• Title/Summary/Keyword: High-throughput analysis

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Effect of Soil Microbial Diversity in Paddy Wetland under Organic Rice-Fish Mixed Farming System (유기농 복합생태 논습지의 토양 미생물 다양성 증진 효과)

  • Han, Yangsoo;Park, Choongbae;Cho, Jung-Lai;Park, Sang-Gu;Kong, Min-Jae;Nam, Hong-Shik;Son, Jinkwan
    • Journal of Wetlands Research
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    • v.24 no.2
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    • pp.69-82
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    • 2022
  • In this study, we investigated the bacterial community structure in organic rice-fish mixed farming paddy soil by using high-throughput sequencing technology. The results showed that compared with the organic rice cultivated soil, the content of AP (available phosphorus) increased by 310.23 % and the content of OM (organic matter) increased by 168.83%. The most abundant phyla in paddy soils were Proteobacteria, Bacteriodetes, and Chloroflexi, whose relative abundance was above 47.83%. Among the dominant genera, the relative abundance of Limisphaera in paddy soils was observed. Alpha diversity indicated that the bacterial diversity of paddy soils was similar among each other. The bacterial community structure was affected by the relative abundance of bacteria, not the species of bacteria. Principal Coordinated Analysis (PCoA) results showed that the bacterial communities in organic rice-fish mixed farming soil and organic paddy soil were correlated to each other; the bacterial community structure was distinctively grouped by four different systems (paddy soil under organic rice-fish mixed farming system, organic rice cultivation, and conventional rice cultivation), where the first two are closely related to each other than the third one. The results provide basal support for organic agri-cultivation while improving an ecological value at the same time.

Analysis of Sinjido Marine Ecosystem in 1994 using a Trophic Flow Model (영양흐름모형을 이용한 1994년 신지도 해양생태계 해석)

  • Kang, Yun-Ho
    • The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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    • v.16 no.4
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    • pp.180-195
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    • 2011
  • A balanced trophic model for Sinjido marine ecosystem was constructed using ECOPATH model and data obtained 1994 in the region. The model integrates available information on biomass and food spectrum, and analyses ecosystem properties, dynamics of the main species populations and the key trophic pathways of the system, and then compares these results with those of other marine environments. The model comprises 17 groups of benthic algae, phytoplankton, zooplankton, gastropoda, polychaeta, bivalvia, echinodermata, crustacean, cephalopoda, goby, flatfish, rays and skates, croaker, blenny, conger, flatheads, and detritus. The model shows trophic levels of 1.0~4.0 from primary producers and detritus to top predator as flathead group. The model estimates total biomass(B) of 0.1 $kgWW/m^2$, total net primary production(PP) of 1.6 $kgWW/m^2/yr$, total system throughput(TST) of 3.4 $kgWW/m^2/yr$ and TST's components of consumption 7%, exports 43%, respiratory flows 4% and flows into detritus 46%. The model also calculates PP/TR of 0.012, PP/B of 0.015, omnivory index(OI) of 0.12, Fin's cycling index(FCI) of 0.7%, Fin's mean path length(MPL) of2.11, ascendancy(A) of 4.1 $kgWW/m^2/yr$ bits, development capacity(C) of 8.2 $kgWW/m^2/yr$ bits and A/C of 51%. In particular this study focuses the analysis of mixed trophic impacts and describes the indirect impact of a groupb upon another through mediating one based on 4 types. A large proportion of total export in TST means higher exchange rate in the study region than in semi enclosed basins, which seems by strong tidal currents along the channels between islands, called Sinjido, Choyakdo and Saengildo. Among ecosystem theory and cycling indices, B, TST, PP/TR, FCI, MPL and OI are shown low, indicating the system is not fully mature according to Odum's theory. Additionally, high A/C reveals the maximum capacity of the region is small. To sum up, the study region has high exports of trophic flow and low capacity to develop, and reaches a development stage in the moment. This is a pilot research applied to the Sinjido in terms of trophic flow and food web system such that it may be helpful for comparison and management of the ecosystem in the future.

