• Korean Journal of Plant Resources
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• v.32 no.5
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• pp.519-542
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• 2019

Twenty soybean cultivars developed recently were assessed using 27 insertion and deletion (InDel) markers derived from dense variation blocks (dVBs) of soybean genome. The objective of this study is to identify the distinctness and genetic relationships among a total of 169 soybean accessions including new cultivars. The genetic homology between 149 accessions in the soybean barcode system and 20 new cultivars was 61.3% on average with the range from 25.9% to 96.3%, demonstrating the versatile application of these markers for cultivars identification. The phylogenic analysis revealed four subgroups related to their usage. The 80% of cultivars for vegetable and early maturity and the 65.9% of cultivars for bean sprouts were clustered in subgroup I-2 and II-2, respectively, indicating of the limited gene pools of their crossing parents in breeding. On the other hands, the cultivars for soy sauce and tofu with considerable gene flow by genome reshuffling were distributed evenly to several subgroups, I-1 (44.4%), I-2 (26.4%) and II-2 (23.6%). We believe that the 27 InDel markers specific to dVBs can be used not only for cultivar identification and genetic diversity, but also in breeding purposes such as introduction of genetic resources and selection of breeding lines with target traits.

• Journal of Life Science
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• v.32 no.12
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• pp.947-955
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• 2022

Silkworms, which have recently shown promise as functional health foods, show functional differences between varieties; therefore, the need for variety identification is emerging. In this study, we analyzed the whole silkworm genome to identify 10 unique silkworm varieties (Baekhwang, Baekok, Daebaek, Daebak, Daehwang, Goldensilk, Hansaeng, Joohwang, Kumkang, and Kumok) using single nucleotide polymorphisms (SNP) present in the genome as biomarkers. In addition, nine SNPs were selected to discriminate between varieties by selecting SNPs specific to each variety. We subsequently created a decision tree capable of cross-verifying each variety and classifying the varieties through sequential analysis. Restriction fragment length polymorphism (RFLP) was used for SNP867 and SNP9183 to differentiate between the varieties of Daehwang and Goldensilk and between Kumkang and Daebak, respectively. A tetra-primer amplification refractory (T-ARMS) mutation was used to analyze the remaining SNPs. As a result, we could isolate the same group or select an individual variety using the nine unique SNPs from SNP780 to SNP9183. Furthermore, nucleotide sequence analysis for the region confirmed that the alleles were identical. In conclusion, our results show that combining SNP analysis of the whole silkworm genome with the decision tree is of high value as a discriminative marker for classifying silkworm varieties.

• Korean Journal of Psychosomatic Medicine
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• v.31 no.2
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• pp.108-117
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• 2023

Objectives : Somatic symptom disorder (SSD) is characterized by the manifestation of a variety of physical symptoms, but little is known about differences in autonomic nervous system activity according to symptom severity, especially within patient groups. In this study, we examined differences in heart rate variability (HRV) across symptom severity in a group of SSD patients to analyze a representative marker of autonomic nervous system changes by symptoms severity. Methods : Medical records were retrospectively reviewed for patients who were diagnosed with SSD based on DSM-5 from September 18, 2020 to October 29, 2021. We applied inverse probability of treatment weighting (IPTW) methods to generate more homogeneous comparisons in HRV parameters by correcting for selection biases due to sociodemographic and clinical characteristic differences between groups. Results : There were statistically significant correlations between the somatic symptom severity and LF (nu), HF (nu), LF/HF, as well as SD1/SD2 and Alpha1/Alpha2. After IPTW estimation, the mild to moderate group was corrected to 27 (53.0%) and the severe group to 24 (47.0%), and homogeneity was achieved as the differences in demographic and clinical characteristics were not significant. The analysis of inverse probability weighted regression adjustment model showed that the severe group was associated with significantly lower RMSSD (β=-0.70, p=0.003) and pNN20 (β=-1.04, p=0.019) in the time domain and higher LF (nu) (β=0.29, p<0.001), lower HF (nu) (β=-0.29, p<0.001), higher LF/HF (β=1.41, p=0.001), and in the nonlinear domain, significant differences were tested for SampEn15 (β=-0.35, p=0.014), SD1/SD2 (β=-0.68, p<0.001), and Alpha1/Alpha2 (ß=0.43, p=0.001). Conclusions : These results suggest that differences in HRV parameters by SSD severity were showed in the time, frequency and nonlinear domains, specific parameters demonstrating significantly higher sympathetic nerve activity and reduced ability of the parasympathetic nervous system in SSD patients with severe symptoms.

