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Find video protocols related to scientific articles indexed in Pubmed.
Analysis of Trace Microcystins in Vegetables Using Solid-phase Extraction Followed by High Performance Liquid Chromatography Triple-quadrupole Mass Spectrometry.
J. Agric. Food Chem.
PUBLISHED: 11-14-2014
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A selective and sensitive method for the simultaneous detection of three common and hazardous microcystins-LR,-RR and -YR in various vegetables was established using solid phase extraction followed by high-performance liquid chromatography coupled with mass spectrometry. The methanol-water proportion ratio of the extraction solvent and its acidity, as well as the efficiencies of solid-phase extraction were evaluated to optimize a pre-treatment procedure for extracting the microcystins from 10 vegetable matrices. The limits of detection and quantitation were below 7.5 µg/kg (dw) and 25 µg/kg (dw) respectively in different vegetable matrices. The recoveries of the microcystins in the 10 vegetable matrices ranged from 61.3 to 117.3%, with RSDs of 0.2-18.3%. The established method was used to analyze 28 field vegetable samples collected from the sides of Lake Dianchi, and microcystin-RR was found in almost all samples at concentrations of 36.4-2352.2 µg/kg (dw).
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[Laser speckle suppression due to dynamic multiple scattering scheme introduced by oblique incidence].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 11-01-2014
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Speckle suppression has been the research focus in laser display technology. In the present paper, the relation between multiple scattering and the size of speckle grains is established by analyzing the properties of speckle generated by the laser beam through SiO2 suspension. Combined with dynamic light scattering theory, laser speckle suppression due to dynamic multiple scattering scheme introduced by oblique incidence is proposed. A speckle suppression element consists of a static diffuser and a light pipe containing the water suspension of SiO2 microspheres with a diameter of 300 nm and a molar concentration of 3.0 x 10(-4) ?m3, which is integrated with the laser display system. The laser beam with different incident angles into the SiO2 suspension affecting the contrast of the speckle images is analyzed by the experiments. The results demonstrate that the contrast of the speckle image can be reduced to 0.067 from 0.43 when the beam with the incident angle of approximately 8 degrees illuminates into the SiO2 suspension. The spatial average of speckle granules and the temporal average of speckle images were achieved by the proposed method, which improved the effect of speckle suppression. The proposed element for speckle suppression improved the reliability and reduced the cost of laser projection system, since no mechanical vibration is needed and it is convenient to integrate the element with the existing projection system.
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Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data.
Genome Biol Evol
PUBLISHED: 10-29-2014
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As an important subtype of structural variations, chromosomal translocation is associated with various diseases, especially cancers, by disrupting gene structures and functions. Traditional methods for identifying translocations are time consuming and have limited resolutions. Recently, a few studies have employed next-generation sequencing (NGS) technology for characterizing chromosomal translocations on human genome, obtaining high-throughput results with high resolutions. However, these studies are mainly focused on mechanism-specific or site-specific translocation mapping. In this study, we conducted a comprehensive genome-wide analysis on the characterization of human chromosomal material exchange with regard to the chromosome translocations. Using NGS data of 1,481 subjects from the 1000 Genomes Project, we identified 15,349,092 translocated DNA fragment pairs, ranging from 65 to 1,886 bp and with an average size of approximately 102 bp. On average, each individual genome carried about 10,364 pairs, covering approximately 0.069% of the genome. We identified 16 translocation hot regions, among which two regions did not contain repetitive fragments. Results of our study overlapped with a majority of previous results, containing approximately 79% of approximately 2,340 translocations characterized in three available translocation databases. In addition, our study identified five novel potential recurrent chromosomal material exchange regions with greater than 20% detection rates. Our results will be helpful for an accurate characterization of translocations in human genomes, and contribute as a resource for future studies of the roles of translocations in human disease etiology and mechanisms.
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[Expression of SLC25A38 in Leukemic Cells from Children with Acute Lymphoblastic Leukemia].
Zhongguo Shi Yan Xue Ye Xue Za Zhi
PUBLISHED: 10-24-2014
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This study was aimed to investigate the SLC25A38 expression in pediatric patients with acute lymphoblastic leukemia (ALL) and its clinical significance. A total of 23 newly diagnosed ALL pedictric patients were enrolled in test group, 10 pediatric patients with non-hematologic malignancies were selected as control group. The expression in protein and mRNA levels of SLC25A38 were detected by Western blot and real-time PCR respectively. The results showed that the SLC25A38 protein was positive in 8 of 23 pediatric ALL patients (34.78%), while no positive case was found in 10 controls. The relative expression level of SLC25A38 mRNA was 0.4673 ± 0.05344 in SLC25A38-protein positive group of ALL patients, while that was 1.296 ± 0.2517 in SLC25A38-protein negative group of ALL patients. The expression level of SLC25A38 mRNA in SLC25A38-protein positive group was significantly lower than that in negative group (P = 0.001) . No statistically significant difference was found in comparison of SLC25A38-protein negative group of ALL patients with the control group (P = 0.1097). The analysis of clinical data showed that there were significantly differences in sex, immunophenotype, initial peripheral white blood cell count and LDH between the SLC25A38-protein positive and SLC25A38-protein negative groups (P < 0.05). It is concluded that as a novel protein, SLC25A38 highly expressed in pediatric ALL patients, indicating that SLC25A38 may serve as a molecular marker and potential therapeutic target for acute lymphoblastic leukemia in children.
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Health-Related and Psychosocial Concerns about Transplantation among Patients Initiating Dialysis.
Clin J Am Soc Nephrol
PUBLISHED: 09-11-2014
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Disparities in kidney transplantation remain; one mechanism for disparities in access to transplantation (ATT) may be patient-perceived concerns about pursuing transplantation. This study sought to characterize prevalence of patient-perceived concerns, explore interrelationships between concerns, determine patient characteristics associated with concerns, and assess the effect of concerns on ATT.
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Synthesis and biological evaluation of liguzinediol mono- and dual ester prodrugs as promising inotropic agents.
Molecules
PUBLISHED: 09-02-2014
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The potent positive inotropic effect, together with the relatively low safety risk of liguzinediol (LZDO), relative to currently available inotropic drugs, has prompted us to intensively research and develop LZDO as a potent positive inotropic agent. In this study, to obtain LZDO alternatives for oral chronic administration, a series of long-chain fatty carboxylic mono- and dual-esters of LZDO were synthesized, and preliminarily evaluated for physicochemical properties and bioconversion. Enhanced lipophilic properties and decreased solubility of the prodrugs were observed as the side chain length increased. All esters showed conspicuous chemical stability in phosphate buffer (pH 7.4). Moreover, the enzymatic hydrolysis of esters in human plasma and human liver microsomes confirmed that the majority of esters were converted to LZDO, with release profiles that varied due to the size and structure of the side chain. In vivo pharmacokinetic studies following oral administration of monopivaloyl (M5), monodecyl (M10) and monododecyl (M12) esters demonstrated the evidently extended half-lives relative to LZDO dosed alone. In particular the monopivaloyl ester M5 exhibited an optimal pharmacokinetic profile with appropriate physiochemical characteristics.
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Stable SET knockdown in breast cell carcinoma inhibits cell migration and invasion.
Biochem. Biophys. Res. Commun.
PUBLISHED: 08-28-2014
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Breast cancer is the most malignant tumor for women, however, the mechanisms underlying this devastating disease remain unclear. SET is an endogenous inhibitor of protein phosphatase 2A (PP2A) and involved in many physiological and pathological processes. SET could promote the occurrence of tumor through inhibiting PP2A. In this study, we explore the role of SET in the migration and invasion of breast cancer cells MDA-MB-231 and ZR-75-30. The stable suppression of SET expression through lentivirus-mediated RNA interference (RNAi) was shown to inhibit the growth, migration and invasion of breast cancer cells. Knockdown of SET increases the activity and expression of PP2Ac and decrease the expression of matrix metalloproteinase 9 (MMP-9). These data demonstrate that SET may be involved in the pathogenic processes of breast cancer, indicating that SET can serve as a potential therapeutic target for the treatment of breast cancer.
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Patient- and Provider-Reported Information about Transplantation and Subsequent Waitlisting.
J. Am. Soc. Nephrol.
PUBLISHED: 08-28-2014
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Because informed consent requires discussion of alternative treatments, proper consent for dialysis should incorporate discussion about other renal replacement options including kidney transplantation (KT). Accordingly, dialysis providers are required to indicate KT provision of information (KTPI) on CMS Form-2728; however, provider-reported KTPI does not necessarily imply adequate provision of information. Furthermore, the effect of KTPI on pursuit of KT remains unclear. We compared provider-reported KTPI (Form-2728) with patient-reported KTPI (in-person survey of whether a nephrologist or dialysis staff had discussed KT) in a prospective ancillary study of 388 hemodialysis initiates. KTPI was reported by both patient and provider for 56.2% of participants, by provider only for 27.8%, by patient only for 8.3%, and by neither for 7.7%. Among participants with provider-reported KTPI, older age was associated with lack of patient-reported KTPI. Linkage with the Scientific Registry for Transplant Recipients showed that 20.9% of participants were subsequently listed for KT. Patient-reported KTPI was independently associated with a 2.95-fold (95% confidence interval [95% CI], 1.54 to 5.66; P=0.001) higher likelihood of KT listing, whereas provider-reported KTPI was not associated with listing (hazard ratio, 1.18; 95% CI, 0.60 to 2.32; P=0.62). Our findings suggest that patient perception of KTPI is more important for KT listing than provider-reported KTPI. Patient-reported and provider-reported KTPI should be collected for quality assessment in dialysis centers because factors associated with discordance between these metrics might inform interventions to improve this process.
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Population clustering based on copy number variations detected from next generation sequencing data.
