• Development and Reproduction
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• v.20 no.2
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• pp.135-140
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• 2016

Genomic DNAs isolated from crucian carp of four rivers, belonging to the family Cyprinidae was amplified by seven oligonucleotides primers. In the present study, we employed hierarchical clustering method in order to reveal genetic distances and variations. Crucian carp was acquired from Hangang river (CAH), Geumgang river (CAG), Nakdonggang river (CAN) and Yeongsangang river (CAY). The primer BION-12 generated the most loci (a total of 50) with an average of 10 in the CAY population. The primer BION-10 generated the least loci (a total of 19), with an average of 3.8 in the CAG population, in comparison to the other primers used. Seven oligonucleotides primers made 16.7 average no. per primer of specific loci in the CAH population, 7.4 in the CAG population, 8.6 in the CAN population and 0.9 in the CAY population, respectively. The specific loci generated by oligonucleotides primers revealed inter-individual-specific characteristics, thus disclosing DNA polymorphisms. The dendrogram obtained by the seven oligonucleotides primers indicates four genetic clusters. The genetic distance that displayed significant molecular differences was between individuals no.06 and no.08 from the CAG population (genetic distance = 0.036), while the genetic distance among the five individuals that displayed significant molecular differences was between individuals no.08 and no.09 from the CAG population (genetic distance = 0.088). With regard to average bandsharing value (BS) results, individuals from CAY population ($0.985{\pm}0.009$) exhibited higher bandsharing values than did individuals from CAH population ($0.779{\pm}0.049$) (P<0.05). Relatively, individuals of CAY population were fairly closely related to that of CAN location (genetic distance between two populations<0.016).

• Korean Journal of Environmental Biology
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• v.38 no.3
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• pp.350-354
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• 2020

Many parrots are considered endangered species due to threats from human activities. Gender determination is of great importance for biological studies and the conservation of endangered parrots. However, like other birds, gender determination in parrots is hindered due to the lack of external dimorphism between males and females. A molecular approach using the chromo-helicase-DNA binding protein 1 (CHD1) gene is commonly used for sexing birds. This study aimed to determine the gender of parrots from Korean zoos based on amplification and visualization of the partial CHD1 gene. The samples of 13 parrot species were collected from three different zoos in Korea and the extracted DNA templates were amplified using CHD1 gene primers. The gender of 27 samples of 13 species was determined by visualizing the PCR products on an agarose gel. While male parrots were indicated by a single band, female parrots were indicated by double bands. The findings provide additional information, which might be helpful for the management and care of parrots in Korean zoos.

• Biomedical Science Letters
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• v.18 no.1
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• pp.49-55
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• 2012

Numerous biochemical molecules have been implicated in the development of muscular atrophy. However, control mechanisms associated with muscular disease are not clear. The present study was conducted to investigate gene expression profiles of rat muscle during the denervation to atrophy transition processes. We isolated total RNA from rats suffering from partial muscle atrophy (P) and electromyostimulated atrophy (PE) and synthesized cDNA using annealing control primers. Using 20 ACPs for PCR, we cloned 18 DEGs using TOPO TA cloning vector, sequenced, and analyzed their identities using BLAST search. Sequences of 14 clones significantly matched database entries, while one clone was ESTs, and 3 clones were unidentified. Different expression profiles of selected DEGs between P and PE were confirmed. The troponin T, Fkbp1a, RGD1307554, Phtf1, Atp1a1 and Commd3 were highly expressed genes in the P and PE groups, while Krox-25 and TCOX2 were only expressed genes in the P group, the Sv2b and Marcks were only expressed genes in PE group. also, Cox8h was highly expressed genes in PE groups. The ASPH, ND1, and ARPL1 were highly expressed genes in the P and PE groups. List of genes obtained from the present study might provide an insight for the study of mechanism regulating muscle atrophy and electrostimulated muscle atrophy transitions. These data suggest that troponin T, Fkbp1a, RGD1307554, Phtf1, Atp1a1, and Commd3 are potentially useful as clinical biomarkers of age-related muscle atrophy and dysfunction.

