• KIPS Transactions on Software and Data Engineering
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• v.8 no.10
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• pp.421-426
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• 2019

In this paper, we propose a method to visualize the geometric features of the contact region between proteins in a protein complex. When proteins or ligands are represented as curved surfaces with irregularities, the property that the two surfaces contact each other without intersections is called shape compatibility. Protein-Protein or Protein-Ligand docking researches have shown that shape complementarity, chemical properties, and entropy play an important role in finding contact regions. Usually, after finding a region with high shape complementarity, we can predict the contact region by using residual polarity and hydrophobicity of amino acids belonging to this region. In the research for predicting the contact region, it is necessary to investigate the geometrical features of the contact region in known protein complexes. For this purpose, it is essential to visualize the geometric features of the molecular surface. In this paper, we propose a method to find the contact region, and visualize the geometric features of it as normal vectors and mean curvatures of the protein complex.

• Journal of Life Science
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• v.31 no.4
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• pp.410-417
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• 2021

Next-generation sequencing (NGS) is a high-throughput technique for sequencing large numbers of DNA fragments that are prepared from a genome. This sequencing technique has been used to elucidate whole genome sequences of living organisms and to analyze complementary DNA (cDNA) or chromatin immunoprecipitated DNA (ChIPed DNA) at the genome level. After NGS, the use of proper tools is important for processing and analyzing data with reasonable parameters. However, handling large-scale sequencing data and programing for data analysis can be difficult. The Galaxy platform, a public web service system, provides many different tools for NGS data analysis, and it allows researchers to analyze their data on a web browser with no deep knowledge about bioinformatics and/or programing. In this study, we explain the procedure for preparing chromatin immunoprecipitation-sequencing (ChIP-seq) libraries and steps for analyzing ChIP-seq data using the Galaxy platform. The data analysis steps include the NGS data upload to Galaxy, quality check of the NGS data, premapping processes, read mapping, the post-mapping process, peak-calling and visualization by window view, heatmaps, average profile, and correlation analysis. Analysis of our histone H3K4me1 ChIP-seq data in K562 cells shows that it correlates with public data. Thus, NGS data analysis using the Galaxy platform can provide an easy approach to bioinformatics.

• Biomedical Science Letters
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• v.8 no.3
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• pp.161-165
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• 2002

Apoptosis can be difficult to detect in routine histological sections. Since extensive DNA fragmentation is an important characteristic of this process, visualization of DNA breaks could greatly facilitate the identification of apoptotic cells. Several techniques for the qualitative and quantitative detection of this process have been established; recently, an in situ nick end-labelling technique based on the detection of DNA fragmentation, which is a molecular characteristic of apoptotic cell death, was described. Applying this method to paraffin sections of rat tissues, sensitivity was observed to be inconsistently low with regard to the expected number of apoptotic cells. I describe a new modified method for formalin-fixed, paraffin-embedded tissue sections, pretense pretreatment to permeate the tissue sections that involves an TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling) is acknowledged as a method of choice in the rapid identification and quantification of the apoptotic cell fraction in paraffin tissue preparations. TUNEL was performed without apoptosis and with apopotosis samples to each of the three concentrations of proteinase K (10, 25, 40 mg/ml) pretreatments. In this study, I show that chemical pretreatments of the tissue sections in proteinase K (25 mg/ml for 15 min at room temperature) considerably enhances the sensitivity of this nick end labelling technique.

• BMB Reports
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• v.51 no.10
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• pp.526-531
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• 2018

Protein-Protein Interactions (PPIs) play essential roles in diverse biological processes and their misregulations are associated with a wide range of diseases. Especially, the growing attention to PPIs as a new class of therapeutic target is increasing the need for an efficient method of cell-based PPI analysis. Thus, we newly developed a robust PPI assay (SeePPI) based on the co-translocation of interacting proteins to the discrete subcellular compartment 'processing body' (p-body) inside living cells, enabling a facile analysis of PPI by the enriched fluorescent signal. The feasibility and strength of SeePPI (${\underline{S}}ignal$ ${\underline{e}}nhancement$ ${\underline{e}}xclusively$ on ${\underline{P}}-body$ for ${\underline{P}}rotein-protein$ ${\underline{I}}nteraction$) assay was firmly demonstrated with FKBP12/FRB interaction induced by rapamycin within seconds in real-time analysis of living cells, indicating its recapitulation of physiological PPI dynamics. In addition, we applied p53/MDM2 interaction and its dissociation by Nutlin-3 to SeePPI assay and further confirmed that SeePPI was quantitative and well reflected the endogenous PPI. Our SeePPI assay will provide another useful tool to achieve an efficient analysis of PPIs and their modulators in cells.

