• Journal of Ecology and Environment
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• 제34권3호
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• pp.323-331
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• 2011

Biodiversity and the community composition of micro-eukaryotic organisms were investigated in the Upo wetland in Korea using molecular analysis. Molecular identification was performed using cytochrome oxidase I (COI) and small subunit ribosomal DNA (SSU rDNA). The genomic DNA was isolated directly from soil samples. The COI and SSU rDNA regions were amplified using universal primers and then sequenced after cloning. In a similarity search of the obtained sequences with BLAST in the Genbank database, the closely related sequences from NCBI were used to identify the amplified sequences. A total of six eukaryotic groups (Annelida, Arthropoda, Rotifera, Chlorophyta, Bacillariophyta, and Stramenopiles) with COI and six groups (Annelida, Arthropoda, Rotifera, Alveolata, Fungi, and Apicomplexa) with SSU rDNA genes were determined in the Upo wetland. Among 38 taxa in 20 genera, which are closely related to the amplified sequences, 10 genera (50%) were newly reported in Korea and five genera (25%) were shown to be distributed in the Upo wetland. This approach is applicable to the development of an efficient method for monitoring biodiversity without traditional taxonomic processes and is expected to produce more accurate results in depositing molecular barcode data in the near future.

• Journal of Microbiology
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• 제45권3호
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• pp.193-198
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• 2007

A marine bacterium was isolated from Mai Po Nature Reserve of Hong Kong and identified as Vibrio cholerae MP-1. It contains a small plasmid designated as pVC of 3.8 kb. Four open reading frames (ORFs) are identified on the plasmid, but none of them shows homology to any known protein. Database search indicated that a 440 bp fragment is 96% identical to a fragment found in a small plasmid of another V. cholerae. Further experiments demonstrated that a 2.3 kb EcoRI fragment containing the complete ORF1, partial ORF4 and their intergenic region could self-replicate. Additional analyses revealed that sequence upstream of ORF1 showed the features characteristic of theta type replicons. Protein encoded by ORF1 has two characteristic motifs existed in most replication initiator proteins (Rep): the leucine zipper (LZ) motif located at the N-terminal region and the alpha helix-turn-alpha helix motif (HTH) located at the C-terminal end. The results suggest that pVC replicates via the theta type mechanism and is likely a novel type of theta replicon.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 추계학술대회
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• pp.32-32
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• 2018

Flora investigations in Korea have been conducted by many researchers for diverse purposes. Accumulated flora investigation data has not been utilized efficiently because there is no accessible database for comparison. To overcome this shortcoming, we constructed web-based database of flora investigation, named as the Integrated Korean Flora Database (IKFD; http://www.floradb.net/intro.php). Until now, 284 flora references (263 papers, 14 reports and books, and 7 unpublished papers written in between 1962 and 2017) were digitalized into the database. From 134,711 records, 4,301 species belonging to 228 families and 1,079 genera were identified via mapping with two major Korean plant species lists. Polygon areas originated from references were used for distribution of plant species, identifying precise distribution area. It will be a better index to show plant ecological characteristics. Collected micro-climate data provided by Korea Meteorology Administration were also integrated in IFKD for understanding correlation between distribution of plants and micro-climate. Cold hardiness zone which has been utilized for classifying climate zones. 12 out of 26 zones identified based on micro-climate data in Korea were mapped with distribution of plants. More than half species were appeared in zone 6a, 6b, 7a, and 7b. Taken together with these results, IKFD will be a fundamental platform for understanding plants in Korea flora investigation as well as a new standard for classifying distribution of plants. Moreover, Biodiversity Observation Database (BODB; http://www.biodiversitydb.info/intro.php) which integrates plant distribution data was also integrated for further studies.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2018년도 춘계학술발표회
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• pp.16-16
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• 2018

Flora investigations have been conducted by many researchers for a long time in Korea. Even though large amount of investigation data has been accumulated, there is no accurate statistics or database because most of data were published in a printed form. We developed a web-based database of flora investigation, named as the Integrated Korean Flora Database (http://www.floradb.net/) to understand distribution patterns and habitats of plants in Korea. Till now, 480 published paper, 356 thesis, 76 reports and books, and 8 unpublished papers written in between 1962 and 2017 were collected and their species lists from 280 papers were parsed into the database. From 124,105 records, 3,100 species belonging to 206 families and 965 genera were identified via comparing with two major Korean plant species lists. 55 endangered species, 159 endemic species, and 367 rare species were identified. The most frequently surveyed species were Commelina communis in herbaceous and Rosa multiflora in woody plants. Microclimate data provided by Korea Meteorological Administration were also integrated and analyzed to assign cold hardness zones for each species. By comparing minimum temperature (<2%) acquired from automated weather stations (AWS) near by plant species, 6a to 10b zones (7b is the most frequent zone) were identified. Integrated Korean Flora Database will be a fundamental platform of korea flora investigation as well as a new standard for classifying distribution of plants based on accurate microclimate data. Moreover, it can also provide evidences of investigated plant species, such as specimen and/or pictures with connecting to the InfoBoss Cyber Herbarium (http://herbarium.infoboss. co.kr/) and Biodiversity Observation Datbase (BODB; http://www.biodiversitydb.org/).

