• The Korean Journal of Mycology
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• v.48 no.3
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• pp.313-323
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• 2020

To investigate the morphological characteristics and genetic relationships among isolate of the artificially cultivated mushroom Hypsizygus marmoreus, 111 isolates were collected from Korea and other countries. Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) and ITS rDNA sequencing were used to confirm the genetic relationships among the collected H. marmoreus isolates. As a result of RAPD analysis using universal rice primer (URP)-PCR, all isolates of H. marmoreus clustered into three groups, which showed high sequence similarity (>90%). In addition, isolates with morphological and geographical differences formed independent clusters. However, it was impossible to distinguish between brown and white strains. Sixteen strains showing morphological and geographic differences were selected, and their ITS region sequences (640 bp) were aligned and compared. The ITS region sequences belonging to these isolates showed 94.8-99.1% similarities to those of publicly available H. marmoreus strains in GenBank. In conclusion, there were differences among isolates in terms of morphology and the area from which they were collected, but all the isolates used in the experiment were classified as H. marmoreus.

• Microbiology and Biotechnology Letters
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• v.40 no.4
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• pp.409-413
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• 2012

Indolicidin (ID) is a 13-residue Trp-rich antimicrobial peptide (AMP) isolated from bovine neutrophils. In addition to having a high antimicrobial potency, it is also toxic to mammalian cells. To develop novel ID-derived AMPs with shorter lengths and enhanced prokaryotic selectivities (meaning potent antimicrobial activity against bacterial cells without toxicity against mammalian cells) over the parental ID, several ID analogs were designed and synthesized. Finally, 10-residue ID analogs (SI, SI-PA, SI-WF and SI-WL) with much higher prokaryotic selectivity than the parental ID were developed. Our results suggest that the hydrophobic and aromatic amino acids at the central position of the analog SI with the highest prokaryotic selectivity are important for potent antimicrobial activity, but two Pro residues do not affect antimicrobial activity. The order of prokaryotic selectivity for ID and its designed analogs was SI > SI-PA > SI-WF > SI-WL > ID > SI-WA. Taken together, our designed short ID analogs could be developed as therapeutic agents for treating bacterial infections.

• Korean Journal of Plant Taxonomy
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• v.37 no.4
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• pp.419-430
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• 2007

This study was conducted to know the taxonomic features of nuclear ribosomal ITS DNA sequences, ITS1, ITS3 and 5.8S regions, as to nine individuals belonging to four Oxalis species in Korea and an induced species. Sequences of the same regions of sixteen taxa deposited in GenBank were also aligned with those of Korean species as outgroups. The length of ITS sequences aligned in this study is 679 by in total. Evidences, from not only the sequence similarities and divergences but also the phylogenetic and statistical treatments with ITS sequences aligned, were useful for the taxonomy of the genus. The similarity of sequences, among both cauline and acauline taxa, is high as 89% and 95% respectively, but between cauline and acauline taxa, relatively low in the range of 64~69%. The sequence divergences, among both cauline and acauline taxa, is also high as much as 0.36~0.42, but between both cauline and both acauline taxa, low as 0.04~0.06. Two groups between cauline and acauline taxa are paraphyletic, and each group makes a single Glade with a high bootstrap value. The analysis of variance, using ITS sequence aligned, revealed that taxa are significantly different in the level of 0.5%, and O. corymbosa, an induced speices, is also separated from the Korean taxa in the Duncan analysis.

• Korean Journal of Microbiology
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• v.34 no.1_2
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• pp.69-73
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• 1998

We have cloned and analyzed cDNA coding for nucleocapsid protein N from infectious hematopoietic necrosis virus(IHNV), IHNV-PRT, which was isolated in Korea. The N gene had open reading frame of 1,176 bp that encoded a 391 amino acids with a molecular weight of 42.3 kDa. The deduced amino acid sequence of N protein was 75-90% identical to those of foreign isolates, IHNV, but was 43% and 38% identical to those of other species of fish rhabdovirus, hirame rhabdovirus(HRV) and viral hemorrahagic septicemia virus(VHSV), respectively. However, it revealed high levels of sequence identity between 214-265 amino acid sequences among all species of fish rhabdovirus.

• The Korean Journal of Zoology
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• v.38 no.1
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• pp.49-54
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• 1995

본 연구자들은 근원세포를 면역시켜 얻은 hybidoma들을 검색하여. 계배 근원세포의 분화와 관련된 단백질을 인지하여 분화를 억제하는 대과가 있는 monoclonal antibody 3H35를 선별하여 그 항원을 확인한 바 있다(Kim et af.. (1992), Korean J. Zool 35 29-36) 본 연구에서는 λZAP에 cloning된 chicken muscle CDNA library들을 lacZ fusion protein으로 발현시켜 항체 3H35로 검색하여 그 유전자를 찾아내었다. 선별한 CDNA clone 중 C59의 삽입 절편은 1.6 kb이었고, 발현시킨 facE fusion protein 은 60 kDa로, f-galactosidase에 대한 항체에 반응하며 3H35와도 반응함을 immunoaffinitv adsorbant와 immunoblot으로 확인하였다 Clone C59의 삽입 절편의 염기서열을 분석한 결과, 실제 유전자는 1.6 kb 이상이며, 알려진 어느 다른 유전자와도 관련이 없는 새로운 근특이 유전자로 판단되었다. 아미노산으로 전환시켰을 때 31개의 특이한 서열이 7차례 반복된 부분이 나타났으며 이 서열의 23개가 일정하게 보존되어있고 나머지 서열의 아미노산의 polarity도 매우 유사하게 효존되어있다. 이들의 보존성이 극히 높은 것으로 보아 독특한 기능을 수행하는 domain으로 추정된다.

