• Genomics & Informatics
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• 제18권4호
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• pp.44.1-44.7
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• 2020

The severity of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), greatly varies from patient to patient. In the present study, we explored and compared mutation profiles of SARS-CoV-2 isolated from mildly affected and severely affected COVID-19 patients in order to explore any relationship between mutation profile and disease severity. Genomic sequences of SARS-CoV-2 were downloaded from Global Initiative on Sharing Avian Influenza Data (GISAID) database. With the help of Genome Detective Coronavirus Typing Tool, genomic sequences were aligned with the Wuhan seafood market pneumonia virus reference sequence and all the mutations were identified. Distribution of mutant variants was then compared between mildly and severely affected groups. Among the numerous mutations detected, 14408C>T and 23403A>G mutations resulting in RNA-dependent RNA polymerase (RdRp) P323L and spike protein D614G mutations, respectively, were found predominantly in severely affected group (>82%) compared with mildly affected group (<46%, p < 0.001). The 241C>T mutation in the non-coding region of the genome was also found predominantly in severely affected group (p < 0.001). The 3037C>T, a silent mutation, also appeared in relatively high frequency in severely affected group compared with mildly affected group, but the difference was not statistically significant (p = 0.06). We concluded that spike protein D614G and RdRp P323L mutations in SARS-CoV-2 are associated with severity of COVID-19. Further studies will be required to explore whether these mutations have any impact on the severity of disease.

• Genomics & Informatics
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• 제7권3호
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• pp.152-158
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• 2009

Although the genetic basis for bone mineral density (BMD) has been studied by many groups so far, genes responsible for this complex trait has not been completely revealed. In order to localize quantitative trait loci (QTLs) for BMD variation in Asian population, the study was designed using a group of Mongolian population, a genetically closed population with a homogeneous lifestyle. BMD was measured at the left and right wrists and ankles using DEXA in 1,082 participants from 142 families. Genotyping of 13 polymorphic microsatellite markers on chromosome 13 (average spacing 8-9 cM) and two-point and multipoint linkage analysis were performed. In two-point linkage analysis, we identified two markers, D13S175 (6.03 cM) and D13S265 (68.73 cM) that had LOD scores greater than 1 for left ankle (LOD=2.09, LOD=1.49, respectively). We also found a marker D13S175 (6.03 cM) with a high LOD for left wrist (LOD=1.49) and the markers D13S265 (68.73 cM) and D13S217 (17.21 cM) for the right wrist (LOD= 1.82, LOD= 1.62, respectively). Among these significant marker regions, only two regions at 17 cM (13p11) and 65 cM (13q21) for the right wrist overlapped with major QTLs reported in following multipoint linkage analysis (LOD= 1.7549, LOD=1.4462, respectively). This study provides the possible evidence of the presence of QTLs affecting right wrist BMD in Mongolian populations on 13p11 and 13q21. Modest evidence was also found for genes affecting left ankle and left wrist BMD on 13p13.

• 한국약용작물학회지
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• 제21권6호
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• pp.455-460
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• 2013

Collected germplasms of five representative species belonging to Curcuma genus (C. longa, C. aromatica, C. zedoaria, C. phaeocaulis and C. kwangsiensis) were 52 samples from different farmhouse in Korea and China. To elucidate the genetic diversity among the species, 52 samples were analyzed by genomic fingerprinting method using amplified fragment length polymorphism (AFLP). AFLP results of 6 primer combinations were revealed 643 total DNA fragments and 349 polymorphic bands with the 54.3% ratio of polymorphism. In the analysis of coefficient similarity using unweight pair group method with arithmetic averages (UPGMA), 52 Curcuma germplasm lines were ranged from 0.60 to 0.99 and clustered distinct five groups according to the species and collected geographical levels. However, the result of principal coordinate analysis (PCA) by multi-variate analysis was shown significantly greater differences among species than geographical origins based on AFLP profiling data of these samples.

