• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.17
• /
• pp.7409-7414
• /
• 2015

Loop-mediated isothermal amplification (LAMP) developed by Notomi et al. (2000) has made it possible to amplify DNA with high specificity, efficiency and rapidity under isothermal conditions. The ultimate products of LAMP are stem-loop structures with several inverted repeats of the target sequence and cauliflower-like patterns with multiple loops shaped by annealing between every other inverted repeats of the amplified target in the similar strand. Because the amplification process in LAMP is achieved by using four to six distinct primers, it is expected to amplify the target region with high selectivity. However, evaluation of reaction accuracy or quantitative inspection make it necessary to append other procedures to scrutinize the amplified products. Hitherto, various techniques such as turbidity assessment in the reaction vessel, post-reaction agarose gel electrophoresis, use of intercalating fluorescent dyes, real-time turbidimetry, addition of cationic polymers to the reaction mixture, polyacrylamide gel-based microchambers, lateral flow dipsticks, fluorescence resonance energy transfer (FRET), enzyme-linked immunosorbent assays and nanoparticle-based colorimetric tests have been utilized for this purpose. In this paper, we reviewed the best-known techniques for evaluation of LAMP amplicons and their applications in molecular biology beside their advantages and deficiencies. Regarding the properties of each technique, the development of innovative prompt, cost-effective and precise molecular detection methods for application in the broad field of cancer research may be feasible.

• Proceedings of the Korean Society for Applied Microbiology Conference
• /
• 2001.06a
• /
• pp.77-80
• /
• 2001

A variety of different methods to generate diverse proteins, including random mutagenesis and recombination, are currently available, and most of them accumulate the mutations on the target gene of a protein, whose sequence space remains unchanged. On the other hand, a pool of diverse genes, which is generated by random insertions, deletions, and exchange of the homologous domains with different lengths in the target gene, would present the protein lineages resulting in new fitness landscapes. Here we report a method to generate a pool of protein variants with different sequence spaces by employing green fluorescent protein (GFP) as a model protein. This process, designated functional salvage screen (FSS), comprises the following procedures： a defective GFP template expressing no fluorescence is firstly constructed by genetically disrupting a predetermined region(s) of the protein, and a library of GFP variants is generated from the defective template by incorporating the randomly fragmented genomic DNA from E. coli into the defined region(s) of the target gene, followed by screening of the functionally salvaged, fluorescence-emitting GFPs. Two approaches, sequence-directed and PCR-coupled methods, were attempted to generate the library of GFP variants with new sequences derived from the genomic segments of E. coli. The functionally salvaged GFPs were selected and analyzed in terms of the sequence space and functional property. The results demonstrate that the functional salvage process not only can be a simple and effective method to create protein lineages with new sequence spaces, but also can be useful in elucidating the involvement of a specific region(s) or domain(s) in the structure and function of protein.

• The Plant Pathology Journal
• /
• v.31 no.1
• /
• pp.25-32
• /
• 2015

Pseudomonas coronafaciens causes halo blight on oats and is a plant quarantine bacterium in many countries, including the Republic of Korea. Using of the certificated seed is important for control of the disease. Since effective detection method of P. coronafaciens is not available yet, PCR and TaqMan PCR assays for specific detection of P. coronafaciens were developed in this study. PCR primers were designed from the draft genome sequence of P. coronafaciens LMG 5060 which was obtained by the next-generation sequencing in this study. The PCR primer set Pc-12-F/Pc-12-R specifically amplified 498 bp from the 13 strains of P. coronafaciens isolated in the seven different countries (Canada, Japan, United Kingdom, Zimbabwe, Kenya, Germany, and New Zealand) and the nested primer set Pc-12-ne-F/Pc-12-ne-R specifically amplified 298 bp from those strains. The target-size PCR product was not amplified from the non-target bacteria with the PCR and nested primer sets. TaqMan PCR with Pc-12-ne-F/Pc-12-ne-R and a TaqMan probe, Pc-taqman, which were designed inside of the nested PCR amplicon, generated Ct values which in a dose-dependent manner to the amount of the target DNA and the Ct values of all the P. coronafaciens strains were above the threshold Ct value for positive detection. The TaqMan PCR generated positive Ct values from the seed extracts of the artificially inoculated oat seeds above 10 cfu/ml inoculation level. PCR and TaqMan PCR assays developed in this study will be useful tools to detect and identify the plant quarantine pathogen, P. coronafaciens.

