in southwestern Pacific Ocean. All CO1 DNA barcodes of A. hourdezi were identical. The interspecies variations of three bythograeid genera were 10.9-13.3% for Austinograea, 6.6-15.7% for Bythograea, and 9.7% for Gandalfus. These results would be helpful to understand taxonomy of brachyuran crabs living in hydrothermal vent fields using CO1 DNA barcodes.

A Quality Comparison of English Translations of Korean Literature between Human Translation and Post-Editing

  • LEE, IL-JAE
    • International Journal of Advanced Culture Technology
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    • v.6 no.4
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    • pp.165-171
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    • 2018
  • As the artificial intelligence (AI) plays a crucial role in machine translation (MT) which has loomed large as a new translation paradigm, concerns have also arisen if MT can produce a quality product as human translation (HT) can. In fact, several MT experimental studies report cases in which the MT product called post-editing (PE) as equally as HT or often superior ([1],[2],[6]). As motivated from those studies on translation quality between HT and PE, this study set up an experimental situation in which Korean literature was translated into English, comparatively, by 3 translators and 3 post-editors. Afterwards, a group of 3 other Koreans checked for accuracy of HT and PE; a group of 3 English native speakers scored for fluency of HT and PE. The findings are (1) HT took the translation time, at least, twice longer than PE. (2) Both HT and PE produced similar error types, and Mistranslation and Omission were the major errors for accuracy and Grammar for fluency. (3) HT turned to be inferior to PE for both accuracy and fluency.

Genome editing of immune cells using CRISPR/Cas9

  • Kim, Segi;Hupperetz, Cedric;Lim, Seongjoon;Kim, Chan Hyuk
    • BMB Reports
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    • v.54 no.1
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    • pp.59-69
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    • 2021
  • The ability to read, write, and edit genomic information in living organisms can have a profound impact on research, health, economic, and environmental issues. The CRISPR/Cas system, recently discovered as an adaptive immune system in prokaryotes, has revolutionized the ease and throughput of genome editing in mammalian cells and has proved itself indispensable to the engineering of immune cells and identification of novel immune mechanisms. In this review, we summarize the CRISPR/Cas9 system and the history of its discovery and optimization. We then focus on engineering T cells and other types of immune cells, with emphasis on therapeutic applications. Last, we describe the different modifications of Cas9 and their recent applications in the genome-wide screening of immune cells.

Genome-wide in-locus epitope tagging of Arabidopsis proteins using prime editors

  • Cheljong Hong;Jun Hee Han;Gue-Ho Hwang;Sangsu Bae;Pil Joon Seo
    • BMB Reports
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    • v.57 no.1
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    • pp.66-70
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    • 2024
  • Prime editors (PEs), which are CRISPR-Cas9 nickase (H840A)-reverse transcriptase fusion proteins programmed with prime editing guide RNAs (pegRNAs), can not only edit bases but also install transversions, insertions, or deletions without both donor DNA and double-strand breaks at the target DNA. As the demand for in-locus tagging is increasing, to reflect gene expression dynamics influenced by endogenous genomic contexts, we demonstrated that PEs can be used to introduce the hemagglutinin (HA) epitope tag to a target gene locus, enabling molecular and biochemical studies using in-locus tagged plants. To promote genome-wide in-locus tagging, we also implemented a publicly available database that designs pegRNAs for in-locus tagging of all the Arabidopsis genes.

Understanding User Motivations and Behavioral Process in Creating Video UGC: Focus on Theory of Implementation Intentions (Video UGC 제작 동기와 행위 과정에 관한 이해: 구현의도이론 (Theory of Implementation Intentions)의 적용을 중심으로)

