• Animal Bioscience
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• v.36 no.9
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• pp.1357-1366
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• 2023

Objective: This study aimed to identify the single-nucleotide polymorphisms (SNPs) in the dual-specificity phosphatase 8 (DUSP8) and insulin-like growth factor 2 (IGF2) genes and to explore their effects on inosine-5'-monophosphate (IMP), inosine, and hypoxanthine contents in Korean native chicken -red-brown line (KNC-R Line). Methods: A total sample of 284 (males, n = 127; females n = 157) and 230 (males, n = 106; females, n = 124) aged of 10 weeks old KNC-R line was used for genotyping of DUSP8 and IGF2 genes, respectively. One SNP (rs313443014 C>T) in DUSP8 gene and two SNPs (rs315806609A/G and rs313810945T/C) in IGF2 gene were used for genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and KASP methods, respectively. The Two-way analysis of variance of the R program was used to associate DUSP8 and IGF2 genotypes with nucleotide contents in KNC-R chickens. Results: The DUSP8 (rs313443014 C>T) was polymorphic in KNC-R line and showed three genotypes: CC, CT, and TT. The IGF2 gene (rs315806609A/G and rs313810945T/C) was also polymorphic and had three genotypes per SNP, including GG, AG, and AA for the SNP rs315806609A/G and genotypes: CC, CT, and TT for the SNP rs313810945T/C. Association resulted into a strong significant association (p<0.01) with IMP, inosine, and hypoxanthine. Moreover, the significant effect of sex (p<0.05) on nucleotide content was also observed. Conclusion: The SNPs in the DUSP8 and IGF2 genes might be used as genetic markers in the selection and production of chickens with highly flavored meat.

• Journal of Crop Science and Biotechnology
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• v.10 no.4
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• pp.249-256
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• 2007

A study was conducted to observe the variation and inheritance of agronomic traits and their interrelationship in mungbean. The objective of the study was to compare agronomic traits and hardseed percentage of 268 recombinant inbred lines(RILs) developed from the cross between wild Vigna subspecies sublobata "ACC 41" with the mungbean cultivar "Berken". The RIL population and their parents were evaluated under controlled conditions in a glass house at the University of Queensland, Brisbane, Australia. The results showed significant differences among the RILs and among the parents in all traits under study. Berken had a longer flowering date and a higher seed weight per plant, but less total leaf number and pod number per plant than ACC 41. A germination test between papers revealed that ACC 41 was 100% hard-seeded and did not germinate at all, while Berken germinated up to 100%. Their RILs distributed well between 0 to 100% hardseed. Upon scarification, all hardseed germinated within seven days. Narrowsense heritability estimates of total leave number, hardseedness, pod length, and pod width were highly heritable at 89.9, 98.9, 93.7, and 93.2%, respectively. The heritability of seed weight per plant and number of seeds per plant were lower at 63.1 and 58.4%, respectively. Seed weight per plant showed positive transgressive segregation when compared with ACC 41 and a positive correlation with 100 seed weight. While the number of seeds per pod showed a negative transgressive segregation when compared with Berken and a negative correlation with pod length and pod width. The RILs gave a 1:1 segregation ratio in leaflet shape, growth habit, and growth pattern, indicating that these traits were controlled by a single dominant gene.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.45 no.1
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• pp.55-58
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• 2000

Germination of sweet and super sweet corn is lower than normal corn due to the higher sugar and lower starch contents of kernels. Sweet corn seeds are easily deteriorated in the field under the unfavorable condition, therefore it is important to identify the optimal harvesting time for seed production. This trial was conducted to investigate the responses of germination percentage of shrunken-2(sh2), brittle(bt), sugary(su), and sugary enhancer(se) hybrids in relation to harvesting dates. Eight hybrids of four different gene sweet corns were harvested at 15, 20, 25, 30, 35, 40, 45, and 50 days after silking(DAS). Germination test was performed using paper towel method. Mean germination percentages across eight hybrids showed the highest value at 45 DAS. There were significant differences among genes and within gene for germination. Shrunken-2 hybrid Mecca was higher than su hybrids for germination, indicating that sh2 would not be poorer than su Late harvesting beyond the optimal harvesting date might not be desirable because of more lodging and ear rots. Theoretical optimal harvesting date estimated from the regression equation was 40.9 DAS, however, practical date for harvesting would be a few days later than the estimated date if seedling vigor might be considered. Kernel dry weight per ear showed similar response to germination. Regression equation showed the highest kernel dry weight at 40.7 DAS. Significant correlations between kernel dry weight and germination were observed, impling that kernel dry matter accumulation would be an important factor for germination.

