Comparison of the MGISEQ-2000 and Illumina HiSeq 4000 sequencing platforms for RNA sequencing

Jeon, Sol A,Park, Jong Lyul,Kim, Jong-Hwan,Kim, Jeong Hwan,Kim, Yong Sung,Kim, Jin Cheon,Kim, Seon-Young Korea Genome Organization 2019 Genomics & informatics Vol.17 No.3

Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.

Genomic and transcriptomic analysis of Korean colorectal cancer patients

Jeon Sol A,Ha Ye Jin,Kim Jong-Hwan,Kim Jeong-Hwan,Kim Seon-Kyu,Kim Yong Sung,Kim Seon-Young,Kim Jin Cheon 한국유전학회 2022 Genes & Genomics Vol.44 No.8

Background: Colorectal cancer (CRC) is the third most common type of diagnosed cancer in the world and has the second-highest mortality rate. Meanwhile, South Korea has the second-highest incidence rate for CRC in the world. Objective: To assess the possible influence of ethnicity on the molecular profile of colorectal cancer, we compared genomic and transcriptomic features of South Korean CRCs with European CRCs. Methods: We assembled a genomic and transcriptomic dataset of South Korean CRC patients (KOCRC; n = 126) from previous studies and European cases (EUCRC; n = 245) selected from The Cancer Genome Atlas (TCGA). Then, we compared the two datasets in terms of clinical data, driver genes, mutational signature, gene sets, consensus molecular subtype, and fusion genes. Results: These two cohorts showed similar profiles in driver mutations but differences in the mutation frequencies of some driver genes (including APC, TP53, PABPC1, FAT4, MUC7, HSPG2, GNAS, DENND5B, and BRAF). Analysis of hallmark pathways using genomic data sets revealed further differences between these populations in the WNT, TP53, and NOTCH signaling pathways. In consensus molecular subtype (CMS) analyses of the study cases, no BRAF mutations were found in the CMS1 subtype of KOCRC, which contrasts with previous findings. Fusion gene analysis identified oncogenic fusion of PTPRK-RSPO3 in a subset of KOCRC patients without APC mutations. Conclusions: This study presents insights into the genomic landscape of KOCRCs and reveals some similarities and differences with EUCRCs at the molecular level.

Improved Thermostability of Glutamate Decarboxylase B from Escherichia coli through Protein Engineering

Chanha JEON,Sol A GU,Jeong Chan JOO,Yong Hwan KIM 한국생물공학회 2012 한국생물공학회 학술대회 Vol.2012 No.4

Enzyme immobilization through biosilicification via R1 silaffin peptide for the enhancement of thermostability

Chanha JEON,Sol A GU,Yong Hwan KIM 한국생물공학회 2011 한국생물공학회 학술대회 Vol.2011 No.10

지금-여기에 ‘로힝야’는 어떻게 도착해 있나 : ‘로힝야 학살’에 대한 한국사회의 반응

이지은전솔비심아정신지영 ( Lee Ji-eun ),( Jeon Sol-bee ),( Sim A-jung ),( Shin Ji-young ) 민족문학사학회·민족문학사연구소 2019 민족문학사연구 Vol.71 No.-

본 논문은 미얀마의 소수민족인 로힝야에 대한 집단학살 및 로힝야 난민의 상황을 전달함으로써, 현재의 로힝야의 고통에 공감하고 알릴 수 있는 ‘청자-증언자’의 확산을 도모하고자 공동으로 집필되었다. 한국에서는 2019년 2월에 아시아인권평화디딤돌(이하 아디)이 작성 공개한 「로힝야 학살 보고서」(『경향신문』게재)를 통해 로힝야가 처한 상황이 집중보도 되었다. 이에 대한 반응 은 2018년 예멘 난민의 유입 후 한국사회가 경험 혹은 학습한‘난민에 대한 공포/혐오’, 로힝 야족이 ‘제국주의의 앞잡이’라는 비난, 무반응과 무관심으로 나타났다. 즉 로힝야 난민은 ‘우리’의 삶과 떨어져 있을 때에는 ‘연민/동정의 대상’이지만, ‘우리’의 삶에 관련된다고 여겨지게 되면 ‘배제/공포의 대상’이 되었다. 이러한 아시아의 소수민족 및 마이너리티의 배제 양상을 페이스북 등을 통한 가짜뉴스와, 시민법 개정·이동권 제한·국경봉쇄 등에 의한 ‘합법적 배제’라는 측면에서 살펴보았다. 이를 통해 ‘국적’과 ‘인권’에 기반한 시민권은 또 하나의 배제 논리임을 밝히고, ‘시민’이라는 위치의 한계를 드러냈다. 더 나아가 난민에 대한 한국사회의 배타성을 아시아의 역사 속에서 조망하면, 아시아의 식민-탈식민의 과정에서 로힝야와 같은 소수민족이나 마이너리 티가 비가시화되어왔다는 사실이 드러난다. 이러한 문제의식을 토대로 한국사회의 민주 화운동 이후에도 지속되는 마이너리티 배제에 대해 자각할 필요성이 있음을 밝혔다. 결론적으로 본 연구는 전형적인 난민재현의 방식을 벗어나 한국, 한국인이라는 독점적 위치를 해체하면서, 로힝야 난민에 대해서 ‘증언하는 청자’가 될 수 있을지를 질문하고 있다. This paper reports on the circumstances under which the Rohingya refugees are and the persecution of the Rohingya, through which we will be able to attract “audience-witnesses” who are able to empathize with and publicize the issue of Rohingya suffering. The Asian Dignity Initiative’s publication of “The Rohingya Massacre Reports” in February 2019 (which was also featured in Kyunghyang Sinmun) was the first extensive coverage of the Rohingya crisis in South Korea. The South Korean response to the Rohingya crisis can be categorized into patterns of phobia and hate speech against refugees ―stemming from the South Korean society’s encounter with the Yemeni refugees in 2018 ―and denunciation of the Rohingya for having been collaborators of imperialism. Whereas the Rohingya are to be sympathized with as long as they are distant from “our lives”, they are to be feared and excluded once the distance is removed. The paper examines the patterns of exclusion through fake news on social media and legal means such as citizenship law amendments, restriction on travel, border closure, etc. The examination reveals how the notion of citizenship based on “nationality” and “human rights” functions as another exclusionary mechanism, and therefore also exposes the limits inherent in the concept of citizen. Once the exclusionary tendency against refugees in South Korean society is set in the historical context, it is revealed that various types of minorities including the Rohingya have been rendered invisible throughout the process of colonization and de-colonization in Asia. Such findings call for the need for acknowledgement of the problem of exclusion against minority groups and the chain of refugee-ization within refugees in South Korea after the democratic transition. Lastly, the paper poses some questions whether we can avoid the stereotypical representation of refugees, dismantle the exclusive position of South Korea and South Korean national, and form an audience who bear witness to the Rohingya crisis.