J Bioinform Comput Biol
PUBLISHED: 08-19-2014
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Copy number variations (CNVs) can be used as significant bio-markers and next generation sequencing (NGS) provides a high resolution detection of these CNVs. But how to extract features from CNVs and further apply them to genomic studies such as population clustering have become a big challenge. In this paper, we propose a novel method for population clustering based on CNVs from NGS. First, CNVs are extracted from each sample to form a feature matrix. Then, this feature matrix is decomposed into the source matrix and weight matrix with non-negative matrix factorization (NMF). The source matrix consists of common CNVs that are shared by all the samples from the same group, and the weight matrix indicates the corresponding level of CNVs from each sample. Therefore, using NMF of CNVs one can differentiate samples from different ethnic groups, i.e. population clustering. To validate the approach, we applied it to the analysis of both simulation data and two real data set from the 1000 Genomes Project. The results on simulation data demonstrate that the proposed method can recover the true common CNVs with high quality. The results on the first real data analysis show that the proposed method can cluster two family trio with different ancestries into two ethnic groups and the results on the second real data analysis show that the proposed method can be applied to the whole-genome with large sample size consisting of multiple groups. Both results demonstrate the potential of the proposed method for population clustering.
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Integrative Analysis of GWASs, Human Protein Interaction, and Gene Expression Identified Gene Modules Associated With BMDs.
J. Clin. Endocrinol. Metab.
PUBLISHED: 08-13-2014
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To date, few systems genetics studies in the bone field have been performed. We designed our study from a systems-level perspective by integrating genome-wide association studies (GWASs), human protein-protein interaction (PPI) network, and gene expression to identify gene modules contributing to osteoporosis risk.
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[Long optical path gas detection based on MEMS infrared light source].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 07-11-2014
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According to the requirements of infrared gas sensor for the light source, a broad wavelength, high modulation frequency, low power consumption and small size MEMS infrared light source is chosen as the radiation source, whose performance meets the requirements of infrared sensing system for the light source greatly. However, the infrared light source with the lamberation radiation characteristics is a surface light source, which is still with a large numerical aperture after shaping. It is difficult to increase the detection sensitivity by using a traditional long optical gas cell in a MEMS infrared light source detection system. Based on the dual-wavelength single beam differential detection method, an integrating sphere as the gas cell for long optical path is designed, which is able to realize long optical path for high sensitivity gas detection. The physical dimension is deduced for the equivalent optical path according to the flux conservation principle in the process of light transmission, solving the calculation problem of equivalent optical path of the integrating sphere cell. Using FPGA control chip, the MEMS infrared light source is droved at high frequency modulation and the detector output signal is processed, which makes the external circuit design much simple and flexible. It turns out that 166.7 cm equivalent optical path and the minimum concentration of methane of 0.001 x 10(-6) are achieved by the use of a 5 cm diameter integrating sphere in the research, improving the sensitivity of infrared detection system greatly.
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An intraoperative device to restore femoral offset in total hip arthroplasty.
J Orthop Surg Res
PUBLISHED: 06-27-2014
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Leg length discrepancy (LLD) after total hip arthroplasty (THA) can lead to unsatisfactory outcome. Our objective was to design and evaluate a simple and reliable intraoperative device (Length-offset Lever) to minimize leg length discrepancy.
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Trans-omics pathway analysis suggests that eQTLs contribute to chondrocyte apoptosis of Kashin-Beck disease through regulating apoptosis pathway expression.
Gene
PUBLISHED: 06-18-2014
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Kashin-Beck disease (KBD) is a serious osteoarthropathia, mainly characterized by excessive chondrocyte necrosis and apoptosis. The molecular signaling pathways underlying KBD excessive chondrocyte apoptosis remain unclear, leading to a lack of effective medical interventions now. To clarify whether expression quantitative trait loci (eQTLs) contribute to excessive chondrocyte apoptosis of Kashin-Beck disease through regulating the expression of apoptosis pathways. We conducted a genome-wide eQTLs based pathway association analysis of KBD using Affymetrix Human SNP Array 6.0 in 1717 Chinese Han subjects. PLINK software was used for genome-wide association study (GWAS) of KBD. A modified gene set enrichment algorithm was applied for pathway association analysis based on GWAS results. The KBD-associated pathways were compared with abnormally expressed pathways in KBD articular cartilage, identified by microarray study of KBD. We identified 4 eQTLs pathways, which were not only significantly associated with KBD, but also abnormally expressed in KBD articular cartilage, including REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS (P=0.008), MAHAJAN _RESPONSE_TO_IL1A_UP (P=0.010), KEGG_PEROXISOME (P=0.005) and MARKS_HDAC_TARGETS_UP (P=0.006). Our results suggest that eQTLs contributed to KBD excessive chondrocyte apoptosis through regulating the expression of apoptosis related pathways. This study provides novel insight into the genetic susceptibility and therapeutic rationale of KBD.
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Age and sex disparities in discussions about kidney transplantation in adults undergoing dialysis.
J Am Geriatr Soc
PUBLISHED: 05-06-2014
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To explore whether disparities in age and sex in access to kidney transplantation (KT) originate at the time of prereferral discussions about KT.
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BS69/ZMYND11 Reads and Connects Histone H3.3 Lysine 36 Trimethylation-Decorated Chromatin to Regulated Pre-mRNA Processing.
Mol. Cell
PUBLISHED: 05-05-2014
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BS69 (also called ZMYND11) contains tandemly arranged PHD, BROMO, and PWWP domains, which are chromatin recognition modalities. Here, we show that BS69 selectively recognizes histone variant H3.3 lysine 36 trimethylation (H3.3K36me3) via its chromatin-binding domains. We further identify BS69 association with RNA splicing regulators, including the U5 snRNP components of the spliceosome, such as EFTUD2. Remarkably, RNA sequencing shows that BS69 mainly regulates intron retention (IR), which is the least understood RNA alternative splicing event in mammalian cells. Biochemical and genetic experiments demonstrate that BS69 promotes IR by antagonizing EFTUD2 through physical interactions. We further show that regulation of IR by BS69 also depends on its binding to H3K36me3-decorated chromatin. Taken together, our study identifies an H3.3K36me3-specific reader and a regulator of IR and reveals that BS69 connects histone H3.3K36me3 to regulated RNA splicing, providing significant, important insights into chromatin regulation of pre-mRNA processing.
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Incidental findings on cardiac computed tomography in incident hemodialysis patients: the predictors of arrhythmic and cardiovascular events in end-stage renal disease (PACE) study.
BMC Nephrol
PUBLISHED: 04-24-2014
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This is the first study that has examined non-cardiac incidental findings in research cardiac computed tomography (CT) of hemodialysis patients and their relationship with patient characteristics.
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Genome-wide association study identifies ITPR2 as a susceptibility gene for Kashin-Beck disease in Han Chinese.
PUBLISHED: 04-09-2014
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Objective. Kashin-Beck Disease (KBD) is a chronic osteochondropathy, the pathogenesis of which remains elusive. To identify susceptibility genes for KBD, we conducted a two-stage genome-wide association study (GWAS) of KBD. Methods. 90 grade II or III KBD patients with extreme KBD phenotypes and 1,627 healthy controls were enrolled in initial GWAS. Affymetrix Genome Wide Human SNP Array 6.0 was applied for genotyping. For replication study, 9 SNPs of significant ITPR2 gene identified by the GWAS were tested in an independent validation sample containing 559 KBD patients and 467 healthy controls. Results. We identified a novel associated locus for KBD (ITRP2, rs10842750, P = 1.58×10(-) (8) ) in the GWAS. Replication study observed significant associations between KBD and the 9 validation SNPs of ITPR2 gene, including rs10842750 (P = 5.97×10(-3) ), rs16931011 (P = 1.29×10(-3) ), rs1531928 (P = 4.95×10(-3) ), rs4414322 (P = 4.40×10(-3) ), rs11048570 (P = 4.53×10(-3) ), rs11048572 (P = 4.43×10(-3) ), rs2017510 (P = 4.58×10(-3) ), rs9669395 (P = 5.77×10(-3) ) and rs1002835 (P = 4.85×10(-3) ). In KBD patients, the genotype score of rs10842750 (P = 0.013) was also correlated with KBD clinical severity grades. Conclusion. Our results strongly suggest that ITPR2 was a novel susceptibility gene for KBD in Han Chinese. This study may provide new insight into the pathogenesis and rationale of therapies for KBD as well as other osteoarthrosis with similar articular cartilage lesions. © 2014 American College of Rheumatology.
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Results from the Atherosclerosis Risk in Communities study suggest that low serum magnesium is associated with incident kidney disease.
Kidney Int.
PUBLISHED: 04-04-2014
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Low serum magnesium has been associated with kidney function decline in persons with diabetes as well as cardiovascular disease in the general population. As the association of serum magnesium with incident kidney disease in the general population is unknown, we assessed this in 13,226 participants (aged 45-65) in the Atherosclerosis Risk in Communities study with baseline estimated glomerular filtration rate of at least 60?ml/min per 1.73?m(2) in years 1987-89 and followed through 2010. The risks for incident chronic kidney disease (CKD) and end-stage renal disease (ESRD) associated with baseline total serum magnesium levels were evaluated using Cox regression. There were 1965 CKD and 208 ESRD events during a median follow-up of 21 years. In adjusted analysis, low serum magnesium levels (0.7?mmol/l or less) had significant associations with incident CKD and ESRD compared with the highest quartile with adjusted hazard ratio of 1.58 (95% CI: 1.35-1.87) for CKD and 2.39 (95% CI: 1.61-3.56) for ESRD. These associations remained significant after excluding users of diuretics and across subgroups stratified by hypertension, diabetes, and self-reported race. Thus, in a large sample of middle-aged adults, low total serum magnesium was independently associated with incident CKD and ESRD. Further studies are needed to determine whether modification of serum magnesium levels might alter subsequent incident kidney disease rates.Kidney International advance online publication, 1 October 2014; doi:10.1038/ki.2014.331.
