• Korean Journal of Clinical Laboratory Science
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• v.52 no.4
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• pp.381-388
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• 2020

The quality control of pathological specimens is important for accurate molecular pathology testing. This study evaluated that specimen factors affecting the DNA quality during tissue processing and sample types for BRAF, EGFR, and KRAS mutations tests. One thousand seven hundred and seventy-two molecular pathology tests were investigated for the factors influencing the DNA quality, such as sample type, formalin fixation time, and reexamination status. Cytology samples stored in a saline solution had better DNA quality than commercial cytology preservation. Tissue samples fixed in formalin within 24 hours had better DNA quality than the samples fixed over 24 hours. Between the types of samples, fresh tissue samples and tissue samples with a high tumor cell density had relatively better DNA quality than the formalin-fixed paraffin-embedded (FFPE) tissues and cytology specimens. Of real-time PCR, the non-PNA Ct value increased proportionally with samples held for longer than 24 hours in formalin, and that the formalin-fixed time affects the sample DNA quality. In conclusion, the appropriate tumor cellularity and 10% neutral formalin fixation time are the most important factors for maintaining the DNA quality. These factors should be managed properly for an accurate pathological molecular test to ensure optimal DNA quality.

• Proceedings of the Korean Society of Crop Science Conference
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• 2006.04a
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• pp.576-577
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• 2006

• Clinical and Experimental Reproductive Medicine
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• v.46 no.4
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• pp.147-151
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• 2019

Objective: The aim of this study was to investigate DNA fragmentation status in human spermatozoa according to specific tail swelling patterns determined via hypo-osmotic swelling test (HOST). Methods: Frozen semen samples from 21 healthy donors were thawed and prepared by the swim-up technique for use in intracytoplasmic sperm injection. The semen samples were treated for 5 minutes as part of the HOST procedure and then underwent the sperm chromatin dispersion test using a Halosperm kit. DNA fragmentation status (large halo, medium halo, small halo, no halo, or degraded) and the specific tail swelling pattern ("a"-"g") were assessed at the level of a single spermatozoon. A total of 42,000 spermatozoa were analyzed, and the percentage of spermatozoa without DNA fragmentation (as evidenced by a large or medium halo) was assessed according to the specific tail swelling patterns observed. Results: The HOST examinations showed that > 93% of spermatozoa across all types displayed no DNA fragmentation. The percentage of spermatozoa without DNA fragmentation was 100% in type "d", 98.67% in type "g", and 98.17% in type "f" spermatozoa. Conclusion: We found that the type "d" spermatozoa displayed no DNA fragmentation, but the other types of spermatozoa also displayed very low rates of DNA fragmentation. This result may be associated with the processing of the spermatozoa by density gradient centrifugation and the swim-up technique.

• The KIPS Transactions:PartB
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• v.13B no.6 s.109
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• pp.579-584
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• 2006

This paper proposes a nonlinear template matching measure, called counting measure, as a signal detection measure that is defined as the number of on pixels in the spot area. It is applied to classify probes for an on-off type DNA chip, where each probe spot is classified as hybridized or not. The counting measure also incorporates the maximum response search method, where the expected signal is obtained by taking the maximum among the measured responses of the various positions and sizes of the spot template. The counting measure was compared to existing signal detection measures such as the normalized correlation and the median for 2390 patient samples tested on the human papiliomavirus (HPV) DNA chip. The counting measure performed the best regardless of whether or not the maximum response search method was used. The experimental results showed that the counting measure combined with the positional search was the most preferable.

• Analytical Science and Technology
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• v.27 no.3
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• pp.147-152
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• 2014

RUVIS(Reflective Ultraviolet Imaging System) is an effective equipment that detects the location of latent fingerprint at crime scene using short wavelength ultraviolet of 254 nm. In this study, the degree of DNA damage in biological samples was compared depending on the distance and time of processing using four commonly used RUVIS. 50% of DNA was damaged by treating 10 seconds at 10 cm distance in 3 types of RUVIS such as Police RUVIS, SIRCHIE mini light and SIRCHIE RUVIS. In addition, the degree of DNA damage was increased as the distance was closer and the treatment time was longer. It showed that short wavelength UV could cause DNA damage when used close to the samples at crime scene. Therefore, it was suggested to use RUVIS at a distance of at least 1 m. The degree of DNA damage was not significant by Polilight which used long wavelength ultraviolet of 350 nm. As a result, the choice and usage of which UV light and RUVIS were critical for detection of fingerprint and successful DNA typing.

• Korean Journal of Medicinal Crop Science
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• v.13 no.5
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• pp.293-297
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• 2005

A thoredoxin (CTRX) gene was cloned and characterized from a full length cDNA library prepared from taproot of three-year old Codonopsis lanceolata. A CTRX was 666 nucleotides long and has an open reading frame of 372 bp with 124 amino acid residues (pI = 4.92). The deduced amino acid sequence of the CTRX matched to the previously reported plant thioredoxin h genes. The deduced amino acid sequence of CTRX exhibited the similarity of 33-67% among previously registered thioredoxin genes. The expression of CTRX in leaves of Codonopsis lanceolata was increased by wounding and 1 mM $H_2O_2$, but decreased by 0.1 mM cadmium.

