• Title/Summary/Keyword: Molecular Cluster

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Molecular Characterization of Small-Spored Alternaria Species (소형의 포자를 형성하는 Alternaria 균류의 분자생물학적 특징)

  • Kim, Byung-Ryun;Park, Myung-Soo;Cho, Hye-Sun;Yu, Seung-Hun
    • Research in Plant Disease
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    • v.11 no.1
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    • pp.56-65
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    • 2005
  • To establish taxonomic system of morphologically similar species of small-spored Alternaria, phylogenetic analysis of internal transcribed spacer (ITS 1, ITS 2 and 5.8S rDNA) and mitochondrial small subunit (mt SSU) rDNA sequences and URP-PCR fingerprinting analysis from 11 species ofAlternaria were performed. Phylogenetic analysis of ITS and mt SSU rDNA sequences revealed that 10 out of 11 species of the smallspored Alternaria were phylogenetically identical with a bootstrap value of 100%. A. infectoria only was phylogenetically differentiated from the other species. The results suggest that the 10 small-spored Alternaria species are very closely related evolutionally and the markers can not be used for differentiation of the smallspored Alternaria species. URP-PCR fingerprinting analysis from eleven species of smallspored Alternaria using 10 URP primers showed that it was possible to differentiate the species, although genetic similarities were found among the species. The Alternaria sp. from common pokeweed could be distinguished from other species by URP-PCR analysis, and it was considered as a new species. A. infectoria could be easily distinguished from the other 10 species by phylogenetic analysis of ITS and mt SSU rDNA sequences and the URPPCR fingerprinting analysis.

Analysis of Genetic Diversity in Thirteen Turfgrass Cultivars Cultivated at Golf Courses Using RAPD Markers (RAPD마커를 이용한 국내골프장의 잔디 13 품종의 유전적 다양성 분석)

  • Kim, Min-Jeong;Kim, Tae-Soo;Shim, Chang-Ki;Kim, Yong-Ki;Jee, Hyeong-Jin
    • Weed & Turfgrass Science
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    • v.1 no.4
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    • pp.57-63
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    • 2012
  • This study was carried our to examine the genetic relationship of 13 commercial turfgrass cultivars using Random Amplified Polymorphic DNA to provide genetic informations more efficient golf course management. Analysis of 56 random hexamer primers generated 13 to 54 polymorphic bands among the 13 cultivars with an average of 30.7 bands per primer. The results of cluster analysis based on RAPDs revealed that three major variety groups: Group I - 'Shadow II', 'Aurora Gold', 'Little Bighorn Blue', 'PennA-1', and 'PennA-4'; Group II - 'Midnight II', 'Prosperity', 'Moon light SLT', 'Bright star SLT', and 'Silver dollar'; and Group III - 'Olympic Gold', 'Silver Star', and 'Tar Heel II'. The genetic similarity coefficients among 13 turfgrass cultivars ranged from 0.039 to 1.0 with highest coefficient in Group III. Studies on morphological characters and the effective molecular markers such as sequence characterized amplified regions are further needed to identify relationships and genetic diversities within species and among species.

Genetic Diversity of Rehmannia glutinosa Genotypes Assessed by Molecular Markers (분자표지자에 의한 지황 유전집단의 유전적 다양성)

  • Bang, Kyong-Hwan;Chung, Jong-Wook;Kim, Young-Chang;Lee, Jei-Wan;Kim, Hong-Sig;Kim, Dong-Hwi
    • Journal of Life Science
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    • v.18 no.4
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    • pp.435-440
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    • 2008
  • Random amplified polymorphic DNA (RAPD) markers were used to identify the genetic diversities among and within varieties and landraces of Rehmannia glutinosa. Polymorphic and reproducible bands were produced by 10 primers out of total 20 primers used in the experiment. In RAPD analysis of the 11 genotypes, 64 fragments out of 73 amplified genomic DNA fragments were polymorphic which represented an average 6.4 polymorphic fragments per primer. Number of amplified fragments with random primers ranged from 2 (OPA-1) to 13 (OPA-11) and varied in size from 200 bp to 1,400 bp. Especially, OPA-10, OPA-11 and OPA-19 primers showed specific bands for varieties of Korea Jiwhang and Jiwhang il ho, which could be useful for discriminating from other varieties and landraces of R. glutinosa. Percentage polymorphism ranged from a minimum of 50% (OPA-1) to a maximum of 100% (OPA-11), with an average of 87.7%. Similarity coefficients were higher in the genotypes of Korea Jiwhang and Jiwhang il ho than in other populations. In cluster analysis, genotypes of Korea Jiwhang, Jiwhang il ho, and Japanese accession were separated from those of other varieties and landraces. Average of genetic diversity within the population $(H_S)$ was 0.110, while average of total genetic diversity $(H_T)$ was 0.229. Across all RAPD makers the $G_{ST}$ value was 0.517, indicating that about 52% of the total genetic variation could be explained by RAPDs differences while the remaining 48% might be attributable to differences among samples. Consequently, RAPD analysis was useful method to discriminate different populations such as domestic varieties and other landraces. The results of the present study will be used to understand the population and evolutionary genetics of R. gllutinosa.

