• Biomolecules & Therapeutics
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• v.27 no.2
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• pp.127-133
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• 2019

The study of the genus Streptomyces is of particular interest because it produces a wide array of clinically important bioactive molecules. The genomic sequencing of many Streptomyces species has revealed unusually large numbers of cytochrome P450 genes, which are involved in the biosynthesis of secondary metabolites. Many macrolide biosynthetic pathways are catalyzed by a series of enzymes in gene clusters including polyketide and non-ribosomal peptide synthesis. In general, Streptomyces P450 enzymes accelerate the final, post-polyketide synthesis steps to enhance the structural architecture of macrolide chemistry. In this review, we discuss the major Streptomyces P450 enzymes research focused on the biosynthetic processing of macrolide therapeutic agents, with an emphasis on their biochemical mechanisms and structural insights.

• BMB Reports
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• v.55 no.7
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• pp.305-315
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• 2022

Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of 'Dissociation (Dc) locus' by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.149.1-149
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• 2003

A lily strain of Cucumber mosaic virus (LK-CMV) was not able to systemically infect zucchini squash (Cucurbita pepo), while Fny strain of CMV (Fny-CMV) caused systemic mosaic and stunting symptom at 4 days post-inoculation on the same host species. The pathogenicity of LK-CMV in zucchini squash was investigated by reassortments of genomic RNAs of LK-CMV and Fny-CMV for infection, as well as by pseudorecombinants generated from biologically active transcripts of CDNA clones of LK-CMV and Fny-CMV, respectively. The assessments of pathogenicity for LK-CMV indicated that RNA2 of LK-CMV was responsible for systemic infection in zucchini squash. In the protoplast of zucchini squash, the RNA accumulations of all constructed pseudorecombinants were indistinguishable and LK-CMV replication was slightly lower than that of Fny-CMV, suggesting that the inability of LK-CMV to infect squash plants was responsible for the poor efficiency of virus movement, rather than the reduction of replication function.

• Journal of Internet Computing and Services
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• v.5 no.5
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• pp.1-15
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• 2004

In this paper, we explain the design and implementation of GWB(Gene WorkBench), which is a web-based, integrated system for efficiently managing and analyzing genomic sequences, Most existing software systems handling genomic sequences rarely provide both managing facilities and analyzing facilities. The analysis programs also tend to be unit programs that include just single or some part of the required functions. Moreover, these programs are widely distributed over Internet and require different execution environments. As lots of manual and conversion works are required for using these programs together, many life science researchers suffer great inconveniences. in order to overcome the problems of existing systems and provide a more convenient one for helping genomic researches in effective ways, this paper integrates both managing facilities and analyzing facilities into a single system called GWB. Most important issues regarding the design of GWB are how to integrate many different analysis programs into a single software system, and how to provide data or databases of different formats required to run these programs. In order to address these issues, GWB integrates different analysis programs byusing common input/output interfaces called wrappers, suggests a common format of genomic sequence data, organizes local databases consisting of a relational database and an indexed sequential file, and provides facilities for converting data among several well-known different formats and exporting local databases into XML files.

• The Korea Journal of Herbology
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• v.29 no.6
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• pp.45-53
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• 2014

Objectives : Due to the morphological similarity of in the roots of herbal medicine, the official herbal medicine is very difficult to authenticate between the original plants of Patriniae Radix and two adulterant Patrinia species. Therefore, we introduced DNA barcode analysis to establish a powerful tool for the authentication of Patriniae Radix from its adulterants. Methods : To analyze DNA barcode regions, genomic DNA was extracted from twenty-nine specimens of Patrinia scabiosaefolia, Patrinia villosa, Patrinia saniculifolia, and Patrinia rupestris, and internal transcribed spacer 2(ITS2), matK and rbcL genes were amplified. For identification of species specific sequences, a comparative analysis was performed by the ClastalW based on entire sequences of ITS2, matK and rbcL genes, respectively. Results : In comparison of three DNA barcode sequences, we identified 22, 22, and 12 species-specific nucleotides enough to distinguish each four species from ITS2, matK and rbcL gene, respectively. The sequence differences at the corresponding positions were available genetic marker nucleotides to discriminate the correct species among analyzed four species. These results indicated that comparative analysis of ITS2, matK and rbcL genes were useful genetic markers to authenticate Patriniae Radix. Conclusions : The marker nucleotides enough to distinguish P. scabiosaefolia, P. villosa, P. saniculifolia, and P. rupestris, were obtained at 22 SNP marker nucleotides from ITS2 and matK DNA barcode sequences, but they were confirmed at 12 SNP marker nucleotides from rbcL. These differences could be used to authenticate Patriniae Radix from its adulterants as well as discriminating each four species.

• The Korea Journal of Herbology
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• v.33 no.3
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• pp.25-35
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• 2018

Objectives : Lepidii seu Descurainiae Semen has been frequently adulterated with the seeds of several inauthentic plant species. However, the accurate identification of these plant seeds is very difficult. To develop a reliable genetic authentication tool for Lepidii seu Descurainiae Semen, we analyzed matK sequence. Methods : To obtain the matK sequences of plant materials, genomic DNA was extracted from 24 samples and PCR amplification was carried out using matK-AF/matK-8R universal primer set and matK-LDSF/matK-LDSR primer set. For identifying species-specific nucleotides and phylogenetic analysis, matK regions were sequenced and comparatively analyzed by the ClustalW and Maximum Likelihood method. Results : We developed a new primer set to amplify matK region in Lepidii seu Descurainiae Semen and closely related plant samples. From the comparative analysis of matK sequences, we identified species-specific marker nucleotides for D. sophia, L. apetalum, L. latifolium, E. cheiranthoides, E. macilentum, and D. nemorosa, respectively. Furthermore, phylogenetic analysis revealed clear classification depending on the species. These results indicated that the matK sequence obtained a new primer set in this study was useful to identify Lepidii seu Descurainiae Semen in species level. Conclusions : We developed a primer set and identified species-specific marker nucleotides enough to distinguish authentic Lepidii seu Descurainiae Semen and adulterants at the species level based on the matK sequences. These genetic tool will be useful to prevent adulteration and to standardize the quality of Lepidii seu Descurainiae Semen.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.5
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• pp.743-748
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• 2014