In silico Analysis of Downstream Target Genes of Transcription Factors (생명정보학을 이용한 전사인자의 하위표적유전자 분석에 관한 연구)

  • Hwang, Sang-Joon;Chun, Sang-Young;Lee, Kyung-Ah
    • Clinical and Experimental Reproductive Medicine
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    • v.33 no.2
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    • pp.125-132
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    • 2006
  • Objective: In the previous study, we complied the differentially expressed genes during early folliculogenesis. Objective of the present study was to identify downstream target genes of transcription factors (TFs) using bioinformatics for selecting the target TFs among the gene lists for further functional analysis. Materials & Methods: By using bioinformatics tools, constituent domains were identified from database searches using Gene Ontology, MGI, and Entrez Gene. Downstream target proteins/genes of each TF were identified from database searches using TF database ($TRANSFAC^{(R)}$ 6.0) and eukaryotic promoter database (EPD). Results: DNA binding and trans-activation domains of all TFs listed previously were identified, and the list of downstream target proteins/genes was obtained from searches of TF database and promoter database. Based on the known function of identified downstream genes and the domains, 3 (HNF4, PPARg, and TBX2) out of 26 TFs were selected for further functional analysis. The genes of wee1-like protein kinase and p21WAF1 (cdk inhibitor) were identified as potential downstream target genes of HNF4 and TBX2, respectively. PPARg, through protein-protein interaction with other protein partners, acts as a transcription regulator of genes of EGFR, p21WAF1, cycD1, p53, and VEGF. Among the selected 3 TFs, further study is in progress for HNF4 and TBX2, since wee1-like protein kinase and cdk inhibitor may involved in regulating maturation promoting factor (MPF) activity during early folliculogenesis. Conclusions: Approach used in the present study, in silico analysis of downstream target genes, was useful for analyzing list of TFs obtained from high-throughput cDNA microarray study. To verify its binding and functions of the selected TFs in early folliculogenesis, EMSA and further relevant characterizations are under investigation.

Diagnostic Accuracy of Rest T1-201/Stress Tc-99m-MIBI Myocardial SPECT in the Diagnosis of Coronary Artery Disease (휴식 T1-201/부하 Tc-99m MIBI 심근 SPECT의 관상동맥질환 진단 정확성)

  • Yeo, Jeong-Seok;Lee, Dong-Soo;Kang, Keon-Wook;Sohn, Dae-Won;Oh, Byung-Hee;Lee, Myung-Mook;Chung, June-Key;Park, Young-Bae;Lee, Myung-Chul;Seo, Jung-Don;Lee, Young-Woo;Koh, Chang-Soon
    • The Korean Journal of Nuclear Medicine
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    • v.30 no.1
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    • pp.112-117
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    • 1996
  • Objective: Standard stress/rest Tc-99m MIBI and T1-201 myocardial perfusion study have some limitations such as stress/rest image overlap for Tc-99m-MIBI, low energy for T1-201 and long period of study time for two separate studies. Separate acquisition rest T1-201/stress Tc-99m MIBI dual isotope study is a potentially efficient myocardial perfusion imaging protocol that combines the high resolution of Tc-99m for stress perfusion assessment and T1-201 for viability assessment. This study assessed the usefulness and diagnostic accuracy for this new approach. Methods: We tried to evaluate sensitivity and specificity of dual isotope separate acquisition protocol in 67 patients. Immediately after resting T1-201 SPECT data was acquired, dipyridamole stress Tc-99m MIBI myocardial perfusion study was performed. Visual analysis was carried out qualitatively with 0 to 3 scoring system for 17 segments of left ventricle in the reconstructed horizontal long axis and short axis slices. Results: Total study was completed within 3 hours. In angiographic correlation, dual isotope SPECT demonstrated high sensitivity(85%) and in a small group of patients, high specificity was also observed (100%). Conclusion: Combined thallium-201/stress Tc-99m MIBI SPECT displayed similiar diagnostic accuracy to protocol using stress/rest Tc-99m MIBI SPECT. This protocol was completed in shorter period than the previous protocols and therefore enhance laboratory throughput and patients convenience.

