• The Korean Journal of Ecology
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• v.23 no.2
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• pp.101-106
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• 2000

The grand challenge for the 21$^{st$ century is to harness knowledge of the earth`s biological and ecological diversity to understand how they shape global environmental systems. This insight benefits both science and society. Biological and ecological data are among the most diverse and complex in the scientific realm. spanning vast temporal and spatial scales, distant localities. and multiple disciplines. Environmental informatics is an emerging discipline applying information science, ecology, and biodiversity to the understanding and solution of environmental problems. In this paper we give an overview of the experiences of the San Diego Supercomputer Center (SDSC) with this new multidisciplinary science, discuss the application of computing resources to the study of environmental systems, and outline strategic partnership activities in environmental iformatics that are underway, We hope to foster interactions between ecology, biodiversity, and conservation researchers in East Asia-Pacific Rim and those at SDSC and the Partnership for Biodiversity Informatics.

• Journal of Korean Society of Forest Science
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• v.110 no.2
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• pp.179-188
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• 2021

Biodiversity informatics applies information technology methods in organizing, accessing, visualizing, and analyzing primary biodiversity data and quantitative data management through the scientific names of accepted names and synonyms. We reviewed the GBIF data published by China, Japan, Taiwan, and internal institutes, such as NIBR, NIE, and KNA of the Republic of Korea, and assessed data in diverse aspects of data quality using BRAHMS software. Most data from four Asian countries have quality problems with the lack of data consistency and missing information on georeferenced data, collectors, collection date, and place names (gazetteers) or other invalid data forms. The major problem is that biodiversity management institutions in East Asia are using unstructured databases and simple spreadsheet-type data. Owing to the nature of the biodiversity information, if data relationships are not structured, it would be impossible to secure the data integrity of scientific names, human names, geographical names, literature, and ecological information. For data quality, it is essential to build data integrity for database management and training systems for taxonomists who are continuous data managers to correct errors. Thus, publishers in East Asia play an essential role not only in using specialized software to manage biodiversity data but also in developing structured databases and ensuring their integration and value within biodiversity publishing platforms.

• Genomics & Informatics
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• v.13 no.3
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• pp.90-92
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• 2015

Biological diversity, also known as biodiversity, is an important criterion for measuring the value of an ecosystem. As biodiversity is closely related to human welfare and quality of life, many efforts to restore and maintain the biodiversity of species have been made by government agencies and non-governmental organizations, thereby drawing a substantial amount of international attention. In the fields of biological research, biodiversity is widely measured using traditional statistical indices such as the Shannon-Wiener index, species richness, evenness, and relative dominance of species. However, some biologists and ecologists have difficulty using these indices because they require advanced mathematical knowledge and computational techniques. Therefore, we developed VBioindex, a user-friendly program that is capable of measuring the Shannon-Wiener index, species richness, evenness, and relative dominance. VBioindex serves as an easy to use interface and visually represents the results in the form of a simple chart and in addition, VBioindex offers functions for long-term investigations of datasets using time-series analyses.

• Journal of Environmental Policy
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• v.13 no.2
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• pp.3-20
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• 2014

Due to habitat damage associated with climate change and human activities, biodiversity has decreased all over the world. In order to prevent further reduction in biodiversity, the international community has endeavored to establish a cooperative system, such as the Convention on Biological Diversity (CBD). Until now, most biodiversity strategic planning has been led by the national government. However, the National Biodiversity Strategy and Action Plan is conservative and its strategic plan is vague. Therefore, we propose a method for managing local biological resources called the Local Biodiversity Strategy and Action Plan. In order to provide the strategic plans and detailed plans for the Local Biodiversity Strategy and Action Plan, the report has examined several cases including Convention on Biological Diversity, Strategic Plan for Biodiversity 2011-2020, and the biodiversity strategies and action plans of the Republic of Korea and several other countries. As a result, the report demonstrates the survey and protection of bio-species, the designation and monitoring of conservation region, the management of the integrated eco-network, the establishment of biodiversity organizations and capacity building, the methods to promote networking and traditional knowledge, and the strategy for development in bioindustry. Consequently, the implementation of biodiversity management strategies by local governments will play a significant role in preserving and increasing biodiversity by realizing the goals of Strategic Plan for Biodiversity 2011-2020.

• Journal of Applied Biological Chemistry
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• v.64 no.1
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• pp.49-55
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• 2021

The diet plays a fundamental role in the formation of the gut microbiota, determining the interrelationship between the gut microbiota and the host. The current study investigated the effect of Chlorella vulgaris on the gut microbiota by using simulated in vitro digestion and colonic fermentation. Bioaccessibility was measured after in vitro digestion, and SCFAs and microbial profiling were analyzed after colonic fermentation. The bioaccessibility of C. vulgaris was 0.24 g/g. The three major SCFAs (acetate, propionate, and butyrate) increased significantly when compared to the control group. In microbial profiling analysis, microorganisms such as Faecalibacterium, Dialister, Megasphaera, Dorea, Odoribacter, Roseburia, Bifidobacterium, Butyricmonas, and Veillonella were high in C. vulgaris group. Among them, Faecalibacterium, Dialister, Megasphaera, Roseburia, and Veillonella were thought to be closely associated with the increased level of SCFAs. Finally, it can be expected to help improve gut microbiota and health through ingestion of C. vulgaris. However, further studies are vital to confirm the changes in the gut microbiota in in vivo, when C. vulgaris is ingested.

