• Title/Summary/Keyword: EST Analysis

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Sympatry and Species Status of Momco Jagowskii and M oxycephalus (Cyprirndae) (버들개(Moroco lagowskii)와 버들치(M.oxcephalus)의 동서지역 분석 및 종 문제에 관하여)

  • 양서영;민미숙
    • The Korean Journal of Zoology
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    • v.31 no.1
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    • pp.56-61
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    • 1988
  • The taxonomic status of Moroco Jagowskii and M oxycephalus a pair of sibling species inhabiting in Korean fresh waters, has been unclear up to date. Recently a sympatric area of these species was found (Kang, 1987). The purpose of this study was to clarify their specific status by analysing specimens collected from the sympatric area of these species. Isozyme analysis and morphometric comparison were performed. Among 26 loci screened 6 loci (Aco, Est-2, E-X, Gk-3, Ipo, Me) showed fixed allelic difference between them and these loci could be used as genetic markers to distinguish them. Isozyme analysis indicates that no hybridization occurs and therefore it is assumed that isolating mechanism is completed and they are distinct species. The mean number of scales above lateral line (SAL) of M Jagowskii and M oxycephalus at sympatric area was 24.93 $\pm$1.95 and 17.33$\pm$0.72 respectively, and it seems as the result of character displacement. A finer microhabitat segregation between them is noticed. M oxycephalus is found along the effluent streams whereas M lagowskii is distributed mostly in the main stream at sympatric area.

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Expressed Sequence Tag Analysis of the Erythrocytic Stage of Plasmodium berghei

  • Seok, Ji-Woong;Lee, Yong-Seok;Moon, Eun-Kyung;Lee, Jung-Yub;Jha, Bijay Kumar;Kong, Hyun-Hee;Chung, Dong-Il;Hong, Yeon-Chul
    • Parasites, Hosts and Diseases
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    • v.49 no.3
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    • pp.221-228
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    • 2011
  • Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.

Isolation and Phylogenetic Analysis of Acyl-CoA-binding Protein Gene from Panax ginseng C.A. Meyer (인삼으로부터 Acyl-CoA-binding Protein 유전자의 동정 및 계통적 분석)

  • 인준교;류명현;최광태;최관삼;김세영;양덕춘
    • Korean Journal of Plant Tissue Culture
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    • v.28 no.4
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    • pp.201-204
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    • 2001
  • Acyl-CoA binding proteins (ACBP) are small highly-conserved cytosolic proteins that bind long-chain acyl-CoAs. A cDNA encoding ACBP was identified from cDNA library constructed from hairy root poly $A^{+}$ RNA in expressed sequence tags (EST) analysis. The cDNA clone was 453 bp long and carried an open reading frame of 264 bp (10 kDa). The ginseng ACBP amino acid sequence was compared with other reported plant ACBPs using the CLUSTALW. Ginseng ACBP is 89%, 81%, 80%, and 73% identical with ACBP from castor bean, lilly, Digitalis and Arabidopsis, respectively. However, ginseng ACBP is 5 amino acids smaller than Arabidopsis and rape seed ACBPs. Also there is no any known signal peptide sequence in ginseng ACBP.

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A New Exploratory Research on Franchisor's Provision of Exclusive Territories (가맹본부의 배타적 영업지역보호에 대한 탐색적 연구)

