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Sample records for methylation analysis periodate

  1. DNA methylation analysis reveals distinct methylation signatures in pediatric germ cell tumors

    International Nuclear Information System (INIS)

    Amatruda, James F; Frazier, A Lindsay; Poynter, Jenny N; Ross, Julie A; Christensen, Brock; Fustino, Nicholas J; Chen, Kenneth S; Hooten, Anthony J; Nelson, Heather; Kuriger, Jacquelyn K; Rakheja, Dinesh

    2013-01-01

    Aberrant DNA methylation is a prominent feature of many cancers, and may be especially relevant in germ cell tumors (GCTs) due to the extensive epigenetic reprogramming that occurs in the germ line during normal development. We used the Illumina GoldenGate Cancer Methylation Panel to compare DNA methylation in the three main histologic subtypes of pediatric GCTs (germinoma, teratoma and yolk sac tumor (YST); N = 51) and used recursively partitioned mixture models (RPMM) to test associations between methylation pattern and tumor and demographic characteristics. We identified genes and pathways that were differentially methylated using generalized linear models and Ingenuity Pathway Analysis. We also measured global DNA methylation at LINE1 elements and evaluated methylation at selected imprinted loci using pyrosequencing. Methylation patterns differed by tumor histology, with 18/19 YSTs forming a distinct methylation class. Four pathways showed significant enrichment for YSTs, including a human embryonic stem cell pluripotency pathway. We identified 190 CpG loci with significant methylation differences in mature and immature teratomas (q < 0.05), including a number of CpGs in stem cell and pluripotency-related pathways. Both YST and germinoma showed significantly lower methylation at LINE1 elements compared with normal adjacent tissue while there was no difference between teratoma (mature and immature) and normal tissue. DNA methylation at imprinted loci differed significantly by tumor histology and location. Understanding methylation patterns may identify the developmental stage at which the GCT arose and the at-risk period when environmental exposures could be most harmful. Further, identification of relevant genetic pathways could lead to the development of new targets for therapy

  2. Methylation analysis of polysaccharides: Technical advice.

    Science.gov (United States)

    Sims, Ian M; Carnachan, Susan M; Bell, Tracey J; Hinkley, Simon F R

    2018-05-15

    Glycosyl linkage (methylation) analysis is used widely for the structural determination of oligo- and poly-saccharides. The procedure involves derivatisation of the individual component sugars of a polysaccharide to partially methylated alditol acetates which are analysed and quantified by gas chromatography-mass spectrometry. The linkage positions for each component sugar can be determined by correctly identifying the partially methylated alditol acetates. Although the methods are well established, there are many technical aspects to this procedure and both careful attention to detail and considerable experience are required to achieve a successful methylation analysis and to correctly interpret the data generated. The aim of this article is to provide the technical details and critical procedural steps necessary for a successful methylation analysis and to assist researchers (a) with interpreting data correctly and (b) in providing the comprehensive data required for reviewers to fully assess the work. Copyright © 2018 Elsevier Ltd. All rights reserved.

  3. Identification of endometrial cancer methylation features using combined methylation analysis methods.

    Directory of Open Access Journals (Sweden)

    Michael P Trimarchi

    Full Text Available DNA methylation is a stable epigenetic mark that is frequently altered in tumors. DNA methylation features are attractive biomarkers for disease states given the stability of DNA methylation in living cells and in biologic specimens typically available for analysis. Widespread accumulation of methylation in regulatory elements in some cancers (specifically the CpG island methylator phenotype, CIMP can play an important role in tumorigenesis. High resolution assessment of CIMP for the entire genome, however, remains cost prohibitive and requires quantities of DNA not available for many tissue samples of interest. Genome-wide scans of methylation have been undertaken for large numbers of tumors, and higher resolution analyses for a limited number of cancer specimens. Methods for analyzing such large datasets and integrating findings from different studies continue to evolve. An approach for comparison of findings from a genome-wide assessment of the methylated component of tumor DNA and more widely applied methylation scans was developed.Methylomes for 76 primary endometrial cancer and 12 normal endometrial samples were generated using methylated fragment capture and second generation sequencing, MethylCap-seq. Publically available Infinium HumanMethylation 450 data from The Cancer Genome Atlas (TCGA were compared to MethylCap-seq data.Analysis of methylation in promoter CpG islands (CGIs identified a subset of tumors with a methylator phenotype. We used a two-stage approach to develop a 13-region methylation signature associated with a "hypermethylator state." High level methylation for the 13-region methylation signatures was associated with mismatch repair deficiency, high mutation rate, and low somatic copy number alteration in the TCGA test set. In addition, the signature devised showed good agreement with previously described methylation clusters devised by TCGA.We identified a methylation signature for a "hypermethylator phenotype" in

  4. Global DNA methylation analysis using methyl-sensitive amplification polymorphism (MSAP).

    Science.gov (United States)

    Yaish, Mahmoud W; Peng, Mingsheng; Rothstein, Steven J

    2014-01-01

    DNA methylation is a crucial epigenetic process which helps control gene transcription activity in eukaryotes. Information regarding the methylation status of a regulatory sequence of a particular gene provides important knowledge of this transcriptional control. DNA methylation can be detected using several methods, including sodium bisulfite sequencing and restriction digestion using methylation-sensitive endonucleases. Methyl-Sensitive Amplification Polymorphism (MSAP) is a technique used to study the global DNA methylation status of an organism and hence to distinguish between two individuals based on the DNA methylation status determined by the differential digestion pattern. Therefore, this technique is a useful method for DNA methylation mapping and positional cloning of differentially methylated genes. In this technique, genomic DNA is first digested with a methylation-sensitive restriction enzyme such as HpaII, and then the DNA fragments are ligated to adaptors in order to facilitate their amplification. Digestion using a methylation-insensitive isoschizomer of HpaII, MspI is used in a parallel digestion reaction as a loading control in the experiment. Subsequently, these fragments are selectively amplified by fluorescently labeled primers. PCR products from different individuals are compared, and once an interesting polymorphic locus is recognized, the desired DNA fragment can be isolated from a denaturing polyacrylamide gel, sequenced and identified based on DNA sequence similarity to other sequences available in the database. We will use analysis of met1, ddm1, and atmbd9 mutants and wild-type plants treated with a cytidine analogue, 5-azaC, or zebularine to demonstrate how to assess the genetic modulation of DNA methylation in Arabidopsis. It should be noted that despite the fact that MSAP is a reliable technique used to fish for polymorphic methylated loci, its power is limited to the restriction recognition sites of the enzymes used in the genomic

  5. Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers.

    Science.gov (United States)

    Cervera, M T; Ruiz-García, L; Martínez-Zapater, J M

    2002-12-01

    AFLP analysis using restriction enzyme isoschizomers that differ in their sensitivity to methylation of their recognition sites has been used to analyse the methylation state of anonymous CCGG sequences in Arabidopsis thaliana. The technique was modified to improve the quality of fingerprints and to visualise larger numbers of scorable fragments. Sequencing of amplified fragments indicated that detection was generally associated with non-methylation of the cytosine to which the isoschizomer is sensitive. Comparison of EcoRI/ HpaII and EcoRI/ MspI patterns in different ecotypes revealed that 35-43% of CCGG sites were differentially digested by the isoschizomers. Interestingly, the pattern of digestion among different plants belonging to the same ecotype is highly conserved, with the rate of intra-ecotype methylation-sensitive polymorphisms being less than 1%. However, pairwise comparisons of methylation patterns between samples belonging to different ecotypes revealed differences in up to 34% of the methylation-sensitive polymorphisms. The lack of correlation between inter-ecotype similarity matrices based on methylation-insensitive or methylation-sensitive polymorphisms suggests that whatever the mechanisms regulating methylation may be, they are not related to nucleotide sequence variation.

  6. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    Directory of Open Access Journals (Sweden)

    Erin M Siegel

    Full Text Available Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2. A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97-1.00, p-value = 0.003. Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.

  7. Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP).

    Science.gov (United States)

    Guevara, María Ángeles; de María, Nuria; Sáez-Laguna, Enrique; Vélez, María Dolores; Cervera, María Teresa; Cabezas, José Antonio

    2017-01-01

    Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.

  8. Analysis of DNA methylation in various swine tissues.

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    Chun Yang

    Full Text Available DNA methylation is known to play an important role in regulating gene expression during biological development and tissue differentiation in eukaryotes. In this study, we used the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP method to assess the extent and pattern of cytosine methylation in muscle, heart, liver, spleen, lung, kidney and stomach from the swine strain Laiwu, and we also examined specific methylation patterns in the seven tissues. In total, 96,371 fragments, each representing a recognition site cleaved by either or both EcoRI + HpaII and EcoRI + MspI, the HpaII and MspI are isoschizomeric enzymes, were amplified using 16 pairs of selective primers. A total of 50,094 sites were found to be methylated at cytosines in seven tissues. The incidence of DNA methylation was approximately 53.99% in muscle, 51.24% in the heart, 50.18% in the liver, 53.31% in the spleen, 51.97% in the lung, 51.15% in the kidney and 53.39% in the stomach, as revealed by the incidence of differential digestion. Additionally, differences in DNA methylation levels imply that such variations may be related to specific gene expression during tissue differentiation, growth and development. Three types of bands were generated in the F-MSAP profile, the total numbers of these three types of bands in the seven tissues were 46,277, 24,801 and 25,293, respectively.In addition, different methylation patterns were observed in seven tissues from pig, and almost all of the methylation patterns detected by F-MSAP could be confirmed by Southern analysis using the isolated amplified fragments as probes. The results clearly demonstrated that the F-MSAP technique can be adapted for use in large-scale DNA methylation detection in the pig genome.

  9. Forward Period Analysis Method of the Periodic Hamiltonian System.

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    Pengfei Wang

    Full Text Available Using the forward period analysis (FPA, we obtain the period of a Morse oscillator and mathematical pendulum system, with the accuracy of 100 significant digits. From these results, the long-term [0, 1060] (time unit solutions, ranging from the Planck time to the age of the universe, are computed reliably and quickly with a parallel multiple-precision Taylor series (PMT scheme. The application of FPA to periodic systems can greatly reduce the computation time of long-term reliable simulations. This scheme provides an efficient way to generate reference solutions, against which long-term simulations using other schemes can be tested.

  10. Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles.

    Science.gov (United States)

    Aiba, Toshiki; Saito, Toshiyuki; Hayashi, Akiko; Sato, Shinji; Yunokawa, Harunobu; Maruyama, Toru; Fujibuchi, Wataru; Kurita, Hisaka; Tohyama, Chiharu; Ohsako, Seiichiroh

    2017-03-09

    It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5' end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research.

