• Research in Plant Disease
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• v.29 no.3
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• pp.286-294
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• 2023

Biological and molecular characterization of a Korean isolate of Orthotospovirus chrysanthinecrocaulis (formerly known as chrysanthemum stem necrosis virus, CSNV) isolated from Chrysanthemum morifolium was determined using host range and sequence analysis in this study. Twenty-three species of indicator plants inoculated mechanically CSNV-Kr was investigated for determination of host range. CSNV-Kr induced various local and systemic symptoms in the inoculated plant species. CSNV-Kr could not infect three plant species and induced symptomless in systemic leaves in Nicotiana tabacum cultivars, though the plant samples reacted positively with the antiserum to CSNV by double-antibody sandwich-enzyme-linked immunosorbent assay. The complete genome sequence of CSNV-Kr was determined. The L RNA of CSNV-Kr consists of 8,959 nucleotides (nt) and encodes a putative RNA-dependent RNA polymerase. The M RNA of CSNV-Kr consists of 4,835 nt and encodes the movement protein (NSm) and the glycoprotein precursor (Gn/Gc protein). The S RNA of CNSV-Kr consists of 2,836 nt and encodes NSs protein and N protein. The Gn/Gc and N sequence of CSNV-Kr were compared with those of previously published CSNV isolates originating from different countries at nucleotide and amino acid levels. The Gn/GC sequence of CSNV-Kr shared 98.8-99.5% identity with CSNV isolated from other countries and the N sequence of CSNV-Kr shared 98.8-99.6% identity. No particular region of variability could be found in either grouping of viruses. All of the CSNV isolates did not show any relationship according to geographical origins and isolation hosts, suggesting no distinct segregation of the CSNV isolates.

• Journal of Microbiology
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• v.39 no.4
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• pp.305-313
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• 2001

The spr D gene encoding Strptomyces griseus protease D(SGPD); a chymotrypsin-like proteae, was cloned from Strptomyces griseus IFO13350 and sequence. Most of the amino-acid sequence deduced from the nucleotide sequence is idential to that Strptomyces griseus IMRU3499 except that one amino acid has been deleted and Trp 369 has been substituted into Cys369 in the SGPD from S. griseus IFO13350 without affecting the protease activity. The spr D gene was overexpressed in Streptomyce liv-idans TK24 as a heterologous host. Various media with different compositions were also used to max-imize the productivity of SGPD inthe heterologous host. The SGPD productivity was best when the transformant S. lividans TK24 was cultivated in R2YE medium. The relative chymotrypsin activity of the culture broth measured with an artificial chromogenic substrate, N-scuccinyl-ala-ala-pro-phe-p-nitroanilide, was 16 units/ml. A high level of SGPD was also produced in YEME and SAAM medial but it was relatively lower that in R2YE medium and negligible amounts of SGPD were produced in GYE, GAE and Benedict media. The growth of S. lividans reacted the maximum level of cell mass at days 3 and 4 of the culture, but SGPD production started in the stationary phase of cell growth and kept increase in till the 10$^{th}$ day of culture in R2YE and YEME medium, but in GYE media the productivity reached maximum level at 8days of cultivation. The introduction of the spr D gene into S. lividans TK24 triggered biosyntheis of the pigmented antibiotic , actinorhodin, which implies some protease may paly a very improtant role in secondary-metabolite formation in sStreptomyces.

• Animal Systematics, Evolution and Diversity
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• v.38 no.4
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• pp.226-237
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• 2022

Arcuospathidium is a haptorian ciliate genus composed of 18 species, and only one species has been reported in Korea. Here, we identify two unrecorded Arcuospathidium subspecies by morphological observation of both living and protargol-impregnated specimens with the small subunit ribosomal RNA (18S rRNA) gene sequence. These subspecies, Arcuospathidium cultriforme cultriforme (Penard, 1922) Foissner, 1984 and A. cultriforme scalpriforme (Kahl, 1930) Foissner, 2003, were isolated from various terrestrial habitats in July and August 2013, respectivley. Arcuospathidium cultriforme cultriforme is similar to A. cultriforme scalpriforme by a knife-shaped body, a twisted-shaped macronucleus, number of dorsal brushes, position of dorsal brushes, and shape of macronucleus but former mainly differs from the body length to oral bulge length ratio (27-38% vs. 41-53%), extrusome (one types vs. three types), cyst shape (roughly faceted wall vs. smooth surface and thin wall) and number of somatic kinety rows(18-30 vs. 30-44). Additionally, we analyzed the 18S rRNA gene sequences of two A. cultriforme subspecies and compared them with the sequences from GenBank to confirm their identification at the molecular level. As the results of genetic analysis, the 18S rRNA gene sequence of the Korean A. cultriforme cultriforme population is most similar to that of Austrian population. Also, the sequence of the Korean A. cultriforme scalpriforme population is most similar to that of another population with some nucleotide differences.

