• ALGAE
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• v.31 no.4
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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.

• The Journal of the Korea Contents Association
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• v.11 no.11
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• pp.503-513
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• 2011

Appreciation of nature and an understanding of the biological sciences by the general public are key to the popularization of modern science. In particular, informal and accessible venues such as museum exhibits occupy a crucial role in science education, and they depend heavily on fields related to macrobiology, including Ecology, Animal Behavior, and Environmental Science. Unfortunately, lack of engaged experts and superficial descriptions of natural phenomena all too often prevent scientific knowledge from being shared effectively with the general public. Raw information itself and knowledge are not in a form or structure accessible to nonspecialists. In order to move successfully deliver substantive comprehension of the biological knowledge to the general public, it is necessary to categorize information from a content-conscious perspective and transform it into useful biological content. Therefore, the role of scientists is critically important in a series of processes that include theme selection, editing, and even graphical layout of contents. These processes require not only a scientific and logical way of thinking, but also an aptitude for artistic presentation and effective communication. The concept of Translation is presented as a theoretical and operational framework for the popularization of science.

• Journal of Species Research
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• v.9 no.4
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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.

• Journal of KIISE:Databases
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• v.32 no.1
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• pp.24-42
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• 2005

Characteristics of biological data including genome sequences are heterogeneous and various. Although the need of management systems for genome sequencing which should reflect biological characteristics has been raised, most current biological databases provide restricted function as repositories for biological data. Therefore, this paper describes a management system of nucleotide sequences at the level of biological laboratories. It includes format transformation, editing, storing and retrieval for collected nucleotide sequences from public databases, and handles sequence produced by experiments. It uses BSML based on XML as a common format in order to extract data fields and transfer heterogeneous sequence formats. To manage sequences and their changes, version management system for originated DNA is required so as to detect transformed new sequencing appearance and trigger database update. Our experimental results show that applying active trigger rules to manage changes of sequences can automatically store changes of sequences into databases.

• Journal of Ecology and Environment
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• v.42 no.2
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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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• v.40 no.2
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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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• v.31 no.4
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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.

• Journal of Korean Biological Nursing Science
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• v.25 no.3
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• pp.183-204
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• 2023

Purpose: The purpose of this study was to evaluate the applicability of ChatGPT in biological nursing science education. Methods: This study was conducted by entering questions about the field of biological nursing science into ChatGPT versions GPT-3.5 and GPT-4 and evaluating the answers. Three questions each related to microbiology and pharmacology were entered, and the generated content was analyzed to determine its applicability to the field of biological nursing science. The questions were of a level that could be presented to nursing students as written test questions. Results: The answers generated in English had 100.0% accuracy in both GPT-3.5 and GPT-4. For the sentences generated in Korean, the accuracy rate of GPT-3.5 was 62.7%, and that of GPT-4 was 100.0%. The total number of Korean sentences in GPT-3.5 was 51, while the total number of Korean sentences in GPT-4 was 68. Likewise, the total number of English sentences in GPT-3.5 was 70, while the total number of English sentences in GPT-4 was 75. This showed that even for the same Korean or English question, GPT-4 tended to be more detailed than GPT-3.5. Conclusion: This study confirmed the advantages of ChatGPT as a tool to improve understanding of various complex concepts in the field of biological nursing science. However, as the answers were based on data collected up to 2021, a guideline reflecting the most up-to-date information is needed. Further research is needed to develop a reliable and valid scale to evaluate ChatGPT's responses.

• Reproductive and Developmental Biology
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• v.29 no.2
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• pp.69-73
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• 2005

The hematopoietic growth factor erythropoietin (EPO) is required for the maintenance, proliferation, and differentiation of the stem cells that produce erythrocytes. To analyse the biological activity of the recombinant human EPO (rec-hEPO), we have cloned the EPO cDNA and genomic DNA and produced rec-hEPO in the CHO cell lines. The growth and differentiation of EPO-dependent human leukemic cell line (F36E) were used to measure cytokine dependency and in vitro bioactivity of rec-hEPO. MIT assay values were increased by survival of F36E cells at 24h or 72h. The hematocrit and RBC values were increased by subcutaneous injection of 20 IU (in mice) and 100IU(in rats) rec-hEPO. Hematocrit values remarkably increased at $13.2\%$ (in mice) and $12.2\%$ (in rats). The pharmacokinetic behavior with injection of 6 IU of rec-hEPO remained detectable after 24 h in all mice tested. The highest peat appeared at 2h after injection. The long half-life of rec-hEPO is likely to confer clinical advantages by allowing less frequent dosing in patients treated for anemia. These data demonstratethat ree-hEPO produced in this study has a potent activity in vivo and in vitro. The results also suggest that biological activity of ree-hEPO could be remarkably enhanced by genetic engineering that affects the potential activity, including mutants with added oligosaccharide chain and designed to produce EPO-EPO fusion protein.

• Journal of Information Science Theory and Practice
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• v.2 no.1
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• pp.6-21
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• 2014

This paper proposes a novel knowledge extraction system, TAKES (Two-step Approach for Knowledge Extraction System), which integrates advanced techniques from Information Retrieval (IR), Information Extraction (IE), and Natural Language Processing (NLP). In particular, TAKES adopts a novel keyphrase extraction-based query expansion technique to collect promising documents. It also uses a Conditional Random Field-based machine learning technique to extract important biological entities and relations. TAKES is applied to biological knowledge extraction, particularly retrieving promising documents that contain Protein-Protein Interaction (PPI) and extracting PPI pairs. TAKES consists of two major components: DocSpotter, which is used to query and retrieve promising documents for extraction, and a Conditional Random Field (CRF)-based entity extraction component known as FCRF. The present paper investigated research problems addressing the issues with a knowledge extraction system and conducted a series of experiments to test our hypotheses. The findings from the experiments are as follows: First, the author verified, using three different test collections to measure the performance of our query expansion technique, that DocSpotter is robust and highly accurate when compared to Okapi BM25 and SLIPPER. Second, the author verified that our relation extraction algorithm, FCRF, is highly accurate in terms of F-Measure compared to four other competitive extraction algorithms: Support Vector Machine, Maximum Entropy, Single POS HMM, and Rapier.