• 한국해양학회지:바다
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• 제15권1호
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• pp.25-35
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• 2010

플랑크톤의 종다양성은 특정 지역의 수계환경 변화 모니터링에 있어 중요 생태지표로써, 환경 평가에 유용한 정보로 사용되고 있다. 기존의 종다양성 평가는 주로 형태학적 형질에 근거한 종동정을 통해 이루어졌으나, 많은 시간과 전문성을 필요로 하고 연구자의 주관적 판단에 의존하는 단점이 있다. 따라서, 본 연구에서는 채수된 환경시료에 대해 보다 빠르고 정확한 플랑크톤 종다양성을 파악하기 위하여 분자마커를 활용한 분자모니터링 기법을 도입하였다. 서낙동강(김해교)과 남해 연얀(남해도) 정점에서 각각 채수된 환경시료에서 DNA를 추출한 후 18S nuclear ribosomal RNA 유전자를 대상으로 중합효소연쇄반응을 수행하였다. 클로닝 과정을 통해 만들어진 각각의 클론 라이브러리에서 클론을 무작위로 선택하여 제한효소절편다형성 패턴분석을 한 후 특이성을 가지는 클론을 선별하였다. 김해교에서는 60개 블론을 대상으로 44개의 특이적 클론을 선별하였고 남해에서는 150개 클론을 대상으토 27개의 클론을 선별하였다. 이틀 클론틀에 대한 염기서열 분석결과 다양한 계통분류군에 속승하는 플랑크톤의 종조성 결과를 보여주었다(김해교: Heterokontophyta(7), Ciliophora(23), Dinophyta(l), Chytridiomycota(l), Rotifera(I), Arthropoda (11), 남해: Ciliophora( 4), Dinophyta(3), Crγptophyta(l)，Arthropoda(19)). 본 연구를 통하여 분자마커를 활용한 분자모니터링 기법이 기존 형태학적 형질에 근거한 분석이 가지는 한계를 보완하여 채수된 환경시료의 종조성 분석에 효율적으로 사용될 수 있다고 판단된다.

• 한국환경복원기술학회지
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• 제27권2호
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• pp.17-28
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• 2024

In order to achieve the management goals (30by30) mandated by the Kunming-Montreal Global Biodiversity Framework, this study established the site-level assessment criteria for OECMs, tailored to domestic circumstances using the Delphi analysis. Subsequently, a site-level assessment was conducted on the National Gariwangsan Natural Recreation Forest. As a result of the study, the initial step involved presenting criteria for the site-level assessment of OECMs, with 'consent for the assessment and recognition of OECM by competent and management authority' proposed as a prerequisite. Subsequently, seven evaluation criteria were established, including 'other than a legally protected area', 'spatially separated area with defined boundaries', 'effective in-situ conservation of biodiversity', 'sustainable management based on the competent and management authority', 'long-term sustainability of conservation outcomes', and 'provision of ecosystem services'. The results of applying site-level assessment criteria to the National Gariwangsan Natural Recreation Forest indicate that six criteria were met, while one criterion (sustainable management based on the competent and management authority) requires further improvement. Specifically, the key competent and management authorities for the National Gariwangsan Natural Recreation Forest are the Korea Forest Service and the National Natural Recreation Forest Management Office, with competent and management organizations established. However, the management focus is primarily on providing forest recreation services centered on users and facilities, making it difficult to confirm the long-term biodiversity conservation plans and implementation by the competent and management authorities. Therefore, it is deemed necessary to improve the long-term biodiversity conservation plans and implementation for the recognition of the National Gariwangsan Natural Recreation Forest as an OECM.

• 식물분류학회지
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• 제37권3호
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• pp.309-321
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• 2007

산림청 국립수목원과 한국식물분류학회가 공동으로 국내 최초로 전산화된 식물목록 데이터베이스를 구축하였다. 그 결과로 재배종을 포함한 약 7,000 분류군을 대상으로 항상 최신의 자료를 갱신할 수 있는 국가표준식물목록을 온라인상에 구현하였다. 국가표준식물목록은 37명의 국내 전문분류학자가 참여한 우리나라 식물목록과 관련된 최대 규모의 프로젝트이다. 본 연구는 국가표준식물목록 생성과정을 분석하고 이를 통해 관계형 데이터베이스 모델을 수립하였다. 개발된 광릉 데이터베이스 모델은 식물목록과 관련된 문헌과 다양한 분류학 자료를 제공할 수 있도록 설계 되었다. 이 모델은 다양한 분류학적 수준의 학명과 잡종명, 재배명, 이명, 기본명, 국명 및 명명법과 관련된 기타 자료를 함께 제공할 수 있다. 따라서, 국가표준식물목록 데이터베이스는 앞으로 개발될 생물정보시스템들의 개발에 있어 식물의 학명과 관련된 정확하고 일관성이 있는 표준 데이터베이스 기반을 제공하게 되었다.

