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Wang X, Zhang XN, Wu ML, Jia LC, Xie LN, Meng Y, Feng SH, Ma W. [Dynamic variation trend and prognostic value of bronchial wall thickness in severely burned patients combined with inhalation injury]. ZHONGHUA SHAO SHANG ZA ZHI = ZHONGHUA SHAOSHANG ZAZHI = CHINESE JOURNAL OF BURNS 2018; 34:208-213. [PMID: 29690738 DOI: 10.3760/cma.j.issn.1009-2587.2018.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the dynamic variation trend of bronchial wall thickness (BWT) in severely burned patients combined with inhalation injury, and to determine the value of BWT to prognosis of patients. Methods: Forty-three severely burned patients with inhalation injury hospitalized in Intensive Burn Department of the Affiliated Hospital of Nankai University (Tianjin No.4 Hospital) from July to November 2016, conforming to the study criteria, were divided into survival group (n=27) and death group (n=16) according to the prognosis of patients within 14 days after admission. All patients underwent fiberoptic bronchoscopy and inhalation injury rating based on abbreviated injury scale at admission. High resolution CT examination was performed in patients of two groups at admission and 24 h post admission, 3, 7, and 14 d post admission to measure the BWT of right superior lobar bronchus trunk opening. Receiver operating characteristic curves of rating of inhalation damage at admission and BWT at admission were drawn to evaluate the predictive value for death of 43 patients. Data were processed with chi-square test, independent sample t test, Wilcoxon rank sum test, analysis of variance for repeated measurement and least-significant difference-t test. Results: (1) The numbers of patients rated as 0, 1, 2, 3, and 4 grade for inhalation injury in survival group and death group were 0, 19, 6, 2, and 0, and 0, 2, 7, 7, and 0, respectively. There were statistically significant differences between the two groups (Z=-3.79, P<0.01). (2) BWT of patients in death group at admission and 24 h post admission, 3, 7, and 14 d post admission was respectively (2.72±0.26), (3.18±0.22), (2.98±0.18), (2.29±0.17), and (1.45±0.21) mm, which was significantly larger than (2.24±0.15), (2.49±0.15), (1.51±0.17), (1.04±0.16), and (1.01±0.13) mm in survival group (t=7.55, 12.14, 27.11, 19.99, 7.11, P<0.01). BWT of patients in survival group and death group at 24 h post admission, 3, 7, and 14 d post admission showed statistically significant difference when compared with that at admission within the corresponding group (t=5.97, 16.63, 28.21, 38.57, 5.34, 3.31, 4.39, 6.48, P<0.01). BWT of patients in survival group and death group on 3, 7, and 14 d post admission was significantly smaller than that at 24 h post admission within the corresponding group (t=22.27, 34.02, 45.03, 2.77, 10.53, 10.59, P<0.01). BWT of patients in survival group and death group on 7 and 14 d post admission was significantly smaller than that on 3 d post admission within the corresponding group (t=10.49, 18.26, 9.57, 11.44, P<0.01). BWT of patients in survival group and death group on 14 d post admission was significantly smaller than that on 7 d post admission within the corresponding group (t=6.97, 6.15, P<0.01). (3) The total areas under ROC curves of inhalation injury rating at admission and BWT at admission for predicting death of 43 patients were 0.880 and 0.956, respectively (with 95% confidence intervals 0.768-0.991, 0.882-1.000, P<0.05). Grade 1.5 and 2.75 mm were respectively chosen as the optimal threshold values of inhalation injury rating at admission and BWT at admission, with sensitivity of 87.50%, 83.33% and specificity of 77.78%, 96.00%, respectively. Conclusions: The BWT of survived and dead patients with severe burn and inhalation injury increases significantly post burn, while the BWT of survived patients restores to normal level faster. BWT can be used to assess the severity of inhalation injury and to predict death in severely burned patients combined with inhalation injury.
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Paz AM, Zhang XN. The GMO Industry: A Neglected Earthly Frontier. JOURNAL OF HUNGER & ENVIRONMENTAL NUTRITION 2018. [DOI: 10.1080/19320248.2016.1227755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ma ZJ, Hu SL, Wang SS, Guo X, Zhang XN, Sun B, Chen LM. [Effects and underlying mechanism of berberine on renal tubulointerstitial injury in diabetic rats]. ZHONGHUA YI XUE ZA ZHI 2018; 96:3072-3077. [PMID: 27784448 DOI: 10.3760/cma.j.issn.0376-2491.2016.38.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the effect of Berberine on renal tubulointerstitial injury and its potential mechanism in rats with type 2 diabetes mellitus (T2DM). Methods: Thirty Sprague-Dawley rats were randomly divided into 3 groups: normal control rats (NC group), diabetic rats without drug treatment (DM group), diabetic rats treated with Berberine (BBR group) for 8 weeks. At the end of the study, blood and urine samples were collected for biochemical examination, and tubulointerstitial fibrosis was quantified by Hematoxylin and Eosin (HE) and Masson staining. The expressions of E-cadherin (E-cad), α-smooth muscle actin (α-SMA), nuclear factor-κB (NF-κB) and monocyte chemoattractant protein 1 (MCP-1) were detected by immunohistochemistry analysis, real-time polymerase chain reaction (RT-PCR) and Western blot analysis. Results: 24 h urinary microalbumin (mAlb)[(170.5±58.1) vs (253.7±53.0) mg]and urinary N-acetyl-glucosaminidase (NAG)[(33.5±7.2) vs (49.5±9.3)U/L]in diabetic rats were significantly decreased by BBR treatment(both P<0.05). The apparent renal tubulointerstitial injury was found in the DM group, which was ameliorated by BBR treatment. The expression of α-SMA, NF-κB and MCP-1 were significantly decreased, accompanied by increased expression of E-cad in BBR-treated DM rats (all P<0.05). Conclusion: BBR could ameliorate renal tubulointerstitial injury in diabetic rats, the mechanism of which may be associated with the amelioration of epithelial-mesenchymal transition (EMT) through suppressing the expression of the NF-κB and MCP-1.
