• Proceedings of the CALSEC Conference
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• 2003.09a
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• pp.197-203
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• 2003

The purpose of the study is to develop an integrated knowledge structuring system for the domain of engineering, in which ontology-based literature mining, knowledge acquisition, knowledge integration, and knowledge retrieval are combined using XML-based tag information and ontology management. The system supports combining different types of databases (papers and patents, technologies and innovations) and retrieving different types of knowledge simultaneously. The main objective of the system is to facilitate knowledge acquisition and knowledge retrieval from documents through an ontology-based dynamic similarity calculation and a visualization of automatically structured knowledge. Through experimentations we conducted using 100,000 words economic documents reported in the "Go！ Japan" project for analyzing Japanese industrial situation, and 100,000 words molecular biology Papers, we show the system is Practical enough for accelerating knowledge acquisition and knowledge discovery from the information sea.

• Vacuum Magazine
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• v.4 no.4
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• pp.18-22
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• 2017

Transmission electron microscopy (TEM) is a versatile and powerful technique that enables direct visualization of biological samples of sizes ranging from whole cell to near-atomic resolution details of a protein molecule. Thanks to numerous technical breakthroughs and monumental discoveries, 3D electron microscopy (3DEM) has become an indispensable tool in the field of structural biology. In particular, development of cryo-electron microscopy(cryo-EM) and computational image processing played pivotal role for the determination of 3D structures of complex biological systems at sub-molecular resolution. Here, basis of TEM and 3DEM will be introduced, especially focusing on technical advancements and practical applications. Also, future prospective of constantly evolving 3DEM field will be discussed, with an anticipation of great biological discoveries that were once considered impossible.

• Applied Microscopy
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• v.45 no.3
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• pp.150-154
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• 2015

Negative staining electron microscopy facilitates the visualization of small bio-materials such as proteins; thus, many electron microscopists have used this conventional method to visualize the morphologies and structures of biological materials. To achieve sufficient contrast of the materials, a number of imaging parameters must be considered. Here, we examined the effects of one of the fundamental imaging parameters, electron beam exposure time, on electron densities generated using transmission electron microscopy. A single site of a negatively stained biological sample was illuminated with the electron beam for different times (1, 2, or 4 seconds) and sets of micrographs were collected. Computational image processing demonstrated that longer exposure times provide better electron densities at the molecular level. This report describes technical procedures for testing parameters that allow enhanced evaluations of the densities of electron microscopy images.

• Journal of Magnetics
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• v.10 no.3
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• pp.103-107
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• 2005

Magnetotransport is a prerequisite to realization of electronic operation of spintronic devices and it would be more useful if realized at room temperature. The effects of Be codoping on GaMnAs on magnetotransport were investigated. Mn flux was varied for growth of precipitated GaMnAs layers under a Be flux for degenerate doping via low-temperature molecular beam epitaxy. Magnetotransport as well as ferromagnetism at room temperature were realized in the precipitated GaAs:(Mn,Be) layers. Codoping of Be was shown to promote formation of MnGa clusters, and annealing process further stabilized the cluster phases. The room-temperature magnetic properties of the layers originate from the ferromagnetic clusters of MnGa and MnAs embedded in GaAs. The degenerately doped metallic GaAs matrix allowed the visualization of the magnetotransport through anomalous Hall effect.

• BMB Reports
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• v.54 no.10
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• pp.489-496
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• 2021

Chromatin has highly organized structures in the nucleus, and these higher-order structures are proposed to regulate gene activities and cellular processes. Sequencing-based techniques, such as Hi-C, and fluorescent in situ hybridization (FISH) have revealed a spatial segregation of active and inactive compartments of chromatin, as well as the non-random positioning of chromosomes in the nucleus, respectively. However, regardless of their efficiency in capturing target genomic sites, these techniques are limited to fixed cells. Since chromatin has dynamic structures, live cell imaging techniques are highlighted for their ability to detect conformational changes in chromatin at a specific time point, or to track various arrangements of chromatin through long-term imaging. Given that the imaging approaches to study live cells are dramatically advanced, we recapitulate methods that are widely used to visualize the dynamics of higher-order chromatin structures.

• Journal of Veterinary Clinics
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• v.35 no.6
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• pp.273-275
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• 2018

A 6-month-old male cat was presented for investigation of depression, loss of appetite, dehydration, pale conjunctival mucous membrane, weight loss, fast heart and respiratory rates, nasal discharge and cough. Nasal swabs collected from the studied cat. As the results of bacterial culture with nasal swabs, it was suspected with Mycoplasma spp. Also, Mycoplasma species was detected by the PCR reaction with Mycoplasma genus primers. At species PCR assay, the specimens evaluated for the presence of M. felis, M. arginini, M. gateae, and Acholeplasma laidlawii and the result was visualization of bands from 238 bp in agarose gel 1.5% showing M. felis amplicons in samples. In conclusion, we detected M. felis in a cat with respiratory disease. PCR was able to detect successfully M. felis infection in cats.

• Molecules and Cells
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• v.42 no.5
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• pp.386-396
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• 2019

Labeling of a protein with a specific dye or tag at defined positions is a critical step in tracing the subtle behavior of the protein and assessing its cellular function. Over the last decade, many strategies have been developed to achieve selective labeling of proteins in living cells. In particular, the site-specific unnatural amino acid (UAA) incorporation technique has gained increasing attention since it enables attachment of various organic probes to a specific position of a protein in a more precise way. In this review, we describe how the UAA incorporation technique has expanded our ability to achieve site-specific labeling and visualization of target proteins for functional analyses in live cells.

