• Title/Summary/Keyword: library 3.0

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Characterization of the pcbD Gene Encoding 2-Hydroxy-6-Ox0-6-Phenylgexa-2,4-Dienoate Hydrolase from Pseudomonas sp. P20

  • Lim, Jong-Chul;Lee, Jeong-Rai;Lim, Jai-Yun;Min, Kyung-Rak;Kim, Chi-Kyung;Ki, Young-Soo
    • Journal of Microbiology and Biotechnology
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    • v.10 no.2
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    • pp.258-263
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    • 2000
  • 2-Hydroxy-6-oxo-6phenylhexa-2,4-dienoate (HOPDA) hydrolase catalyzes the hydrolytic cleavage of HOPDA to bemzpate and 2-hydroxypenta-2, 4-dienoate (HPD) during microbial catabolism of biphenyl and polychlorinated biphenyls. A HOPDA hydrolase gene (pcbD) was isolated from the genomic library of Pseudomonas sp. P20 and designated as pCNUO1201; a 7.5-kb XbaI DNA fragment from Pseudomonas sp. P20 was inserted into the pBluescript SK(+) XbaI site. E. coli HB101 harboring pCNU1201 exhibited HOPDA hydrolase activity. The open reading frame (ORF) corresponding to the pcbD gene consisted of 855 base pairs with an ATG initiation codon and a TGA termination codon. The ORF was preceded by a rebosome-binding sequence of 5'-TGGAGC-3' and its G+C content was 55 mol%. The pcbD gene of Pseudomonas sp. P20 was located immedeately downstream of the pcbC gene encoding 2,3- dihydroxybiphenyl 1,2-dioxygenase, and approximately 4-kb upstream of the pcbE gene encoding HPD hydratase. The pcbK gene was able to encode a polypeptide with a molecular weight of 31,732 containing 284 amino acid residues. The deduced amino acid sequence of the HOPDA hydrolase of Pseudomonas sp. P20 exhibited high identity (62%) with those of the HOPDA hydrolases of P. putida KF715, P. pseudoalcaligenes KF707, and Burkholderia cepacia LB400, and also significant homology with those of other hydrolytic enzymes including esterase, transferase, and peptidase.

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Metabolic Activation of Marijuana Constituents, Cannabinoids, in Relation to Their Toxicity for Human and Its Oxidation Mechanism

  • Ikuo, Yamamoto
    • Proceedings of the PSK Conference
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    • 2002.10a
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    • pp.194-199
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    • 2002
  • Many oxidative metabolites of tetrahydrocannabinols (THCs), active components of marijuana, were pharmacologically active, and 11-hydroxy-THCs, 11-oxo-${\Delta}^8$-THC, 7-oxo-${\Delta}^8$-THC, 8$\beta$, 9$\beta$-epoxyhexahydrocannabinol (EHHC), 9$\alpha$, l0$\alpha$-EHHC and 3'-hydroxy-${\Delta}^9$-THC were more active than THC in pharmacological effects such as catalepsy, hypothermia and barbiturate synergism in mice. Cannabidiol (CBD), another major component, was biotransfomred to two novel metabolites, 6-hydroxymethyl-${\Delta}^9$-THC and 3-pentyl-6, 7, 7a, 8, 9, lla-hexahydro-I, 7-dihydroxy-7, 1O-dimethyldibenzo[b, d]oxepin (PHDO) through 8R, 9-epoxy-CBD and 85, 9-epoxy-CBD, respectively. Both metabolites exhibited some pharmacological effects comparable to d9 - THe. Cannabinol (CBN), the other major component, was mainly metabolized to ll-hydroxy-CBN by hepatic microsomes of animals including humans. The pharmacological effects of the metabolite were higher than those of CBN demonstrating that II-hydroxylation of CBN is metabolic activation pathway of the cannabinoid as is the case in THCs. Tolerance and reciprocal cross-tolerance developed to pharmacological effects d8 - THC and ll-hydroxy-d8-THC , and the magnitude of tolerance development produced by the metabolite was significantly higher than that by d8-THC. The results indicate that ll-hydroxy-d8-THC has an important role not only in the pharmacological effects but also its tolerance development of d8 - THe. THCs and their metabolites competed to the specific binding of CP-55, 940, an agonist of cannabinoid receptor, to synaptic membrane from bovine cerebral cortex. The Ki value of THCs and their metabolites were closely paralleled to their pharmacological effects in mice. A novel cytochrome P450 (cyp2c29) was purified and identified as a major enzyme responsible for the metabolic activation of d8-THC at the II-position in the mouse liver. cDNA of CYP2C29 was cloned from a mouse cDNA library and its sequence was determined. The oxidation mechanism of THC by cyp2c29 was proposed.