  11. Diagnostic markers of urothelial cancer based on DNA methylation analysis

    International Nuclear Information System (INIS)

    Chihara, Yoshitomo; Hirao, Yoshihiko; Kanai, Yae; Fujimoto, Hiroyuki; Sugano, Kokichi; Kawashima, Kiyotaka; Liang, Gangning; Jones, Peter A; Fujimoto, Kiyohide; Kuniyasu, Hiroki

    2013-01-01

    Early detection and risk assessment are crucial for treating urothelial cancer (UC), which is characterized by a high recurrence rate, and necessitates frequent and invasive monitoring. We aimed to establish diagnostic markers for UC based on DNA methylation. In this multi-center study, three independent sample sets were prepared. First, DNA methylation levels at CpG loci were measured in the training sets (tumor samples from 91 UC patients, corresponding normal-appearing tissue from these patients, and 12 normal tissues from age-matched bladder cancer-free patients) using the Illumina Golden Gate methylation assay to identify differentially methylated loci. Next, these methylated loci were validated by quantitative DNA methylation by pyrosequencing, using another cohort of tissue samples (Tissue validation set). Lastly, methylation of these markers was analyzed in the independent urine samples (Urine validation set). ROC analysis was performed to evaluate the diagnostic accuracy of these 12 selected markers. Of the 1303 CpG sites, 158 were hyper ethylated and 356 were hypo ethylated in tumor tissues compared to normal tissues. In the panel analysis, 12 loci showed remarkable alterations between tumor and normal samples, with 94.3% sensitivity and 97.8% specificity. Similarly, corresponding normal tissue could be distinguished from normal tissues with 76.0% sensitivity and 100% specificity. Furthermore, the diagnostic accuracy for UC of these markers determined in urine samples was high, with 100% sensitivity and 100% specificity. Based on these preliminary findings, diagnostic markers based on differential DNA methylation at specific loci can be useful for non-invasive and reliable detection of UC and epigenetic field defect

  12. Differential DNA Methylation Analysis without a Reference Genome

    Directory of Open Access Journals (Sweden)

    Johanna Klughammer

    2015-12-01

    Full Text Available Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS, which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish. Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org. The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome.

  13. Quantitative analysis of DNA methylation in chronic lymphocytic leukemia patients.

    Science.gov (United States)

    Lyko, Frank; Stach, Dirk; Brenner, Axel; Stilgenbauer, Stephan; Döhner, Hartmut; Wirtz, Michaela; Wiessler, Manfred; Schmitz, Oliver J

    2004-06-01

    Changes in the genomic DNA methylation level have been found to be closely associated with tumorigenesis. In order to analyze the relation of aberrant DNA methylation to clinical and biological risk factors, we have determined the cytosine methylation level of 81 patients diagnosed with chronic lymphocytic leukemia (CLL). The analysis was based on DNA hydrolysis followed by derivatization of the 2'-desoxyribonucleoside-3'-monophosphates with BODIPY FL EDA. Derivatives were separated by micellar electrokinetic chromatography, and laser-induced fluorescence was used for detection. We analyzed potential correlations between DNA methylation levels and numerous patient parameters, including clinical observations and biological data. As a result, we observed a significant correlation with the immunoglobulin variable heavy chain gene (VH) mutation status. This factor has been repeatedly proposed as a reliable prognostic marker for CLL, which suggests that the methylation level might be a valuable factor in determining the prognostic outcome of CLL. We are now in the process of refining our method to broaden its application potential. In this context, we show here that the oxidation of the fluorescence marker in the samples and the evaporation of methanol in the electrolytes can be prevented by a film of paraffin oil. In summary, our results thus establish capillary electrophoresis as a valuable tool for analyzing the DNA methylation status of clinical samples.

  14. Analysis of DNA methylation variation in sibling tobacco ( Nicotiana ...

    African Journals Online (AJOL)

    Amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analysis were used to investigate the genome of two sibling tobacco cultivars, Yunyan85 and Yunyan87, their parent K326 and the other tobacco cultivar NC89. AFLP analysis indicated that, the genome primary ...

  15. Cluster analysis for DNA methylation profiles having a detection threshold

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    Siegmund Kimberly D

    2006-07-01

    Full Text Available Abstract Background DNA methylation, a molecular feature used to investigate tumor heterogeneity, can be measured on many genomic regions using the MethyLight technology. Due to the combination of the underlying biology of DNA methylation and the MethyLight technology, the measurements, while being generated on a continuous scale, have a large number of 0 values. This suggests that conventional clustering methodology may not perform well on this data. Results We compare performance of existing methodology (such as k-means with two novel methods that explicitly allow for the preponderance of values at 0. We also consider how the ability to successfully cluster such data depends upon the number of informative genes for which methylation is measured and the correlation structure of the methylation values for those genes. We show that when data is collected for a sufficient number of genes, our models do improve clustering performance compared to methods, such as k-means, that do not explicitly respect the supposed biological realities of the situation. Conclusion The performance of analysis methods depends upon how well the assumptions of those methods reflect the properties of the data being analyzed. Differing technologies will lead to data with differing properties, and should therefore be analyzed differently. Consequently, it is prudent to give thought to what the properties of the data are likely to be, and which analysis method might therefore be likely to best capture those properties.

  16. Periodic nanostructures formed on a poly-methyl methacrylate surface with a femtosecond laser for biocompatibility improvement

    Science.gov (United States)

    Takenaka, Keisuke; Tsukamoto, Masahiro; Sato, Yuji; Ooga, Takahiro; Asai, Satoru; Murai, Kensuke

    2018-06-01

    Poly(methyl methacrylate) (PMMA) is widely used as a biomaterial. The formation of periodic nanostructures on the surface is necessary to improve the biocompatibility. A method was proposed and developed to form periodic nanostructures on a PMMA surface. A PMMA plate was placed on titanium (Ti) plate, and then the Ti plate was irradiated with a laser through the PMMA plate. We try to effectively produce periodic nanostructures on PMMA with a femtosecond laser at a fundamental wavelength by increasing the contact pressure and using titanium (Ti) plate. The contact pressure between PMMA and Ti required to form a periodic nanostructure is 300 kPa, and for a contact pressure of 2400 kPa, periodic nanostructures are formed in 62% of the laser-irradiated area on the PMMA surface. These results suggest that the formation efficiency of the periodic nanostructure depends on the laser conditions and the contact pressure.

  17. Genome-Wide Analysis of DNA Methylation During Ovule Development of Female-Sterile Rice fsv1

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    Helian Liu

    2017-11-01

    Full Text Available The regulation of female fertility is an important field of rice sexual reproduction research. DNA methylation is an essential epigenetic modification that dynamically regulates gene expression during development processes. However, few reports have described the methylation profiles of female-sterile rice during ovule development. In this study, ovules were continuously acquired from the beginning of megaspore mother cell meiosis until the mature female gametophyte formation period, and global DNA methylation patterns were compared in the ovules of a high-frequency female-sterile line (fsv1 and a wild-type rice line (Gui99 using whole-genome bisulfite sequencing (WGBS. Profiling of the global DNA methylation revealed hypo-methylation, and 3471 significantly differentially methylated regions (DMRs were observed in fsv1 ovules compared with Gui99. Based on functional annotation and Kyoto encyclopedia of genes and genomes (KEGG pathway analysis of differentially methylated genes (DMGs, we observed more DMGs enriched in cellular component, reproduction regulation, metabolic pathway, and other pathways. In particular, many ovule development genes and plant hormone-related genes showed significantly different methylation patterns in the two rice lines, and these differences may provide important clues for revealing the mechanism of female gametophyte abortion.

  18. Energetics and Vibrational Analysis of Methyl Salicylate Isomers

    Science.gov (United States)

    Massaro, Richard D.; Dai, Yafei; Blaisten-Barojas, Estela

    2009-08-01

    Energetics and vibrational analysis study of six isomers of methyl salicylate in their singlet ground state and first excited triple state is put forward in this work at the density functional theory level and large basis sets. The ketoB isomer is the lowest energy isomer, followed by its rotamer ketoA. For both ketoB and ketoA their enolized tautomers are found to be stable as well as their open forms that lack the internal hydrogen bond. The calculated vibrational spectra are in excellent agreement with IR experiments of methyl salicylate in the vapor phase. It is demonstrated that solvent effects have a weak influence on the stability of these isomers. The ionization reaction from ketoB to ketoA shows a high barrier of 0.67 eV ensuring that thermal and chemical equilibria yield systems containing mostly the ketoB isomer at normal conditions.

  19. Methylation-sensitive amplified polymorphism-based genome-wide analysis of cytosine methylation profiles in Nicotiana tabacum cultivars.

    Science.gov (United States)

    Jiao, J; Wu, J; Lv, Z; Sun, C; Gao, L; Yan, X; Cui, L; Tang, Z; Yan, B; Jia, Y

    2015-11-26

    This study aimed to investigate cytosine methylation profiles in different tobacco (Nicotiana tabacum) cultivars grown in China. Methylation-sensitive amplified polymorphism was used to analyze genome-wide global methylation profiles in four tobacco cultivars (Yunyan 85, NC89, K326, and Yunyan 87). Amplicons with methylated C motifs were cloned by reamplified polymerase chain reaction, sequenced, and analyzed. The results show that geographical location had a greater effect on methylation patterns in the tobacco genome than did sampling time. Analysis of the CG dinucleotide distribution in methylation-sensitive polymorphic restriction fragments suggested that a CpG dinucleotide cluster-enriched area is a possible site of cytosine methylation in the tobacco genome. The sequence alignments of the Nia1 gene (that encodes nitrate reductase) in Yunyan 87 in different regions indicate that a C-T transition might be responsible for the tobacco phenotype. T-C nucleotide replacement might also be responsible for the tobacco phenotype and may be influenced by geographical location.

  20. Analysis of DNA methylation of maize in response to osmotic and salt stress based on methylation-sensitive amplified polymorphism.

    Science.gov (United States)

    Tan, Ming-pu

    2010-01-01

    Water stress is known to alter cytosine methylation, which generally represses transcription. However, little is known about the role of methylation alteration in maize under osmotic stress. Here, methylation-sensitive amplified polymorphism (MSAP) was used to screen PEG- or NaCl-induced methylation alteration in maize seedlings. The sequences of 25 differentially amplified fragments relevant to stress were successfully obtained. Two stress-specific fragments from leaves, LP166 and LPS911, shown to be homologous to retrotransposon Gag-Pol protein genes, suggested that osmotic stress-induced methylation of retrotransposons. Three MSAP fragments, representing drought-induced or salt-induced methylation in leaves, were homologous to a maize aluminum-induced transporter. Besides these, heat shock protein HSP82, Poly [ADP-ribose] polymerase 2, Lipoxygenase, casein kinase (CK2), and dehydration-responsive element-binding (DREB) factor were also homologs of MSAP sequences from salt-treated roots. One MSAP fragment amplified from salt-treated roots, designated RS39, was homologous to the first intron of maize protein phosphatase 2C (zmPP2C), whereas - LS103, absent from salt-treated leaves, was homologous to maize glutathione S-transferases (zmGST). Expression analysis showed that salt-induced intron methylation of root zmPP2C significantly downregulated its expression, while salt-induced demethylation of leaf zmGST weakly upregulated its expression. The results suggested that salinity-induced methylation downregulated zmPP2C expression, a negative regulator of the stress response, while salinity-induced demethylation upregulated zmGST expression, a positive effecter of the stress response. Altered methylation, in response to stress, might also be involved in stress acclimation. Copyright 2009 Elsevier Masson SAS. All rights reserved.

