• Title/Summary/Keyword: Sequence Analyses

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Structural Analysis of Repeated Tomato Phenylalanine Ammonia-Lyase Gene (PAL X1, PAL X2) (반복배열된 토마토 phenylalanine ammonia-Iyase(p AL X1, PAL X2) 유전자의 구조해석)

  • Lee, Shin-Woo;Yeo, Yun-Soo
    • Applied Biological Chemistry
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    • v.42 no.1
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    • pp.34-38
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    • 1999
  • We observed the structure of phenylalanine ammonia-lyase gene (PAL) which is one of the best studied plant defense-related genes responding to pathogen infection by producing suberin, lignin, and phytoalexins. In tomato, at least 5 different genetic loci have been identified by genomic southern blot hybridization and nucleotide sequence analyses of partially cloned gene fragments (Lee et al. 1992). However, our results suggest that two other isoforms designated as PAL X1 and PAL X2 are located on the chromosome in tomato plant. Furthermore, the preliminary results obtained from southern blot hybridization analyses of subcloned fragment digested with several restriction endonuclease indicated that PAL X1 and PAL X2 clones contain at least two copies of PAL gene and partial nucleotide sequence analyses of each subcloned fragment with the same primer taken from known nucleotide sequence of PAL5 gene indicated that they are located side by side on the same chromosome.

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Applications of Construction Sequence Analyses to Prototype Models of Twisted Tall Buildings (비틀림 초고층 프로토타입 모델에 대한 시공단계해석의 적용)

  • Choe, Mi-Mi;Kim, Jae-Yo;Eom, Tae-Sung;Jang, Dong-Woon
    • Journal of the Computational Structural Engineering Institute of Korea
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    • v.26 no.1
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    • pp.89-97
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    • 2013
  • With regard to complex-shaped tall buildings whose plans and constructions have been gradually on the increase, this study was aimed to analyze their structural behaviors during construction by applications of construction sequences analyses to prototype models. For twisted tall buildings, total 18 models of with three conditions of a lateral load-resisting system, a twisting angle, and a construction method were selected. A diagrid system and a braced tube system were applied as a lateral load-resisting system. For each lateral load-resisting system, three types of plan with $0^{\circ}$, $1^{\circ}$, and $2^{\circ}$ twisting angles and three construction methods with construction sequences of exterior tube and interior frame were assumed. The structural performances of tall buildings under constructions were analyzed with results of lateral displacements from construction sequence analyses. Also, construction performances of the construction period and the maximum lift weight were compared.

Molecular Characterization of Five Potyviruses Infecting Korean Sweet Potatoes Based on Analyses of Complete Genome Sequences

  • Kwak, Hae-Ryun;Kim, Jaedeok;Kim, Mi-Kyeong;Seo, Jang-Kyun;Jung, Mi-Nam;Kim, Jeong-Soo;Lee, Sukchan;Choi, Hong-Soo
    • The Plant Pathology Journal
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    • v.31 no.4
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    • pp.388-401
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    • 2015
  • Sweet potatoes (Ipomea batatas L.) are grown extensively, in tropical and temperate regions, and are important food crops worldwide. In Korea, potyviruses, including Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato virus G (SPVG), Sweet potato virus 2 (SPV2), and Sweet potato latent virus (SPLV), have been detected in sweet potato fields at a high (~95%) incidence. In the present work, complete genome sequences of 18 isolates, representing the five potyviruses mentioned above, were compared with previously reported genome sequences. The complete genomes consisted of 10,081 to 10,830 nucleotides, excluding the poly-A tails. Their genomic organizations were typical of the Potyvirus genus, including one target open reading frame coding for a putative polyprotein. Based on phylogenetic analyses and sequence comparisons, the Korean SPFMV isolates belonged to the strains RC and O with >98% nucleotide sequence identity. Korean SPVC isolates had 99% identity to the Japanese isolate SPVC-Bungo and 70% identity to the SPFMV isolates. The Korean SPVG isolates showed 99% identity to the three previously reported SPVG isolates. Korean SPV2 isolates had 97% identity to the SPV2 GWB-2 isolate from the USA. Korean SPLV isolates had a relatively low (88%) nucleotide sequence identity with the Taiwanese SPLV-TW isolates, and they were phylogenetically distantly related to SPFMV isolates. Recombination analysis revealed that possible recombination events occurred in the P1, HC-Pro and NIa-NIb regions of SPFMV and SPLV isolates and these regions were identified as hotspots for recombination in the sweet potato potyviruses.