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Applications of computer vision for assessing quality of agri-food products: a review of recent research advances.
Crit Rev Food Sci Nutr
PUBLISHED: 04-03-2014
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Abstract With consumer concerns increasing over food quality and safety, the food industry has begun to pay much more attention to the development of rapid and reliable food evaluation systems over the years. As a result, there is a great need for manufacturers and retailers to operate real-time effective assessments for food quality and safety during food producing and processing. Computer vision, as a non-destructive detecting approach, has the aptitude to estimate the characteristics of food products due to its advantages of fast speed, ease of use, and minimal sample preparation. Precisely, computer vision systems are feasible to classify food products into specific grades, detect defects and estimate properties such as color, shape, size, surface defects, and contamination. Thereof, in order to track the latest research developments of this technology in the agri-food industry, this review aims to present the fundamentals and instrumentation of computer vision systems, details of applications in quality assessment of agri-food products from the years 2007 to 2013, and also discuss its future trends in combination with spectroscopy.
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Mutant ZP1 in familial infertility.
N. Engl. J. Med.
PUBLISHED: 03-28-2014
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The human zona pellucida is composed of four glycoproteins (ZP1, ZP2, ZP3, and ZP4) and has an important role in reproduction. Here we describe a form of infertility with an autosomal recessive mode of inheritance, characterized by abnormal eggs that lack a zona pellucida. We identified a homozygous frameshift mutation in ZP1 in six family members. In vitro studies showed that defective ZP1 proteins and normal ZP3 proteins colocalized throughout the cells and were not expressed at the cell surface, suggesting that the aberrant ZP1 results in the sequestration of ZP3 in the cytoplasm, thereby preventing the formation of the zona pellucida around the oocyte.
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Genome-wide Association Studies for Osteoporosis: A 2013 Update.
J Bone Metab
PUBLISHED: 03-23-2014
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In the past few years, the bone field has witnessed great advances in genome-wide association studies (GWASs) of osteoporosis, with a number of promising genes identified. In particular, meta-analysis of GWASs, aimed at increasing the power of studies by combining the results from different study populations, have led to the identification of novel associations that would not otherwise have been identified in individual GWASs. Recently, the first whole genome sequencing study for osteoporosis and fractures was published, reporting a novel rare nonsense mutation. This review summarizes the important and representative findings published by December 2013. Comments are made on the notable findings and representative studies for their potential influence and implications on our present understanding of the genetics of osteoporosis. Potential limitations of GWASs and their meta-analyses are evaluated, with an emphasis on understanding the reasons for inconsistent results between different studies and clarification of misinterpretation of GWAS meta-analysis results. Implications and challenges of GWAS are also discussed, including the need for multi- and inter-disciplinary studies.
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Genome-wide pathway-based association study implicates complement system in the development of Kashin-Beck disease in Han Chinese.
Bone
PUBLISHED: 03-14-2014
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Kashin-Beck disease (KBD) is a chronic osteochondropathy. The pathogenesis of KBD remains unknown. To identify relevant biological pathways for KBD, we conducted a genome-wide pathway-based association study (GWPAS) following by replication analysis, totally using 2,743 Chinese Han adults. A modified gene set enrichment algorithm was used to detect association between KBD and 963 biological pathways. Cartilage gene expression analysis and serum complement measurement were performed to evaluate the functional relevance of identified pathway with KBD. We found that the Complement and Coagulation Cascades (CACC) pathway was significantly associated with KBD (P value=3.09×10(-5), false-discovery rate=0.042). Within the CACC pathway, the most significant association was observed at rs1656966 (P value=1.97×10(-4)) of KNG1 gene. Further replication study observed that rs1656966 (P value=0.037) was significantly associated with KBD in an independent validation sample of 1,026 subjects. Gene expression analysis observed that CFD (ratio=3.39±2.68), A2M (ratio=3.67±5.63), C5 (ratio=2.65±2.52) and CD46 (ratio=2.29±137) genes of the CACC pathway were up-regulated in KBD articular cartilage compared to healthy articular cartilage. The serum level of complement C5 in KBD patients were significantly higher than that in healthy controls (P value=0.038). Our study is the first to suggest that complement system-related CACC pathway contributed to the development of KBD.
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A unified sparse representation for sequence variant identification for complex traits.
Genet. Epidemiol.
PUBLISHED: 03-14-2014
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Joint adjustment of cryptic relatedness and population structure is necessary to reduce bias in DNA sequence analysis; however, existent sparse regression methods model these two confounders separately. Incorporating prior biological information has great potential to enhance statistical power but such information is often overlooked in many existent sparse regression models. We developed a unified sparse regression (USR) to incorporate prior information and jointly adjust for cryptic relatedness, population structure, and other environmental covariates. Our USR models cryptic relatedness as a random effect and population structure as fixed effect, and utilize the weighted penalties to incorporate prior knowledge. As demonstrated by extensive simulations, our USR algorithm can discover more true causal variants and maintain a lower false discovery rate than do several commonly used feature selection methods. It can handle both rare and common variants simultaneously. Applying our USR algorithm to DNA sequence data of Mexican Americans from GAW18, we replicated three hypertension pathways, demonstrating the effectiveness in identifying susceptibility genetic variants.
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Hamstring tendon autograft versus LARS artificial ligament for arthroscopic posterior cruciate ligament reconstruction in a long-term follow-up.
Arch Orthop Trauma Surg
PUBLISHED: 03-10-2014
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Surgical reconstruction has been increasingly recommended for the surgical management of posterior cruciate ligament (PCL) ruptures. While the choice of tissue graft still remains controversial. Currently both hamstring tendon autograft (HTG) and ligament advanced reinforcement system (LARS) artificial ligament are widely used but there are seldom reports on the comparisons of their clinical results. Our study was aimed to assess the effectiveness of these two grafts.
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Novel QTL at chromosome 6p22 for alcohol consumption: Implications for the genetic liability of alcohol use disorders.
Am. J. Med. Genet. B Neuropsychiatr. Genet.
PUBLISHED: 03-10-2014
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Linkage studies of alcoholism have implicated several chromosome regions, leading to the successful identification of susceptibility genes, including ADH4 and GABRA2 on chromosome 4. Quantitative endophenotypes that are potentially closer to gene action than clinical endpoints offer a means of obtaining more refined linkage signals of genes that predispose alcohol use disorders (AUD). In this study we examine a self-reported measure of the maximum number of drinks consumed in a 24-hr period (abbreviated Max Drinks), a significantly heritable phenotype (h(2) ?=?0.32?±?0.05; P?=?4.61?×?10(-14)) with a strong genetic correlation with AUD (?g ?=?0.99?±?0.13) for the San Antonio Family Study (n?=?1,203). Genome-wide SNPs were analyzed using variance components linkage methods in the program SOLAR, revealing a novel, genome-wide significant QTL (LOD?=?4.17; P?=?5.85?×?10(-6)) for Max Drinks at chromosome 6p22.3, a region with a number of compelling candidate genes implicated in neuronal function and psychiatric illness. Joint analysis of Max Drinks and AUD status shows that the QTL has a significant non-zero effect on diagnosis (P?=?4.04?×?10(-3)), accounting for 8.6% of the total variation. Significant SNP associations for Max Drinks were also identified at the linkage region, including one, rs7761213 (P?=?2.14?×?10(-4)), obtained for an independent sample of Chinese families. Thus, our study identifies a potential risk locus for AUD at 6p22.3, with significant pleiotropic effects on the heaviness of alcohol consumption that may not be population specific.
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FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model.
Bioinformatics
PUBLISHED: 03-10-2014
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Fast and accurate genotype imputation is necessary for facilitating gene-mapping studies, especially with the ever increasing numbers of both common and rare variants generated by high-throughput-sequencing experiments. However, most of the existing imputation approaches suffer from either inaccurate results or heavy computational demand.
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Common copy number variation detection from multiple sequenced samples.
IEEE Trans Biomed Eng
PUBLISHED: 02-22-2014
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Common copy number variations (CNVs) are small regions of genomic variations at the same loci across multiple samples, which can be detected with high resolution from next-generation sequencing (NGS) technique. Multiple sequencing data samples are often available from genomic studies; examples include sequences from multiple platforms and sequences from multiple individuals. By integrating complementary information from multiple data samples, detection power can be potentially improved. However, most of current CNV detection methods often process an individual sequence sample, or two samples in an abnormal versus matched normal study; researches on detecting common CNVs across multiple samples have been very limited but are much needed. In this paper, we propose a novel method to detect common CNVs from multiple sequencing samples by exploiting the concurrency of genomic variations in read depth signals derived from multiple NGS data. We use a penalized sparse regression model to fit multiple read depth profiles, based on which common CNV identification is formulated as a change-point detection problem. Finally, we validate the proposed method on both simulation and real data, showing that it can give both higher detection power and better break point estimation over several published CNV detection methods.
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Is GSN significant for hip BMD in female Caucasians?
Bone
PUBLISHED: 02-13-2014
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Low bone mineral density (BMD) is a risk factor for osteoporosis. Osteoporosis is more prevalent in females than in males. So far, the pathophysiological mechanisms underlying osteoporosis are unclear. Peripheral blood monocytes (PBMs) are precursors of bone-resorbing osteoclasts. This study aims to identify PBM-expressed proteins (genes) influencing hip BMD in humans. We utilized three independent study cohorts (N=34, 29, 40), including premenopausal Caucasians with discordant hip BMD. We studied PBM proteome-wide protein expression profiles in cohort 1 and identified 57 differentially expressed proteins (DEPs) between low vs. high BMD subjects. One protein gelsolin (GSN), after validation by Western blotting, was subject to follow-up. We compared GSN mRNA level in PBM between low vs. high BMD subjects in cohorts 2 and 3. We genotyped SNPs across GSN in 2286 unrelated Caucasians (cohort 4) and 1627 Chinese (cohort 5) and tested their association with hip BMD in females and males, respectively. We discovered and validated that GSN protein expression level in PBM was down-regulated 3.0-fold in low vs. high BMD subjects (P<0.05). Down-regulation of GSN in PBM in low BMD subjects was also observed at mRNA level in both cohort 2 and cohort 3. We identified that SNP rs767770 was significantly associated with hip BMD in female Caucasians (P=0.0003) only. Integrating analyses of the datasets at DNA, RNA, and protein levels from female Caucasians substantiated that GSN is highly significant for hip BMD (P=0.0001). We conclude that GSN is a significant gene influencing hip BMD in female Caucasians.