  1. Analysis of DNA methylation of perennial ryegrass under drought using the methylation-sensitive amplification polymorphism (MSAP) technique.

    Science.gov (United States)

    Tang, Xiao-Mei; Tao, Xiang; Wang, Yan; Ma, Dong-Wei; Li, Dan; Yang, Hong; Ma, Xin-Rong

    2014-12-01

    Perennial ryegrass (Lolium perenne), an excellent grass for forage and turf, is widespread in temperate regions. Drought is an important factor that limits its growth, distribution, and yield. DNA methylation affects gene expression and plays an important role in adaptation to adverse environments. In this study, the DNA methylation changes in perennial ryegrass under drought stress were assessed using methylation-sensitive amplified polymorphism (MSAP). After 15 days of drought stress treatment, the plant height was less than half of the control, and the leaves were smaller and darker. Genome-wide, a total of 652 CCGG sites were detected by MSAP. The total methylation level was 57.67 and 47.39 % in the control and drought treatment, respectively, indicating a decrease of 10.28 % due to drought exposure. Fifteen differentially displayed DNA fragments in MSAP profiles were cloned for sequencing analysis. The results showed that most of the genes involved in stress responses. The relative expression levels revealed that three demethylated fragments were up-regulated. The expression of a predicted retrotransposon increased significantly, changing from hypermethylation to non-methylation. Although the extent of methylation in two other genes decreased, the sites of methylation remained, and the expression increased only slightly. All of these results suggested that drought stress decreased the total DNA methylation level in perennial ryegrass and demethylation up-regulated related gene expressions and that the extent of methylation was negatively correlated with expression. Overall, the induced epigenetic changes in genome probably are an important regulatory mechanism for acclimating perennial ryegrass to drought and possibly other environmental stresses.

  2. Methyl Cation Affinities of Neutral and Anionic Maingroup-Element Hydrides: Trends Across the Periodic Table and Correlation with Proton Affinities

    NARCIS (Netherlands)

    Mulder, R. Joshua; Guerra, Celia Fonseca; Bickelhaupt, F. Matthias

    2010-01-01

    We have computed the methyl cation affinities in the gas phase of archetypal anionic and neutral bases across the periodic table using ZORA-relativistic density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. The main purpose of this work is to provide the methyl cation affinities (and

  3. Kernel machine methods for integrative analysis of genome-wide methylation and genotyping studies.

    Science.gov (United States)

    Zhao, Ni; Zhan, Xiang; Huang, Yen-Tsung; Almli, Lynn M; Smith, Alicia; Epstein, Michael P; Conneely, Karen; Wu, Michael C

    2018-03-01

    Many large GWAS consortia are expanding to simultaneously examine the joint role of DNA methylation in addition to genotype in the same subjects. However, integrating information from both data types is challenging. In this paper, we propose a composite kernel machine regression model to test the joint epigenetic and genetic effect. Our approach works at the gene level, which allows for a common unit of analysis across different data types. The model compares the pairwise similarities in the phenotype to the pairwise similarities in the genotype and methylation values; and high correspondence is suggestive of association. A composite kernel is constructed to measure the similarities in the genotype and methylation values between pairs of samples. We demonstrate through simulations and real data applications that the proposed approach can correctly control type I error, and is more robust and powerful than using only the genotype or methylation data in detecting trait-associated genes. We applied our method to investigate the genetic and epigenetic regulation of gene expression in response to stressful life events using data that are collected from the Grady Trauma Project. Within the kernel machine testing framework, our methods allow for heterogeneity in effect sizes, nonlinear, and interactive effects, as well as rapid P-value computation. © 2017 WILEY PERIODICALS, INC.

  4. Diel Periodicity of 3-Methyl-2-Butenyl Butyrate Emissions by Bronze Bug Males Is Suppressed in the Presence of Females.

    Science.gov (United States)

    Groba, H F; Martínez, G; Rossini, C; González, A

    2018-02-07

    The bronze bug, Thaumastocoris peregrinus Carpintero & Dellapé (Heteroptera: Thaumastocoridae), is an exotic emerging pest in Eucalyptus commercial forests in South America, Africa, and southern Europe. Information on the chemical communication system and reproductive ecology of this insect is scant, and it may be relevant for designing management strategies for eucalypt plantations. Males emit large amounts of 3-methyl-2-butenyl butyrate, which attracts conspecific adult males but not females. To learn more about the biological function of this putative male-produced pheromone, we quantified this compound in volatile emissions collected from males, females, and couples, in three 4-h collecting periods during the morning, afternoon, and night of a single 24-h cycle. Our results showed that virgin males emit 3-methyl-2-butenyl butyrate in a diel time pattern, with an almost sevenfold difference between the afternoon emission peak compared to morning or night hours. In addition, we show that in the presence of females, males emit the compound in the same amounts throughout the photocycle. While a definite function cannot yet be attributed to the emission of 3-methyl-2-butenyl butyrate by T. peregrinus males, our findings point to an intraspecific function, possibly one related to male-male competition.

  5. Rapid analysis of heterogeneously methylated DNA using digital methylation-sensitive high resolution melting: application to the CDKN2B (p15) gene

    DEFF Research Database (Denmark)

    Candiloro, Ida Lm; Mikeska, Thomas; Hokland, Peter

    2008-01-01

    ABSTRACT: BACKGROUND: Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (dMS-HRM) t......ABSTRACT: BACKGROUND: Methylation-sensitive high resolution melting (MS-HRM) methodology is able to recognise heterogeneously methylated sequences by their characteristic melting profiles. To further analyse heterogeneously methylated sequences, we adopted a digital approach to MS-HRM (d......MS-HRM) that involves the amplification of single templates after limiting dilution to quantify and to determine the degree of methylation. We used this approach to study methylation of the CDKN2B (p15) cell cycle progression inhibitor gene which is inactivated by DNA methylation in haematological malignancies...... the methylated alleles and assess the degree of methylation. Direct sequencing of selected dMS-HRM products was used to determine the exact DNA methylation pattern and confirmed the degree of methylation estimated by dMS-HRM. CONCLUSION: dMS-HRM is a powerful technique for the analysis of methylation in CDKN2B...

  6. Genome-wide methylation analysis identified sexually dimorphic methylated regions in hybrid tilapia

    Science.gov (United States)

    Wan, Zi Yi; Xia, Jun Hong; Lin, Grace; Wang, Le; Lin, Valerie C. L.; Yue, Gen Hua

    2016-01-01

    Sexual dimorphism is an interesting biological phenomenon. Previous studies showed that DNA methylation might play a role in sexual dimorphism. However, the overall picture of the genome-wide methylation landscape in sexually dimorphic species remains unclear. We analyzed the DNA methylation landscape and transcriptome in hybrid tilapia (Oreochromis spp.) using whole genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). We found 4,757 sexually dimorphic differentially methylated regions (DMRs), with significant clusters of DMRs located on chromosomal regions associated with sex determination. CpG methylation in promoter regions was negatively correlated with the gene expression level. MAPK/ERK pathway was upregulated in male tilapia. We also inferred active cis-regulatory regions (ACRs) in skeletal muscle tissues from WGBS datasets, revealing sexually dimorphic cis-regulatory regions. These results suggest that DNA methylation contribute to sex-specific phenotypes and serve as resources for further investigation to analyze the functions of these regions and their contributions towards sexual dimorphisms. PMID:27782217

  7. Excess of methyl donor in the perinatal period reduces postnatal leptin secretion in rat and interacts with the effect of protein content in diet.

    Directory of Open Access Journals (Sweden)

    Fanny Giudicelli

    Full Text Available Methionine, folic acid, betaine and choline interact in the one-carbon metabolism which provides methyl groups for methylation reactions. An optimal intake of these nutrients during pregnancy is required for successful completion of fetal development and evidence is growing that they could be involved in metabolic long-term programming. However, the biological pathways involved in the action of these nutrients are still poorly known. This study investigated the interaction between methyl donors and protein content in maternal diet during the preconceptual, pregnancy and lactation periods and the consequences on the rat offspring in the short and long term. Methyl donor supplementation reduced leptin secretion in offspring, whereas insulin levels were mostly affected by protein restriction. The joint effect of protein restriction and methyl donor excess strongly impaired postnatal growth in both gender and long term weight gain in male offspring only, without affecting food intake. In addition, rats born from protein restricted and methyl donor supplemented dams gained less weight when fed a hypercaloric diet. Methylation of the leptin gene promoter in adipose tissue was increased in methyl donor supplemented groups but not affected by protein restriction only. These results suggest that maternal methyl donor supplementation may influence energy homeostasis in a gender-dependent manner, without affecting food intake. Moreover, we showed that macronutrients and micronutrients in maternal diet interact to influence the programming of the offspring.

  8. Analysis of DNA methylation related to rice adult plant resistance to bacterial blight based on methylation-sensitive AFLP (MSAP) analysis.

    Science.gov (United States)

    Sha, A H; Lin, X H; Huang, J B; Zhang, D P

    2005-07-01

    DNA methylation is known to play an important role in the regulation of gene expression in eukaryotes. The rice cultivar Wase Aikoku 3 becomes resistant to the blight pathogen Xanthomonas oryzae pv. oryzae at the adult stage. Using methylation-sensitive amplified polymorphism (MSAP) analysis, we compared the patterns of cytosine methylation in seedlings and adult plants of the rice cultivar Wase Aikoku 3 that had been inoculated with the pathogen Xanthomonas oryzae pv. oryzae, subjected to mock inoculation or left untreated. In all, 2000 DNA fragments, each representing a recognition site cleaved by either or both of two isoschizomers, were amplified using 60 pairs of selective primers. A total of 380 sites were found to be methylated. Of these, 45 showed differential cytosine methylation among the seedlings and adult plants subjected to different treatments, and overall levels of methylation were higher in adult plants than in seedlings. All polymorphic fragments were sequenced, and six showed homology to genes that code for products of known function. Northern analysis of three fragments indicated that their expression varied with methylation pattern, with hypermethylation being correlated with repression of transcription, as expected. The results suggest that significant differences in cytosine methylation exist between seedlings and adult plants, and that hypermethylation or hypomethylation of specific genes may be involved in the development of adult plant resistance (APR) in rice plants.

