• Mycobiology
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• v.50 no.4
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• pp.254-257
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• 2022

Wolfiporia cocos is a wood-decay brown rot fungus belonging to the family Polyporaceae. While the fungus grows, the sclerotium body of the strain, dubbed Bokryeong in Korean, is formed around the roots of conifer trees. The dried sclerotium has been widely used as a key component of many medicinal recipes in East Asia. Wolfiporia cocos strain KMCC03342 is the reference strain registered and maintained by the Korea Seed and Variety Service for commercial uses. Here, we present the first draft genome sequence of W. cocos KMCC03342 using a hybrid assembly technique combining both short- and long-read sequences. The genome has a total length of 55.5 Mb comprised of 343 contigs with N50 of 332 kb and 95.8% BUSCO completeness. The GC ratio was 52.2%. We predicted 14,296 protein-coding gene models based on ab initio gene prediction and evidence-based annotation procedure using RNAseq data. The annotated genome was predicted to have 19 terpene biosynthesis gene clusters, which was the same number as the previously sequenced W. cocos strain MD-104 genome but higher than Chinese W. cocos strains. The genome sequence and the predicted gene clusters allow us to study biosynthetic pathways for the active ingredients of W. cocos.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.323-330
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• 2009

Nontuberculous mycobacteria (NTM) are a major cause of opportunistic infections in immunocompromised patients, making the reliable and rapid identification of NTM to the species level very important for the treatment of such patients. Therefore, this study evaluated the usefulness of the novel target genes tuf and tmRNA for the identification of NTM to the species level, using a PCRrestriction fragment length polymorphism analysis (PRA). A total of 44 reference strains and 17 clinical isolates of the genus Mycobacterium were used. The 741 bp or 744 bp tuf genes were amplified, restricted with two restriction enzymes (HaeIII/MboI), and sequenced. The tuf gene-PRA patterns were compared with those for the tmRNA (AvaII), hsp65 (HaeIII/HphI), rpoB (MspI/HaeIII), and 16S rRNA (HaeIII) genes. For the reference strains, the tuf gene-PRA yielded 43 HaeIII patterns, of which 35 (81.4%) showed unique patterns on the species level, whereas the tmRNA, hsp65, rpoB, and 16S rRNA-PRAs only showed 10 (23.3%), 32 (74.4%), 19 (44.2%), and 3 (7%) unique patterns after single digestion, respectively. The tuf gene-PRA produced a clear distinction between closely related NTM species, such as M. abscessus (557-84-58) and M. chelonae (477-84-80-58), and M. kansasii (141-136-80-63-58-54-51) and M. gastri (141-136-117-80-58-51). No difference was observed between the tuf-PRA patterns for the reference strains and clinical isolates. Thus, a diagnostic algorithm using a tuf gene-targeting PRA is a promising tool with more advantages than the previously used hsp65, rpoB, and 16S rRNA genes for the identification of NTM to the species level.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.1
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• pp.371-376
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• 2012

Background: Caveolin-1 (CAV-1), encoding the structural component of cellular caveolae, is a suggested tumor suppressor gene involved in cell signalling. Aberrant promoter methylation of CAV-1 is associated with inactivation of expression. We previously observed CAV-1 mutations in breast cancers and therefore devised this study to examine the hypermethylation status of the promoter region of CAV-1 with reference to breast cancer progression and development. Methods: Hypermethylation status of CAV-1 was analyzed by methylation specific PCR. Loss of expression of the CAV-1 gene was further evaluated by semi-quantitative rt-PCR. Results: 28/130 (21.5%) breast cancer cases showed promoter hypermethylation with reduced CAV-1 expression levels when compared with adjacent normal breast tissue. CAV-1 gene hypermethylation was significantly related to menopausal status, histopathological grade and age. Conclusion: The rationale of our study is that CAV-1 gene is transcriptionally repressed in breast cancer cells due to hypermethylation. Our results reveal that promoter hypermethylation and loss of expression of the CAV-1 gene is an important alternative mechanism for inactivation of CAV-1 leading to complete gene silencing.

• Genomics & Informatics
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• v.11 no.4
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• pp.191-199
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• 2013

High-throughput next-generation sequencing (NGS) technology produces a tremendous amount of raw sequence data. The challenges for researchers are to process the raw data, to map the sequences to genome, to discover variants that are different from the reference genome, and to prioritize/rank the variants for the question of interest. The recent development of many computational algorithms and programs has vastly improved the ability to translate sequence data into valuable information for disease gene identification. However, the NGS data analysis is complex and could be overwhelming for researchers who are not familiar with the process. Here, we outline the analysis pipeline and describe some of the most commonly used principles and tools for analyzing NGS data for disease gene identification.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.8
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• pp.987-992
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• 2010

