• Journal of Life Science
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• v.16 no.2 s.75
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• pp.253-258
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• 2006

Garlic is a perennial herb primarily distributed throughout the world. These plants are regarded as a medically and agricultural important crop in the world. The genetic relationships between cultivated and wild species were investigated at the population levels by constructing tree based on ISSR (inter-simple sequence repeats) markers. In addition, ISSR analysis was also conducted to estimate genetic diversity and population structure of these species. Three wild garlic populations in Korea were found to have more alleles per locus (mean 1.672 vs. 1.510) higher percent polymorphic locus (67.2 vs. 51.0), and higher diversity (0.250 vs. 0.198) than three cultivated populations. The cultivated and wild species in Korea are well separated from each other at phylogenetic trees. Although there is not direct evidence that A. victorialis is an ancestor of Korean A. sativum, there is a possibility that cultivated A. sativum in Korea has evolved from wild A. victorialis in Korea. Populations of A. victorialis may be useful in germ-plasm classification and evolutionary process.

• BMB Reports
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• v.44 no.10
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• pp.680-685
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• 2011

The AT-hook motif is a small DNA-binding protein motif that has been found in the high mobility group of non-histone chromosomal proteins. The Arabidopsis genome contains 29 genes encoding the AT-hook motif DNA-binding protein (AHL). Recent studies of Arabidopsis genes (AtAHLs) have revealed that they might play diverse functional roles during plant growth and development. In this report, we mined 20 AHL genes (OsAHLs) from the rice genome database using AtAHL genes as queries and characterized their molecular features. A phylogenetic tree revealed that OsAHL proteins can be classified into 2 evolutionary clades. Tissue expression pattern analysis revealed that all of the OsAHL genes might be functionally expressed genes with 3 distinct expression patterns. Nuclear localization analysis using transgenic Arabidopsis showed that several OsAHL proteins are exclusively localized in the nucleus, indicating that they may act as architectural transcription factors to regulate expression of their target genes during plant growth and development.

• Computers and Concrete
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• v.8 no.6
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• pp.647-675
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• 2011

Our ability to predict hydration behavior is becoming increasingly relevant to the concrete community as modelers begin to link material performance to the dynamics of material properties and chemistry. At early ages, the properties of concrete are changing rapidly due to chemical transformations that affect mechanical, thermal and transport responses of the composite. At later ages, the resulting, nano-, micro-, meso- and macroscopic structure generated by hydration will control the life-cycle performance of the material in the field. Ultimately, creep, shrinkage, chemical and physical durability, and all manner of mechanical response are linked to hydration. As a way to enable the modeling community to better understand hydration, a review of hydration models is presented offering insights into their mathematical origins and relationships one-to-the-other. The quest for a universal model begins in the 1920's and continues to the present, and is marked by a number of critical milestones. Unfortunately, the origins and physical interpretation of many of the most commonly used models have been lost in their overuse and the trail of citations that vaguely lead to the original manuscripts. To help restore some organization, models were sorted into four categories based primarily on their mathematical and theoretical basis: (1) mass continuity-based, (2) nucleation-based, (3) particle ensembles, and (4) complex multi-physical and simulation environments. This review provides a concise catalogue of models and in most cases enough detail to derive their mathematical form. Furthermore, classes of models are unified by linking them to their theoretical origins, thereby making their derivations and physical interpretations more transparent. Models are also used to fit experimental data so that their characteristics and ability to predict hydration calorimetry curves can be compared. A sort of evolutionary tree showing the progression of models is given along with some insights into the nature of future work yet needed to develop the next generation of cement hydration models.

• Journal of Microbiology and Biotechnology
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• v.17 no.11
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• pp.1743-1750
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• 2007

Two Gram-negative, nonmotile, coccobacilli, SW-$3^T$ and SW-$100^T$, were isolated from sea water of the Yellow Sea in Korea. Strains SW-$3^T$ and SW-$100^T$ contained ubiquinone-9 (Q-9) as the predominant respiratory lipoquinone and $C_{18:1}\;{\omega}9c$ and $C_{16:0}$ as the major fatty acids. The DNA G+C contents of strains SW-$3^T$ and SW- $100^T$ were 44.1 mol% and 41.9 mol%, respectively. A neighbor-joining tree based on l6S rRNA gene sequences showed that the two isolates fell within the evolutionary radiation enclosed by the genus Acinetobacter. Strains SW-$3^T$ and SW-$100^T$ exhibited a l6S rRNA gene similarity value of 95.7% and a mean DNA-DNA relatedness level of 9.2%. Strain SW-$3^T$ exhibited l6S rRNA gene sequence similarity levels of 93.5-96.9% to the validly described Acinetobacter species and fifteen Acinetobacter genomic species. Strain SW-$100^T$ exhibited l6S rRNA gene sequence similarity levels of less than 97.0% to the other Acinetobacter species except Acinetobacter towneri DSM $14962^T$ (98.0% similarity). Strains SW-$3^T$ and SW-$100^T$ exhibited mean levels of DNA-DNA relatedness of 7.3-l6.7% to the type strains of some phylogenetically related Acinetobacter species. On the basis of phenotypic, phylogenetic, and genetic data, strains SW-$3^T$ and SW-$100^T$ were classified in the genus Acinetobacter as two distinct novel species, for which the names Acinetobacter marinus sp. novo (type strain SW-$3^T$=KCTC $12259^T$=DSM $16312^T$) and Acinetobacter seohaensis sp. novo (type strain SW-$100^T$=KCTC $12260^T$=DSM $16313^T$) are proposed, respectively.

