Biomedical subjects

Ji-Young Lee

Publications and source records attributed to Ji-Young Lee.

At least 19 recordsLinked to original sources

PubMed2025

ONAC005 enhances salt stress tolerance by promoting suberin deposition in root endodermis.

Salt stress impairs photosynthetic efficiency and consequently reduces the growth, development, and grain yield of crop plants. The formation of hydrophobic barriers in the root endodermis, including the suberin lamellae and Casparian strips, is a key adaptive strategy for salt stress tolerance. In this study, we identified the role of the rice NAC transcription factor, ONAC005, in salt stress tolerance. ONAC005 expression was induced by NaCl and abscisic acid (ABA). Expression analysis using the β-glucuronidase reporter gene driven by the ONAC005 promoter revealed that ONAC005 is predominantly expressed in the stele and endodermis of rice roots. The null mutation of ONAC005 increased sodium ion levels in the shoots and roots, indicating susceptibility to salt stress, whereas ONAC005 overexpression enhanced tolerance to salt stress by reducing sodium ion accumulation. Yeast one-hybrid, chromatin immunoprecipitation, and dual-luciferase assays demonstrated that ONAC005 upregulates the expression of trehalose-6-phosphate synthase 8 (OsTPS8) by directly binding to its promoter region, leading to increased trehalose accumulation. ONAC005 enhances the formation of the root hydrophobic barrier by upregulating OsTPS8 expression under salt stress. Furthermore, considering the altered expression of ABA signaling and responsive genes, ONAC005 regulates the expression of genes in specific stress-responsive pathways that are independent of OsTPS8-mediated signaling. These results indicate that ONAC005 positively regulates hydrophobic barrier formation in the roots, thereby enhancing salt stress tolerance in rice.

Oryza↗

PubMed2006

Forward chemical genetic approach identifies new role for GAPDH in insulin signaling.

Insulin and insulin-like growth factor have an essential role in growth, development and the maintenance of metabolic homeostasis, including glucose uptake from the bloodstream. Researchers have identified mutations in insulin receptors that cause severe insulin resistance, and a temperature-sensitive daf-2 (a gene encoding an insulin receptor-like protein) mutant in Caenorhabditis elegans has served as an insulin resistance model. Here we report a forward chemical genetic approach with a tagged library that we used to identify a small molecule, GAPDH segregator (GAPDS), that suppresses the dauer formation induced by the daf-2 mutant. Like insulin, GAPDS increased both glucose uptake and the concentration of phosphatidylinositol-3,4,5-trisphosphate (PtdIns(3,4,5)P(3)) in mammalian preadipocytes. Using affinity matrices and RNA interference, we identified glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as a GAPDS target. We discovered that GAPDH stimulates phosphatase activity against not only PtdIns(3,4,5)P(3) but also PtdIns(4,5)P(2). These results suggest that GAPDH is both an active regulator in the phosphoinositide-mediated signaling pathway and a potential new target for insulin resistance treatment.

Adipocytes↗

PubMed2006

Quantitative screening of single copies of human papilloma viral DNA without amplification.

We describe a novel quantitative viral screening method based on single-molecule detection that does not require amplification. DNA of human papilloma virus (HPV), the major etiological agent of cervical cancer, served as the screening target in this study. Eight 100-nucleotide single-stranded DNA probes were designed complementary to the E6-E7 gene of HPV-16 DNA. The probes were covalently stained with Alexa Fluor 532 and hybridized to the target in solution. The individual hybridized molecules were imaged with an intensified charge-coupled device (ICCD) in two ways. In the single-color mode, target molecules were detected via fluorescence from hybridized probes only. This system could detect HPV-16 DNA in the presence of human genomic DNA down to 0.7 copy/cell and had a linear dynamic range of over 6 orders of magnitude. In the dual-color mode, we employed fluorescence resonance energy transfer and added YOYO-3 dye as the acceptor. The two colors from Alexa Fluor 532 and YOYO-3 were dispersed by a transmission grating located in front of the ICCD. With this reinforced criterion for identifying the hybridized molecules, zero false-positive count was achieved. We also showed that DNA extracts from Pap test specimens did not interfere with the measurements.

