• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.347-353
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• 2020

Although sea slaters Ligia have a significant role in rocky shore habitats, their taxonomic entities have not been clearly understood. In this study, we investigated whether genetic variation inferred from a nuclear genetic marker, namely amplified fragment length polymorphism (AFLP), would conform to that of a mitochondrial DNA marker. Using both the mitochondrial DNA marker and the AFLP marker amplified by the six selective primer sets, we analyzed 95 Ligia individuals from eight locations from East Asia. The direct sequencing of mitochondrial 16S rRNA gene revealed three distinct genetic lineages, with 9.8-11.7 Kimura 2-parameter genetic distance. However, the results of AFLP genotyping analysis with 691 loci did not support those of mitochondrial DNA, and revealed an unexpectedly high proportion of shared polymorphisms among lineages. The inconsistency between the two different genetic markers may be explained by difference in DNA evolutionary history, for example inheritance patterns, effective population size, and mutation rate. The other factor is a possible genomic island of speciation, in that most of the genomic parts are shared among lineages, and only a few genomic regions have diverged.

• Journal of Marine Life Science
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• v.7 no.1
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• pp.52-54
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• 2022

Mitochondrial genomes of three specimens of Gadus chalcogrammus Pallas 1,814 from Korea and Japan were completely analyzed by the primer walking method. They were 16,570~16,571 bp in length, each comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Their gene orders were identical to those of conspecific specimens, but exhibited unique haplotypes. In the phylogenetic tree, the juvenile Korean and adult Japanese specimens were separated from the dominant clade composed of specimens from Japan, Korea, the Bering Sea, and the Arctic, including the adult Korean specimen.

• The Plant Pathology Journal
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• v.39 no.1
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• pp.149-157
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• 2023

Phytoplasmas were discovered in diseased Elaeocarpus sylvestris trees growing on Jeju Island that showed symptoms of yellowing and darkening in the leaves. Leaf samples from 14 symptomatic plants in Jeju-si and Seogwipo-si were collected and phytoplasma 16S rRNA was successfully amplified by nested polymerase chain reaction using universal primers. The sequence analysis detected two phytoplasmas, which showed 99.5% identity to 'Candidatus Phytoplasma asteris' and 'Ca. P. malaysianum' affiliated to 16SrI and 16SrXXXII groups, respectively. Through polymerase chain reaction-restriction fragment length polymorphism (RFLP) analyses using the AfaI (RsaI) restriction enzyme, the presence of two phytoplasmas strains as well as cases of mixed infection of these strains was detected. In a virtual RFLP analysis with 17 restriction enzymes, the 16S rRNA sequence of the 'Ca. P. asteris' strain was found to match the pattern of the 16SrI-B subgroup. In addition, the phytoplasmas in the mixed-infection cases could be distinguished using specific primer sets. In conclusion, this study confirmed mixed infection of two phytoplasmas in one E. sylvestris plant, and also the presence of two phytoplasmas (of the 16SrI and 16SrXXXII groups) in Jeju Island (Republic of Korea).

• Korean Journal of Veterinary Research
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• v.35 no.3
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• pp.515-530
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• 1995

Coronaviridae에 속하는 transmissible gastroenteritis virus(TGEV)와 porcine epidemic diarrhea virus(PEDV)를 specific하게 detection할 수 있는 방법을 개발하고자 본 연구를 수행하였다. 두 바이러스 모두 RNA 바이러스이기 때문에 reverse transcription-polymerase chain reaction(RT-PCR)으로 nucleocapsid(N) protein gene의 cDNA를 증폭시켰다. SmaI으로 처리한 pTZ19R에 ligation시킨 후 염기서열을 밝히고자 sequencing하였다. 각각의 prototype virus와 비교하여 상동성을 밝혔다. 두 바이러스에 대한 cDNA probe를 제작하여 Southern blot hybridization을 실시하였다. TGEV의 경우 백신주인 P45와 병독주인 Miller strain을 사용하였다. cDNA를 증폭시키기 위해 N1/N1R과 N2/N2R 두 가지 primer를 이용한 결과, N1/N1R primer의 경우 586bp 크기의 PCR product를 얻을 수 있었고, N2/N2R primers로 582bp의 cDNA를 증폭시킬 수 있었다. PEDV 실험을 위하여 PED 임상 증상을 나타내는 분변을 이용하여 RT-PCR을 실시하였다. P2/P2R primer로 753bp의 PCR product를 얻을 수 있었다. TGEV의 두 가지 strain의 N protein gene을 sequencing하여 prototype인 Purdue strain과 염기서열 상동성을 조사한 결과, 97%이상의 높은 homology를 나타내었다. PED-V 역시 N protein gene을 sequencing하여 CV777과 염기서열 상동성을 조사한 결과 97%이상의 homology로 PEDV임을 알 수 있었다. TGEV와 PEDV의 염기서열을 비교한 결과 29%의 낮은 homology를 관찰할 수 있었다. 두 가지 바이러스의 N protein gene에 대한 cDNA probe를 제작하여 Southern blot hybridization을 한 결과, 각 바이러스에 매우 특이적 반응을 나타내었다.

