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Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines

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Horticultural Plant Journal 2021年第6期7卷 539-551页

作者： Sampath Perumal Nomar Espinosa Waminal Jonghoon Lee hyun-jin koo Boem-soon Choi Jee Young Park Kyounggu Ahn Tae-jin Yang Department of Agriculture Forestry and BioresourcesPlant Genomics and Breeding Instituteand Research Institute of Agriculture and Life SciencesCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Global Institute for Food Security University of Saskatchewan421 Downey RoadSaskatoonSK S7N 4L8Canada Agriculture and Agri-Food Canada 107 Science PlaceSaskatoon S7N 0X2Canada Chromosome Research Institute Department of Life ScienceSahmyook UniversitySeoul 01795Republic of Korea Joeun Seeds.Co. LtdGoesan-GunChungcheongbuk-Do 367-833Republic of Korea Phyzen Genomics Institute 13Seongnam-daero 331beon-gilBundang-guSeongnam-siGyeonggi-do 13558Republic of Korea

Whole-genome shogun sequence(WGS)data generated by next-generation sequencing(NGS)platforms are a valuable resource for crop *** produced 5–6×WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes:cabbage,broccoli,cauliflower,kailan,kale,Brussels sprout,and kohlrabi to systematically evaluate the nuclear and chloroplast(Cp)diversity in the 44 *** breeding *** then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly,annotation of complete chloroplast(Cp)genomes and 45 S nuclear ribosomal DNA(45S nrDNA)sequences,and copy number variation for major *** genome diversity analysis has revealed a total of 496463 SNPs and 37493 indels in the nuclear genome across the 44 ***,some SNPs showed subspecies enrichment at certain chromosomal *** assembly of complete Cp genomes contained 153361–153372 bp with 37 variants including SNPs and *** 45S nrDNA transcription unit was 5802 bp long with a total of 31 SNPs from the 44 *** phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli,cauliflower,and kailan in one group and cabbage,Brussels sprout,kale,and kohlrabi in another *** morphotypes diverged during the last 0.17 million *** Cp genome diversity reflected the unique cytoplasm of each subspecies,and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process *** polymorphic Cp markers provide a classification system for the cytoplasm types in ***,copy numbers of major transposable elements(TEs)showed high diversity among the 44 accessions,indicating that many TEs have become active ***,we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse *** morphotypes.

关键词： Brassica oleracea subspecies Chloroplast genome Nuclear ribosomal DNA Genetic diversity Phylogeny

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Contrast in Fluid M etallogeny between the Tianmashan Au-S Deposit and the Datuanshan Cu Deposit in Tongling,Anhui Province

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Acta Geologica Sinica(English Edition) 2003年第1期77卷 116-124页

作者： LEE hyun koo Depatment of Geology Chungnam National University 220 Kungdong Yuseong Ku Taejon 305-764 Republic of Korea

A comprehensive contrast of ore-forming geological background and ore-forming fluid features, especially fluid ore-forming processes, has been performed between the Tianmashan and the Datuanshan ore deposits in Tongling, Anhui Province. The major reasons for the formation of the stratabound skarn Au-S ore deposit in Tianmashan and the stratabound skarn Cu ore deposit in Datuanshan are analyzed in accordance with this contrast. The magmatic pluton in Tianmashan is rich in Au and poor in Cu, but that in Datuanshan is rich in Cu and Au. The wallrock strata in Tianmashan contain Au-bearing pyrite layers with some organic substance but those in Datuanshan contain no such layers. Moreover, the ore-forming fluids in Tianmashan are dominantly magmatic ones at the oxide and sulfide stages, but those with high content of Cu in Datuanshan are mainly groundwater fluids. In addition, differences in compositional evolution and physicochemical condition variation of the ore-forming fluids result in gradual dispersion

关键词： fluid inclusion fluid ore-forming process contrast in fluid metallogeny Au-S ore deposit Cu ore deposit magmatic fluid groundwater fluid Tongling Anhui Province

