• BMB Reports
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• v.39 no.3
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• pp.240-246
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• 2006

The base compositional correlations that hold among various coding and noncoding regions of the canine genome have been analysed. The distribution pattern of genes, on the basis of $GC_3$ composition, shows a wide range similar to that observed in human. However the occurrence of maximum number of genes was observed in the range of 65-75% of $GC_3$ composition. The correlation between the coding DNA sequences of canine with the different noncoding regions (introns and flanking regions) is found to be significant and in many cases the degree of correlation show similarity to human genome. We found that these correlations are not limited to the GC content alone, but is holding at the level of the frequency of individual bases as well. The present study suggests that canines ideally belong to the predicted 'general mammalian pattern' of genome composition along with human beings.

• Proceedings of the KSRS Conference
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• v.2
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• pp.706-709
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• 2006

Cancer is one of the major causes of death; however, the survival rate can be increased if discovered at an early stage for timely treatment. According to the statistics of the World Health Organization of 2002, breast cancer was the most prevalent cancer for all cancers occurring in women worldwide, and it account for 16.8% of entire cancers inflicting Korean women today. In order to classify the type of breast cancer whether it is benign or malignant, this study was conducted with the use of the discriminant analysis and the decision tree of data mining with the breast cancer data disclosed on the web. The discriminant analysis is a statistical method to seek certain discriminant criteria and discriminant function to separate the population groups on the basis of observation values obtained from two or more population groups, and use the values obtained to allow the existing observation value to the population group thereto. The decision tree analyzes the record of data collected in the part to show it with the pattern existing in between them, namely, the combination of attribute for the characteristics of each class and make the classification model tree. Through this type of analysis, it may obtain the systematic information on the factors that cause the breast cancer in advance and prevent the risk of recurrence after the surgery.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.7
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• pp.4167-4175
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• 2013

A najor current challenge and constraint in cervical cancer research is the development of vaccines against human papilloma virus (HPV) epitopes. Although many studies are done on epitope identification on HPVs, no computational work has been carried out for high risk forms which are considered to cause cervical cancer. Of all the high risk HPVs, HPV 16, HPV 18 and HPV 45 are responsible for 94% of cervical cancers in women worldwide. In this work, we computationally predicted the promiscuous epitopes among the E6 proteins of high risk HPVs. We identified the conserved residues, HLA class I, HLA class II and B-cell epitopes along with their corresponding secondary structure conformations. We used extremely precise bioinformatics tools like ClustalW2, MAPPP, NetMHC, Epi,Jen, EpiTop 1.0, ABCpred, BCpred and PSIPred for achieving this task. Our study identified specific regions 'FAFR(K)DL' followed by 'KLPD(Q)LCTEL' fragments which proved to be promiscuous epitopes present in both human leukocyte antigen (HLA) class I, class II molecules and B cells as well. These fragments also follow every suitable character to be considered as promiscuous epitopes with supporting evidences of previously reported experimental results. Thus, we conclude that these regions should be considered as the important for design of specific therapeutic vaccines for cervical cancer.

• 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.

• Molecules and Cells
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• v.21 no.2
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• pp.302-307
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• 2006

Two Epstein-Barr virus (EBV) types, type 1 and type 2, maintain the same allelic specificity at four genomic loci encoding the EBNA2, -3A, -3B, and -3C proteins. We have previously described 16 EBV-transformed B-lymphoblastoid cell lines derived from Korean cancer patients, and the EBNA2 types of the EBV isolates therein. In this study, the allelic types of the EBNA2, -3A, -3B, and -3C genes of these EBV isolates were determined. We report the identification of two distinct types of naturally occurring intertypic recombinants, one with genotype EBNA2 type1/EBN3A, -3B, -3C type 2 and the other with genotype EBNA2, -3A type 1/EBNA3B, -3C type 2. The existence of these intertypic recombinants indicates that various intertypic EBV strains may be circulating in the human population, in addition to typical EBV-1 and EBV-2 strains.

• Journal of Applied Biological Chemistry
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• v.61 no.4
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• pp.327-334
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• 2018

Monascus is a source of food colorant with high productivity of the pigment azaphilone. Monascus azaphilone (MAz) is biosynthesized through a single non-reducing polyketide pathway, the major components of which are ankaflavin (1), monascin (2), rubropunctatin (3) and monascorubrin (4); valuable biological activities have been reported for these compounds. Thus, various culture conditions were explored to reduce the cost of culture ingredients, enhance productivity and modulate compound composition. In the present study, we examined an extractive fermentation (EF) method with Diaion HP-20 resin (HP20) in direct comparison to a previously explored method involving Triton X-100 (TX100) to explore the modulated production of the major MAzs. We employed wild-type Monascus purpureus as well as two derivative recombinant strains (${\Delta}mppG$ and ${\Delta}mppE$) that are known to have differential MAz profiles as that of the wild-type strain. The HP20 resin was capable of modulating the MAz profile in favor of orange MAzs 3 and 4, oxidized congeners in this class, as was TX100-a phenomenon not previously observed for TX100 EF with Monascus anka. These finding substantiate that HP20 can be employed for the selective production of oxidized MAz and for diversifying the culture conditions used for Az production.

