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Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering in Raphanus sativus in-bred lines for marker-assisted backcross breeding

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Horticulture Research 2019年第1期6卷 248-259页

作者： jinhee Kim Abinaya Manivannan Do-sun Kim eun-Su Lee Hye-eun Lee Vegetable Research Division National Institute of Horticultural and Herbal ScienceRural Development AdministrationJeonju 55365Republic of Korea

The sequencing of radish genome aids in the better understanding and tailoring of traits associated with economic *** order to accelerate the genomics assisted breeding and genetic selection,transcriptomes of 33 radish inbred lines with diverse traits were sequenced for the development of single nucleotide polymorphic(SNP)*** sequence reads ranged from 2,560,543,741 bp to 20,039,688,139 bp with the GC(%)of 47.80–49.34 and phred quality score(Q30)of 96.47–97.54%.A total of 4951 polymorphic SNPs were identified among the accessions after stringent filtering and 298 SNPs with efficient marker assisted backcross breeding(MAB)markers were generated from the polymorphic ***,functional annotations of SNPs revealed the effects and importance of the SNPs identified in the flowering *** SNPs were predominantly associated with the four major flowering related transcription factors such as MYB,MADS box(AG),AP2/EREB,and *** addition,SNPs in the vital flowering integrator gene(FT)and floral repressors(EMBRYONIC FLOWER 1,2,and FRIGIDA)were identified among the radish inbred ***,50 SNPs were randomly selected from 298 SNPs and validated using Kompetitive Allele Specific PCR genotyping system(KASP)in 102 radish inbred *** homozygosity of the inbred lines varied from 56 to 96%and the phylogenetic analysis resulted in the clustering of inbred lines into three *** together,the SNP markers identified in the present study can be utilized for the discrimination,seed purity test,and adjusting parental combinations for breeding in radish.

关键词： breeding Raphanus utilized

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Phosphorylation on TRPV4 Serine Residue 824 Enhances Its Association with PGM1

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American Journal of Molecular Biology 2016年第1期6卷 33-44页

作者： sung Hwa Shin eun Jeoung Lee sunghee Hyun Sang sun Kang Department of Biology Education Chungbuk National University Cheongju Republic of Korea Department of Internal Medicine Chungbuk National University Cheongju Republic of Korea Department of Biomedical Laboratory Science Eulji University Daejeon Republic of Korea

The TRPV4 cation channel is expressed in a broad range of tissues and participates in the generation of a Ca2+ signal and/or depolarization of membrane potential. Here, human phosphoglucomutase- 1 (PGM1), an enzyme that converts glucose-6 phosphate to glucose-1 phosphate in the glycolysis pathway, as the first auxiliary protein of TRPV4 Ca2+ channels, is identified with yeast two hybrid system, coimmunoprecipitation, confocal microscopy, and GST pull-down assays. TRPV4 forms a complex with PGM1 through its C-terminal cytoplasmic domain. Because it is demonstrated that TRPV4 serine residue 824 (S824) is phosphorylated by serum/glucocorticoid regulated kinase 1, we elucidate the effect of TRPV4 S824 phosphorylation on TRPV association with PGM1. Even an inactivated mutant version of TRPV4, S824A, exhibited a decreased ability to bind PGM1, an activated phosphomimetic mutant version of TRPV4, S824D, exhibited enhanced binding to PGM1. Thus, formation of the TRPV4/PGM1 complex and localization of this complex to the plasma membrane appear to be regulated by the phosphorylation status of residue S824 in TRPV4. The newly identified interactor of TRPV4 may help the molecular pathways modulating transport activity or glucose metabolism, respectively.

