• Animal Systematics, Evolution and Diversity
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• v.24 no.3
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• pp.327-332
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• 2008

Soft coral Dendronephthya gigantea (Verrill, 1864) is a conspicuous species dominating shallow sea waters of Jejudo Island, Korea. Recently its whole mitochondrial genome sequencing was completed by us and the sequence information provided an opportunity to test the age of Octocorallia and time of evolutionary separation between some representative orders of the subclass Octocorallia. Molecular phylogenetic analyses based on 13 mitochondrial protein encoding genes revealed a polyphyletic relationship among octocorallians representing two orders (Alcyonacea and Gorgonacea) and four families (Alcyoniidae, Nephtheidae, Briareidae, and Gorgoniidae). Estimates of divergence times among octocorallians indicate that the first splitting might occur around end of or after Cretaceous period (50-79 million years ago (Ma)). The age is relatively young compared to the long history of stony sea corals (>240 Ma). Taken together our result suggests a possible relatively recent radiating evolution at least in the order Alcyonacea and Gorgonacea. Molecular dating and phylogenetic analysis based on much broader taxon sampling and many genes might give an insight into this interesting hypothesis.

• Journal of Ecology and Environment
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• v.38 no.1
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• pp.95-107
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• 2015

Because an ecological community consists of diverse species that vary nonlinearly with environmental variability, its dynamics are complex and difficult to analyze. To investigate temporal variations of benthic macroinvertebrate community, we used the community data that were collected at the sampling site in Baenae Stream near Busan, Korea, which is a clean stream with minimum pollution, from July 2006 to July 2013. First, we used a self-organizing map (SOM) to heuristically derive the states that characterizes the biotic condition of the benthic macroinvertebrate communities in forms of time series data. Next, we applied the hidden Markov model (HMM) to fine-tune the states objectively and to obtain the transition probabilities between the states and the emission probabilities that show the connection of the states with observable events such as the number of species, the diversity measured by Shannon entropy, and the biological water quality index (BMWP). While the number of species apparently addressed the state of the community, the diversity reflected the state changes after the HMM training along with seasonal variations in cyclic manners. The BMWP showed clear characterization of events that correspond to the different states based on the emission probabilities. The environmental factors such as temperature and precipitation also indicated the seasonal and cyclic changes according to the HMM. Though the usage of the HMM alone can guarantee the convergence of the training or the precision of the derived states based on field data in this study, the derivation of the states by the SOM that followed the fine-tuning by the HMM well elucidated the states of the community and could serve as an alternative reference system to reveal the ecological structures in stream communities.

• Korean Journal of Environmental Biology
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• v.33 no.2
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• pp.223-229
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• 2015

Pre-monsoon dynamics of zooplankton community were investigated in the downstream of the Gagok stream flowing into the East Sea of Korea. Monthly sampling was carried out to collect zooplankters at five sites in the stream during the period between April and July 2014. Dissolved oxygen contents exceeded $7.0mg\;L^{-1}$ all the time. Water temperature was in a range of 15.7 to $24.9^{\circ}C$ and pH 7.4 to 8.8, respectively. A total of 75 taxa consisted of 36 species of rotifers, 16 species of cladocerans, 16 species of copepods, four kinds of aquatic insects, two kinds of decapods and one nematod was occurred. One species of marine copepod and one cladoceran, and one species of brackish rotifer and one copepod distributed at the station located in the stream mouth. Zooplankton abundance showed to vary from 42 to 4202 individuals $m^{-3}$ due to the explosion of aquatic insects and Alona sp. at site 2 located in the downstream in April. Heavy rainfall during the monsoon period seems to decrease the zooplankton abundance caused by diffusion and drifting to the sea. Species diversity indices were generally high between 1.2~2.3 and were recorded to be high at the downstream throughout the study period. With the zooplankton dynamics, the influence of the input of sea waters into the stream seemed to be confined to some hundred meters of the stream mouth facing the East Sea.