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Zhang XN, Liu J, Liu Y, Wang Y, Abozeid A, Yu ZG, Tang ZH. Metabolomics Analysis Reveals that Ethylene and Methyl Jasmonate Regulate Different Branch Pathways to Promote the Accumulation of Terpenoid Indole Alkaloids in Catharanthus roseus. JOURNAL OF NATURAL PRODUCTS 2018. [PMID: 29406718 DOI: 10.1021/acs.jnatprod.7b00782/1520-6025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The medicinal plant Catharanthus roseus accumulates large numbers of terpenoid indole alkaloids (TIAs), including the pharmaceutically important vinblastine, vincristine, ajmalicine, and serpentine. The phytohormone ethylene or methyl jasmonate (MeJA) can markedly enhance alkaloid accumulation. The interaction between ethylene or MeJA in the regulation of TIA biosynthesis in C. roseus is unknown. Here, a metabolomics platform is reported that is based on liquid chromatography (LC) coupled with time-of-flight mass spectrometry to study candidate components for TIA biosynthesis, which is controlled by ethylene or MeJA in C. roseus. Multivariate analysis identified 16 potential metabolites mostly associated with TIA metabolic pathways and seven targeted metabolites, outlining the TIA biosynthesis metabolic networks controlled by ethylene or MeJA. Interestingly, ethylene and MeJA regulate the 2-C-methyl-d-erythritol 4-phosphate (MEP) and acetate-mevalonate (MVA) pathways through AACT and HMGS and through DXS, respectively, to induce TIA biosynthesis in C. roseus. Overall, both nontargeted and targeted metabolomics, as well as transcript analysis, were used to reveal that MeJA and ethylene control different metabolic networks to induce TIA biosynthesis.
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Zhang XN, Liu J, Liu Y, Wang Y, Abozeid A, Yu ZG, Tang ZH. Metabolomics Analysis Reveals that Ethylene and Methyl Jasmonate Regulate Different Branch Pathways to Promote the Accumulation of Terpenoid Indole Alkaloids in Catharanthus roseus. JOURNAL OF NATURAL PRODUCTS 2018; 81:335-342. [PMID: 29406718 DOI: 10.1021/acs.jnatprod.7b00782] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The medicinal plant Catharanthus roseus accumulates large numbers of terpenoid indole alkaloids (TIAs), including the pharmaceutically important vinblastine, vincristine, ajmalicine, and serpentine. The phytohormone ethylene or methyl jasmonate (MeJA) can markedly enhance alkaloid accumulation. The interaction between ethylene or MeJA in the regulation of TIA biosynthesis in C. roseus is unknown. Here, a metabolomics platform is reported that is based on liquid chromatography (LC) coupled with time-of-flight mass spectrometry to study candidate components for TIA biosynthesis, which is controlled by ethylene or MeJA in C. roseus. Multivariate analysis identified 16 potential metabolites mostly associated with TIA metabolic pathways and seven targeted metabolites, outlining the TIA biosynthesis metabolic networks controlled by ethylene or MeJA. Interestingly, ethylene and MeJA regulate the 2-C-methyl-d-erythritol 4-phosphate (MEP) and acetate-mevalonate (MVA) pathways through AACT and HMGS and through DXS, respectively, to induce TIA biosynthesis in C. roseus. Overall, both nontargeted and targeted metabolomics, as well as transcript analysis, were used to reveal that MeJA and ethylene control different metabolic networks to induce TIA biosynthesis.
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Su BB, Zhou SW, Gan CB, Zhang XN. MiR-186 inhibits cell proliferation and invasion in human cutaneous malignant melanoma. J Cancer Res Ther 2018; 14:S60-S64. [PMID: 29578151 DOI: 10.4103/0973-1482.157340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AIMS MicroRNA-186 (miR-186) has been shown to be involved in various types of cancer. The purpose of this study was to investigate the expression level and functional role of miR-186 in human cutaneous malignant melanoma cells. SUBJECTS AND METHODS Expression of miR-186 was analyzed in human cutaneous malignant melanoma (CMM) cell lines SK-MEL-1, G-361, A375 and A875, and human normal epidermal melanocytes cell line HEMn-LP by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Additionally, the functional role of miR-186 on melanoma cells was investigated by transfection of miR-186 mimic followed by analyses of cell proliferation, apoptosis, and metastasis. RESULTS We found that the expression levels of miR-186 were decreased in CMM cell lines compared with normal epidermal melanocytes cell line. Moreover, overexpression of miR-186 inhibited cells proliferation through abrogating the G1-S transition, and reduced cells migration and invasion. CONCLUSIONS Our findings suggested that miR-186 exhibit an inhibitory effect on CMM cell proliferation, migration, and invasion; thus, may serve as a potential therapeutic target for human CMM intervention.