  9. Comprehensive analysis of preeclampsia-associated DNA methylation in the placenta.

    Directory of Open Access Journals (Sweden)

    Tianjiao Chu

    Full Text Available A small number of recent reports have suggested that altered placental DNA methylation may be associated with early onset preeclampsia. It is important that further studies be undertaken to confirm and develop these findings. We therefore undertook a systematic analysis of DNA methylation patterns in placental tissue from 24 women with preeclampsia and 24 with uncomplicated pregnancy outcome.We analyzed the DNA methylation status of approximately 27,000 CpG sites in placental tissues in a massively parallel fashion using an oligonucleotide microarray. Follow up analysis of DNA methylation at specific CpG loci was performed using the Epityper MassArray approach and high-throughput bisulfite sequencing.Preeclampsia-specific DNA methylation changes were identified in placental tissue samples irrespective of gestational age of delivery. In addition, we identified a group of CpG sites within specific gene sequences that were only altered in early onset-preeclampsia (EOPET although these DNA methylation changes did not correlate with altered mRNA transcription. We found evidence that fetal gender influences DNA methylation at autosomal loci but could find no clear association between DNA methylation and gestational age.Preeclampsia is associated with altered placental DNA methylation. Fetal gender should be carefully considered during the design of future studies in which placental DNA is analyzed at the level of DNA methylation. Further large-scale analyses of preeclampsia-associated DNA methylation are necessary.

  10. The analysis of methyl salicylate and salicylic acid from Chinese herbal medicine ingestion.

    Science.gov (United States)

    Parker, Dawn; Martinez, Christina; Stanley, Christina; Simmons, Jerry; McIntyre, Iain M

    2004-04-01

    This paper presents a multi-drug fatality in which methyl salicylate was ingested. It is presented to inform the toxicological community that a particularly expeditious method of detection for methyl salicylate exists. Previously published methods for the analysis of methyl salicylate include a gas chromatographic-mass spectrometric method and an alkaline/acidic extraction followed by high-performance liquid chromatographic (HPLC) analysis. This article describes a method for analyzing methyl salicylate using HPLC, in which a simple, rapid extraction procedure is used. Using a previously published HPLC method, methyl salicylate and salicylic acid were easily identified in biological specimens. Methyl salicylate and salicylic acid were detected using an extraction solution of acetonitrile coupled with internal standard and then analyzed by HPLC-diode-array detection. Because of its concentrated liquid form, methyl salicylate ingestion can cause rapid onset salicylate toxicity. As the potentially fatal methyl salicylate forms are readily available and easily found on drugstore shelves, the need to rapidly detect and quantitate salicylic acid concentrations that are due to methyl salicylate ingestion may arise. In the case presented, the peripheral blood concentration of salicylic acid from methyl salicylate ingestion was 320 mg/L, and the concentration in gastric contents was 820 mg. It alone was not the cause of death, however. The discovery of the ability to detect and quantitate methyl salicylate was due to its suspected ingestion.

  11. Methylated DNA Immunoprecipitation Analysis of Mammalian Endogenous Retroviruses.

    Science.gov (United States)

    Rebollo, Rita; Mager, Dixie L

    2016-01-01

    Endogenous retroviruses are repetitive sequences found abundantly in mammalian genomes which are capable of modulating host gene expression. Nevertheless, most endogenous retrovirus copies are under tight epigenetic control via histone-repressive modifications and DNA methylation. Here we describe a common method used in our laboratory to detect, quantify, and compare mammalian endogenous retrovirus DNA methylation. More specifically we describe methylated DNA immunoprecipitation (MeDIP) followed by quantitative PCR.

  12. DNA methylation and genetic diversity analysis of genus Cycas in ...

    African Journals Online (AJOL)

    10 Cycas species as well as one subspecies localized in Thailand were studied using the methylation sensitive amplification polymorphism (MSAP) technique. 11 MSAP primer combinations were used and 720 MSAP bands were generated. The percentages of DNA methylation estimated from MSAP fingerprints were in ...

  13. A relative quantitative Methylation-Sensitive Amplified Polymorphism (MSAP) method for the analysis of abiotic stress

    OpenAIRE

    Bednarek, Piotr T.; Or?owska, Renata; Niedziela, Agnieszka

    2017-01-01

    Background We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied the technique to analyze aluminum (Al)-tolerant and non-tolerant control and Al-stressed inbred triticale lines. The approach is based on detailed analysis of events affecting H...

  14. High-resolution analysis of cytosine methylation in ancient DNA.

    Directory of Open Access Journals (Sweden)

    Bastien Llamas

    Full Text Available Epigenetic changes to gene expression can result in heritable phenotypic characteristics that are not encoded in the DNA itself, but rather by biochemical modifications to the DNA or associated chromatin proteins. Interposed between genes and environment, these epigenetic modifications can be influenced by environmental factors to affect phenotype for multiple generations. This raises the possibility that epigenetic states provide a substrate for natural selection, with the potential to participate in the rapid adaptation of species to changes in environment. Any direct test of this hypothesis would require the ability to measure epigenetic states over evolutionary timescales. Here we describe the first single-base resolution of cytosine methylation patterns in an ancient mammalian genome, by bisulphite allelic sequencing of loci from late Pleistocene Bison priscus remains. Retrotransposons and the differentially methylated regions of imprinted loci displayed methylation patterns identical to those derived from fresh bovine tissue, indicating that methylation patterns are preserved in the ancient DNA. Our findings establish the biochemical stability of methylated cytosines over extensive time frames, and provide the first direct evidence that cytosine methylation patterns are retained in DNA from ancient specimens. The ability to resolve cytosine methylation in ancient DNA provides a powerful means to study the role of epigenetics in evolution.

  15. Functional analysis of a tomato salicylic acid methyl transferase and its role in synthesis of the flavor volatile methyl salicylate.

    Science.gov (United States)

    Tieman, Denise; Zeigler, Michelle; Schmelz, Eric; Taylor, Mark G; Rushing, Sarah; Jones, Jeffrey B; Klee, Harry J

    2010-04-01

    Methyl salicylate (MeSA) is a volatile plant secondary metabolite that is an important contributor to taste and scent of many fruits and flowers. It is synthesized from salicylic acid (SA), a phytohormone that contributes to plant pathogen defense. MeSA is synthesized by members of a family of O-methyltransferases. In order to elaborate the mechanism of MeSA synthesis in tomato, we screened a set of O-methyltransferases for activity against multiple substrates. An enzyme that specifically catalyzes methylation of SA, SlSAMT, as well as enzymes that act upon jasmonic acid and indole-3-acetic acid were identified. Analyses of transgenic over- and under-producing lines validated the function of SlSAMT in vivo. The SlSAMT gene was mapped to a position near the bottom of chromosome 9. Analysis of MeSA emissions from an introgression population derived from a cross with Solanum pennellii revealed a quantitative trait locus (QTL) linked to higher fruit methyl salicylate emissions. The higher MeSA emissions associate with significantly higher SpSAMT expression, consistent with SAMT gene expression being rate limiting for ripening-associated MeSA emissions. Transgenic plants that constitutively over-produce MeSA exhibited only slightly delayed symptom development following infection with the disease-causing bacterial pathogen, Xanthomonas campestris pv. vesicatoria (Xcv). Unexpectedly, pathogen-challenged leaves accumulated significantly higher levels of SA as well as glycosylated forms of SA and MeSA, indicating a disruption in control of the SA-related metabolite pool. Taken together, the results indicate that SlSAMT is critical for methyl salicylate synthesis and methyl salicylate, in turn, likely has an important role in controlling SA synthesis.

  16. Methylation-sensitive amplified polymorphism analysis of Verticillium wilt-stressed cotton (Gossypium).

    Science.gov (United States)

    Wang, W; Zhang, M; Chen, H D; Cai, X X; Xu, M L; Lei, K Y; Niu, J H; Deng, L; Liu, J; Ge, Z J; Yu, S X; Wang, B H

    2016-10-06

    In this study, a methylation-sensitive amplification polymorphism analysis system was used to analyze DNA methylation level in three cotton accessions. Two disease-sensitive near-isogenic lines, PD94042 and IL41, and one disease-resistant Gossypium mustelinum accession were exposed to Verticillium wilt, to investigate molecular disease resistance mechanisms in cotton. We observed multiple different DNA methylation types across the three accessions following Verticillium wilt exposure. These included hypomethylation, hypermethylation, and other patterns. In general, the global DNA methylation level was significantly increased in the disease-resistant accession G. mustelinum following disease exposure. In contrast, there was no significant difference in the disease-sensitive accession PD94042, and a significant decrease was observed in IL41. Our results suggest that disease-resistant cotton might employ a mechanism to increase methylation level in response to disease stress. The differing methylation patterns, together with the increase in global DNA methylation level, might play important roles in tolerance to Verticillium wilt in cotton. Through cloning and analysis of differently methylated DNA sequences, we were also able to identify several genes that may contribute to disease resistance in cotton. Our results revealed the effect of DNA methylation on cotton disease resistance, and also identified genes that played important roles, which may shed light on the future cotton disease-resistant molecular breeding.

  17. Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype.

    Science.gov (United States)

    Moarii, Matahi; Reyal, Fabien; Vert, Jean-Philippe

    2015-10-13

    The CpG island methylator phenotype (CIMP) was first characterized in colorectal cancer but since has been extensively studied in several other tumor types such as breast, bladder, lung, and gastric. CIMP is of clinical importance as it has been reported to be associated with prognosis or response to treatment. However, the identification of a universal molecular basis to define CIMP across tumors has remained elusive. We perform a genome-wide methylation analysis of over 2000 tumor samples from 5 cancer sites to assess the existence of a CIMP with common molecular basis across cancers. We then show that the CIMP phenotype is associated with specific gene expression variations. However, we do not find a common genetic signature in all tissues associated with CIMP. Our results suggest the existence of a universal epigenetic and transcriptomic signature that defines the CIMP across several tumor types but does not indicate the existence of a common genetic signature of CIMP.

  18. Genome-wide DNA methylation patterns and transcription analysis in sheep muscle.

    Directory of Open Access Journals (Sweden)

    Christine Couldrey

    Full Text Available DNA methylation plays a central role in regulating many aspects of growth and development in mammals through regulating gene expression. The development of next generation sequencing technologies have paved the way for genome-wide, high resolution analysis of DNA methylation landscapes using methodology known as reduced representation bisulfite sequencing (RRBS. While RRBS has proven to be effective in understanding DNA methylation landscapes in humans, mice, and rats, to date, few studies have utilised this powerful method for investigating DNA methylation in agricultural animals. Here we describe the utilisation of RRBS to investigate DNA methylation in sheep Longissimus dorsi muscles. RRBS analysis of ∼1% of the genome from Longissimus dorsi muscles provided data of suitably high precision and accuracy for DNA methylation analysis, at all levels of resolution from genome-wide to individual nucleotides. Combining RRBS data with mRNAseq data allowed the sheep Longissimus dorsi muscle methylome to be compared with methylomes from other species. While some species differences were identified, many similarities were observed between DNA methylation patterns in sheep and other more commonly studied species. The RRBS data presented here highlights the complexity of epigenetic regulation of genes. However, the similarities observed across species are promising, in that knowledge gained from epigenetic studies in human and mice may be applied, with caution, to agricultural species. The ability to accurately measure DNA methylation in agricultural animals will contribute an additional layer of information to the genetic analyses currently being used to maximise production gains in these species.

