• Journal of Genetic Medicine
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• v.13 no.2
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• pp.99-104
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• 2016

$Cant{\acute{u}}$ syndrome (CS, OMIM 239850) is a very rare autosomal dominantly inherited genetic disease characterized by congenital hypertrichosis, neonatal macrosomia, a distinct facial features such as macrocephaly, and cardiac defects. Since the first description by $Cant{\acute{u}}$ et al. in 1982, about 50 cases have been reported to date. Recently, two causative genes for CS has been found by using exome sequencing analyses: ABCC9 and KCNJ8. Most cases of clinically diagnosed CS have resulted from de novo mutations in ABCC9. In this study, we report three independent Korean children with CS resulting from de novo ABCC9 mutations. Our patients had common clinical findings such as congenital hypertrichosis, distinctive facial features. One of them showed severe pulmonary hypertension and hypertrophic cardiomyopathy, which require medical treatment. And, two patients had a history of patent ductus arteriosus. Although two of our patients had shown early motor developmental delay, it was gradually improved during follow-up periods. Although CS is quite rare, there are the concerns about development of various cardiac problems in the lifetime. Therefore, an accurate diagnosis followed by appropriate management and genetic counseling should be provided to CS patients.

• KSBB Journal
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• v.18 no.4
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• pp.294-300
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• 2003

In the previous study, we have isolated several vaginal lactobacilli from Korean woman and selected one of them (KLB12) for further study, which was indentified as Lactobacillus fermentum by sequence analysis of 16S rRNA gene. Formulated L. fermentum KLB12 can be used for ecological treatment of bacterial vaginosis. For pharmaceutical formulation, the spray-drying process is required where stress such as high temperature is routinely applied. In this study, we found that heat stress at 60$^{\circ}C$ for 20∼30min reduced the viable cell population of KLB12 by 10$\sub$6/～10$\sub$9/. However, adaptation of KLB12 cells at 52$^{\circ}C$ made them more thermotolerant upon exposure to 60$^{\circ}C$. The level of thermal protection in RSM (reconstituted skim milk) by adaptation in acid (pH 5), cold (4$^{\circ}C$), ethanol (3％), NaCI (0.3M) was also examined. Although not as efficient as the homologous stress, adaptations in both cold and NaCI gave considerable cross protection against heat stress. When chloramphenicol was added during heat adaptation, adaptation effect was abolished. This suggests that de novo protein synthesis is necessary during the adaptation process. Important changes in proteome during heat adaptation was examined with two-dimensional gel electrophoresis.

• Genomics & Informatics
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• v.19 no.1
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• pp.8.1-8.12
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• 2021

Cytorace-3 is a laboratory evolved hybrid lineage of Drosophila nasuta nasuta males and Drosophila nasuta albomicans females currently passing ~850 generations. To assess interracial hybridization effects on gene expression in Cytorace-3 we profiled the transcriptomes of mature ovaries and testes by employing Illumina sequencing technology and de novo transcriptome assembling strategies. We found 26% of the ovarian, and 14% of testis genes to be differentially expressed in Cytorace-3 relative to the expressed genes in the parental gonadal transcriptomes. About 5% of genes exhibited additive gene expression pattern in the ovary and 3% in the testis, while the remaining genes were misexpressed in Cytorace-3. Nearly 772 of these misexpressed genes in the ovary and 413 in the testis were either over-or under-dominant. Genes following D. n. nasuta dominance was twice (270 genes) than D. n. albomicans dominance (133 genes) in the ovary. In contrast, only 105 genes showed D. n. nasuta dominance and 207 showed D. n. albomicans dominance in testis transcriptome. Of the six expression inheritance patterns, conserved inheritance pattern was predominant for both ovary (73%) and testis (85%) in Cytorace-3. This study is the first to provide an overview of the expression divergence and inheritance patterns of the transcriptomes in an independently evolving distinct hybrid lineage of Drosophila. This recorded expression divergence in Cytorace-3 surpasses that between parental lineages illustrating the strong impact of hybridization driving rapid gene expression changes.

• Vascular Specialist International
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• v.34 no.4
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• pp.88-93
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• 2018

Purpose: This study aimed to compare surgical revisions and balloon angioplasty after surgical thrombectomy on thrombosed dialysis access as a first event. Materials and Methods: Records of patients undergoing creation of arteriovenous grafts (AVGs) at the Gachon University Gil Medical Center between March 2008 and February 2016 were reviewed. Among them, patients who underwent treatment on first-time thrombotic occlusion after AVG creation were identified. Outcomes were primary, primary-assisted, and secondary patency. The patency was generated using the Kaplan-Meier method, and patency rates were compared by log-rank test. Results: A total of 59 de novo interventions (n=26, hybrid interventions; n=33, surgical revisions) for occlusive AVGs were identified. The estimated 1-year primary patency rates were 47% and 30% in the surgery and hybrid groups, respectively. The estimated primary patency rates were not different between the two groups (log-rank test, P=0.73). The Kaplan-Meier estimates of 6 and 12 months for primary-assisted patency rates were 68% and 57% in the surgery group and 56% and 56% in the hybrid group. The Kaplan-Meier estimates of 12 and 24 months secondary patency rates were 90% and 71% in the surgery group and 79% and 62% in the hybrid group. There were no differences in the estimated primary-assisted and secondary patency rates between the two groups. Conclusion: Our results showed no significant difference between the two groups in terms of primary patency (P=0.73), primary-assisted patency (P=0.85), and secondary patency (P=0.78). However, percutaneous transluminal angioplasty can give more therapeutic options for both surgeons and patients.