Cell Line, Tumor↗

PubMed2006

In vitro activities of ertapenem against drug-resistant Streptococcus pneumoniae and other respiratory pathogens from 12 Asian countries.

In vitro activities of ertapenem and 11 other comparator agents were tested against 1025 isolates of respiratory pathogens collected from 12 Asian countries. Resistance rate to ertapenem was 1.2% in 602 isolates of Streptococcus pneumoniae (MIC(50), 0.06/MIC(90), 1 microg/mL). Ertapenem was also very active against penicillin-, ciprofloxacin-, erythromycin-, and multidrug-resistant pneumococcal isolates (resistance rate: 3.5%, 2.7%, 1.9%, and 2.7%, respectively). Ertapenem-resistant pneumococcal isolates were found only in Vietnam and Korea. Ertapenem resistance was not found in methicillin-susceptible Staphylococcus aureus, Haemophilus influenzae, Moraxella catarrhalis, and Klebsiella pneumoniae, including extended-spectrum beta-lactamase producers. In vitro data suggest that ertapenem could be a useful treatment option for community-acquired pneumonia.

Anti-Bacterial Agents↗

PubMed2006

Quantification of transcription factor expression from Arabidopsis images.

MOTIVATION: Confocal microscopy has long provided qualitative information for a variety of applications in molecular biology. Recent advances have led to extensive image datasets, which can now serve as new data sources to obtain quantitative gene expression information. In contrast to microarrays, which usually provide data for many genes at one time point, these image data provide us with expression information for only one gene, but with the advantage of high spatial and/or temporal resolution, which is often lostin microarray samples. RESULTS: We have developed a prototype for the automatic analysis of Arabidopsis confocal images, which show the expression of a single transcription factor by means of GFP reporter constructs. Using techniques from image registration, we are able to address inherent problems of non-rigid transformation and partial mapping, and obtain relative expression values for 13 different tissues in Arabidopsis roots. This provides quantitative information with high spatial resolution, which accurately represents the underlying expression values within the organism. We validate our approach on a data set of 122 images depicting expression patterns of 30 transcription factors, both in terms of registration accuracy, as well as correlation with cell-sorted microarray data. Approaches like this will be useful to lay the groundwork to reconstruct regulatory networks on the level of tissues or even individual cells. AVAILABILITY: Upon request from the authors.

Arabidopsis Proteins↗

PubMed2006

In vitro activity of cefditoren: antimicrobial efficacy against major respiratory pathogens from Asian countries.

In this study we evaluated the in vitro activities of cefditoren and 14 other comparator agents against 1025 isolates of major respiratory tract pathogens including Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Klebsiella pneumoniae and Staphylococcus aureus. Bacterial isolates were collected from 11 Asian countries. The majority of S. pneumoniae isolates (98.8%) were susceptible to cefditoren. The MIC(50) and MIC(90) values (minimum inhibitory concentrations for 50% and 90% of the organisms, respectively) of S. pneumoniae were <or=0.06 microg/mL and 1 microg/mL, respectively. These values were 2-32-fold lower than those of the other cephalosporins. Activity against S. pneumoniae was observed irrespective of penicillin or macrolide resistance. Cefditoren was also active against methicillin-susceptible S. aureus (100% susceptible; MIC(90)=1 microg/mL), H. influenzae (100% susceptible; MIC(90)<or=0.016 microg/mL) and M. catarrhalis (MIC(90)=0.016 microg/mL). However, the cefditoren MIC(90) of K. pneumoniae reached only 64 microg/mL (81.4% susceptible), which may be due to the high incidence of extended-spectrum beta-lactamases in Asian countries. Therefore, cefditoren should be considered as a therapeutic option for the treatment of respiratory tract infections in Asian countries.

Anti-Bacterial Agents↗

PubMed2006

Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots.

