• Journal of Life Science
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• v.26 no.4
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• pp.414-418
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• 2016

This study tested the association between genetic polymorphisms of the isocitrate dehydrogenase 3, beta subunit (IDH3B) gene and economic traits in an F₂ crossbred population of Landrace × Jeju (South Korea) Black pigs. A 304-bp insertion/deletion mutation in promoter region was screened for determining genotypes of the IDH3B gene in a total of 1,105 F₂ pigs. Three genotypes (AA, AB, and BB) were identified in the founder, F₁, and F₂ populations. Association analysis showed significant differences in carcass weights (CW), backfat thicknesses in three positions of the body (4^th-5^th ribs, BF5; 11^th-12^th ribs, BF12; 13^th rib-1^st lumbar, BFL), and carcass lengths (CL) (p<0.05), but not in meat color (MC), eye muscle area (EMA), or marbling scores (MARB) (p>0.05). The F₂ IDH3B BB homozygotes showed heavier CW (80.790±0.725 kg) and shorter CL (101.875±0.336 cm) than the other genotypes (p<0.05). In addition, the BF levels between the 4^th - 5^th and 11^th - 12^th vertebrae were thicker in the carcasses of pigs with the IDH3B BB genotype than with the other genotypes (p<0.05). These results suggested that genetic variations in the IDH3B gene may serve as molecular genetic markers for improving the Landrace × Jeju Black pig crossbreeding systems.

• Journal of Life Science
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• v.27 no.3
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• pp.295-300
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• 2017

This study examined the association between genotypes of the isocitrate dehydrogenase 3, beta subunit (IDH3B) gene and economic traits in an $F_2$ population of Duroc and Jeju (South Korea) native black pigs (JBPs). The genotypes was determined the presence/absence of a 304-bp insertion/deletion fragment in the promoter region of the IDH3B gene for JBP, Duroc, and their $F_1$ and $F_2$ progeny. Three genotypes (AA, AB and BB) were found in the $F_1$ and $F_2$ populations, but there was no AA genotype found in JBP and no BB in Duroc. Association analysis results showed the significant differences with carcass weights (CW), backfat thicknesses (BFT) and eye muscle area (EMA) (p<0.05), but not with growth traits including body weights and average daily gains at different stages, reproductive traits including teat numbers, and crude fat contents (CFAT) measured in longissimus dorsi (p>0.05). The $F_2$ pigs possessing the IDH3B BB homozygote had heavier CW ($72.92{\pm}11.133kg$), thicker BFT ($25.75{\pm}6.06mm$), and larger EMA ($23.82{\pm}4.825cm^2$) than those from the other genotypes (p<0.05). These results were estimated that there are biological roles related with IDH3B genotypes resulting development of EMA, BFT, and CW but not with intramuscular fat deposition during late period of pig production. Our findings suggest that the 304-bp insertion allele of porcine IDH3B may be a genetic marker for marker assistant selection for improving meat productivity of the Jeju Black pig and Duroc-related molecular breeding systems.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.27 no.1
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• pp.83-88
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• 1994

For the purpose of genetic stock indentification of three species of salmonid fishs and their hybrid, lactate dehydrogenase(LDH), malate dehydrogenase(MDH), isocitrate dehydrogenase(IDH), a-gylycerophosphate dehydrogenase(a-GPDH), malic enzyme(ME), 6-phospho-gluconate dehydrogenase(6-PGD), phosphoglucose isomerase(PGI) and phospho-glucomutase(PGM) from skeletal muscle, liver, heart and gill tissues in all three species were analyzed. Chum and masu salmon showed no polymorphic patterns in all isozyme loci, however rainbow trout were found to have polymorphic patterns at MDH-B, LDH and IDH loci. Especially, significant differences were found at MDH-B loci between the three species and the IDH patterns of rainbow trout were also different from the other two species. These loci therefore can be utilized as efficient genetic markers for the identification of hybrids and improve the efficiency of fish breeding. There was no difference except PGI between diploid and triploid isozyme patterns but PGI showed some potential as a marker for triploid in masu salmon.

• Korean Journal of Radiology
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• v.24 no.2
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• pp.133-144
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• 2023