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Biofilm three-dimensional architecture influences in situ pH distribution pattern on the human enamel surface

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International Journal of Oral Science 2017年第2期9卷 74-79页

作者： jin Xiao Anderson T Hara Dongyeop Kim Domenick T Zero hyun koo Geelsu Hwang Eastman Institute for Oral Health University of Rochester Medical Center Department of Cariology Operative Dentistry and Dental Public HealthOral Health Research InstituteIndiana University School of Dentistry Biofilm Research Laboratories Levy Center for Oral HealthDepartment of Orthodontics and Divisions of Pediatric Dentistry & Community Oral HealthSchool of Dental MedicineUniversity of Pennsylvania

To investigate how the biofilm three-dimensional(3D) architecture influences in situ pH distribution patterns on the enamel surface. Biofilms were formed on human tooth enamel in the presence of 1% sucrose or 0.5% glucose plus 0.5% fructose. At specific time points, biofilms were exposed to a neutral pH buffer to mimic the buffering of saliva and subsequently pulsed with 1% glucose to induce re-acidification. Simultaneous 3D pH mapping and architecture of intact biofilms was performed using two-photon confocal microscopy. The enamel surface and mineral content characteristics were examined successively via optical profilometry and microradiography analyses. Sucrose-mediated biofilm formation created spatial heterogeneities manifested by complex networks of bacterial clusters(microcolonies). Acidic regions(pH<5.5) were found only in the interior of microcolonies,which impedes rapid neutralization(taking more than 120 min for neutralization). Glucose exposure rapidly re-created the acidic niches, indicating formation of diffusion barriers associated with microcolonies structure. Enamel demineralization(white spots),rougher surface, deeper lesion and more mineral loss appeared to be associated with the localization of these bacterial clusters at the biofilm-enamel interface. Similar 3D architecture was observed in plaque-biofilms formed in vivo in the presence of sucrose. The formation of complex 3D architectures creates spatially heterogeneous acidic microenvironments in close proximity of enamel surface, which might correlate with the localized pattern of the onset of carious lesions(white spot like) on teeth.

关键词： biofilms demineralization dental caries exopolysaccharides microcolonies pH microenvironments plaque Streptococcus mutans

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Clinical applications of fractional flow reserve in bifurcation lesions

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Journal of Geriatric Cardiology 2012年第3期9卷 278-284页

作者： Sang hyun Park Bon-Kwon koo Seoul National University College of Medicine I O1 Daehang-ro Chongno-gu Seoul 110-744 South Korea

Pereutaneous coronary intervention （PCI） for coronary bifurcation lesions has been associated with lower procedural success rates and worse clinical outcomes compared with PCI for simple coronary lesions. Angiographic evaluation alone is sometimes inaccurate and does not reflect the fimctional significance of bifurcation lesions. The fractional flow reserve （FFR） is an easily obtainable, reliable, and reproducible physiologic parameter. This parameter is epicardial lesion specific and reflects both degree of stenosis and the myocardial territory supplied by the specific artery. Recent studies have shown that FFR-guided provisional side branch intervention strategy for bifurcation lesions is feasible and effective and can reduce unnecessary complex interventions and related complications. However, an adequate understanding of coronary physiology and the pitfalls of FFR is essential to properly use FFR for PCI of complex bifurcation lesions.

关键词： Coronary stenosis Bifurcation lesion Physiology Fractional flow reserve

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Beta-nerve growth factor gene therapy alleviates pyridoxine-induced neuropathic damage by increasing doublecortin and tyrosine kinase A in the dorsal root ganglion

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Neural Regeneration Research 2020年第1期15卷 162-168页

作者： hyun-Kee Cho Woosuk Kim Kwon-Young Lee jin-Ok Ahn Jung Hoon Choi In koo Hwang jin-Young Chung Department of Veterinary Internal Medicine and Institute of Veterinary Science College of Veterinary MedicineKangwon National UniversityChuncheonKangwon-doSouth Korea Department of Anatomy and Cell Biology College of Veterinary MedicineResearch Institute for Veterinary ScienceSeoul National UniversitySeoulSouth Korea Department of Anatomy College of Veterinary MedicineKangwon National UniversityChuncheonKangwon-doSouth Korea

