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.

녹동균 세포외막 단백질 백신 CFC-1-101의 안정성 및 면역원성 검토 : 임상 제 Ⅰ/Ⅱa상 시험

장인진,김익상,유경상,임동석,김형기,신상구,장우현,박완제,이나경,정상보,안동호,조양제,안보영,이윤하,김영지,남성우,김현수 대한감염학회 1998 감염 Vol.30 No.3

목적 : 제일제당에서는 녹농균의 세포외막 단밸질을 유효성분으로 하는 백신인 CFC-101을 개발하였으며, 동물시험에서 이 백신의 안전성과 유효성을 입증하였다. 본 연구에서는 이 녹농균 백신의 인체에 대한 안전성과 면역원성을 평가하는 동시에 인체 접종시의 최적 투여 용량을 결정하기 위하여 제 I/Ⅱa상 임상시험을 수행하였다. 방법 : 건강한 성인 남자를 피험자로 선별하여 각 용량군에 백신투여자 6명, 위약투여자 2명을 배정하였다. 백신 투여군은 0.25mg, 0.5mg 또는 1.0mg 용량의 녹농균 백신을 7일 간격으로 3회에 걸쳐 근육주사 하였으며, 위약 투여군에게는 세포외막 단백질을 제외한 동일한 성분을 투여하였다. 백신접종 후 국소적 또는 전신적인 반응의 발생여부를 관찰하고, 혈액시료를 체취하여 백신의 역가와 유효성을 검정하였다. 결과 : 녹농균 백신 CFC-101은 모든 접종자에서 양호한 내약성을 보였다. 또한 0.5mg 과 1.0mg 백신 투여군에서는 100%의 항체양전율을 나타내었다. 생성된 항체는 녹농균 세포외막단백질에 특이성을 보였고, 녹농균 감염에 대해 방어효능이 있었다. 결론 : 이와같은 결과로부터 이 녹농균 백신은 인체에 안전하게 투여할 수 있으며, 높은 항체 생성능으로 감염방어 효능을 보이고 0.5mg과 1.0mg이 최적용량인 것으로 판단되었다. Background : We developed a Pseudomonas aeruginosa outer membrane protein(OMP) vaccine CFC-101, and the prophylactic efficacy of which has been demonstrated in animal models. In order to evaluate the safety and immunogenicity of the P. aeruginosa vaccine, we carried out a phase I/Ⅱa clinical trial in healthy male volunteers. Methods : Groups of eight volunteers, including two placebo subjects, were vaccinated intramuscularly with three doses of 0.25, 0.5 or 1.0 mg of the vaccine at one week intervals. Sings of systemic and local reactions observed after vaccination were recorded for each vaccinee for 5 days. Physical examinations were performed on days 0, 1, 7, 8, 14, 15, 21, and 42, and clinical laboratory tests were done on days 0, 3, and 21. Blood samples for assay of serum antibody levels were obtained up to 42 days after the first vaccination. Results : The vaccine was generally well tolerated by all vaccinees, showing no significant side effects. In the three dosage groups, all vaccinees, except one receiving the 0.25 mg dose, showed significant elevation in serum IgG antibody titers against the vaccine proteins, indicating 100% seroconversion in 0.5 and 1.0 mg groups. The human antibodies induced by the vaccine were specific for P. aeruginosa OMPs, as confirmed by western blot analysis and immunoprecipitation assays. The capacity of the human antisera to enhance opsonophagocytic killing activity by polymorphonuclear leukocytes and to confer protection against P. aeruginosa infections indicates that the antibodies elicited by the vaccine have protective efficacy. Conclusion : We conclude that the P. aeruginosa OMP vaccine is safe and effective for human use and its optimal dose to be 0.5 or 1.0 mg.