Objective: Cyclin-dependent kinase inhibitor (CDKN)2A/B homozygous deletion is a key molecular marker of isocitrate dehydrogenase (IDH)-mutant astrocytomas in the 2021 World Health Organization. We aimed to investigate whether qualitative and quantitative MRI parameters can predict CDKN2A/B homozygous deletion status in IDH-mutant astrocytomas. Materials and Methods: Preoperative MRI data of 88 patients (mean age ± standard deviation, 42.0 ± 11.9 years; 40 females and 48 males) with IDH-mutant astrocytomas (76 without and 12 with CDKN2A/B homozygous deletion) from two institutions were included. A qualitative imaging assessment was performed. Mean apparent diffusion coefficient (ADC), 5th percentile of ADC, mean normalized cerebral blood volume (nCBV), and 95th percentile of nCBV were assessed via automatic tumor segmentation. Logistic regression was performed to determine the factors associated with CDKN2A/B homozygous deletion in all 88 patients and a subgroup of 47 patients with histological grades 3 and 4. The discrimination performance of the logistic regression models was evaluated using the area under the receiver operating characteristic curve (AUC). Results: In multivariable analysis of all patients, infiltrative pattern (odds ratio [OR] = 4.25, p = 0.034), maximal diameter (OR = 1.07, p = 0.013), and 95th percentile of nCBV (OR = 1.34, p = 0.049) were independent predictors of CDKN2A/B homozygous deletion. The AUC, accuracy, sensitivity, and specificity of the corresponding model were 0.83 (95% confidence interval [CI], 0.72-0.91), 90.4%, 83.3%, and 75.0%, respectively. On multivariable analysis of the subgroup with histological grades 3 and 4, infiltrative pattern (OR = 10.39, p = 0.012) and 95th percentile of nCBV (OR = 1.24, p = 0.047) were independent predictors of CDKN2A/B homozygous deletion, with an AUC accuracy, sensitivity, and specificity of the corresponding model of 0.76 (95% CI, 0.60-0.88), 87.8%, 80.0%, and 58.1%, respectively. Conclusion: The presence of an infiltrative pattern, larger maximal diameter, and higher 95th percentile of the nCBV may be useful MRI biomarkers for CDKN2A/B homozygous deletion in IDH-mutant astrocytomas.

• Journal of Korean Society of Forest Science
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• v.89 no.4
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• pp.527-535
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• 2000

Isozyme variants of 15 enzyme systems were analyzed in megagametophytes of Ginkgo biloba L. Five enzyme systems (ADH, G6PD, IDH, MPI, and UGPP) appeared to be monomorphic. Only 11 isozyme zones observed in 10 enzyme systems were polymorphic : ACON-A, FST-B, GDH-A, GOT-B, MDH-B, MDH-C, MNR-A, PGI-B, PGM-A, 6PGD-B and SKDH-B. The segregation ratio and heterogeneity at most polymorphic zones suggested that each isozyme zone was controlled by a single locus with codominant alleles, but significant deviation from 1 : 1 segregation was observed at MDH-B in pooled data. Three pairs of isozyme loci (ACON-A : MDH-B, GOT-B : PGI-B, and MNR-A : SKDH-B) were found to be weakly linked. Recombination frequencies between them ranged from 0.38 to 0.40 (p<0.05).

• Journal of Korean Society of Forest Science
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• v.85 no.3
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• pp.409-415
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• 1996

Isozyme variations in 4 enzyme systems in Pinus densiflora for. multicaulis in 31 individual trees collected throughout the country were studied by starch gel electrophoresis using haploid megagametophyte tissue to compare with those of Pinus densiflora. A minimum of 7 loci were found to code for isozymes of the enzyme systems. No variation was found at locus GOT-A; at the remaining 6 variable loci(GDH-A, GOT-B, GOT-C, IDH-A, LAP-,A, LAP-B) and 2 to 4 alleles were identified. We could not find any marker alleles to distinguish Pinus densiflora for. multicaulis from Pinus densiflora at the isozymes studied here. Allele frequency distributions at each loci were almost all the same as those of P. densiflora. The percentage of polymorphic loci(99% level), the number of alleles per locus, the observed and expected heterozygosities were 85.7, 2.3, 0.165 and 0.186%, respectively. The level of genetic diversity in Pinus densiflora for. multicaulis seemed to be less than that of P. densiflora.

• Journal of Periodontal and Implant Science
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• v.25 no.3
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• pp.487-496
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• 1995

Previous studies have demonstrated that not all A. actinomycetemcomitans produced significant level of leukotoxic factor and its leukotoxicity have associated with serotype and genetic variation. Our aim was to investigate on the interrelationship between serotype and leukotoxicity of an A. actinomycetemcomitans consisting of 13 clinically well characterized. Korean isolates and to evaluate if particular virulent clonal types of A. actinomycetemcomitans are associated with periodontal disease. For this study, 13 strains of A. actinomycetemcomitans from 6 patients with periodontal disease were isolated and identified by using a selective medium(tryptic soy agar supplemented with 10% serum, $75{\mu}g$ of bacitracin and $5{\mu}g$ of vancomycin per ml) in 10% C02 incubator for 3days with routine Gram staining, colony morphology and biochemical test..For serotyping, antisera were prepared from reference strains of 5 serotypes. (ATCC 29523,Y4, SUNY aB 67, IDH 781, IDH 1705) and then ammonium sulfate precipitation, immunoabsorption and indirect immunofluoroscent procedures were done. For analysis of leukotoxicity, sonic extract of A. actinomycetemcomitans exposed to PMN, and trypan blue was stained for counting the cell viability. Finally Southern blot analyses of genomic DNA digested with the restriction enzyme Tag I was done and the Southern blots were hybridized with the 530bp fragment, termed delta 530, originating from the ltx promoter of strain 652 and deleted from strain JP2. Also ltxA-3.1 and SC2 probe from strain JP2 were hybridized with genomic DNA fragments. Results reveal that strains isolated showed approximately equal proportions of 3 serotypes(b, d, e) and serotype b was not detected. 2 patients harbored 2 different serotypes in the same disease site. The prevalence of leukotoxic strain was 23% and there was no relationship between serotype, leukotoxicity and clinical observations. Especially virulent clonal types of Actinobacillus actinomycetemcomitan (JP2 strain) could not found. Further studies are necessary on the genetic polymorphism of leukotoxin and its relations to clinical status.