关键词： Membrane Localization Phosphoglucomutase1 Phosphorylation Protein-Protein Interaction TRPV4

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Anethole improves the developmental competence of porcine embryos by reducing oxidative stress via the sonic hedgehog signaling pathway

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Journal of Animal Science and Biotechnology 2023年第4期14卷 1395-1407页

作者： Ye eun Joo Pil-Soo Jeong Sanghoon Lee Se-Been Jeon Min-Ah Gwon Min Ju Kim Hyo-Gu Kang Bong-Seok Song sun-Uk Kim Seong-Keun Cho Bo-Woong Sim Futuristic Animal Resource and Research Center Korea Research Institute of Bioscience and BiotechnologyCheongjuSouth Korea Department of Animal Science College of Natural Resources and Life SciencePusan National UniversityMiryangSouth Korea Laboratory of Theriogenology College of Veterinary MedicineChungnam National UniversityDaejeonSouth Korea Department of Biotechnology College of EngineeringDaegu UniversityGyeongsanSouth Korea Department of Animal Science and Biotechnology College of Agriculture and Life ScienceChungnam National UniversityDaejeonSouth Korea Department of Functional Genomics University of Science and TechnologyDaejeonSouth Korea Department of Animal Science College of Natural Resources and Life ScienceLife and Industry Convergence Research InstitutePusan National UniversityMiryangSouth Korea

Background Anethole(AN)is an organic antioxidant compound with a benzene ring and is expected to have a positive impact on early embryogenesis in ***,no study has examined the effect of AN on porcine embryonic ***,we investigated the effect of AN on the development of porcine embryos and the underlying *** We cultured porcine in vitro-fertilized embryos in medium with AN(0,0.3,0.5,and 1 mg/mL)for 6 *** at 0.5 mg/mL significantly increased the blastocyst formation rate,trophectoderm cell number,and cellular survival rate compared to the ***-supplemented embryos exhibited significantly lower reactive oxygen species levels and higher glutathione levels than the ***,AN significantly improved the quantity of mitochondria and mitochondrial membrane potential,and increased the lipid droplet,fatty acid,and ATP ***,the levels of proteins and genes related to the sonic hedgehog(SHH)signaling pathway were significantly increased by *** These results revealed that AN improved the developmental competence of porcine preimplantation embryos by activating SHH signaling against oxidative stress and could be used for large-scale production of high-quality porcine embryos.

关键词： Anethole Lipid metabolism Mitochondrial function Porcine embryo development Sonic hedgehog signaling pathway

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Improved Real-time Implementation of Adaptive Gassian Mixture Model-based Object Detection Algorithm for Fixed-point DSP Processors

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Journal of Measurement Science and Instrumentation 2010年第2期1卷 116-120页

作者： Byung-eun LEE Thanh-binh NGUYEN sun-tae CHUNG School of Electronics Engineering University of SoongsilSeoul 156-743Korea

Foreground moving object detection is an important process in various computer vision applications such as intelligent visual surveillance, HCI, object-based video compression, etc. One of the most successful moving object detection algorithms is based on Adaptive Gaussian Mixture Model （AGMM）. Although ACMM-hased object detection shows very good performance with respect to object detection accuracy, AGMM is very complex model requiring lots of floatingpoint arithmetic so that it should pay for expensive computational cost. Thus, direct implementation of the AGMM-based object detection for embedded DSPs without floating-point arithmetic HW support cannot satisfy the real-time processing requirement. This paper presents a novel rcal-time implementation of adaptive Gaussian mixture model-based moving object detection algorithm for fixed-point DSPs. In the proposed implementation, in addition to changes of data types into fixed-point ones, magnification of the Gaussian distribution technique is introduced so that the integer and fixed-point arithmetic can be easily and consistently utilized instead of real nmnher and floatingpoint arithmetic in processing of AGMM algorithm. Experimental results shows that the proposed implementation have a high potential in real-time applications.

