• The Journal of Korean Medicine
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• v.44 no.2
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• pp.106-118
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• 2023

Objectives: Network pharmacology is a method of constructing and analyzing a drug-compound-target network to predict potential efficacy and mechanisms related to drug targets. In that large-scale analysis can be performed in a short time, it is considered a suitable tool to explore the function and role of herbal medicine. Thus, we investigated the potential functions and pathways of Chongmyunggongjin-dan (CMGJD) on Alzheimer's disease (AD) via network pharmacology analysis. Methods: Using public databases and PubChem database, compounds of CMGJD and their target genes were collected. The putative target genes of CMGJD and known target genes of AD were compared and found the correlation. Then, the network was constructed using Cytoscape 3.9.1. and functional enrichment analysis was conducted based on the Gene Ontology (GO) Biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways to predict the mechanisms. Results: The result showed that total 104 compounds and 1157 related genes were gathered from CMGJD. The network consisted of 1157nodes and 10034 edges. 859 genes were interacted with AD gene set, suggesting that the effects of CMGJD are closely related to AD. Target genes of CMGJD are considerably associated with various pathways including 'Positive regulation of chemokine production', 'Cellular response to toxic substance', 'Arachidonic acid metabolic process', 'PI3K-Akt signaling pathway', 'Metabolic pathways', 'IL-17 signaling pathway' and 'Neuroactive ligand-receptor interaction'. Conclusion: Through a network pharmacological method, CMGJD was predicted to have high relevance with AD by regulating inflammation. This study could be used as a basis for effects of CMGJD on AD.

• Applied Biological Chemistry
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• v.50 no.4
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• pp.276-280
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• 2007

Buckwheat often causes severe allergic reactions in sensitive people. One of the major allergenic proteins in common buckwheat (Fagopyrum esculentum) has been found to be a BW10KD protein. In this study, we developed a PCR method to detect buckwheat ingredients in food using primers corresponding to the allergenic BW10KD gene. Five pairs of oligonucleotide primers successfully enabled PCR amplification of the specific regions of the genomic BW10KD DNA from buckwheat, but no amplification from seven other cereals and beans (barley, wheat, German millet, African millet, soybean, red bean, and black bean). The proposed PCR method was applied to analyze 12 processed foods (buckwheat flour, buckwheat noodle, buckwheat jelly, wheat noodle, instant noodle, black sesame gruels, sunsik, cookie, misutkaru, and three kinds of cereal); among them, only three samples including buckwheat flour, buckwheat noodle and buckwheat jelly showed a positive reaction to the detection. This PCR method was able to detect as little as 1 ng of common buckwheat DNA. This rapid and specific PCR method would be applicable to detect allergenic buckwheat ingredients in food.

• Research in Plant Disease
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• v.23 no.2
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• pp.193-201
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• 2017

Major tomato viruses in Korea are Tomato chlorosis virus (ToCV), Tomato spotted wilt virus (TSWV), Cucumber mosaic virus (CMV), Pepper mottle virus (PepMoV), and Tomato mosaic virus (ToMV). RT-PCR conditions for the viruses were examined, especially in primer set and RT-PCR mixture. Total 46 primer sets from the unique sequence of the viruses were tested for nonspecific background products in a RT-PCR mixture without template. Among them 16 primer sets were applied to healthy tomato RNA, resulting the compatibility between RT-PCR mixture and primer set influenced RT-PCR to reduce nonspecific background products. Based on the combinations among cDNA synthesis parameters and RT-PCR mixtures, two reaction mixtures were finally selected for ToCV detection. The condition allowed to determine more specific primer sets; C029 (ToCV), C072 (TSWV), C070 (CMV), C048 (PepMoV), and C065 (ToMV). These primer sets are expected to be of use to specific detection of the major viruses in tomato plants.

• Journal of Life Science
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• v.21 no.7
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• pp.947-952
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• 2011

A number of epidemiological studies have identified human papillomavirus (HPV) types 1, 2, 3, 4, 7, 10, 27, 57, and 65 in cutaneous common warts. However, identification of the HPV subtype by conventional polymerase chain reaction (PCR) is time consuming with its multi-step laboratory process. In this study, we aim to develop a specific one-step multiplex polymerase chain reaction method which capably identifies six different HPV genotypes related to common warts. By HPV DNA sequence analysis, 6 pairs of specific primers were designed from the intergenic regions of genes L1 to E6, and from genes E2 to L2. DNA sequence analysis with the L1 gene sequence of the sample was performed to measure the specificity of multiplex PCR. HPV-1, -2, -3, -4, -27, and -57 were identified without cross amplification in 109 out of 129 samples. The sensitivity and specificity of our set of primers in detecting HPV were 85% and 99.5%, respectively. For the 20 samples where HPV type was not identifiable by our batch of primer sets, multiplex PCR with an additional set of HPV primers was done, where 7 were found positive for HPV-7 or -65. Our results demonstrate that the newly designed multiplex PCR can rapidly detect the specific HPV subtype involved in common warts with high accuracy.

