• Title/Summary/Keyword: Marker density

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Contrasting rice sub-populations to tocols ratio associated with seed longevity

  • Lee, Jae-Sung;Kwak, Jieun;Yoon, Mi-Ra;Lee, Jeom-Sig;Hay, Fiona R.
    • Proceedings of the Korean Society of Crop Science Conference
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    • 2017.06a
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    • pp.31-31
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    • 2017
  • Understanding the mechanism(s) to overcome or prevent seed ageing deterioration during storage is of fundamental interest to seed physiologists. Vitamin E (tocols) is known as a key metabolite to efficiently scavenge lipid peroxy radicals which cause membrane breakdown resulting in seed ageing. However, in rice research this hypothesis has been tested for very few lines only without considering intraspecific variation in genomic structure. Here, we present a correlation study between tocols and seed longevity using a diverse rice panel. Seeds of 20 rice accessions held in the International Rice Genebank at the International Rice Research Institute, representing aus, indica, temperate japonica and tropical japonica subpopulations, were used for tocols analysis (quantification of ${\alpha}$-, ${\beta}$-, ${\gamma}$-, ${\delta}$-tocopherol/tocotrienol by ultra performance liquid chromatography) and storage experiments at $45^{\circ}C$ and 10.9% seed moisture content (sample taken for germination testing every 3 days up to 60 days). To examine interactions between DNA sequences and phenotype, the 700k high-density single-nucleotide polymorphism marker data-set was utilized. Both seed longevity (time for viability to fall to 50%; $p_{50}$) and tocols content varied across subpopulations due to heterogeneity in the genetic architecture. Among eight types of tocol homologues, ${\alpha}$-tocopherol and ${\gamma}$-tocotrienol were significantly correlated with $p_{50}$ (negatively and positively, respectively). While temperate japonica varieties were most abundant in ${\alpha}$-tocopherol, indica varieties recorded 1.3 to 1.7-fold higher ${\gamma}$-tocotrienol than those of other subpopulations. It was highlighted that specific ratio of tocol homologues rather than total tocols content plays an important role in the seed longevity mechanism.

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Genome-wide Linkage Study for Plasma HDL Cholesterol Level in an Isolated Population of Mongolia

  • Park, Han-Soo;Kim, Jong-Il;Cho, Sung-Il;Sung, Joo-Hon;Kim, Hyung-Lae;Ju, Young-Seok;Bayasgalan, Gombojav;Lee, Mi-Kyeong;Seo, Jeong-Sun
    • Genomics & Informatics
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    • v.6 no.1
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    • pp.8-13
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    • 2008
  • High-density lipoprotein (HDL) whose primary role is to transport cholesterol from peripheral tissues to the liver, is associated with the incidence of coronary heart disease. We analyzed HDL cholesterol levels in a genetically isolated population of extended Mongolian families. A total of 1002 individuals (54.5% women) from 95 families were enrolled. After genotyping by use of 1000 microsatellite markers, we performed a genome-wide linkage search with variance component analysis. The estimated heritability of HDL cholesterol was 0.45, revealing that HDL cholesterol was under significant genetic influence. We found peak evidence of linkage (LOD score=1.88) for HDL cholesterol level on chromosome 6 (nearest marker D6S1660) and potential evidences for linkage on chromosomes 1, 12 and 19 with the LOD scores of 1.32, 1.44 and 1.14, respectively. These results should pave the way for the discovery of the relevant genes by fine mapping and association analysis.

GOLPH3, a Good Prognostic Indicator in Early-stage NSCLC Related to Tumor Angiogenesis

