Biomedical subjects

So-Yeon Kim

Publications and source records attributed to So-Yeon Kim.

16 recordsLinked to original sources

PubMed2026

SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.

Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

differential abundance↗

PubMed2006

Honokiol reduces oxidative stress, c-jun-NH2-terminal kinase phosphorylation and protects against glycochenodeoxycholic acid-induced apoptosis in primary cultured rat hepatocytes.

Hydrophobic bile acid-induced apoptosis plays an important role in cholestatic liver disease, and its prevention may be of therapeutic interest. The aim of this study was to investigate the protective effect of honokiol on glycochenodeoxycholic acid-induced apoptosis in primary cultured rat hepatocytes. Glycochenodeoxycholic acid is a hydrophobic bile salt that accumulates intrahepatically during cholestasis and induces hepatocyte apoptosis at pathophysiological concentrations. Primary rat hepatocytes were pretreated with honokiol at concentrations of 40, 20 and 10 microM 5 min before glycochenodeoxycholic acid treatment. Incubation of hepatocytes with glycochenodeoxycholic acid at a concentration of 100 microM for 4 h induced apoptosis as shown by DNA fragmentation, chromatin condensation and cleavage of poly(ADP-ribose) polymerase. Pretreatment with honokiol at concentrations of 40, 20 and 10 microM significantly inhibited the generation of intracellular reactive oxygen species and reduced activation of caspases-8, -9, and -3 and cleavage of poly-(ADP-ribose) polymerase. Glycochenodeoxycholic acid treatment up-regulated phosphorylation of stress-activated protein kinase/c-jun-NH2-terminal kinase which was inhibited by honokiol treatment. Inhibition of stress-activated protein kinase/c-jun-NH2-terminal kinase phosphorylation by SP600125 protected hepatocytes from apoptosis induced by glycochenodeoxycholic acid. These data indicate that honokiol protects hepatocytes from apoptosis induced by glycochenodeoxycholic acid in vitro and this protection may be due to reduced oxidative stress and inhibition of stress-activated protein kinase/c-jun-NH2-terminal kinase phosphorylation.

Animals↗

PubMed2006

Two-dimensional electrophoretic profiling of atopic dermatitis in primary cultured keratinocytes from patients.

Recently, we reported altered protein expression in primary cultured fibroblasts from atopic dermatitis (AD) patients. As a sequential study, we conducted proteomic analysis of primary keratinocytes derived from AD patients to further identify AD-related proteins. Three pH ranges, 4-7, 6-9, and 7-11, were used to profile the altered protein expression in AD. We obtained 46 candidate spots from the 2-D gel image analysis: 18 proteins were up-regulated and 27 proteins were down-regulated. Among the several important candidate proteins, NCC27 showed the same profile of a defect in PTM in both AD-derived keratinocytes and fibroblasts. On the basis of current and previous reports, real-time PCR was performed on select candidate genes to compare RNA and protein expression levels in AD-derived keratinocytes and fibroblasts. Our results provide new clues to aid in understanding the mechanism of atopic alterations in keratinocytes and suggest new AD-associated proteins that are important in AD pathogenesis.

Adolescent↗

PubMed2006

Naringin time-dependently lowers hepatic cholesterol biosynthesis and plasma cholesterol in rats fed high-fat and high-cholesterol diet.

The flavonoid naringin was investigated for its differential effects on hepatic cholesterol regulation when supplemented for 3 weeks and 6 weeks. Sprague-Dawley rats were fed a high-fat and high-cholesterol diet with or without 0.02% naringin supplement for 3 or 6 weeks. Supplementation with naringin resulted in a significant decrease in the plasma cholesterol and triglyceride concentrations in the 6-week trial. Although high-density lipoprotein (HDL)-cholesterol was not altered in either trial, the HDL-cholesterol/total cholesterol ratio (in percent) was significantly higher, and the atherogenic index was significantly lower in the naringin-supplemented groups in the 6-week trial. The hepatic cholesterol content was also lowered by naringin supplementation only in the 6-week trial. The hepatic 3-hydroxy-3-methylglutaryl-coenzyme A reductase activity was lower in the rats supplemented with naringin for 6 weeks, while the hepatic acyl-coenzyme A:cholesterol acyltransferase activity was lower in both the 3-week and 6-week trials. Results indicate that supplementation with naringin for 3 weeks did not exhibit a hypolipidemic effect when given with a HFHC diet. Naringin can, however, be beneficial for lowering hepatic cholesterol biosynthesis and levels of plasma lipids when supplemented for 6 weeks in this animal model.

Animals↗

PubMed2006

Regulation of insulin secretion and beta-cell mass by activating signal cointegrator 2.