• Industrial Engineering and Management Systems
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• v.8 no.3
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• pp.171-180
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• 2009

Population learning algorithm (PLA) is a population-based method that was inspired by the similarities to the phenomenon of social education process in which a diminishing number of individuals enter an increasing number of learning stages. The study aims to develop a framework that repeatedly applying the PLA to solve the discrete resource constrained project scheduling problem with two objectives: minimizing project makespan and renewable resource availability, which are two most common concerns of management when a project is being executed. The PLA looping framework will provide a number of near Pareto optimal schedules for the management to make a choice. Different improvement schemes and learning procedures are applied at different stages of the process. The process gradually becomes more and more sophisticated and time consuming as there are less and less individuals to be taught. An experiment with ProGen generated instances was conducted, and the results demonstrated that the looping framework using PLA outperforms those using genetic local search, particle swarm optimization with local search, scatter search, as well as biased sampling multi-pass algorithm, in terms of several performance measures of proximity. However, the diversity using spread metric does not reveal any significant difference between these five looping algorithms.

• Journal of Biosystems Engineering
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• v.33 no.4
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• pp.276-281
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• 2008

A flow injection analysis method (FIA), which analyzes sample conditions after injecting a sample and reagents into a continuous stream, are recognized as the most adequate analyzing method according to the increase of sampling frequency, the decrease of measuring time and the diversity of measuring targets. Specially, the FIA is considered to be used effectively for the control of a fermentation process to produce fermentation food and useful microbial production by activation of a fermentation industry for development of biological materials. In this study, a flow injection analysis sensor unit was developed for on-line monitoring of the fermentation process. The performance was verified by on-line measuring the concentration of glucose of the fermentation process of wine. The glucose concentrations of the samples were measured every 12 hours during the whole fermentation process and compared with those by a HPLC. The concentration relative errors of glucose on the fermentation process of wine showed below 30% within 72 hours and over 50% after the 72 hours. The sensor unit had potential to on-line monitoring of the fermentation process but some problems to overcome for an commercial application.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.51 no.4
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• pp.426-434
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• 2018

We investigated temporal and depth-related variation in species composition and abundance of the fish assemblage in the southern East Sea. Fish samples were collected seasonally between 2007 and 2008 using a demersal trawl off the southern coast of Korea. We identified 59 fish species belonging to 41 families. The most frequently occurring species was Coelorinchus multispinulosus, followed by Lophius litulon, Acropoma japonicum and Apogon lineatus. The five most abundant species were A. lineatus, A. japonicum, Myctophum nitidulum, Engraulis japonicus and C. multispinulosus, accounting for 87.04% of the total number of individuals collected. The number of species, abundance and diversity fluctuated with sampling location and time. Permutational multivariate analyses of variance revealed that the assemblage structure was influenced by year, season and water depth, with season being the main indicator. These changes were visually emphasized using non-metric multidimensional scaling ordination plots. Fluctuations in assemblage structure were due to differential contributions of the dominant species.

• Journal of Microbiology and Biotechnology
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• v.27 no.10
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• pp.1753-1762
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• 2017

Sea cucumber (Apostichopus japonicus) is a popular seafood source in Asia, including South Korea, and its consumption has recently increased with recognition of its medicinal properties. However, because raw sea cucumber contains various microbes, its ingestion can cause foodborne illness. Therefore, analysis of the microbiota in the whole body of sea cucumber can extend our understanding of foodborne illness caused by microorganisms and help to better manage products. We collected 40 sea cucumbers from four different sites in August and November, which are known as the maximum production areas in Korea. The microbiota was analyzed by an Illumina MiSeq system, and bacterial amounts were quantified by real-time PCR. The diversity and bacterial amounts in sea cucumber were higher in August than in November. Alpha-, Beta-, and Gammaproteobacteria were common dominant classes in all samples. However, the microbiota composition differed according to sampling time and site. Staphylococcus warneri and Propionibacterium acnes were commonly detected potential pathogens in August and November samples, respectively. The effect of experimental Vibrio parahaemolyticus infection on the indigenous microbiota of sea cucumber was analyzed at different temperatures, revealing clear alterations of Psychrobacter and Moraxella; thus, these shifts can be used as indicators for monitoring infection of sea cucumber. Although further studies are needed to clarify and understand the virulence and mechanisms of the identified pathogens of sea cucumber, our study provides a valuable reference for determining the potential of foodborne illness caused by sea cucumber ingestion and to develop monitoring strategies of products using microbiota information.

