• Biomolecules & Therapeutics
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• v.27 no.2
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• pp.201-209
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• 2019

Mixed lineage leukemia proteins (MLL) are the key histone lysine methyltransferases that regulate expression of diverse genes. Aberrant activation of MLL promotes leukemia as well as solid tumors in humans, highlighting the urgent need for the development of an MLL inhibitor. We screened and isolated MLL1-binding ssRNAs using SELEX (${\underline{S}}ystemic$ ${\underline{E}}volution$ of ${\underline{L}}igands$ by ${\underline{E}}xponential$ enrichment) technology. When sequences in sub-libraries were obtained using next-generation sequencing (NGS), the most enriched aptamers-APT1 and APT2-represented about 30% and 26% of sub-library populations, respectively. Motif analysis of the top 50 sequences provided a highly conserved sequence: 5'-A[A/C][C/G][G/U][U/A]ACAGAGGG[U/A]GG[A/C] GAGUGGGU-3'. APT1, APT2, and APT5 embracing this motif generated secondary structures with similar topological characteristics. We found that APT1 and APT2 have a good binding activity and the analysis using mutated aptamer variants showed that the site information in the central region was critical for binding. In vitro enzyme activity assay showed that APT1 and APT2 had MLL1 inhibitory activity. Three-dimensional structure prediction of APT1-MLL1 complex indicates multiple weak interactions formed between MLL1 SET domain and APT1. Our study confirmed that NGS-assisted SELEX is an efficient tool for aptamer screening and that aptamers could be useful in diagnosis and treatment of MLL1-mediated diseases.

• BMB Reports
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• v.43 no.6
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• pp.407-412
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• 2010

Homeodomain (HD) is a highly conserved DNA-binding domain composed of helix-turn-helix motif. Drosophila Vnd (Ventral nervous system defective) containing HD acts as a regulator to either enhance or suppress gene expression upon binding to its target sequence. In this study, kinetic analysis of Vnd binding to DNA was performed. The result demonstrates that DNA-binding affinity of the recombinant protein containing HD and NK2-specific domain (NK2-SD) was higher than that of the full-length Vnd. To access whether phosphorylation sites within HD and NK2-SD affect the interaction of the protein with the target sequence, alanine substitutions were introduced. The result shows that S631A mutation within NK2-SD does not contribute significantly to the DNA-binding affinity. However, S571A and T600A mutations within HD showed lower affinity for DNA binding. In addition, DNA-binding analysis using embryonic nuclear protein also demonstrates that Vnd interacts with other nuclear proteins, suggesting the existence of Vnd as a complex.

• Journal of the Architectural Institute of Korea Planning & Design
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• v.35 no.12
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• pp.3-12
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• 2019

The purpose of this study is to address the Issues on Architectural Plagiarism through the analysis of the discourses written in texts form. This study selected 60 texts of 20 suspected pairs of architectural plagiarism to derive key-words and key-passages to understand the Issues on Architectural Plagiarism. As a result, the Issues on Architectural Plagiarism are categorized into six different topics; Prototype, Archetype, Motif, Expression of Idea, Commodification, and Westernized-modernization. Meanwhile, the six issues were not discussed independently, but several issues were considered simultaneously in individual cases. This study is the first step to establish the objective guideline to judge Architectural Plagiarism and to be a basis in Architectural Plagiarism research.

• Geophysics and Geophysical Exploration
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• v.2 no.1
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• pp.26-32
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• 1999