  • Lim, Young-Kyun;Lee, Su-Dong;Kim, Ju-Young
    • Journal of Distribution Research
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    • v.17 no.1
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    • pp.37-63
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    • 2012
  • In franchise business, exclusive sales territory (sometimes EST in table) protection is a very important issue from an economic, social and political point of view. It affects the growth and survival of both franchisor and franchisee and often raises issues of social and political conflicts. When franchisee is not familiar with related laws and regulations, franchisor has high chance to utilize it. Exclusive sales territory protection by the manufacturer and distributors (wholesalers or retailers) means sales area restriction by which only certain distributors have right to sell products or services. The distributor, who has been granted exclusive sales territories, can protect its own territory, whereas he may be prohibited from entering in other regions. Even though exclusive sales territory is a quite critical problem in franchise business, there is not much rigorous research about the reason, results, evaluation, and future direction based on empirical data. This paper tries to address this problem not only from logical and nomological validity, but from empirical validation. While we purse an empirical analysis, we take into account the difficulties of real data collection and statistical analysis techniques. We use a set of disclosure document data collected by Korea Fair Trade Commission, instead of conventional survey method which is usually criticized for its measurement error. Existing theories about exclusive sales territory can be summarized into two groups as shown in the table below. The first one is about the effectiveness of exclusive sales territory from both franchisor and franchisee point of view. In fact, output of exclusive sales territory can be positive for franchisors but negative for franchisees. Also, it can be positive in terms of sales but negative in terms of profit. Therefore, variables and viewpoints should be set properly. The other one is about the motive or reason why exclusive sales territory is protected. The reasons can be classified into four groups - industry characteristics, franchise systems characteristics, capability to maintain exclusive sales territory, and strategic decision. Within four groups of reasons, there are more specific variables and theories as below. Based on these theories, we develop nine hypotheses which are briefly shown in the last table below with the results. In order to validate the hypothesis, data is collected from government (FTC) homepage which is open source. The sample consists of 1,896 franchisors and it contains about three year operation data, from 2006 to 2008. Within the samples, 627 have exclusive sales territory protection policy and the one with exclusive sales territory policy is not evenly distributed over 19 representative industries. Additional data are also collected from another government agency homepage, like Statistics Korea. Also, we combine data from various secondary sources to create meaningful variables as shown in the table below. All variables are dichotomized by mean or median split if they are not inherently dichotomized by its definition, since each hypothesis is composed by multiple variables and there is no solid statistical technique to incorporate all these conditions to test the hypotheses. This paper uses a simple chi-square test because hypotheses and theories are built upon quite specific conditions such as industry type, economic condition, company history and various strategic purposes. It is almost impossible to find all those samples to satisfy them and it can't be manipulated in experimental settings. However, more advanced statistical techniques are very good on clean data without exogenous variables, but not good with real complex data. The chi-square test is applied in a way that samples are grouped into four with two criteria, whether they use exclusive sales territory protection or not, and whether they satisfy conditions of each hypothesis. So the proportion of sample franchisors which satisfy conditions and protect exclusive sales territory, does significantly exceed the proportion of samples that satisfy condition and do not protect. In fact, chi-square test is equivalent with the Poisson regression which allows more flexible application. As results, only three hypotheses are accepted. When attitude toward the risk is high so loyalty fee is determined according to sales performance, EST protection makes poor results as expected. And when franchisor protects EST in order to recruit franchisee easily, EST protection makes better results. Also, when EST protection is to improve the efficiency of franchise system as a whole, it shows better performances. High efficiency is achieved as EST prohibits the free riding of franchisee who exploits other's marketing efforts, and it encourages proper investments and distributes franchisee into multiple regions evenly. Other hypotheses are not supported in the results of significance testing. Exclusive sales territory should be protected from proper motives and administered for mutual benefits. Legal restrictions driven by the government agency like FTC could be misused and cause mis-understandings. So there need more careful monitoring on real practices and more rigorous studies by both academicians and practitioners.

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Skewed Inheritance of EST-SSR Alleles in Reciprocal Crosses of Cut Roses (절화장미 품종간 정역교배에 있어서 EST-SSR 마커의 유전)

  • Kim, Jin-Ki;Ahn, Dong-Chun;Oh, Hye-Jeong;Kim, Kwang-Hwan;Choi, Young-Mi;Oh, Seung-Yong;Kang, Nam-Jun;Jeong, Byoung-Ryong;Kim, Zhoo-Hyeon;Park, Young-Hoon
    • Horticultural Science & Technology
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    • v.28 no.4
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    • pp.618-626
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    • 2010
  • Matroclinal inheritance of morphological characters in interspecific crosses of Rosa spp. can be influenced by cytoplasmic inheritance, apomixis, and asynaptic heterogamy. In asynaptic heterogamy, which is often observed from interspecific crosses of Rosa sect. $Caninae$, the polyploidy of the seed parent (especially for 5x=35) is recovered in the progeny through the pollens that include only a set of bivalents (x=7) and egg cells that contain a set of bivalents (x=7) and other univalents (3x=21). In this study, we investigated the causes of matroclinal offsprings observed from reciprocal crosses of tetraploid cut rose cultivars ($Rosa$ $hybrida$ L.) by analyzing EST-SSR marker distribution in the progeny populations. From EST-SSR marker analysis of eight offsprings per six reciprocal crosses among six cultivars, cases of cytoplasmic inheritance were not observed. Apomixis was also very rare as compared to the reports on interspecific crosses of sect. $Caninae$; only one apomitic plant was identified from the cross 'Redtem' ${\times}$ 'Red Sandra'. Although a clear-cut pattern of asynaptic heterogamy was not found, cultivar-specific marker transmission skewed to seed parent in four cultivars implied that genetic inheritance can be highly influenced by the seed parent depending on crosses among cut rose cultivars; especially, 10 out of 11 alleles specific to 'Yellow King' distributed in progenies at higher ratios when the cultivars were crossed as the seed parent.