  • Kim, Hyung-Jin;Song, Se-Min;Lee, Ho-Geun
    • Asia pacific journal of information systems
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    • v.19 no.4
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    • pp.125-148
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    • 2009
  • UGC(User Generated Contents) is emerging as the center of e-business in the web 2.0 era. The trend reflects changing roles of users in production and consumption of contents on websites and helps us to understand new strategies of websites such as web portals and social network websites. Nowadays, we consume contents created by other non-professional users for both utilitarian (e.g., knowledge) and hedonic values (e.g., fun). Also, contents produced by ourselves (e.g., photo, video) are posted on websites so that our friends, family, and even the public can consume those contents. This means that non-professionals, who used to be passive audience in the past, are now creating contents and share their UGCs with others in the Web. Accessible media, tools, and applications have also reduced difficulty and complexity in the process of creating contents. Realizing that users create plenty of materials which are very interesting to other people, media companies (i.e., web portals and social networking websites) are adjusting their strategies and business models accordingly. Increased demand of UGC may lead to website visits which are the source of benefits from advertising. Therefore, they put more efforts into making their websites open platforms where UGCs can be created and shared among users without technical and methodological difficulties. Many websites have increasingly adopted new technologies such as RSS and openAPI. Some have even changed the structure of web pages so that UGC can be seen several times to more visitors. This mainstream of UGCs on websites indicates that acquiring more UGCs and supporting participating users have become important things to media companies. Although those companies need to understand why general users have shown increasing interest in creating and posting contents and what is important to them in the process of productions, few research results exist in this area to address these issues. Also, behavioral process in creating video UGCs has not been explored enough for the public to fully understand it. With a solid theoretical background (i.e., theory of implementation intentions), parts of our proposed research model mirror the process of user behaviors in creating video contents, which consist of intention to upload, intention to edit, edit, and upload. In addition, in order to explain how those behavioral intentions are developed, we investigated influences of antecedents from three motivational perspectives (i.e., intrinsic, editing software-oriented, and website's network effect-oriented). First, from the intrinsic motivation perspective, we studied the roles of self-expression, enjoyment, and social attention in forming intention to edit with preferred editing software or in forming intention to upload video contents to preferred websites. Second, we explored the roles of editing software for non-professionals to edit video contents, in terms of how it makes production process easier and how it is useful in the process. Finally, from the website characteristic-oriented perspective, we investigated the role of a website's network externality as an antecedent of users' intention to upload to preferred websites. The rationale is that posting UGCs on websites are basically social-oriented behaviors; thus, users prefer a website with the high level of network externality for contents uploading. This study adopted a longitudinal research design; we emailed recipients twice with different questionnaires. Guided by invitation email including a link to web survey page, respondents answered most of questions except edit and upload at the first survey. They were asked to provide information about UGC editing software they mainly used and preferred website to upload edited contents, and then asked to answer related questions. For example, before answering questions regarding network externality, they individually had to declare the name of the website to which they would be willing to upload. At the end of the first survey, we asked if they agreed to participate in the corresponding survey in a month. During twenty days, 333 complete responses were gathered in the first survey. One month later, we emailed those recipients to ask for participation in the second survey. 185 of the 333 recipients (about 56 percentages) answered in the second survey. Personalized questionnaires were provided for them to remind the names of editing software and website that they reported in the first survey. They answered the degree of editing with the software and the degree of uploading video contents to the website for the past one month. To all recipients of the two surveys, exchange tickets for books (about 5,000~10,000 Korean Won) were provided according to the frequency of participations. PLS analysis shows that user behaviors in creating video contents are well explained by the theory of implementation intentions. In fact, intention to upload significantly influences intention to edit in the process of accomplishing the goal behavior, upload. These relationships show the behavioral process that has been unclear in users' creating video contents for uploading and also highlight important roles of editing in the process. Regarding the intrinsic motivations, the results illustrated that users are likely to edit their own video contents in order to express their own intrinsic traits such as thoughts and feelings. Also, their intention to upload contents in preferred website is formed because they want to attract much attention from others through contents reflecting themselves. This result well corresponds to the roles of the website characteristic, namely, network externality. Based on the PLS results, the network effect of a website has significant influence on users' intention to upload to the preferred website. This indicates that users with social attention motivations are likely to upload their video UGCs to a website whose network size is big enough to realize their motivations easily. Finally, regarding editing software characteristic-oriented motivations, making exclusively-provided editing software more user-friendly (i.e., easy of use, usefulness) plays an important role in leading to users' intention to edit. Our research contributes to both academic scholars and professionals. For researchers, our results show that the theory of implementation intentions is well applied to the video UGC context and very useful to explain the relationship between implementation intentions and goal behaviors. With the theory, this study theoretically and empirically confirmed that editing is a different and important behavior from uploading behavior, and we tested the behavioral process of ordinary users in creating video UGCs, focusing on significant motivational factors in each step. In addition, parts of our research model are also rooted in the solid theoretical background such as the technology acceptance model and the theory of network externality to explain the effects of UGC-related motivations. For practitioners, our results suggest that media companies need to restructure their websites so that users' needs for social interaction through UGC (e.g., self-expression, social attention) are well met. Also, we emphasize strategic importance of the network size of websites in leading non-professionals to upload video contents to the websites. Those websites need to find a way to utilize the network effects for acquiring more UGCs. Finally, we suggest that some ways to improve editing software be considered as a way to increase edit behavior which is a very important process leading to UGC uploading.

Bioinformatics services for analyzing massive genomic datasets

  • Ko, Gunhwan;Kim, Pan-Gyu;Cho, Youngbum;Jeong, Seongmun;Kim, Jae-Yoon;Kim, Kyoung Hyoun;Lee, Ho-Yeon;Han, Jiyeon;Yu, Namhee;Ham, Seokjin;Jang, Insoon;Kang, Byunghee;Shin, Sunguk;Kim, Lian;Lee, Seung-Won;Nam, Dougu;Kim, Jihyun F.;Kim, Namshin;Kim, Seon-Young;Lee, Sanghyuk;Roh, Tae-Young;Lee, Byungwook
    • Genomics & Informatics
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    • v.18 no.1
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    • pp.8.1-8.10
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    • 2020
  • The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www. bioexpress.re.kr/.

