• Molecules and Cells
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• v.26 no.3
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• pp.314-318
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• 2008

Korean long-tailed goral (Nemorhaedus caudatus) is one of the most endangered species in South Korea. However, detailed species distribution and sex ratio data on the elusive goral are still lacking due to difficulty of identification of the species and sex in the field. The primary aim of this study was to develop an economical PCR-RFLP method to identify species using invasive or non-invasive samples from five Korean ungulates: goral (N. caudatus), roe deer (Capreolus pygargus), feral goat (Capra hircus), water deer (Hydropotes inermis) and musk deer (Moschus moschiferus). The secondary aim was to find more efficient molecular sexing techniques that may be applied to invasive or non-invasive samples of ungulate species. We successfully utilized PCR-RFLP of partial mitochondrial cytochrome b gene (376 bp) for species identification, and sex-specific amplification of ZFX/Y and AMELX/Y genes for sexing. Three species (goral, goat and water deer) showed distinctive band patterns by using three restriction enzymes (Xbal, Stul or Sspl). Three different sexing primer sets (LGL331/335 for ZFX/Y gene; SE47/48 or SE47/53 for AMELX/Y gene) produced sex-specific band patterns in goral, goat and roe deer. Our results suggest that the molecular analyses of non-invasive samples might provide us with potential tools for the further genetic and ecological study of Korean goral and related species.

• Journal of Life Science
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• v.13 no.3
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• pp.298-307
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• 2003

To figure out the conserved genes and newly added genes at each phylogenetic level of Archaea, COG (clusters of orthologous groups of proteins) algorithm was applied. The number of conserved genes within 9 species of Archaea was 340 and that of 8 species of Euryarchaeota was 388. Many of conserved 265 COGs, which are specific to Archaea and absent in Bacteria and S. cerevisiae, were concerned with 'information storage and processing' (94 COG, 35.5%) and 'metabolism' (82 COG, 30.9%). COGs related to these functions were assumed as highly conserved and permit peculiar life form to Archaea. It seemed that there was some difference in 'nucleotide transport and metabolism' and there was little difference in 'information storage and processing' between Euryarchaeota and Crenarchaeota. Marine-origin Euryarchaeota showed different conserved COGs with terrestrial Euryarchaeota. Conserved COGs, related to carbohydrate transport and metabolism and others, were different between marine- and terrestrial-origin Euryarchaeota. Hence it was assumed that their physiology might be different. This study may help to understand the origin and conserved genes at each phylogenetic level of marine-origin Euryarchaeota and may help in the mining of useful genes in marine Archaea as Manco et al. (Arch. Biochem. Biophy. 373, 182 (2000)).

• Animal Bioscience
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• v.34 no.4
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• pp.546-557
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• 2021

Objective: If fertilization does not occur within a specific period, the quality of unfertilized oocytes in the oviduct (in vivo aging) or in culture (in vitro aging) will deteriorate over time. Icariin (ICA), found in all species of Epimedium herbs, has strong antioxidant activity, and is thought to exert anti-aging effects in vitro. We asked whether ICA protects oocytes against age-related changes in vitro. Methods: We analyzed the reactive oxygen species (ROS) levels and expression of antioxidant, maternal, and estrogen receptor genes, and along with spindle morphology, and the developmental competence and quality of embryos in the presence and absence of ICA. Results: Treatment with 5 μM ICA (ICA-5) led to a significant reduction in ROS activity, but increased mRNA expression of glutathione and antioxidant genes (superoxide dismutase 1 [SOD1], SOD2, peroxiredoxin 5, and nuclear factor erythroid 2-like 2), during aging in vitro. In addition, ICA-5 prevented defects in spindle formation and chromosomal alignment, and increased mRNA expression of cytoplasmic maturation factor genes (bone morphogenetic protein 15, cyclin B1, MOS proto-oncogene, serine/threonine kinase, and growth differentiation factor-9). It also prevented apoptosis, increased mRNA expression of antiapoptotic genes (BCL2-like 1 and baculoviral IAP repeat-containing 5), and reduced mRNA expression of pro-apoptotic genes (BCL2 antagonist/killer 1 and activation of caspase-3). Although the maturation and cleavage rates were similar in all groups, the total cell number per blastocyst and the percentage of apoptotic cells at the blastocyst stage were higher and lower, respectively, in the control and ICA-5 groups than in the aging group. Conclusion: ICA protects oocytes against damage during aging in vitro; therefore, it can be used to improve assisted reproductive technologies.