• Journal of fish pathology
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• v.17 no.2
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• pp.91-98
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• 2004

This study was performed for the identification of Streptococcus sp. from cultured flounders (Paralichthys olivaceus) showing streptococcosis in the Jeju island. We isolated 10 strains of Streptococcus iniae from the cultured olive flounders with streptococcosis. Isolated strains were identified in S. iniae since they have formed the expected band through performing PCR assay using specific primers, Sin-1 (5'-CTAGAGTACACATGTACT(AGCT)AAG-3') and Sin-2 (5'-GGATTTTCCACTCCCATTAC-3'). In addition to 16S-23S rRNA intergenic spacers (ISR), operon structure of isolated strains showed that all strains had three 16S-23S rRNA ISR band patterns. The 16S-23S rRNA ISR sequence of isolated strains showed 96% sequence identity with S. iniae (GenBank accession number AF 048773). This paper is the first report that S. iniae is associated with streptococcosis of Olive flounder in Korea.

• Korean Journal of Microbiology
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• v.33 no.2
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• pp.86-91
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• 1997

Pseudomonas sp. DJ77로부터 클로닝된 glutathione S-transferase 유전자(phnC)의 염기서열을 결정하였다. 603bp의 open reading frame(ORF)이 존재하였고 개시코돈 앞에서 Shine-Dalgarno sequence를, 종결코돈 뒤에서는 terminator sequence를 발견하였다. phnC 유전자에서 만들어지는 phnC 단백질은 21,416 Da으로 SDS-polyacrylamide gel 전기영동 결과와 일치하였다. PhnC는 Bulkholderia cepacia LB400, Cycloclasticus oligotrophus RB1의 GST와 각각 53.7%, 49%의 높은 상동성을 나타냈다. 아미노산 서열의 상동성과 필수잔기들의 존재유무로 판단할 때 PhnC GST는 theta class GSTs와 진화적으로 유연관계가 높았지만 alpha, mu, pi, sigma class GSTs에서 구조적, 기능적으로 중요하다고 알려진 아미노산 잔기들이 PhnC GST에도 보존되어 있었다. 또한, phnC 유전자의 위치가 C. oligotrophus RB1, B. cepacia LB400 등의 GST 유전자 위치와 유사하다는 점에서 PhnC 효소는 난분해성 방향족 탄화수소의 분해에 관여하는 것으로 생각된다.

• Journal of KIISE:Software and Applications
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• v.37 no.1
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• pp.74-79
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• 2010

The amino acid composition of a protein provides basic information for solving many problems in bioinformatics. We propose a new method that uses biologically relevant similarity between amino acids to determine the amino acid composition, where the BOLOSUM matrix is exploited to define a similarity measure between amino acids. Futhermore, to extract more information from a protein sequence than conventional methods for determining amino acid composition, we exploit the concepts of spectral analysis of signals such as radar and speech signals-the concepts of time-dependent analysis, time resolution, and frequency resolution. The proposed method was applied to predict subcellular localization of proteins, and showed significantly improved performance over previous methods for amino acid composition estimation.

• Korean Journal of Microbiology
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• v.49 no.2
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• pp.211-214
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• 2013

Bisphenol A (BPA) is a highly hazardous component to human since it is regarded as one of endocrine disruptors. For the analysis and/or removal of BPA, the searching for the specific ligand with a selective affinity to target BPA is required. In order to find the peptide moiety that specifically binds to BPA, the ultrasound-assisted biopanning was carried out with a phage-displayed peptide library expressing constrained heptamer. After six rounds of positive screening against BPA particles followed by the negative screening against the surface of eppendorf tube, the peptide sequence (CysLysSerLeuGluAsnSerTyrCys) with affinity to BPA was screened based on the order of frequency from the screened phage clones. To further verify the specificity of screened peptide sequence, the cross-binding affinity of the phage peptide toward BPA analogues such as Bisphenol S (BPS) and Bisphenol F (BPF) was also assessed, where the selected phage peptide showed a higher affinity to BPA over BPS and BPF.

• Parasites, Hosts and Diseases
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• v.31 no.3
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• pp.285-292
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• 1993

C. sinensis total RMh was containing large amount of 185 rRNA but little 285 rRNA. The size of the double-stranded cDNA synthesized from poly $(A)^{+}$ mRNA was 0.4-4.2 kb long with tapering unto 9.5 kb. Degenerated oligonucleotides (as 2 sense and 3 antisense Primers) were designed on the conserved regions of the known tropomyosin amino acid sequences. From one out of the PCR amplifications using total CDNA and matrix of primers, a specific gene product, 580 bp in size, was produced. Upon Southern hybridization of the PCR products with Schistosomn mnnsoni tropomyosin (SMTM) CDNA, only one signal appeared at the band of 580 bp product. This 580 bp product was considered to encode C. sinensis tropomyosin (CSTM) and cloned in pGEM-3Zf(-) for DNA sequencing. CSTM cDNA was 575 bp containing one open reading frame of 191 predicted amino acids, which revealed 86.3% homology with SMTM and 51.1% with rrichostronsylur coeubnlormis tropomyosin. CSTM cDNA obtained will serve as a probe in the studies of molecular cloning of CSTM.