초음파 센서를 이용한 무궤도 반송차의 위치 및 방향제어

안중환,김화영,임한석,김동신 부산대학교 공과대학 1989 硏究報告 Vol.38 No.-

The system that could control a position and a direction of a vehicle by means of supersonic sensors was developed. It is composed of a microcomputer, two couples of supersonic sensor, a vehicle, a power supply and interfaces. Two senders are located at a distance on the vehicle and two receivers are located at two reference coordinate points. Supersonic propagation time from each sender to each receiver was conveniently measured in terms of the repeating number of a short machine language program. Experimental results showed that a repeating number was nearly linear with a corresponding distance. Using four measurements, the present position and direction of the vehicle were calculated .And the amounts of distance to be moved and angles to be rotated to get a destination position and direction were calculated. These data were used for controlling the vehicle driven by two wheel step. Judging from movement tests, the controllability and the accuracy of position an direction of a vehicle using supersonic sensors were quite satisfactory.

원자력현미경 측정정보를 이용한 미세접촉 현상 분석

안효석,장동영 한국공작기계학회 2008 한국공작기계학회 춘계학술대회논문집 Vol.2008 No.-

In micro/nano-scale contacts in MEMS and NEMS, capillary and van der Waals forces generated around contacting micro-asperities significantly influence the performance of concerning device as they are related to adhesion and stiction of interacting surfaces, In this regard, it is of prime importance to accurately estimate the magnitude of surface forces so that an optimal solution for reducing friction and adhesion of micro/nano-surfaces may be obtained. We introduce an effective method to calculate these surface forces based on topography information obtained from an atomic force microscope

男性不育에 關한 文獻的 考察

安世永,曺東鉉,杜鎬京,朴民豪 慶熙大學校韓醫科大學韓醫學硏究所 1995 慶熙韓醫大論文集 Vol.18 No.2

I could get to the conclusions as follows after studying our professors Drs' books and current magazine on Male Infertility. 1. Most of Drs. considered the reason of male infertility as Weakness(虛勞), which specially meant Jung(精)(the essence of life, or in this case could be semen) scarcity, Jung coldness, Jung lackness. They attributed the infertility to the seminal disorder. 2. In the treatment for male infertility, they emphasized the principle of reinforcing Shin(腎) and rearing Jung and presented correcting inclination as the major treatment. 3. In the medication for male infertility, they presented both special decoction and common medication through analyzing clinical symptoms. Especially, they warned to be deliberate in using hot and blazing ingredients. 4. They emphasized the regimen as the way of gathering and preserving Jung. 5. The unification of Oriental and occidental medicine is the current trend in treating the male infertility. And the analysis of the causes using the advanced diagnostic exams is prominent. 6. Spleen weakness(脾虛), liver stagnation(肝鬱) and phligm stasis(痰壅) could be the cause of male infertility, but the main cause was Shin weakness(腎虛). 7. New trials such as Acupoint Injection and Heating Acupunture as well as new decoction, acupuncture and moxibustion are being explored for curing the male infertily.

제주도 주변해역에서 발생하는 해양사고의 유형과 원인에 관한 연구

안영화,최찬문,김동근 제주대학교 해양과환경연구소 2001 해양과환경연구소 연구논문집 Vol.25 No.-

1.380 marine incidents occurred in the adjacent sea of Jeju Island, between 1990 - 1999, these were analysed using data from the National Maritime Police Agency. The occurrence rate of marine incidents is fishing vessels about 93%, which of form is the engine troubles 61.6% of the whole and these are human factors resulting from careless operation and poor engine maintenance, this accounted for the main pattern of incidents and great number of them occurred with fishing vessels per a year average are about 138, that if higher than the another seas. On research about marine security kind of work present condition of fish vessel crew in Juju Island is that each long line and books occupy 42% the whole license of crew is that small vessel driver 60%, six degree 35% and most of marine incidents in the fishing vessel cause frequently the engine troubles, propeller troubles lack of ability of repair and crews almost posses the small license