• Journal of Plant Biotechnology
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• v.48 no.2
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• pp.93-99
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• 2021

This study was conducted to develop an Agrobacterium-mediated genetic transformation protocol for the carnation cv. "Jinju" to counteract its ethylene sensitivity. The new protocol involves the use of an improved shoot regeneration medium, optimized minimal concentrations of the selective agent, a pre-culture period, and co-cultivation periods. Silver nanoparticles (NAg) added at a concentration of 2.0 μM to the Murashige and Skoog (MS) basal shoot regeneration medium supplemented with 0.1 mg/L indole-3-butyric-acid (IBA) and 0.2 mg/L thidiazuron (TDZ) improved the shoot regeneration efficiency, number of shoots per explant, and plant growth compared to the control without the addition of NAg. The phosphinothricin (PPT) concentration of 1.0 mg/L was determined to be the minimal and optimal concentration for the selection of putative transgenic plants. When the explants were infected with Agrobacterium cells harboring the acdS gene, the explants that were pre-cultured for three days induced more putative transgenic plants than those that were co-cultivated for four days. Therefore, we expect that the results of this study will benefit researchers who are developing genetic transformations of carnations.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.2
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• pp.163-169
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• 2001

Despite the high potency of the retrovirus vector system in gene transfer, one of the main drawbacks of has been difficulty in preparing highly concentrated virus stock. Numerous efforts to boost the virus titer have ended in unsatisfactory results mainly due to fragile property of retrovirus envelope protein. In this study, to overcome this problem, we constructed our own retrovirus vector system producing vector viruses encapsulated with VSV-G (vesicular stomatitis virus G glycoprotein). Concentration process of the virus stock by ultracentrifuge did not sacrifice the virus infectivity, resulting in more than 108 to 109 CFU (colony forming unit) per ml on most of the target cell lines tested. Application of this high-titer retrovirus vector system was tested on chicken embryos. Injection of virus stock beneath the blastoderms of pre-incubated fertilized eggs resulted in chick embryos expressing E. coli LacZ gene with 100% efficiency. Therefore, our results suggest that it is possible to transfer the foreign gene into chicken embryo using our high-titer retrovirus vector.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.1
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• pp.36-42
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• 2013

The average twin lambing rate of Bayanbulak sheep is 2% to 3%. However, a flock of sheep with a close genetic relationship and an average of 2 to 3 lambs per birth has been found recently. To determine the major genes controlling the prolificacy of the flock in the present study, the flock was designated A while 100 normal Bayanbulak sheep were randomly selected to comprise the control flock B. Ligase detection reaction method was applied to detect and analyze the 10 mutational loci of the 3 candidate prolificacy genes including bone morphogenetic protein type I receptors, bone morphogenetic protein 15, and growth differentiation factor 9. The 10 mutational loci are as follows: FecB locus of the BMPR-IB gene; $FecX^I$, $FecX^B$, $FecX^L$, $FecX^H$, $FecX^G$, and $FecX^R$ of the BMP15 gene; and G1, G8, and FecTT of the GDF9 gene. Two mutations including BMPR-IB/FecB and GDF9/G1 were found in Bayanbulak sheep. Independence test results of the two flocks demonstrate that the FecB locus has a significant effect on the lambing number of Bayanbulak sheep. However, the mutation frequency of the G1 locus in GDF9 is very low. Independence test results demonstrate that the GDF9 locus does not have a significant impact on the lambing performance of Bayanbulak sheep. Among the 10 detected loci, BMPR-IB/FecB is the major gene that influences the high lambing rate of Bayanbulak sheep.

• Toxicological Research
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• v.22 no.2
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• pp.87-93
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• 2006

The KFDA (Korea Food & Drug Administration) has performed a collaborative toxico-genomics project since 2003. Its aim is to construct a toxicologenomic database of 12 hepatotoxic compounds from mice livers. Phenylbutazone which is non-steroidal anti-inflammatory drug was assigned. It was administered at low (0.0238 mg/kg) and at high (0.238 mg/kg) dose (5 mice per group) orally to the postnatal 6 weeks ICR mice, then the serum and liver were collected at the indicated time (6, 24 and 72 h) after administration. Serum biochemical markers for liver toxicity were measured and histopathologic studies also were carried out. The gene expression profiling was carried out by using Applied Biosystems 1700 Full Genome Expression Mouse. The 2-way ANOVA was used to find genes that reflected phenylbutazone-induced acute toxicity or dose-dependant changes. By self-organization maps (SOM), we identified groups with unique gene expression patterns, some of them are supposed to be related to phenylbutazone induced toxicity, including lipid metabolism abnormality, oxidative stress, cell death and cytoskeleton destruction.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.2
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• pp.835-838
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• 2016

