• Genomics & Informatics
• /
• v.12 no.4
• /
• pp.236-239
• /
• 2014

The genetic regulation of glucose and insulin levels might be modified by adiposity. With regard to the genetic factors that are altered by adiposity, a large meta-analysis on the interactions between genetic variants and body mass index with regard to fasting glucose and insulin levels was reported by the Meta-Analyses of Glucose- and Insulin-related trait Consortium (MAGIC), based on European ancestry. Because no replication study has been performed in other ethnic groups, we first examined the link between reported single-nucleotide polymorphisms (SNPs) and fasting glucose and insulin levels in a large Korean cohort (Korean Genome and Epidemiology Study cohort [KoGES], n = 5,814). The MAGIC study reported 7 novel SNPs for fasting glucose levels and 6 novel SNPs for fasting insulin levels. In this study, we attempted to replicate the association of 5 SNPs with fasting glucose levels and 5 SNPs with fasting insulin levels. One SNP (rs2293941) in PDX1 was identified as a significant obesity-modifiable factor in Koreans. Our results indicate that the novel loci that were identified by MAGIC are poorly replicated in other ethnic groups, although we do not know why.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.4
• /
• pp.682-685
• /
• 2008

Among thirteen strains of the genus Bacillus isolated from Shrimp-jeotkal in our laboratory, a strain BA34 showing good antifungal activity against Phytophthora infestans in a previous experiment was tested for the inhibitory effect against Akt, protein kinase B. Since Akt is known to play an important role in controlling apoptosis, its inhibitors can be used as potential apoptosis-inducing agents in the treatment of cancer. Two active compounds were isolated and their structures were determined. They have similar structures, despite showing different inhibitory effects. In order to elucidate the reasons for these different effects, three-dimensional studies were carried out.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.147-154
• /
• 2003

Microarray information system is a complex system to manage, analyze and interpretate microarray gene expression data. Establishment of well-defined development process is very essential for understanding the complexity and organization of the system. We performed object-oriented analysis using Unified Modeling Language (UML) in specifying, visualizing and documenting microarray information system. The object-oriented analysis consists of three major steps: (i) use case modeling to describe various functionalities from the user's perspective (ii) dynamic modeling to illustrate behavioral aspects of the system (iii) object modeling to represent structural aspects of the system. As a result of our modeling activities we provide the UML diagrams showing various views of the microarray information system. We believe that the object-oriented analysis ensures effective documentations and communication of information system requirements. Another useful feature of object-oriented technique is structural continuity to standard microarray data model MAGE-OM (Microarray Gene Expression Object Model). The proposed modeling e(forts can be applicable for integration of biomedical information system.

• Journal of Applied Biological Chemistry
• /
• v.50 no.4
• /
• pp.293-295
• /
• 2007

• Journal of Microbiology and Biotechnology
• /
• v.14 no.4
• /
• pp.881-884
• /
• 2004

Apoptosis inducers for cancer therapy have been studied. Among hundreds of inducers, peptide anticancer drugs have many advantages such as being not harmful to humans, high selectivity, and dependence on their structures. Naltriben (NTB) is an octapeptide consisting of DPhe-Cys-Tyr-DTrp-Orn-Thr-Pen-Thr-$NH_2$. Several NTB analogues are known. In this experiment, apoptotic activities of NTB analogues with 8 amino acids were tested using flow cytometry. The conformational study of NTB was carried out using NMR spectroscopy and molecular modeling. Here, the relationships between conformations of NTB analogues and their apoptotic effects are reported.

• Bulletin of the Korean Chemical Society
• /
• v.26 no.12
• /
• pp.2065-2068
• /
• 2005

• Genomics & Informatics
• /
• v.3 no.3
• /
• pp.63-67
• /
• 2005

Adaptive responses to diverse microbial pathogens might be limited in relatively few types. Host cell responses to pathogens are believed to be patterned or stereotyped along with species or class. We tried to compose the host response to Mycoplasma in terms of cellular gene expression. Although gene expression profile of two host HeLa and 293 cells were quite different each other, 30 genes were differentially expressed by mycoplasma infection in both of HeLa and 293 cells. Six of them (PR48, MADH4, MKPX, CRK, RBM7, NEK3) were related to cell cycle or proliferation. Another category of genes like IL1 HY1, KLRF1, TNFSF14, GBP1 were host defense to elicit immune responses. With this set of genes, we establish the prediction model for mycoplasma contamination.

• Genomics & Informatics
• /
• v.16 no.4
• /
• pp.40.1-40.3
• /
• 2018

There is a communal need for an annotated corpus consisting of the full texts of biomedical journal articles. In response to community needs, a prototype version of the full-text corpus of Genomics & Informatics, called GNI version 1.0, has recently been published, with 499 annotated full-text articles available as a corpus resource. However, GNI needs to be updated, as the texts were shallow-parsed and annotated with several existing parsers. I list issues associated with upgrading annotations and give an opinion on the methodology for developing the next version of the GNI corpus, based on a semi-automatic strategy for more linguistically rich corpus annotation.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.3
• /
• pp.1333-1336
• /
• 2016

Oral cancer is one of the most prevalent cancers in India but the underlying mechanisms are minimally unraveled. Cancer research has immensely benefited from genome scale high throughput studies which have contributed to expanding the volume of data. Such datasets also exist for oral cancer genes but there has been no consolidated approach to integrate the data to reveal meaningful biological information. OrCanome is one of the largest and comprehensive, user-friendly databases of oral cancer. It features a compilation of over 900 genes dysregulated in oral cancer and provides detailed annotations of the genes, transcripts and proteins along with additional information encompassing expression, inhibitors, epitopes and pathways. The resource has been envisioned as a one-stop solution for genomic, transcriptomic and proteomic annotation of these genes and the integrated approach will facilitate the identification of potential biomarkers and therapeutic targets.

• Proceedings of the IEEK Conference
• /
• 2006.06a
• /
• pp.817-818
• /
• 2006

In Magnetic Resonance Imaging(MRI), the QRS complex of ECG is used as a trigger signal for MRI scan. But, gradient and RF(radio frequency) artifacts which are caused to static and dynamic field in MRI scanner cause interference in the ECG. Also, the signal shape of theses artifacts can be similar to the QRS-complex, causing possible misinterpretation during patient monitoring and false gating of the MRI. In case of using general FIR or IIR band-pass filters for minimizing the artifacts, artifact-reduction-ratio is not excellent. So, an adaptive real-time digital filter is proposed for reduction of noise by gradient and RF(radio frequency) artifacts. The proposed filter for MRI-Gating is based on the noise-canceller with NLMS(Normalized Least Mean Square) algorithm. The reference signals of the adaptive noise canceller are a combination of the noisy three channel ECG signals. In conclusions, the proposed method showed the acceptable quality of ECG signal with sufficient SNR for gating the MRI and possibility of real time implementation.