关键词： background modeling real-time computing object de-tection

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Sensitivity of the suspected blood indicator:An experimental study

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World Journal of Gastroenterology 2012年第31期18卷 4169-4174页

作者： sung Chul Park Hoon Jai Chun eun sun Kim Bora Keum Yeon Seok Seo Yong Sik Kim Yoon Tae Jeen Hong Sik Lee Soon Ho Um Chang Duck Kim Ho Sang Ryu Division of Gastroenterology and Hepatology Department of Internal MedicineKangwon National University School of MedicineChuncheon 200-722South Korea Division of Gastroenterology and Hepatology Department of Internal MedicineKorea University College of MedicineSeoul 136-705South Korea

AIM： To investigate whether suspected blood indicator （SBI） in capsule endoscopy （CE） is affected by back- ground color and capsule passage velocity. METHODS： Experimental models of the small intestine constructed from paper in a variety of colors were used to simulate the background colors observed in CE im- ages. The background colors studied included very pale yellow, yellow, very pale magenta, light grayish pink, burnt sienna, and deep and dark brown, and red spots were attached inside them. An endoscopic capsule was manually passed through the models. The rate of detection of the red spots by the SBI was evaluated based on the colors of the models and the capsule pas- sage velocities （0.5 cm/s, 1 cm/s, and 2 cm/s）.RESULTS： The rate of detection of the red spots byground color of the model （P 〈 0.001）. Detection rates were highest for backgrounds of very pale magenta, burnt sienna, and yellow, in that order. They were lowest for backgrounds of dark brown and very pale yellow. The rate of detection of red spots by the SBI tended to decrease at rapid capsule passage velocities （1-2 cm/s） compared to slow velocities （0.5 cm/s） for backgrounds of very pale yellow （P = 0.042）, yellow （P = 0.001）, very pale magenta （P = 0.002）, and burnt sien- na （P = 0.001）. No significant differences in the rate of detection were observed according to velocity for light grayish pink （P = 0.643） or dark brown （P = 0.396）. CONCLUSION： SBI sensitivity was affected by back- ground color and capsule passage velocity in the models. These findings may facilitate the rapid detection of bleeding lesions by CE.

关键词： Capsule endoscopy Suspected blood indi-cator Sensitivity Background color Passage velocity

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Ablation of TRPV4 in HepG2 with Its CRISPR/Cas9 Enhances Its Wound Healing

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American Journal of Molecular Biology 2020年第1期10卷 74-89页

作者： eun Jeoung Lee sung Hwa Shin sunghee Hyun Sang sun Kang CdmoGen Cheongju Republic of Korea Department of Pre-Medicine School of Medicine Eulji University Daejeon Republic of Korea Department of Biology Education Chungbuk National University Cheongju Republic of Korea

TRPV4 activity modulates cell activities including receptor trafficking and transcriptional or translational regulations. We tested its CRISPR/Cas9 scissor efficacy in HepG2 (HEK293) cell noticed that it worked well in both cell lines to eliminate TRPV4 genome sequences. To confirm TRPV4 functions in the cell morphology maintenance and cell growth (beyond Ca2+ channel), we compared its wound healing, cell surface area, survival property and soft agar growth ability after deletion of TRPV4 gene in the cells with its CRISPR/Cas9 system. With these experiments, we confirmed that TRPV4 is required not only to function as Ca2+ channel but also to maintain its proper cell morphology as a corner stone protein on the cell adhesion junction.

关键词： TRPV4 Ca2+ Ion Channel E-Cadherin Tubulin Soft Agar Growth CRISPR/Cas9 Scissor System

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SGK1 Inhibits ULK2 Autophagy Activity

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American Journal of Molecular Biology 2020年第1期10卷 12-28页

作者： sung Hwa Shin eun Jeoung Lee sunghee Hyun Sang sun Kang Department of Biology Education Chungbuk National University Cheongju Korea Department of Biomedical Laboratory Science Eulji University Daejeon Korea