  19. Synthesis and Analysis of Methacryloyl-L-Alanine Methyl Ester using fourier Transform Nuclear Magnetic Resonance

    International Nuclear Information System (INIS)

    Tri Darwinto

    2008-01-01

    Methacryloyl-L-alanine methyl ester was synthesized by reacting methacrylic acid with L-alanine methyl ester hydrochloride in triethylamine at temperature of 90 o C. Hydrogel polymer of poly(methacryloyl-L-alanine methyl ester) was much used for diagnosis and therapy of vascular tumor. The molecular structure methacryloyl-L-alanine methyl ester analyzed by fourier transform nuclear magnetic resonance (FT-NMR) for analyzing of carbon atom ( 13 C) using Distortionless Enhancement by Polarization Transfer (DEPT) measurement mode with coupling as well as without coupling from proton atom ( 1 H). Molecular structure analysis result showed that DEPT FT-NMR measurement mode with coupling as well as without coupling from 1 H was very fast, exact and accurate method for molecular analysis of organic compound especially methacryloyl-L-alanine methyl ester. (author)

  20. [Comparative analysis of methylation profiles in tissues of oral leukoplakia and oral squamous cell carcinoma].

    Science.gov (United States)

    Fu, J; Su, Y; Liu, Y; Zhang, X Y

    2018-04-09

    Objective: To compare the methylation profiles in tissues of oral leukoplakia (OLK) and oral squamous cell carcinoma (OSCC) with healthy tissues of oral mucosa, in order to identify the role of DNA methylation played in tumorigenesis. Methods: DNA samples extracted from tissues of 4 healthy oral mucosa, 4 OSCC and 4 OLK collected from patients of the Department of Oral Medicine, Capital Medical University School of Stomatology were examined and compared using Methylation 450 Bead Chip. The genes associated with differentially methylated CpG sites were selected for gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment. Results: Multiple differentially methylated CpG sites were identified by using the above mentioned assay. Hypermethylation constitutes 86.18% (23 290/27 025) of methylation changes in OLK and hypomethylation accounts for 13.82% (3 734/27 025) of methylation changes. Both hypermethylated and hypomethylated CpG sites were markedly increased in OSCC tissue compared with OLK tissue. The majority of differentially methylated CpG sites were located outside CpG islands, with approximately one-fourth in CpG shores flanking the islands, which were considered highly important for gene regulation and tumorigenesis. Pathway analysis revealed that differentially methylated CpG sites in both OLK and OSCC patients shared the same pathway enrichments, most of which were correlated with carcinogenesis and cancer progression (e.g., DNA repair, cell cycle, and apoptosis). Conclusions: In the present study, methylation-associated alterations affect almost all pathways in the cellular network in both OLK and OSCC. OLK and OSCC shared similar methylation changes whether in pathways or genes, indicating that epigenetically they might have the same molecular basis for disease progression.

  1. Analysis of RET promoter CpG island methylation using methylation-specific PCR (MSP), pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM): impact on stage II colon cancer patient outcome.

    Science.gov (United States)

    Draht, Muriel X G; Smits, Kim M; Jooste, Valérie; Tournier, Benjamin; Vervoort, Martijn; Ramaekers, Chantal; Chapusot, Caroline; Weijenberg, Matty P; van Engeland, Manon; Melotte, Veerle

    2016-01-01

    Already since the 1990s, promoter CpG island methylation markers have been considered promising diagnostic, prognostic, and predictive cancer biomarkers. However, so far, only a limited number of DNA methylation markers have been introduced into clinical practice. One reason why the vast majority of methylation markers do not translate into clinical applications is lack of independent validation of methylation markers, often caused by differences in methylation analysis techniques. We recently described RET promoter CpG island methylation as a potential prognostic marker in stage II colorectal cancer (CRC) patients of two independent series. In the current study, we analyzed the RET promoter CpG island methylation of 241 stage II colon cancer patients by direct methylation-specific PCR (MSP), nested-MSP, pyrosequencing, and methylation-sensitive high-resolution melting (MS-HRM). All primers were designed as close as possible to the same genomic region. In order to investigate the effect of different DNA methylation assays on patient outcome, we assessed the clinical sensitivity and specificity as well as the association of RET methylation with overall survival for three and five years of follow-up. Using direct-MSP and nested-MSP, 12.0 % (25/209) and 29.6 % (71/240) of the patients showed RET promoter CpG island methylation. Methylation frequencies detected by pyrosequencing were related to the threshold for positivity that defined RET methylation. Methylation frequencies obtained by pyrosequencing (threshold for positivity at 20 %) and MS-HRM were 13.3 % (32/240) and 13.8 % (33/239), respectively. The pyrosequencing threshold for positivity of 20 % showed the best correlation with MS-HRM and direct-MSP results. Nested-MSP detected RET promoter CpG island methylation in deceased patients with a higher sensitivity (33.1 %) compared to direct-MSP (10.7 %), pyrosequencing (14.4 %), and MS-HRM (15.4 %). While RET methylation frequencies detected by nested

  2. CpG island methylator phenotype (CIMP) of colorectal cancer is best characterised by quantitative DNA methylation analysis and prospective cohort studies.

    Science.gov (United States)

    Ogino, S; Cantor, M; Kawasaki, T; Brahmandam, M; Kirkner, G J; Weisenberger, D J; Campan, M; Laird, P W; Loda, M; Fuchs, C S

    2006-07-01

    The concept of CpG island methylator phenotype (CIMP) is not universally accepted. Even if specific clinicopathological features have been associated with CIMP, investigators often failed to demonstrate a bimodal distribution of the number of methylated markers, which would suggest CIMP as a distinct subtype of colorectal cancer. Previous studies primarily used methylation specific polymerase chain reaction which might detect biologically insignificant low levels of methylation. To demonstrate a distinct genetic profile of CIMP colorectal cancer using quantitative DNA methylation analysis that can distinguish high from low levels of DNA methylation. We developed quantitative real time polymerase chain reaction (MethyLight) assays and measured DNA methylation (percentage of methylated reference) of five carefully selected loci (promoters of CACNA1G, CDKN2A (p16), CRABP1, MLH1, and NEUROG1) in 460 colorectal cancers from large prospective cohorts. There was a clear bimodal distribution of 80 microsatellite instability-high (MSI-H) tumours according to the number of methylated promoters, with no tumours showing 3/5 methylated loci. Thus we defined CIMP as having >or=4/5 methylated loci, and 17% (78) of the 460 tumours were classified as CIMP. CIMP was significantly associated with female sex, MSI, BRAF mutations, and wild-type KRAS. Both CIMP MSI-H tumours and CIMP microsatellite stable (MSS) tumours showed much higher frequencies of BRAF mutations (63% and 54%) than non-CIMP counterparts (non-CIMP MSI-H (0%, pCIMP MSS tumours (6.6%, pCIMP is best characterised by quantitative DNA methylation analysis. CIMP is a distinct epigenotype of colorectal cancer and may be less frequent than previously reported.

  3. A relative quantitative Methylation-Sensitive Amplified Polymorphism (MSAP) method for the analysis of abiotic stress.

    Science.gov (United States)

    Bednarek, Piotr T; Orłowska, Renata; Niedziela, Agnieszka

    2017-04-21

    We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied the technique to analyze aluminum (Al)-tolerant and non-tolerant control and Al-stressed inbred triticale lines. The approach is based on detailed analysis of events affecting HpaII and MspI restriction sites in control and stressed samples, and takes advantage of molecular marker profiles generated by EcoRI/HpaII and EcoRI/MspI MSAP platforms. Five Al-tolerant and five non-tolerant triticale lines were exposed to aluminum stress using the physiologicaltest. Total genomic DNA was isolated from root tips of all tolerant and non-tolerant lines before and after Al stress following metAFLP and MSAP approaches. Based on codes reflecting events affecting cytosines within a given restriction site recognized by HpaII and MspI in control and stressed samples demethylation (DM), de novo methylation (DNM), preservation of methylated sites (MSP), and preservation of nonmethylatedsites (NMSP) were evaluated. MSAP profiles were used for Agglomerative hierarchicalclustering (AHC) based on Squared Euclidean distance and Ward's Agglomeration method whereas MSAP characteristics for ANOVA. Relative quantitative MSAP analysis revealed that both Al-tolerant and non-tolerant triticale lines subjected to Al stress underwent demethylation, with demethylation of CG predominating over CHG. The rate of de novo methylation in the CG context was ~3-fold lower than demethylation, whereas de novo methylation of CHG was observed only in Al-tolerant lines. Our relative quantitative MSAP approach, based on methylation events affecting cytosines within HpaII-MspI recognition sequences, was capable of quantifying de novo methylation, demethylation, methylation, and non-methylated status in control

  4. DNA methylation analysis from saliva samples for epidemiological studies.

    Science.gov (United States)

    Nishitani, Shota; Parets, Sasha E; Haas, Brian W; Smith, Alicia K

    2018-06-18

    Saliva is a non-invasive, easily accessible tissue, which is regularly collected in large epidemiological studies to examine genetic questions. Recently, it is becoming more common to use saliva to assess DNA methylation. However, DNA extracted from saliva is a mixture of both bacterial and human DNA derived from epithelial and immune cells in the mouth. Thus, there are unique challenges to using salivary DNA in methylation studies that can influence data quality. This study assesses: (1) quantification of human DNA after extraction; (2) delineation of human and bacterial DNA; (3) bisulfite conversion (BSC); (4) quantification of BSC DNA; (5) PCR amplification of BSC DNA from saliva and; (6) quantitation of DNA methylation with a targeted assay. The framework proposed will allow saliva samples to be more widely used in targeted epigenetic studies.

  5. DNA methylation levels analysis in four tissues of sea cucumber Apostichopus japonicus based on fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) during aestivation.

    Science.gov (United States)

    Zhao, Ye; Chen, Muyan; Storey, Kenneth B; Sun, Lina; Yang, Hongsheng

    2015-03-01

    DNA methylation plays an important role in regulating transcriptional change in response to environmental stimuli. In the present study, DNA methylation levels of tissues of the sea cucumber Apostichopus japonicus were analyzed by the fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP) technique over three stages of the aestivation cycle. Overall, a total of 26,963 fragments were amplified including 9112 methylated fragments among four sea cucumber tissues using 18 pairs of selective primers. Results indicated an average DNA methylation level of 33.79% for A. japonicus. The incidence of DNA methylation was different across tissue types in the non-aestivation stage: intestine (30.16%), respiratory tree (27.61%), muscle (27.94%) and body wall (56.25%). Our results show that hypermethylation accompanied deep-aestivation in A. japonicus, which suggests that DNA methylation may have an important role in regulating global transcriptional suppression during aestivation. Further analysis indicated that the main DNA modification sites were focused on intestine and respiratory tree tissues and that full-methylation but not hemi-methylation levels exhibited significant increases in the deep-aestivation stage. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes.

