• 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 Oral Medicine and Pain
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• v.47 no.1
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• pp.10-26
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• 2022

Purpose: The purpose of this study was to investigate whether various saliva collection methods affect the observed salivary microbiome and whether microbiomes of stimulated and unstimulated saliva and plaque differ in richness and diversity. Methods: Seven sampling methods for unstimulated saliva, stimulated saliva, and plaque samples were applied to six orally and systemically healthy participants. Bacterial 16S ribosomal RNA genes of 10 major oral bacterial species, namely, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, Prevotella intermedia, Prevotella nigrescens, Streptococcus mitis, Streptococcus sobrinus, and Lactobacillus casei, were analyzed by real-time polymerase chain reaction. We comprehensively examined the dependence of the amount of bacterial ribosomal DNA (rDNA), bacterial-community composition, and relative abundance of each species on sample collection methods. Results: There were significant differences in the bacterial rDNA copy number depending on the collection method in three species: F. nucleatum, P. nigrescens, and S. mitis. The species with the highest richness was S. mitis, with the range from 89.31% to 100.00%, followed by F. nucleatum, P. nigrescens, T. denticola, T. forsythia, and P. intermedia, and the sum of the proportions of the remaining five species was less than 1%. The species with the lowest observed richness was P. gingivalis (<0.1%). The Shannon diversity index was the highest in unstimulated saliva collected with a funnel (4.449). The Shannon diversity index was higher in plaque samples (3.623) than in unstimulated (3.171) and stimulated (3.129) saliva and in mouthwash saliva samples (2.061). Conclusions: The oral microbial profile of saliva samples can be affected by sample collection methods, and saliva differs from plaque in the microbiome. An easy and rapid technique for saliva collection is desirable; however, observed microbial-community composition may more accurately reflect the actual microbiome when unstimulated saliva is assayed.

• Journal of Life Science
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• v.29 no.5
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• pp.580-587
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• 2019

Benthic macroinvertebrates were analyzed in March, June, September, and December 2018 to evaluate water quality in the Songji River in Sacheon-ci, Korea. The identified benthic macroinvertebrates included 447 individuals belonging to 20 species, 18 families, 12 orders, 5 classes, and 3 phyla. Various ecological parameters were estimated for evaluation of the river status. The total ecological score of benthic macroinvertebrate community (TESB) varied from 17 (Station D) to 41 (Station A). The saprobic index and ecological score of benthic macroinvertebrate community (ESB) for the evaluation of river status revealed a water quality evaluation at Station A of II (oligosaprobic), indicating some satisfactory water protection. The benthic macroinvertebrate index (BMI) varied from 25.207 (Site C) to 39.348 (Station A). The evaluation of the river status at Stations C and D was polysaprobic, and sensitive taxa were absent. The mean Shannon-Weaver index (H') of diversity varied from 1.288 (Station D) to 2.250 (Station A). The classification of saprobity based on H' was ${\beta}$-mesosaprobic at Station A and ${\alpha}$-mesosaprobic at the other stations. The value of geometric density was varied from 1.229 (Station A) to 2.071 (Station D), with a mean of 1.582. An artificial load is being added to this river. One of load is the rectal river construction which flows straight through the river physics. Thus, the environment of living organisms deteriorates due to insufficient water. In order to secure the quality of the Songji River and a good environmental habitat, several low-height stepped-beam structures are required.

• Korean journal of applied entomology
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• v.34 no.2
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• pp.120-126
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• 1995

This study investigated the soil oribatid mite community at planatations of the Korean white pine, planted in different years. The soil samples $(10\times10\times5cm)$ were taken monthly from Jun 1988 to July 1989, and soil microarthropods in th sample were extracted using the Tullgren funnel for 72 hors. The diversity indices decreased at the older plantation sites with the maximum point in January and the minimum in September. The richness indices showed the maximum point in June and the minimum in may. The dominance indices increased at the older plantation and showed the maximum point in April, May, the minimum in January. The indices of aggregation of Oribatid mites species showed concentrated distribution in the average 1.9. The older plantation, the more indices increase. The seasonal variation of th indices tended to be greatest in April, August and at lowest in January. The richness indices was positively correlated with shannon-wiener, evenness indices. The dominance, aggregation indices was negatively correlated with shannon, evenness, richness indices.

• Journal of Forest and Environmental Science
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• v.22 no.1
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• pp.58-65
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• 2006

This study investigated to distribution of Lepidoptera on the forest stands of cental Gangwon area from July to August in 2005. Collected Lepidoptera in the study area were total 462 individuals 123 genus 15 family and were collected 166 individuals, 66 genus, 15 family in Jumbong Mt., 159 individuals 65 genus 15 family in Eungbok Mt. and 137 individuals 40 genus 9 family in Odae Mt.. Dominant species in study area were Ampelophaga rubiginosa 54 individuals, Antheraea yamamai 35 individuals, Dendrolimus superans 27 individuals, Triphaenopsis jezoensis 14 individuals, Lymantria monacha 13 individuals. Shannon species diversity index(H') and Evenness index (J') were 1.52, 0.84 in Jumbong Mt., 1.69, 0.91 in Eungbok Mt., 1.87, 0.83 in Odae Mt. respectively. Community similarity index showed the lowest value in Jumbong Mt. and Odae Mt. as 0.11, the highest value in Jumbong Mt. and Odae Mt. as 0.28.