• The Korea Journal of Herbology
• /
• v.39 no.3
• /
• pp.37-47
• /
• 2024

Objectives : Because predicting the potential efficacy and mechanisms of Korean medicines is challenging due to their high complexity, employing an approach based on network pharmacology could be effective. In this study, network pharmacological analysis was utilized to anticipate the effects of YunPye-Hwan (YPH) in treating Chronic obstructive pulmonary disease (COPD). Methods : Compounds and their related target genes of YPH were gathered from the TCMSP and PubChem databases. These target genes of YPH were subsequently compared with gene sets associated with COPD to assess correlation. Next, core genes were identified through a two-step screening process, and finally, functional enrichment analysis of these core genes was conducted using both Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathways. Results : A total of 15 compounds and 437 target genes were gathered, resulting in a network comprising 473 nodes and 14,137 edges. Among them, 276 genes overlapped with gene sets associated with COPD, indicating a significant correlation between YPH and COPD. Functional enrichment analysis of the 18 core genes revealed biological processes and pathways such as "miRNA Transcription," "Nucleic Acid-Templated Transcription," "DNA-binding Transcription Factor Activity," "MAPK signaling pathway," and "TNF signaling pathway" were implicated. Conclusion : YPH exhibited significant relevance to COPD by modulating cell proliferation, differentiation, inflammation, and cell death pathways. This study could serve as a foundational framework for further research investigating the potential use of YPH in the treatment of COPD.

• The Journal of Korean Medicine Ophthalmology and Otolaryngology and Dermatology
• /
• v.36 no.4
• /
• pp.30-50
• /
• 2023

Objectives : To investigate the active compounds and therapeutic mechanisms of Atractylodes Lancea(Thunb.) D.C. and Magnolia Officinalis Rehder et Wilson in the treatment of dermatitis accompanied by pruritus, as well as their potential to complement or replace standard drugs. Methods : We conducted the network pharmacological analysis. We selected effective ingredients among the active compounds of research target herbs. Then we explore pathway/terms of the common target proteins among research target herbs, fexofenadine and disease. Results : We selected 9 active compounds are selected from Atractylodes lancea and identified 231 target proteins. Among them, 74 proteins are associated with inflammatory skin diseases that cause pruritus. These proteins are involved in various pathways including, 'Nitric-oxide synthase regulator activity', 'Hydroperoxy icosatetraenoate dehydratase activity, Aromatase activity', 'RNA-directed DNA polymerase activity', 'Arachidonic acid metabolism', 'Peptide hormone processing', 'Chemokine binding' and 'Sterol biosynthetic process'. Additionally, coregenes are involved in 'IL-17 signaling pathway'. Similarly, we selected 2 active compounds from Magnolia officinalis and identified 133 target proteins. Among them, 33 proteins are related to inflammatory skin diseases that cause pruritus. These proteins are primarily involved in 'Vascular associated smooth muscle cell proliferation' and 'Arachidonic acid metabolism'. There is no significant difference between the pathways in which coregenes are involved. Conclusions : It is expected that Atractylodes Lancea will be able to show direct or indirect anti-pruritus and anti-inflammatory effects on skin inflammation accompanied pruritus through suppressing inflammation and protecting skin barrier. Meanwhile, it is expected that Magnolia Officinalis will only be able to show indirect anti-inflammation effects. Therefore, Atractylodes Lancea and fexofenadine are believed to complement each other, whereas Magnolia Officialinalis is expected to provide supplementary support on skin disease.

