• International Journal of Oral Biology
• /
• v.38 no.1
• /
• pp.21-27
• /
• 2013

Anginosus group streptococci (AGS) were classified based on the nucleotide sequences of the 16S rRNA gene (16S rDNA) and comprised Streptococcus anginosus, Streptococcus intermedius, and Streptococcus constellatus. It is known that AGS is a causative factor of oral and systematic diseases. The purpose of this study was to discriminate the 56 clinical strains of AGS isolated from Korean oral cavities using phylogenetic analysis of 16S rDNA and species-specific PCR at the species-level. The 16S rDNA of clinical strains of AGS was sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. PCR was performed to identify the clinical strains using species-specific primers described in previous studies and S. intermedius-specific PCR primers developed in our laboratory. The resulting phylogenetic data showed that the 16S rDNA sequences can delineate the S. anginosus, S. intermedius, and S. constellatus strains even though the 16S rDNA sequence similarity between S. intermedius and S. constellatus is above 98%. The PCR data showed that each species-specific PCR primer pair could discriminate between clinical strains at the species-level through phylogenetic analysis of 16S rDNA nucleotide sequences. These results suggest that phylogenetic analysis of 16S rDNA and PCR are useful tools for discriminating between AGS strains at the species-level.

• Korean Journal Plant Pathology
• /
• v.12 no.1
• /
• pp.11-20
• /
• 1996

한 쌍의 R16-1과 R23-2R primer를 이용한 PCR에 의해 증폭된 16S와 23S rDNA 사이의 rDNA spacer 부위의 다형성들이 Pseudomonas avenae, P. glumae, P. fuscovaginae, P. syringae pv. syrngae, Xanthomonas oryzae pv. oryzae, X. oryzae, Xanthomonas herbicola 등 벼 종자전염성 51개 균주의 구분을 위하여 적용되었다. 증폭산물은 820∼950bp의 크기였으며, 각각의 종에 특이적이었고 구분이 가능하였다. Pseudomonas species의 증폭산물은 P. avenae는 950bp, P. glumae는 850bp, P. fuscovaginae는 770pb 및 P. syringae pv. syringae는 1,240, 1,100 및 820bp로 특이적이었다. P. avenae와 P. glumae의 국내균주들은 다형성에 있어 종내 변이는 없었다. X. oryzae pv. oryzae의 860bp와 X. oryzae pv. oryzicola의 890, 440 및 370bp의 이차산물에서 Xanthomonas species의 종내에서 균주에 관련없이 단일화된 다형성을 보였다. CXO 211을 제외한 모든 국내 균주는 a형에 속한 반면 하나의 국내 균주를 포함하여 4개 균주는 b형이었다. E. herbicola의 spacer 부위 증폭은 여러 개의 band를 보였으며, 증폭상은 각각 동일하였고, strain간의 종내 변이는 없었다. 본 실험 결과에 의하여 16S와 23S rDNAdp R16-1과 R23-2R primer를 이용하여 PCR 증폭된 spacer 다형성의 구별은 종자전염성 세균의 신속한 구별에 이용될 수 있을것이다.

• Parasites, Hosts and Diseases
• /
• v.45 no.3
• /
• pp.181-190
• /
• 2007

The phylogenie relationships existing among 14 parasitic Platyhelminthes in the Republic of Korea were investigated via the use of the partial 28S ribosomal DNA (rDNA) D1 region and the partial mitochondrial cytochrome c oxidase subunit 1 (mCOI) DNA sequences. The nucleotide sequences were analyzed by length, G + C %, nucleotide differences and gaps in order to determine the analyzed phylogenie relationships. The phylogenie patterns of the 28S rDNA D1 and mCOI regions were closely related within the same class and order as analyzed by the PAUP 4.0 program, with the exception of a few species. These findings indicate that the 28S rDNA gene sequence is more highly conserved than are the mCOI gene sequences. The 28S rDNA gene may prove useful in studies of the systematics and population genetic structures of parasitic Platyhelminthes.

