Biomedical subjects

Sun Kim

Publications and source records attributed to Sun Kim.

13 recordsLinked to original sources

PubMed2006

REFINEMENT: a search framework for the identification of interferon-responsive elements in DNA sequences--a case study with ISRE and GAS.

Interferons (IFN) are a family of pleiotropic secreted proteins that play a key role in mediating antiviral and apoptotic responses, and in immune modulation. Interferons induce a large number of genes through activating the janus tyrosine kinase (JAK)-signal transducers and activators of transcription proteins (STAT) pathway, and the binding of transcription factors to upstream regions of the inducible genes (interferon-stimulated gene, ISG) at specific DNA regulatory elements known as interferon-stimulated response element (ISRE) and gamma-activated sequence (GAS). We have previously performed DNA micro-arrays on peripheral blood mononuclear cells (PBMC) treated with interferon-alpha in culture and showed that approximately 700 genes are significantly modulated (P < or = 0.001). In order to search for ISRE and GAS we have developed a framework called regulatory element finding with iteration and effective model refinement (REFINEMENT) using an existing program (HMMER) and a standard discriminating scoring technique. Although REFINEMENT uses existing programs, our framework itself is novel as it effectively discriminates occurrences using an iterative model refinement technique. REFINEMENT has detected either ISRE or GAS sequence in all of the genes shown to be induced at a P-value < or = 0.001. There were far more functional occurrences in ISRE than in GAS, suggesting that ISRE plays a greater role in response to interferon-alpha than GAS sequences. This method can be used to identify such sequences in any set of genes. REFINEMENT is non-commercial and is accessible at .

Base Sequence↗

PubMed2006

A multistate empirical valence bond description of protonatable amino acids.

The multistate empirical valence bond (MS-EVB) model, which was developed for molecular dynamics simulations of proton transport in water and biomolecular systems, is extended for the modeling of protonatable amino acid residues in aqueous environments, specifically histidine and glutamic acid. The parameters of the MS-EVB force field are first determined to reproduce the geometries and energetics of the gas phase amino acid-water clusters. These parameters are then optimized to reproduce experimental pK(a) values. The free energy profiles for acid ionization and the corresponding pK(a) values are calculated by MS-EVB molecular dynamics simulations utilizing the umbrella sampling technique, with the center of excess charge coordinate chosen as the dissociation reaction coordinate. A general procedure for fitting the MS-EVB parameters is formulated, which allows for the parametrization of other amino acid residues with protonatable groups and the subsequent use of the MS-EVB approach for molecular dynamics simulations of proton transfer processes in proteins involving protonation/deprotonation of the protonatable amino acid groups.

Amino Acids↗

PubMed2005

COMPAM :visualization of combining pairwise alignments for multiple genomes.

UNLABELLED: COMPAM is a tool for visualizing relationships among multiple whole genomes by combining all pairwise genome alignments. It displays shared conserved regions (blocks) and where these blocks occur (edges) as block relation graphs which can be explored interactively. An unannotated genome, e.g. can then be explored using information from well-annotated genomes, COG-based genome annotation and genes. COMPAM can run either as a stand-alone application or through an applet that is provided as service to PLATCOM, a toolset for whole genome comparative analysis, where a wide variety of genomes can be easily selected. Features provided by COMPAM include the ability to export genome relationship information into file formats that can be used by other existing tools. AVAILABILITY: http://bio.informatics.indiana.edu/projects/compam/

Algorithms↗

PubMed2005

New anti-cancer strategies: epigenetic therapies and biomarkers.

Epigenetics is the study of chromatin modifications that affect gene expression without altering DNA nucleotide sequences. This review highlights a prominent role for epigenetic therapies, particularly those that reverse aberrant DNA methylation and histone acetylation, in the potential treatment of cancer. Administration of such therapies to reverse epigenetic "silencing" of tumor suppressors, including genes involved in chemotherapy responses, could prove useful in the management of cancer patients. In this review, we summarize recent advances in the use of methyltransferase and histone deacetylase inhibitors and possible synergistic combinations of these to achieve maximal tumor suppressor gene re-expression. Moreover, when used in combination with conventional chemotherapeutic agents, epigenetic-based therapies may provide a means to resensitize drug-resistant tumors to established treatments. As specific, aberrant epigenetic modifications are frequently associated with distinct cancer types, and likely occur early in tumorigenesis, these have potential utility as biomarkers. Finally, future directions are addressed, including alternative epigenetic targets, gene-specific modifications, and the use of bioinformatics.

Acetylation↗

PubMed2005

PLATCOM: a Platform for Computational Comparative Genomics.