• Journal of Photoscience
• /
• v.9 no.2
• /
• pp.138-141
• /
• 2002

A photo-labile compound which is bioinactive but, upon irradiation with light, yields bioactive species is called as "caged compound". Photolysis of caged compounds generating bioactive species, has become a general method to produce a desired amounts of bioactive species in the specific time interval at the desired place or area of the target biological systems. For this purpose, we designed and synthesized caged hydroxyl radical., "Photo-Fenton Reagent" NP-IIl. NP-IIl has a strong absorption maximum at 377 nm and yields hydroxyl radicals upon UV light irradiation. The antioxidant activity of the ${\alpha}$ -lipoic acid and other naturally occurring compounds has been examined by using NP-IIl as a molecular probe. For example, upon photoirradiation of NP-lII with BSA or apolipoprotein of human low density (LDL), the significant oxidative modifications were observed in both cases. The oxidation was completely suppressed in the presence of ${\alpha}$-lipoic acid, which clearly demonstrates the strong hydroxyl radical scavenging activity of ${\alpha}$-lipoic acid. Other applications of NP-lII will also be described

• Asian Journal of Turfgrass Science
• /
• v.15 no.1
• /
• pp.9-14
• /
• 2001

Callus formation and plant regeneration from the seeds of zoysiagrass cv. Zenith was tested on MS basal medium supplemented with various concentrations of 2,4-dichlorophenoxyacetic acid(2,4-D) and of several cytokinins. A concentration of 1mg/L 2,4-D on medium stimulated callus formation. In the presence of 5mg/L 2,4-D, addition of 1mg/L kinetin significantly enhanced callus formation and plant regeneration over 2,4-D alone. To transfer foreign DNA into turfgrass, parameters for the bombardment of embryogenic callus with the particle bombardment were partially optimized using transient expression assay of a $chimeric \beta$-glucuronidase(GUS) gene driven by the CaMV 35S promoter. GUS gene was strongly expressed at helium pressure 1,100 psi and 6~9cm target distance.

• BMB Reports
• /
• v.47 no.6
• /
• pp.299-310
• /
• 2014

Cohesin is a multi-protein complex composed of four core subunits (SMC1A, SMC3, RAD21, and either STAG1 or STAG2) that is responsible for the cohesion of sister chromatids following DNA replication until its cleavage during mitosis thereby enabling faithful segregation of sister chromatids into two daughter cells. Recent cancer genomics analyses have discovered a high frequency of somatic mutations in the genes encoding the core cohesin subunits as well as cohesin regulatory factors (e.g. NIPBL, PDS5B, ESPL1) in a select subset of human tumors including glioblastoma, Ewing sarcoma, urothelial carcinoma, acute myeloid leukemia, and acute megakaryoblastic leukemia. Herein we review these studies including discussion of the functional significance of cohesin inactivation in tumorigenesis and potential therapeutic mechanisms to selectively target cancers harboring cohesin mutations.

• Proceedings of the Korean Society of Toxicology Conference
• /
• 2001.05a
• /
• pp.125-125
• /
• 2001

B cell has been identified as the sensitive cellular target responsible for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) -induced immune suppression. In isolated cell systems, the differentiation of B cells into antibody secreting plasma cells is believed to be inhibited by TCDD. We also have previously demonstrated IgM secretion was suppressed by TCDD in LPS-activated murine B cell line, CH12.LX.(omitted)

• Biomedical Science Letters
• /
• v.26 no.3
• /
• pp.136-148
• /
• 2020

A bispecific antibody (BsAb) is an artificial protein containing two kinds of specific antigen binding sites. BsAb can connect target cells to functional cells or molecules, and thus stimulate a directed immune response. Last several decades a wide variety of bsAb formats and production technologies have been developed. BsAbs are constructed either chemically or biologically, exploiting techniques like cell fusion and recombinant DNA technologies. There are over 100 different formats of bsAb so far developed, but they could be classified into the two main categories such as Fc-based (with a Fc region) bsAbs and fragment-based (without a Fc region) bsAbs. BsAb has a broad application prospect in tumor immunotherapy and drug delivery. Here, we present a brief introduction to the structure of antibody, pharmacological mechanisms of antibodies and the trend in the production technologies of therapeutic antibodies. In addition, we address a review on the current status of various bsAb format development and their production technologies together with global situation in the clinical studies of bsAb.