• Journal of the korean academy of Pediatric Dentistry
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• v.37 no.3
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• pp.275-287
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• 2010

Deep caries may induce pulpitis and the pulpal tissue interacts with microbial invasion. The immune response to protect the pulpal tissue can be mediated by cellular signal molecules produced by the pulpal cells. The understanding of these processes is important to find future therapeutic method for the diseased pulp. The pulp tissue from sound teeth was set as control group (n=30) and the pulp tissue from decayed teeth was set as test group (n=30). Total RNA was extracted from the pulp of each group and it was used for cDNA microarray and reverse transcriptase-polymerase chain reaction(RT-PCR). The expression of TGF-${\beta}1$ was studied by immunohistochemistry. The results were as follows: 1. cDNA microarray analysis identified 520 genes with 6-fold or greater difference in expression level with 143 genes more abundant in health and 377 genes more abundant in disease. 2. The RT-PCR analysis was done for randomly selected 14 genes and the results supported the result of cDNA microarray assay. 3. TGF-${\beta}1$ was highly expressed in the carious pulp and it was found in odontoblast by immunohistochemistry. In conclusion, many cytokines were found to be significantly changed their expression in the diseased pulp(/M/>1.6).

• Journal of Microbiology and Biotechnology
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• v.20 no.10
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• pp.1450-1456
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• 2010

Accurate and rapid diagnosis of Pandemic Influenza A/H1N1 2009 virus (H1N1 2009) infection is important for the prevention and control of influenza epidemics and the timely initiation of antiviral treatment. This study was conducted to evaluate the performance of several diagnostic tools for the detection of H1N1 2009. Flocked nasopharyngeal swabs were collected from 254 outpatients of suspected H1N1 2009 during October 2009. This study analyzed the performances of the RealTime Ready Inf A/H1N1 Detection Set (Roche), Influenza A (H1N1) Real-Time Detection Kit (Bionote), Seeplex Influenza A/B OneStep Typing Set [Seeplex Reverse Transcriptase PCR (RT-PCR)], BinaxNow Influenza A & B Test Kit [Binax Rapid Antigen Test (RAT)], and SD BIOLINE Influenza Ag kit (SD RAT). Roche and Bionote real-time RT-PCR showed identical results for the H1N1 2009 hemagglutinin gene. Compared with real-time RT-PCR, the sensitivities and specificities were 83.7% and 100% for Seeplex RT-PCR, 64.5% and 94.7% for Binax RAT, and 69.5% and 100% for SD RAT. The sensitivities of Seeplex RT-PCR, Binax RAT, and SD RAT in patients aged over 21 years were 73.7%, 47.4%, and 57.9%, respectively. The sensitivities of Seeplex RT-PCR, Binax RAT, and SD RAT on the day of initial symptoms were mostly lower (68.8%, 56.3%, and 31.3%, respectively). In conclusion, multiplex RT-PCR and RAT for the detection of H1N1 2009 were significantly less sensitive than real-time RT-PCR. Moreover, a negative RAT may require more sensitive confirmatory assays, because it cannot be ruled out from influenza infection.

• Korean Journal of Microbiology
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• v.45 no.4
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• pp.306-311
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• 2009

A new PCR method was developed to detect Pectobacterium carotovorum which is the causative agent of soft rot in Brassica pekinensis. A specific detection primer set based on Lytic murein transglycolase gene was designed and evaluated. Using ERB3_F (5'-TGC GAC ACC TCC TCA TCA CG-3') and ERB3_R (5'-CTT ATC ACG CTG TAA CCA GC-3') primers, 437 nucleotides long fragment was specifically amplified. The amplified products were observed in 52 out of 55 strains of P. carotovorum or Pectobacterium carotovorum subsp. carotovorum. On the other hand, no amplification was observed in 8 organisms including Chinese cabbage and potato. The optimal PCR condition for the ERB3_F/ERB3_R primer set was $58^{\circ}C$ for annealing and 15 mM for $MgCl_2$. With serially diluted templates, the specific PCR sensitivitie limit was $2\times10^3$ copies. Also, this method can be applied not only to DNA but also to field samples. This PCR method may be expected to be useful for specific detection of P. carotovorum.