    Science.gov (United States)

    Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare . However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

  7. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    Directory of Open Access Journals (Sweden)

    Karolina Chwialkowska

    2017-11-01

    Full Text Available Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq. We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation

  8. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    Science.gov (United States)

    Chwialkowska, Karolina; Korotko, Urszula; Kosinska, Joanna; Szarejko, Iwona; Kwasniewski, Miroslaw

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop

  9. Association between H3K4 methylation and cancer prognosis: A meta-analysis.

    Science.gov (United States)

    Li, Simin; Shen, Luyan; Chen, Ke-Neng

    2018-05-08

    Histone H3 lysine 4 methylation (H3K4 methylation), including mono-methylation (H3K4me1), di-methylation (H3K4me2), or tri-methylation (H3K4me3), is one of the epigenetic modifications to histone proteins, which are related to the transcriptional activation of genes. H3K4 methylation has both tumor inhibiting and promoting effects, and the prognostic value of H3K4 methylation in cancer remains controversial. Therefore, we performed a systematic review and meta-analysis to examine the association between H3K4 methylation and cancer prognosis. A comprehensive search of PubMed, Web of Science, ScienceDirect, Embase, and Ovid databases was conducted to identify studies investigating the association between H3K4 methylation and prognosis of patients with malignant tumors. The data and characteristics of each study were extracted, and the hazard ratio (HR) at a 95% confidence interval (CI) was calculated to estimate the effect. A total of 1474 patients in 10 studies were enrolled in this meta-analysis. The pooled HR of 1.52 (95% CI 1.02-2.26) indicated that patients with a lower level of H3K4me2 expression were expected to have shorter overall survival, while the pooled HR of 0.45 (95% CI 0.27-0.74) indicated that patients with a lower level of H3K4me3 expression were expected to have longer overall survival. This meta-analysis indicates that increased H3K4me3 expression and decreased H3K4me2 expression might be predictive factors of poor prognosis in cancer. Further large cohort studies are needed to confirm these findings. © 2018 The Authors. Thoracic Cancer published by China Lung Oncology Group and John Wiley & Sons Australia, Ltd.

  10. Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines.

    Science.gov (United States)

    Noor, Dzul Azri Mohamed; Jeyapalan, Jennie N; Alhazmi, Safiah; Carr, Matthew; Squibb, Benjamin; Wallace, Claire; Tan, Christopher; Cusack, Martin; Hughes, Jaime; Reader, Tom; Shipley, Janet; Sheer, Denise; Scotting, Paul J

    2016-01-01

    Silencing of genes by DNA methylation is a common phenomenon in many types of cancer. However, the genome-wide effect of DNA methylation on gene expression has been analysed in relatively few cancers. Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. Previous analyses have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. The genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours' biology have not yet been established. In this study, genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data from primary tumours to address this question. Genome methylation was analysed using the Illumina infinium HumanMethylome450 bead chip system and gene expression was analysed using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Regulation by methylation was confirmed by demethylation using 5-aza-2-deoxycytidine and reverse transcription-quantitative PCR. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested played a role in their silencing in yolk sac tumour cells and many of these genes were also differentially expressed in primary tumours. Genes silenced by methylation in the various GCT cell lines were identified. Several pluripotency-associated genes were identified as a major functional group of silenced genes.

  11. Genome-wide DNA methylation analysis of pseudohypoparathyroidism patients with GNAS imprinting defects.

    Science.gov (United States)

    Rochtus, Anne; Martin-Trujillo, Alejandro; Izzi, Benedetta; Elli, Francesca; Garin, Intza; Linglart, Agnes; Mantovani, Giovanna; Perez de Nanclares, Guiomar; Thiele, Suzanne; Decallonne, Brigitte; Van Geet, Chris; Monk, David; Freson, Kathleen

    2016-01-01

    Pseudohypoparathyroidism (PHP) is caused by (epi)genetic defects in the imprinted GNAS cluster. Current classification of PHP patients is hampered by clinical and molecular diagnostic overlaps. The European Consortium for the study of PHP designed a genome-wide methylation study to improve molecular diagnosis. The HumanMethylation 450K BeadChip was used to analyze genome-wide methylation in 24 PHP patients with parathyroid hormone resistance and 20 age- and gender-matched controls. Patients were previously diagnosed with GNAS-specific differentially methylated regions (DMRs) and include 6 patients with known STX16 deletion (PHP(Δstx16)) and 18 without deletion (PHP(neg)). The array demonstrated that PHP patients do not show DNA methylation differences at the whole-genome level. Unsupervised clustering of GNAS-specific DMRs divides PHP(Δstx16) versus PHP(neg) patients. Interestingly, in contrast to the notion that all PHP patients share methylation defects in the A/B DMR while only PHP(Δstx16) patients have normal NESP, GNAS-AS1 and XL methylation, we found a novel DMR (named GNAS-AS2) in the GNAS-AS1 region that is significantly different in both PHP(Δstx16) and PHP(neg), as validated by Sequenom EpiTYPER in a larger PHP cohort. The analysis of 58 DMRs revealed that 8/18 PHP(neg) and 1/6 PHP(Δstx16) patients have multi-locus methylation defects. Validation was performed for FANCC and SVOPL DMRs. This is the first genome-wide methylation study for PHP patients that confirmed that GNAS is the most significant DMR, and the presence of STX16 deletion divides PHP patients in two groups. Moreover, a novel GNAS-AS2 DMR affects all PHP patients, and PHP patients seem sensitive to multi-locus methylation defects.

  12. Clinical Significance of Retinoic Acid Receptor Beta Promoter Methylation in Prostate Cancer: A Meta-Analysis.

    Science.gov (United States)

    Dou, MengMeng; Zhou, XueLiang; Fan, ZhiRui; Ding, XianFei; Li, LiFeng; Wang, ShuLing; Xue, Wenhua; Wang, Hui; Suo, Zhenhe; Deng, XiaoMing

    2018-01-01

    Retinoic acid receptor beta (RAR beta) is a retinoic acid receptor gene that has been shown to play key roles during multiple cancer processes, including cell proliferation, apoptosis, migration and invasion. Numerous studies have found that methylation of the RAR beta promoter contributed to the occurrence and development of malignant tumors. However, the connection between RAR beta promoter methylation and prostate cancer (PCa) remains unknown. This meta-analysis evaluated the clinical significance of RAR beta promoter methylation in PCa. We searched all published records relevant to RAR beta and PCa in a series of databases, including PubMed, Embase, Cochrane Library, ISI Web of Science and CNKI. The rates of RAR beta promoter methylation in the PCa and control groups (including benign prostatic hyperplasia and normal prostate tissues) were summarized. In addition, we evaluated the source region of available samples and the methods used to detect methylation. To compare the incidence and variation in RAR beta promoter methylation in PCa and non-PCa tissues, the odds ratio (OR) and 95% confidence interval (CI) were calculated accordingly. All the data were analyzed with the statistical software STATA 12.0. Based on the inclusion and exclusion criteria, 15 articles assessing 1,339 samples were further analyzed. These data showed that the RAR beta promoter methylation rates in PCa tissues were significantly higher than the rates in the non-PCa group (OR=21.65, 95% CI: 9.27-50.57). Subgroup analysis according to the source region of samples showed that heterogeneity in Asia was small (I2=0.0%, P=0.430). Additional subgroup analysis based on the method used to detect RAR beta promoter methylation showed that the heterogeneity detected by MSP (methylation-specific PCR) was relatively small (I2=11.3%, P=0.343). Although studies reported different rates for RAR beta promoter methylation in PCa tissues, the total analysis demonstrated that RAR beta promoter methylation

  13. Clinical Significance of Retinoic Acid Receptor Beta Promoter Methylation in Prostate Cancer: A Meta-Analysis

    Directory of Open Access Journals (Sweden)

    MengMeng Dou

    2018-03-01

    Full Text Available Background/Aims: Retinoic acid receptor beta (RAR beta is a retinoic acid receptor gene that has been shown to play key roles during multiple cancer processes, including cell proliferation, apoptosis, migration and invasion. Numerous studies have found that methylation of the RAR beta promoter contributed to the occurrence and development of malignant tumors. However, the connection between RAR beta promoter methylation and prostate cancer (PCa remains unknown. This meta-analysis evaluated the clinical significance of RAR beta promoter methylation in PCa. Materials and Methods: We searched all published records relevant to RAR beta and PCa in a series of databases, including PubMed, Embase, Cochrane Library, ISI Web of Science and CNKI. The rates of RAR beta promoter methylation in the PCa and control groups (including benign prostatic hyperplasia and normal prostate tissues were summarized. In addition, we evaluated the source region of available samples and the methods used to detect methylation. To compare the incidence and variation in RAR beta promoter methylation in PCa and non-PCa tissues, the odds ratio (OR and 95% confidence interval (CI were calculated accordingly. All the data were analyzed with the statistical software STATA 12.0. Results: Based on the inclusion and exclusion criteria, 15 articles assessing 1,339 samples were further analyzed. These data showed that the RAR beta promoter methylation rates in PCa tissues were significantly higher than the rates in the non-PCa group (OR=21.65, 95% CI: 9.27-50.57. Subgroup analysis according to the source region of samples showed that heterogeneity in Asia was small (I2=0.0%, P=0.430. Additional subgroup analysis based on the method used to detect RAR beta promoter methylation showed that the heterogeneity detected by MSP (methylation-specific PCR was relatively small (I2=11.3%, P=0.343. Conclusion: Although studies reported different rates for RAR beta promoter methylation in PCa

  14. Promoter Methylation Analysis of IDH Genes in Human Gliomas

    International Nuclear Information System (INIS)

    Flanagan, Simon; Lee, Maggie; Li, Cheryl C. Y.; Suter, Catherine M.; Buckland, Michael E.

    2012-01-01

    Mutations in isocitrate dehydrogenase (IDH)-1 or -2 are found in the majority of WHO grade II and III astrocytomas and oligodendrogliomas, and secondary glioblastomas. Almost all described mutations are heterozygous missense mutations affecting a conserved arginine residue in the substrate binding site of IDH1 (R132) or IDH2 (R172). But the exact mechanism of IDH mutations in neoplasia is not understood. It has been proposed that IDH mutations impart a “toxic gain-of-function” to the mutant protein, however a dominant-negative effect of mutant IDH has also been described, implying that IDH may function as a tumor suppressor gene. As most, if not all, tumor suppressor genes are inactivated by epigenetic silencing, in a wide variety of tumors, we asked if IDH1 or IDH2 carry the epigenetic signature of a tumor suppressor by assessing cytosine methylation at their promoters. Methylation was quantified in 68 human brain tumors, including both IDH-mutant and IDH wildtype, by bisulfite pyrosequencing. In all tumors examined, CpG methylation levels were less than 8%. Our data demonstrate that inactivation of IDH function through promoter hypermethylation is not common in human gliomas and other brain tumors. These findings do not support a tumor suppressor role for IDH genes in human gliomas.