• 한국균학회소식:학술대회논문집
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• 2015.11a
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• pp.41-41
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• 2015

Oomycetes belong to the kingdom Straminipila, a remarkably diverse group which includes brown algae and planktonic diatoms, although they have previously been classified under the kingdom Fungi. These organisms have evolved both saprophytic and pathogenic lifestyles, and more than 60% of the known species are pathogens on plants, the majority of which are classified into the order Peronosporales (includes downy mildews, Phytophthora, and Pythium). Recent phylogenetic investigations based on DNA sequences have revealed that the diversity of oomycetes has been largely underestimated. Although morphology is the most valuable criterion for their identification and diversity, morphological species identification is time-consuming and in some groups very difficult, especially for non-taxonomists. DNA barcoding is a fast and reliable tool for identification of species, enabling us to unravel the diversity and distribution of oomycetes. Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The mitochondrial cox2 gene has been widely used for identification, taxonomy and phylogeny of various oomycete groups. However, recently the cox1 gene was proposed as a DNA barcode marker instead, together with ITS rDNA. To determine which out of cox1 or cox2 is best suited as universal oomycete barcode, we compared these two genes in terms of (1) PCR efficiency for 31 representative genera, as well as for historic herbarium specimens, and (2) in terms of sequence polymorphism, intra- and interspecific divergence. The primer sets for cox2 successfully amplified all oomycete genera tested, while cox1 failed to amplify three genera. In addition, cox2 exhibited higher PCR efficiency for historic herbarium specimens, providing easier access to barcoding type material. In addition, cox2 yielded higher species identification success, with higher interspecific and lower intraspecific divergences than cox1. Therefore, cox2 is suggested as a partner DNA barcode along with ITS rDNA instead of cox1. Including the two barcoding markers, ITS rDNA and cox2 mtDNA, the multi-locus phylogenetic analyses were performed to resolve two complex clades, Bremia lactucae (lettuce downy mildew) and Peronospora effuse (spinach downy mildew) at the species level and to infer evolutionary relationships within them. The approaches discriminated all currently accepted species and revealed several previously unrecognized lineages, which are specific to a host genus or species. The sequence polymorphisms were useful to develop a real-time quantitative PCR (qPCR) assay for detection of airborne inoculum of B. lactucae and P. effusa. Specificity tests revealed that the qPCR assay is specific for detection of each species. This assay is sensitive, enabling detection of very low levels of inoculum that may be present in the field. Early detection of the pathogen, coupled with knowledge of other factors that favor downy mildew outbreaks, may enable disease forecasting for judicious timing of fungicide applications.

• Journal of Plant Biotechnology
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• v.49 no.3
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• pp.178-186
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• 2022

The tetraploid Solanum acaule is a wild potato species from Bolivia widely used for potato breeding because of its diverse attractive traits, including resistance to frost, late blight, potato virus X, potato virus Y, potato leafroll virus, potato spindle tuber viroid, and cyst nematode. However, the introgression of useful traits into cultivated potatoes via crossing has been limited by differences in endosperm balance number between species. Somatic fusion could be used to overcome sexual reproduction barriers and the development of molecular markers is essential to select proper fusion products. The chloroplast genome of S. acaule was sequenced using next-generation sequencing technology and specific markers for S. acaule were developed by comparing the obtained sequence with those of seven other Solanum species. The total length of the chloroplast genome is 155,570 bp, and 158 genes were annotated. Structure and gene content were very similar to other Solanum species and maximum likelihood phylogenetic analysis with 12 other species belonging to the Solanaceae family revealed that S. acaule is very closely related to other Solanum species. Sequence alignment with the chloroplast genome of seven other Solanum species revealed four InDels and 79 SNPs specific to S. acaule. Based on these InDel and SNP regions, one SCAR marker and one CAPS marker were developed to discriminate S. acaule from other Solanum species. These results will aid in exploring evolutionary aspects of Solanum species and accelerating potato breeding using S. acaule.

• Journal of Photoscience
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• v.9 no.2
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• pp.267-268
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• 2002

A vertebrate retina is an organ belonging to the central nerve system (CNS), and is usually difficult to regenerate except at an embryonic stage in life. However, certain species of urodele amphibians, such as newts and salamanders, possess the ability to regenerate a functional retina from retinal pigment epithelial (RPE) cells even as adults. After surgical removal of neural retinas from adult newt eyes, the remaining RPE cells lose their pigment granules, transdifferentiate into retinal progenitor cells, which further differentiate into various retinal neurons, and then finally reform a functional neural network. To understand the molecular mechanisms of CNS regeneration, we attempted to investigate the genes expressing in regenerating newt retina. mRNAs were isolated from regenerating retinas at 18-19 days after the surgical removal of the normal retina, and a cDNA library (regenerating retinal cDNA library) were constructed. Our EST analysis of 112 clones in the regenerating cDNA library revealed that about 70% clones are closely related to the genes previously identified. About 40% clones are housekeeping genes, and about 15% clones encode proteins related to the regulation of gene expression and to the proliferation of the cells. Sequences similar to neural retina- and RPE-specific genes were not detected at all. These results led us to suppose that the regenerating retinal cells are in a state considerably different from those of neither neural retina nor RPE cells.

