• Mycobiology
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• v.47 no.4
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• pp.466-472
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• 2019

For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders' rights.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.44 no.4
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• pp.352-358
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• 2011

The presence of ISKNV-like viruses in various freshwater ornamental fish species imported from Asia was confirmed by polymerase chain reaction(PCR) amplification of the ATPase(adenosine triphosphatase) gene. Interestingly, molecular analyses of the Open Reading Frame 25(ORF25) region of these isolates based on the ISKNV(Infectious spleen and kidney necrosis virus) genome revealed the presence of various repetitive sequences. ORF25 repeat sequence length had no effect on cumulative mortality of rock bream Oplegnathus fasciatus challenged with tissue homogenates of infected pearl gourami, Trichogaster leeri; silver gourami, Trichogaster microlepis; blue gourami, or Trichogaster trichopterus. All isolates induce cumulative mortalities after 12 days of infection, confirming that ORF25 polymorphism did not affect the pathogenicity of ornamental fish megalocytiviruses that cross infect rock bream, a seawater fish. Also, no statistically significant differences in spleen index or viral copy number in infected tissues was detected between isolates with varying ORF25 repeat sequence lengths. However, further studies are necessary to fully characterize the functional characteristics of these polymorphisms in megalocytivirus disease in ornamental fishes.

• Clinical and Experimental Pediatrics
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• v.52 no.3
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• pp.356-363
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• 2009

Purpose : A polymorphism in the IGF-I gene promoter region is known to be associated with serum IGF-I levels, birth weight, and body length, suggesting that IGF-I gene polymorphism might influence postnatal growth. The present study aimed to investigate the role of this polymorphic cytosine-adenine (CA) repeat of the IGF-I gene in children with idiopathic short stature. Methods : The study involved 131 children (72 boys and 59 girls) diagnosed with idiopathic short stature, aged 715 years. Genomic DNA was extracted from anticoagulated peripheral whole blood. The primers were designed to cover the promoter region containing the polymorphic CA repeat. Data were analyzed using GeneMapper software. The correlations between age and serum IGF-I levels were analyzed using Spearmans correlation coefficient. Results : The CA repeat sequences ranged from 15 to 22, with 19 CA repeats the most common with an allele frequency of 40.6%. Homozygous for 19 CA repeat was 13.0%, heterozygous for 19 CA repeat was 56.5%, and 19 CA non-carrier was 30.5%. The three different genotype groups showed no significant differences in height, body weight and body mass index, and serum IGF-I levels. The serum IGF-I level and age according to the IGF-I genotypes were significantly correlated in the entire group, 19 CA repeat carrier group, and the non-carrier group. The three groups also showed no significant differences in the first year responsiveness to GH treatment. Conclusion : There were no significant different correlations between 19 CA repeat polymorphism and serum IGF-I levels according to genotype. Our results suggest that the IGF-I 19 CA repeat gene polymorphism is not functional in children with idiopathic short stature.

• Applied Biological Chemistry
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• v.38 no.5
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• pp.387-392
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• 1995

To study the regulatory expression mechanism of soybean glycinin gone, Gy2, the 5' upstream region of the gene was searched for the presence of putative regulatory elements by nucleotide sequencing. It revealed various kinds of regulatory sequence elements commonly found in plant storage protein genes. There were canonical promoter sequences, TATA box (TATAAT) and AGGA box (GAAT) which are common in the 5' upstream region of the plant genes. The embryo factor binding sequence, RY repeat, CACA sequences, ${\alpha}$-conglycinin enhancer-like sequences were also found. To delineate the function of these sequences, 5' upstream deletion mutants of Gy2 were prepared and fused to the ${\alpha}$-glucuronidase (GUS) gene. Each chimeric construct was transferred into soybean protoplasts for transient assay, which led to the identification of the sequences between -281 and -223, -170 and -122, of Gy2 promoter as negative regulatory elements, and the sequences between -223 and -170, -122 and -16 as positive regulatory elements. These results are consistent in transformed tobacco plants as well. The serially deleted promoter fragments fused to the GUS were transformed into Nicotiana tabacum by Agrobacterium tumefaciens using the binary vector system. GUS activity of Gy2 promoter deletion constructs was detected only in seeds but not in leaves with different levels of expression as in transient assay. These results suggest that the glycinin Gy2 promoter drives a tissue-specific expression in transgenic tobacco plants.