• International Journal of Industrial Entomology and Biomaterials
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• v.25 no.2
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• pp.195-203
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• 2012

In reared populations of Allomyrina dichotoma, commercial insects, the skin of last instar larvae was changed softer with opaque white, and infested grubs eventually died. To clarify the cause of the symptom, we collected the larvae of A. dichotoma from five farms and examined their intestinal bacterial florae using pyrosequencing technique. From those results, a member of Paenibacillus was found only in the larvae showing the symptom of disease. Through PCR analysis using a Paenibacillus specific primer set, we obtained the partial 16S rRNA gene sequence and confirmed the microbe as Paenibacillus sp. For clear identification, a whole guts was extracted from each larva showing the sign of the disease and incubated at $70^{\circ}C$ for 15 min to isolate spore forming bacteria. After then, each content of guts was cultured on $MYPGP_{NAL}$ agar medium($12.5{\mu}g/ml$ of nalidixic acid) at $30^{\circ}C$. The 16S rRNA gene sequence analysis for the isolated bacteria showed that they were closely related to P. rigui(97.9% similarity), to P. chinjuensis(96.1% similarity), and to P. soli(95.3% similarity). Additional tests including API test and cellular fatty acid composition analysis were performed, but the strain couldn't be identified at species level, suggesting it may represent novel species of the genus Paenibacillus.

• Development and Reproduction
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• v.14 no.4
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• pp.261-268
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• 2010

As in the O. mykiss electrophoretic profiles of RNA, the signals of each RNA sample from 9 individual tissues such as liver, muscle, brain, heart, pituitary gland, kidney, intestine, spleen and gill similar to positive control were obtained. The tissue distributions of the complimentary DNA (cDNA) of O. mykiss four genes were analyzed using quantitative real-time PCR with primer sets for tissue expression analysis. In this rainbow trout species, author obtained bands of various sizes, ranged from 700 bp to 1,400 bp. A dissociation curve was made at the end of each run to make sure that there was no non-specific amplification. Supplementarily, the Ct of each DNA was compared. The Ct values of vinculin with rainbow trout tissues were determined in a manner similar to those for agouti-related protein (AgRP) and melanocortin receptors (MC4R I and MC4R II). Further, obtained Cts for standard curve of each DNA were affected by specific product (vinculin, AgRP and MC4R II genes). After several experiments with four individual genes of rainbow trout, author estimated a variation ratio of the mean Ct value of the DNA extracted using the comparative CTt method was 37.27, and the standard deviation was 5.33. The correlation coefficient between the Ct values and the concentration of cDNA was -0.98, -0.99, -0.91 and -0.86, respectively (vinculin, AgRP, MC4R I and MC4R II genes). Since this correlation showed high linearity, the straight line obtained was used as a standard for the O. mykiss tissues reared in aquarium. A PCR efficiency of 100% is ideally achieved when the slopes are close to the theoretical value of -3.31. According to quantification method, the results of quantification are strongly affected by the DNA fragmentation. The size of most DNA fragments obtained from various tissues of rainbow trout used in the experiment was approximately 100 bp. According to the four slopes, an efficiency of nearly 100% was estimated for four genes detection methods. Additionally, further analysis with more individuals and primers will be required to fully establish optimization in rainbow trout.

• Journal of the Korean Institute of Intelligent Systems
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• v.14 no.5
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• pp.545-550
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• 2004

The study of available genotypes (biodiversity analysis) in bacterial communities is of growing importance in several fields such as ecology, environmental technology, clinical diagnostics, etc. These culture-independent genotyping techniques, especially amplifying 16S rRNA genes, attempt to overcome some shortcomings of conventional cultivation method. Biodiversity analysis based on molecular technique were laborious for base-calling chromatogram, trimming primer sites, correcting strand directions, electing representative operation taxonomic units (OTU), etc. Also, biologists wanted intuitively to confirm results of the above processes. For making up these demands, we developed the web application based on Folder-Process-Filter (FPF) modeling with correspondence to classical Model-View-Controller model. The model of web application leads to keep virtues of simplicity and directness for development and management of the stepwise web interfaces. The web application was developed in Perl and CGI on Linux workstation. It can be freely accessed from http://home.pusan.ac.kr/～genome/tools/rat.htm.

