• Molecules and Cells
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• v.21 no.1
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• pp.63-75
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• 2006

The 5′-region of Potato virus X (PVX) RNA, which contains an AC-rich, single-stranded region and stem-loop structure 1 (SL1), affects RNA replication and assembly. Using Systemic Evolution of Ligands by EXponential enrichment (SELEX) and the electrophoretic mobility shift assay, we demonstrate that SL1 interacts specifically with tobacco protoplast protein extracts (S100). The 36 nucleotides that correspond to the top region of SL1, which comprises stem C, loop C, stem D, and the tetra loop (TL), were randomized and bound to the S100. Remarkably, the wild-type (wt) sequence was selected in the second round, and the number of wt sequences increased as selection proceeded. All of the selected clones from the fifth round contained the wt sequence. Secondary structure predictions (mFOLD) of the recovered sequences revealed relatively stable stem-loop structures that resembled SL1, although the nucleotide sequences therein were different. Moreover, many of the clones selected in the fourth round conserved the TL and C-C mismatch, which suggests the importance of these elements in host protein binding. The SELEX clone that closely resembled the wt SL1 structure with the TL and C-C mismatch was able to replicate and cause systemic symptoms in plants, while most of the other winners replicated poorly only on inoculated leaves. The RNA replication level on protoplasts was also similarly affected. Taken together, these results indicate that the SL1 of PVX interacts with host protein(s) that play important roles related to virus replication.

• Steel and Composite Structures
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• v.25 no.6
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• pp.663-670
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• 2017

The problem of layup optimization of the composite laminates involves a very complex multidimensional solution space which is usually non-exhaustively explored using different heuristic computational methods such as genetic algorithms (GA). To ensure the convergence to the global optimum of the applied heuristic during the optimization process it is necessary to evaluate a lot of layup configurations. As a consequence the analysis of an individual layup configuration should be fast enough to maintain the convergence time range to an acceptable level. On the other hand the mechanical behavior analysis of composite laminates for any geometry and boundary condition is very convoluted and is performed by computational expensive numerical tools such as finite element analysis (FEA). In this respect some studies propose very fast FEA models used in layup optimization. However, the lower bound of the execution time of FEA models is determined by the global linear system solving which in some complex applications can be unacceptable. Moreover, in some situation it may be highly preferred to decrease the optimization time with the cost of a small reduction in the analysis accuracy. In this paper we explore some machine learning techniques in order to estimate the failure of a layup configuration. The estimated response can be qualitative (the configuration fails or not) or quantitative (the value of the failure factor). The procedure consists of generating a population of random observations (configurations) spread across solution space and evaluating using a FEA model. The machine learning method is then trained using this population and the trained model is then used to estimate failure in the optimization process. The results obtained are very promising as illustrated with an example where the misclassification rate of the qualitative response is smaller than 2%.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.11 no.10
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• pp.1937-1943
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• 2007

Given the mountainous nature of Korea, cutting slopes are bound to happen. Every you, slope failures lead to enormous human and material losses. More recently, reckless development and subsequent degradation of forests has brought about soil erosion, which coupled with heavy rainfall, contaminates rivers, raises the level of river bottoms and thereby deteriorates their discharge capacity. In Korea, environmental impact assessments and disaster impact assessments have been conducted to come up with proper countermeasures. In order to perform quantitative analysis for this purpose, reliable slope information is quintessential. This study aims to obtain slope-related digital images using an RC model helicopter with a non-metric camera embedded, and to process these images to gain more accurate slope information. To this end, digital images obtained regarding cutting slopes were processed to gain numerical information of slopes and, on the basis of slope information gained here, reliable soil erosion factors were estimated.

• Elastomers and Composites
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• v.33 no.4
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• pp.231-237
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• 1998

In order to investigate the physical properties of rubber blend compound, this experiment was carried out on the cure rate, loss tangent, reinforcement and abrasion properties of S-SBR (solution styrene-butadiene rubber) blends containing silane coupled silica and E-SBR (emulsion styrene-butadiene rubber) blends containing carbon black as a model compound. E-SBR blend showed the highest total bound rubber(TBR), while S-SBR blends showed constant TBR level regardless of rubber type. Rapid cure rate was achieved when the styrene and vinyl content of rubber microstructure decreased and TBR content of rubber compounds increased. The modulus as the index of rubber reinforcement showed the linear relation with TBR content. The large amount of PICO loss was observed when the styrene and vinyl content of rubber microstructure increased, while the small amount of PICO loss was observed when the ratio of bu-tadiene increased in the S-SBR blends with silane copuled silica. The high loss tangent at $0^{\circ}C$, the low loss tangent at $60^{\circ}C$, and the large difference of loss tangent were shown in the S-SBR blends with high styrene content compared to E-SBR blend.