• Journal of Nutrition and Health
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• v.57 no.1
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• pp.53-64
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• 2024

Purpose: Mitochondria play a crucial role in preserving skeletal muscle mass, and damage to mitochondria leads to muscle mass loss. This study investigated the effects of oxypeucedanin hydrate, a furanocoumarin isolated from Angelica dahurica radix, on myogenesis and mitochondrial function in vitro and in zebrafish models. Methods: C2C12 myotubes cultured in media containing 0.1, 1, 10, or 100 ng/mL oxypeucedanin hydrate were immunostained with myosin heavy chain (MHC), and then multinucleated MHC-positive cells were counted. The expressions of markers related to muscle differentiation, muscle protein degradation, and mitochondrial function were determined by quantitative reverse transcription polymerase chain reaction. To investigate the effects of oxypeucedanin hydrate on mitochondrial dysfunction, Tg(Xla.Eef1a1:mito-EGFP) zebrafish embryos were treated with 5-fluorouracil, leucovorin, and irinotecan (FOLFIRI) with or without oxypeucedanin hydrate and analyzed for mito-EGFP intensity and mitochondrial length. Results: Oxypeucedanin hydrate significantly increased MHC-positive multinucleated myotubes (≥ 3 nuclei) and increased the expression of the myogenic marker myosin heavy chain 4. However, it decreased the expressions of muscle-specific RING finger protein 1 and muscle atrophy f-box (markers of muscle protein degradation). Furthermore, oxypeucedanin hydrate enhanced the expressions of markers of mitochondrial biogenesis (peroxisome proliferator-activated receptor-gamma coactivator 1 alpha, transcription factor a mitochondrial, succinate dehydrogenase complex flavoprotein subunit A, and cytochrome c oxidase subunit 1) and mitochondrial fusion (optic atrophy 1). However, it reduced the expression of dynamin-related protein 1 (a mitochondrial fission regulator). Consistently, oxypeucedanin hydrate reduced FOLFIRI-induced mitochondrial dysfunction in the skeletal muscles of zebrafish embryos. Conclusion: The study indicates that oxypeucedanin hydrate promotes myogenesis by improving mitochondrial function, and thus, suggests oxypeucedanin hydrate has potential use as a nutritional supplement that improves muscle mass and function.

• Tuberculosis and Respiratory Diseases
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• v.53 no.5
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• pp.497-509
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• 2002