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Li Y, He ZC, Zhang XN, Liu Q, Chen C, Zhu Z, Chen Q, Shi Y, Yao XH, Cui YH, Zhang X, Wang Y, Kung HF, Ping YF, Bian XW. Stanniocalcin-1 augments stem-like traits of glioblastoma cells through binding and activating NOTCH1. Cancer Lett 2017; 416:66-74. [PMID: 29196129 DOI: 10.1016/j.canlet.2017.11.033] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/20/2017] [Accepted: 11/25/2017] [Indexed: 12/29/2022]
Abstract
Glioblastoma (GBM) is a fatal tumor and comprises heterogeneous cells in which a subpopulation with stem cell-like properties is included. Cancer cells with stem cell-like properties account for tumor initiation, drug resistance and recurrence. To identify and characterize specific factors in regulating stem-like traits is critical for GBM therapeutic. Here, we showed that Stanniocalcin-1 (STC1), a secretory glycoprotein, functions as a novel stimulator for stem-like traits of GBM cells. We found STC1 was prominently expressed in glioma spheres which are mainly comprised of glioma stem-like cells. The stem-like traits of GBM cells, as determined by the expression of stem cell markers, tumor-sphere formation efficiency and colony-forming ability, were enhanced by STC1 overexpression and inhibited by STC1 knockdown. Furthermore, introduction of STC1 enhanced tumorigenesis in vivo while knockdown of STC1 showed reverse effect. Finally, we demonstrated that STC1 interacted with the extracellular domain of NOTCH1 to activate NOTCH1-SOX2 signaling pathway, by which STC1 augmented the stem-like traits of GBM cells. Taken together, our data herein indicate that STC1 is a novel non-canonical NOTCH ligand and acts as a crucial regulator of stemness in GBM.
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Liu Y, Liu J, Wang Y, Abozeid A, Tian DM, Zhang XN, Tang ZH. The Different Resistance of Two Astragalus Plants to UV-B Stress is Tightly Associated with the Organ-specific Isoflavone Metabolism. Photochem Photobiol 2017; 94:115-125. [PMID: 28881500 DOI: 10.1111/php.12841] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 08/27/2017] [Indexed: 12/24/2022]
Abstract
In this work, the changes in isoflavone levels and the expression of genes involved in their biosynthesis were studied in two Astragalus by UPLC-MS and real-time PCR after 10 days of UV-B treatment (λmax = 313 nm, 804 J m-2 ). Isoflavones were significantly induced by UV-B irradiation. The influence might be activated by the regulation of these target genes. Our results indicate that (1) the resistance of Astragalus membranaceus might not be as good as Astragalus mongholicus in the enhanced UV-B radiation environment; (2) the enhanced accumulation of calycosin and calycosin-7-glucoside with UV-B treatment in roots of A. mongholicus might be derived from formononetin which is synthesized in the leaves; (3) the glycosylation process could be stimulated and activated by the enhanced UV-B radiation in both A. mongholicus and A. membranaceus. In other words, glycosylation of isoflavones might play a crucial role for two Astragalus plants in response to UV-B stress. Overall, this study offered a feasible elicitation strategy to understand the accumulation pattern of isoflavone in A. mongholicus and A. membranaceus, and also provided a reference for the changes in isoflavone levels of Astragalus in UV-B enhanced environment in the future.
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Zhang XN, Shi Y, Powers JJ, Gowda NB, Zhang C, Ibrahim HMM, Ball HB, Chen SL, Lu H, Mount SM. Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana. BMC Genomics 2017; 18:772. [PMID: 29020934 PMCID: PMC5637254 DOI: 10.1186/s12864-017-4183-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/05/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Regulation of pre-mRNA splicing diversifies protein products and affects many biological processes. Arabidopsis thaliana Serine/Arginine-rich 45 (SR45), regulates pre-mRNA splicing by interacting with other regulatory proteins and spliceosomal subunits. Although SR45 has orthologs in diverse eukaryotes, including human RNPS1, the sr45-1 null mutant is viable. Narrow flower petals and reduced seed formation suggest that SR45 regulates genes involved in diverse processes, including reproduction. To understand how SR45 is involved in the regulation of reproductive processes, we studied mRNA from the wild-type and sr45-1 inflorescences using RNA-seq, and identified SR45-bound RNAs by immunoprecipitation. RESULTS Using a variety of bioinformatics tools, we identified a total of 358 SR45 differentially regulated (SDR) genes, 542 SR45-dependent alternative splicing (SAS) events, and 1812 SR45-associated RNAs (SARs). There is little overlap between SDR genes and SAS genes, and neither set of genes is enriched for flower or seed development. However, transcripts from reproductive process genes are significantly overrepresented in SARs. In exploring the fate of SARs, we found that a total of 81 SARs are subject to alternative splicing, while 14 of them are known Nonsense-Mediated Decay (NMD) targets. Motifs related to GGNGG are enriched both in SARs and near different types of SAS events, suggesting that SR45 recognizes this motif directly. Genes involved in plant defense are significantly over-represented among genes whose expression is suppressed by SR45, and sr45-1 plants do indeed show enhanced immunity. CONCLUSION We find that SR45 is a suppressor of innate immunity. We find that a single motif (GGNGG) is highly enriched in both RNAs bound by SR45 and in sequences near SR45- dependent alternative splicing events in inflorescence tissue. We find that the alternative splicing events regulated by SR45 are enriched for this motif whether the effect of SR45 is activation or repression of the particular event. Thus, our data suggests that SR45 acts to control splice site choice in a way that defies simple categorization as an activator or repressor of splicing.