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STAT1-caspase 3 pathway in the apoptotic process associated with steroid-induced necrosis of the femoral head.
J. Mol. Histol.
PUBLISHED: 02-11-2014
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Osteocyte apoptosis is the main manifestation of steroid-induced avascular necrosis of the femoral head (SANFH). STAT1 and caspase 3 participate in the process of apoptosis and STAT1 upregulates the expression of caspase 3. We examined the relationship between the STAT1-caspase 3 pathway and apoptosis in SANFH. All specimens were divided into four groups: the negative control group, Ficat I-II group, Ficat III group, and Ficat IV-V group, and examined histologically, with a TUNEL assay, immunohistochemically, with a caspase 3 activity assay, with ELISAs of STAT1 and phospo-STAT1 (p-STAT1), with a western blotting analysis of p-STAT1 and with real-time RT-PCR. The proportion of empty lacunae increased significantly with the development of SANFH. The proportion of TUNEL-positive cells and immunohistochemical analysis of caspase 3 also increased significantly, although the Ficat I-II group did not differ significantly from the negative control group. Immunohistochemical analysis of STAT1 and p-STAT1, caspase 3 activity all showed significant differences among the groups. An ELISA and a western blotting analysis of p-STAT1 showed significant differences among the groups. An ELISA of STAT1, real-time RT-PCR analysis of caspase 3 and STAT1 all showed significant differences among the groups except between the Ficat I-II and negative control groups. The correlation analysis showed strong positive relationships between the proportion of empty lacunae and the proportion of TUNEL-positive cells between caspase 3 activity and the proportion of TUNEL-positive cells and between the levels of p-STAT1 protein and caspase 3 mRNA. The apoptotic process in SANFH develops with the upregulated expression of caspase 3 via the expression and activation of STAT1. The STATI-caspase 3 pathway plays a critical role in the development of SANFH.
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ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression.
Nature
PUBLISHED: 01-20-2014
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Recognition of modified histones by 'reader' proteins plays a critical role in the regulation of chromatin. H3K36 trimethylation (H3K36me3) is deposited onto the nucleosomes in the transcribed regions after RNA polymerase II elongation. In yeast, this mark in turn recruits epigenetic regulators to reset the chromatin to a relatively repressive state, thus suppressing cryptic transcription. However, much less is known about the role of H3K36me3 in transcription regulation in mammals. This is further complicated by the transcription-coupled incorporation of the histone variant H3.3 in gene bodies. Here we show that the candidate tumour suppressor ZMYND11 specifically recognizes H3K36me3 on H3.3 (H3.3K36me3) and regulates RNA polymerase II elongation. Structural studies show that in addition to the trimethyl-lysine binding by an aromatic cage within the PWWP domain, the H3.3-dependent recognition is mediated by the encapsulation of the H3.3-specific 'Ser?31' residue in a composite pocket formed by the tandem bromo-PWWP domains of ZMYND11. Chromatin immunoprecipitation followed by sequencing shows a genome-wide co-localization of ZMYND11 with H3K36me3 and H3.3 in gene bodies, and its occupancy requires the pre-deposition of H3.3K36me3. Although ZMYND11 is associated with highly expressed genes, it functions as an unconventional transcription co-repressor by modulating RNA polymerase II at the elongation stage. ZMYND11 is critical for the repression of a transcriptional program that is essential for tumour cell growth; low expression levels of ZMYND11 in breast cancer patients correlate with worse prognosis. Consistently, overexpression of ZMYND11 suppresses cancer cell growth in vitro and tumour formation in mice. Together, this study identifies ZMYND11 as an H3.3-specific reader of H3K36me3 that links the histone-variant-mediated transcription elongation control to tumour suppression.
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Qualitative and quantitative analyses of bioactive secolignans from folk medicinal plant Peperomia dindygulensis using UHPLC-UV/Q-TOF-MS.
J Pharm Biomed Anal
PUBLISHED: 01-15-2014
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Peperomia dindygulensis, with secolignans (SLs) as major bioactive constituents, is a commonly used traditional folk medicine in mainland China for treatment of stomach, liver, mammary, and esophageal cancers. However, to date, there is no method available for the qualitative and quantitative analyses of SLs in this medicinal plant. The purpose of this study was to establish a sensitive, selective, and reproducible method for rapidly profiling, identifying, and determining SLs in the whole plant of P. dindygulensis. Ultra high-performance liquid chromatography (UHPLC) coupled with ultraviolet detector (UV) and quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS) were used for this analyses. The fragmentation behaviors of different types of SLs were described. A total of thirteen SLs, including two new derivatives, were identified or tentatively characterized in P. dindygulensis samples. In addition, seven major SLs in herbal samples from different regions in China were successfully determined. The method developed in this study is suitable for the qualitative and quantitative analyses of SLs in P. dindygulensis, and may be applicable for determining or identifying SLs from other Pepermia genus plants.
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The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.
Cell Rep
PUBLISHED: 01-09-2014
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The histone lysine demethylase KDM5B regulates gene transcription and cell differentiation and is implicated in carcinogenesis. It contains multiple conserved chromatin-associated domains, including three PHD fingers of unknown function. Here, we show that the first and third, but not the second, PHD fingers of KDM5B possess histone binding activities. The PHD1 finger is highly specific for unmodified histone H3 (H3K4me0), whereas the PHD3 finger shows preference for the trimethylated histone mark H3K4me3. RNA-seq analysis indicates that KDM5B functions as a transcriptional repressor for genes involved in inflammatory responses, cell proliferation, adhesion, and migration. Biochemical analysis reveals that KDM5B associates with components of the nucleosome remodeling and deacetylase (NuRD) complex and may cooperate with the histone deacetylase 1 (HDAC1) in gene repression. KDM5B is downregulated in triple-negative breast cancer relative to estrogen-receptor-positive breast cancer. Overexpression of KDM5B in the MDA-MB 231 breast cancer cells suppresses cell migration and invasion, and the PHD1-H3K4me0 interaction is essential for inhibiting migration. These findings highlight tumor-suppressive functions of KDM5B in triple-negative breast cancer cells and suggest a multivalent mechanism for KDM5B-mediated transcriptional regulation.
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Metabolite identification of liguzinediol in dogs by ultra-flow liquid chromatography/tandem mass spectrometry.
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.
PUBLISHED: 01-07-2014
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Ultra-flow liquid chromatography/quadrupole-time-of-flight mass spectrometry (UFLC/Q-TOF MS) method combined with metabolitepilot(MT) software was used for analysis of the metabolites of liguzinediol in dogs. Urine, bile, feces and plasma samples were collected after intravenous administration of 8 mg/kg liguzinediol to healthy dogs. Besides liguzinediol, seven metabolites were detected and identified by UFLC/Q-TOF MS method. The results showed that liguzinediol had some main metabolic pathways in dogs including oxidation, sulfation, cysteine conjugation, N-acetylcysteine conjugation and glucuronidation.
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Genome-wide copy number variation study and gene expression analysis identify ABI3BP as a susceptibility gene for Kashin-Beck disease.
Hum. Genet.
PUBLISHED: 01-05-2014
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Kashin-Beck disease (KBD) is a chronic osteochondropathy. In this study, we conducted the first genome-wide copy number variation study (GCNVS) of KBD totally involving 2,743 Chinese Han adults. GCNVS was first performed using Affymetrix Human SNP6.0 Arrays. The identified copy number variations (CNVs) were then replicated in an independent Chinese Han sample containing 1,026 subjects. SNP genotyping, CNV identification and quality control were implemented by Birdsuite. STRUCTURE and EIGENSTRAT were applied for controlling potential population stratification in the GCNVS. Association analysis was conducted using PLINK. Microarray and qRT-PCR were also conducted to compare the expression levels of the genes overlapping with identified CNVs between KBD patients and healthy controls. GCNVS found that CNV452 (P value = 7.78 × 10(-5)) overlapping with ABI3BP gene was significantly associated with KBD. Replication association study observed that rs9850273 (P value = 0.008) and rs7613610 (P value = 0.021) in ABI3BP gene were significantly associated with KBD. Gene expression analysis also found that ABI3BP was up-regulated in KBD patients compared to healthy controls. Our results suggest that ABI3BP was a novel susceptibility gene for KBD.
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Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences.
BMC Bioinformatics
PUBLISHED: 01-03-2014
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Coalescent simulation is pivotal for understanding population evolutionary models and demographic histories, as well as for developing novel analytical methods for genetic association studies for DNA sequence data. A plethora of coalescent simulators are developed, but selecting the most appropriate program remains challenging.
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Circulating MicroRNAs as a Novel Class of Diagnostic Biomarkers in Gastrointestinal Tumors Detection: A Meta-Analysis Based on 42 Articles.
PLoS ONE
PUBLISHED: 01-01-2014
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MicroRNAs (miRNAs) have become the focus of most recent efforts in cancer research. However, there have been inconsistencies in the literature regarding the suitability of circulating miRNAs for early detection of gastrointestinal cancers. This study aims to assess the diagnostic performance of circulating miRNAs in detection of gastrointestinal cancer through a meta-analysis.
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Integrative analysis of multiple diverse omics datasets by sparse group multitask regression.
