• Journal of Microbiology
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• v.33 no.4
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• pp.350-354
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• 1995

Saccharomyces cervisiae has a highly ordered ring of filaments that lies just inside the cytoplasmic membrane in the region of the mother-bud neck. Mutants defective in any one of the our cell division cycle genes (CDC3, CDC10, CDC11, CDC12) fail to form these filaments and exhibit a pleiotropic phenotype that includes failure to complete cytokinesis and abnormal bud growth. However, the role of the filament is not clear. In order to find out the role of filament, the similar gene in S pombe (called cdc103$\^$+) to the CDC3 was cloned and sequenced. Here I report the sequence analysis of the cdc103$\^$+/ ) to the CDC3 was cloned and sequenced. Here I report the sequence analysis of the cdc103$\^$+/. Comparison of the predicted amino acid sequences of cdc103$\^$+/ and CDC3 revealed that they share significant similarity (43% identity and 56% identity or similarity) to each other.

• Genomics & Informatics
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• v.20 no.3
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• pp.36.1-36.6
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• 2022

BLAST, a basic bioinformatics tool for searching local sequence similarity, has been one of the most widely used bioinformatics programs since its introduction in 1990. Users generally use the web-based NCBI-BLAST program for BLAST analysis. However, users with large sequence data are often faced with a problem of upload size limitation while using the web-based BLAST program. This proves inconvenient as scientists often want to run BLAST on their own data, such as transcriptome or whole genome sequences. To overcome this issue, we developed NBLAST, a graphical user interface-based BLAST program that employs a two-way system, allowing the use of input sequences either as "query" or "target" in the BLAST analysis. NBLAST is also equipped with a dot plot viewer, thus allowing researchers to create custom database for BLAST and run a dot plot similarity analysis within a single program. It is available to access to the NBLAST with http://nbitglobal.com/nblast.

• Journal of fish pathology
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• v.35 no.1
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• pp.135-140
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• 2022

In this study, we determined the cause of a disease outbreak in small yellow croaker(Larimichthys polyactis) in Jeju island. The major external signs in the dead fish were hemorrhage of the skin. Vibrio harveyi were isolated from a few fishes and viruses were not detected from the diseased fish. However, flukes were confirmed on the skin and we conducted molecular identification and phylogenetic analysis of the isolated parasites. The obtained 28S rRNA sequence of our specimen(Accession No. OM333244) showed the highest homology with Neobenedenia girellae, while the COI sequence of our specimen showed the highest homology with N. melleni. Further sequence analysis with other genes and morphological observation are necessary for accurate identification.

• Journal of Veterinary Science
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• v.24 no.3
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• pp.40.1-40.6
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• 2023

Analysis of the VP1 gene sequence of the foot and mouth disease virus (FMDV) is critical to understanding viral evolution and disease epidemiology. A standard set of primers have been used for the detection and sequence analysis of the VP1 gene of FMDV directly from suspected clinical samples with limited success. The study validated VP1-specific degenerate primer-based reverse transcription polymerase chain reaction (RT-PCR) for the qualitative detection and sequencing of serotype O FMDV lineages circulating in India. The novel degenerate primer-based RT-PCR amplifying the VP1 gene can circumvent the genetic heterogeneity observed in viruses after cell culture adaptation and facilitate precise viral gene sequence analysis from clinical samples.

• Journal of the Korean Society for Precision Engineering
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• v.14 no.5
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• pp.76-84
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• 1997

A process sequence in precision press forming of electrnic components is investigated by the finite element method. Aperture, a key component of electronic gun, is formed through a sequence of about 15 operation, among which the beading & bending, the first piercing, the first coining, and the second coining operations are expected to be most critical in view of industrial experts opinions. Thus, the analysis per- formed by a commercial code MARC focuses on the three operations, and comparisons are made between the results of the analysis and the measurements of experimental forming of the component.

• Korean Journal of Veterinary Research
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• v.37 no.2
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• pp.367-374
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• 1997

Bovine rotaviruses(A, 288, 55086 strains) isolated from fecal samples in Korea were propagated onto MA104 cells and were confirmed tentatively as G6, G8, and G10, respectively, by RFLP analysis. Full-length VP7 gene of these isolates was amplified by reverse transcriptase polymerase chain reaction(RT-PCR) using VP7 specific primers and cloned into TA vector. Nucleotide and deduced amino acid sequences of VP7 genes of the isolates were determined and compared with those of bovine rotavirus reference strains(NCDV; G6, UK; G6, Cody I-801; G8 and B223; G10). A, 288 and 55086 isolates showed high degree of nucleotide sequence homology with NCDV and UK(93% and 94%), Cody I-801(86%) and B223(97%), respectively, However, they showed 71~74% of nucleotide sequence homlogy with bovine rotavirus reference strains which belong to different serotypes. From the results of deduced amino acid sequence homology analysis, three isolates showed 94~96% of homology with the same serotype reference strains but 80~84% of homology with the different serotype reference strains. Three bovine rotavirus isolates, A, 288 and 55086 strains, were confirmed as G6, G8, and G10, respectively, by nucleotide and deduced amino acid sequence analysis.