  • Lu, Ming;Tian, Yu;Yue, Wei-Ming;Li, Lin;Li, Shu-Hai;Qi, Lei;Hu, Wen-Si;Gao, Cun;Si, Li-Bo;Tian, Hui
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.14
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    • pp.5793-5798
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    • 2014
  • Background: Golgi phosphoprotein-3 (GOLPH3) is implicated in cancer development and progression. The aim of this study was to evaluate the prognostic significance of GOLPH3 protein and its association with tumor angiogenesis in patients with early-stage NSCLC. Materials and Methods: Immunohistochemistry was performed to determine GOLPH3 protein expression and allow assessment of intratumoral microvessel density (MVD) by counting CD-34 positive immunostained endothelial cells. Correlations of expression with MVD, clinicopathologic features and clinical prognosis were analyzed. Results: A notably higher level of GOLPH3 expression was found in early-stage NSCC tissues at the protein level. However, we do not find any correlation between GOLPH3 expression and clinicopathologic features (p>0.05), although higher MVD was positively associated with GOLPH3 overexpression (p<0.001). Expression of GOLPH3 was found to be an independent prognostic factor in early-stage NSCLC patients, those expressing high levels of GOLPH3 exhibiting a substantially lower 5-year overall survival than GOLPH3-negative patients (adjusted HR =1.899, 95% CI: 1.021-3.532, p=0.043). Conclusions: High expression of the GOLPH3 protein is common in early-stage NSCC, and is closely associated with tumor progression, increased tumor angiogenesis, and poor survival. We conclude a possibility of its use as a diagnostic and prognostic marker in early-stage NSCC patients.

Effece of Chlorella Dietary Supplementation on Bone Biochemical Markers of Turnover in Postmenopausal Women

  • Kim, Yong-Ho;Hwang, Yoo-Kyeong;Hwang, Jung-Min;Seoung, Hee-Kyung;Kim, Dong-Uk
    • Biomedical Science Letters
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    • v.9 no.1
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    • pp.9-13
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    • 2003
  • Currently bone biochemical markers are considered to be the best indicators of present and the future state of bone turnover. A recent study has reported that chlorella increases the bone mineral density (BMD) on postmenopausal women, but presently there are no studies on bone biochemical markers treated with chlorella dietary supplementation. The purpose of the present study was to assess the bone biochemical markers for the short term and long term treatment groups, and non-treatment group as a control. Twenty two postmenopausal woman were treated for four months and eighteen for one year with 4 gm of chlorella dietary supplementation per day, and then assessed bone biochemical markers from serum and urine samples. Bone turnover rates calculated with Osteocalcin (OC), bone specific alkaline phosphatase (BAP) as a bone formation markers and deoxypyridinoline (DP), cross-linked N-telopeptides of type I collagen (NTx) as a bone resorption markers, showed 1131$\pm$87% for control group, 61$\pm$11% for short term treated group and 190$\pm$101% for long term treated group. We conclude that chlorella dietary supplementation enhances the bone formation, and NTx as a single markers, OC/Dp as a single markers of bone turnover rate were very useful tools for determine the effectiveness of chlorella dietary supplementation (or the postmenopausal women.

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An Analysis on Positional Accuracy of Urban Control Point for Connecting to Supplementary Control Point (지적도근점과 연계활용을 위한 도시기준점의 위치정확도 분석)

  • Hong, Sung-Eon
    • Journal of Korean Society for Geospatial Information Science
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    • v.17 no.1
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    • pp.97-104
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    • 2009
  • Supplementary control point and urban control point have different purpose and characteristic in the view of installation but their measurement method and permanent marker position are very similar. Therefore if we could use them by connecting those two control point, we would improve the arrangement density as well as minimizing cost of restoration from the loss of control point. So we tried to suggest the possibility of connecting these two control point and usage by analysing positional accuracy of urban control point on the base of supplementary control point in this study. The result of this study is as following. When analysing the positional accuracy of 13 urban control points of the study areas, there were RMSE of connection errors between ${\pm}8cm$ and ${\pm}11cm$ for each measurement point. The result confirmed the possibility of connecting supplementary control point to urban control point and its usage within the allowable error tolerance that the present cadastral law permits.

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Can denosumab be a substitute, competitor, or complement to bisphosphonates?