• Journal of Ecology and Environment
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• v.40 no.1
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• pp.75-83
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• 2016

Background: In order to evaluate the effect of pH, known as a critical factor for shaping the biogeographical microbial patterns in the studies by others, on the bacterial diversity, we selected two sites in a similar geographical location (site 1; north latitude 35.3, longitude 127.8, site 2; north latitude 35.2, longitude 129.2) and compared their soil bacterial diversity between them. The mountain soil at site 1 (Jiri National Park) represented naturally acidic but almost pollution free (pH 5.2) and that at site 2 was neutral but exposed to the pollutants due to the suburban location of a big city (pH 7.7). Methods: Metagenomic DNAs from soil bacteria were extracted and amplified by PCR with 27F/518R primers and pyrosequenced using Roche 454 GS FLX Titanium. Results: Bacterial phyla retrieved from the soil at site 1 were more diverse than those at site 2, and their bacterial compositions were quite different: Almost half of the phyla at site 1 were Proteobacteria (49 %), and the remaining phyla were attributed to 10 other phyla. By contrast, in the soil at site 2, four main phyla (Actinobacteria, Bacteroidetes, Proteobacteria, and Cyanobacteria) composed 94 %; the remainder was attributed to two other phyla. Furthermore, when bacterial composition was examined on the order level, only two Burkholderiales and Rhizobiales were found at both sites. So depending on pH, the bacterial community in soil at site 1 differed from that at site 2, and although the acidic soil of site 1 represented a non-optimal pH for bacterial growth, the bacterial diversity, evenness, and richness at this site were higher than those found in the neutral pH soil at site 2. Conclusions: These results and the indices regarding diversity, richness, and evenness examined in this study indicate that pH alone might not play a main role for bacterial diversity in soil.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.26 no.1
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• pp.45-52
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• 2000

Nowadays, there are a lot of evidence that mutation of the p53 tumor suppressor gene is one of the most common genetic abnormalities in neoplastic progression. In this study, we analyzed 20 specimens of oral tumors(squamous cell carcinoma 14 cases, ameloblastoma 3 cases, adenoid cystic carcinoma 2 cases, malignant schwannoma 1 case)using polymerase chain reaction and direct sequencing which used an automated DNA sequencer and software for detection of mutations. Polymerase chain reactions were performed with 4 sets of primers encompassing exon 5, 6, 7, 8, and direct sequencing method was employed. The results were as followings. 1. We detected 10 point mutations out of 20 specimens (50%). 2. The genetic alterations included 7 mis-sense mutations resulting in single amino acid subtitutions, 2 silent mutations, 1 non-sense mutations encoding a stop codon. 3. Mutations were mostly in exon 7(7 out of 10 mutations, 70%) and involved codons 225, 234, 235, 236, 238, 247. 4. Therse were 4 cases of $T{\rightarrow}A$ transversion, 2 cases of $C{\rightarrow}A$ transversion, $A{\rightarrow}G$ transition, 1 case of $C{\rightarrow}G$, $T{\rightarrow}G$ transversion respectively. 5. We could find out point mutations more conveniently using PCR - Automated Direct Sequencing method.

• The Journal of Korean Society of Virology
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• v.27 no.2
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• pp.217-225
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• 1997

PCR amplication using the primers for gag, pol and env genes in BLV (bovine leukemia virus) proviral DNA and syncytium assay were carried out for the Korean native goats experimentally infected with bovine leukemia virus to investigate pathogenesis of BLV in the goats, and to establish a model animal for BLV infection. The oligonucleotide primers used in PCR revealed very high specificity. The minimal amount of FLK-BLV cellular chromosomal DNA to detect the integrated BLV proviral DNA was 10 ng. The peripheral blood lymphocytes from the goat infected with BLV were examined at regular intervals by PCR amplification and syncytium assay. Pol or gag genes were detected in none of three infected goats at the 1st week post-infection (p.i.). At the 4th week p.i., one of three goats showed the amplified gag gene. Thereafter detection rates for the genes were increased, indicating that the BLV proviral genes were integrated in all of the lymphocytes from three goats, at the 16th weeks p.i., when it was evident in syncytium assay that the lymphocytes from all of three goats were infested with infective BLV. Investigating the tissues from the necropsied goats at the 8th month p.i., the amplified BLV proviral genes and infective BLV were detected in all of the peripheral lymphocytes from three infected-goats. Among various tissues examined, the amplified BLV proviral genes were observed in spleen and superficial cervical, mandibular and retropharyngeal lymph nodes, and the infective BLV, in superficial cervical and mandibular lymph nodes. It was assumed that the Korean native goat was quite susceptible to BLV infection, indicating that the goat could be a good model animal for BLV.

