Lee SJ

References (37)

Title : Immobilized Candida antarctica lipase B as an sn-1,3 regiospecific biocatalyst for the interesterification of triacylglycerols with fatty acid ethyl esters - Hwang_2024_Food.Sci.Biotechnol_33_159
Author(s) : Hwang J , Aum J , Lee SJ , Mun JM , Kim SW , Chung MY , Kim IH , Kim BH
Ref : Food Sci Biotechnol , 33 :159 , 2024
Abstract : Candida antarctica lipase B (CALB) is regarded as non-regiospecific. This study aimed to investigate the regiospecificity of CALB in the solvent-free interesterification of high-oleic sunflower oil with stearic acid ethyl ester for 1,3-distearoyl-2-oleoylglycerol (SOS)-rich fat preparation using a packed bed reactor. The content ratio of 1,2-distearoyl-3-oleoylglycerol (SSO) to SOS (denoted by SSO/SOS content) obtained using Lipozyme 435 (a commercially immobilized CALB; 0-4.1%), at residence times (1-32 min) was similar to that obtained using Lipozyme RM IM (0-3.0%), but lower than that obtained using Lipozyme TL IM (6.0-39.4%). When immobilized on Lewatit VP OC 1600, Lipozyme CALB had an SSO/SOS content of 0-10.4%, which was greater than that of Palatase 20,000 L (0-1.1%) but was lower than that of Lipozyme TL 100 L (8.8-97.7%). Our findings suggest that immobilized CALB shows distinct sn-1,3 regiospecificity in the interesterification of triacylglycerol with fatty acid ethyl esters.
ESTHER : Hwang_2024_Food.Sci.Biotechnol_33_159
PubMedSearch : Hwang_2024_Food.Sci.Biotechnol_33_159
PubMedID: 38186626

Title : Bronchitis, COPD, and pneumonia after viral endemic of patients with leprosy on Sorok Island in South Korea - Lee_2023_Naunyn.Schmiedebergs.Arch.Pharmacol__1
Author(s) : Lee JH , Kanwar B , Khattak A , Altschuler E , Sergi C , Lee SJ , Choi SH , Park J , Coleman M , Bourbeau J
Ref : Naunyn Schmiedebergs Arch Pharmacol , :1 , 2023
Abstract : Viral respiratory diseases (VRDs) cause lung inflammation and inflammatory cytokine production. We study whether dapsone is responsible for its observed preventive treatment effects of the sustained viral RNA interferon response. Around 2008 and 2012, Korea's Dementia Management Act stipulated drastic changes in the administration of dementia medication by medical staff. Participants were randomized and we compared leprosy patients with VRDs after prescribing dapsone as a standard treatment from 2005 to 2019. Significance was evaluated based on the dapsone-prescribed (+) subgroup and the dapsone-unprescribed (-) subgroup of the VRD diagnosed (+) and VRD undiagnosed (-) subgroup. We analyzed VRD ( +)/(- with dapsone (+)/(-) group and used a T-test, and designed the equation of acetylation with dapsone and acetylcholine (AA) equation. The 6394 VRD participants who received the dapsone intervention compared to the 3255 VRD participants in the control group demonstrated at T2 VRD (+) dapsone (-) (mean (M) = 224.80, SD = 97.50): T3 VRD (-) dapsone (+) (M = 110.87, SD = 103.80), proving that VRD is low when dapsone is taken and high when it is not taken. The t value is 3.10, and the p value is 0.004395 (significant at p < 0.05). After an increase in VRDs peaked in 2009, bronchitis, COPD, and pneumonia surged in 2013. The AA equation was strongly negatively correlated with the prevalence of bronchitis and chronic obstructive pulmonary disease (COPD): with bronchitis, r(15) = -0.823189, p = 0.005519, and with COPD, r(15) = -0.8161, p = 0.000207 (significant at p < 0.05). Dapsone treated both bronchitis and COPD. This study provides theoretical clinical data to limit acetylcholine excess during the VRD pandemic for bronchitis, COPD, and pneumonia.
ESTHER : Lee_2023_Naunyn.Schmiedebergs.Arch.Pharmacol__1
PubMedSearch : Lee_2023_Naunyn.Schmiedebergs.Arch.Pharmacol__1
PubMedID: 36773052

Title : Nematicidal Activity of Benzyloxyalkanols against Pine Wood Nematode - Kim_2021_Biomolecules_11_
Author(s) : Kim J , Lee SJ , Park JO , Yoon KA
Ref : Biomolecules , 11 : , 2021
Abstract : Pine wilt disease (PWD) is caused by the pine wood nematode (PWN; Bursaphelenchus xylophilus) and causes severe environmental damage to global pine forest ecosystems. The current strategies used to control PWN are mainly chemical treatments. However, the continuous use of these reagents could result in the development of pesticide-resistant nematodes. Therefore, the present study was undertaken to find potential alternatives to the currently used PWN control agents abamectin and emamectin. Benzyloxyalkanols (BzOROH; R = C(2)-C(9)) were synthesized and the nematicidal activity of the synthetic compounds was investigated. Enzymatic inhibitory assays (acetylcholinesterase (AChE) and glutathione S-transferase (GST)) were performed with BzOC8OH and BzOC9OH to understand their mode of action. The benzyloxyalkanols showed higher nematicidal activity than did benzyl alcohol. Among the tested BzOROHs, BzC8OH and BzC9OH showed the strongest nematicidal activity. The LD(50) values of BzC8OH and BzC9OH were 246.1 and 158.0 ppm, respectively. No enzyme inhibitory activity was observed for BzC8OH and BzC9OH. The results suggested that benzyloxyalcohols could be an alternative nematicidal agent.
ESTHER : Kim_2021_Biomolecules_11_
PubMedSearch : Kim_2021_Biomolecules_11_
PubMedID: 33807784

Title : No Impact of Soluble Epoxide Hydrolase rs4149243, rs2234914 and rs751142 Genetic Variants on the Development of Type II Diabetes and its Hypertensive Complication among Jordanian Patients - Khamees_2021_Int.J.Clin.Pract__e14036
Author(s) : Khamees M , Jarrar Y , Al-Qirim T , Mahmoud IS , Hatmal MM , Alshaer W , Lee SJ
Ref : Int J Clin Pract , :e14036 , 2021
Abstract : BACKGROUND: Human soluble epoxide hydrolase plays a major role in cardiovascular homeostasis. Genetic variants in the EPHX2 gene among different ethnic groups are associated with cardiovascular complications, such as hypertension. However, no reports regarding the association of EPHX2 genotype with hypertension among type II diabetic (T2D) patients of Middle Eastern Jordanian origin exist. OBJECTIVE: The current study aimed to elucidate the association of the EPHX2 allele, genotype, and haplotype with T2D, hypertension, and parameters of lipid profile parameters among Jordanian T2D patients. METHODS: Ninety-three genomic DNA samples of non-diabetic controls and 97 samples from T2D patients were genotyped for EPHX2 rs4149243, rs2234914, and rs751142 genetic variants. The DNA samples were amplified using polymerase chain reaction (PCR) and then sequenced using Applied Biosystems Model (ABI3730x1). The functionality of intronic EPHX2 variants was predicted using the in silico Berkely Drosophila Genome Project software. RESULTS: We found no significant (P > 0.05) association between the EPHX2 rs4149243, rs2234914, and rs751142 allele, genotype, and haplotype and the incidence of T2D and hypertension. Additionally, no association (P > 0.05) between these EPHX2 genetic variants with the baseline total cholesterol, low- and high-density lipoproteins, and triglycerides among both non-diabetic and diabetic volunteers was found. However, we found an inter-ethnic variation ((2) -test, p value 0.05) in the allele frequency of the EPHX2 rs4149243 and rs2234914 variants between Jordanians and other ethnic populations. Also, the in silico Berkely Drosophila Genome Project software predicted that the intronic EPHX2 rs4149243 could alter the splicing of intron 7. CONCLUSIONS: It can be concluded from this study that EPHX2 rs4149243, rs2234914, and rs751142 genetic variants do not play a role in the development of T2D and hypertension among Jordanian T2D patients. Further genetic studies with larger sample sizes are needed to find out the association of other functional EPHX2 variants with cardiovascular diseases among T2D patients in Jordan.
ESTHER : Khamees_2021_Int.J.Clin.Pract__e14036
PubMedSearch : Khamees_2021_Int.J.Clin.Pract__e14036
PubMedID: 33512081

Title : Interactive Gene Expression Between Metarhizium anisopliae JEF-290 and Longhorned Tick Haemaphysalis longicornis at Early Stage of Infection - Lee_2021_Front.Physiol_12_643389
Author(s) : Lee MR , Kim JC , Park SE , Lee SJ , Kim WJ , Lee DH , Kim JS
Ref : Front Physiol , 12 :643389 , 2021
Abstract : The longhorned tick, Haemaphysalis longicornis (Acari: Ixodidae), is a hard tick and a vector for severe fever with thrombocytopenia syndrome (SFTS) virus. The number of patients infected with SFTS is rapidly increasing. Recently, the invertebrate pathogen Metarhizium anisopliae JEF-290 was reported to be useful to control the tick as an alternative to chemical acaricides, which are not easily applicable in human living areas where the tick is widely spread. In this study, we analyzed how the tick and the fungal pathogen interact at the transcriptional level. Field-collected tick nymphs were treated with JEF-290 conidia at 1 x 10(8) conidia/ml. In the early stage of infection with 2.5% mortality, the infected ticks were subjected to RNA sequencing, and non-infected ticks and fungal masses served as controls. Fungus and tick genes were mostly up-regulated at the early stage of infection. In the gene set enrichment analysis of the infecting fungus, catabolic processes that included lipids, phospholipids, and detoxification processes, the response to oxidative stress, and toxic substances were significantly up-regulated. In this fungal up-regulation, various lipase, antioxidant enzyme, and hydrolase genes were highly transcribed. The gene set enrichment analysis of the infected tick showed that many peptide synthesis processes including translation, peptide metabolism, ribonucleotide metabolism, and energy production processes that included ATP generation and ADP metabolism were significantly up-regulated. Structurally, mitochondria and ribosome subunit genes in ticks were highly transcribed to upregulate these processes. Together these results indicate that JEF-290 initiates process that infects the tick while the tick actively defends against the fungal attack. This work provides background to improve our understanding of the early stage of fungal infection in longhorned tick.
ESTHER : Lee_2021_Front.Physiol_12_643389
PubMedSearch : Lee_2021_Front.Physiol_12_643389
PubMedID: 34093222

Title : Identification of a Second Type of AHL-lactonase from Rhodococcus sp. BH4, belonging to the alpha\/beta Hydrolase Superfamily - Ryu_2020_J.Microbiol.Biotechnol__
Author(s) : Ryu DH , Lee SW , Mikolaityte V , Kim YW , Jeong HY , Lee SJ , Lee CH , Lee JK
Ref : J Microbiol Biotechnol , : , 2020
Abstract : N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) plays a major role in development of biofilms, which contribute to rise in infections and biofouling in water-related industries. Interference in QS, called quorum quenching (QQ), has recieved a lot of attention in recent years. Rhodococcus spp. are known to have prominent quorum quenching activity and in previous reports it was suggested that this genus possesses multiple QQ enzymes, but only one gene, qsdA, which encodes an AHL-lactonase belonging to phosphotriesterase family, has been identified. Therefore, we conducted a whole genome sequencing and analysis of Rhodococcus sp. BH4 isolated from a wastewater treatment plant. The sequencing revealed another gene encoding a QQ enzyme (named jydB) that exhibited a high AHL degrading activity. This QQ enzyme had a 46% amino acid sequence similarity with the AHL-lactonase (AidH) of Ochrobactrum sp. T63. HPLC analysis and AHL restoration experiments by acidification revealed that the jydB gene encodes an AHL-lactonase which shares the known characteristics of the alpha/beta hydrolase family. Purified recombinant JydB demonstrated a high hydrolytic activity against various AHLs. Kinetic analysis of JydB revealed a high catalytic efficiency (kcat/KM) against C4-HSL and 3-oxo-C6 HSL, ranging from 1.88 x 10(6) to 1.45 x 10(6) M(-1) s(-1), with distinctly low KM values (0.16 - 0.24 mM). This study affirms that the AHL degrading activity and biofilm inhibition ability of Rhodococcus sp. BH4 may be due to the presence of multiple quorum quenching enzymes, including two types of AHL-lactonases, in addition to AHL-acylase and oxidoreductase, for which the genes have yet to be described.
ESTHER : Ryu_2020_J.Microbiol.Biotechnol__
PubMedSearch : Ryu_2020_J.Microbiol.Biotechnol__
PubMedID: 32160697