• Proceedings of the Korea Information Processing Society Conference
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• 2003.05c
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• pp.1583-1586
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• 2003

DNA 시퀀스는 A, C, G, T 네 개의 문자로 구성된 매우 긴 시퀀스로 볼 수 있다. 고속으로 유사 DNA 시퀀스를 검색하기 위하여 인덱싱 기술을 이용하는 것이 일반적이다. 그러나 검색 대상의 유전체 데이터베이스는 그 크기가 매우 크며, 또한 지수 함수적으로 크기가 급속히 증가하고 있으므로, 기존의 인덱싱 기법을 그대로 적용할 경우, 실용성에 한계가 있다. 본 논문에서는 이와 같은 문제점을 해결할 수 있는 대규모 유전체 데이터베이스를 위한 효율적인 인덱싱 기법과 질의처리 기법을 제안한다. 기본 구조로서 접미어 트라이를 사용하며, 접미어 트리 인덱스 구조의 최대 단점인 인덱스 크기를 줄일 수 있는 데이터 압축 표현 방식을 제안한다. 또한 제안된 데이터 압축 표현 방식의 디스크 기반 인덱스 구성 알고리즘과 이를 활용한 부분 시퀀스 검색 알고리즘을 보이고, 그 저장 성능의 비교 평가결과를 보인다.

• Plant Resources
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• v.8 no.3
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• pp.181-187
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• 2005

A cinnamoyl CoA reductase (CCR) cDNA (ClCCR) was isolated from tabroot mRNAs of Codonopsis lanceolata by cDNA library construction, and its expression was investigated in relation to abiotic stresses. The ClCCR is 1008 bp in length with an open reading frame (ORF) of 336 amino acids. The deduced amino acid sequence was showed high similarity with cinnamoyl-CoA reductases of P. tremuloides (AAF43141) 87%, F.${\times}$aranassa (AAP46143) 83%, L. album (CAD29427) 80%, E. gunnii (CAA66063) 72%, S. tuberosum (AAN71761) 83%. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis was revealed that the ClCCR expression was regulated by abiotic stresses.

• Proceedings of the Korea Information Processing Society Conference
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• 2001.10a
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• pp.105-108
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• 2001

cDNA(complementary DNA)를 복제(cloneing)하여 염기 서열화 한 EST(Expressed Sequence Tag) 데이터는 여러 생물체들의 염기서열 정보들과 비교를 통해 유사점을 찾거나 기능적 부위 검색을 통해 유전자 기능을 추정한 수 있어 기능 유전체 연구에 많이 사용되고 있다. EST 데이터를 식물은 특정종(Species)별로, 동물의 경우 종의 조직별로 클러스터링 함으로써 아직 알려지지 않은 종의 유전자를 밝혀낼 수 있음은 물론 유전자의 발현에 따른 단백질의 기능도 알아낼 수 있다. 따라서 이 논문에서는 NCBI에서 flatfile 형태로 제공하는 EST 데이터를 분석하여 관계형 데이터베이스로 모델링하고 구축하였다. 또한 EST 데이터의 효율적인 사용을 위하여 데이터를 특정 종의 조직별로 클러스터링하여 제공하는 시스템을 설계하고 구현하였다.

• Proceedings of the Korea Information Processing Society Conference
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• 2002.04b
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• pp.1183-1186
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• 2002

DNA 의 염기서열 탐색을 위한 유전체학의 다음 세대인 구조유전체학은 유전체 사업으로 인한 인간 게놈지도의 완성과 축적된 생물정보를 이용한 생물정보학의 발달과 함께 급속한 성장을 계속하고 있다. 포스트 게놈 시대를 맞이하여 생명현상에 대한 궁극적인 이해를 위한 노력으로 단백질의 구조와 기능에 대한 연구가 주목을 받게 되었다. 다양한 구조 규명을 위한 도구들과 단백질 정보를 관리하기 위한 데이터베이스 구축에 따른 관련 기술의 발전은, 앞으로 다가올 생물정보의 방대함을 감안할 때, 가치 있는 지식정보를 얻기 위한 데이터 마이닝 기법들을 통해서만 가능하다. 본 논문은 데이터 마이닝의 근간 기술인 연관규칙 마이닝을 응용한 효율적인 서열 연관 규칙 알고리즘을 제안하며, 단백질 구조의 예측을 위한 단백질 서열 및 DNA 서열간의 패턴 비교 및 연관성을 목적으로 한다. 또한, 공간적 시간적 복잡성을 CMS-tree 라는 자료구조를 통해 알고리즘의 확장성 및 병렬화의 기본 알고리즘으로 사용하도록 개발하였다.