  15. Genome-Wide Methylated DNA Immunoprecipitation Analysis of Patients with Polycystic Ovary Syndrome

    OpenAIRE

    Shen, Hao-ran; Qiu, Li-hua; Zhang, Zhi-qing; Qin, Yuan-yuan; Cao, Cong; Di, Wen

    2013-01-01

    Polycystic ovary syndrome (PCOS) is a complex, heterogeneous disorder of uncertain etiology. Recent studies suggested that insulin resistance (IR) plays an important role in the development of PCOS. In the current study, we aimed to investigate the molecular mechanism of IR in PCOS. We employed genome-wide methylated DNA immunoprecipitation (MeDIP) analysis to characterize genes that are differentially methylated in PCOS patients vs. healthy controls. Besides, we also identified the different...

  16. [Analysis of methylation-sensitive amplified polymorphism in wheat genome under the wheat leaf rust stress].

    Science.gov (United States)

    Fu, Sheng-Jie; Wang, Hui; Feng, Li-Na; Sun, Yi; Yang, Wen-Xiang; Liu, Da-Qun

    2009-03-01

    Intrinsic DNA methylation pattern is an integral component of the epigenetic network in many eukaryotes. DNA methylation plays an important role in regulating gene expression in eukaryotes. Biological stress in plant provides an inherent epigenetic driving force of evolution. Study of DNA methylation patterns arising from biological stress will help us fully understand the epigenetic regulation of gene expression and DNA methylation of biological functions. The wheat near-isogenic lines TcLr19 and TcLr41 were resistant to races THTT and TKTJ, respectively, and Thatcher is compatible in the interaction with Puccinia triticina THTT and TKTJ, respectively. By means of methylation-sensitive amplified polymorphism (MSAP) analysis, the patterns of cytosine methylation in TcLr19, TcLr41, and Thatcher inoculated with P. triticina THTT and TKTJ were compared with those of the untreated samples. All the DNA fragments, each representing a recognition site cleaved by each or both of isoschizomers, were amplified using 60 pairs of selective primers. The results indicated that there was no significant difference between the challenged and unchallenged plants at DNA methylation level. However, epigenetic difference between the near-isogenic line for wheat leaf rust resistance gene Lr41 and Thatcher was present.

  17. [Analysis of genomic DNA methylation level in radish under cadmium stress by methylation-sensitive amplified polymorphism technique].

    Science.gov (United States)

    Yang, Jin-Lan; Liu, Li-Wang; Gong, Yi-Qin; Huang, Dan-Qiong; Wang, Feng; He, Ling-Li

    2007-06-01

    The level of cytosine methylation induced by cadmium in radish (Raphanus sativus L.) genome was analysed using the technique of methylation-sensitive amplified polymorphism (MSAP). The MSAP ratios in radish seedling exposed to cadmium chloride at the concentration of 50, 250 and 500 mg/L were 37%, 43% and 51%, respectively, and the control was 34%; the full methylation levels (C(m)CGG in double strands) were at 23%, 25% and 27%, respectively, while the control was 22%. The level of increase in MSAP and full methylation indicated that de novo methylation occurred in some 5'-CCGG sites under Cd stress. There was significant positive correlation between increase of total DNA methylation level and CdCl(2) concentration. Four types of MSAP patterns: de novo methylation, de-methylation, atypical pattern and no changes of methylation pattern were identified among CdCl(2) treatments and the control. DNA methylation alteration in plants treated with CdCl(2) was mainly through de novo methylation.

  18. Genetic diversity analysis of Jatropha curcas L. (Euphorbiaceae) based on methylation-sensitive amplification polymorphism.

    Science.gov (United States)

    Kanchanaketu, T; Sangduen, N; Toojinda, T; Hongtrakul, V

    2012-04-13

    Genetic analysis of 56 samples of Jatropha curcas L. collected from Thailand and other countries was performed using the methylation-sensitive amplification polymorphism (MSAP) technique. Nine primer combinations were used to generate MSAP fingerprints. When the data were interpreted as amplified fragment length polymorphism (AFLP) markers, 471 markers were scored. All 56 samples were classified into three major groups: γ-irradiated, non-toxic and toxic accessions. Genetic similarity among the samples was extremely high, ranging from 0.95 to 1.00, which indicated very low genetic diversity in this species. The MSAP fingerprint was further analyzed for DNA methylation polymorphisms. The results revealed differences in the DNA methylation level among the samples. However, the samples collected from saline areas and some species hybrids showed specific DNA methylation patterns. AFLP data were used, together with methylation-sensitive AFLP (MS-AFLP) data, to construct a phylogenetic tree, resulting in higher efficiency to distinguish the samples. This combined analysis separated samples previously grouped in the AFLP analysis. This analysis also distinguished some hybrids. Principal component analysis was also performed; the results confirmed the separation in the phylogenetic tree. Some polymorphic bands, involving both nucleotide and DNA methylation polymorphism, that differed between toxic and non-toxic samples were identified, cloned and sequenced. BLAST analysis of these fragments revealed differences in DNA methylation in some known genes and nucleotide polymorphism in chloroplast DNA. We conclude that MSAP is a powerful technique for the study of genetic diversity for organisms that have a narrow genetic base.

  19. Methyl cation affinities of neutral and anionic maingroup-element hydrides: trends across the periodic table and correlation with proton affinities.

    Science.gov (United States)

    Mulder, R Joshua; Guerra, Célia Fonseca; Bickelhaupt, F Matthias

    2010-07-22

    We have computed the methyl cation affinities in the gas phase of archetypal anionic and neutral bases across the periodic table using ZORA-relativistic density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. The main purpose of this work is to provide the methyl cation affinities (and corresponding entropies) at 298 K of all anionic (XH(n-1)(-)) and neutral bases (XH(n)) constituted by maingroup-element hydrides of groups 14-17 and the noble gases (i.e., group 18) along the periods 2-6. The cation affinity of the bases decreases from H(+) to CH(3)(+). To understand this trend, we have carried out quantitative bond energy decomposition analyses (EDA). Quantitative correlations are established between the MCA and PA values.

  20. Factors Affecting Arsenic Methylation in Arsenic-Exposed Humans: A Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Shen, Hui; Niu, Qiang; Xu, Mengchuan; Rui, Dongsheng; Xu, Shangzhi; Feng, Gangling; Ding, Yusong; Li, Shugang; Jing, Mingxia

    2016-02-06

    Chronic arsenic exposure is a critical public health issue in many countries. The metabolism of arsenic in vivo is complicated because it can be influenced by many factors. In the present meta-analysis, two researchers independently searched electronic databases, including the Cochrane Library, PubMed, Springer, Embase, and China National Knowledge Infrastructure, to analyze factors influencing arsenic methylation. The concentrations of the following arsenic metabolites increase (piAs), monomethyl arsenic (MMA), dimethyl arsenic (DMA), and total arsenic. Additionally, the percentages of iAs (standard mean difference (SMD): 1.00; 95% confidence interval (CI): 0.60-1.40; p< 0.00001) and MMA (SMD: 0.49; 95% CI: 0.21-0.77; p = 0.0006) also increase, while the percentage of DMA (SMD: -0.57; 95% CI: -0.80--0.31; p< 0.0001), primary methylation index (SMD: -0.57; 95% CI: -0.94--0.20; p = 0.002), and secondary methylation index (SMD: -0.27; 95% CI: -0.46--0.90; p = 0.004) decrease. Smoking, drinking, and older age can reduce arsenic methylation, and arsenic methylation is more efficient in women than in men. The results of this analysis may provide information regarding the role of arsenic oxidative methylation in the arsenic poisoning process.

  1. Traumatic stress and accelerated DNA methylation age: A meta-analysis.

    Science.gov (United States)

    Wolf, Erika J; Maniates, Hannah; Nugent, Nicole; Maihofer, Adam X; Armstrong, Don; Ratanatharathorn, Andrew; Ashley-Koch, Allison E; Garrett, Melanie; Kimbrel, Nathan A; Lori, Adriana; Va Mid-Atlantic Mirecc Workgroup; Aiello, Allison E; Baker, Dewleen G; Beckham, Jean C; Boks, Marco P; Galea, Sandro; Geuze, Elbert; Hauser, Michael A; Kessler, Ronald C; Koenen, Karestan C; Miller, Mark W; Ressler, Kerry J; Risbrough, Victoria; Rutten, Bart P F; Stein, Murray B; Ursano, Robert J; Vermetten, Eric; Vinkers, Christiaan H; Uddin, Monica; Smith, Alicia K; Nievergelt, Caroline M; Logue, Mark W

    2018-06-01

    Recent studies examining the association between posttraumatic stress disorder (PTSD) and accelerated aging, as defined by DNA methylation-based estimates of cellular age that exceed chronological age, have yielded mixed results. We conducted a meta-analysis of trauma exposure and PTSD diagnosis and symptom severity in association with accelerated DNA methylation age using data from 9 cohorts contributing to the Psychiatric Genomics Consortium PTSD Epigenetics Workgroup (combined N = 2186). Associations between demographic and cellular variables and accelerated DNA methylation age were also examined, as was the moderating influence of demographic variables. Meta-analysis of regression coefficients from contributing cohorts revealed that childhood trauma exposure (when measured with the Childhood Trauma Questionnaire) and lifetime PTSD severity evidenced significant, albeit small, meta-analytic associations with accelerated DNA methylation age (ps = 0.028 and 0.016, respectively). Sex, CD4T cell proportions, and natural killer cell proportions were also significantly associated with accelerated DNA methylation age (all ps age. There was no evidence of moderation of the trauma or PTSD variables by demographic factors. Results suggest that traumatic stress is associated with advanced epigenetic age and raise the possibility that cells integral to immune system maintenance and responsivity play a role in this. This study highlights the need for additional research into the biological mechanisms linking traumatic stress to accelerated DNA methylation age and the importance of furthering our understanding of the neurobiological and health consequences of PTSD. Published by Elsevier Ltd.

  2. Whole Genome DNA Methylation Analysis of Obstructive Sleep Apnea: IL1R2, NPR2, AR, SP140 Methylation and Clinical Phenotype.