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Zhang XN, Matskova L, Zheng BY, Ernberg I, He Z, Huang ZN. 07 The approach to generate oncolytic adenovirus by sirna mediated e1b silencing. J Investig Med 2017. [DOI: 10.1136/jim-2017-mebabstracts.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Zhang BD, Shan YC, Xu LW, Chen H, Zhang XN, Tong CY, Mao YL, Zhou C. [The situation of social support and its relationship with antenatal depression among 1 075 Zhejiang primiparas in their third trimesters]. ZHONGHUA YU FANG YI XUE ZA ZHI [CHINESE JOURNAL OF PREVENTIVE MEDICINE] 2017; 51:740-745. [PMID: 28763925 DOI: 10.3760/cma.j.issn.0253-9624.2017.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the situation of social support (SS), and explore its relationship with antenatal depression (AD) among Zhejiang primiparas in their third trimesters. Methods: From March to August 2016, a cross-sectional study was conducted and the questionnaire was used at the outpatient consulting room of one maternity hospital in Hangzhou. Inclusion criteria includes the primiparas over 18 years old, gestation from 30 to 36 weeks, been able to understand and complete the questionnaires independently, no family history and history of mental disorders and no use of psychotropic drugs, without serious illness and so on. Exclusion criteria was that the primiparas were unable to complete all the contents of the questionnaire and of poor compliance. 1 150 questionnaires were actually given out, and 1 075 questionnaires were valid, so the valid rate was 93.48%. AD was evaluated by the Edinburgh Postnatal Depression Scale (EPDS) and SS was evaluated by the Perceived Social Support Scale (PSSS). SS between the non-AD group and the AD group was compared. The correlation between SS and AD was analyzed. Binary logistic regression model was used to assess the relationship between SS and AD. The level of SS was divided by average scores, groups lower than the average score was defined as the low-score group, groups higher than the average score was defined as the high-score group. Results: The prevalence of AD (score≥9) was 27.3% (293/1 075) among Zhejiang primiparas in their third trimesters. The scores of family support, friend support and other support, and the total score of SS among the non-AD group were 24.80±2.83, 23.40±3.00, 21.91±3.54 and 70.11±7.92, respectively, which were higher than those in the AD group (22.71±3.88, 21.45±3.59, 19.95±3.97, 64.10±10.01), (t values were 8.43, 8.29, 7.83 and 9.25, respectively, P<0.001 for all). The scores of family support, friend support and other support, and the total score of SS were negatively correlated with AD (rs values were-0.26,-0.25,-0.22 and-0.28, respectively, P<0.001 for all). Compared with low-score group, the scores of family support, friend support and other support, and the total score of SS among the high-score group had a lower risk of antenata depression among primiparas in their third trimesters, OR(95%CI) values were 0.56 (0.41-0.77), 0.66(0.47-0.92), 0.57(0.41-0.79) and 0.36(0.27-0.48), respectively. Conclusion: The prevalence of AD among Zhejiang primiparas was relatively high, and AD was negatively associated with SS level. We suggest adding SS in community pregnancy health management service in the future.
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Li FF, Zhao ZX, Yan P, Wang S, Liu Z, Zhang Q, Zhang XN, Sun CH, Wang XS, Wang GY, Liu SL. Different effection of p.1125Val>Ala and rs11954856 in APC on Wnt signaling pathway. Oncotarget 2017; 8:70854-70864. [PMID: 29050326 PMCID: PMC5642601 DOI: 10.18632/oncotarget.20106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 05/23/2017] [Indexed: 01/13/2023] Open
Abstract
Colorectal cancer (CRC) is among the most common and fatal forms of solid tumors worldwide and more than two thirds of CRC and adenomas patients have APC gene mutations. APC is a key regulator in the Wnt/β-catenin signaling pathway but its roles in CRC remains to be elucidated. In this study, we compared APC genes between CRC patients and controls to determine possible associations of nucleotide changes in the APC gene with the pathways involved in CRC pathogenesis. All participants received physical and enteroscopic examinations. The APC gene was sequenced for 300 Chinese Han CRC patients and 411 normal controls, and the expression levels of genes in the signaling pathway were analyzed using Western Blotting. Statistical analyses were conducted using SPSS (version 19.0) software. We found that rs11954856 in the APC gene was associated with colorectal cancer and could increase the expression levels of APC, β-catenin, TCF7L1, TCF7L2 and LEF1 genes in the pathway in the CRC patients, demonstrating the involvement of APC in the pathological processes leading to CRC.
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Shi Y, Ping YF, Zhou W, He ZC, Chen C, Bian BSJ, Zhang L, Chen L, Lan X, Zhang XC, Zhou K, Liu Q, Long H, Fu TW, Zhang XN, Cao MF, Huang Z, Fang X, Wang X, Feng H, Yao XH, Yu SC, Cui YH, Zhang X, Rich JN, Bao S, Bian XW. Tumour-associated macrophages secrete pleiotrophin to promote PTPRZ1 signalling in glioblastoma stem cells for tumour growth. Nat Commun 2017; 8:15080. [PMID: 28569747 PMCID: PMC5461490 DOI: 10.1038/ncomms15080] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 02/28/2017] [Indexed: 12/19/2022] Open
Abstract
Intense infiltration of tumour-associated macrophages (TAMs) facilitates malignant growth of glioblastoma (GBM), but the underlying mechanisms remain undefined. Herein, we report that TAMs secrete abundant pleiotrophin (PTN) to stimulate glioma stem cells (GSCs) through its receptor PTPRZ1 thus promoting GBM malignant growth through PTN–PTPRZ1 paracrine signalling. PTN expression correlates with infiltration of CD11b+/CD163+ TAMs and poor prognosis of GBM patients. Co-implantation of M2-like macrophages (MLCs) promoted GSC-driven tumour growth, but silencing PTN expression in MLCs mitigated their pro-tumorigenic activity. The PTN receptor PTPRZ1 is preferentially expressed in GSCs and also predicts GBM poor prognosis. Disrupting PTPRZ1 abrogated GSC maintenance and tumorigenic potential. Moreover, blocking the PTN–PTPRZ1 signalling by shRNA or anti-PTPRZ1 antibody potently suppressed GBM tumour growth and prolonged animal survival. Our study uncovered a critical molecular crosstalk between TAMs and GSCs through the PTN–PTPRZ1 paracrine signalling to support GBM malignant growth, indicating that targeting this signalling axis may have therapeutic potential. Tumour-associated macrophages (TAMs) facilitate malignant growth of glioblastoma (GBM). Here, the authors show that TAMs support glioma stem cell renewal via paracrine signalling to the pleiotrophin receptor PTPRZ1 and that blocking this axis results in increased survival of tumour-bearing animals.