• Journal of Periodontal and Implant Science
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• v.24 no.3
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• pp.541-560
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• 1994

The present study was performed to evaluate the relationship between the serotype or the genotype of Actnobacillus actinomycetemcomitans (A. a.) and the severity of periodontal disease. Total 64 A. a. clinical isolates were sampled from 46 sites of 20 subjects classified into the group I (1 periodontally healthy subject, 2 gingivitis patients, 5 ealry adult periodontitis patients), group II (3 moderatelly adult periodontitis patients) and group III (1 advanced adult periodontitis patient, 8 RPP patients). Southern bolt hybridization (fingerprinting) patterns of the five reference strains, A. a. strain ATCC 29523 (serotype a), ATCC 29522 (Serotype b), ATCC 43719 (serotype c), IDH 781 (serotype d) and IDH 1705 (serotype e), were used as the five basic genotypic patterns (A, B, C, D, E). NT type was designated as one which did dnot represent any of those five basic types. The serotypes were determined by ELISA technique with the serum samples from pre-immunized rabbit. Based on subject-based analysis, it was noted that genotypes A and C, NT, and B, D, E were significantly related to the disease groups I, II, and III, respectively. It was also noted that both the serotypes a and c were significantly related to the disease group I and II, while serotypes were significantly related bm), and serotypes b and nd were frequently found in sites with severe attachment loss (LA>6mm). The results indicated that the significant relationship can be delineated beteen the genotypes and the serotypes of Acinobacillus actinomycetemcomitans and the periodontal disease severity. The results also indicated that genotyping can provide more detailed information on its relationship with the disease severity based on both the patient-based and the site-based analyses.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.27 no.3
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• pp.306-313
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• 1994

In order to estimate the degree of genetic divergence between the two types of finespotted flounder, Pleuronichthys cornutus which is important commercially in Japan, isozyme analysis was carried out by starch gel electrophoresis. Twenty two loci coding for fourteen enzymes were scored in two types of finespotted flounder and three completely divergent loci (Acp, Idh-2 and Mdh-2), with no common alleles, were observed between these two types. Nei's genetic distance between two types was 0.46592. However, the expected average heterozygosity was 0.120 in type A (Hon meitagarei) and 0.095 in type B (Bake meitagarei) These results mean that the existence of two types of finespotted flounder was established in this study which may have had genetic divergence and the divergence time of these two types may have been about $2.3{\times}10^6$ years ago.

• Journal of Microbiology and Biotechnology
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• v.32 no.3
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• pp.365-377
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• 2022

Mammalian target of rapamycin (mTOR) is a serine-threonine kinase member of the cellular phosphatidylinositol 3-kinase (PI3K) pathway, which is involved in multiple biological functions by transcriptional and translational control. mTOR is a downstream mediator in the PI3K/Akt signaling pathway and plays a critical role in cell survival. In cancer, this pathway can be activated by membrane receptors, including the HER (or ErbB) family of growth factor receptors, the insulin-like growth factor receptor, and the estrogen receptor. In the present work, we congregated an electronic network of mTORC1 built on an assembly of data using natural language processing, consisting of 470 edges (activations/interactions and/or inhibitions) and 206 nodes representing genes/proteins, using the Cytoscape 3.6.0 editor and its plugins for analysis. The experimental design included the extraction of gene expression data related to five distinct types of cancers, namely, pancreatic ductal adenocarcinoma, hepatic cirrhosis, cervical cancer, glioblastoma, and anaplastic thyroid cancer from Gene Expression Omnibus (NCBI GEO) followed by pre-processing and normalization of the data using R & Bioconductor. ExprEssence plugin was used for network condensation to identify differentially expressed genes across the gene expression samples. Gene Ontology (GO) analysis was performed to find out the over-represented GO terms in the network. In addition, pathway enrichment and functional module analysis of the protein-protein interaction (PPI) network were also conducted. Our results indicated NOTCH1, NOTCH3, FLCN, SOD1, SOD2, NF1, and TLR4 as upregulated proteins in different cancer types highlighting their role in cancer progression. The MCODE analysis identified gene clusters for each cancer type with MYC, PCNA, PARP1, IDH1, FGF10, PTEN, and CCND1 as hub genes with high connectivity. MYC for cervical cancer, IDH1 for hepatic cirrhosis, MGMT for glioblastoma and CCND1 for anaplastic thyroid cancer were identified as genes with prognostic importance using survival analysis.