• Korean Journal of Ichthyology
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• v.18 no.4
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• pp.293-299
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• 2006

Copper,zinc superoxide dismutase (Cu,Zn-SOD) plays a key role to the first antioxidant defense system against oxidative stress in diverse aerobic organisms. Due to the housekeeping action of Cu,Zn-SOD, it was reported that the structure and function have been conserved during evolution. In this study Cu,Zn-SOD from cloudy catshark Scyliorhinus torazame was subjected to phylogenetic analyses to know its evolutionary relationship in the vertebrate lineage. Molecular phylogenetic trees inferred by NJ, MP, ML and/or Bayesian analyses showed two shark species, Prionace glauca and S. torazame grouped together with high statistical supports. In general, they placed at the separated position from bony vertebrates. Thereafter, bony vertebrates composed of teleosts and birds/mammals (amniotes) formed a monophyletic group. Each teleost and amniote clade was also supported by relatively high statistical values. These phylogenetic relationships are well congruent with the phylogenetic hypothesis of the ancestral position of cartilaginous fishes to bony vertebrates.

• Journal of the Korean Data and Information Science Society
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• v.27 no.3
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• pp.621-627
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• 2016

A certain professional baseball team tends to be very weak against another particular team. For example, S team, the strongest team in Korea, is relatively weak to H team. In this paper, we carried out clustering the Korean baseball teams based on the records against the team S to investigate whether the pattern of the record of the team H is different from those of the other teams. The technique we have employed is 'time series clustering', or more specifically 'categorical time series clustering'. Three methods have been considered in this paper: (i) distance based method, (ii) genetic sequencing method and (iii) periodogram method. Each method has its own advantages and disadvantages to handle categorical time series, so that it is recommended to draw conclusion by considering the results from the above three methods altogether in a comprehensive manner.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.134-139
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• 2004

Hybrid cluster protein (HCP) was investigated because of its unique iron-sulfur clusters, which have been found in bacteria and archaea. Here, HCP homologous proteins from the third domain, 'eukarya'(3 amitochondriate protozoans, Giardia lamblia, Entamoeba histolytica, and Trichomonas vaginalis), were identified. All three amitochondriate protozoan HCPs (GlHCP, EhHCP, and TvHCP) belonged to Class I on the basis of two key characters, the cysteine spacing, Cys-(Xaa)₂Cys(Xaa)/sub 7-8/-Cys(Xaa)/sub 5/-Cys, and the absence of N-terminal deletion characteristic to the Class III. In phylogenetic analysis performed with amino acid sequences of 3 eukaryal, 5 bacterial, and 4 archaeal HCPs, the maximum likelihood (ML) tree indicated that TvHCP was clustered with Class I HCPs, whereas the other two HCPs (GlHCP and EhHCP) formed an independent clade with a high bootstrapping value (96%) not belonging to any previously recognized HCP class. In spite of the relatively lower bootstrapping value (61%), the position of the new eukaryal GlHCP-EhHCP clade was close to Class I, including the TvHCP, and Classes II and III were closely related with each other. The finding of eukaryal HCPs would help to understand the evolutionary history of HCP.

• Animal cells and systems
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• v.5 no.3
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• pp.243-246
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• 2001

Human endoqenous retroviral long terminal repeats (LTRs) have been found to be coexpressed with sequences of genes closely located nearby. It has been suggested that the LTR elements have contributed to structural changes or genetic variations of human genome connected to various diseases and evolution. Using cDNA library derived from placenta tissue, we performed PCR amplification and identified five new HERV-W LTR elements. Those LTR elements showed a high degree of sequence similarity (98-99%) with HERV-W LTR (AF072500). A phylogenetic tree obtained by the neighbor-joining method revealed that HERV-W LTR elements could be mainly divided into two groups through evolutionary divergence. Five new HERV-W LTR elements (pla-1, 4, 5, 6, 7) belonged to the group I with AX000960, AF072504, and AF072506 from GenBank database. The data suggest that several copy numbers of the HERV-W LTR elements are transcribed in placenta and may contribute to the understanding of biological function such as human placental morphogenesis.

• Animal Bioscience
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• v.34 no.5
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• pp.789-800
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• 2021

Objective: Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. Methods: Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei's genetic distance and Weir and Cockerham's FST. Results: Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was -0.076 for Jeju Black, while -0.018 to -0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. Conclusion: This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.

• The Plant Pathology Journal
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• v.34 no.6
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• pp.514-531
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• 2018

Tomato spotted wilt virus (TSWV; Genus Orthotospovirus: Family Tospoviridae) is one of the most destructive viruses affecting a wide range of horticultural crops on a worldwide basis. In 2015 and 2016, 171 leaf and fruit samples from tomato (Solanum lycopersicum) plants with viral symptoms were collected from the fields in various regions of Iran. ELISA test revealed that the samples were infected by TSWV. The results of RT-PCR showed that the expected DNA fragments of about 819 bp in length were amplified using a pair of universal primer corresponding to the RNA polymerase gene and DNA fragments of ca 777 bp and 724 bp in length were amplified using specific primers that have been designed based on the nucleocapsid (N) and non-structural (NSs) genes, respectively. The amplified fragments were cloned into pTG19-T and sequenced. Sequence comparisons with those available in the GenBank showed that the sequences belong to TSWV. The high nucleotide identity and similarities of new sequences based on the L, N, and NSs genes showed that minor evolutionary differences exist amongst the isolates. The phylogenetic tree grouped all isolates six clades based on N and NSs genes. Phylogenetic analysis showed that the Iranian isolates were composed a new distinct clade based on a part of polymerase, N and NSs genes. To our knowledge, this is the first detailed study on molecular characterization and genetic diversity of TSWV isolates from tomato in Iran that could be known as new clade of TSWV isolates.