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Sun XY, Hai Y, Zhang XN. [Effects of different pelvic incidence minus lumbar lordosis mismatch after long posterior instrumentation and fusion for adult degenerative scoliosis]. ZHONGHUA WAI KE ZA ZHI [CHINESE JOURNAL OF SURGERY] 2017; 55:435-440. [PMID: 28592076 DOI: 10.3760/cma.j.issn.0529-5815.2017.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To evaluate the influence of PI-LL (pelvic incidence minus lumbar lordosis mismatch) on scoliosis correction, living quality and internal fixation related complications for adult degenerative scoliosis (ASD) after long posterior instrumentation and fusion. Methods: A total of 79 patients with ADS underwent long posterior instrumentation and fusion in the Department of Orthopedics at Beijing Chao Yang Hospital from January 2010 to January 2014 were retrospectively reviewed.There were 21 males and 58 females aging from 55 to 72 years with the mean age (63.4±4.8)years. The patients were divided into three groups according to immediately postoperative PI-LL: PI-LL<10°, 10°≤PI-LL≤20°, PI-LL>20°.Compare the Cobb's angles, PI-LL, Japanese Orthopaedic Association (JOA) score, Oswestry Disability Index (ODI), Visual Analog Scale (VAS) and Lumbar Stiffness Disability Index (LSDI). Measurement data were compared via t test and ANOVA, enumeration data were compared via Kruskal-Wallis test, noncontiguous data was performed by χ(2) test. Univariate linear regression equation was performed to investigate the relative influences of postoperative PI-LL on postoperative radiographic parameters and clinical outcome. Results: All the operations were successful without intraoperative complications. The operation time was 145-310 minutes (235.3±42.0) minutes, the intraoperative blood loss was 300-5 300 ml (1 021±787) ml, the duration of hospital was 12-18 d (14.5±1.3) d. A total of 4 to 10 (7.0±1.1) vertebra levels were fused. Compared to preoperative, the Cobb's angle of scoliosis ((4.2±1.8)° vs. (20.1±2.7)°), PI-LL ((16.1±8.6)° vs. (36.0±4.3)°), JOA (3.0±1.3 vs. 5.5±1.2), ODI (24.4±8.1 vs. 62.9±2.7), VAS (3.0±1.0 vs. 6.8±1.3) were significantly decreased postoperative (t=18.539~53.826, P<0.01). Compared to preoperative, postoperative Cobb's angle of scoliosis ((4.1±2.7)° vs. (19.5±2.7)°, (4.0±1.4)° vs. (20.2±2.4)°, (4.7±0.9)° vs. (20.6±3.0)°) (t=21.148-45.355, P<0.01) and PI-LL ((5.2±2.8)° vs. (35.8±4.9)°, (17.9±2.9)° vs. (37.2±3.9)°, (25.8±2.7)° vs. (34.5±4.0)°) (t=7.227-38.250, P<0.01) were significantly reduced postoperative in PI-LL<10° group, 10°≤PI-LL≤20° group and PI-LL>20° group. Compared to preoperative, ODI (27.7±4.9 vs. 63.3±2.6, 17.7±5.9 vs. 63.1±2.8, 30.6±6.5 vs. 62.3±2.5) (t=21.218~50.858, P<0.01), JOA (2.8±1.2 vs. 5.2±1.2, 3.3±1.1 vs. 5.7±1.1, 2.8±1.7 vs. 5.7±1.2) (t=9.042-16.025, P<0.01) and VAS (2.9±1.2 vs.7.0±1.3, 3.3±0.9 vs.7.0±1.4, 2.9±0.8 vs. 6.3±1.2) (t=16.073-22.214, P<0.01) were all significantly reduced at last follow-up. There were statistic differences in ODI and LSDI (F=38.477, P<0.01; F=37.063, P<0.01) at the last follow-up among the three groups. There was a negative correlation in PI-LL and LSDI according to linear regression (B=-5.838, P<0.01) in the last follow-up. All the patients were followed up, the follow-up duration were 2 to 5 years with the mean (3.1±0.7) years. The internal fixation failure related complications in 3 years included proximal junctional kyphosis (PJK) in 19 cases, internal fixation loosening in 6 cases. Eight patients received reoperation for severe local pain and low extremity symptoms. PJK occurrences were significantly different among PI-LL<10° group, 10°≤PI-LL≤20° group and PI-LL>20° group. Conclusions: The PI-LL between 10° and 20° may be the best choice in ADS patients after long posterior instrumentation and fusion for its better clinical outcome and less proximal junctional kyphosis (PJK). The overcorrection of LL may lead to more serious postoperative lumbar stiffness.
