• Journal of Ginseng Research
• /
• v.44 no.1
• /
• pp.161-167
• /
• 2020

Background: The ascomycete fungi Cylindrocarpon destructans (Cd) and Fusarium solani (Fs) cause ginseng root rot and significantly reduce the quality and yield of ginseng. Cd produces the secondary metabolite radicicol, which targets the molecular chaperone Hsp90. Fs is resistant to radicicol, whereas other fungal genera associated with ginseng disease are sensitive to it. Radicicol resistance mechanisms have not yet been elucidated. Methods: Transcriptome analyses of Fs and Cd mycelia treated with or without radicicol were conducted using RNA-seq. All of the differentially expressed genes (DEGs) were functionally annotated using the Fusarium graminearum transcript database. In addition, deletions of two transporter genes identified by RNA-seq were created to confirm their contributions to radicicol resistance. Results: Treatment with radicicol resulted in upregulation of chitin synthase and cell wall integrity genes in Fs and upregulation of nicotinamide adenine dinucleotide dehydrogenase and sugar transporter genes in Cd. Genes encoding an ATP-binding cassette transporter, an aflatoxin efflux pump, ammonium permease 1 (mep1), and nitrilase were differentially expressed in both Fs and Cd. Among these four genes, only the ABC transporter was upregulated in both Fs and Cd. The aflatoxin efflux pump and mep1 were upregulated in Cd, but downregulated in Fs, whereas nitrilase was downregulated in both Fs and Cd. Conclusion: The transcriptome analyses suggested radicicol resistance pathways, and deletions of the transporter genes indicated that they contribute to radicicol resistance.

• Molecules and Cells
• /
• v.38 no.12
• /
• pp.1054-1063
• /
• 2015

Mitochondria play a crucial role in eukaryotic cells; the mitochondrial electron transport chain (ETC) generates adenosine triphosphate (ATP), which serves as an energy source for numerous critical cellular activities. However, the ETC also generates deleterious reactive oxygen species (ROS) as a natural byproduct of oxidative phosphorylation. ROS are considered the major cause of aging because they damage proteins, lipids, and DNA by oxidation. We analyzed the chronological life span, growth phenotype, mitochondrial membrane potential (MMP), and intracellular ATP and mitochondrial superoxide levels of 33 single ETC component-deleted strains during the chronological aging process. Among the ETC mutant strains, 14 ($sdh1{\Delta}$, $sdh2{\Delta}$, $sdh4{\Delta}$, $cor1{\Delta}$, $cyt1{\Delta}$, $qcr7{\Delta}$, $qcr8{\Delta}$, $rip1{\Delta}$, $cox6{\Delta}$, $cox7{\Delta}$, $cox9{\Delta}$, $atp4{\Delta}$, $atp7{\Delta}$, and $atp17{\Delta}$) showed a significantly shorter life span. The deleted genes encode important elements of the ETC components succinate dehydrogenase (complex II) and cytochrome c oxidase (complex IV), and some of the deletions lead to structural instability of the membrane-$F_1F_0$-ATP synthase due to mutations in the stator stalk (complex V). These short-lived strains generated higher superoxide levels and produced lower ATP levels without alteration of MMP. In summary, ETC mutations decreased the life span of yeast due to impaired mitochondrial efficiency.

• Journal of Ginseng Research
• /
• v.45 no.1
• /
• pp.149-155
• /
• 2021

Background: We have reported that internal deletions in the nef, gag, and pol genes in HIV-1-infected patients are induced in those treated with Korean Red Ginseng (KRG). KRG delays the development of resistance mutations to antiretroviral drugs. Methods: The vif-vpr genes over 26 years in 20 hemophiliacs infected with HIV-1 from a single source were sequenced to investigate whether vif-vpr genes were affected by KRG and KRG plus highly active antiretroviral therapy (ART) (hereafter called GCT) and compared the results with our previous data. Results: A significantly higher number of in-frame small deletions were found in the vif-vpr genes of KRG-treated patients than at the baseline, in control patients, and in ART-alone patients (p < 0.001). These were significantly reduced in GCT patients (p < 0.05). In contrast, sequences harboring a premature stop codon (SC) were more significant in GCT patients (10.1%) than in KRG-alone patients, control (p < 0.01), and ART-alone patients (p = 0.078 for peripheral blood mononuclear cells). The proportion of SC in Vpr was similar to that in Vif, whereas the proportion of sequences revealing SC in the env-nef genes was significantly lower than that in the pol-vif-vpr genes (p < 0.01). The genetic distance was 1.8 times higher in the sequences harboring SC than in the sequences without SC (p < 0.001). Q135P in the vif gene is significantly associated with rapid progression to AIDS (p < 0.01). Conclusion: Our data show that KRG might induce sD in the vif-vpr genes and that vif-vpr genes are similarly affected by lethal mutations.

• Journal of Genetic Medicine
• /
• v.21 no.1
• /
• pp.22-30
• /
• 2024

Purpose: Neurofibromatosis 1 (NF1) is one of the most common autosomal dominant diseases caused by heterozygous mutation in the NF1 gene. Mutation detection is complex owing to the large size of the NF1 gene, the presence of a high number of partial pseudogenes, and the great variety of mutations. We aimed to study the mutation spectrum of NF1 gene in Korean patients with NF1. Materials and Methods: We have analyzed total 69 unrelated patients who were clinically diagnosed with NF1. PCR and sequencing of the NF1 gene was performed in all unrelated index patients. Additionally, multiplex ligation-dependent probe amplification (MLPA) test of the NF1 and SPRED1 gene analysis (sequencing and MLPA test) were performed in patients with negative results from NF1 gene sequencing analysis. Results: Fifty-five different variants were identified in 60 individuals, including six novel variants. The mutations included 36 single base substitutions (15 missense and 21 nonsense), eight splicing mutations, 13 small insertion or deletions, and three gross deletions. Most pathogenic variants were unique. The mutations were evenly distributed across exon one through 58 of NF1, and no mutational hot spots were found. When fulfilling the National Institutes of Health criterion for the clinical diagnosis of NF1, the detection rate was 84.1%. Cafe-au-lait macules were observed in all patients with NF1 mutations. There is no clear relationship between specific mutations and clinical features. Conclusion: This study revealed a wide spectrum and genetic basis of patients with NF1 in Korea. Our results aim to contribute genetic management and counseling.

