Biomedical subjects

Sung-Kyu Kim

Publications and source records attributed to Sung-Kyu Kim.

9 recordsLinked to original sources

PubMed2006

Functional study of hot pepper 26S proteasome subunit RPN7 induced by Tobacco mosaic virus from nuclear proteome analysis.

Two-dimensional gel electrophoresis (2-DE) was applied for the screening of Tobacco mosaic virus (TMV)-induced hot pepper (Capsicum annuum cv. Bugang) nuclear proteins. From differentially expressed protein spots, we acquired the matched peptide mass fingerprint (PMF) data, analyzed by MALDI-TOF MS, from the non-redundant hot pepper EST protein FASTA database using the VEMS 2.0 software. Among six identified nuclear proteins, the hot pepper 26S proteasome subunit RPN7 (CaRPN7) was subjected to further study. The level of CaRPN7 mRNA was specifically increased during incompatible TMV-P(0) interaction, but not during compatible TMV-P(1.2) interaction. When CaRPN7::GFP fusion protein was targeted in onion cells, the nuclei had been broken into pieces. In the hot pepper leaves, cell death was exacerbated and genomic DNA laddering was induced by Agrobacterium-mediated transient overexpression of CaPRN7. Thus, this report presents that the TMV-induced CaRPN7 may be involved in programmed cell death (PCD) in the hot pepper plant.

Amino Acid Sequence↗

PubMed2006

miTarget: microRNA target gene prediction using a support vector machine.

BACKGROUND: MicroRNAs (miRNAs) are small noncoding RNAs, which play significant roles as posttranscriptional regulators. The functions of animal miRNAs are generally based on complementarity for their 5' components. Although several computational miRNA target-gene prediction methods have been proposed, they still have limitations in revealing actual target genes. RESULTS: We implemented miTarget, a support vector machine (SVM) classifier for miRNA target gene prediction. It uses a radial basis function kernel as a similarity measure for SVM features, categorized by structural, thermodynamic, and position-based features. The latter features are introduced in this study for the first time and reflect the mechanism of miRNA binding. The SVM classifier produces high performance with a biologically relevant data set obtained from the literature, compared with previous tools. We predicted significant functions for human miR-1, miR-124a, and miR-373 using Gene Ontology (GO) analysis and revealed the importance of pairing at positions 4, 5, and 6 in the 5' region of a miRNA from a feature selection experiment. We also provide a web interface for the program. CONCLUSION: miTarget is a reliable miRNA target gene prediction tool and is a successful application of an SVM classifier. Compared with previous tools, its predictions are meaningful by GO analysis and its performance can be improved given more training examples.

Algorithms↗

PubMed2006

Computed tomographic differentiation between alcoholic and gallstone pancreatitis: Significance of distribution of infiltration or fluid collection.

AIM: To evaluate the usefulness of various computed tomography (CT) findings including distribution of infiltration or fluid collection in differentiating the major etiologies of acute pancreatitis. METHODS: We reviewed 75 relatively severe cases of acute pancreatitis of alcoholic (n = 43) or biliary stone (n = 32) etiology having infiltration or fluid collection on CT. We compared the pancreatic size, CT grading, presence or absence of biliary calculi, and dilatation of pancreatic or bile duct. We also evaluated degree and the distribution of infiltration and fluid collection in each group. RESULTS: The sizes of pancreas were not different between alcohol group and stone group. Alcohol group showed higher CT grading than stone group (P < 0.05). Presence of biliary stone and duct dilatation was statistically significant in differentiating etiology (P < 0.05). Alcohol group showed significantly prominent peripancreatic pathology than stone group only in left peritoneal compartment (P = 0.020). CONCLUSION: Alcoholic pancreatitis tends to form more prominent peripancreatic changes than gallstone pancreatitis in relatively severe cases. This is evident on the anterior aspect of left abdomen. Although clinical history and some CT findings usually are a major determinant of the etiology, this pattern of peripancreatic pathology may have an ancillary role in determining the etiologies of acute pancreatitis in the equivocal cases.

Acute Disease↗

PubMed2006

ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs.