Among the various seismic data processing sequences, the velocity analysis is the most time consuming and man-hour intensive processing steps. For the production seismic data processing, a good velocity analysis tool as well as the high performance computer is required. The tool must give fast and accurate velocity analysis. There are two different approches in the velocity analysis, batch and interactive. In the batch processing, a velocity plot is made at every analysis point. Generally, the plot consisted of a semblance contour, super gather, and a stack pannel. The interpreter chooses the velocity function by analyzing the velocity plot. The technique is highly dependent on the interpreters skill and requires human efforts. As the high speed graphic workstations are becoming more popular, various interactive velocity analysis programs are developed. Although, the programs enabled faster picking of the velocity nodes using mouse, the main improvement of these programs is simply the replacement of the paper plot by the graphic screen. The velocity spectrum is highly sensitive to the presence of the noise, especially the coherent noise often found in the shallow region of the marine seismic data. For the accurate velocity analysis, these noise must be removed before the spectrum is computed. Also, the velocity analysis must be carried out by carefully choosing the location of the analysis point and accuarate computation of the spectrum. The analyzed velocity function must be verified by the mute and stack, and the sequence must be repeated most time. Therefore an iterative, interactive, and unified velocity analysis tool is highly required. An interactive velocity analysis program, xva(X-Window based Velocity Analysis) was invented. The program handles all processes required in the velocity analysis such as composing the super gather, computing the velocity spectrum, NMO correction, mute, and stack. Most of the parameter changes give the final stack via a few mouse clicks thereby enabling the iterative and interactive processing. A simple trace indexing scheme is introduced and a program to nike the index of the Geobit seismic disk file was invented. The index is used to reference the original input, i.e., CDP sort, directly A transformation techinique of the mute function between the T-X domain and NMOC domain is introduced and adopted to the program. The result of the transform is simliar to the remove-NMO technique in suppressing the shallow noise such as direct wave and refracted wave. However, it has two improvements, i.e., no interpolation error and very high speed computing time. By the introduction of the technique, the mute times can be easily designed from the NMOC domain and applied to the super gather in the T-X domain, thereby producing more accurate velocity spectrum interactively. The xva program consists of 28 files, 12,029 lines, 34,990 words and 304,073 characters. The program references Geobit utility libraries and can be installed under Geobit preinstalled environment. The program runs on X-Window/Motif environment. The program menu is designed according to the Motif style guide. A brief usage of the program has been discussed. The program allows fast and accurate seismic velocity analysis, which is necessary computing the AVO (Amplitude Versus Offset) based DHI (Direct Hydrocarn Indicator), and making the high quality seismic sections.

• Genomics & Informatics
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• v.8 no.4
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• pp.170-176
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• 2010

The Ribonucleotide reductases (RNR) are essential enzymes that catalyze the conversion of nucleotides to deoxynucleotides in DNA replication and repair in all living organisms. The RNRs operate by a free radical mechanism but differ in the composition of subunit, cofactor required and regulation by allostery. Based on these differences the RNRs are classified into three classesclass I, class II and class III which depend on oxygen, adenosylcobalamin and S-adenosylmethionine with an iron sulfur cluster respectively for radical generation. In this article thirty seven sequences belonging to each of the three classes of RNR were analyzed by using various tools of bioinformatics. Phylogenetic analysis, dot-plot comparisons and motif analysis was done to identify a number of differences in the three classes of RNRs. In this research article, we have attempted to decipher evolutionary relationship between the three classes of RNR by using bioinformatics approach.

• Bulletin of the Korean Chemical Society
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• v.33 no.4
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• pp.1285-1289
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• 2012

RAP80 plays a key role in DNA damage responses by recognizing K63-linked polyubiquitin moieties through its two ubiquitin-interacting motif (UIM) domains. The linker between the two UIMs possesses a phosphorylation site, but the relationship between phosphorylation and polyubiquitin recognition remains elusive. We investigated the interaction between a phosphorylation-mimic RAP80 mutant S101E and linear polyubiquitins, structurally equivalent to the K63-linked ones, using isothermal titration calorimetry (ITC). ITC analysis revealed differential binding affinities for linear tetraubiquitin by otherwise equivalent UIMs in S101E. Mutational analysis supported such differential polyubiquitin recognition by S101E. Our results suggest a potential crosstalk between polyubiquitin recognition and phosphorylation in RAP80.