Analysis of Expressed Sequence Tags of the Spider, Araneus ventricosus

  • Chung, Eun-Hwa;Lee, Kwang-Sik;Han, Ji-Hee;Sohn, Hung-Dae;Jin, Byung-Rae
    • International Journal of Industrial Entomology and Biomaterials
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    • v.3 no.2
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    • pp.191-199
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    • 2001
  • We have constructed a cDNA library from the whole body of the spider, Araneus ventricosus. Sequence analysis of randomly selected cDNA clones was performed to obtain genetic information on the spider A. ventricosus, of which genetic information is currently not available. We have partially sequenced randomly selected 385 clones of the cDNA library constructed from A. ventricosus. This expressed sequence tags (EST) analysis revealed 383 genes had high homologies to known genes in GenBank. In this report, 241 independent genes were analyzed in detail.

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Structural analysis of expressed sequence tags inimmature seed of Oryza sativa L. (벼 미숙종자의 발현유전자 구조특성분석)

  • Yoon, Ung-Han;Lee, Gang-Seob;Lee, Jung-Sook;Hahn, Jang-Ho;Kim, Chang-Kug;Kikuch, Shoshi;Satoh, Kouji;Kim, Jin-A;Lee, Jeong-Hwa;Lee, Tae-Ho;Kim, Yong-Hwan
    • Journal of Plant Biotechnology
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    • v.36 no.2
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    • pp.130-136
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    • 2009
  • Rice (Oryza sativa) is the most important staple crop in Korea. With its small genome size of 389Mb, rice is a model plant for genome research. We analyzed expressed sequence tag (EST) clones from immature seeds of rice (cv. Ilpum) at 20 days after heading. The 25,668 EST clones were clustered by using SeqMan program and 7,509 clones were selected as unique clones. We compared the 7,509 unique genes with KOME database including the 32,127 FL-cDNA in rice. Finally, 4,990 clones were homologous and 2,519 clones non-homologous to FL-cDNA clones. In addition, we mapped the 7,509 cDNA clones by using TIGR rice pseudomolecule version 5. Ultimately, 7,347 clones were matched to be significant clones related to the TIGR rice pseudomolecules, but 162 clones were unmapped. For the clustering of orthologous group genes, we further analyzed the 7,509 EST clones from immature seeds using NCBI clusters of orthologous groups database. Among the clones, 4,968 clones were categorized into information storage and processing, cellular processes and signaling, metabolism and poorly characterized genes, proportioning 799 (14.89%), 1,536 (28.3%), 1,148 (21.2%) and 1,936 (35.7%) clones to the previous four categories, respectively.

Characterization and Expression of Penaeidin 3-2 from Fleshy Prawn Fenneropenaeus chinensis (대하 Penaeidin 3-2 유전자의 동정 및 발현)