• Journal of Genetic Medicine
• /
• v.5 no.1
• /
• pp.15-20
• /
• 2008

Purpose : Large exon deletions in the DMD gene are found in about 60% of DMD/BMD patients. Multiplex PCR has been employed to detect the deletion mutation, which frequently generates noise PCR products due to the presence of multiple primers in a single reaction as well as the stringency of PCR conditions. This often leads to a false-negative or false-positive result. To address this problematic issue, we introduced the dual primer oligonucleotide (DPO) system. DPO contains two separate priming regions joined by a polydeoxyinosine linker that results in high PCR specificity even under suboptimal PCR conditions. Methods : We tested 50 healthy male controls, 50 patients with deletion mutation as deletion-positive patient controls, and 20 patients with no deletions as deletion-negative patient controls using DPO-multiplex PCR. Both the presence and extent of deletion were verified by simplex PCR spanning the promoter region (PM) and 18 exons including exons 3, 4, 6, 8, 12, 13, 17, 19, 43-48, 50-52, and 60 in all 120 controls. Results : DPO-multiplex PCR showed 100% sensitivity and specificity for the detection a deletion. However, it showed 97.1% sensitivity and 100% specificity for determining the extent of deletions. Conclusion : The DPO-multiplex PCR method is a useful molecular test to detect large deletions of DMD for the diagnosis of patients with DMD/BMD because it is easy to perform, fast, and cost-effective and has excellent sensitivity and specificity.

• Journal of Korean Neurosurgical Society
• /
• v.57 no.4
• /
• pp.295-297
• /
• 2015

We report the case of 57-year-old woman diagnosed with Charcot-Marie-Tooth (CMT) disease and lumbar disk herniation (LDH). She had left leg weakness and foot numbness, foot deformity (muscle atrophy, high arch, and clawed toes). The lumbar spine MRI showed LDH at L4-5. Additionally, electrophysiology results were consistent with chronic peripheral motor-sensory polyneuropathy (axonopathy). In genetic testing, 17p11.2-p12 duplication/deletions characteristic of CMT disease were observed. We confirmed the patient's diagnosis as CMT disease and used conservative treatment.

• Proceedings of the Computational Structural Engineering Institute Conference
• /
• 2008.04a
• /
• pp.458-463
• /
• 2008

An IFC Server is a database management system that stores data complying with a standard data format, called IFC, and keeps track of data transactions, modifications, and deletions. It plays a role as an information hub for storing and sharing information between various parties involved in construction projects. There have been several efforts to develop an IFC Server, however, they suffered from slow performance and long transaction time due to a complex mapping process between IFC files and relational database structures. In this study, we aim to develop an IFC Server using an object-relational database system. Since IFC has an object-flavored data structure, we expect to have a simpler and faster mapping process from IFC to the IFC Server. This paper reviews existing studies and describes the overall framework of the OR-IFC Server.

• Proceedings of the Korean Society of Sericultural Science Conference
• /
• 2003.10a
• /
• pp.23-23
• /
• 2003

We made use of 81, 635 expressed sequence tags (ESTs) derived from 12 different cDNA libraries of Bombyx mori to identify high-quality candidate single nucleotide polymorphisms (SNPs). By PHRAP assembling, we obtained 12, 980 contigs containing 11, 531 contigs assembled by more than one reads. From 117 contig sequences, which were assembled by 1, 576 high-quality reads base-called with PHRED, we identified 101 candidate SNPs and 27 single base insertions/deletions based on a neighborhood quality standard(NQS) of SNP. (omitted)

• Communications for Statistical Applications and Methods
• /
• v.24 no.3
• /
• pp.317-324
• /
• 2017

An influence measure known as Cook's distance has been used for judging the influence of each observation on the least squares estimate of the parameter vector. The distance does not reflect the distributional property of the change in the least squares estimator of the regression coefficients due to case deletions: the distribution has a covariance matrix of rank one and thus it has a support set determined by a line in the multidimensional Euclidean space. As a result, the use of Cook's distance may fail to correctly provide information about influential observations, and we study some reasons for the failure. Three illustrative examples will be provided, in which the use of Cook's distance fails to give the right information about influential observations or it provides the right information about the most influential observation. We will seek some reasons for the wrong or right provision of information.

• Environmental Mutagens and Carcinogens
• /
• v.16 no.2
• /
• pp.117-123
• /
• 1996

This study was carried out to examine the mechanism of Arsenic cytotoxicity through several in vitro test systems. Dose-dependent decrease of cell survival by Arsenic was observed by colony forming assay. Arsenic was weak mutagenic in inducing HGPRT point mutation in CHO cells. The frequency of chromosomal aberrations increased in a dose-dependent manner and the most frequent type of chromosomal aberrations induced by Arsenic were chromatid type deletions. U!trafiltrates of culture media from CHO cells treated with Arsenic induced sister chromatid exchanges(SCE) in CHO cells and Arsenic was able to induce lipid peroxidation in CHO cells. The results suggested that the ultrafiltrates of media from CHO cells treated with Arsenic contain clastogenic factor(CF) and Iipid peroxidation might be involved in the formation of CF.