• Clinical and Experimental Pediatrics
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• v.62 no.5
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• pp.193-197
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• 2019

Alport syndrome (ATS) is an inherited glomerular disease caused by mutations in one of the type IV collagen novel chains (${\alpha}3$, ${\alpha}4$, and ${\alpha}5$). ATS is characterized by persistent microscopic hematuria that starts during infancy, eventually leading to either progressive nephritis or end-stage renal disease. There are 3 known genetic forms of ATS, namely X-linked ATS, autosomal recessive ATS, and autosomal dominant ATS. About 80% of patients with ATS have X-linked ATS, which is caused by mutations in the type IV collagen ${\alpha}5$ chain gene, COL4A5. Although an 80% mutation detection rate is observed in men with X-linked ATS, some difficulties do exist in the genetic diagnosis of ATS. Most mutations are point mutations without hotspots in the COL4A3, COL4A4, and COL4A5 genes. Further, there are insufficient data on the detection of COL4A3 and COL4A4 mutations for their comparison between patients with autosomal recessive or dominant ATS. Therefore, diagnosis of ATS in female patients with no apparent family history can be challenging. Therefore, in this study, we used whole-exome sequencing (WES) to identify mutations in type IV collagen in 2 girls with glomerular basement membrane structural changes suspected to be associated with ATS; these patients had no relevant family history. Our results revealed de novo c.4688G>A (p.Arg1563Gln) and c.2714G>A (p.Gly905Asp) mutations in COL4A5. Therefore, we suggest that WES is an effective approach to obtain genetic information in ATS, particularly in female patients without a relevant family history, to detect unexpected DNA variations.

• Genomics & Informatics
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• v.16 no.4
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• pp.34.1-34.9
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• 2018

Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and antidiabetic and hepatoprotective effects. Silymarin is synthesized by 4-coumaroyl-CoA via both the flavonoid and phenylpropanoid pathways to produce the immediate precursors taxifolin and coniferyl alcohol. Then, the oxidative radicalization of taxifolin and coniferyl alcohol produces silymarin. We identified the expression of genes related to the synthesis of silymarin in C. japonicum in three different tissues, namely, flowers, leaves, and roots, through RNA sequencing. We obtained 51,133 unigenes from transcriptome sequencing by de novo assembly using Trinity v2.1.1, TransDecoder v2.0.1, and CD-HIT v4.6 software. The differentially expressed gene analysis revealed that the expression of genes related to the flavonoid pathway was higher in the flowers, whereas the phenylpropanoid pathway was more highly expressed in the roots. In this study, we established a global transcriptome dataset for C. japonicum. The data shall not only be useful to focus more deeply on the genes related to product medicinal metabolite including flavolignan but also to study the functional genomics for genetic engineering of C. japonicum.

• Mycobiology
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• v.50 no.2
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• pp.121-131
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• 2022

The rare edible and medicinal fungus Antrodia cinnamomea has a substantial potential for development. In this study, Illumina HiSeq 2000 was used to sequence its transcriptome. The results were assembled de novo, and 66,589 unigenes with an N50 of 4413 bp were obtained. Compared with public databases, 6,061, 3,257, and 2,807 unigenes were annotated to the Non-Redundant, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases, respectively. The genes related to terpene biosynthesis in the mycelia of A. cinnamomea were analyzed, and acetyl CoA synthase (ACS2 and ACS4), hydroxymethylglutaryl CoA reductase (HMGR), farnesyl transferase (FTase), and squalene synthase (SQS) were found to be upregulated in XZJ (twig of C. camphora) and NZJ (twig of C. kanehirae). Moreover, ACS5 and 2,3-oxidized squalene cyclase (OCS) were highly expressed in NZJ, while heme IX farnesyl transferase (IX-FIT) and ACS3 were significantly expressed in XZJ. The differential expression of ACS1, ACS2, HMGR, IX-FIT, SQS, and OCS was confirmed by real-time quantitative reverse transcription PCR. This study provides a new concept for the additional exploration of the molecular regulatory mechanism of terpenoid biosynthesis and data for the biotechnology of terpenoid production.