• 정보관리연구
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• 제40권1호
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• pp.217-234
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• 2009

컴퓨터로 옮겨 놓은 생물학 실험실에서 생명과학을 연구하는 연구자가 생명정보를 확인하려면 1차적으로 생물다양성 관련 데이터베이스에서 생명체에 관한 종정보, 생태정보, 분포정보를 검색해야 한다. 그리고 그 생명체를 구성하는 유전자 서열정보와 단백질 구조정보를 Genbank, PDB 등의 유전자/단백질 데이터베이스에서 검색해야 한다. 또한 그 생명체에 관한 학술적 내용이 수록된 학술논문까지 별도로 검색해야만 그 생명체에 관한 포괄적이고도 정확한 정보를 획득하여 연구에 활용할 수 있다. 이런 일련의 과정은 연구자에게 불편함과 함께 많은 시간이 소요됨으로 인해 연구의 효율성을 저하시키는 요인이 되고 있다. 이런 불편함을 해결하기 위하여 통합검색하기 위한 여러 방법을 분석하고, 그중 스키마 통합을 선택하였다. 또한 스키마 통합을 위하여 각각의 데이터베이스의 스키마를 분석하고 메타데이터를 추출하여 Mediated 스키마를 설계하였다. 본 논문에서 설계한 생명정보 검색시스템(BIRS, Biological Information Retrieval System)과 인터페이스를 사용하여 생명과학을 연구하는 연구자들의 연구의 효율성을 향상시킬 수 있을 것이다.

• Journal of Forest and Environmental Science
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• 제28권3호
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• pp.170-178
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• 2012

Dipterocarps or Dipterocarpaceae is a commercially important timber producing and dominant keystone tree family in the rain forests of Borneo. Borneo's landscape is changing at an unprecedented rate in recent years which affects this important biodiversity. This paper attempts to model the natural occurrence (distribution including those areas with natural forests before being converted to other land uses as opposed to current distribution) of dipterocarp species in Sarawak which is important for forest biodiversity conservation and management. Local modeling method of Inverse Distance Weighting was compared with commonly used statistical method (Binary Logistic Regression) to build the best natural distribution models for three genera (12 species) of dipterocarps. Database of species occurrence data and pseudoabsence data were constructed and divided into two halves for model building and validation. For logistic regression modeling, climatic, topographical and edaphic parameters were used. Proxy variables were used to represent the parameters which were highly (p>0.75) correlated to avoid over-fitting. The results show that Inverse Distance Weighting produced the best and consistent prediction with an average accuracy of over 80%. This study demonstrates that local interpolation method can be used for the modeling of natural distribution of dipterocarp species. The Inverse Distance Weighted was proven a better method and the possible reasons are discussed.

• 정보관리연구
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• 제40권4호
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• pp.109-133
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• 2009

생명정보 중에서 미국의 국립생명공학정보센터(NCBI)에서 제공하는 GenBank는 전 세계적으로 연구자들이 가장 많이 사용하는 대표적인 유전자정보 데이터베이스이다. 한국과학기술정보연구원(KISTI)은 GenBank의 최신 버전을 데이터베이스로 재구축하여 Bio-KRISTAL 검색엔진을 이용하여 국내 생명과학 연구자들에게 제공하고 있다. 본 논문에서는 GenBank 데이터베이스를 활용하여 과학기술정보 통합서비스인 NDSL의 논문정보, 특허정보, 생물다양성정보 등의 콘텐트와 GenBank reference 필드와 organism 필드를 상호 연계하는 서비스 모델을 설계하고 프로토타입 시스템을 개발하였다. 이를 위하여 1) NCBI FTP 사이트에서 GenBank 데이터를 수집하여, 2) GenBank 텍스트 파일을 유전자 기본정보와 참고정보로 나누어 데이터베이스로 재구축하여, 3) GenBank reference 필드에서 논문 및 특허 정보 추출을 통한 새로운 테이블을 생성하여, 4) 데이터 맵핑 기술을 이용하여 GenBank 데이터와 NDSL 데이터가 상호 연계되어 서비스되는 프로토타입 시스템을 구현하여 이종의 콘텐트간 연계 및 융합 서비스의 가능성을 확인하였다.