• Genomics & Informatics
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• v.18 no.1
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• pp.7.1-7.7
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• 2020

In this paper, we present few technical notes about the distance distribution paradigm for Mosaab-metric using 1, 2, and 3 grams feature extraction techniques to analyze composite data points in high dimensional feature spaces. This technical analysis will help the specialist in bioinformatics and biotechnology to deeply explore the biodiversity of influenza virus genome as a composite data point. Various technical examples are presented in this paper, in addition, the integrated statistical learning pipeline to process segmented genomes of influenza virus is illustrated as sequential-parallel computational pipeline.

• Journal of Marine Life Science
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• v.8 no.2
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• pp.136-149
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• 2023

Basic bioactivities (antioxidant, anti-inflammatory, antibacterial, anticancer, antiviral) were investigated from 370 strains of marine bacteria, fungi, and microalgae obtained from various marine environmental regions in Korea, and the activity results were obtained at the collection site, isolation source, and species level was compared. In the case of marine bacteria, strains belonging to the generally useful genera Streptomyces and Bacillus were observed to have particularly strong efficacy and useful resources were mainly isolated from marine sediments. In the case of marine fungi and microalgae, results showing strong species-specific activity were confirmed, and results showing efficacy-specific activity were also obtained. Based on these results, it is a research result that can facilitate priority access as a strategic material for industrial revitalization and the establishment of a strategy to secure resources based on usefulness when conducting research on chemicals that are selectively effective against specific diseases or when conducting resource-based research. In addition, we believe that by using these results as material for sale through the Marine BioBank (MBB), academia and industry can use them to help accelerate the revitalization of the marine bio industry.

• Journal of Applied Biological Chemistry
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• v.64 no.1
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• pp.33-38
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• 2021

Marine sponges contain pharmacologically attractive substances that exhibit strong cytotoxicity and are used as materials to isolate potential drug candidates. However, with a growing interest in marine ecosystem conservation, it is becoming increasingly difficult to gather a sponge for natural product research. To build a database to cope with this issue, we measured the neuroprotective and anti-inflammatory activity of 181 sponge extracts. As a result, we found 17 samples with neuroprotective effects and 14 samples with anti-inflammatory effects. In addition, high-performance liquid chromatography (HPLC) analysis was performed to compare the components contained in each sample, and based on HPLC profiles, a dendrogram according to similarity was created. The results of this study suggested the possibility of discovering the active compounds in the sponge and laid the basis for efficient research on the sponge.

• Journal of Applied Biological Chemistry
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• v.64 no.1
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• pp.25-32
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• 2021

Phytochemicals include plant-derived natural products that promote and improve the human metabolism and physiological activity, and there is a lot of research to find the value of the molecules is in progress. Likewise, we obtained 288 fractions of Capsicum annuum L. extract in less than 20 h using HPLC/SPE/HPLC coupling experiment through Sepbox system, an effective separation system to search for active substances in natural resources and ensure efficacy and reliability. Therefore, this experiment allowed rapid identification of biologically active molecules from the extract compared to traditional separation processes. Of the above fractions, eight fractions showed the α-glucosidase inhibitory (AGI) activity and subsequent LC-MS analysis revealed one of the active molecules as luteolin 7-O-glucoside. In addition, we proved the increase in AGI activity according to deglycosylation of flavonoid glycoside. Therefore, this study suggests that the Sepbox system can quickly separate and identify active components from plant extract, and is an effective technique for finding new active substances.

• Genomics & Informatics
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• v.10 no.3
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• pp.206-211
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• 2012

DNA barcoding has been widely used in species identification and biodiversity research. A short fragment of the mitochondrial cytochrome c oxidase subunit I (COI) sequence serves as a DNA bio-barcode. We collected DNA barcodes, based on COI sequences from 156 species (529 sequences) of fish, insects, and shellfish. We present results on phylogenetic relationships to assess biodiversity the in the Korean peninsula. Average GC% contents of the 68 fish species (46.9%), the 59 shellfish species (38.0%), and the 29 insect species (33.2%) are reported. Using the Kimura 2 parameter in all possible pairwise comparisons, the average interspecific distances were compared with the average intraspecific distances in fish (3.22 vs. 0.41), insects (2.06 vs. 0.25), and shellfish (3.58 vs. 0.14). Our results confirm that distance-based DNA barcoding provides sufficient information to identify and delineate fish, insect, and shellfish species by means of all possible pairwise comparisons. These results also confirm that the development of an effective molecular barcode identification system is possible. All DNA barcode sequences collected from our study will be useful for the interpretation of species-level identification and community-level patterns in fish, insects, and shellfish in Korea, although at the species level, the rate of correct identification in a diversified environment might be low.