• Molecules and Cells
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• v.40 no.11
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• pp.828-836
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• 2017

Eukaryotic cells consist of a complex network of thousands of proteins present in different organelles where organelle-specific cellular processes occur. Identification of the subcellular localization of a protein is important for understanding its potential biochemical functions. In the post-genomic era, localization of unknown proteins is achieved using multiple tools including a fluorescent-tagged protein approach. Several fluorescent-tagged protein organelle markers have been introduced into dicot plants, but its use is still limited in monocot plants. Here, we generated a set of multicolored organelle markers (fluorescent-tagged proteins) based on well-established targeting sequences. We used a series of pGWBs binary vectors to ameliorate localization and co-localization experiments using monocot plants. We constructed different fluorescent-tagged markers to visualize rice cell organelles, i.e., nucleus, plastids, mitochondria, peroxisomes, golgi body, endoplasmic reticulum, plasma membrane, and tonoplast, with four different fluorescent proteins (FPs) (G3GFP, mRFP, YFP, and CFP). Visualization of FP-tagged markers in their respective compartments has been reported for dicot and monocot plants. The comparative localization of the nucleus marker with a nucleus localizing sequence, and the similar, characteristic morphology of mCherry-tagged Arabidopsis organelle markers and our generated organelle markers in onion cells, provide further evidence for the correct subcellular localization of the Oryza sativa (rice) organelle marker. The set of eight different rice organelle markers with four different FPs provides a valuable resource for determining the subcellular localization of newly identified proteins, conducting co-localization assays, and generating stable transgenic localization in monocot plants.

• Journal of Korean Neurosurgical Society
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• v.65 no.4
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• pp.572-581
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• 2022

Objective : Compared to microscopes, exoscopes have advantages in field-depth, ergonomics, and educational value. Exoscopes are especially well-poised for adaptation into fluorescence-guided surgery (FGS) due to their excitation source, light path, and image processing capabilities. We evaluated the feasibility of near-infrared FGS using a 3-dimensional (3D), 4 K exoscope with near-infrared fluorescence imaging capability. We then compared it to the most sensitive, commercially-available near-infrared exoscope system (3D and 960 p). In-vitro and intraoperative comparisons were performed. Methods : Serial dilutions of indocyanine-green (1-2000 ㎍/mL) were imaged with the 3D, 4 K Olympus Orbeye (system 1) and the 3D, 960 p VisionSense Iridium (system 2). Near-infrared sensitivity was calculated using signal-to-background ratios (SBRs). In addition, three patients with brain tumors were administered indocyanine-green and imaged with system 1, with two also imaged with system 2 for comparison. Results : Systems 1 and 2 detected near-infrared fluorescence from indocyanine green concentrations of >250 ㎍/L and >31.3 ㎍/L, respectively. Intraoperatively, system 1 visualized strong near-infrared fluorescence from two, strongly gadolinium-enhancing meningiomas (SBR=2.4, 1.7). The high-resolution, bright images were sufficient for the surgeon to appreciate the underlying anatomy in the near-infrared mode. However, system 1 was not able to visualize fluorescence from a weakly-enhancing intraparenchymal metastasis. In contrast, system 2 successfully visualized both the meningioma and the metastasis but lacked high resolution stereopsis. Conclusion : Three-dimensional exoscope systems provide an alternative visualization platform for both standard microsurgery and near-infrared fluorescent guided surgery. However, when tumor fluorescence is weak (i.e., low fluorophore uptake, deep tumors), highly sensitive near-infrared visualization systems may be required.

• Journal of Microbiology and Biotechnology
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• v.28 no.11
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• pp.1928-1936
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• 2018

Recently, human infections caused by severe fever with thrombocytopenia syndrome virus (SFTSV), which can lead to fatality, have dramatically increased in East Asia. With the unavailability of vaccines or antiviral drugs to prevent and/or treat SFTSV infection, early rapid diagnosis is critical for prevention and control of the disease. Here, we report the development of a simple, rapid and sensitive portable detection method for SFTSV infection applying reverse transcription-loop mediated isothermal amplification (RT-LAMP) combined with one-pot colorimetric visualization and electro-free reaction platform. This method utilizes a pocket warmer to facilitate diagnosis in a resource-limited setting. Specific primers were designed to target the highly-conserved region of L gene of SFTSV. The detection limit of the RT-LAMP assay was approximately $10^0$ viral genome copies from three different SFTSV strains. This assay exhibited comparable sensitivity to qRT-PCR and 10-fold more sensitivity than conventional RT-PCR, with a rapid detection time of 30 to 60 minutes. The RT-LAMP assay using SFTSV clinical specimens has demonstrated a similar detection rate to qRT-PCR and a higher detection rate compared to conventional RT-PCR. Moreover, there was no observed cross-reactive amplification of other human infectious viruses including Japanese Encephalitis Virus (JEV), Dengue, Enterovirus, Zika, Influenza and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). This highly sensitive, electro- and equipment-free rapid colorimetric visualization method is feasible for resource-limited SFTSV field diagnosis.