• Journal of Veterinary Clinics
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• v.31 no.1
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• pp.36-39
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• 2014

Many bacteria colonized in the horse semen affect quality of the sperm and some may cause infection in the mare reproductive tract and infertility of susceptible mare. This study was initiated to determine the prevalence of bacteria in testes of Jeju horses by determining rRNA sequence. The samples were swabed from the testes of nine Jeju horses (aged from 8 to 12 months after birth). Bacteria isolated from testes were identified by 16S rDNA sequencing. 1.6-kbp PCR products for 16S rRNA coding region were obtained using the universal primers. The PCR products were further purified and sequenced. Maximum similar species were found by BLAST search in the GenBank DNA database. BLAST results showed that the sequences were similar to those of Acinetobacter sp (A. schindleri, A. ursingii)., Bacillus cereus, Corynebacterium glutamicum, Escherichia coli, Gamma proteobacterium, Micrococcus luteus, Pseudomonas mendocina, Shigella sonnei, Sphingomonas sp., Staphylococcus sp (S. cohnii, S. saprophyticus, S. xylosus)., and Stenotrophomonas maltophilia. DNA sequences for 16S rRNA is provided useful informations for species identification of pathogenic microorganisms for the reproductive organs in horses.

• Journal of Korean Society of Environmental Engineers
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• v.22 no.5
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• pp.939-947
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• 2000

Enhanced biological phosphorus removal (EBPR) was performed in an anaerobic/aerobic sequencing batch reactor (SBR). Influent was a synthetic wastewater based on acetate as a carbon source. The sludge age and hydraulic retention time were kept at 10 days and 16 hrs, respectively, Phosphate release during the anaerobic period and phosphate uptake in aerobic period were increased gradually with time. and after about 200 days, steady-state operation could be achieved with complete removal of influent phosphate. Number distribution of microbial community in the sludge performing EBPR was investigated during the steady state operation. 17 rRNA targeted oligonucleotide probes were designed and slot hybridization technique was used to determine the number distribution of each microorganism. In the acetate fed SBR, rRNA belonging to the beta subclass of proteobacteria was the most dominant in total rRNA and rRNA matching to CTE probe was the second, rRNAs of Acinetobacter, Aeromonas and Pseudomonas, which are usually thought as phosphorus accumulating organisms in EBPR processes, constituted less than 10% of total rRNA. From this community analysis, it was inferred that microorganisms belong to the beta subclass of proteobacteia (BET) and CTE such as Rhodocyclus group were important in biological phosphorus removal. Therefore, the role of Acinetobacter, Aeromonas and Pseudomonas in the EBPR might have been overestimated.

• Journal of Korean Society on Water Environment
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• v.20 no.5
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• pp.506-511
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• 2004

Maintaining dissolved oxygen (DO) at sufficiently low concentration in the aeration tank at a wastewater treatment plant (WWTP) is essential for reduction of the costs of operation and maintenance. On the other hand, the low DO level may result in adverse effect on the integrity of the activated sludge, A typical and disastrous outcome frequently experienced is the outgrowth of filamentous microorganisms, which is called as filamentous bulking, In addition to the traditional methods such as sludge settleability and microscopic observation of the culture, molecular techniques including polymerase chain reaction (PCR) amplification followed by 16S rRNA sequencing were applied to identify filamentous bacteria present in bulking sludge under a condition of low DO concentration, Two morphologically distinct groups, presumably consisting of Sphaerofilus nafans, and Eikelboom Type 1701 or Type 1851, were identified through microscopic observation. They were further confirmed by subsequent 16S rRNA sequencing. Dominant filamentous bacteria identified by the molecular techniques were consisted of three major groups. Sequences of partial 16S rRNA cloned showed that the filamentous bulking organisms were closely related to Eikelboom Type 021N and Eikelboom Type 1701, and Sphaerotilus natans, respectively. Molecular methods were found to possess a strong potential of direct examination of the microbial community of an activated sludge system.