Beta-nerve growth factor(β-NGF) is known to be a major leading cause of neuronal plasticity. To identify the possible action mechanisms of β-NGF gene therapy for sciatic nerve recovery, experimental dogs were randomly divided into control, pyridoxine, and pyridoxine + β-NGF groups. We observed chronological changes of morphology in the dorsal root ganglia in response to pyridoxine toxicity based on cresyl violet staining. The number of large neurons positive for cresyl violet was dramatically decreased after pyridoxine intoxication for 7 days in the dorsal root ganglia and the neuron number was gradually increased after pyridoxine withdrawal. In addition, we also investigated the effects of β-NGF gene therapy on neuronal plasticity in pyridoxine-induced neuropathic dogs. To accomplish this, tyrosine kinase receptor A(TrkA), βIII-tubulin and doublecortin(DCX) immunohistochemical staining was performed at 3 days after the last pyridoxine treatment. TrkA-immunoreactive neurons were dramatically decreased in the pyridoxine group compared to the control group, but strong TrkA immunoreactivity was observed in the small-sized dorsal root ganglia in this group. TrkA immunoreactivity in the dorsal root ganglia was similar between β-NGF and control groups. The numbers of βIII-tubulin-and DCX-immunoreactive cells decreased significantly in the pyridoxine group compared to the control group. However, the reduction of βIII-tubulin-and DCX-immunoreactive cells in the dorsal root ganglia in the β-NGF group was significantly ameliorated than that in the pyridoxine group. These results indicate that β-NGF gene therapy is a powerful treatment of pyridoxine-induced neuropathic damage by increasing the TrkA and DCX levels in the dorsal root ganglia. The experimental protocol was approved by the Institutional Animal Care and Use Committee(IACUC) of Seoul National University, South Korea(approval No. SNU-060623-1, SNU-091009-1) on June 23, 2006 and October 9, 2009, respectively.

关键词： β-nerve growth factor βIII-tubulin doublecortin gene therapy neuron-glial antigen 2 neuropathy pyridoxine

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Extracellular Polysaccharides Matrix—An Often Forgotten Virulence Factor in Oral Biofilm Research

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International Journal of Oral Science 2009年第4期1卷 229-234页

作者： hyun koo Marlise I.Klein Eastman Department of Dentistry and Center for Oral Biology University of Rochester Medical CenterUSA

Oral diseases related to dental biofilms continue to afflict the majority of the world＇s population. Among them, dental caries continues to be the single most prevalent and costly oral infectious disease （Marsh, 2003; Dye et al., 2007）. Dental caries results from the interaction of specific bacteria with constituents of the diet within a dental biofilm known as plaque （Bowen, 2002）. Sucrose is considered to be the ＂arch criminal＂ from the dietary aspect because it serves as a substrate for synthesis of extracellular （EPS） and intracellular （IPS） polysaccharides in dental biofilm and is also fermentable （Bowen, 2002）.

关键词： An Often Forgotten Virulence Factor in Oral Biofilm Research Extracellular Polysaccharides Matrix oral

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Detection of early gastric cancer using hydro-stomach CT:Blinded vs unblinded analysis

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World Journal of Gastroenterology 2011年第8期17卷 1051-1057页

作者： Ki Jeong Park Min Woo Lee Ji hyun koo Yulri Park Heejung Kim Dongil Choi Soon jin Lee Department of Radiol-ogy and Center for Imaging Science Samsung Medical Center Sungkyunkwan University School of Medicine