Activating signal cointegrator 2 (ASC-2) is a transcriptional coactivator of many nuclear receptors (NRs) and other transcription factors and contains two NR-interacting LXXLL motifs (NR boxes). In the pancreas, ASC-2 is expressed only in the endocrine cells of the islets of Langerhans, but not in the exocrine cells. Thus, we examined the potential role of ASC-2 in insulin secretion from pancreatic beta-cells. Overexpressed ASC-2 increased glucose-elicited insulin secretion, whereas insulin secretion was decreased in islets from ASC-2+/- mice. DN1 and DN2 are two dominant-negative fragments of ASC-2 that contain NR boxes 1 and 2, respectively, and block the interactions of cognate NRs with the endogenous ASC-2. Primary rat islets ectopically expressing DN1 or DN2 exhibited decreased insulin secretion. Furthermore, relative to the wild type, ASC-2+/- mice showed reduced islet mass and number, which correlated with increased apoptosis and decreased proliferation of ASC-2+/- islets. These results suggest that ASC-2 regulates insulin secretion and beta-cell survival and that the regulatory role of ASC-2 in insulin secretion appears to involve, at least in part, its interaction with NRs via its two NR boxes.

Amino Acid Motifs↗

PubMed2005

Functional expression of single-chain variable fragment antibody against c-Met in the cytoplasm of Escherichia coli.

c-Met, a high affinity receptor for hepatocyte growth factor/scatter factor, shown to be overexpressed in a variety of malignant cells, is a potential biomarker as well as a therapeutic target. Thus, single-chain antibody fragment (scFv) specific for c-Met is expected to be efficiently employed in the clinical treatment or imaging of many cancer cells. Here, we constructed the expression system for anti-c-Met scFv fused with T7 tag at its N-terminus using pET vector and investigated the expression conditions to achieve a functional and soluble expression of the scFv in the cytoplasm of recombinant Escherichia coli. The redox potential of E. coli cytoplasm was the most critical factor for the functional expression of anti-c-Met scFv. The employment of a host with oxidizing cytoplasm, E. coli trxB/gor double mutant, improved the productivity of functional anti-c-Met scFv by approximately 10-fold compared to the production of anti-c-Met scFv in the reducing cytoplasm of wild type E. coli. Productivity of functional anti-c-Met scFv could be further enhanced by co-expressing molecular chaperones such as GroELS, trigger factor, and DsbC with the scFv. Coexpression of DsbC increased the yield of functional anti-c-Met scFv about 2.5-fold in the cytoplasm of E. coli trxB/gor mutant compared to the production of scFv without DsbC coexpression. Lowering the IPTG concentration from 1 to 0.05 mM led to the slight enhancement, approximately 1.6-fold, of productivity of functional scFv. Although the use of low temperature for anti-c-Met scFv expression increased the ratio of soluble scFv fraction to insoluble fraction, productivity of soluble scFv decreased owing to the significant reduction of expression rate. The addition of 0.5 M sucrose in the medium inhibited the formation of intracellular insoluble anti-c-Met scFv. To purify the anti-c-Met scFv simply, we fused hexahistidine at the C-terminus of scFv and purified the scFv showing 98% of purity through the interaction between Ni2+ and histidine.

Antibodies↗

PubMed2005

Concurrent working memory load can reduce distraction.

People have difficulty performing two tasks at once. For example, maintaining items in working memory (WM) makes people more distractible. However, different types of WM load may have different effects on attentional selection depending on whether WM load overlaps with mechanisms involved in target or distractor processing. Three experiments examined the effect of concurrent WM load on Stroop tasks, a widely used measure of executive control and inhibition. Stroop interference increased when the type of WM load overlapped with the type of information required for the target task (experiment 1). In striking contrast, Stroop interference decreased when the type of WM load overlapped with distractor processing (experiment 2). Experiment 3 replicated these results in a different Stroop task. Thus, concurrent WM load does not always impair executive control; performance depends on how contents of WM and task-relevant information overlap. The results highlight how dissociable components of WM interact with perception and executive control.

Attention↗

PubMed2005

C-terminal domain of hepatitis C virus core protein is essential for secretion.

AIM: We have previously demonstrated that hepatitis C virus (HCV) core protein is efficiently released into the culture medium in insect cells. The objective of this study is to characterize the HCV core secretion in insect cells. METHODS: We constructed recombinant baculoviruses expressing various-length of mutant core proteins, expressed these proteins in insect cells, and examined core protein secretion in insect cells. RESULTS: Only wild type core was efficiently released into the culture medium, although the protein expression level of wild type core was lower than those of other mutant core proteins. We found that the shorter form of the core construct expressed the higher level of protein. However, if more than 18 amino acids of the core were truncated at the C-terminus, core proteins were no longer secreted into the culture medium. Membrane flotation data show that the secreted core proteins are associated with the cellular membrane protein, indicating that HCV core is secreted as a membrane complex. CONCLUSION: The C-terminal 18 amino acids of HCV core were crucial for core secretion into the culture media. Since HCV replication occurs on lipid raft membrane structure, these results suggest that HCV may utilize a unique core release mechanism to escape immune surveillance, thereby potentially representing the feature of HCV morphogenesis.