Understanding how the expression of transcription factor (TF) genes is modulated is essential for reconstructing gene regulatory networks. There is increasing evidence that sequences other than upstream noncoding can contribute to modulating gene expression, but how frequently they do so remains unclear. Here, we investigated the regulation of TFs expressed in a tissue-enriched manner in Arabidopsis roots. For 61 TFs, we created GFP reporter constructs driven by each TF's upstream noncoding sequence (including the 5'UTR) fused to the GFP reporter gene alone or together with the TF's coding sequence. We compared the visually detectable GFP patterns with endogenous mRNA expression patterns, as defined by a genome-wide microarray root expression map. An automated image analysis method for quantifying GFP signals in different tissues was developed and used to validate our visual comparison method. From these combined analyses, we found that (i) the upstream noncoding sequence was sufficient to recapitulate the mRNA expression pattern for 80% (35/44) of the TFs, and (ii) 25% of the TFs undergo posttranscriptional regulation via microRNA-mediated mRNA degradation (2/24) or via intercellular protein movement (6/24). The results suggest that, for Arabidopsis TFs, upstream noncoding sequences are major contributors to mRNA expression pattern establishment, but modulation of transcription factor protein expression pattern after transcription is relatively frequent. This study provides a systematic overview of regulation of TF expression at a cellular level.

Arabidopsis↗

PubMed2006

In vitro evaluation of the antibiotic lock technique (ALT) for the treatment of catheter-related infections caused by staphylococci.

OBJECTIVES: To investigate appropriate antimicrobial agents, the optimal concentration and treatment duration for the antibiotic lock technique (ALT) to treat catheter-related infections caused by Staphylococcus epidermidis and Staphylococcus aureus. METHODS: We evaluated the bacterial killing activity of vancomycin, teicoplanin, ciprofloxacin, rifampicin, cefazolin, gentamicin, nafcillin and erythromycin against biofilms formed by two strains of S. aureus and two strains of S. epidermidis. The effectiveness of the antibiotic lock was assayed after exposure to antibiotics (1, 5 and 10 mg/mL) for 1, 3, 5, 7, 10 or 14 days using an in vitro model of biofilms on polyurethane film. RESULTS: The biofilms were completely sterile after exposure to vancomycin (5 mg/mL) for 5 days and teicoplanin (5 and 10 mg/mL) for 7 days. Ciprofloxacin and rifampicin (both 5 mg/mL) achieved eradication of the biofilms of both staphylococcal species more rapidly than vancomycin or teicoplanin. Significant biofilm eradication was not achieved with cefazolin, nafcillin, gentamicin and erythromycin at any of the time exposures examined. CONCLUSIONS: The data suggest that 5 mg/mL vancomycin, ciprofloxacin or rifampicin can eradicate S. epidermidis and S. aureus biofilms within 5 days. These findings warrant prospective clinical trials for the evaluation of the clinical efficacy of ALT for less than 10 days.

Anti-Bacterial Agents↗

PubMed2006

Expression profiling of mucinous tumors of the ovary identifies genes of clinicopathologic importance.

PURPOSE: To elucidate the molecular mechanisms contributing to the unique clinicopathologic characteristics of mucinous ovarian carcinoma, global gene expression profiling of mucinous ovarian tumors was carried out. EXPERIMENTAL DESIGN: Gene expression profiling was completed for 25 microdissected mucinous tumors [6 cystadenomas, 10 low malignant potential (LMP) tumors, and 9 adenocarcinomas] using Affymetrix U133 Plus 2.0 oligonucleotide microarrays. Hierarchical clustering and binary tree prediction analysis were used to determine the relationships among mucinous specimens and a series of previously profiled microdissected serous tumors and normal ovarian surface epithelium. PathwayAssist software was used to identify putative signaling pathways involved in the development of mucinous LMP tumors and adenocarcinomas. RESULTS: Comparison of the gene profiles between mucinous tumors and normal ovarian epithelial cells identified 1,599, 2,916, and 1,765 differentially expressed in genes in the cystadenomas, LMP tumors, and adenocarcinomas, respectively. Hierarchical clustering showed that mucinous and serous LMP tumors are distinct. In addition, there was a close association of mucinous LMP tumors and adenocarcinomas with serous adenocarcinomas. Binary tree prediction revealed increased heterogeneity among mucinous tumors compared with their serous counterparts. Furthermore, the cystadenomas coexpressed a subset of genes that were differentially regulated in LMP and adenocarcinoma specimens compared with normal ovarian surface epithelium. PathwayAssist highlighted pathways with expression of genes involved in drug resistance in both LMP and adenocarcinoma samples. In addition, genes involved in cytoskeletal regulation were specifically up-regulated in the mucinous adenocarcinomas. CONCLUSIONS: These data provide a useful basis for understanding the molecular events leading to the development and progression of mucinous ovarian cancer.