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Zhou C, Lai RN, Zhang XN, Chen H, Wang WJ, Zhang BD. [Development and evaluation on the primipara social capital scale]. ZHONGHUA YU FANG YI XUE ZA ZHI [CHINESE JOURNAL OF PREVENTIVE MEDICINE] 2017; 51:313-318. [PMID: 28395464 DOI: 10.3760/cma.j.issn.0253-9624.2017.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Objective: To develop the Chinese primipara social capital scale (C-PSCS), and to evaluate its validity and reliability. Methods: The items of C-PSCS were developed based on Social Capital Scale by the World Bank and Social Network Scale. This scale was modified according to the characteristics of primiparas. We selected 10 experts who specialized in related field, and two rounds of seminars about content, cultural compatibility, primiparas' characteristics, and practicability. The finally C-PSCS included four dimensions: social trust, social reciprocity, social network, and social participation. Using purposive sampling to select 1 100 primiparas in their third trimesters (gestational weeks from 30 to 36 weeks). The validity analyses included content validity, construct validity and discriminant validity. The reliability analyses included Cronbach' α coefficient, and split-half reliability. Results: 1 035 questionnaires (94.09%) were qualified and the completion time was (13.23 ± 2.53) minutes. The total score of scale was 195.38 ± 45.98, and scores for social trust, social reciprocity, social network, and social participation were 30.26 ± 4.25, 22.84 ± 4.21, 34.23 ± 7.47, and 108.05 ± 41.96, respectively. The common factor cumulative variance contribution rates of each dimension were from 52.92% to 69.37%, which achieved more than 50% of the approved standard, and all the items held factor loading >0.5 in its relevant common factor, it had good construct validity. The scale had a good content validity, the r values between each dimensions and total scale were range from 0.57 to 0.81, P<0.01. For the high-score group, scores for social trust, social reciprocity, social network, and social participation dimensions were 32.89±3.19, 25.65±3.48, 38.27±6.59, 119.94±36.61, respectively, which were higher than low-score group (27.77±3.58, 20.18±2.91, 30.40±6.13, 96.76 ± 43.60), t-values were -24.23, -27.46, -19.90, and -9.24, respectively, P<0.001. It had good discriminant validity. The Cronbach'α coefficient for the total scale and four dimensions were from 0.76 to 0.86, and whose split-half reliability were from 0.68 to 0.84. Conclusion: The validity and reliability of C-PSCS were excellent, and could be used to evaluate the social capital situation on the Chinese primiparas.
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Hai Y, Meng XL, Li DY, Zhang XN, Wang YS. [Efficacy of Coflex in the treatment of lumbar spondylolisthesis]. ZHONGHUA WAI KE ZA ZHI [CHINESE JOURNAL OF SURGERY] 2017; 55:208-213. [PMID: 28241723 DOI: 10.3760/cma.j.issn.0529-5815.2017.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To study the clinical results of Coflex and lumbar posterior decompression and fusion in the treatment of lumbar degenerative spondylolisthesis at L(4-5). Methods: Thirty-eight patients with Grade Ⅰ degenerative spondylolisthesis, from January 2008 to December 2011 in Beijing Chaoyang Hospital, Capital Medical University were reviewed, and patients were divided into two groups by randomness. Group A was treated with Coflex and group B with pedicle instrumentation and interbody fusion. Fifteen patients were included in group A, and 23 patients were included in group B. In group A, the average age was (56.3±9.1) years. In group B, the average age was (58.2±11.2) years. The clinical results were evaluated by visual analogue scale (VAS) and Oswestry disability index (ODI). Slip distance (SD) was measured before and after surgery, and the changes of intervertebral angle at index level and adjacent level were also recorded. Results: The follow-up period was 36 to 68 months, with the average of (39±14) months in the both groups. The operation time and bleeding volume of patients in group A were significantly less than that of group B (P<0.05). In both groups, the difference of ODI and VAS before operation and postoperative follow-up were statistically significant (P<0.05). There was no significant difference between lumbar intervertebral angle and the sliding distance in group A at all time points. In the group B, there was a significant increase in the intervertebral angle and the sliding distance at L(3-4) and L(5)-S(1 )level after surgery, the difference at upper and below adjacent segment before and after surgery were statistically significant. Conclusions: Coflex interspinous dynamic stabilization system has same excellent clinical results as pedicle screw instrumentation and fusion surgery for the treatment of L(4-5) degenerative spondylolisthesis; no significant progression of spondylolisthesis been observed during more than 3 years follow-up, and no obvious adjacent segment degeneration has been found.
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Han DF, Ma JH, Hao CG, Tuerhong Tuerxun, Du L, Zhang XN. Association and differences in genetic polymorphisms in PCSK9 gene in subjects with lacunar infarction in the Han and Uygur populations of Xinjiang Uygur Autonomous Region of China. Neural Regen Res 2017; 12:1315-1321. [PMID: 28966647 PMCID: PMC5607827 DOI: 10.4103/1673-5374.213552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Polymorphisms in the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene are associated with severe hypercholesterolemia and stroke. Here, we investigated the relationship between single nucleotide polymorphisms in PCSK9 and stroke in 237 patients with lacunar infarction in the Uygur and Han populations in Xinjiang Uygur Autonomous Region of China. Using the SNaPshot single-base terminal extension method, four PCSK9 gene polymorphisms were analyzed. We found a significantly strong relationship between the PCSK9 rs17111503 (G > A) polymorphism and increased susceptibility to lacunar infarction by variant homozygote comparison, and using the dominant and recessive models in the Han population but not in the Uygur population. Low triglyceride levels were found in AA carriers (rs17111503, G > A) in the Han population but not in the Uygur population. Association analysis revealed that the rs17111503 (G > A) polymorphism was not significantly associated with smoking, alcohol drinking, history of hypertension or diabetes in the Han or Uygur lacunar infarction patients. rs11583680, rs483462 and rs505151 were not associated with risk of lacunar infarction in the Han or Uygur populations. Our findings suggest that the PCSK9 rs17111503 (G > A) polymorphism is associated with susceptibility to lacunar infarction in the Han population but not in the Uygur population.
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Zhang WX, Gao ST, Zhang XN, Zhen WF, Zhu Y, Wang N, Shi ZH, Guo Y, Ding DR, Meng XZ. Successful treatment of a severely injured victim from 8.12 Tianjin Port Explosion, China. Chin J Traumatol 2016; 18:320-2. [PMID: 26917020 DOI: 10.1016/j.cjtee.2015.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A male patient, 55 years old, was found from a container yard 65 h later following a chemical warehouse explosion in Tianjin, China on August 12, 2015. He was about 50 m away from the explosion center. He was subjected to compound multiple trauma, multi-viscera function damage, multiple fractures, hemothorax, traumatic wet lung, respiratory failure I, hypovolemic shock and impaired liver and kidney functions. After a series of successful treatments, he was rescued and recovered well.