• Biomedical Science Letters
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• v.24 no.3
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• pp.221-229
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• 2018

Trichophyton rubrum is one of the well-known pathogenic fungi and causes dermatophytosis and cutaneous mycosis in human world widely. However, there are not an available sequence type (ST) classification methods and previous studies for T. rubrum until now. Therefore, currently, molecular biological tools using their DNA sequences are used for genotype identification and classification. In the present study, in order to characterize the genetic diversity and the phylogenetic relation of T. rubrum clinical isolates, five different housekeeping genes, such as actin (ACT), calmodulin (CAL), RNA polymerase II (RPB2), superoxide dismutase 2 (SOD2), and ${\beta}$-tubulin (BT2) were analyzed using by multilocus sequence typing (MLST). Also, DNA sequence analysis was performed to examine the differences between the sequences of Trichophyton strains and the identified genetic variations sequence. As a result, most of the sequences were shown to have highly matched rates in their housekeeping genes. However, genetic variations were found on three different positions of ${\beta}$-tubulin gene and were shown to have changed from $C{\rightarrow}G$ (1766), $G{\rightarrow}T$ (1876), and $C{\rightarrow}A$ (1886). To confirm the association with T. rubrum inheritance, a phylogenetic tree analysis was performed. It was classified as four clusters, but there was little significant correlation. Even so, MLST analysis is believed to be helpful for determining the genetic variations of T. rubrum in cases where there is more large-scale data accumulation. In conclusion, the present study demonstrated the first MLST analysis of T. rubrum in Korea and explored the possibility that MLST could be a useful tool for studying the epidemiology and evolution of T. rubrum through further studies.

• Korean Journal of Breeding Science
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• v.40 no.1
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• pp.1-7
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• 2008

An attempt was made to link rice embryo proteins to DNA sequences and to understand their functions. One hundred of the 700 spots detected on the embryo 2-DE gels were microsequenced. Of these, 28% of the embryo proteins were matched to DNA sequences with known functions, but 72% of the proteins were unknown in functions as previously reported (Woo et al. 2002). In addition, twenty-four protein spots with 100% of homology and nine with over 80% were matched to ESTs (expressed sequence tags) after expanding the amino acid sequences of the protein spots by Database searches using the available rice EST databases at the NCBI (http://www/ncbi.nlm.nih.gov/) and DDBJ (http://www.ddbj.nig.ac.jp/). The chromosomal location of some proteins were also obtained from the rice genetic map provided by Japanese Rice Genome Research Program (http://rgp.dna.affrc.go.jp). The DNA sequence databases including EST have been reported for rice (Oryza sativa L.) now provides whole or partial gene sequence, and recent advances in protein characterization allow the linking proteins to DNA sequences in the functional analysis. This work shows that proteome analysis could be a useful tool strategy to link sequence information and to functional genomics.

• Journal of Veterinary Science
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• v.21 no.6
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• pp.73.1-73.10
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• 2020

Background: Bovine papilloma is a neoplastic disease caused by bovine papillomaviruses (BPVs), which were recently divided into 5 genera and at least 24 genotypes. Objectives: The complete genome sequence of BPV type 15 (BPV Aks-02), a novel putative BPV type from skin samples from infected cows in Southern Xinjiang China, was determined by collecting warty lesions, followed by DNA extraction and amplicon sequencing. Methods: DNA was analyzed initially by polymerase chain reaction (PCR) using the degenerate primers FAP59 and FAP64. The complete genome sequences of the BPV Aks-02 were amplified by PCR using the amplification primers and sequencing primers. Sequence analysis and phylogenetic analysis were performed using bio-informatic software. Results: The nucleotide sequence of the L1 open reading frame (ORF) of BPV Aks-02 was 75% identity to the L1 ORF of BPV-9 reference strain from GenBank. The complete genome consisted of 7,189 base pairs (G + C content of 42.50%) that encoded 5 early (E8, E7, E1, E2, and E4) and 2 late (L1 and L2) genes. The E7 protein contained a consensus CX₂CX₂₉CX₂C zinc-binding domain and a LxCxE motif. Among the different members of this group, the percentages of the complete genome and ORFs (including 5 early and 2 late ORFs) sequence identity of BPV Aks-02 were closer to the genus Xipapillomavirus 1 of the Xipapillomavirus genus. Phylogenetic analysis and sequence similarities based on the L1 ORF of BPV Aks-02 revealed the same cluster. Conclusions: The results suggest that BPV type (BPV Aks-02) clustered with members of the Xipapillomavirus genus as BPV 15 and were closely related to Xipapillomavirus 1.

• The Korean Journal of Mycology
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• v.32 no.1
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• pp.1-7
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• 2004

To establish the phylogenetic relationships of Dictyophora spp., rDNA-ITS regions of 11 strains of veiled lady mushroom collected from various countries were amplified and sequenced. It was observed that the 11 strains were divided into four groups based on PCR band patterns of each ITS region cleaved by eight different restriction enzymes in cleaved amplified polymorphic sequence analysis (CAPS). The phylogenic relationship of each group by cleaved amplified polymorphic sequence (CAPS) analysis matches well with previously reported morphological phylogeny, such as 5 strains of D. indusiata, 4 strains of D. echinovolvata, and a strain of Phallus rugulosus. Sequence analysis using the cluster V methods showed more detail classification than CAPS analysis. The 5.8S region showed two point nucleotide base exchanges from G to A according to four groups, and four groups were subdivided by sequence variation of ITS I and ITS II regions. But sequence variation of Phallus rugulosus was not showed in full ITS region. This study further delineates the taxonomic level at which ITS sequences, in comparison to ribosomal gene sequence, are most useful in systematics and other mushroom study.