• Journal of the Korean Data and Information Science Society
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• 제23권1호
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• pp.39-51
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• 2012

군집분석은 마이크로어레이 발현자료에서 유전자 혹은 표본들의 유사한 특성을 갖는 연관구조를 조사하는데 중요한 도구이다. 본 논문에서는 마이크로어레이 자료에서 계층적 군집방법, K-평균법, PAM (partitioning around medoids), SOM (self-organizing maps) 그리고 모형기반 군집방법 들의 성능을 3가지 군집 타당성 측도인 내적 측도, 안정적 측도 그리고 생물학적 측도를 가지고 비교분석하고자 한다. 모의실험을 통해 생성된 자료와 실제 SRBCT (small round blue cell tumor) 자료를 가지고 여러 가지 군집방법들의 성능을 비교하였으며 그 결과 모의실험 자료에서는 거의 모든 방법들이 3가지 군집측도에서 원래 자료와 일치하는 좋은 군집 결과를 나타내었고 SRBCT 자료에서는 모의실험 자료처럼 명확한 군집화 결과를 보여주지는 않으나 내적측도의 실루엣 너비 (Silhouette width) 관점에서는 PAM 방법, SOM, 모형기반 군집방법 그리고 생물학적 측도에서는 PAM 방법과 모형기반 군집방법이 모의실험 결과와 비슷한 결과를 얻었고 안정적 측도에서 모형기반 군집방법이 다른 방법들보다 좋은 군집결과를 보여주었다.

• 한국정보통신학회논문지
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• 제25권12호
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• pp.1935-1941
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• 2021

최근 다양한 분야에 적용되고 있는 딥러닝을 활용한 알고리즘 개발을 위해서는 양질의 풍부한 학습데이터가 갖춰져야 한다. 본 논문은 딥러닝 알고리즘 개발 시 활용도가 높고 정보 도출 시 유용한 광학 영상, 열화상, 음성 등의 생체신호 데이터를 동시에 수집하여 서버에 전송하는 생체신호 수집시스템을 제안한다. 수집기의 이동성을 높이기 위해 라즈베리 파이를 기반으로 제작하였고, 수집한 데이터는 무선 인터넷을 통해 서버로 전송한다. 복수의 수집기에서 동시에 데이터 수집이 가능하도록 피실험자별로 로그인을 위한 아이디를 부여했고, 이를 데이터베이스에 반영하여 데이터 관리가 용이하게 하였다. 제안하는 수집시스템의 활용방안을 보이기 위해 피로도 측정을 위한 생체신호 데이터 수집의 예시를 보인다.

• ALGAE
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• 제31권4호
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• pp.373-378
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• 2016

Cochlodinium polykrikoides is a red-tide forming dinoflagellate that causes significant worldwide impacts on aquaculture industries and the marine ecosystem. There have been extensive studies on managing and preventing C. polykrikoides blooms, but it has been difficult to identify an effective method to control the bloom development. There is also limited genome information on the molecular mechanisms involved in its various ecophysiology and metabolism processes. Thus, comprehensive genome information is required to better understand harmful algal blooms caused by C. polykrikoides. We estimated the C. polykrikoides genome size using flow cytometry, with detection of the fluorescence of DNA stained with propidium iodide (PI). The nuclear genome size of C. polykrikoides was 100.97 Gb, as calculated by comparing its mean fluorescence intensity (MFI) to the MFI of Mus musculus, which is 2.8 Gb. The exceptionally large genome size of C. polykrikoides might indicate its complex physiological and metabolic characteristics. Our optimized protocol for estimating the nuclear genome size of a dinoflagellate using flow cytometry with PI can be applied in studies of other marine organisms.