  • Kim, Su Young;Ok, Hwoe Gyeong;Birkenmaier, Christof;Kim, Kyung Hoon
    • The Korean Journal of Pain
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    • v.30 no.2
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    • pp.86-92
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    • 2017
  • Osteoblasts, originating from mesenchymal cells, make the receptor activator of the nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG) in order to control differentiation of activated osteoclasts, originating from hematopoietic stem cells. When the RANKL binds to the RANK of the pre-osteoclasts or mature osteoclasts, bone resorption increases. On the contrary, when OPG binds to the RANK, bone resorption decreases. Denosumab (AMG 162), like OPG (a decoy receptor), binds to the RANKL, and reduces binding between the RANK and the RANKL resulting in inhibition of osteoclastogenesis and reduction of bone resorption. Bisphosphonates (BPs), which bind to the bone mineral and occupy the site of resorption performed by activated osteoclasts, are still the drugs of choice to prevent and treat osteoporosis. The merits of denosumab are reversibility targeting the RANKL, lack of adverse gastrointestinal events, improved adherence due to convenient biannual subcutaneous administration, and potential use with impaired renal function. The known adverse reactions are musculoskeletal pain, increased infections with adverse dermatologic reactions, osteonecrosis of the jaw, hypersensitivity reaction, and hypocalcemia. Treatment with 60 mg of denosumab reduces the bone resorption marker, serum type 1 C-telopeptide, by 3 days, with maximum reduction occurring by 1 month. The mean time to maximum denosumab concentration is 10 days with a mean half-life of 25.4 days. In conclusion, the convenient biannual subcutaneous administration of 60 mg of denosumab can be considered as a first-line treatment for osteoporosis in cases of low compliance with BPs due to gastrointestinal trouble and impaired renal function.

Association of Common Vitamin D Receptor Gene Variations with Fracture Risk and Bone Mineral Density in Postmenopausal Korean Population

  • Hwang, Joo-Yeon;Lee, Seung Hun;Kim, Ghi-Su;Koh, Jung-Min;Go, Min-Jin;Kim, Tae-Ho;Hong, Jung-Min;Park, Eui-Kyun;Kim, Shin-Yoon;Lee, Jong-Young
    • Genomics & Informatics
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    • v.7 no.1
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    • pp.13-19
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    • 2009
  • Osteoporosis is characterized by impaired osteogenesis. BMD is a major determinant of bone strength. The role of the VDR gene in predisposition to primary osteoporosis has been recognized. However, population-based case-control studies have been reported controversial results for known candidate genes in an ethnically distinct group. To determine the genetic effects of VDR variants on osteoporosis and BMD, we directly sequenced the VDR gene in 24 unrelated Korean individuals and identified eighteen sequence variants. We investigated the potential involvement of eight SNPs in osteoporosis in postmenopausal women (n = 729). Two SNPs (LD) in intron 2, -5294G>C (rs2238135) and -4817G>A (rs17882443) showed the evidence of association with enhanced BMD of the femoral neck ($p_{additive}$=0.031 for rs2238135; $p_{additive}$=0.017 and $p_{dominant}$= 0.019 for 17882443). Moreover, VDR -4817G>A was significantly associated with protective effect on all fracture risk ($p_{recessive}$=0.035, OR=0.2, 95% CI=$0.05{\sim}0.89$), and tended to be higher BMD values at various proximal femur sites. Therefore, we suggest that the -4817G>A may be useful genetic marker for vitamin D-related metabolism and may have an important role in the increased BMD of the proximal femur in postmenopausal Korean women.

Detection of Escherichia coli O157:H7 Using Combined Procedure of Immunomagnetic Separation and Test Strip Liposome Immunoassay

  • Kim, Myung-Hee;Oh, Se-Jong;Durst, Richard-A.
    • Journal of Microbiology and Biotechnology
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    • v.13 no.4
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    • pp.509-516
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    • 2003
  • A model system for the immnunochemical detection of Escherichia coli O157:H7 using a combined immunomagnetic separation (IMS) and test-strip liposome immunoassay (LIA) procedure was developed. Immunomagnetic beads coated with anti-E. coli O157 IgG antibodies were used to separate the E. coli O157 (including the H7 serotype) from culture. Immunoliposomes, whose surface was conjugated to goat anti-E. coli O157:H7 IgG and which encapsulated the marker dye, sulforhodamine B, were used as a detection label. The test strip, onto which antibodies to goat IgG were immobilized, was the immunosensor capturing immunoliposomes that did not bind to E. coli O157:H7 on the immunomagnetic bead-E. coli O157:H7 complexes. In experiments, pure cell culture suspensions of $10^5 E.$ coli O157:H7 organisms per ml produced a measurable signal inhibition, whereas a weak yet detectable signal inhibition occurred with $10^3CFU/ml$. The inhibition signals increased, when the incubation time for IMS was extended to 90 min and higher IgG-tag density (0.4mol%) was used on the liposomes. With 0.2 and 0.4mol% IgG-tagged liposomes, the IMS-LIA procedure showed more improved signal inhibitions than those of a direct (no IMS) LIA. The combined assay, which measures the instantaneous signal from immunoliposomes, can be completed within 90 min, making it significantly faster than conventional plating methods and enzyme-linked immunosorbent assay (ELISA). Accordingly, it is quite feasible to use the combined immunoassay format of IMS and dye-loaded immunoliposomes for the detection of E. coli O157:H7.