• Journal of Ginseng Research
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• v.45 no.6
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• pp.734-743
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• 2021

Background: The underlying mechanisms of the potential tumor-suppressive effects of ginsenoside Rh2 are complex. N6-methyladenosine (m6A) RNA methylation is usually dysregulated in cancer. This study explored the regulatory effect of ginsenoside Rh2 on m6A RNA methylation in cancer. Methods: m6A RNA quantification and gene-specific m6A RIP-qPCR assays were applied to assess total and gene-specific m6A RNA levels. Co-immunoprecipitation, fractionation western blotting, and immunofluorescence staining were performed to detect protein interactions and distribution. QRT-PCR, dual-luciferase, and ChIP-qPCR assays were conducted to check the transcriptional regulation. Results: Ginsenoside Rh2 reduces m6A RNA methylation and KIF26B expression in a dose-dependent manner in some cancers. KIF26B interacts with ZC3H13 and CBLL1 in the cytoplasm of cancer cells and enhances their nuclear distribution. KIF26B inhibition reduces m6A RNA methylation level in cancer cells. SRF bound to the KIF26B promoter and activated its transcription. SRF mRNA m6A abundance significantly decreased upon KIF26B silencing. SRF knockdown suppressed cancer cell proliferation and growth both in vitro and in vivo, the effect of which was partly rescued by KIF26B overexpression. Conclusion: ginsenoside Rh2 reduces m6A RNA methylation via downregulating KIF26B expression in some cancer cells. KIF26B elevates m6A RNA methylation via enhancing ZC3H13/CBLL1 nuclear localization. KIF26B-SRF forms a positive feedback loop facilitating tumor growth.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.1-8
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• 2019

Due to the major role played by several species of Streptococcus in the etiology of periodontitis, it is important to assess the pattern of Streptococcus pathogenic pathways within the infected subgingival pockets using a bacterial specific 16S rRNA fragment. From the total of 50 patients with periodontitis included in the study, only 23 Streptococcal isolates were considered for further analyses, in which their 16S rRNA fragments were amplified and sequenced. Then, a comprehensive phylogenetic tree was constructed and in silico prediction was performed for the observed Streptococcal species. The phylogenetic analysis of the subgingival Streptococcal species revealed a high discrimination power of the 16S rRNA fragment to accurately identify three groups of Streptococcus on the species level, including S. salivarius (14 isolates), S. anginosus (5 isolates), and S. gordonii (4 isolates). The employment of state-of-art in silico tools indicated that each Streptococcal species group was characterized with particular transcription factors that bound exclusively with a different 16S rRNA-based secondary structure. In conclusion, the observed data of the present study provided in-depth insights into the mechanism of each Streptococcal species in its pathogenesis, which differ in each observed group, according to the differences in the 16S rRNA secondary structure it takes, and the consequent binding with its corresponding transcription factors. This study paves the way for further interventions of the in silico prediction, with the main conventional in vitro microbiota identification to present an interesting insight in terms of the gene expression pattern and the signaling pathway that each pathogenic species follows in the infected subgingival site.

• Molecules and Cells
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• v.42 no.1
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• pp.36-44
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• 2019

Alzheimer's disease (AD) is the most frequent age-related human neurological disorder. The characteristics of AD include senile plaques, neurofibrillary tangles, and loss of synapses and neurons in the brain. ${\beta}-Amyloid$ ($A{\beta}$) peptide is the predominant proteinaceous component of senile plaques. The amyloid hypothesis states that $A{\beta}$ initiates the cascade of events that result in AD. Amyloid precursor protein (APP) processing plays an important role in $A{\beta}$ production, which initiates synaptic and neuronal damage. ${\delta}-Catenin$ is known to be bound to presenilin-1 (PS-1), which is the main component of the ${\gamma}-secretase$ complex that regulates APP cleavage. Because PS-1 interacts with both APP and ${\delta}-catenin$, it is worth studying their interactive mechanism and/or effects on each other. Our immunoprecipitation data showed that there was no physical association between ${\delta}-catenin$ and APP. However, we observed that ${\delta}-catenin$ could reduce the binding between PS-1 and APP, thus decreasing the PS-1 mediated APP processing activity. Furthermore, ${\delta}-catenin$ reduced PS-1-mediated stabilization of APP. The results suggest that ${\delta}-catenin$ can influence the APP processing and its level by interacting with PS-1, which may eventually play a protective role in the degeneration of an Alzheimer's disease patient.