Background : The mechanisms through which cellular activation results in intracellular mycobacterial killing is only partially understood. However, in vitro studies of human immunity to Mycobacterium tuberculosis have been largely modeled on the work reported by Crowle, which is complicated by several factors. The whole blood culture is simple and allows the simultaneous analysis of the relationship between bacterial killing and the effect of effector cells and humoral factors. In this study, we attempted to determine the extent to which M. tuberculosis is killed in a human whole blood culture and to explore the role of the host and microbial factor in this process. Methods : The PPD positive subject were compared to the umbilical cord blood and patients with tuberculosis, diabetes and lung cancer. The culture is performed using heparinized whole blood diluted with a culture medium and infected with a low number of M. avium or M. tuberculosis $H_{37}Ra$ for 4 days by rotating the culture in a $37^{\circ}C$, 5% $CO_2$ incubator. In some experiments, methlprednisolone- or pentoxifyline were used to inhibit the immune response. To assess the role of the T-cell subsets, CD4+, CD8+ T-cells or both were removed from the blood using magnetic beads. The ${\Delta}$ log killing ratio was defined using a CFU assay as the difference in the log number of viable organisms in the completed culture compared to the inoculum. Results : 1. A trend was noted toward the improved killing of mycobacteria in PPD+ subjects comparing to the umbilical cord blood but there was no specific difference in the patients with tuberculosis, diabetes and lung cancer. 2. Methylprednisolone and pentoxifyline adversely affected the killing in the PPD+ subjects umbilical cord blood and patients with tuberculosis. 3. The deletion of CD4+ or CD8+ T-lymphocytes adversely affected the killing of M. avium and M. tuberculosis $H_{37}Ra$ by PPD+ subjects. Deletion of both cell types had an additive effect, particularly in M. tuberculosis $H_{37}Ra$. 4. A significantly improved mycobacterial killing was noted after chemotherapy in patients with tuberculosis and the ${\Delta}$ logKR continuously decreased in a 3 and 4 days of whole blood culture. Conclusion : The in vitro bactericidal assay by human whole blood culture model was settled using a CFU assay. However, the host immunity to M. tuberculosis was not apparent in the human whole blood culture bactericidal assay, and patients with tuberculosis showed markedly improved bacterial killing after anti-tuberculous chemotherapy compared to before. The simplicity of a whole blood culture facilitates its inclusion in a clinical trial and it may have a potential role as a surrogate marker in a TB vaccine trial.

• The Korean Journal of Nuclear Medicine Technology
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• v.21 no.1
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• pp.39-43
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• 2017

Purpose Thyroglobulin (Tg) is a biologic marker of differentiated thyroid carcinoma (DTC), produced by normal thyroid tissue or thyroid cancer tissue. Therefore, the Tg values of DTC patients is the most specific indicator for judging whether recurrence occur or whether the remaining thyroid cancer is present. Thyroid cancer is currently the most common cancer in Korea, of which 90% is differentiated thyroid cancer. The number of patients with thyroid disease of this application also increased, and an accurate and prompt results are required. However, the incubation time of the Tg commonly takes about 24 hours in our hospital, and the result reporting time is delayed, and We could not satisfied with the requirements of clinical departments and patients. In order to fulfill these requirements, experiments were conducted by shortening the incubation time between company B's Kit currently in use and company C's Kit used in other hospitals. Through these experiments, we could perform the correlation with the original method and shortening method, and could find the optimum reaction time to satisfy the needs of the departments and the patients, and we will improve the competitiveness with the EIA examination. Materials and Methods In September 2016, we tested 65 patients company B's kit and company C's kit by three incubation ways. First method $37^{\circ}C$ shaking 2hr/2hr, Second method RT shaking 3hr/2hr, Third method 1hr/1hr shaking at $37^{\circ}C$. Fourth method RT shaking 3hr method which is the original method of Company C's Kit. Fifth method, the incubation time was shortened under room temperature shaking 2hr, Sixth method $37^{\circ}C$ shaking 2hr. And we performed and compared the correlation and coefficient of each methods. Results As a result of performing shortening method on company B currently in use, when comparing the Original method of company B kit, First method $37^{\circ}C$ shaking 2hr/2hr was less than Tg 1.0 ng/mL and the ratio of $R^2=0.5906$, above 1.0 ng/mL In the value, $R^2=0.9597$. Second method RT shaking 3hr/2hr was $R^2=0.7262$ less than value of 1.0 ng/mL, $R^2=0.9566$ above than value of 1.0 ng/mL. Third method $37^{\circ}C$ shaking 1hr/1hr was $R^2=0.7728$ less than value of 1.0 ng/mL, $R^2=0.8904$ above than value of 1.0 ng/mL. Forth, Company C's The original method, RT shaking 3hr was $R^2=0.7542$ less than value of 1.0 ng/mL, and $R^2=0.9711$ above than value of 1.0 ng/mL. Fifth method RT shaking 2hr was $R^2=0.5477$ less than value of 1.0 ng/mL, $R^2=0.9231$ above than value of 1.0 ng/mL. Sixth method $37^{\circ}C$ shaking 2hr showed $R^2=0.2848$ less than value of 1.0 ng/mL, $R^2=0.9028$ above than value of 1.0 ng/mL. Conclusion Samples with both values of 1.0 ng/mL or higher in both of the six methods showed relatively high correlation, but the correlation was relatively low less than value of 1.0 ng/mL. Especially, the $37^{\circ}C$ shaking 2hr method of company C showed a sharp fluctuation from the low concentration value of 1.0 ng/mL or less. Therefore, we are planning to continuously test the time, equipment, incubation temperature and so on for the room temperature shaking 2hr method and $37^{\circ}C$ shaking 1hr/1hr of company C which showed a relatively high correlation. After that, we can search for an appropriate shortening method through additional experiments such as recovery test, dilution test, sensitivity test, and provide more accurate and prompt results to the department of medical treatment, It is competitive with EIA test.