Serum- and glucocorticoid-induced kinase 1 (SGK1) is known to have consensus sequence of phosphorylation site R-x-R-x-x-(S/T)-Φ, where Φ is any hydrophobic amino acid and arginine residues are conserved at positions −5 and −3 relative to positions of Ser/Thr residues that are phosphorylated in the presence of SGK1. UNC-21-like kinase 2 (ULK2) also harbors putative SGK1 phosphorylation sites at both Ser507 (502RsRnsSG508) and Ser750 (745RtRttSV751) residues. Thus, the objective of this study was to determine whether Ser507 and Ser750 residues of ULK2 could be phosphorylation sites of SGK1 as one of its authentic substrate proteins. Using ULK2 507 and 750 serine residue un- or phosphorylation analog (S507AS750A or 507DS750D), we observed that modification of Ser507 or Ser750 residue was required to activate the kinase activity of ULK2 and sensitize ULK2 to stress or starvation while simultaneously enhancing its active state and autophagy characteristics, suggesting that phosphorylation at Ser750 or Ser507 residue could modulate its subcellular localization and protein interaction with AMPK1α to activate ULK2. We also observed that ULK2 autophagy activity was enhanced by GSK650394 (an SGK1 inhibitor) to compensate survival capacity through increasing its association with LC3 and phosphorylation. When SGK1 known to be associated with cell survival was inhibited by GSK650394, ULK2 autophagy pathway was activated to avoid cell death alternatively. Thus, our observations indicate that phosphorylation of ULK2 by SGK1 can regulate cell survival as an alternative modulation of ULK2 functions.

关键词： ULK-2 SGK1 Phosphorylation Autophagy Cell Survival Signal Transduction

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Optimal initiation of Helicobacter pylori eradication in patients with peptic ulcer bleeding

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World Journal of Gastroenterology 2015年第8期21卷 2497-2503页

作者： Hyuk Yoon Dong Ho Lee eun sun Jang Jaihwan Kim Cheol Min Shin Young Soo Park jin-Hyeok Hwang jin-Wook Kim Sook-Hayng Jeong Nayoung Kim Departments of Internal Medicine Seoul National University Bundang Hospital

AIM:To evaluate when Helicobacter pylori(***)eradication therapy(ET)should be started in patients with peptic ulcer bleeding(PUB).METHODS:Clinical data concerning adults hospitalizedwith PUB were retrospectively collected and ***,sex,type and stage of peptic ulcer,whether endoscopic therapy was performed or not,methods of *** detection,duration of hospitalization,and specialty of the attending physician were *** influencing the confirmation of *** infection prior to discharge were determined using multiple logistic regression *** *** eradication rates of patients who received ET during hospitalization and those who commenced ET as outpatients were ***:A total of 232 patients with PUB were evaluated for *** infection by histology and/or rapid urease *** these patients,53.7%(127/232)had confirmed results of *** infection prior to *** multivariate analysis,duration of hospitalization and ulcer stage were factors independently influencing whether *** infection was confirmed before or after *** the patients discharged before confirmation of *** infection,13.3%(14/105)were lost to *** the patients found to be ***-positive after discharge,41.4%(12/29)did not receive *** was no significant difference in the *** eradication rate between patients who received ET during hospitalization a n d t h o s e w h o c o m m e n c e d E T a s o u t p a t i e n t s[intention-to-treat:68.8%(53/77)vs 60%(12/20),P=0.594;per-protocol:82.8%(53/64)vs 80%(12/15),P=0.723].CONCLUSION:Because many patients with PUB who were discharged before *** infection status was confirmed lost an opportunity to receive ET,we should confirm *** infection and start ET prior to discharge.