Adenocarcinoma, Mucinous↗

PubMed2006

Candidate tumor-suppressor gene DLEC1 is frequently downregulated by promoter hypermethylation and histone hypoacetylation in human epithelial ovarian cancer.

Suppression of ovarian tumor growth by chromosome 3p was demonstrated in a previous study. Deleted in Lung and Esophageal Cancer 1 (DLEC1) on 3p22.3 is a candidate tumor suppressor in lung, esophageal, and renal cancers. The potential involvement of DLEC1 in epithelial ovarian cancer remains unknown. In the present study, DLEC1 downregulation was found in ovarian cancer cell lines and primary ovarian tumors. Focus-expressed DLEC1 in two ovarian cancer cell lines resulted in 41% to 52% inhibition of colony formation. No chromosomal loss of chromosome 3p22.3 in any ovarian cancer cell line or tissue was found. Promoter hypermethylation of DLEC1 was detected in ovarian cancer cell lines with reduced DLEC1 transcripts, whereas methylation was not detected in normal ovarian epithelium and DLEC1-expressing ovarian cancer cell lines. Treatment with demethylating agent enhanced DLEC1 expression in 90% (9 of 10) of ovarian cancer cell lines. DLEC1 promoter methylation was examined in 13 high-grade ovarian tumor tissues with DLEC1 downregulation, in which 54% of the tumors showed DLEC1 methylation. In addition, 80% of ovarian cancer cell lines significantly upregulated DLEC1 transcripts after histone deacetylase inhibitor treatment. Therefore, our results suggested that DLEC1 suppressed the growth of ovarian cancer cells and that its downregulation was closely associated with promoter hypermethylation and histone hypoacetylation.

Cell Line, Tumor↗

PubMed2005

Expression profiling of serous low malignant potential, low-grade, and high-grade tumors of the ovary.

Papillary serous low malignant potential (LMP) tumors are characterized by malignant features and metastatic potential yet display a benign clinical course. The role of LMP tumors in the development of invasive epithelial cancer of the ovary is not clearly defined. The aim of this study is to determine the relationships among LMP tumors and invasive ovarian cancers and identify genes contributing to their phenotypes. Affymetrix U133 Plus 2.0 microarrays (Santa Clara, CA) were used to interrogate 80 microdissected serous LMP tumors and invasive ovarian malignancies along with 10 ovarian surface epithelium (OSE) brushings. Gene expression profiles for each tumor class were used to complete unsupervised hierarchical clustering analyses and identify differentially expressed genes contributing to these associations. Unsupervised hierarchical clustering analysis revealed a distinct separation between clusters containing borderline and high-grade lesions. The majority of low-grade tumors clustered with LMP tumors. Comparing OSE with high-grade and LMP expression profiles revealed enhanced expression of genes linked to cell proliferation, chromosomal instability, and epigenetic silencing in high-grade cancers, whereas LMP tumors displayed activated p53 signaling. The expression profiles of LMP, low-grade, and high-grade papillary serous ovarian carcinomas suggest that LMP tumors are distinct from high-grade cancers; however, they are remarkably similar to low-grade cancers. Prominent expression of p53 pathway members may play an important role in the LMP tumor phenotype.

Carcinoma, Papillary↗

PubMed2005

Recruitment of CRABS CLAW to promote nectary development within the eudicot clade.

Nectaries are secretory organs that are widely present in flowering plants that function to attract floral pollinators. Owing to diversity in nectary positions and structures, they are thought to have originated multiple times during angiosperm evolution, with their potential contribution to the diversification of flowering plants and pollinating animals being considerable. We investigated the genetic basis of diverse nectary forms in eudicot angiosperm species using CRABS CLAW (CRC), a gene required for nectaries in Arabidopsis. CRC expression is conserved in morphologically different nectaries from several core eudicot species and is required for nectary development in both rosids and asterids, two major phylogenetic lineages of eudicots. However, in a basal eudicot species, no evidence of CRC expression in nectaries was found. Considering the phylogenetic distribution of nectary positions and CRC expression analyses in eudicots, we propose that diverse nectaries in core eudicots share conserved CRC gene regulation, and that derived nectary positions in eudicots have altered regulation of CRC. As the ancestral function of CRC lies in the regulation of carpel development, it may have been co-opted as a regulator of nectary development within the eudicots, concomitant with the association of nectaries with reproductive organs in derived lineages.