Title : Effect of acetylcholinesterase inhibitors on post-stroke cognitive impairment and vascular dementia: A meta-analysis - Kim_2020_PLoS.One_15_e0227820
Author(s) : Kim JO , Lee SJ , Pyo JS
Ref : PLoS ONE , 15 :e0227820 , 2020
Abstract : Cognitive impairment is a common complication observed after a stroke. Currently there are no definitively proven pharmacologic therapies for recovery from post-stroke cognitive impairment and vascular dementia. In this meta-analysis, we evaluated the efficacy and safety of cholinesterase inhibitors in their improvement of cognition in patients with post-stroke cognitive impairment and vascular dementia. We conducted a meta-analysis using seven eligible studies from 305 published articles. We investigated the differences in Mini-Mental State Examination (MMSE) and Alzheimer's Disease Assessment Scale-Cognitive subscale (ADAS-Cog) scores, before and after cholinergic augmentation in patients with post-stroke cognitive impairment and vascular dementia. MMSE and ADAS-cog scores were also compared during the subsequent follow-up periods. MMSE score of patients with post-stroke cognitive impairment was increased after cholinergic augmentation throughout the 24 weeks with mean differences [MD] of 3.000, 1.732, 1.578 1.516, and 1.222, at 4, 4-8, 8-12, 12-18, and 18-24 weeks, respectively. In addition, ADAS-cog scores decreased at 6, 12, 18, and 24 weeks by pharmaceutical augmentation, but not with placebo with mean differences [MD] of -2.333, -2.913, -2.767, -2.416, and -1.859, respectively. This meta-analysis shows that acetylcholinesterase inhibitors maintain a stable pattern of improved cognitive function in patients with post stroke cognitive impairment and vascular dementia without the increased risk of side effects.
ESTHER : Kim_2020_PLoS.One_15_e0227820
PubMedSearch : Kim_2020_PLoS.One_15_e0227820
PubMedID: 32032361

Title : Inhibition of Salmonella Typhimurium adhesion, invasion, and intracellular survival via treatment with methyl gallate alone and in combination with marbofloxacin - Birhanu_2018_Vet.Res_49_101
Author(s) : Birhanu BT , Park NH , Lee SJ , Hossain MA , Park SC
Ref : Vet Res , 49 :101 , 2018
Abstract : Salmonella enterica serovar Typhimurium infects intestinal epithelia and macrophages, which is prevented by inhibiting adhesion and cell invasion. This study aimed to investigate the role of methyl gallate (MG) in adhesion, invasion, and intracellular survival of Salmonella Typhimurium in Caco-2 and RAW 264.7 cells via a gentamicin protection assay, confocal microscopy, and quantitative reverse-transcription polymerase chain reaction. MG (30 microg/mL) inhibited adhesion and invasion of Salmonella Typhimurium by 54.01% and 60.5% in RAW 264.7 cells, respectively. The combination of MG with sub-minimum inhibitory concentration (MIC) of marbofloxacin (MRB) inhibited the adhesion, invasion, and intracellular survival by 70.49%, 67.36%, and 74%, respectively. Confocal microscopy further revealed reductions in bacterial count in Caco-2 cells treated with MG alone or with sub-MIC of MRB. Furthermore, MG alone or in combination with sub-MIC of MRB decreased the motility of Salmonella Typhimurium. Quorum sensing genes including sdiA, srgE, and rck were downregulated by 52.8%, 61.7%, and 22.2%, respectively. Moreover, rac-1 was downregulated by 56.9% and 71.9% for MG alone and combined with sub-MIC of MRB, respectively, in mammalian cells. Furthermore, MG downregulated virulence genes of Salmonella Typhimurium including cheY, ompD, sipB, lexA, and ompF by 59.6%, 60.2%, 20.5%, 31.4%, and 16.2%, respectively. Together, the present results indicate that MG alone or in combination with a sub-MIC of MRB effectively inhibited the adhesion, invasion, and intracellular survival of Salmonella Typhimurium in vitro by downregulating quorum sensing and virulence genes.
ESTHER : Birhanu_2018_Vet.Res_49_101
PubMedSearch : Birhanu_2018_Vet.Res_49_101
PubMedID: 30286813

Title : Observational Study of Clinical and Functional Progression Based on Initial Brain MRI Characteristics in Patients with Alzheimer's Disease - Choi_2018_J.Alzheimers.Dis_66_1721
Author(s) : Choi H , Yang Y , Han HJ , Jeong JH , Park MY , Kim YB , Jo KD , Choi JY , Kang KH , Kang H , Kwon DY , Yoo BG , Lee HJ , Shin BS , Jeon SM , Kwon OD , Kim JS , Lee SJ , Kim Y , Park TH , Kim YJ , Yang HJ , Park HY , Shin HE , Lee JS , Jung YH , Lee AY , Shin DI , Shin KJ , Park KH
Ref : J Alzheimers Dis , 66 :1721 , 2018
Abstract : BACKGROUND: Magnetic resonance imaging (MRI) is a useful tool to predict the diagnosis and progression of Alzheimer's disease (AD), especially for primary physicians. However, the correlation between baseline MRI findings and AD progression has not been fully established. OBJECTIVE: To investigate the correlation between hippocampal atrophy (HA) and white matter hyperintensities (WMH) on initial brain MRI images and the degree of cognitive decline and functional changes over 1 year. METHODS: In this prospective, 12-month observational study, dementia outpatients were recruited from 29 centers across South Korea. Baseline assessments of HA and WMH on baseline brain MRI were derived as well as cognitive function, dementia severity, activities of daily living, and acetylcholinesterase inhibitor (AChEI) use. Follow-up assessments were conducted at 6 and 12 months. RESULTS: Among 899 enrolled dementia patients, 748 were diagnosed with AD of whom 654 (87%) were taking AChEIs. Baseline WMH showed significant correlations with age, current alcohol consumption, and Clinical Dementia Rating score; baseline HA was correlated with age, family history, physical exercise, and the results of cognitive assessments. Among the AChEI group, changes in the Korean version of the Instrumental Activities of Daily Living (K-IADL) were correlated with the severity of HA on baseline brain MRI, but not with the baseline severity of WMH. In the no AChEI group, changes in K-IADL were correlated with the severity of WMH and HA at baseline. CONCLUSION: Baseline MRI findings could be a useful tool for predicting future clinical outcomes by primary physicians, especially in relation to patients' functional status.
ESTHER : Choi_2018_J.Alzheimers.Dis_66_1721
PubMedSearch : Choi_2018_J.Alzheimers.Dis_66_1721
PubMedID: 30452413

Title : Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta - Lee_2018_Mol.Biol.Evol_35_1869
Author(s) : Lee J , Yang EC , Graf L , Yang JH , Qiu H , Zelzion U , Chan CX , Stephens TG , Weber APM , Boo GH , Boo SM , Kim KM , Shin Y , Jung M , Lee SJ , Yim HS , Lee JH , Bhattacharya D , Yoon HS
Ref : Molecular Biology Evolution , 35 :1869 , 2018
Abstract : Red algae (Rhodophyta) underwent two phases of large-scale genome reduction during their early evolution. The red seaweeds did not attain genome sizes or gene inventories typical of other multicellular eukaryotes. We generated a high-quality 92.1 Mb draft genome assembly from the red seaweed Gracilariopsis chorda, including methylation and small (s)RNA data. We analyzed these and other Archaeplastida genomes to address three questions: 1) What is the role of repeats and transposable elements (TEs) in explaining Rhodophyta genome size variation, 2) what is the history of genome duplication and gene family expansion/reduction in these taxa, and 3) is there evidence for TE suppression in red algae? We find that the number of predicted genes in red algae is relatively small (4,803-13,125 genes), particularly when compared with land plants, with no evidence of polyploidization. Genome size variation is primarily explained by TE expansion with the red seaweeds having the largest genomes. Long terminal repeat elements and DNA repeats are the major contributors to genome size growth. About 8.3% of the G. chorda genome undergoes cytosine methylation among gene bodies, promoters, and TEs, and 71.5% of TEs contain methylated-DNA with 57% of these regions associated with sRNAs. These latter results suggest a role for TE-associated sRNAs in RNA-dependent DNA methylation to facilitate silencing. We postulate that the evolution of genome size in red algae is the result of the combined action of TE spread and the concomitant emergence of its epigenetic suppression, together with other important factors such as changes in population size.
ESTHER : Lee_2018_Mol.Biol.Evol_35_1869
PubMedSearch : Lee_2018_Mol.Biol.Evol_35_1869
PubMedID: 29688518
Gene_locus related to this paper: 9flor-a0a2v3j1b8

Title : Characterization of T-DNA insertion mutants with decreased virulence in the entomopathogenic fungus Beauveria bassiana JEF-007 - Kim_2016_Appl.Microbiol.Biotechnol_100_8889
Author(s) : Kim S , Lee SJ , Nai YS , Yu JS , Lee MR , Yang YT , Kim JS
Ref : Applied Microbiology & Biotechnology , 100 :8889 , 2016
Abstract : The bean bug, Riptortus pedestris, is a major agricultural pest that reduces crop quality and value. Chemical pesticides have contributed to pest management, but resistance to these chemicals has significantly limited their use. Alternative strategies with different modes of action, such as entomopathogenic fungi, are therefore of great interest. Herein, we explored how entomopathogenic fungi can potentially be used to control the bean bug and focused on identifying virulence-related genes. Beauveria bassiana (JEF isolates) were assayed against bean bugs under laboratory conditions. One isolate, JEF-007, showed >80 % virulence by both spray and contact exposure methods. Agrobacterium tumefaciens-mediated transformation (AtMT) of JEF-007 generated 249 random transformants, two of which (B1-06 and C1-49) showed significantly reduced virulence against Tenebrio molitor and R. pedestris immatures. Both species were used for rapid screening of virulence-reduced mutants. The two transformants had different morphologies, conidial production, and thermotolerance than the wild type. To determine the localization of the randomly inserted T-DNA, thermal asymmetric interlaced (TAIL) PCR was conducted and analysis of the two clones found multiple T-DNA insertions (two in B1-06 and three in C1-49). Genes encoding complex I intermediate-associated protein 30 (CIA30) and the autophagy protein (Atg22) were possibly disrupted by the T-DNA insertion and might be involved in the virulence. This work provides a strong platform for future functional genetic studies of bean bug-pathogenic B. bassiana. The genes putatively involved in fungal virulence should be experimentally validated by knockdown in future studies.
ESTHER : Kim_2016_Appl.Microbiol.Biotechnol_100_8889
PubMedSearch : Kim_2016_Appl.Microbiol.Biotechnol_100_8889
PubMedID: 27470140
Gene_locus related to this paper: beaba-a0a2s7xwt2 , beaba-a0a2n6n8e6

Title : Pathogenic mechanism of an autism-associated neuroligin mutation involves altered AMPA-receptor trafficking - Chanda_2016_Mol.Psychiatry_21_169
Author(s) : Chanda S , Aoto J , Lee SJ , Wernig M , Sudhof TC
Ref : Mol Psychiatry , 21 :169 , 2016
Abstract : Neuroligins are postsynaptic cell-adhesion molecules that bind to presynaptic neurexins. Although the general synaptic role of neuroligins is undisputed, their specific functions at a synapse remain unclear, even controversial. Moreover, many neuroligin gene mutations were associated with autism, but the pathophysiological relevance of these mutations is often unknown, and their mechanisms of action uninvestigated. Here, we examine the synaptic effects of an autism-associated neuroligin-4 substitution (called R704C), which mutates a cytoplasmic arginine residue that is conserved in all neuroligins. We show that the R704C mutation, when introduced into neuroligin-3, enhances the interaction between neuroligin-3 and AMPA receptors, increases AMPA-receptor internalization and decreases postsynaptic AMPA-receptor levels. When introduced into neuroligin-4, conversely, the R704C mutation unexpectedly elevated AMPA-receptor-mediated synaptic responses. These results suggest a general functional link between neuroligins and AMPA receptors, indicate that both neuroligin-3 and -4 act at excitatory synapses but perform surprisingly distinct functions, and demonstrate that the R704C mutation significantly impairs the normal function of neuroligin-4, thereby validating its pathogenicity.
ESTHER : Chanda_2016_Mol.Psychiatry_21_169
PubMedSearch : Chanda_2016_Mol.Psychiatry_21_169
PubMedID: 25778475