Quantitative Analysis and Antioxidant Effects of Gyejibokryeong-hwan (LC-MS/MS를 이용한 계지복령환(桂枝茯苓丸)의 동시분석 및 항산화 효능 연구)

  • Seo, Chang-Seob;Kim, Ohn Soon;Shin, Hyeun-Kyoo
    • Korean Journal of Pharmacognosy
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    • v.45 no.3
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    • pp.240-248
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    • 2014
  • Gyejibokryeong-hwan (GJBRH) has been used for treatment of patients with climacteric syndrome. In this study, an ultra-performance liquid chromatography-electrospray ionization-mass spectrometer (UPLC-ESI-MS) method was established for the simultaneous quantification of seven marker compounds in GJBRH extract. In addition, we assessed the antioxidant effects of GJBRH. All analytes were separated by gradient elution using two mobile phases on a UPLC BEH $C_{18}$ column and maintained at $45^{\circ}C$. The antioxidant activities of GJBRH were evaluated by measuring free radical scavenging activities on 2,2'-azinobis-3-ethyl-benzothiazoline-6-sulfonic acid (ABTS) and 1-1-diphenyl-2-picrylhydrazyl (DPPH). The inhibitory effects on low-density lipoprotein (LDL) oxidation were evaluated by the formation of thiobarbituric acid relative substances (TBARS) and relative electrophoretic mobility (REM). Regression equations of the seven compounds were acquired with $r^2$ values ${\geq}0.9988$. The amounts of the seven compounds, amygdalin, albiflorin, paeoniflorin, coumarin, cinnamic acid, cinnamaldehyde, and paeonol in GJBRH water extract were 21.71, 2.16, 17.17, 1.97, 0.40, 0.78, and 3.42 mg/g, respectively. The GJBRH showed the radical scavenging activity in a dose-dependent manner. The concentration required for 50% reduction ($RC_{50}$) against ABTS and DPPH radicals were $54.18{\mu}g/mL$ and $79.53{\mu}g/mL$. Furthermore, GJBRH reduced the oxidation properties of LDL induced by $CuSO_4$.

A Case of MALT Lymphoma in Parotid Gland Duct (이하선관에 발생한 MALT 림프종 1예)

  • Kim, Ki Yup;Yang, Won Yong;Kwon, Seok Min;Kang, Sang Yoon
    • Archives of Plastic Surgery
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    • v.36 no.5
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    • pp.663-666
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    • 2009
  • Purpose: Primary malignant lymphomas of the salivary glands are uncommon. The parotid gland was most frequently involved, followed by the submandibular gland, minor salivary gland and sublingual gland. The most common subtype is mucosa - associated lymphoid tissue(MALT) lymphoma. We experienced a case of salivary MALT lymphoma involving parotid gland duct, so report a case with a review of the literature. Methods: A 65 year old female presented with a palpable mass on the left side of her cheek. There was no clinical or laboratory evidence of pre - existing autoimmune disease. Preoperative facial and neck CT with contrast showed $2.1{\times}1.7cm$ sized, ill defined, homogeneous low density mass near left masseter muscle, and no evidence of other enlarged lymph nodes. Results: At operation, a yellowish oval shaped mass was found slightly adhered to middle portion of the parotid gland duct, meaduring $2{\times}1.5{\times}0.7cm$. Microscopic finding showed that centrocyte - like cells, monocyte B cells and plasma cells were diffusely infiltrated. Immunophenotyping was preformed on fixed section. The majority of the small cells were immunoreactive for the B cell marker CD20. Based on the typical histological findings supported by immunostaining, the mass was defined as MALT lymphoma. Conclusion: We report that very rare case of MALT lymphoma involving parotid gland duct in 65 year old female patient was experienced with clinical characteristics, histologic features and references.