关键词： Helicobacter pylori Peptic ulcer hemorrhage Diseas

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Lens culinaris agglutinin-reactive fraction of alpha-fetoprotein improves diagnostic accuracy for hepatocellular carcinoma

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World Journal of Gastroenterology 2021年第28期27卷 4687-4696页

作者： Han Ah Lee Yoo Ra Lee Young-sun Lee Young Kul Jung Ji Hoon Kim Hyunggin An Hyung Joon Yim Yoon Tae Jeen Jong eun Yeon Kwan Soo Byun Yeon Seok Seo Department of Internal Medicine Korea University College of MedicineSeoul 02841South Korea Department of Biostatistics Korea University Anam HospitalSeoul 02841South Korea

BACKGROUND Diagnostic accuracy of various tumor markers and their combinations for hepatocellular carcinoma(HCC)was not fully *** To evaluate the diagnostic accuracy of alpha-fetoprotein(AFP),the Lens culinaris agglutinin-reactive fraction of AFP(AFP-L3),and protein induced by vitamin K absence or antagonist-II(PIVKA-II)and their combination for HCC *** Patients with newly detected liver mass or elevated serum AFP levels were considered *** AFP level,AFP-L3 fraction,and PIVKA-II level were measured at the first *** In total,622 patients were included;355 patients(57.1%)had chronic liver disease,and 208(33.4%)had liver *** was diagnosed in 160 patients(25.7%).The area under the receiver operating characteristics curves(AUROCs)of the serum AFP,AFP-L3 fraction,AFP-L3,and PIVKA-II levels for the diagnosis of HCC were 0.775,0.792,0.814,and 0.834,respectively.A novel diagnostic model was developed by classifying patients in a 1:1 ratio into training and validation *** the binary regression analysis of the training cohort,the AFP,AFP-L3 fraction,and PIVKA-II(ALPs)score was calculated as follows:ALPs score=3.8×[serum AFP level(ng/mL)×AFP-L3 fraction(%)×0.01]+0.2×PIVKA-II level(mAU/mL).The AUROC of the ALPs score for diagnosis of HCC was 0.878,significantly higher than that of serum AFP level(P<0.001),AFP-L3 fraction(P<0.001),PIVKA-II level(P=0.036),and AFP-L3 level(P=0.006).The optimal ALPs score cut-off was 5.3(sensitivity,85.0%,specificity 80.1%).The validation cohort showed similar *** The ALPs score calculated using serum AFP level,AFP-L3 fraction,and PIVKA-II level showed improved accuracy in HCC diagnosis.

关键词： Alpha-fetoprotein Lens culinaris agglutinin-reactive fraction of alphafetoprotein Protein induced by vitamin K absence or antagonist-II Hepatocellular carcinoma

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Self-expandable metal stents in patients with postoperative delayed gastric emptying after distal gastrectomy

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World Journal of Gastroenterology 2018年第40期24卷 4578-4585页

作者： Seung Han Kim Bora Keum Hyuk Soon Choi eun sun Kim Yeon Seok Seo Yoon Tae Jeen Hong Sik Lee Hoon Jai Chun Soon Ho Um Chang Duck Kim sungsoo Park Division of Gastroenterology and Hepatology Department of Internal MedicineInstitute of Gastrointestinal Medical Instrument ResearchKorea University College of MedicineSeoul 02841South Korea Department of Surgery Korea University College of MedicineSeoul 02841South Korea

AIM To investigate the efficacy and safety of endoscopic stent insertion in patients with delayed gastric emptying after *** In this study, we prospectively collected data from patients who underwent stent placement for delayed gastric emptying(DGE) after distal gastrectomy between June 2010 and April 2017, at a tertiary referral academic center. Clinical improvement, complications, and consequences after stent insertion were *** Technical success was achieved in all patients(100%). Early symptom improvement was observed in 15 of 20 patients(75%) and clinical success was achieved in all patients. Mean follow-up period was 1178.3 ± 844.1 d and median stent maintenance period was 51 d(range 6-2114 d). During the follow-up period, inserted stents were passed spontaneously per rectum without any complications in 14 of 20 patients(70%). Symptom improvement was maintained after stent placement without the requirement of any additional intervention in 19 of 20 patients(95%).CONCLUSION Endoscopic stent placement provides prompt relief of obstructive symptoms. Thus, it can be considered an effective and safe salvage technique for post-operative DGE.

关键词： Self-expandable metal stent Delayed gastric emptying Gastrectomy Salvage technique Symptom improvement

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