Cinematic Method on Kihachiro Kawamoto's works (카와모토 키하치로 작품의 영화적 표현 기법)

  • Park, Gi-Ryung
    • Cartoon and Animation Studies
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    • s.25
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    • pp.65-85
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    • 2011
  • In this essay, Japanese animator Kihachiro Kawamoto's works will be analyzed. Kawamoto made Breaking of Branches is Forbidden in 1968 and was famous for puppet animation as The Demon(1972), Dojoji Temple(1976) and House of Flame(1979) used Japanese traditional elements in his works. The themes are the agony and despair of a human being, and the narrative is developed dramatically. This is possible through a variety of techniques in animation expression. For example of this are the movement of the puppets and the lighting. In the case of Kawamoto's works, above all, it can be said that the dramatic development depends on editing - the relation of each shot to the next shot. Therefore, this analysis will focus especially on the editing of The Demon, Dojoji Temple and House of Flame. Kawamoto's method of editing will be examed and the analysis will confirm that classical continuity edting by controling space and time has been used. Namely that the effect of editing enhances dramatic development of the narrative on Kawamoto's works. This study will also discuss the benefit of using cinematic methods of in animation. Eventhough it is not essential, Kawamoto chooses cinematic method editing. Through their use, he is able to absorb the audience in the traditional Japanese world which ordinarily could be too difficult to understand through puppet animation.

Whole genome MBD-seq and RRBS analyses reveal that hypermethylation of gastrointestinal hormone receptors is associated with gastric carcinogenesis

  • Kim, Hee-Jin;Kang, Tae-Wook;Haam, Keeok;Kim, Mirang;Kim, Seon-Kyu;Kim, Seon-Young;Lee, Sang-Il;Song, Kyu-Sang;Jeong, Hyun-Yong;Kim, Yong Sung
    • Experimental and Molecular Medicine
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    • v.50 no.12
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    • pp.1.1-1.14
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    • 2018
  • DNA methylation is a regulatory mechanism in epigenetics that is frequently altered during human carcinogenesis. To detect critical methylation events associated with gastric cancer (GC), we compared three DNA methylomes from gastric mucosa (GM), intestinal metaplasia (IM), and gastric tumor (GT) cells that were microscopically dissected from an intestinal-type early gastric cancer (EGC) using methylated DNA binding domain sequencing (MBD-seq) and reduced representation bisulfite sequencing (RRBS) analysis. In this study, we focused on differentially methylated promoters (DMPs) that could be directly associated with gene expression. We detected 2,761 and 677 DMPs between the GT and GM by MBD-seq and RRBS, respectively, and for a total of 3,035 DMPs. Then, 514 (17%) of all DMPs were detected in the IM genome, which is a precancer of GC, supporting that some DMPs might represent an early event in gastric carcinogenesis. A pathway analysis of all DMPs demonstrated that 59 G protein-coupled receptor (GPCR) genes linked to the hypermethylated DMPs were significantly enriched in a neuroactive ligand-receptor interaction pathway. Furthermore, among the 59 GPCRs, six GI hormone receptor genes (NPY1R, PPYR1, PTGDR, PTGER2, PTGER3, and SSTR2) that play an inhibitory role in the secretion of gastrin or gastric acid were selected and validated as potential biomarkers for the diagnosis or prognosis of GC patients in two cohorts. These data suggest that the loss of function of gastrointestinal (GI) hormone receptors by promoter methylation may lead to gastric carcinogenesis because gastrin and gastric acid have been known to play a role in cell differentiation and carcinogenesis in the GI tract.

Automatic Drawing and Structural Editing of Road Lane Markings for High-Definition Road Maps (정밀도로지도 제작을 위한 도로 노면선 표시의 자동 도화 및 구조화)

  • Choi, In Ha;Kim, Eui Myoung
    • Journal of the Korean Society of Surveying, Geodesy, Photogrammetry and Cartography
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    • v.39 no.6
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    • pp.363-369
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    • 2021
  • High-definition road maps are used as the basic infrastructure for autonomous vehicles, so the latest road information must be quickly reflected. However, the current drawing and structural editing process of high-definition road maps are manually performed. In addition, it takes the longest time to generate road lanes, which are the main construction targets. In this study, the point cloud of the road lane markings, in which color types(white, blue, and yellow) were predicted through the PointNet model pre-trained in previous studies, were used as input data. Based on the point cloud, this study proposed a methodology for automatically drawing and structural editing of the layer of road lane markings. To verify the usability of the 3D vector data constructed through the proposed methodology, the accuracy was analyzed according to the quality inspection criteria of high-definition road maps. In the positional accuracy test of the vector data, the RMSE (Root Mean Square Error) for horizontal and vertical errors were within 0.1m to verify suitability. In the structural editing accuracy test of the vector data, the structural editing accuracy of the road lane markings type and kind were 88.235%, respectively, and the usability was verified. Therefore, it was found that the methodology proposed in this study can efficiently construct vector data of road lanes for high-definition road maps.