• Tuberculosis and Respiratory Diseases
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• v.44 no.3
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• pp.534-546
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• 1997

Background : The p53 and retinoblastoma(Rb) tumor suppressor genes are associated with the pathogenesis of several types of human cancer. Substantial proportion of the primary lung cancers or cell lines have been reported to have the p53 and/or the Rb gene mutations. But, so far there is no report on the analysis of the Rb gene polymorphism as one of the genetic susceptibility marker. This study was undertaken to establish the gene frequencies of the polymorphic genotypes of the p53 and Rb genes in Koreans to evaluate the possible involvement of these genotypes as a risk factor of lung cancer. Methods : In this study 145 controls without previous and present tumor history and 128 lung cancer patients were subjected to analysis. The two intragenic polymorphisms of the p53 gene(exon 4/ AccII, intron 6/MspI) and one intron 17/XbaI polymorphism of the Rb gene were analysed by the method of polymersae chain reaction- restriction fragment length polymorphisms(PCR-RFLPs). The genotype of the intron 3/16 bp repeat polymorphism of p53 was determined by PCR and direct gel electrophoresis. Results : There were no significant differences in the genotype distributions of the p53 gene between lung cancer patients and controls. But heterozygotes(Arg/Pro) of the exon 4/AccII polymorphisms were slightly over-represented than controls, especially in the Kreyberg type I cancer, which was known to be associated with smoking. The intron 3/16 bp duplication and the intron 6/MspI polymorphisms were in complete linkage disequilibrium. About 95% of the individuals were homozygotes of the common alleles both in the 16 duplication and MspI polymorphisms, and no differences were deteced in the genotype distributions between lung cancer patients and controls. Overall genotype distributions of the Rb gene polymorphisms between lung cancer patients and controls were not significantly different However, the genotype distributions in the Kreyberg type I cancer were significantly different from those of controls(p = 0.0297) or adenocarcinomas(p = 0.0008). It was noticeable that 73.4% of the patients with adenocarcinomas were heterozygotes(r1/r2) whereas 39.2% of the Kreyberg type I cancer were heterozygous at this polymorphisms. In the lung cancer patients, significant differences were also noted between the high dose smokers and low dose smokers including non-smokers(p = 0.0258). The relative risk to Kreyberg type I cancer was significantly reduced in the individuals with the genotype of r1/r2(odds ratio = 0.46, 95% C.I. = 0.25-0.86, p = 0.0124). The combined genotype distribution of the exon 4 AccII of the p53 and the intron 17 Rb gene polymorphisms in Kreyberg type I cancers were significantly different from dose of controls or adenocarcinomas. The highest odds ratio were observed in the individuals with the genotypes of Arg/Pro and r2/r2(odds ratio = 1.97,95% C.I. = 0.84-4.59) and lowest one was in the patients with Arg/Arg, r1/r2 genotype(odds ratio = 0.54, 95% C.I. = 0.25-1.14). Conclusion : The p53 and the Rb gene polymorphisms modulate the risk of smoking induced lung cancer development in Koeans. However, the exact mechanism of risk modulation by these polymorphism remains to be determined. For more discrete clarification of associations between specific genotypes and lung cancer risk, the evaluations of these polymorphisms in other ethnics and more number of patients will be needed.