Title : Neuroligins Sculpt Cerebellar Purkinje-Cell Circuits by Differential Control of Distinct Classes of Synapses - Zhang_2015_Neuron_87_781
Author(s) : Zhang B , Chen LY , Liu X , Maxeiner S , Lee SJ , Gokce O , Sudhof TC
Ref : Neuron , 87 :781 , 2015
Abstract : Neuroligins are postsynaptic cell-adhesion molecules that bind presynaptic neurexins and are genetically linked to autism. Neuroligins are proposed to organize synaptogenesis and/or synaptic transmission, but no systematic analysis of neuroligins in a defined circuit is available. Here, we show that conditional deletion of all neuroligins in cerebellar Purkinje cells caused loss of distal climbing-fiber synapses and weakened climbing-fiber but not parallel-fiber synapses, consistent with alternative use of neuroligins and cerebellins as neurexin ligands for the excitatory climbing-fiber versus parallel-fiber synapses. Moreover, deletion of neuroligins increased the size of inhibitory basket/stellate-cell synapses but simultaneously severely impaired their function. Multiple neuroligin isoforms differentially contributed to climbing-fiber and basket/stellate-cell synapse functions, such that inhibitory synapse-specific neuroligin-2 was unexpectedly essential for maintaining normal climbing-fiber synapse numbers. Using systematic analyses of all neuroligins in a defined neural circuit, our data thus show that neuroligins differentially contribute to various Purkinje-cell synapses in the cerebellum in vivo.
ESTHER : Zhang_2015_Neuron_87_781
PubMedSearch : Zhang_2015_Neuron_87_781
PubMedID: 26291161

Title : Terrein reduces age-related inflammation induced by oxidative stress through Nrf2\/ERK1\/2\/HO-1 signalling in aged HDF cells - Lee_2015_Cell.Biochem.Funct_33_479
Author(s) : Lee YH , Lee SJ , Jung JE , Kim JS , Lee NH , Yi HK
Ref : Cell Biochemistry & Function , 33 :479 , 2015
Abstract : This study investigated whether multiple bioactivity of terrein such as anti-inflammatory and anti-oxidant inhibits age-related inflammation by promoting an antioxidant response in aged human diploid fibroblast (HDF) cells. HDF cells were cultured serially for in vitro replicative senescence. To create the ageing cell phenotype, intermediate stage (PD31) HDF cells were brought to stress-induced premature senescence (SIPS) using hydrogen peroxide (H2 O2). Terrein increased cell viability even with H2O2 stress and reduced inflammatory molecules such as intracellular adhesion molecule-1 (ICAM-1), cyclooxygenase-2 (COX-2), interleukin-1beta (IL-1beta) and tumour necrosis factor-alpha (TNF-alpha). Terrein reduced also phospho-extracellular kinase receptor1/2 (p-EKR1/2) signalling in aged HDF cells. SIPS cells were attenuated for age-related biological markers including reactive oxygen species (ROS), senescence associated beta-galactosidase (SA beta-gal.) and the aforementioned inflammatory molecules. Terrein induced the induction of anti-oxidant molecules, copper/zinc-superoxide defence (Cu/ZnSOD), manganese superoxide dismutase (MnSOD) and heme oxygenase-1 (HO-1) in SIPS cells. Terrein also alleviated reactive oxygen species formation through the Nrf2/HO-1/p-ERK1/2 pathway in aged cells. The results indicate that terrein has an alleviative function of age-related inflammation characterized as an anti-oxidant. Terrein might be a useful nutraceutical compound for anti-ageing.
ESTHER : Lee_2015_Cell.Biochem.Funct_33_479
PubMedSearch : Lee_2015_Cell.Biochem.Funct_33_479
PubMedID: 26416516
Gene_locus related to this paper: aspte-AT1

Title : Lipoprotein-associated phospholipase A is related to plaque stability and is a potential biomarker for acute coronary syndrome - Chung_2014_Yonsei.Med.J_55_1507
Author(s) : Chung H , Kwon HM , Kim JY , Yoon YW , Rhee J , Choi EY , Min PK , Hong BK , Rim SJ , Yoon JH , Lee SJ , Park JK , Kim MH , Jo M , Yang JH , Lee BK
Ref : Yonsei Med J , 55 :1507 , 2014
Abstract : PURPOSE: Plasma lipoprotein-associated phospholipase A (Lp-PLA) binds to low-density lipoprotein. The levels of Lp-PLA reflect the plaque burden, and are upregulated in acute coronary syndrome (ACS). We investigated the diagnostic value of Lp-PLA2 levels and found that it might be a potential biomarker for ACS. MATERIALS AND METHODS: We classified 226 study participants into three groups: patients without significant stenosis (control group), patients with significant stenosis with stable angina (SA group), and patients with ACS (ACS group). RESULTS: Lp-PLA and high-sensitivity C-reactive protein (hs-CRP) levels were significantly greater in the ACS group than in the SA group (p=0.044 and p=0.029, respectively). Multivariate logistic regression analysis revealed that Lp-PLA levels are significantly associated with ACS (odds ratio=1.047, p=0.013). The addition of Lp-PLA to the ACS model significantly increased the global ^2 value over traditional risk factors (28.14 to 35.602, p=0.006). The area under the receiver operating characteristic curve for Lp-PLA was 0.624 (p=0.004). The addition of Lp-PLA level to serum hs-CRP concentration yielded an integrated discrimination improvement of 0.0368 (p=0.0093, standard error: 0.0142) and improved the ability to diagnose ACS. CONCLUSION: Lp-PLA levels are related to plaque stability and might be a diagnostic biomarker for ACS.
ESTHER : Chung_2014_Yonsei.Med.J_55_1507
PubMedSearch : Chung_2014_Yonsei.Med.J_55_1507
PubMedID: 25323886

Title : Multiple Cytochrome P450 Isoforms Are Involved in the Generation of a Pharmacologically Active Thiol Metabolite, whereas Paraoxonase 1 and Carboxylesterase 1 Catalyze the Formation of a Thiol Metabolite Isomer from Ticlopidine - Kim_2014_Drug.Metab.Dispos_42_141
Author(s) : Kim MJ , Jeong ES , Park JS , Lee SJ , Ghim JL , Choi CS , Shin JG , Kim DH
Ref : Drug Metabolism & Disposition: The Biological Fate of Chemicals , 42 :141 , 2014
Abstract : Ticlopidine is a first-generation thienopyridine antiplatelet drug that prevents adenosine 5'-diphosphate (ADP)-induced platelet aggregation. We identified the enzymes responsible for the two-step metabolic bioactivation of ticlopidine in human liver microsomes and plasma. Formation of 2-oxo-ticlopidine, an intermediate metabolite, was NADPH dependent and cytochrome P450 (CYP) 1A2, 2B6, 2C19, and 2D6 were involved in this reaction. Conversion of 2-oxo-ticlopidine to thiol metabolites was observed in both microsomes (M1 and M2) and plasma (M1). These two metabolites were considered as isomers, and mass spectral analysis suggested that M2 was a thiol metabolite bearing an exocyclic double bond, whereas M1 was an isomer in which the double bond was migrated to an endocyclic position in the piperidine ring. The conversion of 2-oxo-ticlopidine to M1 in plasma was significantly increased by the addition of 1 mM CaCl2. In contrast, the activity in microsomes was not changed in the presence of CaCl2. M1 formation in plasma was inhibited by EDTA but not by other esterase inhibitors, whereas this activity in microsomes was substantially inhibited by carboxylesterase (CES) inhibitors such as bis-(p-nitrophenyl)phosphate (BNPP), diisopropylphosphorofluoride (DFP), and clopidogrel. The conversion of 2-oxo-ticlopidine to M1 was further confirmed with recombinant paraoxonase 1 (PON1) and CES1. However, M2 was detected only in NADPH-dependent microsomal incubation, and multiple CYP isoforms were involved in M2 formation with highest contribution of CYP2B6. In vitro platelet aggregation assay demonstrated that M2 was pharmacologically active. These results collectively indicated that the formation of M2 was mediated by CYP isoforms whereas M1, an isomer of M2, was generated either by human PON1 in plasma or by CES1 in the human liver.
ESTHER : Kim_2014_Drug.Metab.Dispos_42_141
PubMedSearch : Kim_2014_Drug.Metab.Dispos_42_141
PubMedID: 24170778
Gene_locus related to this paper: human-CES1

Title : MDGAs interact selectively with neuroligin-2 but not other neuroligins to regulate inhibitory synapse development - Lee_2013_Proc.Natl.Acad.Sci.U.S.A_110_336
Author(s) : Lee K , Kim Y , Lee SJ , Qiang Y , Lee D , Lee HW , Kim H , Je HS , Sudhof TC , Ko J
Ref : Proc Natl Acad Sci U S A , 110 :336 , 2013
Abstract : The MAM domain-containing GPI anchor proteins MDGA1 and MDGA2 are Ig superfamily adhesion molecules composed of six IG domains, a fibronectin III domain, a MAM domain, and a GPI anchor. MDGAs contribute to the radial migration and positioning of a subset of cortical neurons during early neural development. However, MDGAs continue to be expressed in postnatal brain, and their functions during postnatal neural development remain unknown. Here, we demonstrate that MDGAs specifically and with a nanomolar affinity bind to neuroligin-2, a cell-adhesion molecule of inhibitory synapses, but do not bind detectably to neuroligin-1 or neuroligin-3. We observed no cell adhesion between cells expressing neuroligin-2 and MDGA1, suggesting a cis interaction. Importantly, RNAi-mediated knockdown of MDGAs increased the abundance of inhibitory but not excitatory synapses in a neuroligin-2-dependent manner. Conversely, overexpression of MDGA1 decreased the numbers of functional inhibitory synapses. Likewise, coexpression of both MDGA1 and neuroligin-2 reduced the synaptogenic capacity of neuroligin-2 in an artificial synapse-formation assay by abolishing the ability of neuroligin-2 to form an adhesion complex with neurexins. Taken together, our data suggest that MDGAs inhibit the activity of neuroligin-2 in controlling the function of inhibitory synapses and that MDGAs do so by binding to neuroligin-2.
ESTHER : Lee_2013_Proc.Natl.Acad.Sci.U.S.A_110_336
PubMedSearch : Lee_2013_Proc.Natl.Acad.Sci.U.S.A_110_336
PubMedID: 23248271

Title : Gene cloning and characterization of a cold-adapted esterase from Acinetobacter venetianus V28 - Kim_2012_J.Microbiol.Biotechnol_22_1245
Author(s) : Kim YO , Heo YL , Kim HK , Nam BH , Kong HJ , Kim DG , Kim WJ , Kim BS , Jee YJ , Lee SJ
Ref : J Microbiol Biotechnol , 22 :1245 , 2012
Abstract : Acinetobacter venetians V28 was isolated from the intestine of righteye flounder, Poecilopsetta plinthus caught in Vietnam seawater, and the esterase gene was cloned using a shotgun method. The amino acid sequence deduced from the nucleotide sequence (1,017 bp) corresponded to a protein of 338 amino acid residues with a molecular weight of 37,186. The esterase had 87% and 72% identities with the lipases of A. junii SH205 and A. calcoaceticus RUH2202, respectively. The esterase contained a putative leader sequence, as well as the conserved catalytic triad (Ser, His, Asp), consensus pentapeptide GXSXG, and oxyanion hole sequence (HG). The protein from the strain V28 was produced in both a soluble and an insoluble form when the Escherichia coli cells harboring the gene were cultured at 18 degrees C. The maximal activity of the purified enzyme was observed at a temperature of 40 degrees C and pH 9.0 using p-NP-caprylate as substrate; however, relative activity still reached to 70% even at 5 degrees C with an activation energy of 3.36 kcal/mol, which indicated that it was a cold-adapted enzyme. The enzyme was a nonmetalloprotein and was active against p-nitrophenyl esters of C4, C8, and C14. Remarkably, this enzyme retained much of its activity in the presence of commercial detergents and organic solvents. This cold-adapted esterase will be applicable as catalysts for reaction in the presence of organic solvents and detergents.
ESTHER : Kim_2012_J.Microbiol.Biotechnol_22_1245
PubMedSearch : Kim_2012_J.Microbiol.Biotechnol_22_1245
PubMedID: 22814499