• Journal of the Korea Organic Resources Recycling Association
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• v.16 no.4
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• pp.64-73
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• 2008

The cDNA of CCF (coelomic cytolytic factor)-like gene (EC 3.2.1.16), a kind of glycosyl hydorlase, was isolated and cloned from the midgut of the earthworm Eisenia anderi. The size of nucleotide sequence appeared to be 1,152 bp and its predicted coding region was composed of 384 amino acid residues including the initiation methionine. The 17 residues at N-terminal end in the deduced amino acid sequence were regarded to be a signal peptide. Based on the amino acid sequence analysis, it appeared that this CCF-like protein could belong to glycosyl hydrolase family 16 (GHF16) and showed a high sequence homology of about 79~99% with CCF and CCF-like proteins from other earthworm species. The CCFs and CCF-like proteins from various earthworm species exhibited a 100% homology in the polysacchride-binding motif and glucanase motif. It has been reported that the CCFs isolated from E. fedita appeared to show a broader pattern recognition specificity than those from other earthworm species because this species resides in decaying organic matter showing very high microbial activity, implying that CCF-like protein isolated in this study from E. andrei might exhibit a broad substrate specificity that is a useful characteristic for industrial application. A phylogenetic analysis using the deduced amino acid sequences of CCF-related proteins through the BLASTX revealed that GHF16 families could be divided into three groups of metazoa, viriplantae and eubacteria subfamily. Subsequently the CCF-related proteins of metazoa subfamily could clearly be subgroup into lophotrochozoan and edysozoan type including a deuterostome origin. Further understanding of the biological properties of E. andrei CCF-like protein should be addressed to regulate the ${\beta}$-D-glucan hydrolysis and production for the industrial uses.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.21-22
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• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.

• Korean Journal of Remote Sensing
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• v.10 no.2
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• pp.121-132
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• 1994

A GIS based tactical terrain analysis system named ATTAS(Army Tactical Terrain Analysis Software) has been designed and implemented to support the field commanders for enhancing the capabiliy of their unit and efficiency of weapon system. This system is designed to provide computer graphics environment in which the analyst can interactively operate the entire analyzing process such as selecting the area of interest, performing analysis functions, simulating required battlefield operation and display the results. This system can be divided into three major sections; the terrain analysis modules, utilites, and graphic editor. The terrain analysis module inclused surface analysis, line of sight analysis, enemy disposition, 3D display, radar coverage, logistic route analysis, shortest path analysis, atmospheric phenomena prediction, automated IPB (Inteligence preparation of Battlefield), and other applied analysis. A combination of 2D and 3D computer graphics techniques using the X-window system with OSF/Motif in UNIX workstation was adopted as the user interface. The integration technique of remotely sensed images and GIS data such as precision registration, overlay, and on-line editing was developed and implemented. An efficient image and GIS data management technique was also developed and implemented using Oracle Database Management System.

• Journal of Microbiology and Biotechnology
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• v.28 no.8
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• pp.1376-1383
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• 2018

The hepatitis B virus (HBV) envelope contains small (S), middle (M), and large (L) proteins. PreS1 of the L protein contains a receptor-binding motif crucial for HBV infection. This motif is highly conserved among 10 HBV genotypes (A-J), making it a potential target for the prevention of HBV infection. In this study, we successfully generated a neutralizing human monoclonal antibody (mAb), 1A8 (IgG1), that recognizes the receptor-binding motif of preS1 using a phage-displayed human synthetic Fab library. Analysis of the antigen-binding activity of 1A8 for different genotypes indicated that it can specifically bind to the preS1 of major HBV genotypes (A-D). Based on Bio-Layer interferometry, the affinity ($K_D$) of 1A8 for the preS1 of genotype C was 3.55 nM. 1A8 immunoprecipitated the hepatitis B virions of genotypes C and D. In an in vitro neutralization assay using HepG2 cells overexpressing the cellular receptor sodium taurocholate cotransporting polypeptide, 1A8 effectively neutralized HBV infection with genotype D. Taken together, the results suggest that 1A8 may neutralize the four HBV genotypes. Considering that genotypes A-D are most prevalent, 1A8 may be a neutralizing human mAb with promising potential in the prevention and treatment of HBV infection.