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Dong QY, Zhao CX, Zheng H, Chen FZ, Li ZM, Li YH, Ji HX, Hao HY, Zhao W, Gao JQ, Liu HT, He J, Zhang XN, Li JG, Yuan JX. [Application of benchmark dose on renal injury in people chronically exposed to lead]. ZHONGHUA LAO DONG WEI SHENG ZHI YE BING ZA ZHI = ZHONGHUA LAODONG WEISHENG ZHIYEBING ZAZHI = CHINESE JOURNAL OF INDUSTRIAL HYGIENE AND OCCUPATIONAL DISEASES 2016; 34:494-497. [PMID: 27682482 DOI: 10.3760/cma.j.issn.1001-9391.2016.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Objective: To screen sensitive indicators of renal injury in lead workers using benchmark dose method. Methods: Of the 486 subjects,116 did not occupationally contact to lead as a control. The blood lead was considered as exposure biomarker, while Uβ2-MG and UNAG as effect biomarkers for renal injury. The BMD and BMDL of blood lead were estimated at the 10% benchmark response using BMDS Version 2.6. Results: There was statistical rise in blood lead between the lead group and control group (P<0.05) ; and the blood lead level was divided into four groups by quarterback spacing method, among which UNAG was statistically different (P<0.05) . There was an increased prevalence of abnormal rates of Uβ2-MG and UNAG with increasing blood lead concentration (P<0.05) , after trend chi-square test. BMD and BMDL of UNAG and Uβ2-MG were 602.784/431.838 μg/L and 130.398/100.981 μg/L caculated by Log-Probit model, respectively. Conclusions: Occupational lead exposure may cause kidney damage, and UNAG could be as a more sensitive marker for monitoring early renal injury than Uβ2-MG.
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Su BB, Zhou SW, Gan CB, Zhang XN. MiR-330-5p regulates tyrosinase and PDIA3 expression and suppresses cell proliferation and invasion in cutaneous malignant melanoma. J Surg Res 2016; 203:434-40. [PMID: 27363653 DOI: 10.1016/j.jss.2016.03.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/21/2016] [Accepted: 03/10/2016] [Indexed: 01/25/2023]
Abstract
BACKGROUND Increasing evidence has suggested that miR-330-5p can function as a tumor suppressor in different types of cancers. However, the effects and underlying mechanisms of miR-330-5p in the development of cutaneous malignant melanoma (CMM) remain largely unknown. The aim of the present study was to investigate the role of miR-330-5p in CMM and to determine the molecular mechanisms underlying its action. MATERIALS AND METHODS The expression level of miR-330-5p was detected in 26 cases of primary CMM tissues and cell lines by real-time quantitative polymerase chain reaction. We also assessed whether overexpression of miR-330-5p influences in vitro cell proliferation, invasion, and migration. Western blotting analysis was used to detect the influence of miR-330-5p on the targets, and Pearson analysis was used to calculate the correlation between the expression of targets gene and miR-330-5p in CMM tissues. RESULTS Our study showed that miR-330-5p was downregulated in CMM tissues (P = 0.010) and cell lines (P < 0.05), and patients with high mitotic activity showed lower miR-330-5p expression levels (P = 0.002). Enforced expression of miR-330-5p inhibits malignant CMM cells proliferation and migration and led to downregulation of the TYR and PDIA3 protein. Moreover, the expression level of miR-330-5p in CMM tissues showed inverse relationship with the expression level of TYR and PDIA3 protein. CONCLUSIONS In conclusion, our findings suggested that miR-330-5p represents a potential tumor-suppressive miRNA and plays an important role in CMM progression by suppressing TYR and PDIA3 expression.
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Cilano K, Mazanek Z, Khan M, Metcalfe S, Zhang XN. A New Mutation, hap1-2, Reveals a C Terminal Domain Function in AtMago Protein and Its Biological Effects in Male Gametophyte Development in Arabidopsis thaliana. PLoS One 2016; 11:e0148200. [PMID: 26867216 PMCID: PMC4750992 DOI: 10.1371/journal.pone.0148200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/14/2016] [Indexed: 01/02/2023] Open
Abstract
The exon-exon junction complex (EJC) is a conserved eukaryotic multiprotein complex that examines the quality of and determines the availability of messenger RNAs (mRNAs) posttranscriptionally. Four proteins, MAGO, Y14, eIF4AIII and BTZ, function as core components of the EJC. The mechanisms of their interactions and the biological indications of these interactions are still poorly understood in plants. A new mutation, hap1-2. leads to premature pollen death and a reduced seed production in Arabidopsis. This mutation introduces a viable truncated transcript AtMagoΔC. This truncation abolishes the interaction between AtMago and AtY14 in vitro, but not the interaction between AtMago and AteIF4AIII. In addition to a strong nuclear presence of AtMago, both AtMago and AtMagoΔC exhibit processing-body (P-body) localization. This indicates that AtMagoΔC may replace AtMago in the EJC when aberrant transcripts are to be degraded. When introducing an NMD mutation, upf3-1, into the existing HAP1/hap1-2 mutant, plants showed a severely reduced fertility. However, the change of splicing pattern of a subset of SR protein transcripts is mostly correlated with the sr45-1 and upf3-1 mutations, not the hap1-2 mutation. These results imply that the C terminal domain (CTD) of AtMago is required for the AtMago-AtY14 heterodimerization during EJC assembly, UPF3-mediated NMD pathway and the AtMago-AtY14 heterodimerization work synergistically to regulate male gametophyte development in plants.