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An Empirical Study on the Determinants of Supply Chain Management Systems Success from Vendor's Perspective (참여자관점에서 공급사슬관리 시스템의 성공에 영향을 미치는 요인에 관한 실증연구)

  • Kang, Sung-Bae;Moon, Tae-Soo;Chung, Yoon
    • Asia pacific journal of information systems
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    • v.20 no.3
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    • pp.139-166
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    • 2010
  • The supply chain management (SCM) systems have emerged as strong managerial tools for manufacturing firms in enhancing competitive strength. Despite of large investments in the SCM systems, many companies are not fully realizing the promised benefits from the systems. A review of literature on adoption, implementation and success factor of IOS (inter-organization systems), EDI (electronic data interchange) systems, shows that this issue has been examined from multiple theoretic perspectives. And many researchers have attempted to identify the factors which influence the success of system implementation. However, the existing studies have two drawbacks in revealing the determinants of systems implementation success. First, previous researches raise questions as to the appropriateness of research subjects selected. Most SCM systems are operating in the form of private industrial networks, where the participants of the systems consist of two distinct groups: focus companies and vendors. The focus companies are the primary actors in developing and operating the systems, while vendors are passive participants which are connected to the system in order to supply raw materials and parts to the focus companies. Under the circumstance, there are three ways in selecting the research subjects; focus companies only, vendors only, or two parties grouped together. It is hard to find researches that use the focus companies exclusively as the subjects probably due to the insufficient sample size for statistic analysis. Most researches have been conducted using the data collected from both groups. We argue that the SCM success factors cannot be correctly indentified in this case. The focus companies and the vendors are in different positions in many areas regarding the system implementation: firm size, managerial resources, bargaining power, organizational maturity, and etc. There are no obvious reasons to believe that the success factors of the two groups are identical. Grouping the two groups also raises questions on measuring the system success. The benefits from utilizing the systems may not be commonly distributed to the two groups. One group's benefits might be realized at the expenses of the other group considering the situation where vendors participating in SCM systems are under continuous pressures from the focus companies with respect to prices, quality, and delivery time. Therefore, by combining the system outcomes of both groups we cannot measure the system benefits obtained by each group correctly. Second, the measures of system success adopted in the previous researches have shortcoming in measuring the SCM success. User satisfaction, system utilization, and user attitudes toward the systems are most commonly used success measures in the existing studies. These measures have been developed as proxy variables in the studies of decision support systems (DSS) where the contribution of the systems to the organization performance is very difficult to measure. Unlike the DSS, the SCM systems have more specific goals, such as cost saving, inventory reduction, quality improvement, rapid time, and higher customer service. We maintain that more specific measures can be developed instead of proxy variables in order to measure the system benefits correctly. The purpose of this study is to find the determinants of SCM systems success in the perspective of vendor companies. In developing the research model, we have focused on selecting the success factors appropriate for the vendors through reviewing past researches and on developing more accurate success measures. The variables can be classified into following: technological, organizational, and environmental factors on the basis of TOE (Technology-Organization-Environment) framework. The model consists of three independent variables (competition intensity, top management support, and information system maturity), one mediating variable (collaboration), one moderating variable (government support), and a dependent variable (system success). The systems success measures have been developed to reflect the operational benefits of the SCM systems; improvement in planning and analysis capabilities, faster throughput, cost reduction, task integration, and improved product and customer service. The model has been validated using the survey data collected from 122 vendors participating in the SCM systems in Korea. To test for mediation, one should estimate the hierarchical regression analysis on the collaboration. And moderating effect analysis should estimate the moderated multiple regression, examines the effect of the government support. The result shows that information system maturity and top management support are the most important determinants of SCM system success. Supply chain technologies that standardize data formats and enhance information sharing may be adopted by supply chain leader organization because of the influence of focal company in the private industrial networks in order to streamline transactions and improve inter-organization communication. Specially, the need to develop and sustain an information system maturity will provide the focus and purpose to successfully overcome information system obstacles and resistance to innovation diffusion within the supply chain network organization. The support of top management will help focus efforts toward the realization of inter-organizational benefits and lend credibility to functional managers responsible for its implementation. The active involvement, vision, and direction of high level executives provide the impetus needed to sustain the implementation of SCM. The quality of collaboration relationships also is positively related to outcome variable. Collaboration variable is found to have a mediation effect between on influencing factors and implementation success. Higher levels of inter-organizational collaboration behaviors such as shared planning and flexibility in coordinating activities were found to be strongly linked to the vendors trust in the supply chain network. Government support moderates the effect of the IS maturity, competitive intensity, top management support on collaboration and implementation success of SCM. In general, the vendor companies face substantially greater risks in SCM implementation than the larger companies do because of severe constraints on financial and human resources and limited education on SCM systems. Besides resources, Vendors generally lack computer experience and do not have sufficient internal SCM expertise. For these reasons, government supports may establish requirements for firms doing business with the government or provide incentives to adopt, implementation SCM or practices. Government support provides significant improvements in implementation success of SCM when IS maturity, competitive intensity, top management support and collaboration are low. The environmental characteristic of competition intensity has no direct effect on vendor perspective of SCM system success. But, vendors facing above average competition intensity will have a greater need for changing technology. This suggests that companies trying to implement SCM systems should set up compatible supply chain networks and a high-quality collaboration relationship for implementation and performance.