• Korean Journal of Medicinal Crop Science
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• v.17 no.1
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• pp.26-32
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• 2009

The region containing 18S rRNA gene, ITS 1 and part of the 5.8S rRNA gene of the Atractylodes japonica Koidz was amplified by PCR and the product cloned in a pBluescript SK II plasmid. DNA sequence of the cloned DNA was determined and submitted to the GenBank (accession number EU678363). Phylogenetic analysis of the ITS 1 DNA showed close similarity with the other plant species of the family Compositae. The extract of the plant materials of five different members of the family Compositae was analyzed by HPLC to detect atractylon. Extract of the A. japonica Koidz showed presence of significant amount of atractylon. However, noticeable amount of atractylon was not detected by the same analyses from the extracts of the other plants belonging to the family Compositae including Artemisia capillaris, Chrysantemum zawadskii, Eclipta prostrata or Taraxacum platycarpum.

• Proceedings of the Zoological Society Korea Conference
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• 1995.10b
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• pp.312.1-312
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• 1995

• 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.

• Korean Journal of Microbiology
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• v.30 no.6
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• pp.479-482
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• 1992

The sequence of the cytoplasmic 5S-rRNA from Trimorphomyces papilionaceus, a basidiomycetous yeast, was determined by the direct chemical method for sequencing RNA and compared to known 5S rRNA sequences of 19 basidiomycetous fuungi. There were 26 nucleotide differences between T. papilionaceus and Tremella mesenterica both of which belong to the Tremellaceae of the Tremellales. Based on Knuc values, the closest fungus was Tilletiaria anomala, another basidiomycetous yeast which belong to the Sporbolomycetaceae of the Sporobolomycetales. T. papilionaceus did not show any significant phylogenetic relationship with other fungi.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.812-822
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• 2014

Metagenomic analysis of the human intestinal microbiota has extended our understanding of the role of these bacteria in improving human intestinal health; however, a number of reports have shown that current total fecal DNA extraction methods and 16S rRNA universal primer sets could affect the species coverage and resolution of these analyses. Here, we improved the extraction method for total DNA from human fecal samples by optimization of the lysis buffer, boiling time (10 min), and bead-beating time (0 min). In addition, we developed a new long-range 16S rRNA universal PCR primer set targeting the V6 to V9 regions with a 580 bp DNA product length. This new 16S rRNA primer set was evaluated by comparison with two previously developed 16S rRNA universal primer sets and showed high species coverage and resolution. The optimized total fecal DNA extraction method and newly designed long-range 16S rRNA universal primer set will be useful for the highly accurate metagenomic analysis of adult and infant intestinal microbiota with minimization of any bias.

• Mycobiology
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• v.33 no.2
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• pp.109-112
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• 2005

The internal transcribed spacer (ITS) regions including the 3'-end of 18S rRNA gene, 5.8S rRNA gene and the 5'-end of the 28S rRNA gene of Rhizopus spp. were amplified by PCR and analyzed by DNASIS program. Length polymorphism of these region ranged from 564 bp in R. oryzae to 789bp in R. stolonifer. The length and sequence of 5.8S was very conserved with $154{\sim}155\;bp$. The sequence of ITS2 was more variable than that of ITS1. The base substitution rates were ranged from 0 to 0.6069 per site, and higher rate was found in R. stolonifer. In general, transition was usually more frequent than transversion. On the basis of sequencing results, four groups were clustered with value of 61.9% similarity; R. oryzae, R. micros pores, R. homothallicus, and R. stolonifer groups.

• Journal of Species Research
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• v.13 no.2
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• pp.127-130
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• 2024

The first complete mitogenome sequence of the Red-tongue Pit Viper (Gloydius ussuriensis) from Korea was characterized using next-generation sequencing. The mitogenome is a circular molecule (17,209 bp) with a typical vertebrate mitogenome arrangement, which consists of 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), two non-coding regions (D-loop), and 13 protein-coding genes (PCGs). The base composition of the mitogenome is 32.7% of A, 27.5% of C, 13.9% of G, and 25.9% of T, with a slight AT bias(58.6%). This phylogenetic analysis infers that G. ussuriensis is in the same group as the Chinese G. ussuriensis (Accession No. KP262412) and is closely related to G. blomhoffi and other species of the genus Gloydius. In our study, the complete mitogenome sequence of Korean G. ussuriensis was characterized and we provided basic genetic information on this species.