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Antiviral activity of sertindole, raloxifene and ibutamoren against transcription and replication-competent Ebola virus-like particles

  • Yoon, Yi-Seul;Jang, Yejin;Hoenen, Thomas;Shin, Heegwon;Lee, Younghoon;Kim, Meehyein
    • BMB Reports
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    • v.53 no.3
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    • pp.166-171
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    • 2020
  • A chemical library comprising 2,354 drug-like compounds was screened using a transcription and replication-competent viruslike particle (trVLP) system implementing the whole Ebola virus (EBOV) life cycle. Dose-dependent inhibition of Ebola trVLP replication was induced by 15 hit compounds, which primarily target different types of G protein-coupled receptors (GPCRs). Based on the chemical structure, the compounds were divided into three groups, diphenylmethane derivatives, promazine derivatives and chemicals with no conserved skeletons. The third group included sertindole, raloxifene, and ibutamoren showing prominent antiviral effects in cells. They downregulated the expression of viral proteins, including the VP40 matrix protein and the envelope glycoprotein. They also reduced the amount of EBOV-derived tetracistronic minigenome RNA incorporated into progeny trVLPs in the culture supernatant. Particularly, ibutamoren, which is a known agonist of growth hormone secretagogue receptor (GHSR), showed the most promising antiviral activity with a 50% effective concentration of 0.2 μM, a 50% cytotoxic concentration of 42.4 μM, and a selectivity index of 222.8. Here, we suggest a strategy for development of anti-EBOV therapeutics by adopting GHSR agonists as hit compounds.

Evaluation of Glucosinolate Content and Composition Contained in Korean Leaf Mustard (Brassica juncea var. integrifolia) Germplasm Using Liquid Chromatography Electrospray Ionization Mass Spectrometry(LC-ESI-MS/MS)

  • Kim, Jung-Bong;Kim, Heon-Woong;Ko, Ho-Cheol;Kim, So-Young;Kim, Se-Na;Jin, Yong-Xie;Kim, Jae-Hyun
    • Proceedings of the Plant Resources Society of Korea Conference
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    • 2010.05a
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    • pp.18-18
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    • 2010
  • Glucosinolates(GSLs) are major secondary products($\beta$-thioglucoside N-hydroxysulfates) containing sulfates that are found mainly in Cruciferae family such as cabbage, broccoli, radish, turnip, kale, mustard and rapeseed as the important crops in agronomic and economic aspects. Especially, isothiocyanates(ITCs) have been shown to inhibit carcinogenesis with regulation cancer cell development followed by regulating target enzymes, inducing cell cycle arrest and apoptosis against various human cancer cell lines. Total desulfo(DS)-GSLs of nine type in 210 Korean leaf mustard accessions were isolated and confirmed using electrospray ionization mass spectrometric(ESI-MS/MS) method and DS-GSLs powerful library maked from several reference data. The isolated individual DS-GSLs were identified by removed $\beta$-D-glucopyranose residue ($C_6H_{11}O_5$, MW 163) from MS/MS data. Among them sinigrin(41.7%), glucoiberverin(21.7%) and gluconasturtiin(12.6%) were major components, Especially, despite gluconapin was minor component, accession K046197-1 and K046197-2 showed higher content of 4.11 and 3.31 mg/g(DW), respectively. The total GSLs contents in 210 accessions were ranged from 5.3 to 23.2 mg/g(DW) with a mean value of 13.0 mg/g(DW). As a result of principal component analysis(PCA), the individual GSLs loading plots were composed of three groups and components belonged to each group showed correlationship in quantitative pattern.

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Identification of Proteins Interacting with C- Terminal Region of Human Ankyrin-G

  • Lee, Yeong-Mi;Lee, Min-A;Park, Jae-Kyoung;Kim, Myong-Shin;Jeon, Eun-Bee;Park, Su-Il;Kim, Chong-Rak
    • Biomedical Science Letters
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    • v.9 no.3
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    • pp.159-165
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    • 2003
  • Ankyrins are a ubiquitously expressed family of intracellular adaptor proteins involved in targeting diverse proteins to specialized membrane domains in both the plasma membrane and the endoplasmic reticulum. Recently, the studies with C-terminus of ankyrins have identified that ankyrin-B is capable of interacting with Hsp40 and sAnkl is capable of interacting with obscurin and titin, but the function of C-terminal domain of ankyrin-G remains unknown. To identify proteins interacting C-terminus of ankyrin-G, we used the C-terminus of ankyrin-G as a bait for a yeast two-hybrid screen of brain cDNA library. Approximately 1.33$\times$l0$^6$ transformants were screened, of which 13 positive clones were obtained as determined by activation of HIS3, ADE2 and MELl reporter genes. Sequence analyses of these 13 plasmids revealed that cDNA inserts of 13 colonies showed highly homologous to 11 genes, including 5 known (i.e., Na$^+$/K$^+$ ATPase $\beta$1, SERBPl, UTF2, cytochrome C oxidase and collagen IV $\alpha$2) and 6 unknown genes. The evaluation of the proteins that emerge from these experiments provides a rational approach to investigate the those proteins significant in interaction with ankyrin-G.