The Robust Phylogeny of Korean Wild Boar (Sus scrofa coreanus) Using Partial D-Loop Sequence of mtDNA

  • Cho, In-Cheol;Han, Sang-Hyun;Fang, Meiying;Lee, Sung-Soo;Ko, Moon-Suck;Lee, Hang;Lim, Hyun-Tae;Yoo, Chae-Kyoung;Lee, Jun-Heon;Jeon, Jin-Tae
    • Molecules and Cells
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    • v.28 no.5
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    • pp.423-430
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    • 2009
  • In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.

Classification of Rices on the Basis of Sensory Properties of Cooked Rices and the Physicochemical Properties of Rice Starches (취반미의 관능적 특성에 따른 쌀의 분류 및 쌀전분의 이화학적 특성)

  • Jang, Kyung-Ah;Shin, Myung-Gon;Hong, Sung-Hee;Min, Bong-Ki;Kim, Kwang-Ok
    • Korean Journal of Food Science and Technology
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    • v.28 no.1
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    • pp.44-52
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    • 1996
  • Sensory properties of cooked rice were affected by the varieties and growing environments of the rice. Moistness, cohesiveness, and adhesiveness of cooked rice were highly and positively correlated each other, whereas firmness was negatively correlated with these attributes. Sixty rice samples which differed in varieties and/or growing environments were divided into four groups based on their textural properties through principal component analysis and cluster analysis. Quality type I showed the highest values for moistness, cohesiveness, and adhesiveness, and the lowest values for firmness of cooked rice. On the other hand, quality type IV showed just the opposite values. There was no significant difference among rice starches in amylose content (P<0.05). A17 (type III) and A09 (type IV) had higher blue values for starch and amylopectin than the other samples (type I and II). On the amylogram, these samples showed lower values for breakdown and higher values for setback than the other samples. Average degree of polymerization, average chain length, and average number of chains for amylose and amylopectin were 597-878 and 2660-3140, 140-230 and 17-19, and 3.1-4.9 and 140-170, respectively.

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Use of Microsatellite Markers Derived from Genomic and Expressed Sequence Tag (EST) Data to Identify Commercial Watermelon Cultivars (수박 시판 품종의 식별을 위한 Genomic과 Expressed Sequence Tag (EST)에서 유래된 Microsatellite Marker의 이용)

  • Kwon, Yong-Sham;Hong, Jee-Hwa;Kim, Du-Hyun;Kim, Do-Hoon
    • Horticultural Science & Technology
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    • v.33 no.5
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    • pp.737-750
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    • 2015
  • This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard's genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation ($r{\geq}0.80$). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

The Chemical Bond of Cu Atom in Layer and Chain for Y123 and Y124 Superconductors (Y123 초전도체 및 Y124 초전도체에서 층과 사슬에 존재하는 구리 원자의 화학결합)

  • Man Shick Son;U-Hyon Paek;Lee Kee-Hag
    • Journal of the Korean Chemical Society
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    • v.36 no.4
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    • pp.477-484
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    • 1992
  • Using semiempirical molecular orbital method, ASED-MO of extended Huckel Theory, we were investigated chemical bonds and electronic properties of Cu atom in a chain and a layer for Y123 and Y124 superconductors from VEP (valence electron population), DOS (density of state), and COOP (crystal orbital overlap population). In order to investigate environmental effects of Cu atom for Y123 and Y124 superconductors, we introduced charged cluster models with point charge and without point charge into our calculations. As a result of ASED-MO calculations, the Cu atom in the layer acts as electron acceptor and the Cu atom in the chain acts as electron donor for Y123 and Y124 superconductors. The oxidation state of Cu atom for Y123 and Y124 superconductors without point charge is higher in the chain than in the layer. The oxidation state of Cu atom in the layer for Y123 superconductor is higher than that in the layer for Y124 superconductor. The Cu atom in the layer and the chain for Y123 superconductor does not largely affect on the environmental effect. However, the Cu atom in the layer and the chain for Y124 superconductor does largely affect on it. Also, electron population and chemical bonding of Cu1-O4, Cu2-O4, and Cu1-Cu2 for Y123 superconductor are far different from Y124 superconductor.

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Crystal Structure of Xenon Encapsulate within Na-A Zeolite