Front Cell Dev Biol
PUBLISHED: 01-01-2014
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A variety of high throughput genome-wide assays enable the exploration of genetic risk factors underlying complex traits. Although these studies have remarkable impact on identifying susceptible biomarkers, they suffer from issues such as limited sample size and low reproducibility. Combining individual studies of different genetic levels/platforms has the promise to improve the power and consistency of biomarker identification. In this paper, we propose a novel integrative method, namely sparse group multitask regression, for integrating diverse omics datasets, platforms, and populations to identify risk genes/factors of complex diseases. This method combines multitask learning with sparse group regularization, which will: (1) treat the biomarker identification in each single study as a task and then combine them by multitask learning; (2) group variables from all studies for identifying significant genes; (3) enforce sparse constraint on groups of variables to overcome the "small sample, but large variables" problem. We introduce two sparse group penalties: sparse group lasso and sparse group ridge in our multitask model, and provide an effective algorithm for each model. In addition, we propose a significance test for the identification of potential risk genes. Two simulation studies are performed to evaluate the performance of our integrative method by comparing it with conventional meta-analysis method. The results show that our sparse group multitask method outperforms meta-analysis method significantly. In an application to our osteoporosis studies, 7 genes are identified as significant genes by our method and are found to have significant effects in other three independent studies for validation. The most significant gene SOD2 has been identified in our previous osteoporosis study involving the same expression dataset. Several other genes such as TREML2, HTR1E, and GLO1 are shown to be novel susceptible genes for osteoporosis, as confirmed from other studies.
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Serum amyloid A and clusterin as potential predictive biomarkers for severe hand, foot and mouth disease by 2D-DIGE proteomics analysis.
PLoS ONE
PUBLISHED: 01-01-2014
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Hand, foot, and mouth disease (HFMD) affects more than one million children, is responsible for several hundred child deaths every year in China and is the cause of widespread concerns in society. Only a small fraction of HFMD cases will develop further into severe HFMD with neurologic complications. A timely and accurate diagnosis of severe HFMD is essential for assessing the risk of progression and planning the appropriate treatment. Human serum can reflect the physiological or pathological states, which is expected to be an excellent source of disease-specific biomarkers. In the present study, a comparative serological proteome analysis between severe HFMD patients and healthy controls was performed via a two-dimensional difference gel electrophoresis (2D-DIGE) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) strategy. Fifteen proteins were identified as differentially expressed in the sera of the severe HFMD patients compared with the controls. The identified proteins were classified into different groups according to their molecular functions, biological processes, protein classes and physiological pathways by bioinformatics analysis. The up-regulations of two identified proteins, serum amyloid A (SAA) and clusterin (CLU), were confirmed in the sera of the HFMD patients by ELISA assay. This study not only increases our background knowledge about and scientific insight into the mechanisms of HFMD, but also reveals novel potential biomarkers for the clinical diagnosis of severe HFMD.
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Replication of 6 obesity genes in a meta-analysis of genome-wide association studies from diverse ancestries.
PLoS ONE
PUBLISHED: 01-01-2014
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Obesity is a major public health problem with a significant genetic component. Multiple DNA polymorphisms/genes have been shown to be strongly associated with obesity, typically in populations of European descent. The aim of this study was to verify the extent to which 6 confirmed obesity genes (FTO, CTNNBL1, ADRB2, LEPR, PPARG and UCP2 genes) could be replicated in 8 different samples (n?=?11,161) and to explore whether the same genes contribute to obesity-susceptibility in populations of different ancestries (five Caucasian, one Chinese, one African-American and one Hispanic population). GWAS-based data sets with 1000 G imputed variants were tested for association with obesity phenotypes individually in each population, and subsequently combined in a meta-analysis. Multiple variants at the FTO locus showed significant associations with BMI, fat mass (FM) and percentage of body fat (PBF) in meta-analysis. The strongest association was detected at rs7185735 (P-value?=?1.01×10(-7) for BMI, 1.80×10(-6) for FM, and 5.29×10(-4) for PBF). Variants at the CTNNBL1, LEPR and PPARG loci demonstrated nominal association with obesity phenotypes (meta-analysis P-values ranging from 1.15×10(-3) to 4.94×10(-2)). There was no evidence of association with variants at ADRB2 and UCP2 genes. When stratified by sex and ethnicity, FTO variants showed sex-specific and ethnic-specific effects on obesity traits. Thus, it is likely that FTO has an important role in the sex- and ethnic-specific risk of obesity. Our data confirmed the role of FTO, CTNNBL1, LEPR and PPARG in obesity predisposition. These findings enhanced our knowledge of genetic associations between these genes and obesity-related phenotypes, and provided further justification for pursuing functional studies of these genes in the pathophysiology of obesity. Sex and ethnic differences in genetic susceptibility across populations of diverse ancestries may contribute to a more targeted prevention and customized treatment of obesity.
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Genome-wide association study identified copy number variants important for appendicular lean mass.
PLoS ONE
PUBLISHED: 01-01-2014
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Skeletal muscle is a major component of the human body. Age-related loss of muscle mass and function contributes to some public health problems such as sarcopenia and osteoporosis. Skeletal muscle, mainly composed of appendicular lean mass (ALM), is a heritable trait. Copy number variation (CNV) is a common type of human genome variant which may play an important role in the etiology of many human diseases. In this study, we performed genome-wide association analyses of CNV for ALM in 2,286 Caucasian subjects. We then replicated the major findings in 1,627 Chinese subjects. Two CNVs, CNV1191 and CNV2580, were detected to be associated with ALM (p?=?2.26×10(-2) and 3.34×10(-3), respectively). In the Chinese replication sample, the two CNVs achieved p-values of 3.26×10(-2) and 0.107, respectively. CNV1191 covers a gene, GTPase of the immunity-associated protein family (GIMAP1), which is important for skeletal muscle cell survival/death in humans. CNV2580 is located in the Serine hydrolase-like protein (SERHL) gene, which plays an important role in normal peroxisome function and skeletal muscle growth in response to mechanical stimuli. In summary, our study suggested two novel CNVs and the related genes that may contribute to variation in ALM.
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[Study on spermdamage caused by trichloroethylene in male rats].
Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi
PUBLISHED: 12-28-2013
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To study in vitro sperm damage caused by trichloroethylene in male rats.
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Multistage genome-wide association meta-analyses identified two new loci for bone mineral density.
Hum. Mol. Genet.
PUBLISHED: 11-17-2013
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Aiming to identify novel genetic variants and to confirm previously identified genetic variants associated with bone mineral density (BMD), we conducted a three-stage genome-wide association (GWA) meta-analysis in 27 061 study subjects. Stage 1 meta-analyzed seven GWA samples and 11 140 subjects for BMDs at the lumbar spine, hip and femoral neck, followed by a Stage 2 in silico replication of 33 SNPs in 9258 subjects, and by a Stage 3 de novo validation of three SNPs in 6663 subjects. Combining evidence from all the stages, we have identified two novel loci that have not been reported previously at the genome-wide significance (GWS; 5.0 × 10(-8)) level: 14q24.2 (rs227425, P-value 3.98 × 10(-13), SMOC1) in the combined sample of males and females and 21q22.13 (rs170183, P-value 4.15 × 10(-9), CLDN14) in the female-specific sample. The two newly identified SNPs were also significant in the GEnetic Factors for OSteoporosis consortium (GEFOS, n = 32 960) summary results. We have also independently confirmed 13 previously reported loci at the GWS level: 1p36.12 (ZBTB40), 1p31.3 (GPR177), 4p16.3 (FGFRL1), 4q22.1 (MEPE), 5q14.3 (MEF2C), 6q25.1 (C6orf97, ESR1), 7q21.3 (FLJ42280, SHFM1), 7q31.31 (FAM3C, WNT16), 8q24.12 (TNFRSF11B), 11p15.3 (SOX6), 11q13.4 (LRP5), 13q14.11 (AKAP11) and 16q24 (FOXL1). Gene expression analysis in osteogenic cells implied potential functional association of the two candidate genes (SMOC1 and CLDN14) in bone metabolism. Our findings independently confirm previously identified biological pathways underlying bone metabolism and contribute to the discovery of novel pathways, thus providing valuable insights into the intervention and treatment of osteoporosis.
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[Characteristics of prospective memory impairments in patients with severe traumatic brain injury during recovery stage].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 10-16-2013
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To explore the characteristics of time-based prospective memory (TBPM) and event-based prospective memory (EBPM) in patients with severe traumatic brain injury (TBI) during recovery stage.
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Regulation of estrogen receptor ? by histone methyltransferase SMYD2-mediated protein methylation.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 10-07-2013
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Estrogen receptor alpha (ER?) is a ligand-activated transcription factor. Upon estrogen stimulation, ER? recruits a number of coregulators, including both coactivators and corepressors, to the estrogen response elements, modulating gene activation or repression. Most coregulator complexes contain histone-modifying enzymes to control ER? target gene expression in an epigenetic manner. In addition to histones, these epigenetic modifiers can modify nonhistone proteins including ER?, thereby constituting another layer of transcriptional regulation. Here we show that SET and MYND domain containing 2 (SMYD2), a histone H3K4 and H3K36 methyltransferase, directly methylates ER? protein at lysine 266 (K266) both in vitro and in cells. In breast cancer MCF7 cells, SMYD2 attenuates the chromatin recruitment of ER? to prevent ER? target gene activation under an estrogen-depleted condition. Importantly, the SMYD2-mediated repression of ER? target gene expression is mediated by the methylation of ER? at K266 in the nucleus, but not the methylation of histone H3K4. Upon estrogen stimulation, ER?-K266 methylation is diminished, thereby enabling p300/cAMP response element-binding protein-binding protein to acetylate ER? at K266, which is known to promote ER? transactivation activity. Our study identifies a previously undescribed inhibitory methylation event on ER?. Our data suggest that the dynamic cross-talk between SMYD2-mediated ER? protein methylation and p300/cAMP response element-binding protein-binding protein-dependent ER? acetylation plays an important role in fine-tuning the functions of ER? at chromatin and the estrogen-induced gene expression profiles.