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Effectiveness of exercise for improving physical and renal function in older adults with pre-dialysis chronic kidney disease: A systematic review and meta-analysis (운동중재가 투석 전단계 만성 신질환 노인의 신체기능 및 신기능 향상에 미치는 효과: 체계적 문헌고찰 및 메타분석)

  • Lee, Hyeon-Ju;Son, Youn-Jung;Jang, So Eun
    • Journal of Korean Critical Care Nursing
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    • v.16 no.3
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    • pp.34-47
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    • 2023
  • Purpose : Exercise may prevent the worsening of chronic kidney disease (CKD) and progression of cardiovascular diseases in patients with CKD. This review aims to identify the best type of exercise modality and summarizes the beneficial effects of exercise on physical and renal function among older adults with pre-dialysis CKD. Methods : A systematic search of PubMed, Embase, CINAHL, Cochrane Library, Web of Science, SCOPUS, and domestic database was performed for randomized controlled trials (RCTs) assessing the effect of exercise intervention on older adults with pre-dialysis CKD published until February 2023. A random-effects meta-analysis was conducted. The risk of bias was assessed using a Cochrane tool for assessing the risk of bias in RCTs (RoB 2.0). Results : The systematic review included 11 RCTs (n = 591, average age 60.2-76), of which 8 could be included for meta-analysis. Exercise was significant in increasing peak oxygen consumption and knee muscle strength among physical functions, and also in improving glomerular filtration rate among kidney functions. Conclusion : Exercise has beneficial effects on physical and renal function among older adults with pre-dialysis CKD. In the future, it is necessary to verify the effectiveness of exercise by subdividing it by type, intensity, duration, and delivery.

Exploring the Potential of Natural Products as FoxO1 Inhibitors: an In Silico Approach

  • Anugya Gupta;Rajesh Haldhar;Vipul Agarwal;Dharmendra Singh Rajput;Kyung-Soo Chun;Sang Beom Han;Vinit Raj;Sangkil Lee
    • Biomolecules & Therapeutics
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    • v.32 no.3
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    • pp.390-398
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    • 2024
  • FoxO1, a member of the Forkhead transcription factor family subgroup O (FoxO), is expressed in a range of cell types and is crucial for various pathophysiological processes, such as apoptosis and inflammation. While FoxO1's roles in multiple diseases have been recognized, the target has remained largely unexplored due to the absence of cost-effective and efficient inhibitors. Therefore, there is a need for natural FoxO1 inhibitors with minimal adverse effects. In this study, docking, MMGBSA, and ADMET analyses were performed to identify natural compounds that exhibit strong binding affinity to FoxO1. The top candidates were then subjected to molecular dynamics (MD) simulations. A natural product library was screened for interaction with FoxO1 (PDB ID-3CO6) using the Glide module of the Schrödinger suite. In silico ADMET profiling was conducted using SwissADME and pkCSM web servers. Binding free energies of the selected compounds were assessed with the Prime-MMGBSA module, while the dynamics of the top hits were analyzed using the Desmond module of the Schrödinger suite. Several natural products demonstrated high docking scores with FoxO1, indicating their potential as FoxO1 inhibitors. Specifically, the docking scores of neochlorogenic acid and fraxin were both below -6.0. These compounds also exhibit favorable drug-like properties, and a 25 ns MD study revealed a stable interaction between fraxin and FoxO1. Our findings highlight the potential of various natural products, particularly fraxin, as effective FoxO1 inhibitors with strong binding affinity, dynamic stability, and suitable ADMET profiles.