• Proceedings of the KSRS Conference
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• 2005.10a
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• pp.770-773
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• 2005

In most biological laboratory, sequences from sequence machine are stored into file disks as simple files. It will be hard work to store and manage the sequence data with consistency and integrity such as storing redundant files. It is required needed to develop a system which integrated and managed genome data with consistency and integrity for accurate sequence analysis. There fore, in this paper, we not only store gene and protein sequence data through sequencing but also manage them. We also make a integrate schema for transforming the file formats and design database system using it. As integrated schema is designed as a BSML, it is possible to apply a style language of XSL. From this, we can transfer among heterogeneous sequence formats.

• Research in Plant Disease
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• v.21 no.3
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• pp.222-226
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• 2015

The chitinase-producing bacterial strain C-1 is one of the key chitinase-producing biocontrol agents used for effective bioformulations for biological control. These bioformulations are mixed cultures of various chitinolytic bacteria. However, the precise identification, biocontrol activity, and the underlying mechanisms of the strain C-1 have not been investigated so far. Therefore, we evaluated in planta biocontrol efficacies of C-1 and determined the draft genome sequence of the strain in this study. The bacterial C-1 strain was identified as a novel Serratia sp. by a phylogenic analysis of its 16S rRNA sequence. The Serratia sp. C-1 bacterial cultures showed strong in planta biocontrol efficacies against some major phytopathogenic fungal diseases. The draft genome sequence of Serratia sp. C-1 indicated that the C-1 strain is a novel strain harboring a subset of genes that may be involved in its biocontrol activities.

• Journal of Korea Society of Industrial Information Systems
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• v.17 no.6
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• pp.41-50
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• 2012

This paper presents a new sequence alignment method using the divide approach, which solves the problem by decomposing sequence alignment into several sub-alignments with respect to exact matching subsequences. Exact matching subsequences in the proposed method are bounded on the generalized suffix tree of two sequences, such as protein domain length more than 7 and less than 7. Experiment results show that protein sequence pairs chosen in PFAM database can be aligned using this method. In addition, this method reduces the time about 15% and space of the conventional dynamic programming approach. And the sequences were classified with 94% of accuracy.

• Genomics & Informatics
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• v.6 no.3
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• pp.157-159
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• 2008

Multiple sequence alignment (MSA) is the most important step for many of biological sequence analyses, homology search, and protein structural assignments. However, large amount of data make biologists difficult to perform MSA analyses and it requires much computational time to align many sequences. Here, we have developed a simple and fast web alignment tool for aligning, editing, and visualizing large amount of sequence data. We used a cluster server installed ClustalW-MPI using web services and message passing interface (MPI). It also enables users to edit multiple sequence alignments for manual editing and to download the input data and results such as alignments and phylogenetic tree.

• Proceedings of the Microbiological Society of Korea Conference
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• 2005.05a
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• pp.182.2-182
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• 2005

• Journal of Species Research
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• v.1 no.1
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• pp.1-3
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• 2012

A new species, Zabelia densipila M.-P. Hong, Y.-C. Kim & B.Y. Lee (Linnaeaceae) is described from Gangwon-do, Korea and illustrated. The new taxon resembles Z. biflora (Turcz.) Makino, but it can be distinguished by its different flowering seasons, ovaries with densely long-pilose hairs, and sequence differences in nuclear ribosomal DNA and chloroplast DNA coding regions.

• Journal of Species Research
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• v.3 no.1
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• pp.27-34
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• 2014

Two species of Tortanus (Eutortanus) are newly recorded from shallow Korean waters: T. (E.) vermiculus Shen, 1955 and T. (E.) komachi Itoh, Ohtsuka and Sato, 2001. As a result of this study, five species are reported in the subgenus of the family Tortanidae in Korea. The sequence of cytochrome c oxidase subunit 1 (CO1) is also provided as a molecular characteristic.