• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3425-3428
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• 2013

Approximately, 15-20% of all cancers worldwide are caused by infectious agents. Understanding the role of infectious agents on cancer development might be useful for developing new approaches to its prevention. Mycoplasma genitalium is a clinically important sexually transmitted pathogen that has been associated with several human diseases. There have been a few studies suggestive of probable roles of Mycoplasma genitalium in cancer development, including prostate and ovarian cancers and lymphomas, but the role of this microorganism like other Mycoplasma species in neoplasia is still conjectural. Considering the prevalence of Mycoplasma genitalium infections and also the emergence of resistant strains, Mycoplasma genitalium needs more attention in the infectious agent cancer-causing research area.

• Journal of Life Science
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• v.28 no.3
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• pp.369-375
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• 2018

Mycoplasma genitalium has 367 conserved genes and the smallest genome among mono-culturable prokaryotes. Conservative metabolic pathways were examined among M. genitalium and 14 prokaryotes, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans and 13 intracellular eubacteria of plants or insects, with fewer conserved genes than M. genitalium. They have 11 to 71 metabolic pathways, however complete metabolic pathways ranged from 1 to 24. Totally, metabolic pathway hole is very high due to the lack of 45.8% of the enzymes required for the whole metabolic pathways and it could be suggested that the shared metabolic pathway with the host's enzyme would work or the essential substances are host dependent. The number of genes necessary for mass transfer through the cell membrane is also very low, and it may be considered that the simple diffusion or the protein of the host will function in the cell membrane of these prokaryotes. Although the tRNA charging pathway was distributed in all 15 prokaryotes, each has 5-20 tRNA charging genes. This study would give clues to the understanding of the metabolic pathways of intracellular parasitic bacteria of plant and endosymbiotic bacteria of insects, and could provide basic data for prevention of crop damage, development of insect pests and human medicines.

• Journal of Life Science
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• v.27 no.6
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• pp.694-701
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• 2017

Mycoplasma genitalium represents the smallest genome among mono-cultivable prokaryotes. To discover and compare the orthologs (conservative genes) among M. genitalium and 14 prokaryotes that are uncultivable and have less orthologs than M. genitalium, COG (clusters of orthologous groups of protein) analyses were applied. The analyzed prokaryotes were M. genitalium, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans, four intracellular plant pathogenic eubacteria of Candidatus Phytoplasma genus, and nine endosymbiotic eubacteria of phloem- and xylem-feeding insects. Among 367 orthologs of M. genitalium, 284 orthologs were conservative between M. genitalium and at least one other prokaryote. All 15 prokaryotes commonly have 29 orthologs, representing the significance of proteins in life. They belong to 25 translation-related, including 22 ribosomal proteins, 3 subunits of RNA polymerase, and 1 protein-folding-related. Among the 15 prokaryotes, 40 orthologs were only found in all four Candidatus Phytoplasma. The other nine Candidatus, all endosymbionts with insects, showed only a single common COG0539 (ribosomal protein S1), representing the diversity of orthologs among them. These results might provide clues to understand conservative genes in uncultivable prokaryotes, and may be helpful in industrial areas, such as handling prokaryotes producing amino acids and antibiotics, and as precursors of organic synthesis.

• 한국생물공학회:학술대회논문집
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• 2003.04a
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• pp.686-689
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• 2003

A Gene content phylogenetic tree and a 16S rRNA based phylogenetic tree were compared for 9 Archaea and 15 Proteobacteria, whole-genome sequenced, by neighbor joining and bootstrap methods (n=1000). Ratio of conserved COG (clusters of orthologous groups of proteins) to ortholog revealed that they were within the range of 4.60% (Mezorhizobium loti) or 56.57% (Mycoplasma genitalium), The diversity of ratio meant the Possibility of searching for useful genes, as they possess peculiar genes. The gene content tree and the 16S rDNA tree showed coincidence and discordance in Archaea and Proteobacteria.

• Clinical and Experimental Reproductive Medicine
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• v.44 no.4
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• pp.207-213
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• 2017

Objective: This study investigated the prevalence of infections with human papillomavirus, Chlamydia trachomatis, Ureaplasma urealyticum, Mycoplasma hominis, and Mycoplasma genitalium in the semen of Korean infertile couples and their associations with sperm quality. Methods: Semen specimens were collected from 400 men who underwent a fertility evaluation. Infection with above five pathogens was assessed in each specimen. Sperm quality was compared in the pathogen-infected group and the non-infected group. Results: The infection rates of human papillomavirus, C. trachomatis, U. urealyticum, M. hominis, and M. genitalium in the study subjects were 1.57%, 0.79%, 16.80%, 4.46%, and 1.31%, respectively. The rate of morphological normality in the U. urealyticum-infected group was significantly lower than in those not infected with U. urealyticum. In a subgroup analysis of normozoospermic samples, the semen volume and the total sperm count in the pathogen-infected group were significantly lower than in the non-infected group. Conclusion: Our results suggest that infection with U. urealyticum alone and any of the five sexually transmitted infections are likely to affect sperm morphology and semen volume, respectively.