AIM:To evaluate the difference in diagnostic performance of hydro-stomach computed tomography(CT) to detect early gastric cancer(EGC) between blinded and unblinded analysis and to assess independent factors affecting visibility of cancer ***:Two radiologists initially blinded and then unblinded to gastroscopic and surgical-histological findings independently reviewed hydro-stomach CT images of 110 patients with single *** graded the visibility of cancer foci for each of three gastric segments(upper,middle and lower thirds) using a 4-point scale(1:definitely absent,2:probably absent,3:probably present,and 4:definitely present).The sensitivity and specificity for detecting an EGC were *** and interobserver agreements were *** visibility of an EGC was evaluated with regard to tumor size,invasion depth,gastric segments,histological type and gross morphology using univariate and multivariate ***:The respective sensitivities and specificities [reviewer 1:blinded,20%(22/110) and 98%(215/220);unblinded,27%(30/110) and 100%(219/220)/reviewer 2:blinded,19%(21/110) and 98%(216/220);unblinded,25%(27/110) and 98%(215/220)] were not significantly *** intraobserver agreements were good(weighted κ = 0.677 and 0.666),interobserver agreements were fair(blinded,0.371) or moderate(unblinded,0.558).For both univariate and multivariate analyses,the tumor size and invasion depth were statistically significant factors affecting ***:The diagnostic performance of hydrostomach CT to detect an EGC was not significantly different between blinded and unblinded *** tumor size and invasion depth were independent factors for visibility.

关键词： Stomach neoplasm Computed tomography Water Early detection of cancer Sensitivity

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Expression of E-cadherin and α-catenin in a varicocele-induced infertility rat model

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Asian Journal of Andrology 2011年第3期13卷 470-475,514页

作者： Hong koo Ha hyun Jun Park Nam Cheol Park Department of Urology Pusan National University School of Medicine Busan 602739 Korea Medical Research Institute Pusan National University Hospital Busan 602739 Korea

The roles of E-cadherin and α-catenin were evaluated in the development of varicocele-induced infertility. Analysis of the association between the expression of E-cadherinla-catenin and clinical/pathological parameters was performed. Thirty lO-week-old male rats （experimental group） were used for the experiments; the left renal vein was ligated to form a varicocele. The abdomen was incised in 30 rats （control group） and no procedure was performed on 10 rats （baseline group）. The weights of the left testis, serum reactive oxygen species （ROS）, testosterone, luteinizing hormone （LH）, follicle-stimulating hormone （FSH） and degenerative changes in the seminiferous tubules after 4 and 8 weeks were recorded. The expression of E-cadherin and α-catenin was evaluated by immunohistochemical （IHC） staining and Western blot analysis. The ROS increased in the 8-week experimental group, compared with the baseline and control groups （P〈0.001 for both）. Additionally, FSH significantly increased in the 4- and 8-week experimental group compared with the control groups （P= 0.013 and P= 0.032, respectively）. The ratio of degenerative changes in the seminiferous tubules of the experimental groups increased. The IHC staining showed that the expression of E-cadherin and a-catenin decreased in the 4- and 8-week experimental groups. Similar to the IHC staining, the experimental group had decreased reactivity on Western blot analysis. The expression of E-cadherin and a-catenin was significantly associated with the ROS and degenerative changes in the seminiferous tubules. The results of this study suggest that damage to the blood-testis barrier （BTB） is associated with varicocele-induced male infertility, and that ROS may cause damage to the BTB.

关键词： α-catenin blood-testis barrier E-cadherin varicocele infertility

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Ethanol extract from Gynostemma pentaphyllum ameliorates dopaminergic neuronal cell death in transgenic mice expressing mutant A53T human alpha-synuclein

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Neural Regeneration Research 2020年第2期15卷 361-368页

作者： hyun jin Park Ting Ting Zhao Seung Hwan Kim Chong Kil Lee Bang Yeon Hwang Kyung Eun Lee Myung koo Lee Department of Pharmacy College of PharmacyChungbuk National UniversityCheongjuRepublic of Korea 2Research Center for Bioresource and Health College of PharmacyChungbuk National UniversityCheongjuRepublic of Korea Department of Social Physical Education Songwon UniversityGwangjuRepublic of Korea

