• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2003년도 춘계 학술발표대회
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• pp.125-125
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• 2003

To assist genetic study of the root development in Panax ginseng, which is one of the most important medicinal plant, expressed sequence tags (EST) analysis was carried out. We constructed a cDNA library using the 14-year ginseng root. Partial sequences were obtained from 2,975 clone. The ESTs could be clustered into 1,991 (70.2%) non-redundant groups. Similarity search of the non-redundant ESTs against public non-redundant databases of both protein and DNA indicated that 1,553 groups show similarity to genes of blown function. These ESTs clones were divided into sixteen categories depending upon gene function. The most abundant transcripts were ribonuclease 1 (67) and ribonuclease 2 (65). Our extensive EST analysis of genes expressed in 14-year ginseng root not only contributes to the understanding of the dynamics of genome expression patterns in root organ but also adds data to the reperoire of all genomic genes.

• Genomics & Informatics
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• 제8권2호
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• pp.90-93
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• 2010

A-kinase-anchoring proteins (AKAPs) are scaffold proteins which compartmentalize protein kinase A (PKA, cAMP-dependent protein kinase) and other enzymes to specific subcellular sites. The spatiotemporal control of these enzymes by AKAPs is important for cellular function like cell growth and development etc. Hence, it is important to understand the basic function of AKAPs and their functional domains. However, diverse names, function, cellular localizations and many members of AKAPs increase difficulties when researchers search appropriate AKAPs for their experimental purpose. Nevertheless, there was no previous AKAPs-related database regardless of their important cellular functions and difficulty of finding appropriate AKAPs. So, we developed AKAPs database (AKAPDB), which contains their sequence information, functions and other information derived from prediction programs and other databases. Therefore, we propose that AKAPDB can be an important tool to researchers in the related fields. AKAPDB is available via the internet at http://plaza3.snu.ac.kr/akapdb/.

• Journal of information and communication convergence engineering
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• 제11권2호
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• pp.124-131
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• 2013

Extraction and representation of postures and/or gestures from human activities in videos have been a focus of research in this area of action recognition. With various applications cropping up from different fields, this paper seeks to improve the performance of these action recognition machines by proposing a shape-based silhouette-edge descriptor for the human body. Information entropy, a method to measure the randomness of a sequence of symbols, is used to aid the selection of vital key postures from video frames. Morphological operations are applied to extract and stack edges to uniquely represent different actions shape-wise. To classify an action from a new input video, a Hausdorff distance measure is applied between the gallery representations and the query images formed from the proposed procedure. The method is tested on known public databases for its validation. An effective method of human action annotation and description has been effectively achieved.

• The Plant Pathology Journal
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• 제17권2호
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• pp.67-70
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• 2001

Medicago truncatula is a diploid legume plant related to the forage crop alfalfa. Recently, it has been chosen as a model species for genomic studies due to its small genome, self-fertility, short generation time, and high transformation efficiency. M. truncatula engages in symbiosis with nitrogen-fixing soil bacterium Rhizobium meliloti. M. truncatula mutants that are defective in nodulation and developmental processes have been generated. Some of these mutants exhibited altered phenotypes in symbiotic responses such as root hair deformation, expression of nodulin genes, and calcium spiking. Thus, the genes controlling these traits are likely to encode functions that are required for Nod-factor signal transduction pathways. To facilitate genome analysis and map-based cloning of symbiotic genes, a bacterial artificial chromosome library was constructed. An efficient polymerase chain reaction-based screening of the library was devised to fasten physical mapping of specific genomic regions. As a genomics approach, comparative mapping revealed high levels of macro- and microsynteny between M. truncatula and other legume genomes. Expressed sequence tags and microarray profiles reflecting the genetic and biochemical events associated with the development and environmental interactions of M. truncatula are assembled in the databases. Together, these genomics programs will help enrich our understanding of the legume biology.

• ALGAE
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• 제21권2호
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• pp.169-174
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• 2006

We have cultured more than 100 Arctic and Antarctic cryophilic microalgal strains in KOPRI culture collections of polar microorganisms (KCCPM). Among them, we tried to identify an Antarctic strain, KOPRI AnM0008 by morphological and molecular analysis. Nuclear SSU rDNA and plastid rbcL sequences were used to identify the strain. It was identified as Porosira pseudodenticulata based on SSU sequence data showing 99% identity with GenBank X85398. This result was supported by morphological features like solitary labiate process, external foramina and internal cribra by optical and scanning electron microscope. Morphological identification and molecular analysis on polar cryophilic microalgae will be accomplished to construct the databases for KCCPM.

