• 응용통계연구
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• 제22권1호
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• pp.115-127
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• 2009

The purpose of statistical analyses of array-CGH experiment data is to divide the whole genome into regions of equal copy number, to quantify the copy number in each region and finally to evaluate its significance of being different from two. Several statistical procedures have been proposed which include the circular binary segmentation, and a Gaussian based local regression for detecting break points (GLAD) by estimating a piecewise constant function. We propose in this note a penalized spline regression and its simultaneous confidence band(SCB) approach to evaluate the statistical significance of regions of genetic gain/loss. The region of which the simultaneous confidence band stays above 0 or below 0 can be considered as a region of genetic gain or loss. We compare the performance of the SCB procedure with GLAD and hidden Markov model approaches through a simulation study in which the data were generated from AR(1) and AR(2) models to reflect spatial dependence of the array-CGH data in addition to the independence model. We found that the SCB method is more sensitive in detecting the low level copy number alterations.

• Genomics & Informatics
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• 제12권4호
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• pp.136-144
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• 2014

Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs), are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.

• ALGAE
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• 제32권3호
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• pp.189-197
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• 2017

To quantify the abundance of the harmful dinoflagellate Cochlodinium polykrikoides in natural seawaters, we developed the innovative procedure using a droplet digital PCR (ddPCR) with C. polykrikoides-specific primers targeting the internal transcription sequence (ITS). The abundance of C. polykrikoides was estimated by the specific copy number of target ITS DNA segments per cell in cultures and natural water samples. The copy number per C. polykrikoides cell as acquired by ddPCR was $157{\pm}16$, which was evaluated against known cell numbers through a simplified protocol preparing DNAs. The abundances of C. polykrikoides in the waters of different locations estimated by ddPCR agreed with the number of cells visually counted under a microscope. This protocol was used to measure the abundance of C. polykrikoides close to and further off the southern coast of Korea in August of 2016 and 2017. The practical application showed that this method can reduce time for analysis and increase accuracy.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2001년도 추계학술발표대회
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• pp.99-102
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• 2001

본 연구에서는 히루딘을 생산할 수 있는 재조합 S. cerevisiae 에서 ‘히루딘 유전자의 copy number 와 히루딘 발현양과의 관계를 규명하였으며 , ${\delta}$ 서열을 이중으로 사용한 히루딘 발현벡터를 제조하여 히루딘 유전자의 효모염색체로의 도입효율을 증가시켰다. 숙주세포인 효모의 GALl 유전자를 파쇄하여 균체에 의한 갈락토스 소모를 방지하여 보다 경제적으로 히루딘을 생산할 수 있는 시스템을 개발하였으며, 재조합 H. polymorpha을 이용한 발효공정에서 히루딘 생산을 위한 최적의 메탄올 농도를 결정하였다.

• ALGAE
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• 제37권4호
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• pp.281-291
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• 2022

Quantifying the abundance of Chattonella species is necessary to effectively manage the threats from ichthyotoxic raphidophytes, which can cause large-scale mortality of aquacultured fish in temperate waters. The identification and cell counting of Chattonella species have been conducted primarily on living cells without fixation by light microscopy because routine fixatives do not retain their morphological features. Species belonging to the Chattonella marina complex, including C. marina and C. marina var. ovata, had high genetic similarities and the lack of clear morphological delimitations between the species. To estimate the abundance of C. marina complex in marine plankton samples, we developed a protocol based on the droplet digital polymerase chain reaction (ddPCR) assay, with C. marina complex-specific primers targeting the internal transcribed spacer (ITS) region of the rDNA. Cell abundance of the C. marina complex can be determined using the ITS copy number per cell, ranging from 25 ± 1 for C. marina to 112 ± 7 for C. marina var. ovata. There were no significant differences in ITS copies estimated by the ddPCR assay between environmental DNA samples from various localities spiked with the same number of cells of culture strains. This approach can be employed to improve the monitoring efficiency of various marine protists and to support the implementation of management for harmful algal blooms, which are difficult to analyze using microscopy alone.

• 미생물학회지
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• 제32권2호
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• pp.115-119
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• 1994

Staphylococcus aureus DH1에서 분리된 R-plasmid pSBK203상의 복제개시 인자인 rep 유전자산물의 발현이 어떻게 조절되는가를 밝히기 위해 관련 부위를 확인하고 cloning한 후 그 염기서열을 결정하였으며 이를 같은 계열에 속하는 pT181족 plasmid들의 서열과 그 상동성을 비교 분석하였다. 복제 조절 관련 부위에 염기 삽입 및 염기 결손을 유도함으로써 얻어진 변이체들의 copy수를 측정하여 그 복제 조절 기능에 초래된 변화를 확인하였다.