Development of Agrobacterium-mediated Transformation Method for Domestically Bred Chrysanthemum Cultivar 'Moulinrouge' and Genetic Change of Leaf Morphology Using AtSICKLE Gene (아그로박테리움를 이용한 국내개발 국화품종 '무랑루즈'의 형질전환 기술 및 AtSICKLE 유전자를 이용한 엽형 변화 국화 형질전환체 개발)

  • Kim, Yun-Hye;Park, Hyun-Myung;Jung, Ji-Yong;Kwon, Tack-Min;Jeung, Soon-Jae;Yi, Young-Byung;Kim, Gyung-Tae;Nam, Jae-Sung
    • Horticultural Science & Technology
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    • v.28 no.3
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    • pp.449-455
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    • 2010
  • 'Moulinrouge' was selected as the best regenerating cultivar among 18 different spray-type chrysanthemum cultivars bred in the Gyeongnam Flowers Breeding Research Institute. When the leaf explants from standard- and spray-type chrysanthemum 'Jinba' and 'Moulinrouge' were incubated on MS basal medium supplemented with $0.5mg{\cdot}L^{-1}$ BA and $1.0mg{\cdot}L^{-1}$ NAA, both 'Jinba' and 'Moulinrouge' induced adventitious shoots that can be regenerated into plantlets. Based on these regeneration conditions, we developed an efficient $Agrobacterium$-mediated chrysanthemum 'Moulinrouge' transformation method by using sequential selection of shoots from low ($10mg{\cdot}L^{-1}$) to high ($30mg{\cdot}L^{-1}$) concentrations of kanamycin after co-cultivation of leaf explants with $Agrobacterium$ for 10 days and induction of shoots. All kanamycin resistant plants investigated with genomic PCR analysis carried the report gene, $AtSICKLE$, in their genome. Although expression levels of the report gene in the transgenic plants investigated with RT-PCR were relatively low because of inefficiency of CaMV 35S promoter in chrysanthemum, transgenic lines expressing $AtSICKLE$ efficiently showed leaf epinasty phenotype. We expect that our results will provide a useful method that can perform a high-throughput investigation of genes isolated and studied well in model plants for molecular breeding of chrysanthemum.

Identification of a Locus Associated with Resistance to Phytophthora sojae in the Soybean Elite Line 'CheonAl' (콩 우수 계통 '천알'에서 발견한 역병 저항성 유전자좌)

  • Hee Jin You;Eun Ji Kang;In Jeong Kang;Ji-Min Kim;Sung-Taeg Kang;Sungwoo Lee
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.68 no.3
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    • pp.134-146
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    • 2023
  • Phytophthora root rot (PRR) is a major soybean disease caused by an oomycete, Phytophthora sojae. PRR can be severe in poorly drained fields or wet soils. The disease management primarily relies on resistance genes called Rps (resistance to P. sojae). This study aimed to identify resistance loci associated with resistance to P. sojae isolate 40468 in Daepung × CheonAl recombinant inbred line (RIL) population. CheonAl is resistant to the isolate, while Daepung is generally susceptible. We genotyped the parents and RIL population via high-throughput single nucleotide polymorphism genotyping and constructed a set of genetic maps. The presence or absence of resistance to P. sojae was evaluated via hypocotyl inoculation technique, and phenotypic distribution fit to a ratio of 1:1 (R:S) (χ2 = 0.57, p = 0.75), indicating single gene mediated inheritance. Single-marker association and the linkage analysis identified a highly significant genomic region of 55.9~56.4 megabase pairs on chromosome 18 that explained ~98% of phenotypic variance. Many previous studies have reported several Rps genes in this region, and also it contains nine genes that are annotated to code leucine-rich repeat or serine/threonine kinase within the approximate 500 kilobase pairs interval based on the reference genome database. CheonAl is the first domestic soybean genotype characterized for resistance against P. sojae isolate 40468. Therefore, CheonAl could be a valuable genetic source for breeding resistance to P. sojae.