NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations from next-generation sequencing data

Dong‑Jun Lee,Taesoo Kwon,Chang‑Kug Kim,Young‑Joo Seol,Dong‑Suk Park,Tae‑Ho Lee,Byung‑Ohg Ahn 한국유전학회 2020 Genes & Genomics Vol.42 No.11

Background Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Therefore, identifying sequence variations is one of the main objectives of several genome projects. Although most genomeproject consortiums provide standard operation procedures for sequence variation detection methods, there may be differencesin the results because of human selection or error. Objective To standardize the procedure for sequence variation detection and help researchers who are not formally trainedin bioinformatics, we developed the NGS_SNPAnalyzer, a desktop software and fully automated graphical pipeline. Methods The NGS_SNPAnalyzer is implemented using JavaFX (version 1.8); therefore, it is not limited to any operatingsystem (OS). The tools employed in the NGS_SNPAnalyzer were compiled on Microsoft Windows (version 7, 10) andUbuntu Linux (version 16.04, 17.0.4). Results The NGS_SNPAnalyzer not only includes the functionalities for variant calling and annotation but also providesquality control, mapping, and filtering details to support all procedures from next-generation sequencing (NGS) data to variantvisualization. It can be executed using pre-set pipelines and options and customized via user-specified options. Additionally,the NGS_SNPAnalyzer provides a user-friendly graphical interface and can be installed on any OS that supports JAVA. Conclusions Although there are several pipelines and visualization tools available for NGS data analysis, we developedthe NGS_SNPAnalyzer to provide the user with an easy-to-use interface. The benchmark test results indicate that theNGS_SNPAnayzer achieves better performance than other open source tools.

가축분뇨를 이용한 SCP 생산 균주의 분리 및 균체 단백질 생산

한석균,고유석,안태영,배동훈 한국미생물생명공학회 ( 구 한국산업미생물학회 ) 1996 한국미생물·생명공학회지 Vol.24 No.6

질소원으로서 계분을 이용하는 균주를 선별하고 계분배지에서 균체의 생육속도가 다른 균주에 비하여 우수한 균주를 분리하였다. 형태·생리학적 특성을 기초로 하여 yeast의 분류 기준과 비교하여 본 균주를 Candida sp.로 동정하였으며 본 균주를 Candida sp. D116으로 명명하였다. Poultry feces extract medium에서 4% 농도의 glucose 첨가가 균체 생육에 효과적이었다. D116 균주를 액체 발효하여 균체생산능, 요산 그리고 가용성 단백질의 변화를 조사하였다. 그 결과 약 60시간이 경과하면 액체 발효 배지내의 거의 모든 가용성 단백질 및 요산의 감소를 보였으며 균체생육은 약 36시간 배양하였을 때 최고조에 도달하였고 그 후에는 점차 감소하는 경향을 보였다. SCP의 대량생산의 결과 50%의 계분혼합 배지와 30℃의 배양 온도에서 36시간 배양하여 균주의 생육수준이 3.8×10^9 CFU/ml 농도의 균체를 생산하였고 200 L의 배양액중 약 870 g-dw의 균체를 얻었으며 생산된 군체의 조단백질 함량은 67%이었다. Production of Single Cell Protein from Poultry Feces. Suk-kyun Han, You-Suk Go, Tae-Young Ahn and Dong-Hoon Bal^1*. Deparment of Microbioligy, College of Natural Sciences, Dankook Univerity, Cheonan 330-714 and Research Center for Molecular Microbiology, Seoul Nationa University, Seoul 151-742, Korea, ^1Department of Food Engineering. College of Engineering, Dankook University, Cheonan 330-714 and Bioproducts Research Center of Yonsei University, Seoul 120-749, Korea - From the soil collected form provincial area of South Korea, a microorganisms which have been shown good growth in the minimal poultry feces extract medium was isolated. Supplement of glucose to the poultry feces extract medium helped the complete degraded during the microbial growth. Maximum cell growth (3.8×10^9 CFU/ml) obtained at 36 hours of incubation after inoculation. Uric acid was degraded faster in minimal medium that in the glucose complement medium. VFA (volatile fatty acid), which are known as major compounds of poultry feces odor, were almost removed from the minimal poultry feces extract medium. Glucose supplement to the minimal medium enhanced the growth of microbial cells. Addition of 4% of glucose and 4% of neopeptone to the minimal poultry feces extract medium helped the maximal growth of cells.