• ALGAE
• /
• v.19 no.2
• /
• pp.79-90
• /
• 2004

Nuclear DNA contents of spermatia from eight ceramiacean and four dasyacean algae (Ceramiales, Rhodophyta) and microspores from two land plants were estimated by fluorescence microscopic image processing and their nuclear SSU rDNA sequence data were analyzed. In frequency distribution patterns, the DAPI-stained nuclear volume (NV) of spermatia showed two peaks corresponding to 1C and 2C. Nuclear 2C DNA contents estimated from NV were 0.45-2.31 pg in ceramiacean and 0.40-0.57 pg in dasyacean algae and 8.42-9.51 pg in two land plants, Capsicum annuum and Nicotiana tabacum. By nuclear patterning of vegetative cells derived from an apical cell, 2C DNA contents of spermatia were 2.31 pg in an alga having uninucleate and non-polyploid nucleus (Aglaothamnion callophyllidicola), 0.45-1.94 pg in algae having uninucleate and polyploid nucleus (Antithamnion spp. and Pterothamnion yezoense), and 0.40-0.62 pg in algae having multinucleate and non-polyploid nuclei (Griffithsia japonica and dasyacean algae). Each mature spermatium and microspore (pollen grain) seemed to have a 2C nucleus, which may provide a genetic buffering system to protect the genetic content of a spermatium and microspore from potentially lethal mutations. Nuclear DNA content and SSU rDNA sequence of Antithamnion sparsum from Korea were reasonably different from those of Antithamnion densum from France. The data did not support the previous taxonomic studies that these two taxa could be conspecific.

• Mycobiology
• /
• v.31 no.1
• /
• pp.23-31
• /
• 2003

With universal primer ITS1-F, the specific DHJ2 primer was developed to detect the Ectomycorrhizal(ECM) root tips in soil and to identify the species of ECM fungi, as based on DNA sequences of rDNA stored in GeneBank of NCBI. This primer was designed with the common sites of rDNA of Amanita and Boletus, and was also designed with several DNA programs provided by NCBI. The DNA fragments synthesized by PCR were calculated to be 1,000 to 1,200 bps of DNA located to 18s to 28s rDNA to contain two variable sites of ITS, indicating much diversities for specific species or ecotypes of ECM fungi. The primer DHJ2 reacted with the genomic DNA's extracted from the tissues of basidiocarp at the rate of 73 of 80 fungi collected produced single bands with a 1,100 bps length. The DNA fragment synthesized with the genomic DNA that extracted from eight ECM tips of Pinus densiflora was confirmed and analysized to the rDNAs of ECM in full sequences, and informed to be a ECM fungal species in the forest.

• Korean Journal of Ecology and Environment
• /
• v.55 no.4
• /
• pp.352-359
• /
• 2022

Recently, with the development of genetic technology, interest in environmental DNA (eDNA) to study biodiversity according to molecular biological approaches is increasing. Environmental DNA has many advantages over traditional research methods for biological communities distributed in the environment but highly depends on the established base sequence database. This study conducted a comprehensive analysis of the habitat status and classification at the genus level, which is mainly used in eDNA (12S rRNA, 16S rRNA, 18S rRNA, COI, and CYTB), focusing on Korean registration taxon groups (phytoplankton, zooplankton, macroinvertebrates, and fish). As a result, phytoplankton and zooplankton showed the highest taxa proportion in 18S rRNA, and macroinvertebrates observed the highest ratio in the nucleotide sequence database in COI. In fish, all genes except 18S rRNA showed a high taxon ratio. Based on the Korean registration taxon group, the gene construction of the top 20 genera according to bio density observed that most of the phytoplankton were registered in 18S rRNA, and the most significant number of COI nucleotide sequences were established in macroinvertebrates. In addition, it was confirmed that there is a nucleotide sequence for the top 20 genera in 12S rRNA, 16S rRNA, and CYTB in fish. These results provided comprehensive information on the genes suitable for eDNA research for each taxon group.

