• BMB Reports
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• v.37 no.4
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• pp.493-502
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• 2004

The genetic diversity and species-diagnostic markers in the introduced apple snail, Pomacea canaliculata and in the native Thai apple snails; Pila ampullacea, P. angelica, P. pesmei, and P. polita, were investigated by restriction analysis of COI and are reported for the first time. Twenty-one composite haplotypes showing non-overlapping distributions among species were found. Genetic heterogeneity analysis indicated significant differences between species (P < 0.0001) and within P. pesmei (P < 0.0001) and P. angelica (P < 0.0004). No such heterogeneity was observed in Pomacea canaliculata (P > 0.0036 as modified by the Bonferroni procedure), P. ampullacea (P = 0.0824-1.000) and P. polita (P = 1.0000). A neighbor-joining tree based on genetic distance between pairs of composite haplotypes differentiated all species and indicated that P. angelica and P. pesmei are closely related phylogenetically. In addition, the 16S rDNA of these species was cloned and sequenced. A species-specific PCR for P. canaliculata was successfully developed with a sensitivity of detection of approximately 50 pg of the target DNA template. The amplification of genomic DNA (50 pg and 25 ng) isolated from the fertilized eggs, and juveniles (1, 7, and 15 d after hatching) of Pomacea canaliculata was also successful, and suggested that Pomacea canaliculata and Pila species can be discriminated from the early stages of development.

• The Plant Pathology Journal
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• v.38 no.6
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• pp.656-664
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• 2022

Pectobacterium odoriferum is the primary causative agent in Kimchi cabbage soft-rot diseases. The pathogenic bacteria Pectobacterium genera are responsible for significant yield losses in crops. However, P. odoriferum shares a vast range of hosts with P. carotovorum, P. versatile, and P. brasiliense, and has similar biochemical, phenotypic, and genetic characteristics to these species. Therefore, it is essential to develop a P. odoriferumspecific diagnostic method for soft-rot disease because of the complicated diagnostic process and management as described above. Therefore, in this study, to select P. odoriferum-specific genes, species-specific genes were selected using the data of the P. odoriferum JK2.1 whole genome and similar bacterial species registered with NCBI. Thereafter, the specificity of the selected gene was tested through blast analysis. We identified novel species-specific genes to detect and quantify targeted P. odoriferum and designed specific primer sets targeting HAD family hydrolases. It was confirmed that the selected primer set formed a specific amplicon of 360 bp only in the DNA of P. odoriferum using 29 Pectobacterium species and related species. Furthermore, the population density of P. odoriferum can be estimated without genomic DNA extraction through SYBR Green-based real-time quantitative PCR using a primer set in plants. As a result, the newly developed diagnostic method enables rapid and accurate diagnosis and continuous monitoring of soft-rot disease in Kimchi cabbage without additional procedures from the plant tissue.

• The Korea Journal of Herbology
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• v.28 no.6
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• pp.53-58
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• 2013

Objectives : Pinelliae Tuber has been used as a typical unauthentic herbal medicines. Due to the morphological similarity between Pinelliae Tuber and adulterants, the correct authentication is very difficult. Therefore, we introduced DNA barcode to establish a powerful tool for the authentication of Pinelliae Tuner from adulterants. Methods : To obtain DNA barcode regions, genomic DNA was extracted from nineteen specimens of Pinellia ternata, Pinellia pedatisecta, Pinellia tripartita, and Typhonium flagelliforme, and matK and rbcL genes were amplified. For identification of species specific sequences and analysis phylogenetic relationship, a comparative analysis were performed by the ClastalW and UPGMA based on entire sequences of matK and rbcL genes, respectively. Results : In comparison of two DNA barcode sequences, we elucidated the phylogenetic relationship showing distinct four groups depending on species and identified 40 and 20 species specific nucleotides enough to distinguish each species from matK and rbcL gene, respectively. The sequence differences at the corresponding positions were avaliable genetic marker nulceotides to discriminate the correct species among analyzed four species. These results indicated that phylogentic and comparative analysis of matK and rbcL genes are useful genetic markers to authenticate Pinelliae Tubers. Conclusions : The marker nucleotides enough to distinguish P. ternata, P. tripatrita, P. peditisecta, and T. flagelliform, were observed at 40 positions in matK gene and 20 positions in rbcL gene sequence, respectively. These differences can be used to authenticate Pinelliae Tuber from adulterants as well as discriminate each four species.