• 한국콘텐츠학회논문지
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• 제11권11호
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• pp.503-513
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• 2011

일반인들의 자연에 대한 감상과 생명과학의 이해는 오늘날 과학의 대중화에서 큰 역할을 차지하고 있다. 특히 일반인의 관심이 높은 전시와 같은 비형식 과학교육은 생태학, 동물행동학, 환경학 등 거시생물학적 분야의 내용이 주를 이루고 있다. 그렇지만 전문가의 참여 부재, 자연 현상의 피상적인 기술 등의 이유로 대중에게 효과적으로 전달되고 있지 않다. 정보와 지식은 그 자체로는 수용자가 곧바로 이해하고 받아 들일 만한 형태 및 구조를 가지지 못하다. 생명과학 지식을 일반인에게 효과적으로 전달하기 위해서는 콘텐츠를 유형별로 분류하고 콘텐츠화 하는 가공 과정이 필요하다. 주제의 선정 단계에서부터 내용의 편집 및 표현 단계까지의 일련의 과정으로서 관련 분야의 전문가인 과학자의 적극적인 역할이 강조된다. 콘텐츠화 과정은 과학적, 논리적 사고방식과 더불어 예술적 표현 및 소통 능력을 필요로 한다. 과학의 대중화를 위한 이론적 및 실천적 틀로서 통역의 개념을 제안한다.

• Journal of Species Research
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• 제9권4호
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• pp.492-531
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• 2020

This study is based on crane fly specimens collected from 1936-2019 and are in collections maintained at the United States National Museum, Smithsonian Institution, Washington DC, USA; the Snow Entomological Museum, University of Kansas, Lawrence, KS, USA; the Hungarian Natural History Museum in Budapest, Hungary, and the National Institute of Biological Resources, Incheon, South Korea. The genus Dicranophragma Osten Sacken, 1860 with two species D. (Brachylimnophila) transitorium (Alexander, 1941) and D. (Dicranophragma) melaleucum melaleucum (Alexander, 1933), is a new record for the Korean Peninsula. New findings of Dicranomyia (Erostrata) submelas Kato et al., 2018, Dicranoptycha venosa Alexander, 1924a, Austrolimnophila (Archilimnophila) subunicoides(Alexander, 1950b), A. (A.) unica (Osten Sacken, 1869), A. (Austrolimnophila) asiatica (Alexander, 1925), Conosia irrorata (Wiedemann, 1828), Eloeophila persalsa (Alexander, 1940), E. serenensis (Alexander, 1940), E. subaprilina (Alexander, 1919), E. ussuriana ussuriana (Alexander, 1933), E. yezoensis (Alexander, 1924b), Paradelphomyia chosenica Alexander, 1950b, and P. macracantha Alexander, 1957 are discussed. General information on genera and subgenera morphological characters, redescriptions of species based on Korean specimens, illustrations of both sexes, elevation range, period of activity, habitat information, general distribution, and a distribution map for the Korean Peninsula (including North Korea) are presented for each species.

• 한국정보과학회논문지:데이타베이스
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• 제32권1호
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• pp.24-42
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• 2005

유전체 서열을 포함하는 생물정보는 지속적으로 변화하며 이질적이고 다양하다는 특성을 갖는다. 이러한 생물 정보의 특성을 반영한 관리시스템이 요구되지만 현재 대부분의 기존 생물정보 데이타베이스는 생물 데이타에 대한 저장소로만 이용된다. 따라서 이 논문에서는 생물학 연구실 수준에서 시퀀싱 실험을 통해 생산되거나 다양한 공개용 데이타베이스로부터 수집된 염기 서열 데이타를 파일 포맷 변환, 편집, 저장 및 검색을 수행하는 서열정보관리 시스템을 제시한다. 이질적인 서열 포맷간의 파일 변환을 위하여 XML기반 BSML을 공통 포맷으로 이용한다. 서열 저장관리에서는 동일한 DNA 조각에 대한 서열 구성의 변경정보를 저장하기 위해 서열 버전을 정의하고 능동 트리거 규칙을 이용하여 변경 정보 검출 및 생성 방법을 보여준다. 트리거 기능을 이용하여 서열의 변경 정보를 자동적으로 데이타베이스에서 저장관리 할 수 있음을 보이고 성능을 평가하였다.