• Food Science and Biotechnology
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• v.15 no.6
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• pp.967-974
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• 2006

Cyclomaltodextrinases (CDases), maitogenic amylases, and neopullulanases share highly conserved primary structures and similar characteristics, and are thus classified into the same family. BLAST search has showed that a variety of bacterial strains harbor putative CDase family genes with several well-conserved motif amino acid sequences. In this study, four degenerate polymerase chain reaction (PCR) primer sets were designed for the detection of CDase genes, on the basis of their highly conserved amino acid blocks (WYQIFP, DGWRLD, LGSHDT, and KCMVW). The PCR detection conditions were optimized and the detection specificity of each for the primer sets was tested against the genomic DNAs isolated from 23 different Bacillus-associated species. Consequently, all tested primer sets evidenced successful amplification of specific PCR products in length, which share 55-98% amino acid sequence identity with known and putative CDases. The primers developed herein, therefore, can be applied for the easy and efficient detection and isolation of CDase family genes for the modification of functional food carbohydrates.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.1
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• pp.33-38
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• 2004

This study was aimed at testing the gene expression of antioxidant enzymes and apoptosis genes for in vitro culture in porcine embryos produced by in vitro maturation/in vitro fertilization (IVM/IVF). Pocine preimplantation embryos obtainted from IVM/IVF can be successfully culture in vitro, but they are delayed or stop to develop at specific developmental stage. Many factors such as reactive oxygen species and apoptosis in an IVM/IVF system followed by in vitro culture influence the rate of production of viable blastocysts. Porcine embryos derived from IVM/IVF were cultured in the atmosphere of 5% $CO_2$ and 20% $O_2$ at $38.5^{\circ}C$ in NCSU23 medium. The patterns of gene expression for antioxidant enzymes and apoptosis genes during in vitro culture in pocine IVM/IVF embryos were examined by the modified semi-quantitative single cell reverse transcriptase-polymerase chain reaction (RT-PCR). Porcine embryos produced by in vitro procedures were expressed mRNAs for CuZn-SOD, GAPDH and GPX, whereas transcripts for Mn-SOD and catalase were not detected at any developmental stages. Expression of caspase-3 mRNA was detected at 2 cell, 8 cell 16 cell and blastocyst, but p53 mRNA was not detected at any stages. The fas transcripts was only detected in blastocyst stage. These results suggest that various antioxidant enzymes and apoptosis genes play crucial roles in vitro culture of porcine IVM/IVF embryos.

• Korean Journal of Environmental Agriculture
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• v.37 no.4
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• pp.324-332
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• 2018

BACKGROUND: Insects are ectothermic organisms in terrestrial ecosystems and play various roles such as controlling plant biomass and maintaining species diversity. Because insects are ectothermic, their physiological responses are very sensitive to environmental temperature which determines survival and distribution of insect population and that affects climate change. This study aimed to identification of genes contributing to fitness under high temperature. METHODS AND RESULTS: To identify genes contributing to fitness under high temperature, the transcriptomes of fat body in Plutella xyostella larva have been analyzed via next generation sequencing. From the fat body transcriptomes, structure-related proteins, heat shock proteins, antioxidant enzymes and detoxification proteins were identified. Genes encoding proteins such as structural proteins (cuticular proteins, chitin synthase and actin), stress-related protein (cytochrome P450), heat shock protein and antioxidant enzyme (catalase) were up-regulated at high temperature. In contrast expression of glutathione S transferase was down-regulated. CONCLUSION: Identifications of temperature-specific up- or down-regulated genes can be useful for detecting temperature adaptation and understanding physiological responses in insect pests.

• Journal of Plant Biotechnology
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• v.49 no.4
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• pp.271-291
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• 2022

Pectin methylesterase (PME) plays an important role in vegetative and reproductive development and biotic/abiotic stress responses by regulating the degree of methyl-esterification of pectic polysaccharides in the plant cell wall. PMEs are encoded by a large multigene family in higher land plant genomes. In general, the expression of plant PME genes shows tissue- or cell-specific patterns and is induced by endogenous and exogenous stimuli. In this study, we identified PME multigene family members (CsPMEs) from the sweet orange genome and report detailed molecular characterization and expression profiling in different citrus tissues and two fruit developmental stages. We also discussed the possible functional roles of some CsPME genes by comparing them with the known functions of PMEs from other plant species. We identified 48 CsPME genes from the citrus genome. A phylogenetic tree analysis revealed that the identified CsPMEs were divided into two groups/types. Some CsPMEs showed very close phylogenetic relationships with the PMEs whose functions were formerly addressed in Arabidopsis, tomato, and maize. Expression profiling showed that some CsPME genes are highly or specifically expressed in the leaf, root, flower, or fruit. Based on the phylogenetic relationships and gene expression profiling results, we suggest that some CsPMEs could play functional roles in pollen development, pollen tube growth, cross incompatibility, root development, embryo/seed development, stomata movement, and biotic/abiotic stress responses. Our results shed light on the biological roles of individual CsPME isoforms and contribute to the search for genetic variations in citrus genetic resources.