• Fisheries and Aquatic Sciences
• /
• v.9 no.2
• /
• pp.70-74
• /
• 2006

DNA sequence-based typing is considered a robust tool for the discrimination of dinoflagellate species because of the availability of extensive rDNA sequences. Here, we present a rapid, cost-effective DNA-sequencing technique for various PCR products. This sequencing strategy relies on 'nested' or 'tailed' primer labeled with near-infrared dye, and uses a minimal volume of unpurified PCR product (ca. $5{\mu}L$) as the DNA template for sequencing reactions. Reliable and accurate base identification was obtained for several hundred PCR fragments of rRNA genes. This quick, inexpensive technique is widely applicable to sequence-based typing in clinical applications, as well as to large-scale DNA sequencing of the same genomic regions from related species for studies of molecular evolution.

• Korean journal of applied entomology
• /
• v.37 no.1
• /
• pp.23-30
• /
• 1998

Restriction fragment length polymorphism (RFLP) of a DNA has been a useful tool for analyzing genetic variation. This research was performed to establish an RFLP analytic method on the mitochondrial DNA (mtDNA) of the beet armyworm, Spodoptera exigua (Hiibner). To do this, total size of the mtDNA was measured and polymerase chain reaction (PCR) primers were selected. Its mitochondrial genome size was ca. 16kb. From a serial PCR test of 29 primers refered to the compilation of Simon et al. (1994), 22 primers were selected to amplify its mtDNA fragments. These primers resulted in short (300-700 bp) or long (1000-2000 bp) DNA products which represented a total or partial sequence of each of CO-I, CO-11, Cyt-B, ND-1, 12s rRNA, 16s rRNA, and some tRNAs. PCR-RFLP was performed in some variable mtDNA regions with 8 kinds of 4bp recognizing restriction enzymes. Different populations from Andong, Kyungsan, and Sunchun did not show any restriction site polymorphisms but had some length variation in certain regions of mtDNA.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.34 no.2
• /
• pp.137-144
• /
• 2001

Sequences of partial 18S rDNA have been analyzed to elucidate genetic diversity of scallops collected around Korean sea, The scallops used in genetic comparison are Argopecten irradians concentricus, Amusium japonicum japonicum, Chlamys farreri farreri, Chlamys (Swiftopecten) swifti and Patinopecten yessoensis. The 18S rDNA sequences were aligned by Clustalx program. Phylogenetic tree was drawn by Treecon program, The scallops were divided into two groups-the Family Pectinidae containing A. japonicum japonicum and the Family Propeamussiidae containing Argopecten, Chlamys and Patinopecten genera. The Family Propeamussiidae was also divided into the Supergenera Aequipecten containing A. irradians concentricus and Supergenera Chlamys containing C. farreri farreri, C. swifti and P. yessoensis. The species of C. swifti was closer to the P. yessoensis rather than C. farreri farreri in respect to nuclear 18S rDNA sequence.

• The Korean Journal of Zoology
• /
• v.15 no.1
• /
• pp.1-14
• /
• 1972

The effect of 400 R of whole-body X-irradiation on DNA synthesis, DNA degradation, CdR-aminohydrolase activity and oxygen uptake in the liver, spleen and thymus of the rat has been studied in connection with the radiosensitivity of these tissues. The rate of CdR-2-$^14 C$ incorporation has been followed during the postirradiation period and has been correlated with the increased levels of CdR-aminohydrolase activity druing this period. The postirradiation period comprises radiation reaction and tissue regeneration periods. During the period of radiation reaction, markedly decreased precursor incorporation, decreased tissue levels of DNA and decreased uptake of oxygen are noted as well as an increase in the CdR-aminohydrolase activity. The period of regeneration appears to consist in two discrete phases. The first phase reveals a return of CdR-aminohydrolase activity and the second phase is highlighted by a markedly increased rate of labeled CdR incorporation. Various events occurring during the radiation reaction period and the regeneration period in the three tissues studied can be considered qualitatively the same, differing only in the degree of acute cell death, in the duration of the delay of DNA synthesis in the sruviving cells, and in the rate of recovery resulting from accelerated cell replication during the period of regeneration. A possible biochemical mechanism involved in the DNA synthesis and degradation, in connection with the inreased levels of CdR-aminohydrolase after irradiation, has been briefly discussed.