Title : Gene cloning and catalytic characterization of cold-adapted lipase of Photobacterium sp. MA1-3 isolated from blood clam - Kim_2012_J.Biosci.Bioeng_114_589
Author(s) : Kim YO , Khosasih V , Nam BH , Lee SJ , Suwanto A , Kim HK
Ref : J Biosci Bioeng , 114 :589 , 2012
Abstract : A lipase-producing Photobacterium strain (MA1-3) was isolated from the intestine of a blood clam caught at Namhae, Korea. The lipase gene was cloned by shotgun cloning and encoded 340 amino acids with a molecular mass of 38,015 Da. It had a very low sequence identity with other bacterial lipases, with the exception of that of Photobacterium lipolyticum M37 (83.2%). The MA1-3 lipase was produced in soluble form when Escherichia coli cells harboring the gene were cultured at 18 degrees C. Its optimum temperature and pH were 45 degrees C and pH 8.5, respectively. Its activation energy was calculated to be 2.69 kcal/mol, suggesting it to be a cold-adapted lipase. Its optimum temperature, temperature stability, and substrate specificity were quite different from those of M37 lipase, despite the considerable sequence similarities. Meanwhile, MA1-3 lipase performed a transesterification reaction using olive oil and various alcohols including methanol, ethanol, 1-propanol, and 1-butanol. In the presence of t-butanol as a co-solvent, this lipase produced biodiesel using methanol and plant or waste oils. The highest biodiesel conversion yield (73%) was achieved using waste soybean oil and methanol at a molar ratio of 1:5 after 12 h using 5 units of lipase.
ESTHER : Kim_2012_J.Biosci.Bioeng_114_589
PubMedSearch : Kim_2012_J.Biosci.Bioeng_114_589
PubMedID: 22841866

Title : NDRG2 and PRA1 interact and synergistically inhibit T-cell factor\/beta-catenin signaling. - Kim_2012_FEBS.Lett_586_3962
Author(s) : Kim JT , Kim JW , Kang YH , Kim KD , Lee SJ , Choi SC , Kim KS , Chae SK , Lim JS , Lee HG
Ref : FEBS Letters , 586 :3962 , 2012
Abstract : NDRG2 is a member of the N-myc downstream regulated gene (NDRG) family, implicated in cell growth and differentiation. Investigation of NDRG2 molecular interactions by yeast two-hybrid screening identified prenylated Rab acceptor-1 (PRA1), involved in vesicle trafficking and protein transport, as binding partner. Binding of NDRG2 (and NDRG1-4) with PRA1 in vitro was confirmed by GST pull-down assay and immunoprecipitation, and colocalization was verified by confocal microscopy in HCT116 cells. Intracellular coexpression showed that NDRG2 and PRA1 synergistically downregulate T-cell factor (TCF) promoter activity and GSK3beta phosphorylation. Results suggest that NDRG2 and PRA1 might act synergistically to prevent signaling of TCF/beta-catenin.
ESTHER : Kim_2012_FEBS.Lett_586_3962
PubMedSearch : Kim_2012_FEBS.Lett_586_3962
PubMedID: 23068607

Title : A novel cold-adapted esterase from Salinisphaera sp. P7-4: gene cloning, overproduction, and characterization - Kim_2011_J.Gen.Appl.Microbiol_57_357
Author(s) : Kim YO , Park IS , Kim HK , Nam BH , Jeong Kong H , Kim WJ , Kim DG , Kim KK , Lee SJ
Ref : J Gen Appl Microbiol , 57 :357 , 2011
Abstract : Salinisphaera sp. P7-4 was isolated from the intestine of silver whiting, Sillago japonicas caught in the Pacific Ocean, and the esterase gene was cloned using the shotgun method. The amino acid sequence deduced from the nucleotide sequence (951 bp) corresponded to a protein of 316 amino acid residues with a molecular weight of 34,443. The esterase had 46 and 44% identities with the esterase enzymes of Ralstonia eutropha JMP134 and Rhodopseudomonas palustris HaA2, respectively. The primary structure of P7-4 esterase showed the conserved catalytic triad (Ser, Asp, His), consensus pentapeptide GXSXG, and oxyanion hole sequence (HG). The protein P7-4 was successfully expressed in Escherichia coli in a biologically active form. The enzyme showed high catalytic activity at low temperatures (5-25 degrees C) with an activation energy of 2.18 kcal/mol. This result indicated that the esterase from Salinisphaera sp. P7-4 is a new cold-adapted enzyme. The enzyme preferentially hydrolyzed acyl-group chains with short chain lengths of </=10 carbon. Metal ions such as Cd2(+), Co2(+), Cu2(+), Hg2(+), Ni2(+) and Zn2(+) inhibited enzymatic activity. Additionally, EDTA has no effect on its activity, whereas inhibition was observed with PMSF, a serine hydrolase inhibitor.
ESTHER : Kim_2011_J.Gen.Appl.Microbiol_57_357
PubMedSearch : Kim_2011_J.Gen.Appl.Microbiol_57_357
PubMedID: 22353741
Gene_locus related to this paper: 9gamm-h8ypm9

Title : Protein-stabilized nanoemulsions and emulsions: comparison of physicochemical stability, lipid oxidation, and lipase digestibility - Lee_2011_J.Agric.Food.Chem_59_415
Author(s) : Lee SJ , Choi SJ , Li Y , Decker EA , McClements DJ
Ref : Journal of Agricultural and Food Chemistry , 59 :415 , 2011
Abstract : The properties of whey protein isolate (WPI) stabilized oil-in-water (O/W) nanoemulsions (d(43) approximately 66 nm; 0.5% oil, 0.9% WPI) and emulsions (d(43) approximately 325 nm; 0.5% oil, 0.045% WPI) were compared. Emulsions were prepared by high-pressure homogenization, while nanoemulsions were prepared by high-pressure homogenization and solvent (ethyl acetate) evaporation. The effects of pH, ionic strength (0-500 mM NaCl), thermal treatment (30-90 degrees C), and freezing/thawing on the stability and properties of the nanoemulsions and emulsions were compared. In general, nanoemulsions had better stability to droplet aggregation and creaming than emulsions. The nanoemulsions were unstable to droplet flocculation near the isoelectric point of WPI but remained stable at higher or lower pH values. In addition, the nanoemulsions were stable to salt addition, thermal treatment, and freezing/thawing (pH 7). Lipid oxidation was faster in nanoemulsions than emulsions, which was attributed to the increased surface area. Lipase digestibility of lipids was slower in nanoemulsions than emulsions, which was attributed to changes in interfacial structure and protein content. These results have important consequences for the design and utilization of food-grade nanoemulsions.
ESTHER : Lee_2011_J.Agric.Food.Chem_59_415
PubMedSearch : Lee_2011_J.Agric.Food.Chem_59_415
PubMedID: 21133433

Title : Genome sequencing and analysis of the model grass Brachypodium distachyon. -
Author(s) : Vogel JP , Garvin DF , Mockler TC , Schmutz J , Rokhsar D , Bevan MW , Barry K , Lucas S , Harmon-Smith M , Lail K , Tice H , Grimwood J , McKenzie N , Huo N , Gu YQ , Lazo GR , Anderson OD , You FM , Luo MC , Dvorak J , Wright J , Febrer M , Idziak D , Hasterok R , Lindquist E , Wang M , Fox SE , Priest HD , Filichkin SA , Givan SA , Bryant DW , Chang JH , Wu H , Wu W , Hsia AP , Schnable PS , Kalyanaraman A , Barbazuk B , Michael TP , Hazen SP , Bragg JN , Laudencia-Chingcuanco D , Weng Y , Haberer G , Spannagl M , Mayer K , Rattei T , Mitros T , Lee SJ , Rose JK , Mueller LA , York TL , Wicker T , Buchmann JP , Tanskanen J , Schulman AH , Gundlach H , Bevan M , de Oliveira AC , Maia Lda C , Belknap W , Jiang N , Lai J , Zhu L , Ma J , Sun C , Pritham E , Salse J , Murat F , Abrouk M , Bruggmann R , Messing J , Fahlgren N , Sullivan CM , Carrington JC , Chapman EJ , May GD , Zhai J , Ganssmann M , Gurazada SG , German M , Meyers BC , Green PJ , Tyler L , Wu J , Thomson J , Chen S , Scheller HV , Harholt J , Ulvskov P , Kimbrel JA , Bartley LE , Cao P , Jung KH , Sharma MK , Vega-Sanchez M , Ronald P , Dardick CD , De Bodt S , Verelst W , Inz D , Heese M , Schnittger A , Yang X , Kalluri UC , Tuskan GA , Hua Z , Vierstra RD , Cui Y , Ouyang S , Sun Q , Liu Z , Yilmaz A , Grotewold E , Sibout R , Hematy K , Mouille G , Hofte H , Michael T , Pelloux J , O'Connor D , Schnable J , Rowe S , Harmon F , Cass CL , Sedbrook JC , Byrne ME , Walsh S , Higgins J , Li P , Brutnell T , Unver T , Budak H , Belcram H , Charles M , Chalhoub B , Baxter I
Ref : Nature , 463 :763 , 2010
PubMedID: 20148030
Gene_locus related to this paper: bradi-i1grm0 , bradi-i1gx82 , bradi-i1hb80 , bradi-i1hkv6 , bradi-i1hpu6 , bradi-i1i3e4 , bradi-i1i9i0 , bradi-i1i435 , bradi-i1ix93 , bradi-i1gsk6 , bradi-i1hk44 , bradi-i1hk45 , bradi-i1hnk7 , bradi-i1hsd5 , bradi-i1huy4 , bradi-i1huy9 , bradi-i1huz0 , bradi-i1gxx9 , bradi-i1hl25 , bradi-i1hcw7 , bradi-i1hyv6 , bradi-i1hyb5 , bradi-i1hvr8 , bradi-i1hmu2 , bradi-i1hf05 , bradi-i1gry7 , bradi-i1hf06 , bradi-i1i5z8 , bradi-i1icy3 , bradi-i1j1h3 , bradi-i1h1e3 , bradi-i1hvr9 , bradi-a0a0q3r7i7 , bradi-i1i377 , bradi-i1hjg5 , bradi-i1h3i9 , bradi-i1gsg5 , bradi-a0a0q3mph9 , bradi-i1h682 , bradi-a0a0q3lc91 , bradi-i1gx49 , bradi-i1i839 , bradi-a0a2k2dsp5 , bradi-i1gsb5