MOTIVATION: As more whole genome sequences become available, comparing multiple genomes at the sequence level can provide insight into new biological discovery. However, there are significant challenges for genome comparison. The challenge includes requirement for computational resources owing to the large volume of genome data. More importantly, since the choice of genomes to be compared is entirely subjective, there are too many choices for genome comparison. For these reasons, there is pressing need for bioinformatics systems for comparing multiple genomes where users can choose genomes to be compared freely. RESULTS: PLATCOM (Platform for Computational Comparative Genomics) is an integrated system for the comparative analysis of multiple genomes. The system is built on several public databases and a suite of genome analysis applications are provided as exemplary genome data mining tools over these internal databases. Researchers are able to visually investigate genomic sequence similarities, conserved gene neighborhoods, conserved metabolic pathways and putative gene fusion events among a set of selected multiple genomes. AVAILABILITY: http://platcom.informatics.indiana.edu/platcom

Chromosome Mapping↗

PubMed2005

GAME: a simple and efficient whole genome alignment method using maximal exact match filtering.

In this paper, we present a simple and efficient whole genome alignment method using maximal exact match (MEM). The major problem with the use of MEM anchor is that the number of hits in non-homologous regions increases exponentially when shorter MEM anchors are used to detect more homologous regions. To deal with this problem, we have developed a fast and accurate anchor filtering scheme based on simple match extension with minimum percent identity and extension length criteria. Due to its simplicity and accuracy, all MEM anchors in a pair of genomes can be exhaustively tested and filtered. In addition, by incorporating the translation technique, the alignment quality and speed of our genome alignment algorithm have been further improved. As a result, our genome alignment algorithm, GAME (Genome Alignment by Match Extension), performs competitively over existing algorithms and can align large whole genomes, e.g., A. thaliana, without the requirement of typical large memory and parallel processors. This is shown using an experiment which compares the performance of BLAST, BLASTZ, PatternHunter, MUMmer and our algorithm in aligning all 45 pairs of 10 microbial genomes. The scalability of our algorithm is shown in another experiment where all pairs of five chromosomes in A. thaliana were compared.

Algorithms↗

PubMed2005

Diversification of non-TIR class NB-LRR genes in relation to whole-genome duplication events in Arabidopsis.

Arabidopsis thaliana is believed to have experienced at least two and possibly three whole-genome duplication events in its evolutionary history. In order to investigate the evolutionary relationships between these duplication events and diversification of disease resistance (R) genes, segmental-duplication events containing R genes belonging to the nucleotide binding-leucine rich repeat (NB-LRR) class were identified. Of 153 segmental-duplication events containing NB-LRR genes, only 22 contained NB-LRR genes in both members of the duplication pair, indicating a high frequency of NB-LRR gene loss after whole-genome duplication. The relative age of the duplication events was estimated based on the average synonymous substitution rate of the duplicated gene pairs in the segments. These data were combined with phylogenetic analyses. NB-LRR genes present in segment pairs derived from the most recent whole-genome duplication event, estimated to have occurred only 20 to 40 million years ago, occupy very distant branches of the NB-LRR phylogenetic tree. These data suggest that when NB-LRR clusters are duplicated as part of a whole-genome duplication, homoeologous NB-LRR genes are preferentially lost, either by eliminating one copy of the cluster or by eliminating individual genes such that only paralogous NB-LRR genes are maintained.

Arabidopsis↗

PubMed2005

Gene teams with relaxed proximity constraint.

Functionally related genes co-evolve, probably due to the strong selection pressure in evolution. Thus we expect that they are present in multiple genomes. Physical proximity among genes, known as gene team, is a very useful concept to discover functionally related genes in multiple genomes. However, there are also many gene sets that do not preserve physical proximity. In this paper, we generalized the gene team model, that looks for gene clusters in a physically clustered form, to multiple genome cases with relaxed constraint. We propose a novel hybrid pattern model that combines the set and the sequential pattern models. Our model searches for gene clusters with and/or without physical proximity constraint. This model is implemented and tested with 97 genomes (120 replicons). The result was analyzed to show the usefulness of our model. Especially, analysis of gene clusters that belong to B. subtilis and E. coli demonstrated that our model predicted many experimentally verified operons and functionally related clusters. Our program is fast enough to provide a sevice on the web at http://platcom. informatics.indiana.edu/platcom/. Users can select any combination of 97 genomes to predict gene teams.

Algorithms↗

PubMed2003

Increased translocation of cardiac protein kinase C beta2 accompanies mild cardiac hypertrophy in rats fed saturated fat.

Signal transduction through protein kinase C (PKC) beta2 may modulate cardiac hypertrophy in pressure-overloaded rat myocardium. Because PKC beta2 can be activated by fatty acids and diacylglycerol, we hypothesized that altering the level and type of dietary fat might modulate cardiac PKC activation and stimulate hypertrophy in otherwise normal rat myocardium. Male Sprague-Dawley rats (n = 32) were randomly assigned to either a low fat [10% total energy intake (TEI)] or high fat diet (40% TEI) based on corn or coconut oil as a source of saturated or unsaturated fat. After 40 d of isoenergetic diet consumption, the heart/body weight ratio was slightly greater in rats fed saturated fat diets compared with those fed unsaturated fat (P = 0.05). Increased activation of PKC beta2, as evidenced by greater membrane translocation, was also observed in all rats fed saturated fat diets (P < 0.01). PKC alpha, beta1 and epsilon did not change. These results suggest that dietary fat type can alter PKC beta2 activation in the heart, and exert a mild hypertrophic effect on the heart.