Arabidopsis↗

PubMed2005

A phenolic compound, 5-caffeoylquinic acid (chlorogenic acid), is a new type and strong matrix metalloproteinase-9 inhibitor: isolation and identification from methanol extract of Euonymus alatus.

A phenolic compound responsible for anti-MMP-9, which is known to be involved in tumor cell invasion and metastasis, has been isolated from methanol extracts prepared from stem barks of Euonymus alatus by assay-guided fractionation. The compound has been identified as 5-caffeoylquinic acid (chlorogenic acid; CHA) by NMR and FAB-MS. CHA showed a strong inhibitory effect of matrix metalloproteinase (MMP)-9 activity in a concentration-dependent manner on zymography. The purified CHA inhibited MMP-9 activity with the IC50 of 30-50 nM. Furthermore, the cytotoxic survival curve showed that CHA does not have cytotoxic effects on cellular proliferation, when Hep3B cells were treated with various concentrations of CHA and cell viability was measured using the XTT assay. The present data suggest a clue for possible mechanisms of cancer chemoprevention by CHA and other naturally occurring phenolic compounds. The results also imply that useful cancer chemopreventive agents can be further identified by combinations of in vitro (as a first screen) and in vivo studies.

Cell Line, Tumor↗

PubMed2005

HDLs in apoA-I transgenic Abca1 knockout mice are remodeled normally in plasma but are hypercatabolized by the kidney.

Patients homozygous for Tangier disease have a near absence of plasma HDL as a result of mutations in ABCA1 and hypercatabolize normal HDL particles. To determine the relationship between ABCA1 expression and HDL catabolism, we investigated intravascular remodeling, plasma clearance, and organ-specific uptake of HDL in mice expressing the human apolipoprotein A-I (apoA-I) transgene in the Abca1 knockout background. Small HDL particles (7.5 nm), radiolabeled with (125)I-tyramine cellobiose, were injected into recipient mice to quantify plasma turnover and the organ uptake of tracer. Small HDL tracer was remodeled to 8.2 nm diameter particles within 5 min in human apolipoprotein A-I transgenic (hA-I(Tg)) mice (control) and knockout mice. Decay of tracer from plasma was 1.6-fold more rapid in knockout mice (P < 0.05) and kidney uptake was twice that of controls, with no difference in liver uptake. We also observed 2-fold greater hepatic expression of ABCA1 protein in hA-I(Tg) mice compared with nontransgenic mice, suggesting that overexpression of human apoA-I stabilized hepatic ABCA1 protein in vivo. We conclude that ABCA1 is not required for in vivo remodeling of small HDLs to larger HDL subfractions and that the hypercatabolism of normal HDL particles in knockout mice is attributable to a selective catabolism of HDL apoA-I by the kidney.

ATP Binding Cassette Transporter 1↗

PubMed2005

Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis.

To find potential targets of novel antimicrobial agents, we identified essential genes of Streptococcus pneumoniae using comparative genomics and allelic replacement mutagenesis. We compared the genome of S. pneumoniae R6 with those of Bacillus subtilis, Enterococcus faecalis, Escherichia coli, and Staphylococcus aureus, and selected 693 candidate target genes with > 40% amino acid sequence identity to the corresponding genes in at least two of the other species. The 693 genes were disrupted and 133 were found to be essential for growth. Of these, 32 encoded proteins of unknown function, and we were able to identify orthologues of 22 of these genes by genomic comparisons. The experimental method used in this study is easy to perform, rapid and efficient for identifying essential genes of bacterial pathogens.

Genes, Bacterial↗

PubMed2005

Changes in antioxidant defense systems by 2,2',5,5'-tetrachlorobiphenyl exposure in neuronal SK-N-MC cells.