• The Korean Journal of Food And Nutrition
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• v.15 no.2
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• pp.104-111
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• 2002

The peptidyl prolyl sis-trans isomerase (PPIase, EC 5.2.1.8) from bacillus stearothermophilus was extracted from the cells treated with by lysozyme. PPIase was purified from the cell extracts by heat treatment, ammonium sulfate precipitation, ion exchange chromatography and finally gel filtration, sodium dodecyl sulfate polyacrylamide gel electrophoresis(SDS-PAGE). The molecular weight of the purified PPIase was estimated as 18kDa by SDS-PAGE. The 39 amino acid residues from the N-terminus were determined by the protein sequencer. The enzyme showed the optimum pH at 8.0 and was stable at the range of pH 7.0∼8.0. The enzyme was considerably stable after heat treatment at 60$\^{C}$ for 30minutes, and the enzyme was quite stable up to 65$\^{C}$. The presence of the PPIase in the refolding solution accelerated the isomerization rate of the assay peptide. PPIase gene of Bacillus stearothermophilus was screened from a genomic library by plaque hybridization using the A-l primer as a probe. A PPIase positive plaque contained a 3.0kb insert of the chromosomal DNA. A 3.0kb fragment was subcloned into pUC18, resulting pPI-40. A DNA fragment encoding the N-terminal portion of the PPIase in pPI-40 was amplified by polymerase chain reaction(PCR) method using the A-1 and B-2 primers. The amplified fragment was cloned into the Sma I site of pUC18 and recombinant plasmid was designated as pSN-18. The nucleotide sequence of 167bp fragment was determined. The deduced amino acid sequence of PPIase was completely matched with the determined N-terminal amino acid sequence of PPIase B. stearothermophilus.

• Journal of Photoscience
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• v.11 no.3
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• pp.115-120
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• 2004

For the expression study of antioxidant isoenzyme genes in rice (Oryza sativa L.) plants, extensive searches for genes of superoxide dismutase (SOD), ascorbate peroxidase (APX), and catalase (CAT) isoforms were performed through the GenBank database. The genes for two cytosolic and one plastidic CuZn-SOD, one Fe-SOD, two Mn-SOD, two cytosolic and two chloroplastic (stromal and thylakoid) APX, and three CAT isoforms were available in japonica-type rice. These isoforms were named as cCuZn-SOD1, cCuZn-SOD2, pCuZn-SOD, Fe-SOD, Mn-SOD1, Mn-SOD2, cAPXa, cAPXb, Chl_sAPX, Chl_tAPX, CATa, CATb, and CATc, respectively. Since they shared a high degree of homology in the nucleotide and amino acid sequences, the gene-specific primers for the genes were designed directly from their full-length cDNAs found in the database except for the CATa gene. These primers were used in the RT-PCR analysis to investigate the differential expression of antioxidant isoenzyme genes in rice plants from the seeds irradiated with low doses (2, 4, 8, and 16 Gy) of gamma-radiation. The gammairradiation slightly increased the transcripts of pCuZn-SOD, while those of Fe-SOD, cAPXb, and CATb decreased. However, no substantial differences were observed in the expression of all the isoenzyme genes between the control and irradiated groups. In this study, gene specific primers for thirteen SOD, APX and CAT isoenzymes were constructed from the full-length cDNAs. The results of RT-PCR analysis obtained by using these primers suggests that the expression levels of SOD, APX, and CAT isoenzyme genes in rice seedlings were hardly affected by gamma-irradiation at the seed stage.

• Mycobiology
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• v.37 no.2
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• pp.103-108
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• 2009

The principal objective of this study was to acquire basic data regarding the mycelial growth characteristics for the artificial cultivation of Coprinus comatus. 12 URP primers were employed to evaluate the genetic relationships of C. comatus, and the results were divided into three groups. Among six kinds of mushroom media, MYP medium was selected as the most favorable culture medium for C. comatus. The optimal temperature and pH ranges for the mycelial growth of C. comatus were $23{\sim}26^{\circ}C$ and pH 6${\sim}$8, respectively. The carbon and nitrogen sources for optimal mycelial growth were sucrose and tryptone, respectively.

• Asian-Australasian Journal of Animal Sciences
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• v.16 no.5
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• pp.650-654
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• 2003

The accuracy of Polymerase chain reaction (PCR) assay in sexing of sheep embryos was assessed in this study. A total of 174 ovine embryos produced in vitro at different stages of development (2, 4-8 cell stages, morula and blastocyst) were sexed. The universal primers (P1-5EZ and P2-3EZ) used in this assay amplified ZFY/ZFX-specific sequences and yielded a 445 bp fragment in both sexes. Restriction enzyme analysis of ZFY/ZFX-amplified fragments with Sac I exhibited polymorphism between sexes, three and two fragments in males and in females, respectively. For verification of accuracy, blood samples of known sex were utilized as positive controls in each test. The mean percentages of sex identification by this method at 2 cell, 4-8 cell, morula and blastocyst were $73.00{\pm}5.72$, $89.77{\pm}3.79$, $3.33{\pm}8.08$ and $79.6{\pm}9.09$, espectively with the over all male to female ratio of 1:0.87. It is concluded that the ZFY/ZFX based method is highly reliable for the sexing of sheep embryos.