• Genomics & Informatics
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• v.20 no.4
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• pp.41.1-41.9
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• 2022

The pathogen Gallibacterium anatis has caused heavy economic losses for commercial poultry farms around the world. However, despite its importance, the functions of its hypothetical proteins (HPs) have been poorly characterized. The present study analyzed the functions and structures of HPs obtained from Gallibacterium anatis (NCTC11413) using various bioinformatics tools. Initially, all the functions of HPs were predicted using the VICMpred tool, and the physicochemical properties of the identified virulence proteins were then analyzed using Expasy's ProtParam server. A virulence protein (WP_013745346.1) that can act as a potential drug target was further analyzed for its secondary structure, followed by homology modeling and three-dimensional (3D) structure determination using the Swiss-Model and Phyre2 servers. The quality assessment and validation of the 3D model were conducted using ERRAT, Verify3D, and PROCHECK programs. The functional and phylogenetic analysis was conducted using ProFunc, STRING, KEGG servers, and MEGA software. The bioinformatics analysis revealed 201 HPs related to cellular processes (n = 119), metabolism (n = 61), virulence (n = 11), and information/storage molecules (n = 10). Among the virulence proteins, three were detected as drug targets and six as vaccine targets. The characterized virulence protein WP_013745346.1 is proven to be stable, a drug target, and an enzyme related to the citrate cycle in the present pathogen. This enzyme was also found to facilitate other metabolic pathways, the biosynthesis of secondary metabolites, and the biosynthesis of amino acids.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2005.06a
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• pp.903-906
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• 2005

The purpose of this study was to analyze the muscular force of swing using the soft golf club in comparison with the muscular force of swing using normal golf club. The subject was normal adult (twenties) and performed swing motion using normal and soft golf club. And then we compared muscular power soft golf club with normal golf club of the subject. The muscular power of the subject was measured by MP 100(BIOPAC Systems, Inc.). For the analysis of muscular power of swing using soft golf club, we measured EMG(Electromyography) of the subject. The position of muscle was deltoid, latissimus dorsi, external oblique and rectus abdominis of the upper limbs and rectus femoris, biceps femoris, gastrocnemius and soleus of the lower limbs. The result of experiment, muscle pattern of swing using soft golf club was similar to pattern of swing using normal golf club and muscular power of subjects using the soft golf was smaller than normal golf.

• Reproductive and Developmental Biology
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• v.39 no.4
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• pp.105-115
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• 2015

Toll-like receptor 7 (TLR7) is critical for the triggering of innate immune response by recognizing the conserved molecular patterns of single-stranded RNA (ssRNA) viruses and mediated antigenic adaptive immunity. To understand how TLR7 distinguish pathogen-derived molecular patterns from the host self, it is essential to be able to identify TLR7 receptor interaction interfaces, such as active sites or R848-agonist binding sites. The functional interfaces of TLR7 can serve as targets for structure-based drug design in studying the TLR7 receptor's structure-function relationship. In contrast to mammalian TLR7, chicken TLR7 (chTLR7) is unknown for its important biological function. Therefore, it has been targeted to mediate contrasting evolutionary patterns of positive selection into non-synonymous SNPs across eleven species using TLR7 conservation patterns (evolutionary conserved and class-specific trace residues), where protein sequence differences to the TLR7 receptors of interest record mutation that have passed positive section across the species. In this study, we characterized the Lys609 residue on chTLR7-ECD homodimer interfaces to reflect the current tendency of evolving positive selection to be transfer into a stabilization direction of the R848-agonist/chTLR7-ECDs complex under the phylogenetically variable position across species and we suggest a potential indicator for contrasting evolutionary patterns of both the species TLR-ECDs.

• Journal of Computing Science and Engineering
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• v.1 no.1
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• pp.1-30
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• 2007

In this paper we have provided an extensive survey of the databases and other resources related to the current research in bioinformatics and the issues that confront the database researcher in helping the biologists. Initially we give an overview of the concepts and principles that are fundamental in understanding the basis of the data that has been captured in these databases. We briefly trace the evolution of biological advances and point out the importance of capturing data about genes, the fundamental building blocks that encode the characteristics of life and proteins that are the essential ingredients for sustaining life. The study of genes and proteins is becoming extremely important and is being known as genomics and proteomics, respectively. Whereas there are numerous databases related to various subfields of biology, we have maintained a focus on genomic and proteomic databases which are the crucial stepping stones for other fields and are expected to play an important role in the future applications of biology and medicine. A detailed listing of these databases with information about their sizes, formats and current status is presented. Related databases like molecular pathways and interconnection network databases are mentioned, but their full coverage would be beyond the scope of a single paper. We comment on the peculiar nature of the data in biology that presents special problems in organizing and accessing these databases. We also discuss the capabilities needed for database development and information management in the bioinformatics arena with particular attention to ontology development. Two research case studies based on our own research are summarized dealing with the development of a new genome database called Mitomap and the creation of a framework for discovery of relationships among genes from the biomedical literature. The paper concludes with an overview of the applications that will be driven from these databases in medicine and healthcare. A glossary of important terms is provided at the end of the paper.