Polychlorinated biphenyls (PCBs) are known to alter the mammalian antioxidant defense system. To determine whether similar detoxification processes are activated in human neuronal cells, we investigated activities of antioxidant enzymes and the glutathione status (i.e., the levels of reduced and oxidized glutathione, GSH and GSSG) in human neuronal SK-N-MC cells exposed to 2,2',5,5'-tetrachlorobiphenyl (PCB 52). Upon PCB 52 treatment, time- and concentration-dependent inhibitions of cell viability were observed. PCB 52 did not affect GSH contents upon increasing the concentration up to 15 microg/ml, but significant depletions in GSH were observed at the concentrations of 20 and 25 microg/ml. PCB 52 exposure increased GSSG levels in the SK-N-MC cells, while GSH levels were decreased, and these changes naturally modified the GSSG/GSH ratios. Cytosolic glutathione S-transferase (GST) activity with 1-chloro-2,4-dinitrobenzene as substrate was enhanced by two-fold in neuronal cells after exposure to PCB 52 versus controls. In contrast, neuronal cells showed a sustained decrease in glutathione peroxidase activity with increasing concentrations of PCB 52, and a sustained decrease in Cu/Zn-superoxide dismutase (SOD) activity with increasing concentrations of PCB 52. Catalase activity was increased until 12 h after exposure to PCB 52, but was decreased 24 h after exposure. Overall, these results imply a major effect of PCB 52 on GSH status and upon the activities of antioxidant enzymes in human neuronal SK-N-MC cells, and upon the overall process of detoxification in human neuronal cells.

Antioxidants↗

PubMed2005

Transcriptional profile of the Arabidopsis root quiescent center.

The self-renewal characteristics of stem cells render them vital engines of development. To better understand the molecular mechanisms that determine the properties of stem cells, transcript profiling was conducted on quiescent center (QC) cells from the Arabidopsis thaliana root meristem. The AGAMOUS-LIKE 42 (AGL42) gene, which encodes a MADS box transcription factor whose expression is enriched in the QC, was used to mark these cells. RNA was isolated from sorted cells, labeled, and hybridized to Affymetrix microarrays. Comparisons with digital in situ expression profiles of surrounding tissues identified a set of genes enriched in the QC. Promoter regions from a subset of transcription factors identified as enriched in the QC conferred expression in the QC. These studies demonstrated that it is possible to successfully isolate and profile a rare cell type in the plant. Mutations in all enriched transcription factor genes including AGL42 exhibited no detectable root phenotype, raising the possibility of a high degree of functional redundancy in the QC.

Arabidopsis↗

PubMed2005

Targeted inactivation of hepatic Abca1 causes profound hypoalphalipoproteinemia and kidney hypercatabolism of apoA-I.

Patients with Tangier disease exhibit extremely low plasma HDL concentrations resulting from mutations in the ATP-binding cassette, sub-family A, member 1 (ABCA1) protein. ABCA1 controls the rate-limiting step in HDL particle assembly by mediating efflux of cholesterol and phospholipid from cells to lipid-free apoA-I, which forms nascent HDL particles. ABCA1 is widely expressed; however, the specific tissues involved in HDL biogenesis are unknown. To determine the role of the liver in HDL biogenesis, we generated mice with targeted deletion of the second nucleotide-binding domain of Abca1 in liver only (Abca1(-L/-L)). Abca1(-L/-L) mice had total plasma and HDL cholesterol concentrations that were 19% and 17% those of wild-type littermates, respectively. In vivo catabolism of HDL apoA-I from wild-type mice or human lipid-free apoA-I was 2-fold higher in Abca1(-L/-L) mice compared with controls due to a 2-fold increase in the catabolism of apoA-I by the kidney, with no change in liver catabolism. We conclude that in chow-fed mice, the liver is the single most important source of plasma HDL. Furthermore, hepatic, but not extrahepatic, Abca1 is critical in maintaining the circulation of mature HDL particles by direct lipidation of hepatic lipid-poor apoA-I, slowing its catabolism by the kidney and prolonging its plasma residence time.

ATP Binding Cassette Transporter 1↗