• Korean Journal of Environmental Biology
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• v.25 no.4
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• pp.326-335
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• 2007

This study was conducted to assess the environmental risks of anthracnose resistant transgenic chili peppers with the PepEST gene on non-target organisms in the agroecosystem environments during the chili pepper growing seasons in 2006. We quantitatively collected arthropods assemblages living on leaves and flowers of chili peppers on June 20, July 25, and August 25 by using an insect vacuum collector to compare the patterns of arthropod community structures between non-transgenic chili peppers (nTR, WT512) and anthracnose resistant transgenic chili peppers (TR, line 68). We found the seasonal difference with the highest species richness and Shannon's diversity in July's sampling among the growing seasons (P<0.05) and each sampling season showed the different arthropod community composition. We also found there was no statistical difference between the two types of crops, nTR and TR, at each sampling time (P>0.05). The significance level of arthropod community showed that there were lots of seasonal difference of functional groups as well as taxa but only the herbivore group in the functional groups was significantly different for the types of plants (P<0.05). So, we further examined the herbivore groups to find any potential damage and identified the possibility of herbivorous damage from some herbivores, grasshoppers, aphids and thrips. Although we couldn't find any adverse effects from the environmental risk assessment between the arthropod community structures on two types of plants from our results, we should keep working for the environmental risk assessment because of the herbivorous potential risk possibility.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.16 no.4
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• pp.238-245
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• 2011

Phytoplankton community composition was investigated in the Asan Bay (South) Korea. Water samples were collected monthly from five stations during January to December 2008. Phytoplankton blooms were observed in February and in August but the location of the bloom varied with the sampling time. A total of 134 phytoplankton species from seven classes (Bacillariophyceae, Chlorophyceae, Chrysophyceae, Cryptophyceae, Cyanophyceae, Dinophyceae, Euglenophyceae) were observed. Diatoms were dominant in all stations through-out the year except in summer when dinoflagellates were numerous and highly distributed within the outer bay rather than in the river mouth. Dominant and subdominant species were composed mostly of diatoms but were replaced by dinoflagellates in June and July. Results of ecological index showed that the diversity indices were increasing toward outer bay but the dominance indices showed a reverse trend.

• Journal of Korean Neurosurgical Society
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• v.64 no.4
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• pp.505-513
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• 2021

Objective : The adaptive immune response following subarachnoid hemorrhage (SAH) is not well understood. We evaluated and compared the T cell receptor (TCR) immune repertoire of good-grade and poor-grade SAH patients to elucidate the T cell immunology after ictus. Methods : Peripheral blood from six SAH patients was collected at two different times, admission and at the 7-day follow-up. Composition and variation of the TCR β-chain (TCRB) complimentary determining regions (CDR) 3 repertoire was examined using high-throughput sequencing; the analysis was based on sampling time and disease severity (good vs. poor-grade SAH). Results : Clonality at admission and follow-up were 0.059 (0.037-0.038) and 0.027 (0.014-0.082) (median, 25th-75th percentile). Poor-grade SAH (0.025 [0.011-0.038]) was associated with significantly lower clonality than good-grade SAH (0.095 [0.079-0.101]). Poor-grade SAH patients had higher diversity scores than good-grade SAH patients. CDR length was shorter in good-grade SAH vs. poor-grade SAH. Differences in clonotype distribution were more prominent in TCRBV gene segments than TCRBJ segments. TCRBV19-01/TCRBJ02-04 and TCRBV28-01/TCRBJ02-04 were the most increased and the most decreased V-J pairs in the 7-day follow-up compared to admission in good-grade SAH. The most increased and decreased V-J pairs in poor-grade SAH patients were TCRBV28-01/TCRBJ02-06 and TCRBV30-01/TCRBJ02-04, respectively. Conclusion : The TCRB repertoire is dynamic in nature following SAH. TCRB repertoire may facilitate our understanding of adaptive immune response according to SAH severity.