CYB5R3 functions as a tumor suppressor by inducing ER stress-mediated apoptosis in lung cancer cells via the PERK-ATF4 and IRE1α-JNK pathways

Im Joo-Young,Kim Soo Jin,Park Jong-Lyul,Han Tae-Hee,Kim Woo-il,Kim Inhyub,Ko Bomin,Chun So-Young,Kang Mi-Jung,Kim Bo-Kyung,Jeon Sol A.,Kim Seon-Kyu,Ryu Incheol,Kim Seon-Young,Nam Ki-Hoan,Hwang Inah,Ba 생화학분자생물학회 2024 Experimental and molecular medicine Vol.56 No.-

Cytochrome b5 reductase 3 (CYB5R3) is involved in various cellular metabolic processes, including fatty acid synthesis and drug metabolism. However, the role of CYB5R3 in cancer development remains poorly understood. Here, we show that CYB5R3 expression is downregulated in human lung cancer cell lines and tissues. Adenoviral overexpression of CYB5R3 suppresses lung cancer cell growth in vitro and in vivo. However, CYB5R3 deficiency promotes tumorigenesis and metastasis in mouse models. Transcriptome analysis revealed that apoptosis- and endoplasmic reticulum (ER) stress-related genes are upregulated in CYB5R3-overexpressing lung cancer cells. Metabolomic analysis revealed that CYB5R3 overexpression increased the production of nicotinamide adenine dinucleotide (NAD+) and oxidized glutathione (GSSG). Ectopic CYB5R3 is mainly localized in the ER, where CYB5R3-dependent ER stress signaling is induced via activation of protein kinase RNA-like ER kinase (PERK) and inositol-requiring enzyme 1 alpha (IRE1α). Moreover, NAD+ activates poly (ADP-ribose) polymerase16 (PARP16), an ER-resident protein, to promote ADP-ribosylation of PERK and IRE1α and induce ER stress. In addition, CYB5R3 induces the generation of reactive oxygen species and caspase-9-dependent intrinsic cell death. Our findings highlight the importance of CYB5R3 as a tumor suppressor for the development of CYB5R3-based therapeutics for lung cancer.

간호대학생의 환자안전에 대한 지식, 간호전문직관과 환자안전관리활동의 관련성

김철규,유하민,김혜원,남아연,노희성,방다솔,신진의,이아현,이은경,전한용,정세림,정유정,Kim, Chul-Gyu,Yu, Ha-Min,Kim, Hye-Won,Nam, A-Yeon,Roh, Hee-Sung,Bang, Da-Sol,Sin, Jin-Ui,Lee, A-Hyun,Lee, Eun-Gyeong,Jeon, Han-yong,Jeong, Se-Lim,Jung, 한국의료질향상학회 2018 한국의료질향상학회지 Vol.24 No.2

Purpose: The objective of this study was to identify the relationship between knowledge of patient safety, nursing professionalism and patient safety management activities of nursing students with clinical practical experience. Methods: Self-administered questionnaires survey on knowledge of patient safety, nursing professionalism, and patient safety management activities were conducted for the $3^{rd}-year$ and $3^{th}-year$ nursing students. 139 questionnaires were distributed, of which, 131 were used for data analysis. Results: The scores of nursing students' knowledge of patient safety, nursing professionalism and patient safety management activities were $6.76{\pm}1.26$, $65.11{\pm}7.97$ and $67.99{\pm}7.26$, respectively. Knowledge of patient safety differed significantly according to the grade. Nursing professionalism had a difference with major satisfaction, clinical practical satisfaction, and experience of patient safety accident. Patient safety management activities were positively correlated (p<.01) with knowledge of patient safety and nursing professionalism. Patient safety management activities increased significantly with increase in the scores of knowledge of patient safety and nursing professionals. The factors that were related to patient safety management activities of nursing students were knowledge of patient safety and nursing professionalism. Knowledge of patient safety and nursing professionalism were selected as significant variables for explaining the patient safety management activities of nursing students, of which the coefficient of determination was 9.8%. Conclusion: To promote patient safety management activities of nursing students, training programs for patient safety management activities are required. Also, there is the need to increase the knowledge of patient safety and nursing professionalism of nursing students using various educational method.