Animals↗

PubMed2003

Suppression of rat and human growth hormone and prolactin secretion by a novel somatostatin/dopaminergic chimeric ligand.

As cotreatment of somatostatin (SRIF) and dopamine (DA) agonists reduces GH in acromegaly more effectively than either agonist alone, SRIF and DA receptors (SSTR and DAR) may interact with enhanced functional activity. The selective SSTR2 agonist, BIM-23023 (50% effective dose, 0.42), and the DAR2 agonist, BIM-53097 (50% effective dose, 22.1), dose- dependently inhibited GH secretion in cultured primary rat and human fetal as well as in human pituitary tumor cells derived from GH-secreting adenomas. The combination of individual SSTR2 and DAR2 agonists was additive for suppressing GH secretion in both rat and human pituitary cells. BIM-23A387 is a chimeric compound that contains structural elements of both SRIF and DA in a single molecule and retains potent, selective binding to DAR2 and SSTR2. BIM-23A387 (50% effective dose, 0.16 for SSTR2 and 24.5 for DAR2), displayed similar efficacy in suppressing GH secretion from rat pituitary cells as the combination of the two individual agonists. In contrast, the chimeric molecule was more potent than individual selective analogs in suppressing GH secretion by human fetal pituitary and GH-secreting adenoma cells (P < 0.05). Although the DAR2 antagonist, sulpiride, reversed BIM-23A387-induced GH suppression, blockade of SSTR2 by the selective SSTR antagonist, BIM-23454, did not block BIM-23A387-suppressed GH secretion. These results indicate that mechanisms by which the chimeric molecule suppresses pituitary GH secretion may not be mediated by individual SSTR2 or DAR2 signaling, respectively. Functional interaction of the two receptors may explain the clinical observation that more effective GH suppression is achieved when DAR2 and SSTR2 agonists are administered in combination. The SRIF/DA chimeric molecule, BIM-23A387, represents a novel tool for effective drug treatment of acromegaly and for prolactinomas otherwise resistant to dopaminergic therapy.

Animals↗

PubMed2002

Curriculum design for problem-based learning on a volunteer basis: a Yonsei approach.

Innovative new medical programs such as Problem Based Learning (PBL) are being developed worldwide. An increasing number of medical schools are starting to introduce these programs into or even to replace the existing curriculum. At Yonsei University College of Medicine (YUCM), we developed our own PBL curriculum and evaluation method. In order to develop a program suitable for our school, we suggest that for trial purposes, a small number of student and teacher volunteers should be selected and that the tutors involved in the program be given adequate training.

Education, Medical↗

PubMed2001

Meningioangiomatosis: MR imaging and pathological correlation in two cases.

Meningioangiomatosis is a rare, benign neoplastic disorder involving the cortex and leptomeninges. The pathological findings are characterised by proliferation of meningothelial cells and leptomeningeal vessels and calcifications within the mass. We experienced two cases of pathologically confirmed meningioangiomatosis, one as a solitary cortical mass with calcification and the other as a cortical lesion manifested as extensive intracranial haemorrhage. On MRI, the first case showed an isointense cortical mass in the left frontal lobe and homogeneous enhancement on the contrast-enhanced study. The second case showed a target-like lesion with a peripheral dark signal rim on T2-weighted images accompanied by extensive haemorrhage in the adjacent frontal lobe and lateral ventricles.

Child↗

PubMedDate not supplied

Postpartum emotional distress in mothers with multiple sclerosis.

OBJECTIVE: To determine the impact of multiple sclerosis (MS)-related symptoms and both received social support and perceived deficits in social support on emotional distress in mothers with MS at 1, 3, and 6 months postpartum. DESIGN: Longitudinal correlation descriptive study. SETTING: Community-residing women in North America. PARTICIPANTS: Convenience sample of 174 postpartum mothers with MS. METHOD: Mothers completed the MS-Related Symptom Scale and Postpartum Support Questionnaire at 1, 3, and 6 months postpartum. Bivariate correlations and hierarchical regression analyses determined relationships between the dependent variable, emotional distress, and independent variables: participant characteristics, MS-related symptoms, and social support. RESULTS: The authors found moderately strong positive correlations between MS-related symptoms and emotional distress at each assessment. Significant negative correlations existed between received social support and emotional distress at 1 month but not at 3 and 6 months. Significant positive correlations existed between MS-related symptoms and social support deficits at each assessment. Explained variance in emotional distress across the three assessments ranged between 2% and 4% for participant characteristics, 49% and 60% for MS-related symptoms, 2% and 7% for social support, and 57% and 66% for total variance. CONCLUSION: MS-related symptoms created considerable emotional distress in mothers that was minimally alleviated by the support given them. In fact, many needed more support than they received.

Adaptation, Psychological↗