• Journal of the Computational Structural Engineering Institute of Korea
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• v.20 no.3
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• pp.365-370
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• 2007

Many engineering problems often require the large amount of computing resources for iterative simulations of problems treating many parameters and input files. In order to overcome the situation, this paper proposes an e-Science based computational system. The system exploits the Grid computing technology to establish an integrated web service environment which supports distributed high throughput computational simulations and remote executions. The proposed system provides an easy-to-use parametric study service where a computational service includes real time monitoring. To verify usability of the proposed system, two kinds of applications were introduced. The first application is an Aerospace Integrated Research System (e-AIRS). The e-AIRS adapts the proposed computational system to solve CFD problems. The second one is design and optimization of protein 3-dimensional structures in structural biology.

• KSBB Journal
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• v.22 no.6
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• pp.393-400
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• 2007

Analysis of protein interactions/functions in a microarray format has been of great potential in drug discovery, diagnostics, and cell biology, because it is amenable to large-scale and high-throughput biological assays in a rapid and economical way. In recent years, the protein microarray have broaden their utility towards the global analysis of protein interactions on a proteome scale, the functional activity analysis based on protein interactions and post-translational modifications (PTMs), and the discovery of biomarkers through profiling of protein expression between sample and reference pool. As a promising tool for proteomics, the protein microarray technology has advanced outstandingly over the past decade in terms of surface chemistry, acquisition of relevant proteins on a proteomic level, and detection methods. In this article, we briefly describe various techniques for development of protein microarray, and introduce developmental state of protein microarray and its applications.

• Molecules and Cells
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• v.23 no.3
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• pp.357-362
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• 2007

There is an increasing demand for high throughput (HTP) methods for gene analysis on a genome-wide scale. However, the current repertoire of HTP detection methodologies allows only a limited range of cellular phenotypes to be studied. We have constructed two HTP-optimized expression vectors generated from the red fluorescent reporter protein (RFP) gene. These vectors produce RFP-tagged target proteins in a multiple expression system using gateway cloning technology (GCT). The RFP tag was fused with the cloned genes, thereby allowing us localize the expressed proteins in mammalian cells. The effectiveness of the vectors was evaluated using an HTP-screening system. Sixty representative human C2 domains were tagged with RFP and overexpressed in HiB5 neuronal progenitor cells, and we studied in detail two C2 domains that promoted the neuronal differentiation of HiB5 cells. Our results show that the two vectors developed in this study are useful for functional gene analysis using an HTP-screening system on a genome-wide scale.

• BMB Reports
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• v.45 no.4
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• pp.233-238
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• 2012

We present a top down separation platform for yeast ribosomal proteins using affinity chromatography and capillary electrophoresis which is designed to allow deposition of proteins onto a substrate. FLAG tagged ribosomes were affinity purified, and rRNA acid precipitation was performed on the ribosomes followed by capillary electrophoresis to separate the ribosomal proteins. Over 26 peaks were detected with excellent reproducibility (<0.5% RSD migration time). This is the first reported separation of eukaryotic ribosomal proteins using capillary electrophoresis. The two stages in this workflow, affinity chromatography and capillary electrophoresis, share the advantages that they are fast, flexible and have small sample requirements in comparison to more commonly used techniques. This method is a remarkably quick route from cell to separation that has the potential to be coupled to high throughput readout platforms for studies of the ribosomal proteome.

• The Korean Journal of Food & Health Convergence
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• v.10 no.3
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• pp.19-22
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• 2024

The field of synthetic biology has emerged in response to the ongoing progress in the life sciences. Advances have been made in medicine, farming, eating, making materials, and more. Synthetic biology is the exploration of using living organisms to create new organisms. By manipulating specific genes to express targeted proteins, proteins can be created that are both productive and cost-effective. Solid-phase extraction (SPE) and liquid-liquid extraction (LLE) are employed for protein separation during the production process involving microorganisms. This study centers on Scanning Probe Microscopy (SPM) to showcase its utility in the food industry and food management. SPE is predominantly utilized as a pretreatment method to eliminate impurities from samples. In comparison to LLE, this method presents benefits such as decreased time and labor requirements, streamlined solvent extraction, automation capabilities, and compatibility with various other analytical instruments. Anion exchange chromatography (AEC) utilizes a similar methodology. Pharmaceutical companies utilize these technologies to improve the purity of biopharmaceuticals, thereby guaranteeing their quality. Used in the food and beverage industry to test chemical properties of raw materials and finished products. This exemplifies the potential of these technologies to enhance industrial development and broaden the scope of applications in synthetic biology.