• Asian-Australasian Journal of Animal Sciences
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• 제19권11호
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• pp.1561-1565
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• 2006

The objective of this study was to investigate the anti-oxidative effects of taurine on sperm characteristics for in vitro storage of boar semen. Semen was randomly divided into 10 groups in conical tubes and treated with different concentrations of taurine (25-100 mM) with or without $250{\mu}M$ $H_2O_2$. The percentage of motile spermatozoa in taurine groups after 6 and 9 h were significantly higher at >94% and 87%, respectively, compared to the control group ($85.1{\pm}0.5$ and $72.4{\pm}0.3$, p<0.05). The sperm motility in taurine with $H_2O_2$ after 6 h incubation was slightly decreased compared to the taurine alone treatment, but after 9 and 12 h incubation % sperm motility dropped sharply in taurine with $H_2O_2$ ($75.3{\pm}0.3$ and $69.6{\pm}2.9$, p<0.05). For 3, 9 and 12 h incubation, sperm viability in the control was lower than in taurine groups, irrespective of taurine concentration. In eosin Y and nigrosin staining (ENS), the sperm survival rates (%) for 6 h incubation were significantly higher in 25 mM ($76.0{\pm}0.6$) and 50 mM taurine groups ($78.0{\pm}0.7$), respectively. Sperm survival rates for 9 and 12 h incubation were higher in taurine groups (${\geq}48%$ in 9 h and ${\geq}42%$ in 12 h) compared to controls ($43.0{\pm}2.1$ and $31.0{\pm}0.6$, respectively). In the hyoosmotic swelling test (HOST), sperm membrane integrity was similar to the results of sperm survival. These experiments indicate that supplementation of taurine to the semen extender can increase the sperm characteristics(motility, viability, survival and membrane integrity).

• Asian-Australasian Journal of Animal Sciences
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• 제19권11호
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• pp.1546-1550
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• 2006

The purpose of this study was to assess the genetic variation and establish the relationship amongst breeds and strains using 15 chicken specific microsatellite markers. A total of 285 unrelated DNA samples from four Korean native chicken strains (Black strain of Korean native chicken; KL, Red Brown strain of Korean native chicken; KR, Ogol strain of Korean native chicken; KS and Yellow Brown strain of Korean native chicken; KY) and three introduced chicken breeds (F strain of White Leghorn; LF, K strain of White Leghorn; LK, Rhode Island Red; RC and Cornish; CN) were genotyped to estimate within and between breed genetic diversity indices. All the loci analyzed in 15 microsatellite markers showed a polymorphic pattern and the number of alleles ranged from 5 to 14. The polymorphism information content (PIC) of UMA1019 was the highest (0.872) and that of ADL0234 was the lowest (0.562). The expected total heterozygosity (He) within breed and mean number of observed alleles ranged from 0.540 (LF) to 0.689 (KY), and from 3.47 (LK) to 6.07 (KR), respectively. The genetic variation of KR and KY were the highest and the lowest within Korean native strains, respectively. The genetic distance results showed that Korean native chicken strains were separated with the three introduced chicken breeds clustered into another group. The lowest distance (0.149) was observed between the KR and KL breeds and the highest distance (0.855) between the KR and LK breeds. The microsatellite polymorphism data were shown to be useful for assessing the genetic relationship between Korean native strains and other foreign breeds.

• 한국발생생물학회:학술대회논문집
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• 한국발생생물학회 2003년도 제3회 국제심포지움 및 학술대회
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• pp.109-109
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• 2003