• KSBB Journal
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• v.14 no.6
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• pp.702-706
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• 1999

The genetic responses of aquaculturable seaweed Prophyra yezoensis tissue by acid shock have been compared using differential display technique. The tissue has been challenged in seawater containing 0.05% hydrogen chloride(pH 3.0) for 5 min, then rehabilitated in normal seawater for 10 min, 30 min, 60 min and 4 hrs, respectively. Total RNA was extracted by LiCl-guanidinium method. The cDNA was synthesized by reverse transcription with random hexamers and amplified by PCR with arbitrary primers. The genetic fragment disappeared by acid shock was selectively isolated from agarose gel and sequenced with a DNA auto sequencer. One of the acid-labile gene(605 bp) was identified as a dethiobiotin synthetase gene according to sequence alignment analysis by the NCBI BLAST search program.

• Biomedical Science Letters
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• v.12 no.3
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• pp.131-137
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• 2006

RGS is a negative regulator of G-protein signaling and can be identified by the presence of a conserved $120{sim}125$ amino acid motif, which is referred to as the RGS box. A number of RGSs are induced in response to a wide variety of stimuli. Increased levels of RGSs lead to significant decreases in GPCR responsiveness. To obtain further evidence of a role of RGS proteins in rat C6 astrocytoma cells, we first determined the expression profile of RGS-specific mRNA in C6 cells using reverse transcription-polymerase chain reaction (RT-PCR) with a poly dT18 primer and transcript-specific primers. We found that RGS2, RGS3, RGS6, RGS9, RGS10, RGS12, and RGS16 were differentially expressed in C6 astrocytoma cells. The highest expression rate was found for RGS3, followed by RGS16, RGS10 and RGS9, whereas the expression level for RGS2 was barely detectable. We next assessed whether forskolin regulated the expression of RGSs expressed in C6 astrocytoma cells. The present study found that forskolin dose-dependently stimulated the expression of RGS2 transcripts. This up-regulation of RGS2 gene was abrogated by H-89, potent and broad-spectrum protein kinase A (PKA) inhibitors. Actinomycin D completely inhibited the up-regulation of RGS2 gene induced by forskolin $(10{\mu}M)$, indicating that the regulation of RGS2 gene is controlled at the transcriptional level. In addition, forskolin did significantly activate transcriptional cAMP response element (CRE) in either HEK 293 cells or C6 cells and did not modulate the $NF-{\kappa}B$ and AP-l activity as measured by luciferase reporter gene assay. Finally, forskolin induced the expression of RGS2 mRNA in C6 astrocytoma cells, which depend on the PKA pathway and CRE transcriptional pathways.

• Journal of Physiology & Pathology in Korean Medicine
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• v.17 no.3
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• pp.684-692
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• 2003

The herbal extract(YMT_02) is a modified extracts from Yukmijihwang-tang(YMJ) to promote memory-enhancing. The YMJ extracts has been widely used as replenishing yin and tonifying the kidneys herbal medicine for hundred years ia Asian countries. The purpose of this study is to: 1) quantitatively evaluate the memory-enhancing effect of YMT_02 by passive avoidance test, 2) statistical evaluation of candidate gene expression (pentraxin. PEP-19, transthyretin) in rat hippocampus. The hippocampi of YMT_02 and control group were dissected and mRNA was further purified. After synthesizing cDNA using oligo-dT primer, the cDNA were applied to Real Time PCR. The results were as follows : 1) passive avoidance test showed enhancing memory retentin by YMT_02 treatment, 2) expression of pentraxin, that accelerate degenerating of neuronal cell, was significantly decreased, 3) the mRNA of genes that has been known to be associated with protecting neuronal cell degeneration, such as PEP-19 and transthyretin, were significantly increased upon YMT_02 treatment. From above results, the administration of YMT_02 which tonify the function of Kidneys could enhance the ability of memory and learning. In addition, the administration of YMT_02 enhance memory retention through modulating particular gene (pentraxin, PEP-19, transthyretin) expressions in hippocampu.