• Genomics & Informatics
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• 제13권3호
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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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• 제47권1호
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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.

• 생명과학회지
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• 제29권5호
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• pp.580-587
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• 2019

저서성대형무척추동물은 수질 평가를 위해 다년간 이용되었다. 본 연구는 한국 송지천에서 저서성대형무척추동물을 이용하여 이 하천의 수질을 평가하고자 수행되었다. 동정된 동물은 3문 5강 12목 18과 20종 447개체였다. 집모기류(Culicini sp.)가 가장 우점종이었고(203개체), 두번째 우점종은 집파리(Musca do­mestica)였다. 다양한 생태학적 척도로 수질의 상태를 평가하였다. 전체 생태 점수(total ecological score of benthic macroinvertebrate community, TESB)은 17(St. D)에서 41(St. A)으로 평균은 29였다. St. A에서 부수성 지수와 저서성 대형무척추동물생태 점수(ESB)는 II 등급으로 빈부수성, 수질은 약간 만족이며 보호가 요청되는 수질에 해당되었다. 저서성동물지수(benthic macroinvertebrate index, BMI)은 25.207(St. C)에서 39.348(St. A)까지 이며 평균은 31.810였다. St. C와 St. D의 하천 상태 평가는 강부수성이며 민감종이 결여되어 있었다. 다양도를 나타내는 Shannon-Weaver index (H')는 1.288(St. D)에서 2.250(St. A)였다. H'에 근거한 부수성 정도는 St. A에서는 ${\beta}$-중부수성이었으며 나머지 지점은 ${\alpha}$-중부수성이었다. 지리적 밀도는 1.229(St. A)에서 2.071(St. D)으로 평균은 1.582였다. 송지천에서 사용한 무척추동물을 이용한 여러 수질의 척도는 한국 내 다른 하천에서도 적용할 수 있을 것이다.

• 한국응용곤충학회지
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• 제34권2호
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• pp.120-126
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• 1995

잣나부 인공조임지의 식생과 임상 토질에 서식하는 날개응애류의 군집지수를 분석한 결과를 요약하면 다음과 같다. 종다양도의 Shannon-Wiener index와 균등도지수는 조임년수가 경과할수톡 낮아지는 경향이었으며 1월에 최고치를, 9月에 최저치를 나타냈다. 종풍부경지수는 6월에 최고치를 5月에 최저치를 나타냈다. 우점도지수는 조림연수가 경과할수록 증가하는 경향이고, 4월과 5월에 최고치를, 1월에 최저치를 나타냈다. 집중도지수는 평균 1.9로서 집중분포를 나타냈으며, 조림연수가 경과할수록 증가하는 경향이고, 4월과 8월에 최고치를 1월에 최저치를 나타냈다. 군집지수간의 상관관계에 있어서는 고도의 유의성이 인정되었으며 풍부도지수와 Shannon-Wiener, 균등도지수는 I정의 상관관계가 우점도, 집중도지수와 Shannon-Wiener, 균등도, 풍부도지수는 부의상관 관계가 인정되었다.

• Journal of Forest and Environmental Science
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• 제22권1호
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• pp.58-65
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• 2006

본 연구는 백두대간에 서식하는 나비목 곤충의 분포를 파악하기 위하여 2005년 7월과 8월에 수행되었다. 총 15과 123속 462개체가 채집되었으며, 점봉산(인제군 인제읍 귀둔리) 15과 63속 166개체, 응복산(홍천군 내면 명계리) 15과 65 속 159개체, 오대산(평창군 도암면 병내리) 9과 40속 137개체가 채집되었다. 조사지역에서 채집된 종들 중 우점하고 있는 5종은 머루박각시 (Ampelophaga rubiginosa) 54개체, 참나무산누에나방 (Antheraea yamamai) 35개체, 솔송나방 (Dendrolimus superans) 27개체, 북방뒷노랑밤나방 (Triphaenopsis jezoensis) 14개체, 얼룩매미나방 (Lymantria monacha) 13개체였다. Shannon(H') 지수와 균등도지수 (J') 는 점봉산 1.52, 0.84, 응복산1.69, 0.91, 오대산 1.37, 0.83, 유사도지수 (QS)는 점봉산과 응복산이 0.28로 다소 높았으며, 점봉산과 오대산이 0.11로 낮게 나타났다.

• Environmental Engineering Research
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• 제17권3호
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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.

• 한국물환경학회지
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• 제31권6호
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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.

• 한국환경생태학회지
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• 제13권4호
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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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• 제27권12호
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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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• 제42권4호
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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.