Animals↗

PubMed2005

Cilostazol inhibits vascular smooth muscle cell growth by downregulation of the transcription factor E2F.

Neointimal formation, the leading cause of restenosis, is caused by proliferation of vascular smooth muscle cells (VSMCs). Patients with diabetes mellitus have higher restenosis rates after coronary angioplasty than nondiabetic patients. Cilostazol, a selective type 3 phosphodiesterase inhibitor, is currently used to treat patients with diabetic vascular complications. Cilostazol is a potent antiplatelet agent that inhibits VSMC proliferation. In the present study, we examine whether the antiproliferative effect of cilostazol on VSMCs is mediated by inhibition of an important cell cycle transcription factor, E2F. Cilostazol inhibited the proliferation of human VSMCs in response to high glucose in vitro and virtually abolished neointimal formation in rats subjected to carotid artery injury in vivo. Moreover, the compound suppressed high-glucose-induced E2F-DNA binding activity, and the expression of E2F1, E2F2, cyclin A, and PCNA proteins. These data suggest that the beneficial effects of cilostazol on high-glucose-stimulated proliferation of VSMCs are mediated by the downregulation of E2F activity and expression of its downstream target genes, including E2F1, E2F2, cyclin A, and PCNA.

8-Bromo Cyclic Adenosine Monophosphate↗

PubMed2005

A new type of uncompetitive inhibition of tyrosinase induced by Cl- binding.

A new type of Cl- induced inhibition of mushroom derived tyrosinase has been detected in this study, and it is defined as the reversible partial hyperbolic uncompetitive inhibition. The Cl- binding site was only induced at the state of the enzyme-substrate complex, and this was confirmed with the intrinsic fluorescence changes. As the oxygen bridge is broken by L-DOPA binding, Cl- simultaneously binds to the ES state to form the ESI complex. It is worth noticing that tyrosinase reacts sensitively to Cl- in the manner of a complex interaction, and this indicates that Cl- might be physiologically involved in the regulation of tyrosinase activity.

Ammonium Chloride↗

PubMed2004

Taurine increases glucose sensitivity of UCP2-overexpressing beta-cells by ameliorating mitochondrial metabolism.

A low-taurine diet during fetal or early postnatal life causes abnormal pancreatic beta-cell development. Tissue and plasma taurine concentrations can also be low in diabetic patients. We examined the effect of taurine on impaired glucose responses in diabetic rat beta-cells adenovirally overexpressing uncoupling protein (UCP)2, which is upregulated in obesity-related type 2 diabetes. We found that taurine pretreatment restored the ATP-to-ADP (ATP/ADP) ratio and glucose-stimulated insulin secretion in UCP2-infected islets. ATP-sensitive K(+) channel sensitivity to dihydroxyacetone, another insulin secretagogue, was similar in both UCP2-infected and control beta-cells. In freshly isolated mitochondria from UCP2-overexpressing insulin-secreting (INS)-1 beta-cells, methyl pyruvate-mediated mitochondrial Ca(2+) increase was significantly ameliorated by taurine. A mitochondrial Ca(2+) uniporter blocker, ruthenium red, inhibited the action of taurine. This study suggests that taurine enhances the glucose sensitivity of UCP2-overexpressing beta-cells, probably by increasing mitochondrial Ca(2+) influx through the Ca(2+) uniporter, thereby enhancing mitochondrial metabolic function and increasing the ATP/ADP ratio.

Adenosine Diphosphate↗

PubMed2004

Inhibition of ATP-sensitive K+ channels by taurine through a benzamido-binding site on sulfonylurea receptor 1.

ATP-sensitive potassium (K(ATP)) channels in pancreatic beta-cells comprise sulfonylurea receptor (SUR) 1 and inwardly-rectifying potassium channel (Kir) 6.2 subunits. We have evaluated the effect of intracellular taurine on K(ATP) channel activity in rat pancreatic beta-cells using the patch-clamp technique. The mechanism of taurine action was also examined using recombinant K(ATP) channels. The islets and single beta-cells from male Sprague-Dawley rats were collected by collagenase digestion technique. Single K(ATP) channel currents were recorded by the inside-out mode at a membrane potential of -60mV. Cytosolic free-Ca(2+) concentration ([Ca(2+)](c)) and insulin secretory capacity were measured by the dual-excitation fluorimetry and radioimmunoassay, respectively. The native beta-cell K(ATP) channel was directly inhibited by taurine in a dose-dependent manner. Taurine did not influence ATP-mediated inhibition or MgADP-induced activation of the channel activity. The sensitivity of the K(ATP) channel to glybenclamide, but not gliclazide, was enhanced by taurine. Glybenclamide elicited a greater increase in [Ca(2+)](c) and increased insulin secretion in the beta-cells when pretreated with taurine. Taurine did not inhibit Kir6.2DeltaC36 currents, a truncated form of Kir6.2, expressed in Xenopus oocytes without SUR. These results demonstrate that taurine inhibits the K(ATP) channel activity in the beta-cells, interacting with a benzamido-binding site on SUR1, but not Kir6.2.