  • Park, Eun-Mi;Cho, Hyun Kook;Hong, Gyeong-Eun;Nam, Bo-Hye;Kim, Young-Ok;Kim, Woo-Jin;Lee, Sang-Jun;Han, Hyon Sob;Lee, Jae Yong;Kim, Jong-Sheek;Jang, In-Kwon;Cheong, JaeHun;Choi, Tae-Jin;Kong, Hee Jeong
    • Journal of Marine Bioscience and Biotechnology
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    • v.2 no.1
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    • pp.34-39
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    • 2007
  • Penaeidins are members of a special family of antimicrobial peptides existing in several species of shrimp and play a crucial role in the immunological defense of shrimp. In this study, we isolated and characterized one EST clone (penaeidin) from cDNA library of fleshy prawn Fenneropenaeus chinensis hemocytes. Amino acids sequence comparison and phylogenetic analysis with other known penaeidins revealed that our clone was completely identical to F. chinensis Penaeidin 3-2 (Accession no. ABC33920), which composed of 71 amino acids with a putative signal peptide (1-19) and a cysteine-rich domain (C-terminal part). The expression and distribution of Penaeidin 3-2 transcripts in shrimp were detected in hemocytes, hepatopancreas, and muscles, and that Penaeidin 3-2 was constitutively expressed mainly in hemocytes. The artificial infection of white spot syndrome virus to F. chinensis resulted in Penaeidin 3-2 mRNA up-regulation in hemocytes, suggesting that the possible role of Penaeidin 3-2 in host defense system of F. chinensis.

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Functional analysis of expressed sequence tags from the liver and brain of Korean Jindo dogs

  • Kim, Jae-Young;Park, Hye-Sun;Lim, Da-Jeong;Jang, Hong-Chul;Park, Hae-Suk;Lee, Kyung-Tai;Kim, Jong-Seok;Oh, Seok-Il;Kweon, Mu-Sik;Kim, Tae-Hun;Choi, Bong-Hwan
    • BMB Reports
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    • v.44 no.4
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    • pp.238-243
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    • 2011
  • We generated 16,993 expressed sequence tags (ESTs) from two libraries containing full-length cDNAs from the brain and liver of the Korean Jindo dog. An additional 365,909 ESTs from other dog breeds were identified from the NCBI dbEST database, and all ESTs were clustered into 28,514 consensus sequences using StackPack. We selected the 7,305 consensus sequences that could be assembled from at least five ESTs and estimated that 12,533 high-quality single nucleotide polymorphisms (SNPs) were present in 97,835 putative SNPs from the 7,305 consensus sequences. We identified 58 Jindo dog-specific SNPs in comparison to other breeds and predicted seven synonymous SNPs and ten non-synonymous SNPs. Using PolyPhen, a program that predicts changes in protein structure and potential effects on protein function caused by amino acid substitutions, three of the non-synonymous SNPs were predicted to result in changes in protein function for proteins expressed by three different genes (TUSC3, ITIH2, and NAT2).

Gene Expression Profiling of Eukaryotic Microalga, Haematococcus pluvialis

  • EOM HYUNSUK;PARK SEUNGHYE;LEE CHOUL-GYUN;JIN EONSEON
    • Journal of Microbiology and Biotechnology
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    • v.15 no.5
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    • pp.1060-1066
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    • 2005
  • Under environmental stress, such as strong irradiance or nitrogen deficiency, unicellular green algae of the genus Haematococcus accumulate secondary carotenoids, i.e. astaxanthin, in the cytosol. The induction and regulation of astaxanthin biosynthesis in microalgae has recently received considerable attention owing to the increasing use of secondary carotenoids as a source of pigmentation for fish aquacultures, and as a potential drug in cancer prevention as a free-radical quencher. Accordingly, this study generated expressed sequence tags (ESTs) from a library constructed from astaxanthin-induced Haematococcus pluvialis. Partial sequences were obtained from the 5' ends of 1,858 individual cDNAs, and then grouped into 1,025 non-overlapping sequences, among which 708 sequences were singletons, while the remainder fell into 317 clusters. Approximately $63\%$ of the EST sequences showed similarity to previously described sequences in public databases. H. pluvialis was found to consist of a relatively high percentage of genes involved in genetic information processing ($15\%$) and metabolism ($11\%$), whereas a relatively low percentage of sequences was involved in the signal transduction ($3\%$), structure ($2\%$), and environmental information process ($3\%$). In addition, a relatively large fraction of H. pluvialis sequences was classified as genes involved in photosynthesis ($9\%$) and cellular process ($9\%$). Based on this EST analysis, the full-length cDNA sequence for superoxide dismutase (SOD) of H. pluvialis was cloned, and the expression of this gene was investigated. The abundance of SOD changed substantially in response to different culture conditions, indicating the possible regulation of this gene in H. pluvialis.