A Study on the Automation of Field Instrumentation and the Analysis of MPBX Displacement (지중변위 계측자동화 및 3차원 유한요소해석에 관한 연구)

  • 정용복;정현기;정소걸;김동현;이희근
    • Tunnel and Underground Space
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    • v.6 no.4
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    • pp.287-297
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    • 1996
  • Input data play an important role in numerical analyses. However, it is difficult to obtain appropriate data for many reasons. In order to overcome those difficulties, an automatic MPBX(Multi-Position Borehole Extensometer) monitoring system is developed. This system can be applied to the analyses of measured data which include evaluation of the stabiliyt, efficiency of construction and the validity of numerical analyses. At first, the MPBX among field measurement tools is considered in this study. Also, 3-dimension finite element analyses are carried out to verify the influence of geological conditions and excavation sequence on the MPBX displacement. The effect of geological conditons on the displacement can be estimated qualitatively qualitavely from the measured data by plotting displacement vs. depth.

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A Gradient Analsis of the Mixed Forest of Seonusan Area in Southwestern Korea (선운산지역 삼림군집의 경도분석)

  • Kim, Jeong-Un;Yim, Yang-Jai
    • The Korean Journal of Ecology
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    • v.9 no.4
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    • pp.225-230
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    • 1986
  • The environmental gradient analyses and the continum analyses were applied for the ordinationa of forest vegetation in Seonunsan area. In the soil moisture gradient, mesic to xeric, Zelkova serrata, Carpinus tschonoskii, Quercus aliena, Carpinus laxiflora, Quercus serrata, Quercus variabilis and Pinus densiflora type were arranged as a series of sequence along the gradient. In two dimensional analyses of soil moisture and organic matter gradients seven vegetation types mentioned above were also separated one another. Especially Carpinus tschonoskii in mesic-fertile sites adn Pinus densiflora in xeric-sterile were noticeable. The results of continum analyses were corresponded to those of environmental gradient analses for the forest vegetation.

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Genomic Analyses of Toll-like Receptor 4 and 7 Exons of Bos indicus from Temperate Sub-himalayan Region of India

  • Malik, Y.P.S.;Chakravarti, S.;Sharma, K.;Vaid, N.;Rajak, K.K.;Balamurugan, V.;Biswas, S.K.;Mondal, B.;Kataria, R.S.;Singh, R.K.
    • Asian-Australasian Journal of Animal Sciences
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    • v.24 no.7
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    • pp.1019-1025
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    • 2011
  • Toll-like receptors (TLRs) play an important role in the recognition of invading pathogens and the modulation of innate immune responses in mammals. The TLR4 and TLR7 are well known to recognize the bacterial lipopolysaccharide (LPS) and single stranded (ssRNA) ligands, respectively and play important role in host defense against Gram-negative bacteria and ssRNA viruses. In the present study, coding exon fragments of these two TLRs were identified, cloned, sequenced and analyzed in terms of insertion-deletion polymorphism, within bovine TLRs 4 and 7, thereby facilitating future TLR signaling and association studies relevant to bovine innate immunity. Comparative sequence analysis of TLR 4 exons revealed that this gene is more variable, particularly the coding frame (E3P1), while other parts showed percent identity of 95.7% to 100% at nucleotide and amino acid level, respectivley with other Bos indicus and Bos taurus breeds from different parts of the world. In comparison to TLR4, sequence analysis of TLR7 showed more conservation among different B. indicus and B. taurus breeds, except single point mutation at 324 nucleotide position (AAA to AAM) altering a single amino acid at 108 position (K to X). Percent identity of TLR7 sequences (all 3 exons) was between 99.2% to 100% at nucleotide and amino acid level, when compared with available sequence database of B. indicus and B. taurus. Simple Modular Architecture Research Tool (SMART) analysis showed variations in the exon fragments located in the Leucine Rich Repeat (LRR) region, which is responsible for binding with the microbial associated molecular patterns and further, downstream signaling to initiate anti-microbial response. Considering importance of TLR polymorphism in terms of innate immunity, further research is warranted.

Genetic Relationships of Four Korean Oysters Based on RAPD and Nuclear rDNA ITS Sequence Analyses

  • Kim, Woo-Jin;Lee, Jeong-Ho;Kim, Kyung-Kil;Kim, Young-Ok;Nam, Bo-Hye;Kong, Hee-Jeong;Jung, Hyung-Taek
    • The Korean Journal of Malacology
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    • v.25 no.1
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    • pp.41-49
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    • 2009
  • Random amplified polymorphic DNA (RAPD) marker and sequence analyses of the internal transcribed spacer (ITS) region of ribosomal DNA were used to assess phylogenetic relationships of four Korean oyster species. The average number of species-specific markers identified from five universal rice primers (URPs) by RAPD-PCR was 1.8 for Crassostrea gigas, 3.2 for C. nippona, 3.6 for C. ariakensis, and 4.6 for Ostrea denselamellosa. The length of the ITS (ITS1-5.8S-ITS2) region ranged from 1,001 to 1,206 bp (ITS1, 426-518 bp; 5.8S, 157 bp; and ITS2, 418-536 bp), while the GC content ranged from 55.5-61.1% (ITS1, 56.8-61.8%; 5.8S, 56-57.3%; and ITS2, 54.1-62.2%). A phylogenetic analysis of the oysters based on our RAPD, ITS1, and ITS2 sequence data revealed a close relationship between C. gigas and C. nippona and a distant relationship between the genera Crassostrea and Ostrea. Our results indicated that RAPD and ITS sequence analysis was a useful tool for the elucidation of phylogenetic relationships and for the selection of species-specific markers in Korean oysters.