• Mycobiology
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• v.51 no.1
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• pp.49-59
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• 2023

Antrodia cinnamomea, an edible and medicinal fungus with significant economic value and application prospects, is rich in terpenoids, benzenoids, lignans, polysaccharides, and benzoquinone, succinic and maleic derivatives. In this study, the transcriptome of A. cinnamomea cultured on the wood substrates of Cinnamomum glanduliferum (YZM), C. camphora (XZM), and C. kanehirae (NZM) was sequenced using the high-throughput sequencing technology Illumina HiSeq 2000, and the data were assembled by de novo strategy to obtain 78,729 Unigenes with an N50 of 4,463 bp. Compared with public databases, about 11,435, 6,947, and 5,994 Unigenes were annotated to the Non-Redundant (NR), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genome (KEGG), respectively. The comprehensive analysis of the mycelium terpene biosynthesis-related genes in A. cinnamomea revealed that the expression of acetyl-CoA acetyltransferase (AACT), acyl-CoA dehydrogenase (MCAD), 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA), mevalonate pyrophosphate decarboxylase (MVD), and isopentenyl diphosphate isomerase (IDI) was significantly higher on NZM compared to the other two wood substrates. Similarly, the expression of geranylgeranyltransferase (GGT) was significantly higher on YZM compared to NZM and XZM, and the expression of farnesyl transferase (FTase) was significantly higher on XZM. Furthermore, the expressions of 2,3-oxidized squalene cyclase (OCS), squalene synthase (SQS), and squalene epoxidase (SE) were significantly higher on NZM. Overall, this study provides a potential approach to explore the molecular regulation mechanism of terpenoid biosynthesis in A. cinnamomea.

• Journal of Preventive Medicine and Public Health
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• v.56 no.1
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• pp.1-11
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• 2023

In 1945, atomic bombs were dropped on Hiroshima and Nagasaki. Approximately 70 000 Koreans are estimated to have been exposed to radiation from atomic bombs at that time. After Korea's Liberation Day, approximately 23 000 of these people returned to Korea. To investigate the long-term health and hereditary effects of atomic bomb exposure on the offspring, cohort studies have been conducted on atomic bomb survivors in Japan. This study is an ongoing cohort study to determine the health status of Korean atomic bomb survivors and investigate whether any health effects were inherited by their offspring. Atomic bomb survivors are defined by the Special Act On the Support for Korean Atomic Bomb Victims, and their offspring are identified by participating atomic bomb survivors. As of 2024, we plan to recruit 1500 atomic bomb survivors and their offspring, including 200 trios with more than 300 people. Questionnaires regarding socio-demographic factors, health behaviors, past medical history, laboratory tests, and pedigree information comprise the data collected to minimize survival bias. For the 200 trios, whole-genome analysis is planned to identify de novo mutations in atomic bomb survivors and to compare the prevalence of de novo mutations with trios in the general population. Active follow-up based on telephone surveys and passive follow-up with linkage to the Korean Red Cross, National Health Insurance Service, death registry, and Korea Central Cancer Registry data are ongoing. By combining pedigree information with the findings of trio-based whole-genome analysis, the results will elucidate the hereditary health effects of atomic bomb exposure.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.28-28
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• 2022

This paper presents the first genome assemblies of Philippine mangoes that provide valuable reference for varietal improvement and genomic studies on mango and related fruit crops. WE sequenced whole genomes of3 species, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica 'Carabao' (Sweet Elena). 'Carabao' is the major export variety of the Philippines; Paho is identified as vulnerable by the IUCN Red List of Threatened Species; Huani has fruit sap acrid which is the primary defense mechanism against insects and birds. We used Falcon, a diploid aware -de novo assembler to assemble SMRT generated long-read sequences. Falcon-unzip was employed to phase the output assembly producing larger contig sets (primary contigs) and shorter contigs corresponding to haplotypes (haplotigs). Assembly statistics were generated by comparing the assembly to a reference genome, Tommy Atkins, using Quality Assessment Tool (QUAST). Moreover, the extent of duplication and completeness of gene content was measured using Benchmarking Universal Single-Copy Orthologs (BUSCO). Draft assemblies with high duplications were processed using Purge Haplotigs and Purge Dups to lessen duplications with minimal impact on genome completeness. De novo assemblies of Huani, Paho and 'Carabao' were then generated with primary contig sizes of 463.64 Mb, 508.95 Mb and 401.51 Mb respectively. These draft assemblies of Huani, Paho and 'Carabao' showed 96.90%, 95.17% and 99.07% complete BUSCOs respectively which is comparable to 'Tommy Atkins' genome (98.6%). Using two mango transcriptome data (pooled RNA-seq from different mango varieties and tissues), 91-96% or 24-30 million reads were successfully mapped back for each generated assembly indicating high degree of completeness. The results obtained demonstrated the highly contiguous, phased, and near complete genome assembly of three Philippine mango species for structural and functional annotation of gene units, especially those with economic importance.