• Journal of Microbiology
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• v.44 no.1
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• pp.42-49
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• 2006

In this study, we describe our newly-developed sensitive two-stage PCR procedure for the detection of 13 common mycoplasmal contaminants (M. arthritidis, M. bovis, M. fermentans, M. genitalium, M. hominis, M. hyorhinis, M. neurolyticum, M. orale, M. pirum, M. pneumoniae, M. pulmonis, M. salivarium, U. urealyticum). For primary amplification, the DNA regions encompassing the 16S and 23S rRNA genes of 13 species were targeted using general mycoplasma primers. The primary PCR products were then subjected to secondary nested PCR, using two different primer pair sets, designed via the multiple alignment of nucleotide sequences obtained from the 13 mycoplasmal species. The nested PCR, which generated DNA fragments of 165-353 bp, was found to be able to detect 1-2 copies of the target DNA, and evidenced no cross-reactivity with the generated DNA of related microorganisms or of human cell lines, thereby confirming the sensitivity and specificity of the primers used. The identification of contaminated species was' achieved via the performance of restriction fragment length polymorphism (RFLP) coupled with Sau3AI digestion. The results obtained in this study furnish evidence suggesting that the employed assay system constitutes an effective tool for the disagnosis of mycoplasmal contamination in cell culture systems.

• KSBB Journal
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• v.18 no.1
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• pp.39-44
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• 2003

A Gene content phylogenetic tree and a 16s rRNA based phylogenetic tree were compared for 33 whole-genome sequenced procaryotes, neighbor joining and bootstrap methods (n=1,000). Ratio of conserved COG (clusters of orthologous groups of proteins) to orthologs revealed that they were within the range of 4.60% (Mezorhizobium loti) or 56.57% (Mycopiasma genitalium). This meant that the ratio was diverse among analyzed procaryotes and indicated the possibility of searching for useful genes. Over 20% of orthologs were independent among the same species. The gene content tree and the 16s rDNA tree showed coincidence and discordance in Archaeabacteria, Proteobacteria and Firmicutes. This might have resulted from non-conservative genes in the gene content phylogenetic tree and horizontal gene transfer. The COG based gene content tree could be regarded as a midway phylogeny based on biochemical tests and nucleotide sequences.

• Journal of Microbiology and Biotechnology
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• v.23 no.10
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• pp.1484-1490
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• 2013

A lack of investigation in specific regions has impeded the understanding of epidemiological trends in the prevalence of sexually transmitted infections (STIs) in South Korea. To help fill this research gap, this study used multiplex polymerase chain reaction (mPCR) to determine the prevalence of STIs detected in clinical specimens collected from women in Cheonan, South Korea between August 2006 and November 2012, and analyzed the prevalence of STIs according to age, bacterial pathogen, and time period. Of the 1,618 specimens collected from 1,523 patients, 536 (35.2%) tested positive for at least 1 pathogen, with 407 (25.2%) testing positive for 1 pathogen, 103 (6.4%) for 2 pathogens, 20 (1.2%) for 3 pathogens, and 6 (0.4%) for 4 pathogens (n = 697 pathogens total). The median ages of all patients and of STI-positive patients were 37.8 and 33.3 years, respectively, and both decreased annually over the study period. Mycoplasma hominis (MH) was detected in 62.1% of the positive specimens, Ureaplasma urealyticum (UU) in 28.4%, Chlamydia trachomatis (CT) in 23.1%, Trichomonas vaginalis (TV) in 7.8%, Mycoplasma genitalium (MG) in 6.5%, and Neisseria gonorrhoeae (NG) in 2.1%. Whereas the prevalence of MH, MG, and TV infection did not vary greatly over the study period, that of UU decreased by one-fifth and that of both CT and NG increased 4-fold. The results indicate great variability in the rates of infection with each pathogen and a decreasing trend in overall STI prevalence, age of patients seeking STI testing, and age of STI-positive patients.

• Journal of Microbiology
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• v.45 no.5
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• pp.453-459
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• 2007

We developed a multiplex PCR (mPCR) assay to simultaneously detect Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Ureaplasma urealyticum, Corynebacterium spp. and seudomona aeruginosa. This method employs a single tube and multiple specific primers which yield 200, 281, 346, 423, 542, and 1,427 bp PCR products, respectively. All the PCR products were easily detected by agarose gel electrophoresis and were sequenced to confirm the specificity of the reactions. To test this method, DNA extracted from urine samples was collected from 96 sexually transmitted disease or prostatitis patients at a local hospital clinical center, and were subjected to the mPCR assay. The resulting amplicons were cloned and sequenced to exactly match the sequences of known pathogenic isolates. N. gonorrhoeae and Corynebacterium spp. were the most frequently observed pathogens found in the STDs and prostatitis patients, respectively. Unexpectedly, P. aeruginosa was also detected in some of the STD and prostatitis samples. More than one pathogen species was found in 10% and 80.7% of STD and prostatitis samples, respectively, indicating that STD and prostatitis patients may have other undiagnosed and associates. The sensitivity of the assay was determined by sing purified DNA from six pathogenic laboratory strains and revealed that this technique could detect pathogenic DNA at concentrations ranging from 0.018 to $1.899\;pg/{\mu}l$. Moreover, the specificities of this assay were found to be highly efficient. Thus, this mPCR assay may be useful for the rapid diagnosis of causative infectious STDs and prostatitis. useful for the infectious STDs and prostatitis.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.65-65
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• 2003

After many genome projects, algorithms and software to process explosively growing biological information have been developed. To process huge amount of biological information, high performance computing equipments are essential. If we use the remote resources such as computing power, storages etc., through a Grid to share the resources in the Internet environment, we will be able to obtain great efficiency to process data at a low cost. Here we present the performance improvement of the protein secondary structure prediction (PSIPred) by using the Grid platform, distributing protein sequence data on the Grid where each computer node analyzes its own part of protein sequence data to speed up the structure prediction. On the Grid, genome scale secondary structure prediction for Mycoplasma genitalium, Escherichia coli, Helicobacter pylori, Saccharomyces cerevisiae and Caenorhabditis slogans were performed and analyzed by a statistical way to show the protein structural deviation and comparison between the genomes. Experimental results show that the Grid is a viable platform to speed up the protein structure prediction and from the predicted structures.