• ETRI Journal
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• 제43권3호
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• pp.483-510
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• 2021

In computational biology, desired patterns are searched in large text databases, and an exact match is preferable. Classical benchmark algorithms obtain competent solutions for pattern matching in O (N) time, whereas quantum algorithm design is based on Grover's method, which completes the search in $O(\sqrt{N})$ time. This paper briefly explains existing quantum algorithms and defines their processing limitations. Our initial work overcomes existing algorithmic constraints by proposing the quantum-based combined exact (QBCE) algorithm for the pattern-matching problem to process exact patterns. Next, quantum random access memory (QRAM) processing is discussed, and based on it, we propose the QRAM processing-based exact (QPBE) pattern-matching algorithm. We show that to find all t occurrences of a pattern, the best case time complexities of the QBCE and QPBE algorithms are $O(\sqrt{t})$ and $O(\sqrt{N})$, and the exceptional worst case is bounded by O (t) and O (N). Thus, the proposed quantum algorithms achieve computational speedup. Our work is proved mathematically and validated with simulation, and complexity analysis demonstrates that our quantum algorithms are better than existing pattern-matching methods.

• Journal of Ecology and Environment
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• 제46권2호
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• pp.126-135
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• 2022

Background: Pollinators are important ecological elements due to their role in the maintenance of ecosystem health, wild plant reproduction, crop production and food security. The pollinator-plant interaction supports the preservation of plant and animal populations and it also improves the yield in pollination dependent crops. Having knowledge about the plant-pollinator interaction is necessary for development of pesticide risk assessment of pollinators and conservation of endangering species. Results: Traditional methods to discover the relatedness of insects and plants are based on tracing the visiting pollinators by field observations as well as palynology. These methods are time-consuming and needs expert taxonomists to identify different groups of pollinators such as insects or identify flowering plants through palynology. With pace of technology, using molecular methods become popular in identification and classification of organisms. DNA metabarcoding, which is the combination of DNA barcoding and high throughput sequencing, can be applied as an alternative method in identification of mixed origin environmental samples such as pollen loads attached to the body of insects and has been used in DNA-based discovery of plant-pollinator relationship. Conclusions: DNA metabarcoding is practical for plant-pollinator studies, however, lack of reference sequence in online databases, taxonomic resolution, universality of primers are the most crucial limitations. Using multiple molecular markers is preferable due to the limitations of developed universal primers, which improves taxa richness and taxonomic resolution of the studied community.

• 한국정보과학회논문지:데이타베이스
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• 제41권4호
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• pp.249-255
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• 2014

유전체 단위 반복 변이(CNV)는 유전적 구조변이의 하나로서, 암을 포함하는 인간의 질병과 밀접한 연관성이 있는 것으로 알려져 있다. 암 유전자를 규명하기 위하여, 연구자는 특정 암 환자의 대규모 유전체 데이터를 분석하여 CNV를 찾아내야하며, 동시에 대규모 유전/임상 데이터를 연계 분석하여야 한다. 본 연구는 NGS 데이터로부터 CNV를 추출하고, 추출된 CNV와 관련된 유전/임상 정보를 체계적으로 연계 분석하는 기능을 제공하는 새로운 분석 툴 CNVDAT를 제안한다. CNV 추출 모듈은 스케일 스페이스 필터링 기법을 이용하여 CNV를 추출하며, 리드 데이터에 잡음이 포함된 경우에도 CNV의 타입/위치를 정확히 추출해낸다. 또한 시퀀스 분석 모듈은 변이 영역의 브라우징 및 상호 비교를 지원하는 사용자 친화적 프로그램으로서, 암/정상 샘플의 변이 영역의 동시 분석 기능과 refGene, OMIM DB를 기반으로 하는 CNV-유전자-표현형 매핑의 연관성 분석 기능을 제공한다. 본 프로그램의 소스 코드와 샘플프로그램은 http://dblab.hallym.ac.kr/CNVDAT/에서 다운 받을 수 있다.

• Journal of Microbiology and Biotechnology
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• 제22권4호
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• pp.555-562
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• 2012