Electroacupuncture for Rotator Cuff Disorder: A Systematic Review and Meta-Analysis (회전근개 질환의 전침 치료에 대한 체계적 문헌고찰 및 메타분석)

  • Bok-Yeon Na;Sang-Hoon Lee;Chang-Hoon Woo;Young-Jun Kim
    • Journal of Korean Medicine Rehabilitation
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    • v.34 no.3
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    • pp.27-41
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    • 2024
  • Objectives This study aims to evaluate the efficacy and safety of electroacupuncture for rotator cuff disorder. Methods We searched nine online databases (PubMed, Embase, Cochrane Library, Chinese Academic Journals, Korean studies Information Service System, Rsearch Information Sharing Service, ScienceON, KMbase, Oriental Medicine Advanced Searching Integrated System) and two related journals up to April 2024 to identify randomized controlled trials that applied electroacupuncture to rotator cuff disorder. Selected studies were analyzed for risk of bias using the Cochrane risk of bias tool, and a meta-analysis was performed with RevMan version 5.4.1. Results Out of 175 studies, eleven randomized controlled trials were selected for final analysis. Most studies showed that electroacupuncture had effect on rotator cuff disorder. In the meta-analysis, electroacupuncture combined with rehabilitation treatment was significantly more effective than rehabilitation treatment alone in improving visual analog scale (p<0.00001). Almost studies did not report any side effects or adverse reactions to electroacupuncture treatment. Conclusions This systematic review suggests that electroacupuncture is an effective treatment for pain management in rotator cuff disorder. However, the lack of adverse effect reporting and a high risk of bias indicate the need for high-quality randomized controlled trials from various countries.

Prediction of East Asian Brain Age using Machine Learning Algorithms Trained With Community-based Healthy Brain MRI

  • Chanda Simfukwe;Young Chul Youn
    • Dementia and Neurocognitive Disorders
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    • v.21 no.4
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    • pp.138-146
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    • 2022
  • Background and Purpose: Magnetic resonance imaging (MRI) helps with brain development analysis and disease diagnosis. Brain volumes measured from different ages using MRI provides useful information in clinical evaluation and research. Therefore, we trained machine learning models that predict the brain age gap of healthy subjects in the East Asian population using T1 brain MRI volume images. Methods: In total, 154 T1-weighted MRIs of healthy subjects (55-83 years of age) were collected from an East Asian community. The information of age, gender, and education level was collected for each participant. The MRIs of the participants were preprocessed using FreeSurfer(https://surfer.nmr.mgh.harvard.edu/) to collect the brain volume data. We trained the models using different supervised machine learning regression algorithms from the scikit-learn (https://scikit-learn.org/) library. Results: The trained models comprised 19 features that had been reduced from 55 brain volume labels. The algorithm BayesianRidge (BR) achieved a mean absolute error (MAE) and r squared (R2) of 3 and 0.3 years, respectively, in predicting the age of the new subjects compared to other regression methods. The results of feature importance analysis showed that the right pallidum, white matter hypointensities on T1-MRI scans, and left hippocampus comprise some of the essential features in predicting brain age. Conclusions: The MAE and R2 accuracies of the BR model predicting brain age gap in the East Asian population showed that the model could reduce the dimensionality of neuroimaging data to provide a meaningful biomarker for individual brain aging.

Implementation of WLAN Baseband Processor Based on Space-Frequency OFDM Transmit Diversity Scheme (공간-주파수 OFDM 전송 다이버시티 기법 기반 무선 LAN 기저대역 프로세서의 구현)

  • Jung Yunho;Noh Seungpyo;Yoon Hongil;Kim Jaeseok
    • Journal of the Institute of Electronics Engineers of Korea SD
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    • v.42 no.5 s.335
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    • pp.55-62
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    • 2005
  • In this paper, we propose an efficient symbol detection algorithm for space-frequency OFDM (SF-OFDM) transmit diversity scheme and present the implementation results of the SF-OFDM WLAN baseband processor with the proposed algorithm. When the number of sub-carriers in SF-OFDM scheme is small, the interference between adjacent sub-carriers may be generated. The proposed algorithm eliminates this interference in a parallel manner and obtains a considerable performance improvement over the conventional detection algorithm. The bit error rate (BER) performance of the proposed detection algorithm is evaluated by the simulation. In the case of 2 transmit and 2 receive antennas, at $BER=10^{-4}$ the proposed algorithm obtains about 3 dB gain over the conventional detection algorithm. The packet error rate (PER), link throughput, and coverage performance of the SF-OFDM WLAN with the proposed detection algorithm are also estimated. For the target throughput at $80\%$ of the peak data rate, the SF-OFDM WLAN achieves the average SNR gain of about 5.95 dB and the average coverage gain of 3.98 meter. The SF-OFDM WLAN baseband processor with the proposed algorithm was designed in a hardware description language and synthesized to gate-level circuits using 0.18um 1.8V CMOS standard cell library. With the division-free architecture, the total logic gate count for the processor is 945K. The real-time operation is verified and evaluated using a FPGA test system.