• BMB Reports
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• v.53 no.7
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• pp.357-366
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• 2020

Currently, most biological research relies on conventional experimental techniques that allow only static analyses at certain time points in vitro or ex vivo. However, if one could visualize cellular dynamics in living organisms, that would provide a unique opportunity to study key biological phenomena in vivo. Intravital microscopy (IVM) encompasses diverse optical systems for direct viewing of objects, including biological structures and individual cells in live animals. With the current development of devices and techniques, IVM addresses important questions in various fields of biological and biomedical sciences. In this mini-review, we provide a general introduction to IVM and examples of recent applications in the field of immunology, oncology, and vascular biology. We also introduce an advanced type of IVM, dubbed real-time IVM, equipped with video-rate resonant scanning. Since the realt-ime IVM can render cellular dynamics with high temporal resolution in vivo, it allows visualization and analysis of rapid biological processes.

• BMB Reports
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• v.46 no.8
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• pp.416-421
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• 2013

Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

• Journal of ILASS-Korea
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• v.15 no.1
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• pp.31-37
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• 2010

The aim of this work is to investigate the spray and combustion characteristics of dimethyl-ether (DME) at various injection conditions. The spray characteristics such as spray tip penetration and spray cone angle were experimentally studied from the spray images which obtained from the spray visualization system. Combustion and emissions characteristics were numerically investigated by using KIVA-3V code coupled with Chemkin chemistry solver. From these results, it revealed that DME spray had a shorter spray tip penetration and wider spray cone angle than that of diesel spray due to the low density, low surface tension, and fast evaporation characteristics. At the constant heating value condition, DME fuel showed higher peak combustion pressure and earlier ignition timing, because of high cetane number and superior evaporation characteristics. In addition, the combustion of DME exhausted more $NO_x$ emission and lower HC emission due to the active combustion reaction in the combustion chamber. The result shows that DME had a little soot emission due to its molecular structure characteristics with no direct connection between carbons.

• Genomics & Informatics
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• v.11 no.4
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• pp.186-190
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• 2013

The advances in electronic medical records (EMRs) and bioinformatics (BI) represent two significant trends in healthcare. The widespread adoption of EMR systems and the completion of the Human Genome Project developed the technologies for data acquisition, analysis, and visualization in two different domains. The massive amount of data from both clinical and biology domains is expected to provide personalized, preventive, and predictive healthcare services in the near future. The integrated use of EMR and BI data needs to consider four key informatics areas: data modeling, analytics, standardization, and privacy. Bioclinical data warehouses integrating heterogeneous patient-related clinical or omics data should be considered. The representative standardization effort by the Clinical Bioinformatics Ontology (CBO) aims to provide uniquely identified concepts to include molecular pathology terminologies. Since individual genome data are easily used to predict current and future health status, different safeguards to ensure confidentiality should be considered. In this paper, we focused on the informatics aspects of integrating the EMR community and BI community by identifying opportunities, challenges, and approaches to provide the best possible care service for our patients and the population.

• Microbiology and Biotechnology Letters
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• v.13 no.3
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• pp.315-319
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• 1985

Delta-endotoxin crystals of B. thuringiensis var. kurstari and B. thuringiensis var. israelensis were purified by NaBr density gradient centrifigation and the wet weight of the BTK endotoxin was approximately 23.79％ of the cell wet weight and that of BTI was 25％. The shape of BTK crystal was bipyramidal, whose size was 1.7${\mu}{\textrm}{m}$ $\times$ 0.9${\mu}{\textrm}{m}$ and that of BTI was a spheroid, whose size was about 1.6$\times$0.45${\mu}{\textrm}{m}$. The molecular weight of BTK crystal protein was approximately 134,000 daltons and that of BTI was about 128,000 daltons.

• Parasites, Hosts and Diseases
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• v.57 no.6
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• pp.581-585
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• 2019

Confocal laser scanning microscopy (CLSM) was used to examine archaeoparasitological specimens from coprolites associated with La Cueva de los Muertos Chiquitos (CMC) located near present-day Durango, Mexico. The eggs for 4 different types of parasites recovered from CMC coprolites were imaged using CLSM to assist with identification efforts. While some of the parasite eggs recovered from CMC coprolites were readily identified using standard light microscopy (LM), CLSM provided useful data for more challenging identifications by highlighting subtle morphological features and enhancing visualization of parasite egg anatomy. While other advanced microscopy techniques, such as scanning electron microscopy (SEM), may also detect cryptic identifying characters, CLSM is less destructive to the specimens. Utilizing CLSM allows for subsequent examinations, such as molecular analyses, that cannot be performed following SEM sample preparation and imaging. Furthermore, CLSM detects intrinsic autofluorescence molecules, making improved identification independent of resource and time-intensive protocols. These aspects of CLSM make it an excellent method for assisting in taxonomic identification and for acquiring more detailed images of archaeoparasitological specimens.