ProMiR is a web-based service for the prediction of potential microRNAs (miRNAs) in a query sequence of 60-150 nt, using a probabilistic colearning model. Identification of miRNAs requires a computational method to predict clustered and nonclustered, conserved and nonconserved miRNAs in various species. Here we present an improved version of ProMiR for identifying new clusters near known or unknown miRNAs. This new version, ProMiR II, integrates additional evidence, such as free energy data, G/C ratio, conservation score and entropy of candidate sequences, for more controllable prediction of miRNAs in mouse and human genomes. It also provides a wider range of services, e.g. the prediction of miRNA genes in long nonrelated sequences such as viral genomes. Importantly, we have validated this method using several case studies. All data used in ProMiR II are structured in the MySQL database for efficient analysis. The ProMiR II web server is available at http://cbit.snu.ac.kr/~ProMiR2/.

Animals↗

PubMed2006

In vivo binding of hot pepper bZIP transcription factor CabZIP1 to the G-box region of pathogenesis-related protein 1 promoter.

We find that salicylic acid and ethephon treatment in hot pepper increases the expression of a putative basic/leucine zipper (bZIP) transcription factor gene, CabZIP1. CabZIP1 mRNA is expressed ubiquitously in various organs. The green fluorescent protein-fused transcription factor, CabZIP1::GFP, can be specifically localized to the nucleus, an action that is consistent with the presence of a nuclear localization signal in its protein sequence. Transient overexpression of the CabZIP1 transcription factor results in an increase in PR-1 transcripts level in Nicotiana benthamiana leaves. Using chromatin immunoprecipitation, we demonstrate that CabZIP1 binds to the G-box elements in native promoter of the hot pepper pathogenesis-related protein 1 (CaPR-1) gene in vivo. Taken together, our results suggest that CabZIP1 plays a role as a transcriptional regulator of the CaPR-1 gene.

Amino Acid Sequence↗

PubMed2006

Characteristics of pixel arrangements in various rhombuses for full-parallax three-dimensional image generation.

In full-parallax three-dimensional (3-D) imaging systems, the pixel cells often have the shape of a rhombus. Proper arrangement of pixels in these rhombic-shaped cells is important to maximize the quality of displayable 3-D images with a given display panel. The possible number of pixel arrangements in a rhombic cell with a definite dimension is found by considering the number of possible crossings between parallel line families forming the pixel cells, when the slopes of the lines are approximated by the ratio between the number of pixels in the vertical and horizontal directions. To make the rhombic cell have a uniquely defined pixel arrangement, its horizontal and vertical dimensions should be equal to the even multiple of the pixel dimension in their corresponding direction.

Algorithms↗

PubMed2005

Analysis of color distortions in a transmission-type holographic screen.

Full-color transmission-type holographic screens for displaying stereoscopic and multiview images suffer color distortions, especially at their edges. These distortions arise because the reconstructed image of the diffuser appears not at a specified location at different locations for different parts of the screen. Analysis shows that the diffuser strip, which is an object that records the screen, should be extended further in the photoplate direction than in the conventional position to remove the distortions and that use of a short-wavelength laser in the blue spectral region, along with extending the diffuser, is recommended for recording large-sized screens. The analysis also allows the largest sizes of screens that can be recorded for a given set of parameters to be calculated. A comparison of the quality of the images displayed on the screens recorded in the conventional position and in the newly developed position has shown distinctive improvements for the new position.

Journal Article↗

PubMed2004

Pulse-laser electroholography by use of interference fringe patterns captured by a CCD.

Digital holography is combined with a pulse-laser electroholographic system for a real-time three-dimensional display. Owing to the one-dimensional characteristics of the Bragg-regime acousto-optic spatial-light modulator, vertical parallax cannot be generated from the acoustic signal propagating along the fan-shaped beam direction of the incident laser. To obtain a proper interference pattern, we attach a horizontal slit to the confocal lens system for recording the fringe data, significantly reducing the bandwidth of the vertical fringe data. When the bandwidth-reduced fringe data are displayed by use of a pulse-laser electroholographic system, the clarity and the quality of the image are found to be appreciably improved.

Journal Article↗

PubMed2003

N-nitration of secondary amines with 4-chloro-5-methoxy-2-nitropyridazin-3-one.

N-Nitration of 4-chloro-5-substituted-pyridazin-3-one with copper nitrate trihydrate in acetic anhydride gave the corresponding 4-chloro-2-nitro-5-substituted-pyridazin-3-one. 4-Chloro-5-alkoxy-2-nitropyridazin-3-ones such as 5-methoxy (2b) and 5-ethoxy (2d) derivatives showed excellent nitro group transfer potentiality. N-Nitration of some secondary amines with 2b gave the corresponding N-nitramines under mild neutral condition in good yields.

Journal Article↗