• Journal of Microbiology and Biotechnology
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• v.32 no.9
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• pp.1134-1145
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• 2022

SCO6993 (606 amino acids) in Streptomyces coelicolor belongs to the large ATP-binding regulators of the LuxR family regulators having one DNA-binding motif. Our previous findings predicted that SCO6993 may suppress the production of pigmented antibiotics, actinorhodin, and undecylprodigiosin, in S. coelicolor, resulting in the characterization of its properties at the molecular level. SCO6993-disruptant, S. coelicolor ΔSCO6993 produced excess pigments in R2YE plates as early as the third day of culture and showed 9.0-fold and 1.8-fold increased production of actinorhodin and undecylprodigiosin in R2YE broth, respectively, compared with that by the wild strain and S. coelicolor ΔSCO6993/SCO6993⁺. Real-time polymerase chain reaction analysis showed that the transcription of actA and actII-ORF4 in the actinorhodin biosynthetic gene cluster and that of redD and redQ in the undecylprodigiosin biosynthetic gene cluster were significantly increased by SCO6993-disruptant. Electrophoretic mobility shift assay and DNase footprinting analysis confirmed that SCO6993 protein could bind only to the promoters of pathway-specific transcriptional activator genes, actII-ORF4 and redD, and a specific palindromic sequence is essential for SCO6993 binding. Moreover, SCO6993 bound to two palindromic sequences on its promoter region. These results indicate that SCO6993 suppresses the expression of other biosynthetic genes in the cluster by repressing the transcription of actII-ORF4 and redD and consequently negatively regulating antibiotic production.

• Journal of Radiation Protection and Research
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• v.46 no.2
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• pp.39-47
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• 2021

Background: The National Institutes for Quantum and Radiological Science and Technology-National Institute of Radiological Sciences (QST-NIRS) has continuously investigated the undesired radiation exposure in ion beam radiotherapy mainly in carbon-ion radiotherapy (CIRT). This review introduces our investigations on the secondary neutron dose in CIRT with the broad and scanning beam methods. Materials and Methods: The neutron ambient dose equivalents in CIRT are evaluated based on rem meter (WENDI-II) measurements. The out-of-field organ doses assuming prostate cancer and pediatric brain tumor treatments are also evaluated through the Monte Carlo simulation. This evaluation of the out-of-field dose includes contributions from secondary neutrons and secondary charged particles. Results and Discussion: The measurements of the neutron ambient dose equivalents at a 90#x00B0; angle to the beam axis in CIRT with the broad beam method show that the neutron dose per treatment dose in CIRT is lower than that in proton radiotherapy (PRT). For the scanning beam with the energy scanning technique, the neutron dose per treatment dose in CIRT is lower than that in PRT. Moreover, the out-of-field organ doses in CIRT decreased with distance to the target and are less than the lower bound in intensity-modulated radiotherapy (IMRT) shown in AAPM TG-158 (American Association of Physicists in Medicine Task Group). Conclusion: The evaluation of the out-of-field doses is important from the viewpoint of secondary cancer risk after radiotherapy. Secondary neutrons are the major source in CIRT, especially in the distant area from the target volume. However, the dose level in CIRT is similar or lower than that in PRT and IMRT, even if the contributions from all radiation species are included in the evaluation.

• Iberoamérica
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• v.23 no.1
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• pp.1-31
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• 2021

The main purpose of this study is to examine the use of 'a gente' in Portuguese, and to discuss what to consider educationally. We examined the origin and style of 'a gente', grammaticalization process phase, personalization level, and variations in use in terms of linguistic and social aspects, and confirmed that 'a gente' is showing an increasingly high frequency of use in Brazil. And in order to find educational considerations, we observed how 'a gente' was handled in Portuguese textbooks for foreigners, and analyzed data obtained through interviews with three Korean students studying Portuguese in Brazil. Considering the importance and frequency of use of 'a gente', which is used in the third-person singular form, the section about 'a gente' in grammar and textbooks seems to be very insufficient. Therefore, the contents of textbooks that do not correspond to the actual use of language should be actively revised according to changes in the reality of language use. In addition, the instructor should not be bound by traditional use, but must include 'a gente' in the personal pronoun section of the textbook for efficient education, and actively reflect the more practical usage to educate.