Title : Effects of soy phytoestrogens on reference memory and neuronal cholinergic enzymes in ovariectomized rats - Lee_2009_J.Med.Food_12_64
Author(s) : Lee YB , Lee KH , Sohn HS , Lee SJ , Cho KH , Kang IJ , Kim DW , Shin YK , Pai T , Hwang IK , Won MH
Ref : J Med Food , 12 :64 , 2009
Abstract : The effects of soy phytoestrogens on Morris water maze (MWM) performance and neuronal cholinergic enzyme activities and immunoreactivity were studied in ovariectomized (OVX) rats. The rats were assigned to four groups fed control diet (CD), 3.9 mg/kg 17beta-estradiol diet (E2), 263.4 mg/kg soy phytoestrogens diet (SP1), and 526.9 mg/kg soy phytoestrogens diet (SP2). In the MWM task, escape latency and path length were significantly less in the E2 and SP2 groups than in the CD group on the second day. Choline acetyltransferase (ChAT) activity in the cerebral cortex and ChAT immunoreactivity in the diagonal band of Broca were significantly greater in the E2, SP1, and SP2 groups than in the CD group. Acetylcholinesterase activity in the hippocampus in the E2, SP1, and SP2 groups was significantly lower than in the CD group. This study suggests that soy phytoestrogens affect the reference memory and neuronal cholinergic system in OVX rats.
ESTHER : Lee_2009_J.Med.Food_12_64
PubMedSearch : Lee_2009_J.Med.Food_12_64
PubMedID: 19298197

Title : De Novo Next Generation Sequencing of Plant Genomes - Rounsley_2009_Rice_2_35
Author(s) : Rounsley S , Marri PR , Yu Y , He R , Sisneros N , Goicoechea JL , Lee SJ , Angelova A , Kudrna D , Luo M , Affourtit J , Desany B , Knight J , Niazi F , Egholm M , Wing RA
Ref : Rice , 2 :35 , 2009
Abstract :
ESTHER : Rounsley_2009_Rice_2_35
PubMedSearch : Rounsley_2009_Rice_2_35
PubMedID:
Gene_locus related to this paper: orysa-Q0JK71 , orysj-q6yse8 , orysa-q65xp3 , 9oryz-a0a0e0aui2 , orysi-b8bly4 , 9oryz-a0a0d9zru5

Title : A three-dimensional pharmacophore model for dipeptidyl peptidase IV inhibitors - Lu_2008_Eur.J.Med.Chem_43_1603
Author(s) : Lu IL , Tsai KC , Chiang YK , Jiaang WT , Wu SH , Mahindroo N , Chien CH , Lee SJ , Chen X , Chao YS , Wu SY
Ref : Eur Journal of Medicinal Chemistry , 43 :1603 , 2008
Abstract : Dipeptidyl peptidase IV (DPP-IV) is a valid drug target for type-2 diabetes and DPP-IV inhibitors have been proven to efficiently improve glucose tolerance. In our study, 3D pharmacophore models were generated using a training set of 22 DPP-IV inhibitors. The best model consisted of important chemical features and mapped well into the active site of DPP-IV. The model gave high correlation coefficients of 0.97 and 0.84 for the training set and the test set, respectively, showing its good predictive ability for biological activity. Furthermore, the pharmacophore model demonstrated the capability to retrieve inhibitors from database with a high enrichment factor of 42.58. All results suggest that the model provides a useful tool for designing novel DPP-IV inhibitors.
ESTHER : Lu_2008_Eur.J.Med.Chem_43_1603
PubMedSearch : Lu_2008_Eur.J.Med.Chem_43_1603
PubMedID: 18207285