혈우병 소견을 가진 뇌출혈 환자 치험(治驗) 1례(例)

정인태,서병관,이현종,하지영,강미경,홍장무,백용현,박동석,최도영,Jung, In-tae,Seo, Byung-kwan,Lee, Hyun-jong,Ha, Ji-young,Kang, Mi-kyeong,Hong, Jang-moo,Baek, Yong-hyeon,Park, Dong-suk,Choi, Do-young 대한침구의학회 2003 대한침구의학회지 Vol.20 No.4

Objective : Hemophilia, a genetically determined disorder, is characterized by abnormality of the coagulation mechanism due to functional deficiency of a specific factor, namely VIII or IX. In this study, the effect of Dong-Si acupuncture therapy on the cerebral hemorrhage patient with hemophilia was evaluated. Methods : We treated him with acupuncture by stimulating Dong-Si acupuncture point(Yuk Wan) and assessed the effect by using manual dynamic evaluation of MRC(Medical Research Council) and Modified Barthel Index. Results : After treatment, the bleeding tendency was grossly reduced and bleeding lesion was absorbed gradually. And manual dynamic evaluation of the upper extremity increased from 4 grade to 5 grade. Conclusions : This result suggest that Dong-Si acupuncture therapy on the cerebral hemorrhage patient with hemophilia was effective. And futher studies are required to concretely prove the effectiveness of Dong-Si acupuncture therapy for treating hemorrhagic diseases.

원위 대퇴골의 고립성 골연골종에서 발생한 속발성 연골 육종 1례 보고

정필현,황장수,강석,김용민,오형호,채동주,김종필 동국대학교 경주대학 1996 東國論集 Vol.15 No.-

연골육종은 비교적 서서히 자라며 늦게 전이하는 악성 연골 종양으로 알려져 있다. 골 연골종에서 발생한 속발성 연골육종은 발생빈도는 드물며 타부위로의 전이가 적고 악성도가 낮은 경우가 많아 적합한 수술적 치료로서 좋은 예후를 보이는 것으로 보고되고 있다. 본 동국대학교 정형외과학 교실에서는 우측 대퇴골 원위부 골간단부에 생긴 고립성 골 연골종에서 이차적으로 발생한 연골육종을 치험한 바 문헌고찰과 함께 보고하는 바이다. A case of Secondary Chondrosarcoma Arising from Solitary Osteochondroma of the Distal Femur Department of Orthopaedic Surgery, College of Medicine, DongGuk University Phil Hyun Chung M.D., Jung Su Hwang M.D., Suk Kang M.D., Yang Mln Kim M.D., Hyung Ho Oh M.D., Dong Ju Chae M.D., Jong Pil Kim M.D. Chondrpsarcoma is a malignant cartilage-forming tumor that grows slowly and metastasis of this tumor occurs in late stage. Secondary chondrosarcomas arising from a solitary osteocartilaginous exostosis are rare and those have a better prognosis than other chondrosarcomas, and they rarely metastasize. We present our experience with a case of secondary chondrpsarcoma arising in solitary osteochondroma of distal metaphysis of right femur with clinical details.

Plenary Session 2 : PS-2-1 ; Outcomes of hepatitis B virus recurrence after liver transplantation: a multicenter analysis in Korea

( Hee Yeon Kim ),( Jong Young Choi ),( Dong Goo Kim ),( Myoung Soo Kim ),( Soon Il Kim ),( Shin Hwang ),( Sung Gyu Lee ),( Kwang Woong Lee ),( Kyung Suk Suh ),( Young Seok Han ),( Dong Lak Choi ),( Se 대한간학회 2012 춘·추계 학술대회 (KASL) Vol.2012 No.-