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MESH Headings
- Amino Acid Sequence
- Animals
- Arabidopsis/genetics
- Arabidopsis/physiology
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/physiology
- Base Sequence
- Cloning, Molecular
- Crosses, Genetic
- DNA Primers/genetics
- DNA, Complementary/metabolism
- Dimerization
- Exons
- Genes, Plant
- Germ Cells, Plant
- Humans
- Microscopy, Confocal
- Molecular Sequence Data
- Mutation
- Nuclear Proteins/genetics
- Nuclear Proteins/physiology
- Plants, Genetically Modified
- Pollen/physiology
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA Processing, Post-Transcriptional
- RNA Splicing
- RNA Stability
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/metabolism
- Seeds/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
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Li WQ, Wang G, Zhang XN, Geng HP, Shen JL, Wang LS, Zhao J, Xu LF, Zhang LJ, Wu YQ, Tai RZ, Chen G. Geometrical and morphological optimizations of plasmonic nanoarrays for high-performance SERS detection. NANOSCALE 2015; 7:15487-94. [PMID: 26274048 DOI: 10.1039/c5nr03140k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Here we present an in-depth and comprehensive study of the effect of the geometry and morphology of nanoarray (NA) substrates on their surface-enhanced Raman scattering (SERS) performance. The high-quality SERS-active NA substrates of various unit shapes and pitches are assembled through electron beam lithography and fabricated by electron beam physical vapor deposition. Good agreement is found on comparing the Raman scattering results with the integrals of the fourth power of local electric fields from the three-dimensional numerical simulations. A novel type of hybrid NA substrate composed of disordered nanoparticles and a periodic NA is fabricated and characterized. The morphology of NAs has little influence on the SERS performance of hybrid NA substrates and they perform better than both their counterparts pure NA and disordered nanoparticle substrates.
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Li W, Li Y, Wu Y, Liao J, Qi T, Li H, Li J, Zhang X, Qian Z. A Nonenzymatic Electrochemical Immunosensor for Ultrasensitive Detection of Tumor Biomarkers Based on Palladium Nanoparticles Conjugated Reduced Graphene Nanosheets. J Biomed Nanotechnol 2015; 11:2050-6. [DOI: 10.1166/jbn.2015.2104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Wang YF, Liu WT, Chen CY, Ke HP, Jiang HL, Chen XL, Shi SY, Wei W, Zhang XN. Anti-osteoporosis activity of red yeast rice extract on ovariectomy-induced bone loss in rats. GENETICS AND MOLECULAR RESEARCH 2015; 14:8137-46. [PMID: 26345740 DOI: 10.4238/2015.july.27.2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Osteoporosis is the most common bone disease, affecting millions of people worldwide and leading to significant morbidity and high costs. Monacolin K, an extract of red yeast rice (RYR, Hongqu), plays important roles in the management of dyslipidemia, coronary heart disease, and diabetes. Our study aimed to investigate the protective effect of monacolin K on ovariectomy-induced bone loss in rats. Fifty female Sprague-Dawley rats were randomly divided into a sham-operated and five ovariectomized (OVX) groups: OVX with vehicle, OVX with fluvastatin, and OVX with RYR extract of three graded doses. Bone mineral density (BMD), biochemical markers, and cell viability were analyzed by dual energy X-ray absorptiometry, enzyme-linked immunosorbent assay, and 3(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assays. Gene expression was evaluated by real-time polymerase chain reaction amplification and western blot. Our results showed that administration of RYR extract markedly increased the bone mineral density in OVX rats. Moreover, RYR extract decreased the levels of bone turnover markers, including osteocalcin and tartrate resistant acid phosphatase activity. The MMT assay revealed that RYR extract treatment significantly improved the osteoblast viabilities in a dose-dependent manner (P < 0.05). At the molecular level, we further demonstrated that RYR extract enhanced the expression of Bmp2 and Bmp4 both at the mRNA and protein levels. Collectively, these data suggested RYR extract could protect against osteoporosis in ovariectomized rats, most likely through activation of BMP2/4 expression.
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Srinivasan P, Zhang XN, Bouten R, Chang C. Ferret: a sentence-based literature scanning system. BMC Bioinformatics 2015; 16:198. [PMID: 26091670 PMCID: PMC4474359 DOI: 10.1186/s12859-015-0630-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 05/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The rapid pace of bioscience research makes it very challenging to track relevant articles in one's area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million citations with three-quarters of a million new ones added each year. Thus it is not surprising to see active research in building new document retrieval and sentence retrieval systems. We present Ferret, a prototype retrieval system, designed to retrieve and rank sentences (and their documents) conveying gene-centric relationships of interest to a scientist. The prototype has several features. For example, it is designed to handle gene name ambiguity and perform query expansion. Inputs can be a list of genes with an optional list of keywords. Sentences are retrieved across species but the species discussed in the records are identified. Results are presented in the form of a heat map and sentences corresponding to specific cells of the heat map may be selected for display. Ferret is designed to assist bio scientists at different stages of research from early idea exploration to advanced analysis of results from bench experiments. RESULTS Three live case studies in the field of plant biology are presented related to Arabidopsis thaliana. The first is to discover genes that may relate to the phenotype of open immature flower in Arabidopsis. The second case is about finding associations reported between ethylene signaling and a set of 300+ Arabidopsis genes. The third case is on searching for potential gene targets of an Arabidopsis transcription factor hypothesized to be involved in plant stress responses. Ferret was successful in finding valuable information in all three cases. In the first case the bZIP family of genes was identified. In the second case sentences indicating relevant associations were found in other species such as potato and jasmine. In the third sentences led to new research questions about the plant hormone salicylic acid. CONCLUSIONS Ferret successfully retrieved relevant gene-centric sentences from PubMed records. The three case studies demonstrate end user satisfaction with the system.
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