The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene ($VEGF{\alpha}$) by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog), we constructed a phylogenetic tree which showed that equine $VEGF{\alpha}$ belonged to the same clade of the pig $VEGF{\alpha}$. Analysis for synonymous (Ks) and non-synonymous substitution ratios (Ka) revealed that the horse $VEGF{\alpha}$ underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR) and quantitative-polymerase chain reaction (qPCR) showed ubiquitous expression of $VEGF{\alpha}$ mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of $VEGF{\alpha}$ gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

• Journal of Periodontal and Implant Science
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• v.25 no.1
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• pp.89-98
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• 1995

P. intermedia are considered an important pathogen in adult periodontitis, rapidly progressing periodontitis, refractory periodontitis, pregnancy gingivitis, acute necrotizing ulcerative gingivitis, pubertal gingivitis. So far 2 DNA homology groups and 3 serotypes of P. intermedia have been reported but there is no data available as yet regarding genetic diversity for the species P. intermedia. The purpose of this study is to investigate, using bacterial DNA restriction endonuclease analysis, genetic diversity between individual strains of P. intermedia which are indistinguishable by serotyping and biotyping, occurrence of an intrafamilial transmission and genetic heterogeneity between P. intermedia strains isolated within a patient and within the same serotypes. The families who have had no systemic disease, no experience of periodontal treatment for the previous 1 year and no experience of antibiotics for the previous 6 months were selected and subgingival plaque was collected at 4 sites in each person and incubated in the anaerobic chamber. P. intermedia were identified by colony shape, gram stain, biochemical test, SK-I03(Sunstar Inc.) test and IIF using monoclonal antibody was perfomed for the determination of serotypes. P. intermedia strains were grown in BHI broth and whole genomic DNA was extracted and digested by restriction endonuclease. The resulting DNA fragments were separated by agarose gel electrophoresis, stained and photographed under UV. As the results of this study, intrafamilial vertial transmissions could be assessed in 2 families and horizintal transmissions in another 2 families. There were different DNA digest patterns within a patient, so P. intermedia showed that individuals could be colonized by multiple clonal types at anyone time. And different serotypes could be found within a patient and in the same serotype within a patient, obvius genetic heterogeneity could not be assessed. But in the same serotype in different famies, there were differences in the DNA digest patterns.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.7-8
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• 2003

Since it was first reported in 1997, somatic cell cloning has been demonstrated in several other mammalian species. On the mouse, it can be cloned from embryonic stem (ES) cells, fetus-derived cells, and adult-derived cells, both male and female. While cloning efficiencies range from 0 to 20%, rates of just 1-2% are typical (i.e. one or two live offspring per one hundred initial embryos). Recently, abnormalities in mice cloned from somatic cells have been reported, such as abnormal gene expression in embryo (Boiani et al., 2001, Bortvin et al., 2003), abnormal placenta (Wakayama and Yanagimachi 1999), obesity (Tamashiro et ai, 2000, 2002) or early death (Ogonuki et al., 2002). Such abnormalities notwithstanding, success in generating cloned offspring has opened new avenues of investigation and provides a valuable tool that basic research scientists have employed to study complex processes such as genomic reprogramming, imprinting and embryonic development. On the other hand, mouse ES cell lines can also be generated from adult somatic cells via nuclear transfer. These 'ntES cells' are capable of differentiation into an extensive variety of cell types in vitro, as well assperm and oocytes in vivo. Interestingly, the establish rate of ntES cell line from cloned blastocyst is much higher than the success rate of cloned mouse. It is also possible to make cloned mice from ntES cell nuclei as donor, but this serial nuclear transfer method could not improved the cloning efficiency. Might be ntES cell has both character between ES cell and somatic cell. A number of potential agricultural and clinical applications are also are being explored, including the reproductive cloning of farm animals and therapeutic cloning for human cell, tissue, and organ replacement. This talk seeks to describe both the relationship between nucleus donor cell type and cloning success rate, and methods for establishing ntES cell lines. (중략)

• Journal of Periodontal and Implant Science
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• v.32 no.2
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• pp.281-290
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• 2002

The purpose of this study is to develop species-specific DNA probe for detection and identification of Prevotella intermedia (P. intermedia) G8-9K-3. This study procedure includes (1) whole-genomic DNA extraction of P. intermedia G8-9K-3 (2) construction of the genomic DNA library, (3) screening of strain-specific DNA probe by reverse dot hybridization, (4) confirmation of strain-specific DNA probe by Southern blot hybridization, (5) determination of nucleotide sequences of strain-specific DNA probe. Twenty-eight recombinant plasmids containing Hind III-digested DNA fragments of P. intermedia G8-9K-3 were obtained. Reverse Dot Hybridization and Southern blot analysis data showed that one of them, Pig3, could be P. intermedia G8-9K-3-specific DNA probe. This datum indicates that this Pig3 DNA probe could be useful in detection and identification of the P. intermedia G8-9K-3 strain.