  • Im, U Taek;Park, Man;Heo, Nam Ho
    • Bulletin of the Korean Chemical Society
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    • v.21 no.1
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    • pp.75-80
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    • 2000
  • The positions of Xe atoms encapsulated in the molecular-dimensioned cavities of fully dehydrated Na-A have been determined. Na-A was exposed to 1050atm of xenon gas at 400 $^{\circ}C$ for seven days, followed by cooling at pressure to encapsulate Xe atoms. The resulting crystal structure of Na-A(7Xe) (a = 12.249(1) $\AA$, $R_1$ = 0.065, and $R_2$ = 0.066) were determined by single-crystal X-ray diffraction techniques in the cubic space group Pm3m at 21(1) $^{\circ}C$ and 1 atm. In the crystal structure of Na-A(7Xe), seven Xe atoms per unit cell are distributed over four crystallographically distinct positions: one Xe atom at Xe(1) lies at the center of the sodalite unit, two Xe atoms at Xe(4) are found opposite four-rings in the large cavity, and four Xe atoms, two at Xe(2) and others at Xe(3), respectively, occupy positions opposite and between eight- and six-rings in the large cavity. Relatively strong interactions of Xe atoms at Xe(2) and Xe(3) with $Na^+$ ions of four-, eight-, and six-rings are observed:Na(1)-Xe(2) = 3.09(6), Na(2)-Xe(3) = 3.11(2), and Na(3)-Xe(2) = 3.37(8) $\AA$. In each sodalite unit, one Xe atom is located at its center. In each large cavity, six Xe atoms are found, forming a distorted octahedral arrangement with four Xe atoms, at equatorial positions (each two at Xe(2) and Xe(3)) and the other two at axial positions (at Xe(4)). With various reasonable distances and angles, the existence of $(Xe)_6$ cluster is proposed (Xe(2)-Xe(3) = 4.78(6) and 4.94(7), Xe(2)-Xe(4) = 4.71(6) and 5.06(6), Xe(3)-Xe(4) = 4.11(3) and 5.32(4) $\AA$, Xe(2)-Xe(3)-Xe(2) = 93(1), Xe(3)-Xe(2)-Xe(3) = 87(1), Xe(2)-Xe(4)-Xe(2) = 91(4), Xe(2)-Xe(4)-Xe(3) = 55(2), 59(1), 61(1), and 68(1), and Xe(3)-Xe(4)-Xe(3) = 89($^{\circ}1$)). These arrangements of the encapsulated Xe atoms in the large cavity are stabilized by alternating dipoles induced on Xe(2), Xe(3), and Xe(4) by eight- and six-ring $Na^+$ ions as well as four-ring oxygens, respectively.

Coronaviruses: SARS, MERS and COVID-19 (코로나바이러스: 사스, 메르스 그리고 코비드-19)

  • Kim, Eun-Joong;Lee, Dongsup
    • Korean Journal of Clinical Laboratory Science
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    • v.52 no.4
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    • pp.297-309
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    • 2020
  • Coronaviruses were originally discovered as enzootic infections that limited to their natural animal hosts, but some strains have since crossed the animal-human species barrier and progressed to establish zoonotic diseases. Accordingly, cross-species barrier jumps resulted in the appearance of SARS-CoV, MERS-CoV, and SARS-CoV-2 that manifest as virulent human viruses. Coronaviruses contain four main structural proteins: spike, membrane, envelope, and nucleocapsid protein. The replication cycle is as follows: cell entry, genome translation, replication, assembly, and release. They were not considered highly pathogenic to humans until the outbreaks of SARS-CoV in 2002 in Guangdong province, China. The consequent outbreak of SARS in 2002 led to an epidemic with 8,422 cases, and a reported worldwide mortality rate of 11%. MERS-CoVs is highly related to camel CoVs. In 2019, a cluster of patients infected with 2019-nCoV was identified in an outbreak in Wuhan, China, and soon spread worldwide. 2019-nCoV is transmitted through the respiratory tract and then induced pneumonia. Molecular diagnosis based on upper respiratory region swabs is used for confirmation of this virus. This review examines the structure and genomic makeup of the viruses as well as the life cycle, diagnosis, and potential therapy.

Function and Molecular Ecology Significance of Two Catechol-Degrading Gene Clusters in Pseudomonas putida ND6

  • Shi, Sanyuan;Yang, Liu;Yang, Chen;Li, Shanshan;Zhao, Hong;Ren, Lu;Wang, Xiaokang;Lu, Fuping;Li, Ying;Zhao, Huabing
    • Journal of Microbiology and Biotechnology
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    • v.31 no.2
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    • pp.259-271
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    • 2021
  • Many bacteria metabolize aromatic compounds via catechol as a catabolic intermediate, and possess multiple genes or clusters encoding catechol-cleavage enzymes. The presence of multiple isozyme-encoding genes is a widespread phenomenon that seems to give the carrying strains a selective advantage in the natural environment over those with only a single copy. In the naphthalene-degrading strain Pseudomonas putida ND6, catechol can be converted into intermediates of the tricarboxylic acid cycle via either the ortho- or meta-cleavage pathways. In this study, we demonstrated that the catechol ortho-cleavage pathway genes (catBICIAI and catBIICIIAII) on the chromosome play an important role. The catI and catII operons are co-transcribed, whereas catAI and catAII are under independent transcriptional regulation. We examined the binding of regulatory proteins to promoters. In the presence of cis-cis-muconate, a well-studied inducer of the cat gene cluster, CatRI and CatRII occupy an additional downstream site, designated as the activation binding site. Notably, CatRI binds to both the catI and catII promoters with high affinity, while CatRII binds weakly. This is likely caused by a T to G mutation in the G/T-N11-A motif. Specifically, we found that CatRI and CatRII regulate catBICIAI and catBIICIIAII in a cooperative manner, which provides new insights into naphthalene degradation.