• Journal of Life Science
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• v.28 no.1
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• pp.130-139
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• 2018

In ancient times, horse racing was done in ancient European countries in the form of wagon races or mountain races, and wagon racing was adopted as a regular event at the Greek Olympic Games. Thoroughbred horse has been bred since 17th century by intensive selective breeding for its speed, stamina, and racing ability. Then, in the 18th century, horse racing using the Thoroughbred species began to gain popularity among nobles. Since then, horse racing has developed into various forms in various countries and have developed into flat racing, steeplechasing, and harness racing. Thoroughbred racehorse has excellent racing abilities because of powerful selection breeding strategy for 300 years. It is necessary to maintain and maximize horses' ability to race, because horse industries produce enormous economic benefits through breeding, training, and horse racing. Next-generation sequencing (NGS) methods which process large amounts of genomic data have been developed recently. Based on the remarkable development of these genomic analytical techniques, it is now possible to easily carry out animal breeding strategies with superior traits. In order to select breeding racehorse with superior racing traits, the latest genomic analysis techniques have to be introduced. In this paper, we will review the current efforts to improve race performance for racehorses and to examine the research trends of genomic analysis. Finally, we suggest to utilize genomic analysis in Thoroughbred racehorse and Jeju horse, and propose a strategy for selective breeding for Jeju horse, which contributes job creation of Korea.

• Applied Biological Chemistry
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• v.37 no.5
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• pp.361-369
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• 1994

To study the light-induced expression mechanism and protein transport into the chloroplast, a rice genomic clone (GrbcS) for the small subunit of ribulose 1,5-bisphosphate carboxylase (rbcS) was isolated and its nucleotide sequence was determined. Nucleotide sequence analysis of GrbcS revealed that the gene consists of two exons interrupted by an intron, encoding a protein of 175 amino acids including a transit peptide of 47 amino acids. These structural features of GrbcS are consistent with those of other rbcS genes from monocot species. Genomic Southern blot analysis suggested that the rbcS genes are present as a relatively small multigene family in the rice genome. Comparison of the nucleotide and deduced amino acid sequences to other rice rbcSs shows close sequence similaritiy. Conserved DNA sequences present in other light-responsive genes are also found in the 5’ upstream region of GrbcS such as G-box, 3AF1-binding site and GATA site. The possible function of these putative regulatory elements are discussed.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.8
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• pp.1183-1189
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• 2017

Objective: Owing to the public availability of complete genome sequences, including avian species, massive bioinformatics analyses may be conducted for computational gene prediction and the identification of gene regulatory networks through various informatics tools. However, to evaluate the biofunctional activity of a predicted target gene, in vivo and in vitro functional genomic analyses should be a prerequisite. Methods: Due to a lack of quail genomic sequence information, we first identified the partial genomic structure and sequences of the quail SH3 domain containing ring finger 2 (SH3RF2) gene. Subsequently, SH3RF2 was knocked out using clustered regularly interspaced short palindromic repeat/Cas9 technology and single cell-derived SH3RF2 mutant sublines were established to study the biofunctional activity of SH3RF2 in quail myoblast (QM7) cells during muscle differentiation. Results: Through a T7 endonuclease I assay and genotyping analysis, we established an SH3RF2 knockout (KO) QM7#4 subline with 61 and 155 nucleotide deletion mutations in SH3RF2. After the induction of myotube differentiation, the expression profiles were analyzed and compared between regular QM7 and SH3RF2 KO QM7#4 cells by global RNA sequencing and bioinformatics analysis. Conclusion: We did not detect any statistically significant role of SH3RF2 during myotube differentiation in QM7 myoblast cells. However, additional experiments are necessary to examine the biofunctional activity of SH3RF2 in cell proliferation and muscle growth.