Background: Lung cancer remains one of the most common cancers in the world, both in terms of new cases (about 13% of total per year) and deaths (nearly one cancer death in five), because of the high case fatality. Errors in lung cancer type or malignant growth determination lead to degraded treatment efficacy, because anticancer strategy depends on tumor morphology. Materials and Methods: We have made an attempt to evaluate effectiveness of machine learning algorithms in the task of lung cancer classification based on gene expression levels. We processed four publicly available data sets. The Dana-Farber Cancer Institute data set contains 203 samples and the task was to classify four cancer types and sound tissue samples. With the University of Michigan data set of 96 samples, the task was to execute a binary classification of adenocarcinoma and non-neoplastic tissues. The University of Toronto data set contains 39 samples and the task was to detect recurrence, while with the Brigham and Women's Hospital data set of 181 samples it was to make a binary classification of malignant pleural mesothelioma and adenocarcinoma. We used the k-nearest neighbor algorithm (k=1, k=5, k=10), naive Bayes classifier with assumption of both a normal distribution of attributes and a distribution through histograms, support vector machine and C4.5 decision tree. Effectiveness of machine learning algorithms was evaluated with the Matthews correlation coefficient. Results: The support vector machine method showed best results among data sets from the Dana-Farber Cancer Institute and Brigham and Women's Hospital. All algorithms with the exception of the C4.5 decision tree showed maximum potential effectiveness in the University of Michigan data set. However, the C4.5 decision tree showed best results for the University of Toronto data set. Conclusions: Machine learning algorithms can be used for lung cancer morphology classification and similar tasks based on gene expression level evaluation.

• Toxicological Research
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• v.21 no.3
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• pp.209-218
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• 2005

We investigated effects of recombinant human erythropoietin (rHuEPO) on profiles of mRNA transcripts in 6 male cynomolgus (M. fascicularis) monkey's spleen for 4 weeks. Six monkeys, composed of control and treatment group (Control : M1, M2, M3: Treatment : M4, M5, M6) were intravenously administered 3 times per week without or with a dose of rHuEPO 2730 IU/0.1 ml/kg. After 4 weeks rHuEPO treatment, spleen was removed for RNA isolation. Splenic gene expression was assessed using Affymetrix U133A 2.0 arrays containing 18,400 transcripts and variants, including 14,500 well-characterized human genes. Gene expression pattern was very different between individuals even in same treatment. In rHuEPO treated groups showed number of genes were up- or down-regulated (M4: 79: M5: 48; M6: 73 genes). Six genes (epidermal growth factor receptor, calgranulin A, estrogen receptor binding site associated antigen, matrix metalloproteinase 19, zinc finger and BTB domain containing 16, progestin and adipoQ receptor) were commonly expressed in rHuEPO treated group. The different individual response could be major considering factor in monkey experiment. Further study is needed to clarify the different individual response to rHuEPO in molecular level. This study will be valuable in the fundamental understanding and validation of molecular toxicology for bio-generic drugs including rHuEPO in cynomolgus monkey.

• International Journal of Industrial Entomology and Biomaterials
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• v.27 no.1
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• pp.142-158
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• 2013

The bumblebee, Bombus ignitus (Hymenoptera: Apidae), is a valuable natural resource that is widely utilized for greenhouse pollination in South Korea. Understanding the magnitude of genetic diversity and geographic relationships is of fundamental importance for long term preservation and utilization. As a first step, we sequenced a partial COI gene of mitochondrial DNA (mtDNA) corresponding to the "DNA barcode" region and the complete internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA from 88 individuals collected in nine South Korean localities. The complete ITS2 sequences were longest among known insects, ranging in size from 2,034 bp ~ 2,052 bp, harboring two duplicated 112-bp long repeats. The 658-bp long mtDNA sequences provided only six haplotypes with a maximum sequence divergence of 0.61% (4 bp), whereas the ITS sequences provided 84 sequence types with a maximum sequence divergence of 1.02% (21 sites). The combination of the current COI data with those of published data suggest that the B. ignitus in South Korea and China are genetically a large group, but those in Japan can be roughly separated into another group. Overall, a very high per generation migration ratio, a very low level of genetic fixation, and no discernable hierarchical population were found to exist among the South Korean populations of B. ignitus, which suggests panmixia. This finding is consistent with our understanding of the dispersal capability of the species.