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[UFLC/Q-TOF-MS based analysis on material base of atractylodis macrocephalae rhizoma stir-fried with wheat bran].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 09-27-2013
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To establish a fingerprint spectrum for Atractylodis Macrocephalae Rhizoma stir-fried with wheat bran based on UFLC/Q-TOF-MS, and make a principal component analysis (PCA) with Markview software, in order to compare the changes of components between raw and processed Atractylodis Macrocephalae Rhizoma with raw wheat bran as the blank. The results showed that the changed in components raw Atractylodis Macrocephalae Rhizoma and Atractylodis Macrocephalae Rhizoma stir-fried with wheat bran were apparently observed by PCA. Six compounds were identified to have significant changes in mass fraction before and after being stir-fried, namely atractylenolide-I, atractylenolide-II, atractylenolide-III, atractylentrid, atractylon and an unknown compound. Among them, atractylenolide-I and atractylenolide-II generated from dehydration and dehydrogenation of atractylenolide-III may be the material base of Atractylodis Macrocephalae Rhizoma stir-fried with wheat bran for strengthening spleen.
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Meta-analysis of genome-wide association data identifies novel susceptibility loci for obesity.
Hum. Mol. Genet.
PUBLISHED: 09-23-2013
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Obesity is a major public health problem with strong genetic determination. Multiple genetic variants have been implicated for obesity by conducting genome-wide association (GWA) studies, primarily focused on body mass index (BMI). Fat body mass (FBM) is phenotypically more homogeneous than BMI and is more appropriate for obesity research; however, relatively few studies have been conducted on FBM. Aiming to identify variants associated with obesity, we carried out meta-analyses of seven GWA studies for BMI-related traits including FBM, and followed these analyses by de novo replication. The discovery cohorts consisted of 21 969 individuals from diverse ethnic populations and a total of over 4 million genotyped or imputed SNPs. The de novo replication cohorts consisted of 6663 subjects from two independent samples. To complement individual SNP-based association analyses, we also carried out gene-based GWA analyses in which all variations within a gene were considered jointly. Individual SNP-based association analyses identified a novel locus 1q21 [rs2230061, CTSS (Cathepsin S)] that was associated with FBM after the adjustment of lean body mass (LBM) (P = 3.57 × 10(-8)) at the genome-wide significance level. Gene-based association analyses identified a novel gene NLK (nemo-like kinase) in 17q11 that was significantly associated with FBM adjusted by LBM. In addition, we confirmed three previously reported obesity susceptibility loci: 16q12 [rs62033400, P = 1.97 × 10(-14), FTO (fat mass and obesity associated)], 18q22 [rs6567160, P = 8.09 × 10(-19), MC4R (melanocortin 4 receptor)] and 2p25 [rs939583, P = 1.07 × 10(-7), TMEM18 (transmembrane protein 18)]. We also found that rs6567160 may exert pleiotropic effects to both FBM and LBM. Our results provide additional insights into the molecular genetic basis of obesity and may provide future targets for effective prevention and therapeutic intervention.
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Simultaneous determination of five bioactive secolignans in rat plasma by LC-MS/MS for pharmacokinetic studies following oral administration of Peperomia dindygulensis Miq. extract.
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.
PUBLISHED: 09-06-2013
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A rapid and sensitive ultra fast performance liquid chromatography-tandem mass spectrometry method was developed for the simultaneous determination of five bioactive secolignans in Peperomia dindygulensis extract, including peperomin A, peperomin B, peperomin C, 4?-hydroxypeperomin B and 4?-hydroxypeperomin C in rat plasma. Arctigenin was used as the internal standard. The separation was performed on an Innovation™ Polar-RP C18 column by a gradient elution within a runtime of 7min. The mobile phase consisted of A (methanol) and B (0.1% formic acid in water) at a flow rate of 0.4mL/min. The detection was accomplished by using positive ion TurboIonSpray ionization in multiple reaction monitoring mode. The method was linear for all analytes over investigated range with all correlation coefficients greater than 0.9972. The lower limits of quantification were 1.1ng/mL for peperomin A, 1.24ng/mL for peperomin B, 1.02ng/mL for peperomin C, 1.91ng/mL for 4?-hydroxypeperomin B and 1.27ng/mL for 4?-hydroxypeperomin C. The intra- and inter-day precision (RSD%) was within 15% and the accuracy (RE%) ranged from -11.7% to 10.3%. This simple and sensitive method was fully validated and successfully applied to the pharmacokinetic study of peperomin A, peperomin B, peperomin C, 4?-hydroxypeperomin B and 4?-hydroxypeperomin C in rat plasma after oral administration of P. dindygulensis extract.
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SLCO1B1 variants and urine arsenic metabolites in the Strong Heart Family Study.
Toxicol. Sci.
PUBLISHED: 08-22-2013
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Arsenic species patterns in urine are associated with risk for cancer and cardiovascular diseases. The organic anion transporter coded by the gene SLCO1B1 may transport arsenic species, but its association with arsenic metabolites in human urine has not yet been studied. The objective of this study is to evaluate associations of urine arsenic metabolites with variants in the candidate gene SLCO1B1 in adults from the Strong Heart Family Study. We estimated associations between % arsenic species biomarker traits and 5 single-nucleotide polymorphisms (SNPs) in the SLCO1B1 gene in 157 participants, assuming additive genetics. Linear regression models for each SNP accounted for kinships and were adjusted for sex, body mass index, and study center. The minor allele of rs1564370 was associated with lower %MMA (p = .0003) and higher %DMA (p = .0002), accounting for 8% of the variance for %MMA and 9% for %DMA. The rs1564370 minor allele homozygote frequency was 17% and the heterozygote frequency was 43%. The minor allele of rs2291075 was associated with lower %MMA (p = .0006) and higher %DMA (p = .0014), accounting for 7% of the variance for %MMA and 5% for %DMA. The frequency of rs2291075 minor allele homozygotes was 1% and of heterozygotes was 15%. Common variants in SLCO1B1 were associated with differences in arsenic metabolites in a preliminary candidate gene study. Replication of this finding in other populations and analyses with respect to disease outcomes are needed to determine whether this novel candidate gene is important for arsenic-associated disease risks.
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ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural chinese sample.
Am. J. Med. Genet. B Neuropsychiatr. Genet.
PUBLISHED: 08-02-2013
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Alcohol dependence (AD) is a moderately heritable phenotype with a small number of known risk genes mapped via linkage or candidate gene studies. We considered 313 males from among 595 members of documented, extended pedigrees in which AD segregates collected in Northern Hunan Province, China. A joint analysis of both males and females could not be performed as the difference in alcohol consumption variance was too large. Genome-wide association analyses were performed for approximately 300,000 single nucleotide polymorphisms (SNPs). Significant associations found in the ALDH2 region for AD (minimum P?=?4.73?×?10(-8) ) and two AD-related phenotypes: flushing response (minimum P?=?4.75?×?10(-26) ) and maximum drinks in a 24-hr period (minimum P?=?1.54?×?10(-16) ). Association of previous candidate SNP, rs10774610 in CCDC63, was confirmed but resulted from linkage disequilibrium with ALDH2. ALDH2 is strongly associated with flushing response, AD, and maximum drinks in males, with nonsynonymous SNP rs671 explaining 29.2%, 7.9%, and 22.9% of phenotypic variation, respectively, in this sample. When rs671 was considered as a candidate SNP in females, it explained 23.6% of the variation in flushing response, but alcohol consumption rates were too low among females-despite familial enrichment for AD-for an adequate test of association for either AD or maximum drinks. These results support a mediating effect of aldehyde dehydrogenase deficiency on alcohol consumption in males and a secondary, culturally mediated limitation on alcohol consumption by females that should be appropriately modeled in future studies of alcohol consumption in populations where this may be a factor. © 2013 Wiley Periodicals, Inc.
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DNA methylation levels of CYP2R1 and CYP24A1 predict vitamin D response variation.
J. Steroid Biochem. Mol. Biol.
PUBLISHED: 08-01-2013
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Factors contributing to the variability of serum 25-hydroxyvitamin D [25(OH)D] in response to a given dose of vitamin D supplementation are largely unknown. We examined whether DNA methylation levels of Cytochrome P450 (CYP) enzymes (CYP2R1, CYP24A1, CYP27A1, and CYP27B1) are potential biomarkers predicting vitamin D response variation. We randomized 446 white postmenopausal women to a calcium and vitamin D (1100IU/day) intervention for at least 12 months. From these subjects, 18 with the highest 12-month increase in serum 25(OH)D were selected as "responders." Another 18 with the lowest 12-month increase in serum 25(OH)D were selected as "non-responders." DNA methylation levels between the groups were compared. To validate findings in the first study, association between DNA methylation levels and vitamin D response variation was studied in another 145 extended independent white postmenopausal women. In the first study, compared to non-responders, responders had significantly lower baseline DNA methylation levels in the promoter region of CYP2R1 (8% in the responders vs. 30% in the non-responders, P=0.004), and CYP24A1 (13% in the responders vs. 32% in the non-responders, P=0.001). In the validation study, for CYP2R1, baseline DNA methylation levels at eight CpG sites were negatively associated with 12-month increases in serum 25(OH)D (P<0.05). For CYP24A1, baseline DNA methylation levels at two CpG sites were also negatively associated with vitamin D response variation (r=-0.151, P=0.011; r=-0.131, P=0.025). These negative associations were consistent with the first studys results. Our findings indicate that baseline DNA methylation levels of CYP2R1 and CYP24A1 may predict vitamin D response variation. This article is part of a Special Issue entitled 16th Vitamin D Workshop.