Even though success in birth of live offspring from nuclear transfer(NT) using somatic cells in many species, detailed information on processes or mechanisms of development are not well known. Cytoplasm of bovine oocyte has been known to support the development of nuclear transferred embryos using nuclear donor cells from different species. Therefore, interspecies NT might be used to find answers of some questions in basic aspect of nuclear transfer In this study, we examined the developmental potential of reconstructed embryos when bovine oocyte as a cytoplasm recipient and mouse embryonic fibroblast as a nuclear donor were used. The nuclear transfer units were aliocated in Group 1 (murine block media and normal media) and Group 2. (bovine block media and normal media). NT units were not blocked at 2-cell stage regardless of types of medium. On mouse media, poor development of interspecies NT units was observed compared to bovine media. However, as NT units cultured in bovine normal medium, embryos developed over 8-cell stage. Further studies performed to increase the developmental rate in condition of antioxidant treatment. Despite low development, bovine-murine interspecies nuclear transferred embryos could develop to blastocysts and they showed that blastocyts rate of antioxidant group was superior to those of non-antioxidant group. Next, we investigated gene expression pattern which is carried out for zygotic activation. The Xist gene is expressed in female mouse embryo after zygotic activation of 4-cell stage. But interspecies nuclear transferred embryos do not express Xist gene at 4-cell stage. As a result, it is suggested that the bovine cytoplasm controls the early preimplantation development in interspecies NT However, the development of later stages might require genomic control from transferred donor nucleus. Therefore, even though the involvement of several other factors such as mitochondrial incompatibility, effective development of embryos produced by interspecies NT requires proper genomic activation of donor nucleus after overcoming the cytoplasmic control of recipient oocytes.

• Asian-Australasian Journal of Animal Sciences
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• 제21권7호
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• pp.980-987
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• 2008

The objective of this study was to investigate the effects of cell status of BOEC on development of bovine IVM/IVF embryos and gene expression in BOEC before or after culturing of embryos. The developmental rates beyond morula stage in the BOEC co-culture group was significantly higher than in the control group (p<0.05). In particular, blastocyst production in the BOEC co-culture group (28.3%) was dramatically increased compared with the control group (7.2%). In the in vitro development of bovine IVM/IVF embryos according to cell status, the developmental rates beyond morula stage in the primary culture cell (PCC) co-culture group were the highest of all experimental groups. Expression of genes related to growth (TGF-${\beta}$ EGF and IGFBP), apoptosis (Bax, Caspase-3 and p53) and antioxidation (CuZnSOD, MnSOD, Catalase and GPx) in different status cells of BOEC for embryo culture was detected by RT-PCR. While EGF gene was detected in isolated fresh cells (IFC) and PCC, TGF-${\beta}$ and IGFBP were found in IFC or PCC after use in the embryo culture, respectively. Caspase-3 and Bax genes were detected in all experimental groups regardless of whether the BOEC was used or not used in the embryo culture. However, p53 gene was found in IFC of both conditions for embryo culture and in frozen/thawed culture cells (FPCC) after use in the embryo culture. Although antioxidant genes examined were detected in all experimental groups before using for the embryo culture, these genes were not detected after use. This study indicated that the BOEC co-culture system used for in vitro culture of bovine IVF embryos can increase the developmental rates, and cell generations and status of BOEC might affect the in vitro development of bovine embryos. The BOEC monolayer used in the embryo culture did not express the growth factors (TGF-${\beta}$ and EGF) and enzymatic antioxidant genes, thereby improving embryo development in vitro.

• 농업과학연구
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• 제26권2호
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• pp.39-48
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• 1999