• Biomedical Science Letters
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• v.15 no.2
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• pp.167-170
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• 2009

Nitric oxide is an important factor to regulate the biochemical reactions in the body such as expansion of blood vessel, neural conduction and antimicrobial activity. There are two forms of nitric oxide synthase and iNOS has attracted most attention because it is involved in the development of diabetes and cardiac disease condition. There are several regulatory sequences in the promoter region of iNOS gene. One of them is (CCTTT)n. It has been reported that the number of tandem repeat of (CCTTT)n varies from population to population. So, we analyzed (CCTTT)n polymorphism in Korean genome for the purpose of comparison. According to our present study Koreans are different from other Asians reported previously because $(CCTTT)_{10}$ is the highest incidence as opposed to $(CCTTT)_{12}$ for other countries. This study should facilitate the understanding of the expression of iNOS gene in different population.

• Journal of Aquaculture
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• v.9 no.1
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• pp.93-100
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• 1996

Previously, as an effort to make an autonomously replicating expression vector in fish, an ARS (autonomously replicating sequence) was cloned from MAR (matrix attachment region) of Misgurnus mizolepis. The DNA fragment composed of 443 base pairs contains ARS core consensus sequences, topoisomerase II consensus sequences, and A or T box sequences which are homologous to the known consensus sequences originated from other organisms. The clond ARS, as other DNA replication origins, contains inverted repeat sequences and several potential hairpin loop structures. These consensus sequences and hairpin structures may serve as recognition signals for regulatory proteins of DNA replication initiation.

• Microbiology and Biotechnology Letters
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• v.34 no.3
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• pp.278-287
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• 2006

Cycloinulooligosaccharide fructanotransferase (CFTase) converts inulin into cycloinulooligosaccharides (cyclofructan, CF) of ${\beta}-(2{\to}1)$-linked D-fructofuranose as well as hydrolysis of cyclofructan. Sequences analysis indicated that CFTase was divided into five distinct regions containing three repeated sequences (R1, R3, and R4) at the N-terminus and C-terminus. Each domain function was investigated by comparison of wild type CFTase enzyme (CFT148) and deletion mutant proteins (CFT108: R1 and R3 deletion; CFT130: R4 deletion; and CFT88: R1, R3, and R4 deletion) of CFTase. The CFT108 mutant had both CFTase and CF hydrolyzing activity as CFT148 did. CFTase activities and CF hydrolysing activities were disappeared in CFT130 and CFT88 mutants. These results indicated that the C-terminal R4 region of P. polymyxa CFTase is necessary for cyclization and hydrolyzing activity.

• Korean Journal of Microbiology
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• v.26 no.2
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• pp.101-105
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• 1988

6M-MuLV mutants containing deldtions around the putative packaging signal were constructed by using recombinant DNA technique and transfected into NIH/3T3 cell. 2 of 6 mutants can not be packaged into virions even in the presence of the wild type helper virus. The boundary between the packagible and the non-packagible genome is located around Pvu I site, 421 nucleotide downstream from the 5' end of M-MuLV genome. 10 base pair inverted repeat sequence (GAGUCCAAAA) which can make stem structure around Pvu Isite could be the putative packaging signal.

• Fisheries and Aquatic Sciences
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• v.5 no.1
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• pp.54-58
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• 2002

The polymerase chain reaction (PCR) amplification technique was used for comparison of Listeria monocytogenes serotypes. PCR primers for the fragment of invasion-associated protein (iap) gene were highly specific for all the serotypes of L. monocytogenes. Other Listeria spp., such as Listeria ivanovii and Listeria innocua were not produced the PCR fragments by above primer set. The nucleotide sequences of PCR products showed high homologies in comparison of all the isolated serotypes except unknown type II-2. The deduced amino acid sequences of the PCR products also showed similar to one another. The various region of the PCR products, called a Thr-Asn repeat region was presented. All of isolated L. monocytogenes serotypes possessed 16 to 20 Thr-Asn repeats.

• Genomics & Informatics
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• v.4 no.4
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• pp.167-169
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• 2006

PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user-defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users.