Title : Evolution of genes and genomes on the Drosophila phylogeny - Clark_2007_Nature_450_203
Author(s) : Clark AG , Eisen MB , Smith DR , Bergman CM , Oliver B , Markow TA , Kaufman TC , Kellis M , Gelbart W , Iyer VN , Pollard DA , Sackton TB , Larracuente AM , Singh ND , Abad JP , Abt DN , Adryan B , Aguade M , Akashi H , Anderson WW , Aquadro CF , Ardell DH , Arguello R , Artieri CG , Barbash DA , Barker D , Barsanti P , Batterham P , Batzoglou S , Begun D , Bhutkar A , Blanco E , Bosak SA , Bradley RK , Brand AD , Brent MR , Brooks AN , Brown RH , Butlin RK , Caggese C , Calvi BR , Bernardo de Carvalho A , Caspi A , Castrezana S , Celniker SE , Chang JL , Chapple C , Chatterji S , Chinwalla A , Civetta A , Clifton SW , Comeron JM , Costello JC , Coyne JA , Daub J , David RG , Delcher AL , Delehaunty K , Do CB , Ebling H , Edwards K , Eickbush T , Evans JD , Filipski A , Findeiss S , Freyhult E , Fulton L , Fulton R , Garcia AC , Gardiner A , Garfield DA , Garvin BE , Gibson G , Gilbert D , Gnerre S , Godfrey J , Good R , Gotea V , Gravely B , Greenberg AJ , Griffiths-Jones S , Gross S , Guigo R , Gustafson EA , Haerty W , Hahn MW , Halligan DL , Halpern AL , Halter GM , Han MV , Heger A , Hillier L , Hinrichs AS , Holmes I , Hoskins RA , Hubisz MJ , Hultmark D , Huntley MA , Jaffe DB , Jagadeeshan S , Jeck WR , Johnson J , Jones CD , Jordan WC , Karpen GH , Kataoka E , Keightley PD , Kheradpour P , Kirkness EF , Koerich LB , Kristiansen K , Kudrna D , Kulathinal RJ , Kumar S , Kwok R , Lander E , Langley CH , Lapoint R , Lazzaro BP , Lee SJ , Levesque L , Li R , Lin CF , Lin MF , Lindblad-Toh K , Llopart A , Long M , Low L , Lozovsky E , Lu J , Luo M , Machado CA , Makalowski W , Marzo M , Matsuda M , Matzkin L , McAllister B , McBride CS , McKernan B , McKernan K , Mendez-Lago M , Minx P , Mollenhauer MU , Montooth K , Mount SM , Mu X , Myers E , Negre B , Newfeld S , Nielsen R , Noor MA , O'Grady P , Pachter L , Papaceit M , Parisi MJ , Parisi M , Parts L , Pedersen JS , Pesole G , Phillippy AM , Ponting CP , Pop M , Porcelli D , Powell JR , Prohaska S , Pruitt K , Puig M , Quesneville H , Ram KR , Rand D , Rasmussen MD , Reed LK , Reenan R , Reily A , Remington KA , Rieger TT , Ritchie MG , Robin C , Rogers YH , Rohde C , Rozas J , Rubenfield MJ , Ruiz A , Russo S , Salzberg SL , Sanchez-Gracia A , Saranga DJ , Sato H , Schaeffer SW , Schatz MC , Schlenke T , Schwartz R , Segarra C , Singh RS , Sirot L , Sirota M , Sisneros NB , Smith CD , Smith TF , Spieth J , Stage DE , Stark A , Stephan W , Strausberg RL , Strempel S , Sturgill D , Sutton G , Sutton GG , Tao W , Teichmann S , Tobari YN , Tomimura Y , Tsolas JM , Valente VL , Venter E , Venter JC , Vicario S , Vieira FG , Vilella AJ , Villasante A , Walenz B , Wang J , Wasserman M , Watts T , Wilson D , Wilson RK , Wing RA , Wolfner MF , Wong A , Wong GK , Wu CI , Wu G , Yamamoto D , Yang HP , Yang SP , Yorke JA , Yoshida K , Zdobnov E , Zhang P , Zhang Y , Zimin AV , Baldwin J , Abdouelleil A , Abdulkadir J , Abebe A , Abera B , Abreu J , Acer SC , Aftuck L , Alexander A , An P , Anderson E , Anderson S , Arachi H , Azer M , Bachantsang P , Barry A , Bayul T , Berlin A , Bessette D , Bloom T , Blye J , Boguslavskiy L , Bonnet C , Boukhgalter B , Bourzgui I , Brown A , Cahill P , Channer S , Cheshatsang Y , Chuda L , Citroen M , Collymore A , Cooke P , Costello M , D'Aco K , Daza R , De Haan G , DeGray S , DeMaso C , Dhargay N , Dooley K , Dooley E , Doricent M , Dorje P , Dorjee K , Dupes A , Elong R , Falk J , Farina A , Faro S , Ferguson D , Fisher S , Foley CD , Franke A , Friedrich D , Gadbois L , Gearin G , Gearin CR , Giannoukos G , Goode T , Graham J , Grandbois E , Grewal S , Gyaltsen K , Hafez N , Hagos B , Hall J , Henson C , Hollinger A , Honan T , Huard MD , Hughes L , Hurhula B , Husby ME , Kamat A , Kanga B , Kashin S , Khazanovich D , Kisner P , Lance K , Lara M , Lee W , Lennon N , Letendre F , LeVine R , Lipovsky A , Liu X , Liu J , Liu S , Lokyitsang T , Lokyitsang Y , Lubonja R , Lui A , Macdonald P , Magnisalis V , Maru K , Matthews C , McCusker W , McDonough S , Mehta T , Meldrim J , Meneus L , Mihai O , Mihalev A , Mihova T , Mittelman R , Mlenga V , Montmayeur A , Mulrain L , Navidi A , Naylor J , Negash T , Nguyen T , Nguyen N , Nicol R , Norbu C , Norbu N , Novod N , O'Neill B , Osman S , Markiewicz E , Oyono OL , Patti C , Phunkhang P , Pierre F , Priest M , Raghuraman S , Rege F , Reyes R , Rise C , Rogov P , Ross K , Ryan E , Settipalli S , Shea T , Sherpa N , Shi L , Shih D , Sparrow T , Spaulding J , Stalker J , Stange-Thomann N , Stavropoulos S , Stone C , Strader C , Tesfaye S , Thomson T , Thoulutsang Y , Thoulutsang D , Topham K , Topping I , Tsamla T , Vassiliev H , Vo A , Wangchuk T , Wangdi T , Weiand M , Wilkinson J , Wilson A , Yadav S , Young G , Yu Q , Zembek L , Zhong D , Zimmer A , Zwirko Z , Alvarez P , Brockman W , Butler J , Chin C , Grabherr M , Kleber M , Mauceli E , MacCallum I
Ref : Nature , 450 :203 , 2007
Abstract : Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
ESTHER : Clark_2007_Nature_450_203
PubMedSearch : Clark_2007_Nature_450_203
PubMedID: 17994087
Gene_locus related to this paper: droan-ACHE , droan-b3lx10 , droan-b3lx75 , droan-b3lxv7 , droan-b3ly87 , droan-b3lyh4 , droan-b3lyh5 , droan-b3lyh7 , droan-b3lyh9 , droan-b3lyi0 , droan-b3lyi2 , droan-b3lyi3 , droan-b3lyi4 , droan-b3lyj8 , droan-b3lyj9 , droan-b3lyx4 , droan-b3lyx5 , droan-b3lyx6 , droan-b3lyx7 , droan-b3lyx9 , droan-b3lz72 , droan-b3m1x3 , droan-b3m2d4 , droan-b3m3d9 , droan-b3m4e3 , droan-b3m5w1 , droan-b3m6i7 , droan-b3m7v2 , droan-b3m9a5 , droan-b3m9f4 , droan-b3m9p3 , droan-b3m254 , droan-b3m259 , droan-b3m260 , droan-b3m262 , droan-b3m524 , droan-b3m635 , droan-b3m845 , droan-b3m846 , droan-b3md01 , droan-b3mdh7 , droan-b3mdm6 , droan-b3mdw8 , droan-b3mee1 , droan-b3mf47 , droan-b3mf48 , droan-b3mg94 , droan-b3mgk2 , droan-b3mgn6 , droan-b3mii3 , droan-b3mjk2 , droan-b3mjk3 , droan-b3mjk4 , droan-b3mjk5 , droan-b3mjl2 , droan-b3mjl4 , droan-b3mjl7 , droan-b3mjl9 , droan-b3mjm8 , droan-b3mjm9 , droan-b3mjs6 , droan-b3mkr0 , droan-b3ml20 , droan-b3mly4 , droan-b3mly5 , droan-b3mly6 , droan-b3mmm8 , droan-b3mnb5 , droan-b3mny9 , droan-b3mtj5 , droan-b3muw4 , droan-b3muw8 , droan-b3n0e7 , droan-b3n2j7 , droan-b3n247 , droan-c5idb2 , droer-ACHE , droer-b3n5c7 , droer-b3n5d0 , droer-b3n5d8 , droer-b3n5d9 , droer-b3n5t7 , droer-b3n5y4 , droer-b3n7d2 , droer-b3n7d3 , droer-b3n7d4 , droer-b3n7k8 , droer-b3n8e4 , droer-b3n8f7 , droer-b3n8f8 , droer-b3n9e1 , droer-b3n319 , droer-b3n547 , droer-b3n549 , droer-b3n558 , droer-b3n560 , droer-b3n577 , droer-b3n612 , droer-b3nar5 , droer-b3nb91 , droer-b3nct9 , droer-b3nd53 , droer-b3ndh9 , droer-b3ndq8 , droer-b3ne66 , droer-b3ne67 , droer-b3ne97 , droer-b3nfk3 , droer-b3nfq9 , droer-b3nim7 , droer-b3nkn2 , droer-b3nm11 , droer-b3nmh4 , droer-b3nmy2 , droer-b3npx2 , droer-b3npx3 , droer-b3nq76 , droer-b3nqg9 , droer-b3nqm8 , droer-b3nr28 , droer-b3nrd3 , droer-b3nst4 , droer-b3nwa7 , droer-b3nyp5.1 , droer-b3nyp5.2 , droer-b3nyp6 , droer-b3nyp7 , droer-b3nyp8 , droer-b3nyp9 , droer-b3nyq3 , droer-b3nz06 , droer-b3nz14 , droer-b3nzj0 , droer-b3p0c0 , droer-b3p0c1 , droer-b3p0c2 , droer-b3p2x6 , droer-b3p2x7 , droer-b3p2x9 , droer-b3p2y1 , droer-b3p2y2 , droer-b3p6d4 , droer-b3p6d5 , droer-b3p6w3 , droer-b3p7b4 , droer-b3p7h9 , droer-b3p152 , droer-b3p486 , droer-b3p487 , droer-b3p488 , droer-b3p489 , droer-EST6 , droer-q670j5 , drogr-ACHE , drogr-b4iwp3 , drogr-b4iww3 , drogr-b4iwy3 , drogr-b4ixf7 , drogr-b4ixh4 , drogr-b4iyz5 , drogr-b4j2s2 , drogr-b4j2u8 , drogr-b4j3u1 , drogr-b4j3v3 , drogr-b4j4g7 , drogr-b4j4x9 , drogr-b4j6e6 , drogr-b4j9c9 , drogr-b4j9y4 , drogr-b4j156 , drogr-b4j384 , drogr-b4j605 , drogr-b4j685 , drogr-b4ja76 , drogr-b4jay5 , drogr-b4jcf0 , drogr-b4jcf1 , drogr-b4jdg6 , drogr-b4jdg7 , drogr-b4jdh6 , drogr-b4jdz1 , drogr-b4jdz2 , drogr-b4jdz4 , drogr-b4je66 , drogr-b4je79 , drogr-b4je82 , drogr-b4je88 , drogr-b4je89 , drogr-b4je90 , drogr-b4je91 , drogr-b4jf76 , drogr-b4jf79 , drogr-b4jf80 , drogr-b4jf81 , drogr-b4jf82 , drogr-b4jf83 , drogr-b4jf84 , drogr-b4jf85 , drogr-b4jf87 , drogr-b4jf91 , drogr-b4jf92 , drogr-b4jg66 , drogr-b4jgh0 , drogr-b4jgh1 , drogr-b4jgr9 , drogr-b4ji67 , drogr-b4jls2 , drogr-b4jnh9 , drogr-b4jpc6 , drogr-b4jpq3 , drogr-b4jpx9 , drogr-b4jql2 , drogr-b4jrh5 , drogr-b4jsb2 , drogr-b4jth3 , drogr-b4jti1 , drogr-b4jul5 , drogr-b4jur4 , drogr-b4jvh3 , drogr-b4jz00 , drogr-b4jz03 , drogr-b4jz04 , drogr-b4jz05 , drogr-b4jzh2 , drogr-b4k0u2 , drogr-b4k2r1 , drogr-b4k234 , drogr-b4k235 , drome-BEM46 , drome-CG3734 , drome-CG9953 , drome-CG11626 , drome-GH02439 , dromo-ACHE , dromo-b4k6a7 , dromo-b4k6a8 , dromo-b4k6q8 , dromo-b4k6q9 , dromo-b4k6r1 , dromo-b4k6r3 , dromo-b4k6r4 , dromo-b4k6r5 , dromo-b4k6r6 , dromo-b4k6r7 , dromo-b4k6r8 , dromo-b4k6r9 , dromo-b4k6s0 , dromo-b4k6s1 , dromo-b4k6s2 , dromo-b4k9c7 , dromo-b4k9d3 , dromo-b4k571 , dromo-b4k721 , dromo-b4ka74 , dromo-b4ka89 , dromo-b4kaj4 , dromo-b4kc20 , dromo-b4kcl2 , dromo-b4kcl3 , dromo-b4kd55.1 , dromo-b4kd55.2 , dromo-b4kd56 , dromo-b4kd57 , dromo-b4kde1 , dromo-b4kdg2 , dromo-b4kdh4 , dromo-b4kdh5 , dromo-b4kdh6 , dromo-A0A0Q9XDF2 , dromo-b4kdh8.1 , dromo-b4kdh8.2 , dromo-b4kg04 , dromo-b4kg05 , dromo-b4kg06 , dromo-b4kg16 , dromo-b4kg44 , dromo-b4kg90 , dromo-b4kh20 , dromo-b4kh21 , dromo-b4kht7 , dromo-b4kid3 , dromo-b4kik0 , dromo-b4kjx0 , dromo-b4kki1 , dromo-b4kkp6 , dromo-b4kkp8 , dromo-b4kkq8 , dromo-b4kkr0 , dromo-b4kkr3 , dromo-b4kkr4 , dromo-b4kks0 , dromo-b4kks1 , dromo-b4kks2 , dromo-b4kla1 , dromo-b4klv8 , dromo-b4knt4 , dromo-b4kp08 , dromo-b4kp16 , dromo-b4kqa6 , dromo-b4kqa7 , dromo-b4kqa8 , dromo-b4kqh1 , dromo-b4kst4 , dromo-b4ksy6 , dromo-b4kt84 , dromo-b4ktf5 , dromo-b4ktf6 , dromo-b4kvl3 , dromo-b4kvw2 , dromo-b4kwv4 , dromo-b4kwv5 , dromo-b4kxz6 , dromo-b4ky12 , dromo-b4ky36 , dromo-b4ky44 , dromo-b4kzu7 , dromo-b4l0n8 , dromo-b4l4u5 , dromo-b4l6l9 , dromo-b4l084 , drope-ACHE , drope-b4g3s6 , drope-b4g4p7 , drope-b4g6v4 , drope-b4g8m0 , drope-b4g8n6 , drope-b4g8n7 , drope-b4g9p2 , drope-b4g815 , drope-b4g816 , drope-b4gat7 , drope-b4gav5 , drope-b4gb05 , drope-b4gc08 , drope-b4gcr3 , drope-b4gdk2 , drope-b4gdl9 , drope-b4gdv9 , drope-b4gei8 , drope-b4gei9 , drope-b4gej0 , drope-b4ghz9 , drope-b4gj62 , drope-b4gj64 , drope-b4gj74 , drope-b4gkf4 , drope-b4gkv2 , drope-b4gky9 , drope-b4gl76 , drope-b4glf3 , drope-b4gmt3 , drope-b4gmt7 , drope-b4gmt9 , drope-b4gmu2 , drope-b4gmu3 , drope-b4gmu4 , drope-b4gmu5 , drope-b4gmu6 , drope-b4gmu7 , drope-b4gmv1 , drope-b4gn08 , drope-b4gpa7 , drope-b4gq13 , drope-b4grh7 , drope-b4gsf9 , drope-b4gsw4 , drope-b4gsw5 , drope-b4gsx2 , drope-b4gsx7 , drope-b4gsy6 , drope-b4gsy7 , drope-b4guj8 , drope-b4gw36 , drope-b4gzc2 , drope-b4gzc6 , drope-b4gzc7 , drope-b4h4p9 , drope-b4h5l3 , drope-b4h6a0 , drope-b4h6a8 , drope-b4h6a9 , drope-b4h6b0 , drope-b4h7m7 , drope-b4h462 , drope-b4h601 , drope-b4h602 , drope-b4hay1 , drope-b4hb18 , drope-est5a , drope-est5b , drope-est5c , drops-ACHE , drops-b5dhd2 , drops-b5dk96 , drops-b5dpe3 , drops-b5drp9 , drops-b5dwa7 , drops-b5dwa8 , drops-b5dz85 , drops-b5dz86 , drops-est5a , drops-est5b , drops-q29bq2 , drops-q29dd7 , drops-q29ew0 , drops-q291d5 , drops-q291e8 , drops-q293n1 , drops-q293n4 , drops-q293n5 , drops-q293n6 , drops-q294n6 , drops-q294n7 , drops-q294n9 , drops-q294p4 , drose-b4he97 , drose-b4hfu2 , drose-b4hg54 , drose-b4hga0 , drose-b4hgu9 , drose-b4hgv0 , drose-b4hgv3 , drose-b4hgv4 , drose-b4hhm8 , drose-b4hhs6 , drose-b4hie4 , drose-b4him9 , drose-b4hk63 , drose-b4hkj5 , drose-b4hr07 , drose-b4hr81 , drose-b4hre7 , drose-b4hs13 , drose-b4hsj9 , drose-b4hsk0 , drose-b4hsm8 , drose-b4hvr5 , drose-b4hwr7 , drose-b4hwr8 , drose-b4hwr9 , drose-b4hws6 , drose-b4hws7 , drose-b4hwt0 , drose-b4hwt2 , drose-b4hwu1 , drose-b4hwu2 , drose-b4hxs9 , drose-b4hxu4 , drose-b4hxz1 , drose-b4hyp8 , drose-b4hyp9 , drose-b4hyq0 , drose-b4hyz4 , drose-b4hyz5 , drose-b4i1k8 , drose-b4i2f3 , drose-b4i2w5 , drose-b4i4u3 , drose-b4i4u7 , drose-b4i4u9 , drose-b4i4v0 , drose-b4i4v1 , drose-b4i4v4 , drose-b4i4v5 , drose-b4i4v6 , drose-b4i4v7 , drose-b4i4v8 , drose-b4i4w0 , drose-b4i7s6 , drose-b4i133 , drose-b4i857 , drose-b4iam7 , drose-b4iam9 , drose-b4iaq6 , drose-b4icf6 , drose-b4icf7 , drose-b4id80 , drose-b4ifc5 , drose-b4ihv9 , drose-b4iie9 , drose-b4ilj8 , drose-b4in13 , drose-b4inj9 , drosi-ACHE , drosi-aes04a , drosi-b4nsh8 , drosi-b4q3d7 , drosi-b4q4w5 , drosi-b4q4y7 , drosi-b4q6h6 , drosi-b4q7u2 , drosi-b4q7u3 , drosi-b4q9c6 , drosi-b4q9c7 , drosi-b4q9d3 , drosi-b4q9d4 , drosi-b4q9r0 , drosi-b4q9r1 , drosi-b4q9r3 , drosi-b4q9s2 , drosi-b4q9s3 , drosi-b4q429 , drosi-b4q530 , drosi-b4q734 , drosi-b4q782 , drosi-b4q783 , drosi-b4q942 , drosi-b4qet1 , drosi-b4qfv6 , drosi-b4qge5 , drosi-b4qgh5 , drosi-b4qgs5 , drosi-b4qhf3 , drosi-b4qhf4 , drosi-b4qhi5 , drosi-b4qjr2 , drosi-b4qjr3 , drosi-b4qjv6 , drosi-b4qk23 , drosi-b4qk51 , drosi-b4qlt1 , drosi-b4qlz9 , drosi-b4qmn9 , drosi-b4qrq7 , drosi-b4qs01 , drosi-b4qs57 , drosi-b4qs82 , drosi-b4qs83 , drosi-b4qs84 , drosi-b4qs85 , drosi-b4qs86 , drosi-b4qsq1 , drosi-b4quk6 , drosi-b4qvg5 , drosi-b4qvg6 , drosi-b4qzn2 , drosi-b4qzn3 , drosi-b4qzn5 , drosi-b4qzn7 , drosi-b4qzn8 , drosi-b4qzp2 , drosi-b4qzp3 , drosi-b4qzp4 , drosi-b4qzp5 , drosi-b4qzp6 , drosi-b4qzp7 , drosi-b4r1a4 , drosi-b4r025 , drosi-b4r207 , drosi-b4r662 , drosi-este6 , drosi-q670k8 , drovi-ACHE , drovi-b4lev2 , drovi-b4lf33 , drovi-b4lf51 , drovi-b4lg54 , drovi-b4lg72 , drovi-b4lgc6 , drovi-b4lgd5 , drovi-b4lgg0 , drovi-b4lgk5 , drovi-b4lgn2 , drovi-b4lh17 , drovi-b4lh18 , drovi-b4lk43 , drovi-b4ll59 , drovi-b4ll60 , drovi-b4llm5 , drovi-b4lln3 , drovi-b4lmk4 , drovi-b4lmp0 , drovi-b4lnr4 , drovi-b4lp47 , drovi-b4lpd0 , drovi-b4lps0 , drovi-b4lqc6 , drovi-b4lr00 , drovi-b4lrp6 , drovi-b4lrw2 , drovi-b4lse7 , drovi-b4lse9 , drovi-b4lsf0 , drovi-b4lsn0 , drovi-b4lsq5 , drovi-b4lt32 , drovi-b4ltr1 , drovi-b4lui7 , drovi-b4lui9 , drovi-b4luj8 , drovi-b4luk0 , drovi-b4luk3 , drovi-b4luk8 , drovi-b4luk9 , drovi-b4lul0 , drovi-b4lve2 , drovi-b4lxi9 , drovi-b4lxj8 , drovi-b4lyf3 , drovi-b4lyq2 , drovi-b4lyq3 , drovi-b4lz07 , drovi-b4lz13 , drovi-b4lz14 , drovi-b4lz15 , drovi-b4m0j7 , drovi-b4m0s0 , drovi-b4m2b6 , drovi-b4m4h7 , drovi-b4m4h8 , drovi-b4m4i0 , drovi-b4m4i2 , drovi-b4m4i3.A , drovi-b4m4i3.B , drovi-b4m4i4 , drovi-b4m4i5 , drovi-b4m4i6 , drovi-b4m4i7 , drovi-b4m4i8 , drovi-b4m4i9 , drovi-b4m4j2 , drovi-b4m5a0 , drovi-b4m5a1 , drovi-b4m5a2 , drovi-b4m6b9 , drovi-b4m7k9 , drovi-b4m9g9 , drovi-b4m9h0 , drovi-b4m564 , drovi-b4m599 , drovi-b4m918 , drovi-b4mb87 , drovi-b4mc71 , drovi-b4mfa4 , drowi-ACHE , drowi-b4mjb9 , drowi-b4mkt7 , drowi-b4mlc1 , drowi-b4mp68 , drowi-b4mqe9 , drowi-b4mqf0.2 , drowi-b4mqf1 , drowi-b4mqf3 , drowi-b4mqf4 , drowi-b4mqf5 , drowi-b4mqq6 , drowi-b4mrd1 , drowi-b4mrk3 , drowi-b4mtl5 , drowi-b4mug2 , drowi-b4muj8 , drowi-b4mv18 , drowi-b4mw32 , drowi-b4mw85 , drowi-b4mwp2 , drowi-b4mwp6 , drowi-b4mwq5 , drowi-b4mwr0 , drowi-b4mwr8 , drowi-b4mwr9 , drowi-b4mwt1 , drowi-b4mwz7 , drowi-b4mxn5 , drowi-b4my54 , drowi-b4myg1 , drowi-b4myh5 , drowi-b4n0d4 , drowi-b4n1a7 , drowi-b4n1c8 , drowi-b4n3s9 , drowi-b4n3x7 , drowi-b4n4x9 , drowi-b4n4y0 , drowi-b4n6m1 , drowi-b4n6n0 , drowi-b4n6n7 , drowi-b4n6u6 , drowi-b4n7s6 , drowi-b4n7s7 , drowi-b4n7s8 , drowi-b4n899.1 , drowi-b4n8a1 , drowi-b4n8a2 , drowi-b4n8a3 , drowi-b4n8a4 , drowi-b4n8a9 , drowi-b4n023 , drowi-b4n075 , drowi-b4n543 , drowi-b4n888 , drowi-b4n889 , drowi-b4n891 , drowi-b4n893 , drowi-b4n895 , drowi-b4n897 , drowi-b4n898 , drowi-b4n899.2 , drowi-b4nae3 , drowi-b4ner8 , drowi-b4ng76 , drowi-b4nga7 , drowi-b4ngb5 , drowi-b4nhz9 , drowi-b4nj18 , drowi-b4nj19 , drowi-b4nja7 , drowi-b4nja8 , drowi-b4nja9 , drowi-b4njk8 , drowi-b4nkc8 , drowi-b4nky0 , drowi-b4nl36 , drowi-b4nm27 , drowi-b4nn59 , drowi-b4nnc1 , drowi-b4nng1 , drowi-b4nng2 , droya-ACHE , droya-aes04 , droya-b4itg2 , droya-b4itg6 , droya-b4itu9 , droya-b4iuv4 , droya-b4iuv5 , droya-b4nxe6 , droya-b4nxg5 , droya-b4nxg6 , droya-b4nxg8 , droya-b4nxw4 , droya-b4ny57 , droya-b4ny58 , droya-b4ny86 , droya-b4nzz8 , droya-b4p0b5 , droya-b4p0q9 , droya-b4p0r0 , droya-b4p0r7 , droya-b4p0r8 , droya-b4p0r9 , droya-b4p0s0 , droya-b4p0s2 , droya-b4p0t0 , droya-b4p0t1 , droya-b4p3h4 , droya-b4p3x8 , droya-b4p5g8 , droya-b4p6c9 , droya-b4p6l9 , droya-b4p6r1 , droya-b4p6r2 , droya-b4p7u4 , droya-b4p8w7 , droya-b4p023 , droya-b4p241 , droya-b4p774 , droya-b4pat9 , droya-b4pbl1 , droya-b4pd22 , droya-b4pd70 , droya-b4pdm8 , droya-b4pet9 , droya-b4pff9 , droya-b4pga7 , droya-b4pgu0 , droya-b4pig3 , droya-b4pjt8 , droya-b4pka2 , droya-b4plh2 , droya-b4pma3 , droya-b4pmv3 , droya-b4pmv4 , droya-b4pmv5 , droya-b4pn92 , droya-b4pp65 , droya-b4ppc5 , droya-b4ppc6 , droya-b4ppc7 , droya-b4ppc8 , droya-b4pq03 , droya-b4prg6B , droya-b4prg9 , droya-b4prh3 , droya-b4prh4 , droya-b4prh6 , droya-b4prh7 , droya-b4psz8 , droya-b4psz9 , droya-b4pv22 , droya-b4q0g5 , droya-b4q246 , droya-EST6 , droya-q71d76 , drowi-b4n7m9 , drope-b4gkk1 , droer-b3n5s3 , drose-b4i1w5 , drowi-a0a0q9x0t3 , drogr-b4jvm7 , dromo-b4ku70 , drovi-b4mcn9 , drovi-b4lty2 , drogr-b4jdu1 , drovi-a0a0q9wiq8 , dromo-b4kf70 , drosi-b2zi86 , droya-b4p2y4 , drose-b2zic5 , droer-b3n895