PCR was performed to analyze the ${\beta}$-lactamase genes carried by ampicillin-resistant Vibrio spp. strains isolated from marine environments in Korea between 2006 and 2009. All 36 strains tested showed negative results in PCR with the primers designed from the nucleotide sequences of various known ${\beta}$-lactamase genes. This prompted us to screen new ${\beta}$-lactamase genes. A novel ${\beta}$-lactamase gene was cloned from Vibrio alginolyticus KV3 isolated from the aquaculture water of Geoje Island of Korea. The determined nucleotide sequence (VAK-3 ${\beta}$-lactamase) revealed an open reading frame (ORF) of 852 bp, encoding a protein of 283 amino acids (aa), which displayed low homology to any other ${\beta}$-lactamase genes reported in public databases. The deduced 283 aa sequence of VAK-3, consisting of a 19 aa signal peptide and a 264 aa mature protein, contained highly conserved peptide segments specific to class A ${\beta}$-lactamases including the specific amino acid residues STFK (62-65), SDN (122-124), E (158), and RTG (226-228). Results from PCR performed with primers specific to the VAK-3 ${\beta}$-lactamase gene identified 3 of the 36 isolated strains as V. alginolyticus, Vibrio cholerae, and Photobacterium damselae subsp. damselae, indicating the utilization of various ${\beta}$-lactamase genes including unidentified ones in ampicillin-resistant Vibrio spp. strains from the marine environment. In a mating experiment, none of the isolates transfered the VAK-3 ${\beta}$-lactamase gene to the Escherichia coli recipient. This lack of mobility, and the presence of a chromosomal acyl-CoA flanking sequence upstream of the VAK-3 ${\beta}$-lactamase gene, led to the assumption that the location of this new ${\beta}$-lactamase gene was in the chromosome, rather than the mobile plasmid. Antibiotic susceptibility of VAK-3 ${\beta}$-lactamase was indicated by elevated levels of resistance to penicillins, but not to cephalosporins in the wild type and E. coli harboring recombinant plasmid pKV-3, compared with those of the host strain alone. Phylogenetic analysis showed that VAK-3 ${\beta}$-lactamase is a new and separate member of class A ${\beta}$-lactamases.

• 한국정보과학회논문지:데이타베이스
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• 제31권5호
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• pp.468-478
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• 2004

시퀀스 데이타베이스로부터 원하는 질의 패턴과 일치하는 모든 서브 시퀀스를 검색하는 것은 데이타 마이닝이나 바이오 인포매틱스 등 응용 분야에서 필수적인 연산이다. 예를 들어, 특정한 이벤트가 발생할 때마다 이벤트의 유형과 발생 시각을 기록하는 네트웍 이벤트 관리 시스템에서 네트웍 이벤트들의 연관 관계를 발견하기 위한 전형적인 질의 형태는 다음과 같다: 'CiscoDCDLinkUp이 발생한 후 MLMStatusUP과 TCPConnectionClose가 각각 20초 이내와 40초 이내에 순차적으로 발생하는 모든 경우를 검색하라.' 본 논문에서는 대규모 이벤트 시퀀스 데이타베이스를 대상으로 하여 위와 같은 질의를 효율적으로 처리할 수 있는 인덱싱 방법을 제안한다. 기존의 방법들이 비효율적인 순차적 검색이나 페이지화 하기 어려운 인덱스 구조에 의존하는데 반하여, 제안하는 방법은 저장 및 검색 효율이 입증된 다차원 공간 인덱스를 사용하여 질의를 만족하는 모든 서브 시퀀스를 착오 기각(false dismissal) 없이 신속하게 검색한다. 다차원 공간 인덱스의 입력은 이벤트 시퀀스 데이타베이스 상의 슬라이딩 윈도우 내에서 각 이벤트 유형이 최초로 발생한 시각을 기록한 n 차원 벡터가 된다. 여기서 n은 발생 가능한 이벤트 유형의 수이다. n이 큰 경우는 차원 저주(dimensionality curse) 문제가 발생할 수 있으므로 차원 선택이나 이벤트유형 그루핑을 이용하여 차원을 축소한다. 실험 결과에 의하면 제안된 방법은 순차적 검색이나 ISO-Depth 인덱스 기법에 비하여 몇 배에서 몇 십 배의 성능 향상 효과를 갖는 것으로 나타났다. 것으로 나타났다.예측치가 비교적 유사한 것으로 나타났으며, 평균 절도오차도 10% 수준이었다.HNP 처리구에서 가장 많았던 것으로 나타났다. 지상부 식생에 대한 총 양분함량은(N+P+K+Ca+Mg) 리기다소 나무가 703kg/ha 그리고 낙엽송이 869kg/ha였다.여 주었다.능성을 시도하였고, 그 결과는 다음과 같다. 1. Cholesterol을 제거한 cheese의 제조에서 최적조건은 균질압력 1200psi(70kg$cm^2$), 균질온도 $70^{\circ}$, $\beta$-cyclodextrin 첨가량 2%였으며, 이때 우유의 cholesterol의 제거율이 86.05%로 가장 높게 나타났다. 2. Cholesterol을 제거한 cheese들의 수율은 모두 12.53%(control 10.54%) 이상으로 균질 처리가 cheese의 수율을 18.88%이상 향상시키는 것으로 나타났다. 3. 유지방 함량 23.80%인 control 치즈의 cholesterol 함량은 81.47mg/100g이었고, 균질압력 1200psi(91kg/$cm^2$)에 $\beta$-cyclodextrin 2%를 첨가한 cheese에서는 cholesterol 함량이 20.15mg/100g으로 cholesterol 제거율이 75.27%로 가장 높게 나타났다. 4. Meltability는 균질압력 1200psi(91kg/$cm^2$)에 $\beta$-cyclodextrin 1과 2%로 처리한 치즈에서 2.25cm(control 3.34cm)로 가장 낮았으며,