• Clinical and Experimental Pediatrics
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• v.50 no.10
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• pp.1024-1029
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• 2007

Costello syndrome (CS) is a rare multiple congenital abnormality syndrome characterized by a typical coarse face, developmental delay, psychomotor and growth retardation, neurologic abnormalities, cardiac and cutaneous anomalies, severe feeding difficulties with postnatal growth failure, and increased risk of tumors. Since Costello first described it in 1971 and again in 1977, over 100 cases have been reported worldwide. It was recently shown that CS is a congenital condition caused by heterozygous de novo missense mutations affecting the codon for glycine 12 or 13 of the HRAS gene. We experienced three unrelated cases with coarse faces, developmental delays, short statures, macrocephaly, and redundant skin with deep palmar and plantar creases, hypertrophic cardiomyopathy and atrial tachycardia, which are characteristic of CS.

• Molecules and Cells
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• v.39 no.2
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• pp.141-148
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• 2016

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.

• Biomolecules & Therapeutics
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• v.16 no.4
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• pp.431-436
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• 2008

To identify genes whose expression correlated with biological features of therapy-related AML (t-AML), we analyzed the expression profiles of de novo AML t(9;11) and t-AML t(9;11) bone marrow samples using previously published SAGE data. Three-hundred twenty-nine transcripts that satisfied statistical (P<0.05) and magnitude-of-change ($\geq$ 4-fold) criteria were identified as differentially expressed between de novo AML t(9;11) and t-AML t(9;11) cells. Of these transcripts, 301 (91%) matched known genes or ESTs and were classified according to functional categories (http://david.abcc.ncifcrf.gov/). The majority of differentially expressed genes in t-AML t(9;11) were involved in the regulation of biological and metabolic processes. Especially prominent among these were genes related to immune and drug responses. These results establish a framework for developing new drugs for the treatment of t-AML.

• Journal of Life Science
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• v.25 no.3
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• pp.357-367
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• 2015

With the ongoing development of next-generation sequencing (NGS) platforms and advancements in the latest bioinformatics tools at an unprecedented pace, the ultimate goal of sequencing the human genome for less than $1,000 can be feasible in the near future. The rapid technological advances in NGS have brought about increasing demands for statistical methods and bioinformatics tools for the analysis and management of NGS data. Even in the early stages of the commercial availability of NGS platforms, a large number of applications or tools already existed for analyzing, interpreting, and visualizing NGS data. However, the availability of this plethora of NGS data presents a significant challenge for storage, analyses, and data management. Intrinsically, the analysis of NGS data includes the alignment of sequence reads to a reference, base-calling, and/or polymorphism detection, de novo assembly from paired or unpaired reads, structural variant detection, and genome browsing. While the NGS technologies have allowed a massive increase in available raw sequence data, a number of new informatics challenges and difficulties must be addressed to improve the current state and fulfill the promise of genome research. This review aims to provide an overview of major NGS technologies and bioinformatics tools for NGS data analyses.

• YAKHAK HOEJI
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• v.41 no.6
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• pp.782-788
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• 1997

This study was designed to characterize glucose-enhancing effects on endotoxin-induced prostaglandin production in primary cultured rat vascular smooth muscle cells (VSMC). High glucose treatment significantly augmented prostaglandin (PG) synthesis in lipopolysaccharide (LPS)-stimulated VSMC and this effect was maximal at the concentration of 4mg/ml. It has been reported that increases in glucose metabolism through sorbitol pathway could alter the cytosolic $NADH/NAD^+$ ratio and this change favors de novo synthesis of diacylglycerol (DAG) and, in turn. Results in the activation of protein kinase C (PKC) in vascular tissues. Protein kinase C (PKC) inhibitors, staurosporin and H7, blocked the glucose enhancing effect, and DAG, a PKC activator, significantly increased the PG production stimuated by LPS. Sodium pyruvate, which can reverse the alteration in cytosolic NADH/NAD+ ratio, reduced the high glucose effect on PG production. And also, zopolrestat, a strong aldose reductase inhibitor, almost completely blocked the augmentation effect of glucose on PG synthesis. Arachidonic acid release was significantly increased in high glucose treated group, which implied the increase in $PLA_2$ activity was associated with glucose enhancing effect. Metabloic, labeling study clearly showed that de novo synthesis of prostaglandin H synthase-2 (PGHS-2) is greatly increased in high glucose treated group and this was mitigated by the treatment of zopolrestat. Taken together, the activation of PKC through sorbitol pathway increased the activities of $PLA_2$ and PGHS which resulted in the augmentation in LPS-induced PG production in high glucose treated VSMC.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.36 no.3
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• pp.172-176
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• 2010

Postirradiation extraosseous osteogenic sarcomas are uncommon in the head and neck, despite the extensive use of high-dose radiation. It has been described as de novo radiation-induced neoplasm. We present a 73-year-old male who had been treated by radiotherapy for gingival cancer 7 years earlier and later developed extraosseous osteogenic sarcomas (EOSs) of the neck. Microscopically, the neck mass was composed with mesenchymal malignant cells with cartilaginous and osteogenic differentiation. Immunohistochemical stain demonstrated strong positivity of tumor cells for Snail, the one of major epithelial-mesenchymal transition (EMT) inducer. The E-cadherin expression was scarce, showing inverse relationship to Snail expression. Compared with previous squamous cell carcinoma (SCC) of the gingiva, the present EOS sample revealed the remained epithelial cells on cytokeratin immunohistochemistry, suggesting the tumor arise from the cells of epithelial origin. We have also reviewed the previous 6 cases of head and neck EOSs carefully. The clinicopathologic features of the unusual lesion suggest that it is an incomplete EMT of precedent epithelial malignancy rather than de novo pathology.

• 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.