Title : Cloning, expression and enantioselective hydrolytic catalysis of a microsomal epoxide hydrolase from a marine fish, Mugil cephalus - Lee_2007_Biotechnol.Lett_29_237
Author(s) : Lee SJ , Kim HS , Kim SJ , Park S , Kim BJ , Shuler ML , Lee EY
Ref : Biotechnol Lett , 29 :237 , 2007
Abstract : The cDNA of a marine fish microsomal epoxide hydrolase (mEH) gene from Mugil cephalus was cloned by rapid amplification of cDNA ends (RACE) techniques. The homology model for the mEH of M. cephalus showed a characteristic structure of alpha/beta-hydrolase-fold main domain with a lid domain over the active site. The characteristic catalytic triad, consisting of Asp(238), His(444), and Glu(417), was highly conserved. The cloned mEH gene was expressed in Escherichia coli and the recombinant mEH exhibited (R)-preferred hydrolysis activity toward racemic styrene oxide. We obtained enantiopure (S)-styrene oxide with a high enantiopurity of more than 99% enantiomeric excess and yield of 15.4% by batch kinetic resolution of 20 mM racemic styrene oxide.
ESTHER : Lee_2007_Biotechnol.Lett_29_237
PubMedSearch : Lee_2007_Biotechnol.Lett_29_237
PubMedID: 17151961
Gene_locus related to this paper: mucge-c4paw7

Title : The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes - Cho_2007_Proc.Natl.Acad.Sci.U.S.A_104_7981
Author(s) : Cho NH , Kim HR , Lee JH , Kim SY , Kim J , Cha S , Darby AC , Fuxelius HH , Yin J , Kim JH , Lee SJ , Koh YS , Jang WJ , Park KH , Andersson SG , Choi MS , Kim IS
Ref : Proc Natl Acad Sci U S A , 104 :7981 , 2007
Abstract : Scrub typhus is caused by the obligate intracellular rickettsia Orientia tsutsugamushi (previously called Rickettsia tsutsugamushi). The bacterium is maternally inherited in trombicuid mites and transmitted to humans by feeding larvae. We report here the 2,127,051-bp genome of the Boryong strain, which represents the most highly repeated bacterial genome sequenced to date. The repeat density of the scrub typhus pathogen is 200-fold higher than that of its close relative Rickettsia prowazekii, the agent of epidemic typhus. A total of 359 tra genes for components of conjugative type IV secretion systems were identified at 79 sites in the genome. Associated with these are >200 genes for signaling and host-cell interaction proteins, such as histidine kinases, ankyrin-repeat proteins, and tetratrico peptide-repeat proteins. Additionally, the O. tsutsugamushi genome contains >400 transposases, 60 phage integrases, and 70 reverse transcriptases. Deletions and rearrangements have yielded unique gene combinations as well as frequent pseudogenization in the tra clusters. A comparative analysis of the tra clusters within the genome and across strains indicates sequence homogenization by gene conversion, whereas complexity, diversity, and pseudogenization are acquired by duplications, deletions, and transposon integrations into the amplified segments. The results suggest intragenomic duplications or multiple integrations of a massively proliferating conjugative transfer system. Diversifying selection on host-cell interaction genes along with repeated population bottlenecks may drive rare genome variants to fixation, thereby short-circuiting selection for low complexity in bacterial genomes.
ESTHER : Cho_2007_Proc.Natl.Acad.Sci.U.S.A_104_7981
PubMedSearch : Cho_2007_Proc.Natl.Acad.Sci.U.S.A_104_7981
PubMedID: 17483455

Title : 2-[3-[2-[(2S)-2-Cyano-1-pyrrolidinyl]-2-oxoethylamino]-3-methyl-1-oxobutyl]- 1,2,3,4-tetrahydroisoquinoline: a potent, selective, and orally bioavailable dipeptide-derived inhibitor of dipeptidyl peptidase IV - Tsu_2006_J.Med.Chem_49_373
Author(s) : Tsu H , Chen X , Chen CT , Lee SJ , Chang CN , Kao KH , Coumar MS , Yeh YT , Chien CH , Wang HS , Lin KT , Chang YY , Wu SH , Chen YS , Lu IL , Wu SY , Tsai TY , Chen WC , Hsieh HP , Chao YS , Jiaang WT
Ref : Journal of Medicinal Chemistry , 49 :373 , 2006
Abstract : Dipeptidyl peptidase IV (DPP-IV) inhibitors are expected to become a new type of antidiabetic drugs. Most known DPP-IV inhibitors often resemble the dipeptide cleavage products, with a proline mimic at the P1 site. As off-target inhibitions of DPP8 and/or DPP9 have shown profound toxicities in the in vivo studies, it is important to develop selective DPP-IV inhibitors for clinical usage. To achieve this, a new class of 2-[3-[[2-[(2S)-2-cyano-1-pyrrolidinyl]-2-oxoethyl]amino]-1-oxopropyl]-based DPP-IV inhibitors was synthesized. SAR studies resulted in a number of DPP-IV inhibitors, having IC(50) values of <50 nM with excellent selectivity over both DPP8 (IC(50) > 100 microM) and DPP-II (IC(50) > 30 microM). Compound 21a suppressed the blood glucose elevation after an oral glucose challenge in Wistar rats and also inhibited plasma DPP-IV activity for up to 4 h in BALB/c mice. The results show that compound 21a possesses in vitro and in vivo activities comparable to those of NVP-LAF237 (4), which is in clinical development.
ESTHER : Tsu_2006_J.Med.Chem_49_373
PubMedSearch : Tsu_2006_J.Med.Chem_49_373
PubMedID: 16392822