This study was to detect the expression of heart fatty acid-binding protein (H-FABP) and adipocyte fatty acid-binding protein (A-FABP) gene mRNA in different tissues of Rugao and Luyuan chickens at 56 d and 120 d by real-time fluorescence quantitative reverse transcription polymerase-chain reaction (FQ-RT-PCR). The primers were designed according to the sequences of HFABP, A-FABP and GAPDH genes in Gallus gallus, which were used as target genes and internal reference gene, respectively. The levels of H-FABP and A-FABP gene expression were detected by SYBR Green I FQ-RT-PCR. The relative H-FABP and A-FABP gene mRNA expression level was calculated with 2-$^{{\Delta}Ct}$. Melting curve analysis showed a single peak of three genes. Intramuscular fat (IMF) content in breast muscle and leg muscle of the two chicken breeds at 120 d was higher than at 56 d. IMF content in breast muscle and leg muscle at 56 d and 120 d in Luyuan was significantly higher than in Rugao, however, abdominal fat of Luyuan was significantly lower than that of Rugao. The relative H-FABP gene mRNA expression level in cardiac muscle was the highest in both chicken breeds. The relative H-FABP and A-FABP gene expression of different tissues in Luyuan was higher than in Rugao. H-FABP gene mRNA expression had a negative effect on IMF of leg and breast muscles, and was significantly negatively correlated with IMF content. The relative A-FABP gene mRNA level in abdominal fat was higher than in liver. The A-FABP gene mRNA was not expressed in leg, breast and cardiac muscles. A-FABP gene mRNA expression level was significantly positively correlated with abdominal fat and had a significant effect on abdominal fat but not IMF content.

• Journal of Information Processing Systems
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• v.12 no.1
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• pp.1-34
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• 2016

Gene identification is at the center of genomic studies. Although the first phase of the Encyclopedia of DNA Elements (ENCODE) project has been claimed to be complete, the annotation of the functional elements is far from being so. Computational methods in gene identification continue to play important roles in this area and other relevant issues. So far, a lot of work has been performed on this area, and a plethora of computational methods and avenues have been developed. Many review papers have summarized these methods and other related work. However, most of them focus on the methodologies from a particular aspect or perspective. Different from these existing bodies of research, this paper aims to comprehensively summarize the mainstream computational methods in gene identification and tries to provide a short but concise technical reference for future studies. Moreover, this review sheds light on the emerging trends and cutting-edge techniques that are believed to be capable of leading the research on this field in the future.

• 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.

• Journal of Veterinary Clinics
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• v.23 no.4
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• pp.405-410
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• 2006

Using internal transcribed spacer 1 (ITS1) region ribosomal DNA sequences from 9 strains of Microsporum canis and 5 strains of Microsporum gypseum isolated from dogs and a cat with dermatophytosis, we demonstrated the mutual phylogenetic relationship of these strains. Nucleotide sequence analysis of the ITS 1 gene fragments from the 9 strains of M canis had the 100% nucleotide sequence similarities and the 5 strains of M gypseum also had the 100% nucleotide sequence similarities. The phylogenetic analysis of the nucleotide sequences of the 9 strains of M canis formed a nested cluster with the reference strains of M canis originating from USA, Australia, Japan, and Europe. M canis were genetically distinct from the other reference strains of Microsporum spp, but M distortum, M equinum, and M. ferrugineum were genetically very close to M canis. M gypseum from a cluster in the phylogenetic tree with M canis as an outgroup. The molecular analysis of ITS 1 genes provided the useful information for the identification of these microsporum species and the understanding of their relationship.

• Journal of Periodontal and Implant Science
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• v.39 no.sup2
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• pp.269-278
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• 2009

Purpose: The aim of this study was to investigate matrix metalloproteinase 1 (MMP-1) gene polymorphism (1G/2G at -1607 and A/G at -519) in Korean subject and to assess the association between polymorphism and periodontal status. Methods: Forty nine generalized aggressive periodontitis (GAP) patients and 57 periodontally healthy children were recruited and genomic DNA was extracted from buccal swab. The polymorphisms of MMP-1 promoter genes were determined by polymerase chain reaction and restriction fragment length product (PCR-RFLP) method. The distribution of genotype and allele frequency was compared between 2 groups by ${\chi}^2$ test. Results: There was a significant difference in the distribution of genotypes and frequency of alleles between the GAP and reference groups at the position - 519 of MMP-1 gene promoter (P<0.05). Allele G carrier rate was significantly lower in GAP group than that of the reference group (P< 0.001). At the position -1607 of MMP-1 gene promoter, genotype distribution and allele frequency showed no statistically significant difference between the groups. However, in the female group, a significant difference was observed between the groups for the genotype distribution, allele frequency and allele 1G carrier rate (P< 0.05). Conclusions: The DNA polymorphism at the MMP-1 gene promoter might be associated with GAP in Korean.

• Journal of Marine Bioscience and Biotechnology
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• v.1 no.3
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• pp.163-169
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• 2006

In the survey of the samples infected by iridovirus, we found the natural outbreak of iridovirus disease in the ornamental fish, pearl gourami (Trichogaster leeri) in Korea. It was characterized by the appearance of enlarged cells and necrosis in the observation of the imprinted spleen cells under iridovirus. To determine the infection of iridovirus more accurately, PCR using 2 different primer sets for MCP and ATPase gene used for the diagnosis of iridovirus infection was done and found the produced fragments matched with the size of expectation. Partially determined nucleotide sequences of the MCP gene of the iridovirus isolated in this study showed very high homology (99.6%) with that of ISKNV as a reference strain. In challenge experiment with the iridovirus isolated from the moribund of pearl gourami, the pathogenicity of the isolated iridovirus was confirmed and suggested the potential of the risk associated the transfer of iridovirus from the ornamental fishes to the marine culturing fishes.