• The Plant Pathology Journal
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• v.22 no.1
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• pp.36-45
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• 2006

Twenty isolates of Didymella bryoniae were isolated from infected cucurbit plants in various growing areas of southern Korea in 2001 and 2002. Random Amplified Polymorphic DNA (RAPD) group [RG] I of D. bryoniae was more virulent than RG IV to watermelon. Virulence of the RG I isolate was strong to moderate to cucumber, whereas that of the RG IV varied from strong, moderate to weak. Two hundred seventy-three amplified fragments were produced with 40 primers, and were analyzed by a cluster analysis using UPGMA method with an arithmetic average program of NTSYSPC. At the distance level of 0.7, two major genomic DNA RAPD groups were differentiated among 20 isolates. The RG I included 7 isolates from watermelon and one isolate from melon, whereas the RG IV included 12 isolates from squash, cucumber, watermelon and melon. Amplification of internal transcribed spacer (ITS) region and small subunit rRNA region from the 20 isolates yielded respectively a single fragment. Restriction pattern with 12 restriction enzymes was identical for all isolates tested, suggesting that variation in the ITS and small subunit within the D. bryoniae were low. Amplification of the genomic DNAs of the tested isolates with the sequence characterized amplified regions (SCAR) primer RG IF-RG IR specific for RG I group resulted in a single band of 650bp fragment for 8 isolates out of the 20 isolates. Therefore, these 8 isolates could be assigned into RG I. The same experiments done with RG IIF-RG IIR resulted in no amplified PCR product for the 20 isolates tested. An about 1.4 kb-fragment amplified from the RG IV isolates was specifically hybridized with PCR fragments amplified from genomic DNAs of the RG IV isolates only, suggesting that this PCR product could be used for discriminating the RG IV isolates from the RG I isolates as well other fungal species.

• Mycobiology
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• v.45 no.2
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• pp.105-109
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• 2017

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

• Molecular & Cellular Toxicology
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• v.1 no.2
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• pp.73-77
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• 2005

Nickel is the one of potent environmental, the occupational pollutants and the classified human carcinogens. It is a serious hazard to human health, when the metal exposure. To prevent human diseases from the heavy metals, it is seemingly important that understanding of how nickel exerts their toxicity and carcinogenic effect at a molecular and a genomic level. The process of nickel absorption has been demonstrated as phagocytosis, iron channel and diffusion. Uptaked nickel has been suggested to induce carcinogenesis via two pathways, a direct DNA damaging pathway and an indirect DNA damaging pathway. The former was originated from the ability of metal to generate Reactive Oxygen Species (ROS) and the reactive intermediates to interact with DNA directly. Ni-generated ROS or Nickel itself, interacts with DNAs and histones to cause DNA damage and chromosomal abnormality. The latter was originated from an indirect DNA damage via inhibition of DNA repair, or condensation and methylation of DNA. Cells have ability to protect from the genotoxic stresses by changing gene expression. Microarray analysis of the cells treated with nickel or nickel compounds, show the specific altered gene expression profile. For example, HIF-I (Hypoxia-Inducible Factor I) and p53 were well known as transcription factors, which are upregulated in response to stress and activated by both soluble and insoluble nickel compounds. The induction of these important transcription factors exert potent selective pressure and leading to cell transformation. Genes of metallothionein and family of heat shock proteins which have been known to play role in protection and damage control, were also induced by nickel treatment. These gene expressions may give us a clue to understand of the carcinogenesis mechanism of nickel. Further discussions on molecular and genomic, are need in order to understand the specific mechanism of nickel toxicity and carcinogenicity.

• Journal of Science and Technology Studies
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• v.16 no.2
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• pp.33-63
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• 2016

This paper compares and contrasts the concept of nature and the theory of evolution held by leading synthetic biologists and transhumanists in the post-genomic era. Synthetic biology, which emerged in the early 2000s, aims to design biological systems that perform specific functions with the two key concepts of "rational design" and "directed evolution". However, synthetic biology has also raised serious concerns about the creation of man-made biological materials and the manipulation of the direction and speed of evolution. It is no wonder that transhumanists, who dream of creating new, enhanced human species, have welcomed the arrival of synthetic biology. How, then, can we deal with the nature reinvented by synthetic biology? By what means can one justify research that may affect the process of evolution? What intellectual resources do synthetic biology and transhumanism share in common? What influence would the new trend of commercialization of science and technology exert upon the development of synthetic biology? Addressing those questions, this paper argues that the moral authority of nature can be restored in this post-genomic era.