Title : Novel isoindoline compounds for potent and selective inhibition of prolyl dipeptidase DPP8 - Jiaang_2005_Bioorg.Med.Chem.Lett_15_687
Author(s) : Jiaang WT , Chen YS , Hsu T , Wu SH , Chien CH , Chang CN , Chang SP , Lee SJ , Chen X
Ref : Bioorganic & Medicinal Chemistry Lett , 15 :687 , 2005
Abstract : DPP8 is a prolyl dipeptidase homologous to DPP-IV, which is a drug target for Type II diabetes. The biological function of DPP8 is not known. To identify potent and selective chemical compounds against DPP8, we have synthesized a series of isoquinoline and isoindoline derivatives and have tested their inhibitory activity against DPP8, DPP-IV and DPP-II. Isoindoline derivatives were found to be more potent DPP8 inhibitors than isoquinoline derivatives. Isoindoline with a 1-(4,4'-difluor-benzhydryl)-piperazine group at the P2 site was observed to be a very potent DPP8 inhibitor, having an IC(50) value of 14nM with at least a 2500-fold selectivity over either DPP-IV or DPP-II. From SAR results, we speculate that the S1 site of DPP8 may be larger than that of DPP-IV, which would allow the accommodation of larger C-terminal residues, such as isoquinoline or isoindoline.
ESTHER : Jiaang_2005_Bioorg.Med.Chem.Lett_15_687
PubMedSearch : Jiaang_2005_Bioorg.Med.Chem.Lett_15_687
PubMedID: 15664838
Gene_locus related to this paper: human-DPP8

Title : Glutamic acid analogues as potent dipeptidyl peptidase IV and 8 inhibitors - Lu_2005_Bioorg.Med.Chem.Lett_15_3271
Author(s) : Lu IL , Lee SJ , Tsu H , Wu SY , Kao KH , Chien CH , Chang YY , Chen YS , Cheng JH , Chang CN , Chen TW , Chang SP , Chen X , Jiaang WT
Ref : Bioorganic & Medicinal Chemistry Lett , 15 :3271 , 2005
Abstract : To find potent and selective inhibitors of dipeptidyl peptidase IV (DPP-IV), we synthesized a series of 2-cyanopyrrolidine with P2-site 4-substituted glutamic acid derivatives and tested their activities against DPP-IV, DPP8, and DPP-II. Analogues that incorporated a bulky substituent at the first carbon position of benzylamine or isoquinoline showed over 30-fold selectivity for DPP-IV over both DPP8 and DPP-II. From structure-activity relationship studies, we speculate that the S2 site of DPP8 might be similar to that of DPP-IV, while DPP-IV inhibitor with N-substituted glycine in the P2 site and/or with a moiety involving in hydrophobic interaction with the side chain of Phe357 might provide a better selectivity for DPP-IV over DPP8.
ESTHER : Lu_2005_Bioorg.Med.Chem.Lett_15_3271
PubMedSearch : Lu_2005_Bioorg.Med.Chem.Lett_15_3271
PubMedID: 15927466

Title : Production of (S)-styrene oxide by recombinant Pichia pastoris containing epoxide hydrolase from Rhodotorula glutinis - Lee_2004_Enzyme.Microb.Technol_35_624
Author(s) : Lee EY , Yoo SS , Kim HS , Lee SJ , Oh YK , Park S
Ref : Enzyme Microb Technol , 35 :624 , 2004
Abstract : A recombinant yeast Pichia pastoris carrying the gene encoding epoxide hydrolase (EH) of Rhodotorula glutinis was constructed and used for producing (S)-styrene oxide by enantioselective hydrolysis of racemic mixtures of styrene oxides. The EH gene was obtained by PCR amplification of cDNA of R. glutinis and integrated into the chromosomal DNA of P. pastoris to express EH under the control of AOX promoter. The recombinant yeast has a high hydrolytic activity toward (R)-styrene oxide as 358 nmol min-1 (mg cell)-1, which is about 10-fold higher than that of wild type R. glutinis. When kinetic resolution was conducted by the recombinant yeast at a high initial epoxides concentration of 526 mM that constitutes an epoxidewater two-liquid phase, chiral (S)-styrene oxide with an enantiomeric excess (e.e.) higher than 98% was obtained as 36% yield (theoretical, 50%) at 16 h
ESTHER : Lee_2004_Enzyme.Microb.Technol_35_624
PubMedSearch : Lee_2004_Enzyme.Microb.Technol_35_624
PubMedID:
Gene_locus related to this paper: rhogl-EPH1

Title : Association of hepatic lipase with proteoglycans stimulates the production of proteoglycans in vivo and in vitro - Lee_2004_J.Lipid.Res_45_1266
Author(s) : Lee SJ , Kadambi S , David C , Cooper AD , Choi SY
Ref : J Lipid Res , 45 :1266 , 2004
Abstract : HL is synthesized in hepatocytes and functions while bound to heparan sulfate proteoglycans (HSPGs) in sinusoidal endothelial cells. The HL-mediated uptake of lipoprotein requires cell-surface HSPG. The present study tested whether HL plays a role in the production of HSPG. The production of HSPG in Chinese hamster ovary (CHO) cells was determined by measuring the incorporation of (35)SO(4) into PGs. HL-producing HL-CHO cells showed approximately 30% more cellular PG than did wild-type (WT) cells. In contrast, PG production in cells producing a membrane-anchored HL-glycophosphatidylinositol (GPI) that was not bound to HSPG was virtually identical to that in WT cells. When purified HL was added to the WT- or HL-GPI cells, PG production increased significantly to a level similar to that of the HL-secreting cells, suggesting that the binding of HL to HSPG triggered the increased HSPG production. Heparin reduced PG production in HL-producing cells, confirming that PG production is stimulated only when HL is present as a ligand for HSPG. Real-time PCR and Northern blots demonstrated that PG production was significantly reduced in animals lacking HL. Together, these data suggest that the binding of HL to PG on the cell surface exerts a positive feedback on cellular PG production.
ESTHER : Lee_2004_J.Lipid.Res_45_1266
PubMedSearch : Lee_2004_J.Lipid.Res_45_1266
PubMedID: 15102889

Title : Nereistoxin and cartap neurotoxicity attributable to direct block of the insect nicotinic receptor\/channel - Lee_2003_J.Agric.Food.Chem_51_2646
Author(s) : Lee SJ , Tomizawa M , Casida JE
Ref : Journal of Agricultural and Food Chemistry , 51 :2646 , 2003
Abstract : Nereistoxin (NTX) (4-dimethylamino-1,2-dithiolane) is the naturally occurring prototype for cartap [the bis(thiocarbamate) derivative of the NTX dithiol], which is generally regarded as a proinsecticide reverting to NTX. The aim of this study is to define the target site(s) for dithiolanes and dithiol esters. The affinity of [(3)H]NTX was not suitable for binding assays with honeybee (Apis mellifera) head membranes. However, NTX and cartap are equally potent, direct-acting, and competitive displacers of [(3)H]thienylcyclohexylpiperidine binding at the noncompetitive blocker (NCB) site of the Apis nicotinic acetylcholine receptor (nAChR)/channel. NTX also binds at the Apis [(3)H]imidacloprid agonist site, but cartap does not. As candidate metabolic pathways, sequential N-desmethylation and S-oxidation of NTX progressively reduce its potency at the NCB site and toxicity to houseflies. A P450 inhibitor reduces the toxicity of NTX and enhances it with cartap. Surprisingly, cartap is not just a pro-NTX but instead directly induces inhibitory neurotoxicity by blocking the nAChR/channel, whereas NTX may have dual NCB and agonist targets.
ESTHER : Lee_2003_J.Agric.Food.Chem_51_2646
PubMedSearch : Lee_2003_J.Agric.Food.Chem_51_2646
PubMedID: 12696952

Title : Sequential structural changes of Escherichia coli thioesterase\/protease I in the serial formation of Michaelis and tetrahedral complexes with diethyl p-nitrophenyl phosphate - Tyukhtenko_2003_Biochemistry_42_8289
Author(s) : Tyukhtenko SI , Litvinchuk AV , Chang CF , Lo YC , Lee SJ , Shaw JF , Liaw YC , Huang TH
Ref : Biochemistry , 42 :8289 , 2003
Abstract : Escherichia coli thioesterase/protease I (TEP-I) belongs to a new subclass of lipolytic enzymes of the serine hydrolase superfamily. Here we report the first direct NMR observation of the formation of the Michaelis complex (MC) between TEP-I and diethyl p-nitrophenyl phosphate (DENP), an active site directed inhibitor of serine protease, and its subsequent conversion to the tetrahedral complex (TC). NMR, ESI-MS, and kinetic data showed that DENP binds to TEP-I in a two-step process, a fast formation of MC followed by a slow conversion to TC. NMR chemical shift perturbation further revealed that perturbations were confined mainly to four conserved segments comprising the active site. Comparable magnitudes of chemical shift perturbations were detected in both steps. The largest chemical shift perturbation occurred around the catalytic Ser(10). In MC, the conformation of the mobile Ser(10) was stabilized, and its amide resonance became observable. From the large chemical shift perturbation upon conversion from MC to TC, we propose that the amide protons of Ser(10) and Gly(44) serve as the oxyanion hole proton donors that stabilize the tetrahedral adduct. The pattern of residues perturbed in both steps suggests a sequential, stepwise structural change upon binding of DENP. The present study also demonstrates the important catalytic roles of conserved residues in the SGNH family of proteins.
ESTHER : Tyukhtenko_2003_Biochemistry_42_8289
PubMedSearch : Tyukhtenko_2003_Biochemistry_42_8289
PubMedID: 12846577

Title : Identification of radiation-specific responses from gene expression profile - Park_2002_Oncogene_21_8521
Author(s) : Park WY , Hwang CI , Im CN , Kang MJ , Woo JH , Kim JH , Kim YS , Kim H , Kim KA , Yu HJ , Lee SJ , Lee YS , Seo JS
Ref : Oncogene , 21 :8521 , 2002
Abstract : The responses to ionizing radiation (IR) in tumors are dependent on cellular context. We investigated radiation-related expression patterns in Jurkat T cells with nonsense mutation in p53 using cDNA microarray. Expression of 2400 genes in gamma-irradiated cells was distinct from other stimulations like anti-CD3, phetohemagglutinin (PHA) and concanavalin A (ConA) in unsupervised clustering analysis. Among them, 384 genes were selected for their IR-specific changes to make 'RadChip'. In spite of p53 status, every type of cells showed similar patterns in expression of these genes upon gamma-radiation. Moreover, radiation-induced responses were clearly separated from the responses to other genotoxic stress like UV radiation, cisplatin and doxorubicin. We focused on two IR-related genes, phospholipase Cgamma2 (PLCG2) and cytosolic epoxide hydrolase (EPHX2), which were increased at 12 h after gamma-radiation in RT-PCR. TPCK could suppress the induction of these two genes in either of Jurkat T cells and PBMCs, which might suggest the transcriptional regulation of PLCG2 and EPHX2 by NF-kappaB upon gamma-radiation. From these results, we could identify the IR-specific genes from expression profiling, which can be used as radiation biomarkers to screen radiation exposure as well as probing the mechanism of cellular responses to ionizing radiation.
ESTHER : Park_2002_Oncogene_21_8521
PubMedSearch : Park_2002_Oncogene_21_8521
PubMedID: 12466973