Adenosine Diphosphate↗

PubMed2004

Towards a proteomic analysis of atopic dermatitis: a two-dimensional-polyacrylamide gel electrophoresis/mass spectrometric analysis of cultured patient-derived fibroblasts.

Atopic dermatitis (AD) is a chronic relapsing inflammatory skin disease typically characterized by a distribution of eczematous skin lesions with lichenification, pruritic excoriations, and dry skin with wide varieties of pathophysiologic aspects. Recently, AD was divided into extrinsic and intrinsic forms according to the presence or absence of an allergy. We investigated alterations in protein expression in primary cultured AD cells from the patient biopsy samples by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight. In the primary cultured fibroblasts, we obtained 31 candidate proteins from the two-dimensional gel image analysis in which 18 proteins were up-regulated, eight proteins were down-regulated and five proteins were post-translationally modified. From these 2-DE results, we found several candidate genes matched proteomic expression patterns by semiquantitative reverse transcription PCR. Since the exact mechanism of atopic alterations in fibroblasts remains unknown, our results may provide new clues to aid in understanding AD.

DNA, Complementary↗

PubMed2004

Enhancing effect of taurine on glucose response in UCP2-overexpressing beta cells.

Uncoupling protein 2 (UCP2) is up-regulated in pancreatic beta cells when exposed to long-term high glucose or free fatty acids, which results in impaired glucose-induced insulin secretion (GIIS). We have evaluated whether taurine pretreatment can restore impaired GIIS of beta cells overexpressing UCP2 by adenovirus (Ad)-mediated transfection technique. In Ad-Null control cells, externally applied glucose (10 mM) inhibited ATP-sensitive potassium (K(ATP)) channel activity even in the presence of 300 microM diazoxide. In Ad-UCP2 cells, however, glucose failed to inhibit K(ATP) channel activity; despite the response of K(ATP) channel itself to glibenclamide was normal. The glucose-stimulated increase of cytosolic Ca2+ concentration ([Ca2+]c) and insulin secretion was also diminished (P < 0.05). When taurine (3 mM) was pretreated for 24 h, the glucose responses of Ad-UCP2 cells were remarkably restored. The effect of taurine was, however, blocked by CCCP (carbonyl cyanide p-chlorophenylhydrazone; 2 microM), a mitochondrial Ca2+ uniporter inhibitor. These results suggest that taurine restores impaired GIIS in Ad-UCP2 cells, at least partially, by acting on the mechanism for Ca2+ sequestration into the mitochondrial matrix.

ATP-Binding Cassette Transporters↗

PubMed2003

Proteome changes induced by expression of tumor suppressor PTEN.

The tumor suppressor, PTEN, located at 10q23, is one of the most frequently mutated tumor suppressors in a number of sporadic cancers and in two autosomal dominant harmatomas. It is considered one of the most important tumor suppressors in the post p53 era. To identify the molecules involved in the signal network regulated by PTEN using proteomic tools, a PTEN-inducible expression system was established in NIH 3T3 mouse embryonic fibroblast cells. We compared proteome images of PTEN-induced and non-induced cells by 2-dimensional electrophoresis. Twenty-nine differentially expressed protein spots were identified by MALDI-TOF MS and NSI MS/MS. We conclude that expression of PTEN by itself leads to protein profile changes, and those proteins affected are likely to be directly and/or indirectly involved in the function and physiology of the tumor suppressor.

Animals↗

PubMed2002

Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature.

A large group of hydrolytic enzymes, which contain a conserved stretch of approximately 130 amino acids designated the amidase signature (AS) sequence, constitutes a super family that is distinct from any other known hydrolase family. AS family enzymes are widespread in nature, ranging from bacteria to humans, and exhibit a variety of biological functions. Here we report the first structure of an AS family enzyme provided by the crystal structure of malonamidase E2 from Bradyrhizobium japonicum. The structure, representing a new protein fold, reveals a previously unidentified Ser-cisSer-Lys catalytic machinery that is absolutely conserved throughout the family. This family of enzymes appears to be evolutionarily distinct but has diverged to acquire a wide spectrum of individual substrate specificities, while maintaining a core structure that supports the catalytic function of the unique triad. Based of the structures of the enzyme in two different inhibited states, an unusual action mechanism of the triad is proposed that accounts for the role of the cis conformation in the triad.

Amidohydrolases↗