• Clinical and Experimental Pediatrics
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• v.61 no.12
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• pp.403-406
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• 2018

Floating-Harbor syndrome is a rare autosomal dominant genetic disorder associated with SRCAP mutation. To date, approximately 50 cases of Floating-Harbor syndrome have been reported, but none have been reported in Korea yet. Floating-Harbor syndrome is characterized by delayed bony maturation, unique facial features, and language impairment. Here, we present a 6-year-old boy with a triangular face, deep-set protruding eyes, low-set ears, wide nose with narrow nasal bridge, short philtrum, long thin lips, clinodactyly, and developmental delay that was transferred to our pediatric clinic for genetic evaluation. He showed progressive delay in the area of language and cognition-adaption as he grew. He had previously undergone chromosomal analysis at another hospital due to his language delay, but his karyotype was normal. We performed targeted exome sequencing, considering several syndromes with similar phenotypes. Library preparation was performed with the TruSight One sequencing panel, which enriches the sample for about 4,800 genes of clinical relevance. Massively parallel sequencing was conducted with NextSeq. An identified variant was confirmed by Sanger sequencing of the patient and his parents. Finally, the patient was confirmed as the first Korean case of Floating-Harbor syndrome with a novel SRCAP (Snf2 related CREBBP activator protein) mutation (c.7732dupT, p.Ser2578Phefs*6), resulting in early termination of the protein; it was not found in either of his healthy parents or a control population. To our knowledge, this is the first study to describe a boy with Floating-Harbor syndrome with a novel SRCAP mutation diagnosed by targeted exome sequencing in Korea.

• Journal of Microbiology and Biotechnology
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• v.17 no.8
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• pp.1330-1337
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• 2007

To better understand the gene expression of the cold-adapted polar diatom, we conducted a survey of the Chaetoceros neogracile transcriptome by cDNA sequencing and expression of interested cDNAs from the Antarctic diatom. A non-normalized cDNA library was constructed from the C. neogracile, and a total of 2,500 cDNAs were sequenced to generate 1,881 high-quality expressed sequence tags (ESTs) (accession numbers EL620615-EL622495). Based on their clustering, we identified 154 unique clusters comprising 342 ESTs. The remaining 1,540 ESTs did not cluster. The number of unique genes identified in the data set is thus estimated to be 1,694. Taking advantage of various tools and databases, putative functions were assigned to 939 (55.4%) of these genes. Of the remaining 540 (31.9%) unknown sequences, 215 (12.7%) appeared to be C. neogracile-specific since they lacked any significant sequence similarity to any sequence available in the public databases. C. neogracile consisted of a relatively high percentage of genes involved in metabolism, genetic information processing, cellular processes, defense or stress resistance, photosynthesis, structure, and signal transduction. From the ESTs, the expression of these putative C. neogracile genes was investigated: fucoxanthin chlorophyll (chl) a,c-binding protein (FCP), ascorbate peroxidase (ASP), and heat-shock protein 90 (HSP90). The abundance of ASP and HSP90 changed substantially in response to different culture conditions, indicating the possible regulation of these genes in C. neogracile.

• The Plant Pathology Journal
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• v.31 no.3
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• pp.245-251
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• 2015

Alternative hosts increase the difficulty of disease management in crops because these alternate hosts provide additional sources of primary inoculum or refuges for diversity in the pathogen gene pool. Agropyron cristatum (crested wheatgrass), Bromus inermis (smooth bromegrass), Pascopyrum smithii (western wheatgrass), Stipa viridula (green needlegrass), and Thinopyrum intermedium (intermediate wheatgrass), commonly identified in range, prairie, verge, and soil reclamation habitats, serve as additional hosts for Pyrenophora tritici-repentis, the cause of tan spot in wheat (Triticum aestivum L.). A. cristatum (five lines), B. inermis (seven lines), P. smithii (four lines), S. viridula (two lines), and T. intermedium (six lines) were tested for their reactions to 30 representative P. tritici-repentis isolates from races 1-5. Plants were grown until the two-three-leaf stage in a greenhouse, inoculated individually with the 30 isolates, held at high humidity for 24 h, and rated after 7 days. All lines developed lesion types 1-2 (resistant) based on a 1-5 rating scale. Also, leaves from an additional plant set were infiltrated with two host selective toxins, Ptr ToxA as a pure preparation and Ptr ToxB as a dilute crude culture filtrate. All lines were insensitive to the toxins. Results indicate that these grass hosts have a limited or nonsignificant role in tan spot epidemiology on wheat in the northern Great Plains. Additionally, the resistant reactions demonstrated by the grass species in this research indicate the presence of resistance genes that can be valuable to wheat breeding programs for improving wheat resistance to P. tritici-repentis.