Background: The outcome of hepatitis B virus (HBV) infection after liver transplantation (LT) was improved by hepatitis B immunoglobulin (HBIG) and nucles(t)ide analogue (NUA). However, HBV recurrence after LT is critical because the recurrence is occasionally accompanied by a progressive destruction of graft and poor survival. The aims of this study were to investigate the significance HBV recurrence and identity factors associated with HBV recurrence. Methods: From October 1999 to February 2011, a total of 2684 consecutive LT recipients who underwent HBV-associated LT were retrospectively enrolled from 7 transplantation centers in Korea. Results: Prophylaxis regimens were HBIG monotherapy (67.7%) or a combination of HBIG with NUA (22.3%). The recurrence rate of HBV was 6.1% (164 recipients) during mean follow-up duration of 10.9 years. The median time from transplantation to recurrence was 2.1 years (0.1-7.9 years). Of the 1,071 patients with hepatocellular carcinoma (HCC) prior to LT, 155 patients (14.5%) had HCC recurrence after transplantation, and 48 patients (31.0%) had HBV recurrence. Of the 48 patients with recurrence of both HBV and HCC, 25 patients (52.1%) experienced HBV recurrence after HCC recurrence. In the multivariate analysis, pretransplant HCC, pretransplant HBV DNA above 5.5 log copies/mL was independent clinical factors influencing HBV recurrence after LT. The mortality rate among the recipients with HBV recurrence was 34.1% (56 recipients). Mean overall survival was 6.4 years in the HBV-recurrence group and 9.9 years in the HBV-nonrecurrence group (p<0.001). HBV recurrence was not an independent prognostic factor for overall survival. HCC recurrence was the most important factor for overall survival. Conclusions: The overall outcome of LT in HBV-related liver disease was excellent with the current prophylaxis regimen Choon Hyuck David Kwon,8 Suk-Koo Lee8 Pretransplant HBV DNA and HCC were important factors for HBV recurrence. HBV recurrence after LT did not significantly influence on the overall survival without combining of HCC recurrence.

事故와 月經週期간의 相互關係

石在鎬,咸雄,朴東哲 大韓神經精神醫學會 1981 신경정신의학 Vol.20 No.1

Although there have been many studies in the accident proneness, little attention appears to have been given to the part possibly played by menstruation. In some previous studies of menstrual disorders, it was observed that the reaction time was slow and the judgement impaired during the premenstrual period. As both judgement and reaction time are important factors in the avoidance of accidents, it was felt that a study of women involved in accidents might reveal a correlation between accident and menstruation. The author surveyed menstrual cycle of 90 patients with accidents who visited Han Gang Sacred Heart Hospital from 1st June 1979... to 31st Aug. 1980. In order to determine the phase in which they met the accidents and to explore the correlation between accident and menstruation, the menstruation cycle of 28 days was divided into seven, 4-day periods by Dalton's method. The results were as follows: The accidents of 90 patients were found to have ocurred most frequently during menstrual period(18.9%), followed by the period of the 5th day through the 8th day (16.7%), mid-cycle period (16.7%), and premenstrual period (16.7%). A total of 35.6% of the patients had accidents during menstrual and premenstrual period. The author, therefore, suggested that there was a relationship between the phases of the menstrual cycle and accidents.

3-Acetamidophenyl Acetate의 Fries Rearrangement 반응 연구

김동현, 만노즈 마니캄, 풀라레디 보꾸, 이상윤, 조정석, 정상헌 충남대학교 약학대학 의약품개발연구소 2017 藥學論文集 Vol.32 No.-

Fries rearrangement has been known as highly useful reaction for the synthesis of ortho-or para-hydroxyacylbenzene from phenyl ester in the presence of Lewis acid catalyst. Conventionally, aluminum chloride was used as catalyst. For obtaining N-(4-acetyl-3-hydroxyphenyl)acetamide, 3-acetamidophenyl acetate was subjected to Fries Rearrangement reaction using aluminum chloride. Although the desired N-( 4-acetyl-3-hydroxyphenyl)acetamide was obtained, yield was very low. In addition, regioisomer N-(2-acetyl-5-hydroxyphenyl)acetamide and unexpected N-(2-methyl-4-oxo-4H-chromen-7-yl) acet-amide were obtained. NMR study and conversion to known compollnds confirmed the substitlltion pattern of these phenylacetamides and the structure of chromen-4-ones. Under this Fries Rearrangement condition, formation of chromen-4-one was newly discovered.