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On genome-wide association studies and their meta-analyses: lessons learned from osteoporosis studies.
J. Clin. Endocrinol. Metab.
PUBLISHED: 06-19-2013
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Genome-wide association studies (GWASs) and meta-analyses of GWASs have led to the identification of a number of promising genes for osteoporosis. However, inconsistent findings are seen among and between GWASs and meta-analyses, and inconsistencies have even been observed between meta-analyses whose samples overlapped to a large extent.
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Characterization of the DNA methylome and its interindividual variation in human peripheral blood monocytes.
Epigenomics
PUBLISHED: 06-12-2013
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Peripheral blood monocytes (PBMs) play multiple and critical roles in the immune response, and abnormalities in PBMs have been linked to a variety of human disorders. However, the DNA methylation landscape in PBMs is largely unknown. In this study, we characterized epigenome-wide DNA methylation profiles in purified PBMs.
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CNV-TV: a robust method to discover copy number variation from short sequencing reads.
BMC Bioinformatics
PUBLISHED: 04-19-2013
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Copy number variation (CNV) is an important structural variation (SV) in human genome. Various studies have shown that CNVs are associated with complex diseases. Traditional CNV detection methods such as fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) suffer from low resolution. The next generation sequencing (NGS) technique promises a higher resolution detection of CNVs and several methods were recently proposed for realizing such a promise. However, the performances of these methods are not robust under some conditions, e.g., some of them may fail to detect CNVs of short sizes. There has been a strong demand for reliable detection of CNVs from high resolution NGS data.
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Gene-gene interaction between RBMS3 and ZNF516 influences bone mineral density.
J. Bone Miner. Res.
PUBLISHED: 04-12-2013
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Osteoporosis is characterized by low bone mineral density (BMD), a highly heritable trait that is determined, in part, by the actions and interactions of multiple genes. Although an increasing number of genes have been identified to have independent effects on BMD, few studies have been performed to identify genes that interact with one another to affect BMD. In this study, we performed gene-gene interaction analyses in selected candidate genes in individuals with extremely high versus low hip BMD (20% tails of the distributions), in two independent U.S. Caucasian samples. The first sample contained 916 unrelated subjects with extreme hip BMD Z-scores selected from a population composed of 2286 subjects. The second sample consisted of 400 unrelated subjects with extreme hip BMD Z-scores selected from a population composed of 1000 subjects. Combining results from these two samples, we found one interacting gene pair (RBMS3 versus ZNF516) which, even after Bonferroni correction for multiple testing, showed consistently significant effects on hip BMD. RMBS3 harbored two single-nucleotide polymorphisms (SNPs), rs6549904 and rs7640046, both of which had significant interactions with an SNP, rs4891159, located on ZNF516 (p?=?7.04?×?10(-11) and 1.03?×?10(-10) ). We further validated these results in two additional samples of Caucasian and African descent. The gene pair, RBMS3 versus ZNF516, was successfully replicated in the Caucasian sample (p?=?8.07?×?10(-3) and 2.91?×?10(-3) ). For the African sample, a significant interaction was also detected (p?=?0.031 and 0.043), but the direction of the effect was opposite to that observed in the three Caucasian samples. By providing evidence for genetic interactions underlying BMD, this study further delineates the genetic architecture of osteoporosis.
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Group sparse canonical correlation analysis for genomic data integration.
BMC Bioinformatics
PUBLISHED: 04-01-2013
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The emergence of high-throughput genomic datasets from different sources and platforms (e.g., gene expression, single nucleotide polymorphisms (SNP), and copy number variation (CNV)) has greatly enhanced our understandings of the interplay of these genomic factors as well as their influences on the complex diseases. It is challenging to explore the relationship between these different types of genomic data sets. In this paper, we focus on a multivariate statistical method, canonical correlation analysis (CCA) method for this problem. Conventional CCA method does not work effectively if the number of data samples is significantly less than that of biomarkers, which is a typical case for genomic data (e.g., SNPs). Sparse CCA (sCCA) methods were introduced to overcome such difficulty, mostly using penalizations with l-1 norm (CCA-l1) or the combination of l-1and l-2 norm (CCA-elastic net). However, they overlook the structural or group effect within genomic data in the analysis, which often exist and are important (e.g., SNPs spanning a gene interact and work together as a group).
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SNP rs6265 Regulates Protein Phosphorylation and Osteoblast Differentiation and Influences BMD in Humans.
J. Bone Miner. Res.
PUBLISHED: 03-17-2013
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Bone mineral density (BMD) is a major index for diagnosing osteoporosis. PhosSNPs are nonsynonymous SNPs that affect protein phosphorylation. The relevance and significance of phosSNPs to BMD and osteoporosis is unknown. This study aimed to identify and characterize phosSNPs significant for BMD in humans. We conducted a pilot genomewide phosSNP association study for BMD in three independent population samples, involving ?5000 unrelated individuals. We identified and replicated three phosSNPs associated with both spine BMD and hip BMD in Caucasians. Association with hip BMD for one of these phosSNPs, ie, rs6265 (major/minor allele: G/A) in BDNF gene, was also suggested in Chinese. Consistently in both ethnicities, individuals carrying the AA genotype have significantly lower hip BMD than carriers of the GA and GG genotypes. Through in vitro molecular and cellular studies, we found that compared to osteoblastic cells transfected with wild-type BDNF-Val66 (encoded with allele G at rs6265), transfection of variant BDNF-Met66 (encoded with allele A at rs6265) significantly decreased BDNF protein phosphorylation (at amino acid residue T62), expression of osteoblastic genes (OPN, BMP2, and ALP), and osteoblastic activity. The findings are consistent with and explain our prior observations in general human populations. We conclude that phosSNP rs6265, by regulating BDNF protein phosphorylation and osteoblast differentiation, influences hip BMD in humans. This study represents our first endeavor to dissect the functions of phosSNPs in bone, which might stimulate extended large-scale studies on bone or similar studies on other human complex traits and diseases. © 2013 American Society for Bone and Mineral Research.
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Synthesis, biological evaluation, and pharmacokinetic study of novel liguzinediol prodrugs.
Molecules
PUBLISHED: 03-15-2013
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Liguzinediol (LZDO) ester prodrugs 3-5 were synthesized and evaluated in vitro and in vivo for their potential use in prolonging the half-life of the parent drug LZDO (1a) in vivo. Prodrugs 3-5 were found to display a potent positive inotropic effect on the myocardium, without the risk of arrhythmia. Prodrugs 3-5 rapidly underwent enzymatic hydrolysis to release the parent compound LZDO in 1-3 h in rat liver microsomes and rat plasma. The half-life of the parent compound was prolonged after intragastric administration of prodrug 3, which was found to be a superior prodrug candidate for increasing myocardial contractility.
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Telmisartan protects against microvascular dysfunction during myocardial ischemia/reperfusion injury by activation of peroxisome proliferator-activated receptor gamma.
BMC Cardiovasc Disord
PUBLISHED: 03-03-2013
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We investigated the potential of telmisartan to improve microvascular dysfunction induced by myocardial ischemia/reperfusion (I/R) injury by activating the peroxisome proliferator-activated receptor gamma (PPARG) pathway.
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On individual genome-wide association studies and their meta-analysis.
Hum. Genet.
PUBLISHED: 02-27-2013
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Individual genome-wide association (GWA) studies and their meta-analyses represent two approaches for identifying genetic loci associated with complex diseases/traits. Inconsistent findings and non-replicability between individual GWA studies and meta-analyses are commonly observed, hence posing the critical question as to how to interpret their respective results properly. In this study, we performed a series of simulation studies to investigate and compare the statistical properties of the two approaches. Our results show that (1) as expected, meta-analysis of larger sample size is more powerful than individual GWA studies under the ideal setting of population homogeneity among individual studies; (2) under the realistic setting of heterogeneity among individual studies, detection of heterogeneity is usually difficult and meta-analysis (even with the random-effects model) may introduce elevated false positive and/or negative rates; (3) despite relatively small sample size, well-designed individual GWA study has the capacity to identify novel loci for complex traits; (4) replicability between meta-analysis and independent individual studies or between independent meta-analyses is limited, and thus inconsistent findings are not unexpected.
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Using multiple measures for quantitative trait association analyses: application to estimated glomerular filtration rate.
J. Hum. Genet.
PUBLISHED: 02-27-2013
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Studies of multiple measures of a quantitative trait can have greater precision and thus statistical power compared with single-measure studies, but this has rarely been studied in the relation to quantitative trait measurement error models in genetic association studies. Using estimated glomerular filtration rate (eGFR), a quantitative measure of kidney function, as an example we constructed measurement error models of a quantitative trait with systematic and random error components. We then examined the effects on precision of the parameter estimate between genetic loci and eGFR, resulting from varying the correlation and contribution of the error components. We also compared the empirical results from three genome-wide association studies (GWAS) of kidney function in 9049 European Americans: a single measure model, a three-measure model of the same biomarker of kidney function and a six-measure model of different biomarkers of kidney function. Simulations showed that given the same amount of overall errors, inclusion of measures with less correlated systematic errors led to greater gain in precision. The empirical GWAS results confirmed that both the three- and six-measure models detected more eGFR-associated genomic loci with stronger statistical association than the single-measure model despite some heterogeneity among the measures. Multiple measures of a quantitative trait can increase the statistical power of a study without additional participant recruitment. However, careful attention must be paid to the correlation of systematic errors and inconsistent associations when different biomarkers or methods are used to measure the quantitative trait.
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The complex containing Drosophila Myb and RB/E2F2 regulates cytokinesis in a histone H2Av-dependent manner.
Mol. Cell. Biol.