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Molecular Systematics of the Genus Megoura (Hemiptera: Aphididae) Using Mitochondrial and Nuclear DNA Sequences

  • Kim, Hyojoong;Lee, Seunghwan
    • Molecules and Cells
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    • v.25 no.4
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    • pp.510-522
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    • 2008
  • To construct the molecular systematics of the genus Megoura (Hemiptera: Aphididae), DNA based-identification was performed using four mitochondrial and three nuclear DNA regions: partial cytochrome c oxidase I (COI), partial tRNA-leucine + cytochrome c oxidase II (tRNA/COII), cytochrome b (CytB), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S), elongation factor-1 alpha ($EF1{\alpha}$), and the internal transcribed spacers 1 and 2 (ITS1, ITS2). Pairwise sequence divergences between taxa were compared, and phylogenetic analyses were performed based on each DNA region separately, and the combined datasets. COI, CytB, $EF1{\alpha}$, ITS1, and ITS2 were relatively effective in determining species and resolving their relationships. By contrast, the sequences of tRNA/COII and 12S/16S were not able to separate the closely related species. CytB and $EF1{\alpha}$ gave better resolution with higher average sequence divergences (4.7% for CytB, 5.2% for $EF1{\alpha}$). The sequence divergence of COI (3.0%) was moderate, and those of the two ITS regions (1.8% for ITS1, 2.0% for ITS2) were very low. Phylogenetic trees were constructed by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses. The results indicated that the phylogenetic relationships between Megoura species were associated with their host preferences. Megoura brevipilosa and M. lespedezae living on Lespedeza were closely related, and M. nigra, monophagous on Vicia venosa, was rather different from M. crassicauda, M. litoralis, and M. viciae, which are oligophagous on Lathyrus and Vicia. The three populations of M. crassicauda formed a clade separated from M. litoralis and M. viciae. Nevertheless M. litoralis and M. viciae, which are morphologically similar, were not separated due to negligible sequence divergence. We discuss the phylogenetic relationships of the Megoura, and the usefulness of the seven DNA regions for determining the species level phylogeny of aphids.

Safety analysis of marine nuclear reactor in severe accident with dynamic fault trees based on cut sequence method

  • Fang Zhao ;Shuliang Zou ;Shoulong Xu ;Junlong Wang;Tao Xu;Dewen Tang
    • Nuclear Engineering and Technology
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    • v.54 no.12
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    • pp.4560-4570
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    • 2022
  • Dynamic fault tree (DFT) and its related research methods have received extensive attention in safety analysis and reliability engineering. DFT can perform reliability modelling for systems with sequential correlation, resource sharing, and cold and hot spare parts. A technical modelling method of DFT is proposed for modelling ship collision accidents and loss-of-coolant accidents (LOCAs). Qualitative and quantitative analyses of DFT were carried out using the cutting sequence (CS)/extended cutting sequence (ECS) method. The results show nine types of dynamic fault failure modes in ship collision accidents, describing the fault propagation process of a dynamic system and reflect the dynamic changes of the entire accident system. The probability of a ship collision accident is 2.378 × 10-9 by using CS. This failure mode cannot be expressed by a combination of basic events within the same event frame after an LOCA occurs in a marine nuclear reactor because the system contains warm spare parts. Therefore, the probability of losing reactor control was calculated as 8.125 × 10-6 using the ECS. Compared with CS, ECS is more efficient considering expression and processing capabilities, and has a significant advantage considering cost.

Morphological and Genetic Characterization of Penicillium spp. associated with post - harvest decay of fruits. (oral)

  • Oh, S.Y.;Yu, S.H.
    • Proceedings of the Korean Society of Plant Pathology Conference
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    • 2003.10a
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    • pp.115.1-115
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    • 2003
  • Post-harvest decay, caused by Penicillium spp. is a serious problem of fruits worldwide. Morphological characteristics and molecular markers were used to characterize 22 Penicillium isolates from apples, 18 isolates from pears, 60 from oranges and 18 from grapes and 23reference isolates representing related Penicillium spp. to assess their diversity and resolve their taxonomy. Based on morphological and physiological characteristics, the isolates were grouped as identical or very similar to P. digitatum, P. italicum, P. ulaiense or very similar to P. crustosum, P. expansum, P. solitum and unidentified Penicillium spp. Based on sequence comparisons of ITS region, variable site were presented within and among the species, but there variation were not correlated with the species. Cluster analyses of AP-PCR fragment patterns using UP and L45 primer and the -tubulin gene sequence, the Penicillium species were segregated into distinct groups. Particularly. the -tubulin partial sequence data provided support for species concepts based on morphological and physiological characteristics.

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