청각장애학생의 조사 사용 능력

석동일,유재이 大邱大學校 再活科學硏究所 1992 再活科學硏究 Vol.10 No.1

This trestise analyzes the deaf student's capacity in use of postposition by comparing with that of normal student. Their issue contents are can be summarized into the following two points. 1.In their frequency of the use of postposition, both deaf-students and normal students have a aqual post position. But in the misuse of those deaf student's postposition is high particulary until the students of middle school, the postposition of misuse does not decrease and aqual to that of students of elelmentary school, but up to the student of high school in minute decrease. Thus we can define that deaf student's composition ability is low in quality when compared with that of normal students. 2.the analysis of deaf student's misuse of postposition shows that the misuse of adjective postposition most frequently arises, and that of subjective postposition, postposition omission, postposition addition, objective postposition are following successively. On the contarary, the misuses of indeclinable adjective postposition, descriptive postposition, subsidiary postposition are more appear in students of milddle and high school.

티탄자철석의 수성 저온산화 예비 실험

석동우 한양대학교 이학기술연구소 2001 이학기술연구지 Vol.3 No.-

티탄자철석 (titanomaghemite)은 해양지각을 이루는 현무암에 존재하는 중요한 자성광물로서 일반적으로 저온산화에 의해 양이온이 결핍된(cation-deficient) 티탄맥히마이트(titanomaghemite)로 변한다. 실험실에서 pH3.0인 반응용액을 이용하여 철성분 제거방식(removal of iron mechanism)을 통해 자연에서 일어나는 티탄맥히마이트의 자기적 특성이 민감하게 변화하는 것을 관찰하였다. 본 실험 결과는 pH 값이 다른 반응용액을 이용하여 티탄자철석에 대한 수성 저온산화 실험을 시행하면 연속적으로 증가하는 산화계수를 갖는 일련의 티탄맥히마이트를 얻을 수 있음을 지시하고 있다. Titanomagnetites, the primary magnetic mineral in submarine basalts, generally has undergone some degree of low temperature oxidation to cation-deficient titanomaghemites. Preliminary experiments of the low-temperature oxidation of titanomagnetite by the removal of iron mechanism using pH3.0 solution reveal that magnetic properties of titanomagnetite change sensitively. The results indicate that the low-temperature aqueous oxidation experiments using solutions of different pH values will yield titanomaghemite with continuously increasing oxidation parameters.

聽覺障碍兒 敎育 敎師養成 制度 및 過程의 改善

石東一 又石大學校 1988 論文集 Vol.10 No.-

In this study, I have assumed that teachers training system in the hearing-impaired education should be reformed to competency-bassed. The main purpose of this study is the presentation of a model of major study for the hearing-impaired deucation. A systematic approach to determine the curriculum by techers of the hearing-hanicapped investigated the curriculum and program of Japan, American, and German. The tendencies of foreign curriculum and program are as follows. 1. Basically, course of depth for the each handicpped is specialized. 2. According to preschool, elementary school, and secondary school, subject education is established by major study course. 3. Course of depth for the each handicapped should be given much more weight than basic common course. 4. There is a tendency of the train of audidogist in a post graduate course. 5. Especially, clinical training is weighted. According to above tendencies, I presented the model of major study for the hearing-handicapped education as follows. <elementary school> (1) Education foundation and Psychological aspects (2) Speech teaching of the hearing handicapped (Ⅰ) (3) Speech teaching of the hearing handicapped (Ⅱ) (4) Curriculum and instruction of the hearing handicapped (5) Media of the hearing handicapped education (6) Clinical trining <secondary school> (1) Education foundation and Psychlogical aspects (2) speech teaching of the hearing handicapped (3) Curriculum and Instruction of the hearing handicapped (4) Guidance of vocational and career activites (5) Media of the hearing handicappe education (6) Clinical training