Gynostemma(G.) pentaphyllum(Cucurbitaceae) contains various bioactive gypenosides. Ethanol extract from G. pentaphyllum(GP-EX) has been shown to have ameliorative effects on the death of dopaminergic neurons in animal models of Parkinson’s disease(PD) induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-and 6-hydroxydopamine. PD patients exhibit multiple symptoms, so PD-related research should combine neurotoxin models with genetic models. In the present study, we investigated the ameliorative effects of GP-EX, including gypenosides, on the cell death of dopaminergic neurons in the midbrain of A53 T α-synuclein transgenic mouse models of PD(A53 T). Both GP-EX and gypenosides at 50 mg/kg per day were orally administered to the A53 T mice for 20 weeks.α-Synuclein-immunopositive cells and α-synuclein phosphorylation were increased in the midbrain of A53 T mice, which was reduced following treatment with GP-EX. Treatment with GP-EX modulated the reduced phosphorylation of tyrosine hydroxylase, extracellular signal-regulated kinase(ERK1/2), Bcl-2-associated death promoter(Bad) at Ser112, and c-Jun N-terminal kinase(JNK1/2) due to α-synuclein overexpression. In the A53 T group, GP-EX treatment prolonged the latency of the step-through passive avoidance test and shortened the transfer latency of the elevated plus maze test. Gypenosides treatment exhibited the effects and efficacy similar to those of GP-EX. Taken together, GP-EX, including gypenosides, has ameliorative effects on dopaminergic neuronal cell death due to the overexpression of α-synuclein by modulating ERK1/2, Bad at Ser112, and JNK1/2 signaling in the midbrain of A53 T mouse model of PD. Further studies are needed to investigate GP-EX as a treatment for neurodegenerative synucleinopathies, including PD. This study was approved by the Animal Ethics Committee of Chungbuk National University(approval No. CBNUA-956-16-01) on September 21, 2016.

关键词： A53T α-synuclein genetic mice ERK1/2 gynostemma pentaphyllum gypenosides Parkinson’s disease retention transfer latency time

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Intra-abdominal desmoid tumors mimicking gastrointestinal stromal tumors——8 cases: A case report

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World Journal of Gastroenterology 2019年第16期25卷 2010-2018页

作者： Jwa Hoon Kim Min-Hee Ryu Young Soo Park hyun jin Kim Hyojung Park Yoon-koo Kang Department of Oncology Asan Medical CenterUniversity of Ulsan College of Medicine Department of Pathology Asan Medical Center University of Ulsan College of Medicine Department of Radiology Asan Medical Center University of Ulsan College of Medicine

BACKGROUND Intra-abdominal desmoid tumors(DTs) can mimic recurrence or progression of gastrointestinal stromal tumors(GISTs). Differential diagnosis is important to avoid unnecessary or inappropriate *** SUMMARY All 8 patients experienced surgical resection of GIST, and median time to diagnosis of DT was 1.8 years after surgical resection. All sites of DT were in the peritoneum around the surgical sites of GIST. The following clinical suspicion coupled with radiological findings contributed to the suspicion of intraabdominal DTs:(1) Occurrence of a new single lesion in the peritoneum around the surgical sites of GIST;(2) uncontrolled lesion with imatinib while other lesions being controlled with imatinib;(3) well-defined ovoid shaped lesion with delayed or mild enhancement and absence of necrosis, hemorrhage, and cystic change on computed tomography; and(4) a lesion showing mild or no hypermetabolic activity on 18 fluorodeoxyglucose-positron emission tomography,contrary to initially hyperactive lesion of GIST. All DTs were surgically removed except for one unresectable DT and only one DT recurred at another site of peritoneum, which was also surgically *** Intra-abdominal DT should be a differential diagnosis for a new single lesion in patients with GIST.

关键词： Desmoid tumor Gastrointestinal stromal tumor Radiology Surgicalresection Imatinib mesylate Case report

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