• Journal of Ecology and Environment
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• 제48권2호
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• pp.163-172
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• 2024

Background: Fruit bats are natural carriers of Nipah virus (NiV). The primary objective of this study is to identify potential reservoir species in a selected geographic regions. It is necessary to determine an accurate species identification of the associated reservoir bat species distributed in a specific region. Results: In this study, we collected 20 different bat specimens from the NiV-prone area of the Kushtia district. Among these, 14 were tissue samples (BT-1-14) and six were fecal samples (BF-1-6). We used the mitochondrial gene cytochrome b, one of the most abundant and frequently used genetic markers, for polymerase chain reaction amplification and sequencing. Out of the 20 samples, 12 tissue samples and 2 fecal samples were successfully amplified and sequenced. However, two tissue samples and four fecal samples yielded chimeric sequences, rendering them unsuitable for annotation. The sequences of the successfully amplified samples were compared to those deposited in the National Center for Biotechnology Information database using basic local alignment search tool to identify the bat specimen collected. The study identified six different bat species using both morphological and genetic data, which may carriers of the NiV. Conclusions: Our results suggest that additional research should be conducted to gather more information on fruit bats from different localities across the country. The study contributes to the establishment of appropriate measures for NiV carrying disease control and management.

• Journal of Ecology and Environment
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• 제42권2호
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• pp.85-89
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• 2018

Observations and video documentation of interactions between animals living in dens, cavities, and other enclosed spaces are difficult, but they play an important role in field biology, ecology, and conservation. For example, bird parents visiting nests and feeding their nestlings may provide crucial information for testing of ecological hypotheses and may easily attract attention of participants of citizen-science ecological and conservation projects. Because of the nest concealment of cavity-nesting birds, their behaviors in the nest can only be studied by using video surveillance. Professional wildlife surveillance systems are extremely expensive. Here, we describe an inexpensive video setup that can be constructed with relatively little effort and is more affordable than any previously described system. We anticipate that the relatively low cost of about 250 USD for a battery-operated system is an important feature for citizen-science type of projects and for applications in heavily populated areas where the potential for theft and vandalism may be high. Based on our experiences, we provide methodological advice on practical aspects of using this system in the field for ecological research on birds. We highlight the low cost, easiness of construction, and potential availability to a large number of observers taking part in wildlife monitoring projects, and we offer technical help to participants of such research projects.

• Journal of Ecology and Environment
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• 제40권2호
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• pp.107-119
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• 2016

Background: Previous studies on the biological integrity on habitat and landuse patterns demonstrated ecological stream health in the view of regional or macrohabitat scale, thus ignored the mesoscale habitat patterns of pool, riffle, and runs in the stream health analysis. The objective of this study was to analyze influences on the mesohabitat structures of pool, riffle, and run reaches on the fish guilds and biological integrity in Geum-River Watershed. Results: The mesohabitat structures of pool, riffle, and run reaches influenced the ecological stream health along with some close relations on the fish trophic and tolerance guilds. The mesoscale components altered chemical water quality such as nutrients (TN, TP) and BOD and these, then, determined the primary productions, based on the sestonic chlorophyll-a. The riffle-reach had good chemical conditions, but the pool-reach had nutrient enrichments. The riffle-reach had a predominance of insectivores, while the pool-reach has a predominance of omnivores. Also, the riffle-reach had high proportions of sensitive fish and insectivore fish, and the pool-reach had high proportions of tolerant species in the community composition. The intermediate fish species in tolerance and omnivorous fish species in the food linkage dominated the community in the watershed, and the sensitive and insectivorous fishes decreased rapidly with a degradation of the water quality. All the habitat patterns were largely determined by the land-use patterns in the watershed. Conclusions: Trophic guilds and tolerance guilds of fish were determined by land-use pattern and these determined the stream health, based on the Index of Biological Integrity. This study remarks the necessity to include additional variables to consider information provided by mesohabitats and land-use distributions within the selected stream stretch. Overall, our data suggest that land-use pattern and mesohabitat distribution are important factors to be considered for the trophic and tolerance fish compositions and chemical gradients as well as ecological stream health in the watershed.

• Journal of Microbiology and Biotechnology
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• 제31권4호
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• pp.601-609
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• 2021

Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan-genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.