• Environmental Engineering Research
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• v.17 no.3
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• pp.167-174
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• 2012

In situ particle size spectra are obtained from two sequent cruises in order to evaluate the physical consequences of suspended particulate matters caused by episodic storm runoff from the Santa Ana River watershed, an urbanized coastal watershed. Suspended particles from various sources including surface runoff, near-bed resuspension, and phytoplankton are identified in empirical orthogonal function (EOF) analysis and an entropy-based parameterization (Shannon entropy). The first EOF mode is associated with high turbidity and fine particles as indicated by the elevated beam attenuation near the Santa Ana River and Newport Bay outlets, and the second EOF mode explains the suspended sediment dispersal and particle coarsening at the near-surface plume. Chlorophyll particles are also distinguished by negative magnitudes of the first EOF mode, which is supported by the relationship between fluorescence and beam attenuation. The integrated observation between the first EOF mode and the Shannon entropy index accentuates the characteristics of two different structures and/or sources of sediment particles; the near-surface plumes are originated from runoff water outflow, while the near-bottom particles are resuspended due to increased wave heights or mobilizing bottom turbidity currents. In a coastal pollution context, these methods may offer useful means of characterizing particle-associated pollutants for purposes of source tracking and environmental interpretation.

• Journal of Korean Society on Water Environment
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• v.31 no.6
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• pp.610-618
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• 2015

This study was conducted to find out the influence of sample size (accumulated survey areas) on the seven biological indices of benthic macroinvertebrates. BMI, the index similar to Zeilika-Marvan’s saprobic index, tended to be independent on the variations of sample size. The other indices (Shannon-Weaver’s diversity, Margalef’s richness, Menhinick’s richness, Pielou’s evenness, and Lenat’s EPT index) showed the considerable variations along with the increase of sample size and environmental conditions. To get the appropriate index values, it should be sampled at least 6 replicates more based on 30×30cm Surber sampler. In addition, the habitat heterogeneity index of benthic macroinvertebrates suggested in this study, it will be able to be used for evaluating the heterogeneity of habitats.

• Korean Journal of Environment and Ecology
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• v.13 no.4
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• pp.382-391
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• 2000

지리산국립공원 연하천계곡의 식물군집구조를 조사하기 위해서 48개의 조사구(1개 조사구 단위면적 100m2)를 설정하고 식생조사를 하였다 48개의 조사구는 DCA 분석에 의하여 2개의 군집(들메나무군집 시날나무군집)으로 분류되었다 층위별상대우점치와 흉고직경급별 분포 분석결과 들메나무와 신갈나무는 현상태를 계속유지할 것으로 보이며 들메나무군집은 계곡부 토지극상림을 이루고 있었다 연하천계곡의 Shannon 종다양도지수는 들메나무군집은 1.0810 신갈나무군집은 0.2468이었다 들메나무는 함박꽃나무 물참대 참회나무 바위 마발도리 개회나무와 정의 상관관계를 보였으며 신갈나무 생강나무, 조릿대, 노린재 , 당단풍과 부의상관관계를 보였다.

• Journal of Microbiology and Biotechnology
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• v.27 no.12
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• pp.2089-2093
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• 2017

The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using culturein-dependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon-Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon-Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

• Journal of Ecology and Environment
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• v.42 no.4
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• pp.183-190
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• 2018

Backgrounds: The main purpose of this research was to assess changes in vegetation structure, wetland index, and diversity index for a 15-year-old created wetland in Jincheon, South Korea. The created wetland consists of four sub-wetlands: a kidney-shaped wetland, a ditch, an ecological pond, and a square wetland. Vegetation and water depth data were collected at each site in 1999 and 2013, and Shannon diversity and wetland indices were calculated. Results: The total number of plant species increased from 18 in 1999 to 50 in 2013, and the ecological pond in 1999 and the ditch in 2013 presented the highest diversity indices (2.5 and 3.2, respectively). Plant species were less diverse in 1999 than in 2013, presumably because these initial wetlands were managed periodically for water purification and installation of test beds. The proportion of wetland plants, including obligate wetland and facultative wetland species, decreased from 83 to 56%, whereas upland plants, including obligate upland and facultative upland species, increased from 17 to 44%. After ceasing water supply, water depth in all four sub-wetlands declined in 2013. Thus, upland plants established more readily at these sites, resulting in higher diversity and lower wetland indices than in 1999. Conclusions: The major floristic differences between 1999 and 2013 were an increase in the number of upland plants and a decrease in wetland species. Although wetland indices were lower in 2013, the created wetland performed important ecosystem functions by providing habitats for wetland and upland plants, and the overall species diversity was high.