• Bioinformatics and Biosystems
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• v.2 no.2
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• pp.46-51
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• 2007

In the proteomics research using mass spectrometry, the protein database search gives the protein information from the peptide sequences that show the best match with the tandem mass spectra. The protein sequence database has been a powerful knowledgebase for this protein identification. However, as we accumulate the protein sequence information in the database, the database size gets to be huge. Now it becomes hard to consider all the protein sequences in the database search because it consumes much computing time. For the high-throughput analysis of the proteome, usually we have used the non-redundant refined database such as IPI human database of European Bioinformatics Institute. While the non-redundant database can supply the search result in high speed, it misses the variation of the protein sequences. In this study, we have concerned the proteomics data in the point of protein similarities and used the network analysis tool to build a new analysis method. This method will be able to save the computing time for the database search and keep the sequence variation to catch the modified peptides.

• BMB Reports
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• v.35 no.3
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• pp.262-266
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• 2002

A non-isotopic neutravidin-based reverse transcriptase (RT) assay adapted for high throughput screening of HIV activity is described. Using a 96-well microtitre plate, HIV particles are lysed and the RT enzyme released into a reaction mixture containing poly(A) RNA, biotinylated oligo d(T) and fluorescein-labelled dUTP (FI-dUTP). With poly(A) as a template and oligo d(T) as primer, the viron RT incorporates FI-dUTP into an elongating DNA strand. The resulting product is captured on a neutravidin-coated 96-well plate and the unincorporated nucleotides removed by a series of washing steps. A simple ELISA is subsequently performed using a monoclonal antifluorescein antibody conjugated to alkaline phosphatase. Quantification of RT activity is facilitated by a colorimetric readout. The assay was validated in the context of a diagnostic HIV-1 phenotyping assay. Using supernatants from HIV-1 infected lymphocyte cultures the assay was shown to be as sensitive as a radioactive assay and the RT activity correlated well with levels of cell-asociated HIV-p24. Importantly, even minor reductions of RT activity by virus variants with reduced fitness could be distinguished.

• BMB Reports
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• v.44 no.12
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• pp.811-815
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• 2011

Inhalational anthrax is caused by B. anthracis, a virulent sporeforming bacterium which secretes anthrax toxins consisting of protective antigen (PA), lethal factor (LF) and edema factor (EF). LF is a Zn-dependent metalloprotease and is the main determinant in the pathogenesis of anthrax. Here we report the identification of a lead small-molecule inhibitor of anthrax lethal factor by screening an available synthetic small-molecule inhibitor library using fluorescence-based high-throughput screening (HTS) approach. Seven small molecules were found to have inhibitory effect against LF activity, among which SM157 had the highest inhibitory activity. All theses small molecule inhibitors inhibited LF in a noncompetitive inhibition mode. SM157 and SM167 are from the same family, both having an identical group complex, which is predicted to insert into S1' pocket of LF. More potent small-molecule inhibitors could be developed by modifying SM157 based on this identical group complex.

• Biomolecules & Therapeutics
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• v.19 no.1
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• pp.1-8
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• 2011

G-protein coupled receptors (GPCRs) constitute an important class of drug targets and are involved in every aspect of human physiology including sleep regulation, blood pressure, mood, food intake, perception of pain, control of cancer growth, and immune response. Radiometric assays have been the classic method used during the search for potential therapeutics acting at various GPCRs for most GPCR-based drug discovery research programs. An increasing number of diverse small molecules, together with novel GPCR targets identified from genomics efforts, necessitates the use of high-throughput assays with a good sensitivity and specificity. Currently, a wide array of high-throughput tools for research on GPCRs is available and can be used to study receptor-ligand interaction, receptor driven functional response, receptor-receptor interaction,and receptor internalization. Many of the assay technologies are based on luminescence or fluorescence and can be easily applied in cell based models to reduce gaps between in vitro and in vivo studies for drug discovery processes. Especially, cell based models for GPCR can be efficiently employed to deconvolute the integrated information concerning the ligand-receptor-function axis obtained from label-free detection technology. This review covers various platform technologies used for the research of GPCRs, concentrating on the principal, non-radiometric homogeneous assay technologies. As current technology is rapidly advancing, the combination of probe chemistry, optical instruments, and GPCR biology will provide us with many new technologies to apply in the future.

• Molecules and Cells
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• v.23 no.2
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• pp.170-174
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• 2007

High-throughput subcellular imaging is a powerful tool for investigating the function of genes. In order to identify novel regulators of apoptosis we transiently transfected HeLa cells with 938 hypothetical genes of unknown function, and captured their nuclear images with an automated fluorescence microscope. We selected genes that induced greater than 3-fold increase in the percentage of apoptotic nuclei compared with vector-transfected cells. The full-length genes C10orf61, MGC 26717, and FLJ13855 were identified as candidate proapoptotic genes, and their apoptotic effects were confirmed by DNA fragmentation ELISAs and Western blotting for caspase-7 and PARP. We conclude that a subcellular image-based apoptotic screen is useful for identifying genes with proapoptotic activity.