딤플형 내부구조체를 가진 Isb 판넬의 정적 굽힘 특성

안동규,문경제,한길영 朝鮮大學校 機械技術硏究所 2006 機械技術硏究 Vol.9 No.1

본 연구에서는 덤플형 내부 구조제를 가진 ISB 판넬의 굽힘 및 파손 특성을 분석/고찰하고자 한다. 딩플형 내부 구조체를 가진 ISB 판넬의 설계조건에 따른 변형 형상, 최대하중 및 최대하중에서의 변위와 같은 특성치 및 파손 형태를 분석하기 위하여 정적 3접 굽힘 시 험을 통한 하중-변위 곡선과 파손 형상을 얻었다. 또한, 본 실험 결과를 이용하여 ISB 판 넬 설계 변수의 굽힘 특성 및 파손 모드 영향성을 분석하였다. 본 연구 결과 딩플형 내부 구조체를 가진 ISB 판넬의 굽힘 및 파손 특성은 덤플형 내부구조체의 반경비와 ISB 판넬 의 재료 방향에 따라 제어 가능함을 알 수 있었다. The objective of this pater is to investigate into bending and failure characteristics of ISB panel with dimple shapes as inner structures. Through three-points bending test, the force-displacement curve and the failure shape are obtained to examine the deformation pattern, characteristic data including maximum load and displacement at the maximum load and failure pattern for the ISB panel. In addition, the influence of design parameters for ISB panel on the bending stiffness and failure mode has been found. From the results of the experiments, it has been shown that bending and failure characteristics of the ISB panel can be controlled by the ratio of radius and the direction of the material.

파라캇에 의한 대뇌 피질 손상 : 증례 보고

안미영,신동익,이형석,백신혜,이성현,이상수 충북대학교 의과대학 충북대학교 의학연구소 2010 忠北醫大學術誌 Vol.20 No.1

Paraquat is widely used as a universal herbicide. Paraquat induces brain damage in case of fatal poisoning. It is well documented that paraquat exposure is associated with Parkinson's disease. However, many reports suggest paraquat is not selective for the dopaminergic nigro-strial system. Preferably, there are reports that cortical neurons were found to be more sensitive to paraquat. A39-year-old woman committed suicide by drinking 20 ml of a 20% solution of Paraquat. After 5 days, she had a convulsive seizure and lost consciousness. Brain MRI showed diffuse cerebral cortical edema of bilateral frontal and temporal lobes. She died 2 days after progressive pulmonary fibrosis. Here, we report a patient with paraquat induced cortical lesion. 파라캇은 세계적으로 널리 쓰이는 제초제이다. 파라캇은 중독되었을 경우 뇌손상을 일으키기도 한다. 파라캇과 파킨슨병과의 관련성은 비교적 잘 알려져 있다. 하지만, 파라캇이 도파민 줄무늬흑체 계통(dopaminergic nifro-striatal system)에 선택적이지 않다는 많은 보고들이 있다. 오히려, 대뇌피질이 파라캇 중독에 더욱 민감하다는 일부 보고들도 있다. 39세 여자환자가 자살할 목적으로 20% 농도의 파라캇 20 ml를 마시고 본원에 내원하였다. 환자는 입원 5일째 갑자기 전신 발작 증상과 함께 의식 저하 소견을 보였다. 다음날 시행한 뇌자기공명영상 촬영상 양쪽 측두엽과 전두엽에 대칭성 세포 도겅부종 소견을 보이고 있었다. 그녀는 2일 후 폐섬유화증에 의한 호흡부전으로 사망하였다. 저자들은 파라캇 중독 환자에서 대뇌 피질 손상을 확인한 1예를 경험하였기에 보고하는 바이다.

사람-사람 하이브리도마의 생산을 위한 fusion partner cell의 개발

안지영,김혜원,서동상 성균관대학교 생명과학자원연구소 1995 生命資源科學硏究 Vol.2 No.1

This study was performed to establish human hybridmyeloma cell lines as fusion partner cells for producing human-human hybridoma. Human myeloma, SKO-007(J3), and human cervix epitheloid carcinoma cell line, HeLa MR, were fused by using with 50% PEG, and cultured in RPMI 1640 medium containing 15% FBS. Hybrids of SKO-007(J3) and HeLa MR were selected in RPMI 1640 media containing 6-thioguanine(6-TG ; gradually increasing concentration from 10 ㎍/ml to 20 ㎍/ml, and then gradually decreasing to 10 ㎍/ml) for 6 weeks. 6-TG resistant cells were collected and cloned by limiting dilution method. The fused myelomas with HeLa MR grew more rapidly than the fused cells with a small number of HeLa MR. Their doubling time was 72 hours.