PUBLISHED: 02-25-2013
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In Drosophila, mutation of the oncogene Myb reduced the expression of mitotic genes, such as polo and ial, and caused multiple mitotic defects, including disrupted chromosome condensation and abnormal spindles. We now show that binucleate cells, the hallmark phenotype of cytokinesis failure, accumulate in Myb-null ovarian follicle cell and wing disc epithelia. Myb functions as an activator in the generally repressive Drosophila RBF, E2F2, and Myb (dREAM)/Myb-MuvB complex. Absence of the dREAM subunit Mip130 or E2F2 suppressed the Myb-null cytokinesis defect. Therefore, we used Myb-null binucleate cells as a quantitative phenotypic readout of transcriptional repression by the dREAM complex. In the absence of Myb, the complex was sensitive to the dose of the subunits E2F2, Mip120, Caf1, and Lin-52 but not Mip130 or Mip40. Surprisingly, reduction of the dose of His2Av/H2A.z also suppressed the Myb-null binucleate cell phenotype, suggesting a novel role for this variant histone in transcriptional repression by the dREAM complex.
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Comprehensive characterization of human genome variation by high coverage whole-genome sequencing of forty four Caucasians.
PLoS ONE
PUBLISHED: 02-14-2013
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Whole genome sequencing studies are essential to obtain a comprehensive understanding of the vast pattern of human genomic variations. Here we report the results of a high-coverage whole genome sequencing study for 44 unrelated healthy Caucasian adults, each sequenced to over 50-fold coverage (averaging 65.8×). We identified approximately 11 million single nucleotide polymorphisms (SNPs), 2.8 million short insertions and deletions, and over 500,000 block substitutions. We showed that, although previous studies, including the 1000 Genomes Project Phase 1 study, have catalogued the vast majority of common SNPs, many of the low-frequency and rare variants remain undiscovered. For instance, approximately 1.4 million SNPs and 1.3 million short indels that we found were novel to both the dbSNP and the 1000 Genomes Project Phase 1 data sets, and the majority of which (?96%) have a minor allele frequency less than 5%. On average, each individual genome carried ?3.3 million SNPs and ?492,000 indels/block substitutions, including approximately 179 variants that were predicted to cause loss of function of the gene products. Moreover, each individual genome carried an average of 44 such loss-of-function variants in a homozygous state, which would completely "knock out" the corresponding genes. Across all the 44 genomes, a total of 182 genes were "knocked-out" in at least one individual genome, among which 46 genes were "knocked out" in over 30% of our samples, suggesting that a number of genes are commonly "knocked-out" in general populations. Gene ontology analysis suggested that these commonly "knocked-out" genes are enriched in biological process related to antigen processing and immune response. Our results contribute towards a comprehensive characterization of human genomic variation, especially for less-common and rare variants, and provide an invaluable resource for future genetic studies of human variation and diseases.
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Comparative studies of copy number variation detection methods for next-generation sequencing technologies.
PLoS ONE
PUBLISHED: 02-12-2013
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Copy number variation (CNV) has played an important role in studies of susceptibility or resistance to complex diseases. Traditional methods such as fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) suffer from low resolution of genomic regions. Following the emergence of next generation sequencing (NGS) technologies, CNV detection methods based on the short read data have recently been developed. However, due to the relatively young age of the procedures, their performance is not fully understood. To help investigators choose suitable methods to detect CNVs, comparative studies are needed. We compared six publicly available CNV detection methods: CNV-seq, FREEC, readDepth, CNVnator, SegSeq and event-wise testing (EWT). They are evaluated both on simulated and real data with different experiment settings. The receiver operating characteristic (ROC) curve is employed to demonstrate the detection performance in terms of sensitivity and specificity, box plot is employed to compare their performances in terms of breakpoint and copy number estimation, Venn diagram is employed to show the consistency among these methods, and F-score is employed to show the overlapping quality of detected CNVs. The computational demands are also studied. The results of our work provide a comprehensive evaluation on the performances of the selected CNV detection methods, which will help biological investigators choose the best possible method.
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Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin.
Hum. Genet.
PUBLISHED: 02-06-2013
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Beta-2 microglobulin (B2M) is a component of the major histocompatibility complex (MHC) class I molecule and has been studied as a biomarker of kidney function, cardiovascular diseases and mortality. Little is known about the genes influencing its levels directly or through glomerular filtration rate (GFR). We conducted a genome-wide association study of plasma B2M levels in 6738 European Americans from the Atherosclerosis Risk in Communities study to identify novel loci for B2M and assessed its association with known estimated GFR (eGFR) loci. We identified 2 genome-wide significant loci. One was in the human leukocyte antigen (HLA) region on chromosome 6 (lowest p value = 1.8 × 10(-23) for rs9264638). At this locus, 6 index SNPs accounted for 3.2 % of log(B2M) variance, and their association with B2M could largely be explained by imputed classical alleles of the MHC class I genes: HLA-A, HLA-B, or HLA-C. The index SNPs at this locus were not associated with eGFR based on serum creatinine (eGFRcr). The other locus of B2M was on chromosome 12 (rs3184504 at SH2B3, beta = 0.02, p value = 3.1 × 10(-8)), which was previously implicated as an eGFR locus. In conclusion, although B2M is known to be a component of MHC class I molecule, the association between HLA class I alleles and plasma B2M levels in a community-based population is novel. The identification of the two novel loci for B2M extends our understanding of its metabolism and informs its use as a kidney filtration biomarker.
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On combining reference data to improve imputation accuracy.
PLoS ONE
PUBLISHED: 01-30-2013
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Genotype imputation is an important tool in human genetics studies, which uses reference sets with known genotypes and prior knowledge on linkage disequilibrium and recombination rates to infer un-typed alleles for human genetic variations at a low cost. The reference sets used by current imputation approaches are based on HapMap data, and/or based on recently available next-generation sequencing (NGS) data such as data generated by the 1000 Genomes Project. However, with different coverage and call rates for different NGS data sets, how to integrate NGS data sets of different accuracy as well as previously available reference data as references in imputation is not an easy task and has not been systematically investigated. In this study, we performed a comprehensive assessment of three strategies on using NGS data and previously available reference data in genotype imputation for both simulated data and empirical data, in order to obtain guidelines for optimal reference set construction. Briefly, we considered three strategies: strategy 1 uses one NGS data as a reference; strategy 2 imputes samples by using multiple individual data sets of different accuracy as independent references and then combines the imputed samples with samples based on the high accuracy reference selected when overlapping occurs; and strategy 3 combines multiple available data sets as a single reference after imputing each other. We used three software (MACH, IMPUTE2 and BEAGLE) for assessing the performances of these three strategies. Our results show that strategy 2 and strategy 3 have higher imputation accuracy than strategy 1. Particularly, strategy 2 is the best strategy across all the conditions that we have investigated, producing the best accuracy of imputation for rare variant. Our study is helpful in guiding application of imputation methods in next generation association analyses.
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Meta-analysis identifies a MECOM gene as a novel predisposing factor of osteoporotic fracture.
J. Med. Genet.
PUBLISHED: 01-24-2013
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Osteoporotic fracture (OF) as a clinical endpoint is a major complication of osteoporosis. To screen for OF susceptibility genes, we performed a genome-wide association study and carried out de novo replication analysis of an East Asian population.
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The effects of Rhizoma Zingiberis on pharmacokinetics of six Aconitum alkaloids in herb couple of Radix Aconiti Lateralis-Rhizoma Zingiberis.
J Ethnopharmacol
PUBLISHED: 01-15-2013
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Radix Aconiti Lateralis (Fuzi in Chinese, derived from the lateral roots of Aconitum Carmichaeli Debx.) is widely used for the treatment of heart failure, internal cold, arthralgia, diarrhea and edema for thousands of years. It was usually prescribed in combination with Rhizoma Zingiberis (Ganjiang in Chinese, derived from the dry rhizome of Zingiber officinale Rosc.) to decrease toxicity and increase efficacy.
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Association between variants in or near PNPLA3, GCKR, and PPP1R3B with ultrasound-defined steatosis based on data from the third national health and nutrition examination survey.
Clin. Gastroenterol. Hepatol.
PUBLISHED: 01-07-2013
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A genome-wide association study associated 5 genetic variants with hepatic steatosis (identified by computerized tomography) in individuals of European ancestry. We investigated whether these variants were associated with measures of hepatic steatosis (HS) in non-Hispanic white (NHW), non-Hispanic black, and Mexican American (MA) participants in the US population-based National Health and Nutrition Examination Survey III, phase 2.
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The rs1142345 in TPMT Affects the Therapeutic Effect of Traditional Hypoglycemic Herbs in Prediabetes.
Evid Based Complement Alternat Med
PUBLISHED: 01-06-2013
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Therapeutic interventions in prediabetes are important in the primary prevention of type 2 diabetes (T2D) and its chronic complications. However, little is known about the pharmacogenetic effect of traditional herbs on prediabetes treatment. A total of 194 impaired glucose tolerance (IGT) subjects were treated with traditional hypoglycemic herbs (Tianqi Jiangtang) for 12 months in this study. DNA samples were genotyped for 184 mutations in 34 genes involved in drug metabolism or transportation. Multinomial logistic regression analysis indicated that rs1142345 (A > G) in the thiopurine S-methyltransferase (TPMT) gene was significantly associated with the hypoglycemic effect of the drug (P = 0.001, FDR P = 0.043). The "G" allele frequencies of rs1142345 in the healthy (subjects reverted from IGT to normal glucose tolerance), maintenance (subjects still had IGT), and deterioration (subjects progressed from IGT to T2D) groups were 0.094, 0.214, and 0.542, respectively. Binary logistic regression analysis indicated that rs1142345 was also significantly associated with the hypoglycemic effect of the drug between the healthy and maintenance groups (P = 0.027, OR = 4.828) and between the healthy and deterioration groups (P = 0.001, OR = 7.811). Therefore, rs1142345 was associated with the clinical effect of traditional hypoglycemic herbs. Results also suggested that TPMT was probably involved in the pharmacological mechanisms of T2D.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.