본 연구는 축우 품종의 유전적 다형성을 분석하여 분자유전수준에서 축우의 품종간 판별과 유전적 유사성을 구명하고자 Holstein종과 한우, Charolais종 및 한우 교잡종의 혈액에서 DNA를 추출하여, PCR(polymerase chain reaction) 기법에 의한 RAPD(random amplified polymorphic DNAs)분석을 실시하고, 소 품종간의 유사도 지수를 추정한 후 UPGMA(unweighted pair-group method using average)방법으로 유사도를 추정하였으며 그 결과를 요약하면 다음과 같다. 1. 축우 품종들로부터 추출된 genomic DNA를 1.5% agarose gel에서 전기영동한 결과, 12.2kb 이상의 단일밴드로 나타났으며, genomic DNA의 순도는 DNA 흡광도 $A_{260}$과 $A_{280}$의 비율로 측정한 결과 그 비율은 1.75~2.10이었다. 2. RAPD기법에 의한 축우 품종의 유전적 다형성을 분석한 결과, 품종판별을 위한 가장 유용한 random primer는 5'-GAC CGC TTG T-3'인 것으로 판명되었다. 3. Primer 부착 온도에 따른 band 양상에 있어서 $33.0^{\circ}C$인 경우는 약 340bp에서 Holstein종과 Charolais종에서는 band가 출현되었으나, 한우와 한우 교잡종에서는 밴드가 나타나지 않았으며, $37.5^{\circ}C$의 경우에는 340bp에서 Holstein종과 한우에서는 밴드가 나타났으나, Charolais종과 한우 교잡종에서는 band가 출현되지 않아 이들 밴드의 유무가 소 품종판별을 위한 유용한 유전적 표지로서의 이용이 가능할 것으로 사료되었다. 4. 축우 품종의 유사도 지수에 있어서는 primer 부착온도를 $33.0^{\circ}C$와 $37.5^{\circ}C$을 종합하였을때 Holstein종과 한우간에는 0.666~0.777이었으며, Charolais종간에는 0.615~0.666이었고, 한우와 Charolais종간에는 0.400~0.461로 다소 낮은 수치를 보였으나, 한우와 한우 교잡종간에는 0.857~0.888로 대체로 높은 계수를 보였다. 5. 이상의 결과를 종합하여 보면 RAPD기법에 의하여 random primer 5'-GAC CGC TTG T-3'으로 축우 품종의 판별이 가능하며, UPGMA에 의한 축우 품종의 유사도는 Holstein종과 한우 및 Charolais종간 보다는 한우와 한우 교잡종 및 Charolais종간의 유전적 유사도가 높은 것으로 나타났다.

• Molecules and Cells
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• 제37권2호
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• pp.161-171
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• 2014

In several lysosomal storage disorders, including Niemann-Pick disease Type C (NP-C), sphingolipids, including glycosphingolipids, particularly gangliosides, are the predominant storage materials in the brain, raising the possibility that accumulation of these lipids may be involved in the NP-C neurodegenerative process. However, correlation of these accumulations and NP-C neuropathology has not been fully characterized. Here we derived NP-C mice with complete and partial deletion of the Siat9 (encoding GM3 synthase) gene in order to investigate the role of ganglioside in NP-C pathogenesis. According to our results, NP-C mice with homozygotic deletion of GM3 synthase exhibited an enhanced neuropathological phenotype and died significantly earlier than NP-C mice. Notably, in contrast to complete depletion, NP-C mice with partial deletion of the GM3 synthase gene showed ameliorated NP-C neuropathology, including motor disability, demyelination, and abnormal accumulation of cholesterol and sphingolipids. These findings indicate the crucial role of GM3 synthesis in the NP-C phenotype and progression of CNS pathologic abnormality, suggesting that well-controlled inhibition of GM3 synthesis could be used as a therapeutic strategy.

• Journal of Microbiology and Biotechnology
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• 제28권8호
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• pp.1352-1359
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• 2018

Lactobacillus plantarum is a lactic acid bacterium that promotes animal intestinal health as a probiotic and is found in a wide variety of habitats. Here, we investigated the genomic features of different clusters of L. plantarum strains via pan-genomic analysis. We compared the genomes of 108 L. plantarum strains that were available from the NCBI GenBank database. These genomes were 2.9-3.7 Mbp in size and 44-45% in G+C content. A total of 8,847 orthologs were collected, and 1,709 genes were identified to be shared as core genes by all the strains analyzed. On the basis of SNPs from the core genes, 108 strains were clustered into five major groups (G1-G5) that are different from previous reports and are not clearly associated with habitats. Analysis of group-specific enriched or depleted genes revealed that G1 and G2 were rich in genes for carbohydrate utilization (${\text\tiny{L}}-arabinose$, ${\text\tiny{L}}-rhamnose$, and fructooligosaccharides) and that G3, G4, and G5 possessed more genes for the restriction-modification system and MazEF toxin-antitoxin. These results indicate that there are critical differences in gene content and survival strategies among genetically clustered L. plantarum strains, regardless of habitats.