• 전자공학회논문지S
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• 제35S권10호
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• pp.52-63
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• 1998

본 논문에서는 기존의 멀티캐스트 패킷 교환기의 문제점에 대한 개선 방안을 제안한다. 오버플로우에 의해 야기 되는 입력포트의 공평성 문제는 임의의 입력 포트로부터 복사 수를 가산 할 수 있는 동적 시작점 결정기에 의해 해결된다. 시작점은 매 타임 슬롯 마다 입력 버퍼의 점유도와 이전 타임 슬롯의 오버플로우를 기반으로 가변 된다. 입력 버퍼의 점유도를 이용함으로서 제안된 복사망은 기존의 방식에 비해 입력 트래픽의 변동에 대하여 우수한 적응성을 제공한다. 동적 시작점 결정기는 입력 트래픽의 양에 따라 복사 요청의 수를 제어하며 이것은 복사망의 전체 스루풋을 제고하는 필수적인 기능 이다. 오버플로우 발생시에 멀티캐스트 스위치의 스루풋을 향상시키는 호-분할(call-splitting) 방식도 동적 시작점 결정기에 의해 제공된다. 동적 시작점 결정기의 하드웨어는 고속 동작에 적합한 단순한 구조로 도출된다. 제안된 방식의 성능 평가를 위해 다양한 트래픽에 대한 모의 실험 결과가 제공된다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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• pp.125-126
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• 2006

NimbleGen has developed strategies to use its high-density oligonucleotide microarray platform (385,000 probes per array) to map both promoter binding sites and copy number variation at very high-resolution in the human genome. Here we describe a genome-wide map of active promoters determined by experimentally locating the sites of transcription imitation complex binding throughout the human genome using microarrays combined with chromatin immunoprecipitation. This map defines 10,567 active promoters corresponding to 6,763 known genes and at least 1,196 un-annotated transcriptional units. Microarray-based comparative genomic hybridisation (CGH) is animportant research tool for investigating chromosomal aberrations frequently associated with complex diseases such as cancer, neuropsychiatric disorders, and congenital developmental disorders. NimbleGen array CGH is an ultra-high resolution (0.5-50 Kb) oligo array platform that can be used to detect amplifications and deletions and map the associated breakpoints on the whole-genome level or with custom fine-tiling arrays. For whole-genome array CGH, probes are tiled through genic and intergenic regions with a median probe spacing of 6 Kb, which provides a comprehensive, unbiased analysis of the genome.

• 한국유기농업학회지
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• 제23권4호
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• pp.847-858
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• 2015

인삼뿌리썩음병에 길항력이 있는 Bacillus amyloliquefaciens GR4-5 균주 처리 전 후의 토양 내 Bacillus spp. 밀도 변화를 qPCR을 이용하여 분석하였다. 실내배양시험에서는 GR4-5 균주 처리 직후부터 4주째까지 Bacillus sp. group의 유전자 수가 무처리구보다 약 100배 이상으로 유지되는 경향이었다. 실외매몰시험과 포장시험에서는 유의차는 없었지만 경향으로 보아 GR4-5 처리구와 무처리구의 B. subtilis group 유전자 수가 비슷한 수준이 되는데 걸리는 시간은 7일 내외로 나타났다. 토양에 접종된 미생물의 생존에는 환경요인이 큰 영향을 미치며 그 중에서도 온도와 미생물의 격리 정도가 가장 큰 인자로 추정된다. 또한 GR4-5 균주의 생존에는 토양의 수분 함량 변화보다는 균주 처리 방법에 의한 영향이 더 크게 작용하는 것으로 보인다. 본 연구결과를 고려하면, B. amyloliquefaciens GR4-5 균주를 생물적 방제제로 사용하고자 한다면 7일 간격으로 관주 처리하는 것이 식물병원균 억제 및 근권 정착에 유리한 환경을 조성할 수 있을 것으로 판단된다. 또한 본 연구에서 제작한 실외 마이크로코즘 시스템은 제어하기 어려운 외부 환경 요인을 최소로 하여 유용미생물의 토양 내 생존 패턴을 분석하기 위한 간편한 방법으로서 유용하게 사용될 수 있을 것으로 판단된다.

• Journal of information and communication convergence engineering
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• 제12권3호
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• pp.181-185
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• 2014

The lifetime of a solid-state drive (SSD) is limited because of the number of program and erase cycles allowed on its NAND flash blocks. Data cannot be overwritten in an SSD, leading to an out-of-place update every time the data are modified. This result in two copies of the data: the original copy and a modified copy. This phenomenon is known as write amplification and adversely affects the endurance of the memory. In this study, we address the issue of reducing wear leveling through efficient handling of write requests. This results in even wearing of all the blocks, thereby increasing the endurance period. The focus of our work is to logically divert the write requests, which are concentrated to limited blocks, to the less-worn blocks and then measure the maximum number of write requests that the memory can handle. A memory without the proposed algorithm wears out prematurely as compared to that with the algorithm. The main feature of the proposed algorithm is to delay out-of-place updates till the threshold is reached, which results in a low overhead. Further, the algorithm increases endurance by a factor of the threshold level multiplied by the number of blocks in the memory.