    Science.gov (United States)

    Chen, Yung-Che; Chen, Ting-Wen; Su, Mao-Chang; Chen, Chung-Jen; Chen, Kuang-Den; Liou, Chia-Wei; Tang, Petrus; Wang, Ting-Ya; Chang, Jen-Chieh; Wang, Chin-Chou; Lin, Hsin-Ching; Chin, Chien-Hung; Huang, Kuo-Tung; Lin, Meng-Chih; Hsiao, Chang-Chun

    2016-04-01

    We hypothesized that DNA methylation patterns may contribute to disease severity or the development of hypertension and excessive daytime sleepiness (EDS) in patients with obstructive sleep apnea (OSA). Illumina's (San Diego, CA, USA) DNA methylation 27-K assay was used to identify differentially methylated loci (DML). DNA methylation levels were validated by pyrosequencing. A discovery cohort of 15 patients with OSA and 6 healthy subjects, and a validation cohort of 72 patients with sleep disordered breathing (SDB). Microarray analysis identified 636 DMLs in patients with OSA versus healthy subjects, and 327 DMLs in patients with OSA and hypertension versus those without hypertension. In the validation cohort, no significant difference in DNA methylation levels of six selected genes was found between the primary snoring subjects and OSA patients (primary outcome). However, a secondary outcome analysis showed that interleukin-1 receptor 2 (IL1R2) promoter methylation (-114 cytosine followed by guanine dinucleotide sequence [CpG] site) was decreased and IL1R2 protein levels were increased in the patients with SDB with an oxygen desaturation index > 30. Androgen receptor (AR) promoter methylation (-531 CpG site) and AR protein levels were both increased in the patients with SDB with an oxygen desaturation index > 30. Natriuretic peptide receptor 2 (NPR2) promoter methylation (-608/-618 CpG sites) were decreased, whereas levels of both NPR2 and serum C type natriuretic peptide protein were increased in the SDB patients with EDS. Speckled protein 140 (SP140) promoter methylation (-194 CpG site) was increased, and SP140 protein levels were decreased in the patients with SDB and EDS. IL1R2 hypomethylation and AR hypermethylation may constitute an important determinant of disease severity, whereas NPR2 hypomethylation and SP140 hypermethylation may provide a biomarker for vulnerability to EDS in OSA. A commentary on this article appears in this issue on page 723. © 2016

  3. The application of methylation specific electrophoresis (MSE to DNA methylation analysis of the 5' CpG island of mucin in cancer cells

    Directory of Open Access Journals (Sweden)

    Yokoyama Seiya

    2012-02-01

    Full Text Available Abstract Background Methylation of CpG sites in genomic DNA plays an important role in gene regulation and especially in gene silencing. We have reported mechanisms of epigenetic regulation for expression of mucins, which are markers of malignancy potential and early detection of human neoplasms. Epigenetic changes in promoter regions appear to be the first step in expression of mucins. Thus, detection of promoter methylation status is important for early diagnosis of cancer, monitoring of tumor behavior, and evaluating the response of tumors to targeted therapy. However, conventional analytical methods for DNA methylation require a large amount of DNA and have low sensitivity. Methods Here, we report a modified version of the bisulfite-DGGE (denaturing gradient gel electrophoresis using a nested PCR approach. We designated this method as methylation specific electrophoresis (MSE. The MSE method is comprised of the following steps: (a bisulfite treatment of genomic DNA, (b amplification of the target DNA by a nested PCR approach and (c applying to DGGE. To examine whether the MSE method is able to analyze DNA methylation of mucin genes in various samples, we apply it to DNA obtained from state cell lines, ethanol-fixed colonic crypts and human pancreatic juices. Result The MSE method greatly decreases the amount of input DNA. The lower detection limit for distinguishing different methylation status is Conclusions The MSE method can provide a qualitative information of methylated sequence profile. The MSE method allows sensitive and specific analysis of the DNA methylation pattern of almost any block of multiple CpG sites. The MSE method can be applied to analysis of DNA methylation status in many different clinical samples, and this may facilitate identification of new risk markers.

  4. An integrative analysis of DNA methylation and RNA-Seq data for human heart, kidney and liver

    Directory of Open Access Journals (Sweden)

    Xie Linglin

    2011-12-01

    Full Text Available Abstract Background Many groups, including our own, have proposed the use of DNA methylation profiles as biomarkers for various disease states. While much research has been done identifying DNA methylation signatures in cancer vs. normal etc., we still lack sufficient knowledge of the role that differential methylation plays during normal cellular differentiation and tissue specification. We also need thorough, genome level studies to determine the meaning of methylation of individual CpG dinucleotides in terms of gene expression. Results In this study, we have used (insert statistical method here to compile unique DNA methylation signatures from normal human heart, lung, and kidney using the Illumina Infinium 27 K methylation arraysand compared those to gene expression by RNA sequencing. We have identified unique signatures of global DNA methylation for human heart, kidney and liver, and showed that DNA methylation data can be used to correctly classify various tissues. It indicates that DNA methylation reflects tissue specificity and may play an important role in tissue differentiation. The integrative analysis of methylation and RNA-Seq data showed that gene methylation and its transcriptional levels were comprehensively correlated. The location of methylation markers in terms of distance to transcription start site and CpG island showed no effects on the regulation of gene expression by DNA methylation in normal tissues. Conclusions This study showed that an integrative analysis of methylation array and RNA-Seq data can be utilized to discover the global regulation of gene expression by DNA methylation and suggests that DNA methylation plays an important role in normal tissue differentiation via modulation of gene expression.

  5. [Novel Approaches in DNA Methylation Studies - MS-HRM Analysis and Electrochemistry].

    Science.gov (United States)

    Bartošík, M; Ondroušková, E

    Cytosine methylation in DNA is an epigenetic mechanism regulating gene expression and plays a vital role in cell differentiation or proliferation. Tumor cells often exhibit aberrant DNA methylation, e.g. hypermethylation of tumor suppressor gene promoters. New methods, capable of determining methylation status of specific DNA sequences, are thus being developed. Among them, MS-HRM (methylation-specific high resolution melting) and electrochemistry offer relatively inexpensive instrumentation, fast assay times and possibility of screening multiple samples/DNA regions simultaneously. MS-HRM is due to its sensitivity and simplicity an interesting alternative to already established techniques, including methylation-specific PCR or bisulfite sequencing. Electrochemistry, when combined with suitable electroactive labels and electrode surfaces, has been applied in several unique strategies for discrimination of cytosines and methylcytosines. Both techniques were successfully tested in analysis of DNA methylation within promoters of important tumor suppressor genes and could thus help in achieving more precise diagnostics and prognostics of cancer. Aberrant methylation of promoters has already been described in hundreds of genes associated with tumorigenesis and could serve as important biomarker if new methods applicable into clinical practice are sufficiently advanced.Key words: DNA methylation - 5-methylcytosine - HRM analysis - melting temperature - DNA duplex - electrochemistry - nucleic acid hybridizationThis work was supported by MEYS - NPS I - LO1413.The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 6. 5. 2016Accepted: 16. 5. 2016.

  6. Meta-analysis of the association between APC promoter methylation and colorectal cancer.

    Science.gov (United States)

    Ding, Zhenyu; Jiang, Tong; Piao, Ying; Han, Tao; Han, Yaling; Xie, Xiaodong

    2015-01-01

    Previous studies investigating the association between adenomatous polyposis coli (APC) gene promoter methylation and colorectal cancer (CRC) have yielded conflicting results. The aim of this study was to comprehensively evaluate the potential application of the detection of APC promoter methylation to the prevention and treatment of CRC. PubMed, Embase, and MEDLINE (results updated to October 2014) were searched for relevant studies. The effect size was defined as the weighted odds ratio (OR), which was calculated using either the fixed-effects or random-effects model. Prespecified subgroup and sensitivity analyses were conducted to evaluate potential heterogeneity among the included studies. Nineteen studies comprising 2,426 participants were selected for our meta-analysis. The pooled results of nine studies comprising a total of 740 subjects indicated that APC promoter methylation was significantly associated with CRC risk (pooled OR 5.53; 95% confidence interval [CI] 3.50-8.76; PAPC promoter methylation and the presence of CRC metastasis, and the pooled OR was 0.80 (95% CI 0.44-1.46; P=0.47). A meta-analysis conducted with four studies with a total of 467 patients found no significant correlation between APC promoter methylation and the presence of colorectal adenoma (pooled OR 1.85; 95% CI 0.67-5.10; P=0.23). No significant correlation between APC promoter methylation and patients' Dukes' stage, TNM stage, differentiation grade, age, or sex was identified. In conclusion, APC promoter methylation was found to be significantly associated with a higher risk of developing CRC. The findings indicate that APC promoter methylation may be a potential biomarker for the carcinogenesis of CRC.

  7. Comparative methylome analysis in solid tumors reveals aberrant methylation at chromosome 6p in nasopharyngeal carcinoma

    International Nuclear Information System (INIS)

    Dai, Wei; Cheung, Arthur Kwok Leung; Ko, Josephine Mun Yee; Cheng, Yue; Zheng, Hong; Ngan, Roger Kai Cheong; Ng, Wai Tong; Lee, Anne Wing Mui; Yau, Chun Chung; Lee, Victor Ho Fu; Lung, Maria Li

    2015-01-01

    Altered patterns of DNA methylation are key features of cancer. Nasopharyngeal carcinoma (NPC) has the highest incidence in Southern China. Aberrant methylation at the promoter region of tumor suppressors is frequently reported in NPC; however, genome-wide methylation changes have not been comprehensively investigated. Therefore, we systematically analyzed methylome data in 25 primary NPC tumors and nontumor counterparts using a high-throughput approach with the Illumina HumanMethylation450 BeadChip. Comparatively, we examined the methylome data of 11 types of solid tumors collected by The Cancer Genome Atlas (TCGA). In NPC, the hypermethylation pattern was more dominant than hypomethylation and the majority of de novo methylated loci were within or close to CpG islands in tumors. The comparative methylome analysis reveals hypermethylation at chromosome 6p21.3 frequently occurred in NPC (false discovery rate; FDR=1.33 × 10 −9 ), but was less obvious in other types of solid tumors except for prostate and Epstein–Barr virus (EBV)-positive gastric cancer (FDR<10 −3 ). Bisulfite pyrosequencing results further confirmed the aberrant methylation at 6p in an additional patient cohort. Evident enrichment of the repressive mark H3K27me3 and active mark H3K4me3 derived from human embryonic stem cells were found at these regions, indicating both DNA methylation and histone modification function together, leading to epigenetic deregulation in NPC. Our study highlights the importance of epigenetic deregulation in NPC. Polycomb Complex 2 (PRC2), responsible for H3K27 trimethylation, is a promising therapeutic target. A key genomic region on 6p with aberrant methylation was identified. This region contains several important genes having potential use as biomarkers for NPC detection

  8. Genome-Wide DNA Methylation Analysis and Epigenetic Variations Associated with Congenital Aortic Valve Stenosis (AVS.

    Directory of Open Access Journals (Sweden)

    Uppala Radhakrishna

    Full Text Available Congenital heart defect (CHD is the most common cause of death from congenital anomaly. Among several candidate epigenetic mechanisms, DNA methylation may play an important role in the etiology of CHDs. We conducted a genome-wide DNA methylation analysis using an Illumina Infinium 450k human methylation assay in a cohort of 24 newborns who had aortic valve stenosis (AVS, with gestational-age matched controls. The study identified significantly-altered CpG methylation at 59 sites in 52 genes in AVS subjects as compared to controls (either hypermethylated or demethylated. Gene Ontology analysis identified biological processes and functions for these genes including positive regulation of receptor-mediated endocytosis. Consistent with prior clinical data, the molecular function categories as determined using DAVID identified low-density lipoprotein receptor binding, lipoprotein receptor binding and identical protein binding to be over-represented in the AVS group. A significant epigenetic change in the APOA5 and PCSK9 genes known to be involved in AVS was also observed. A large number CpG methylation sites individually demonstrated good to excellent diagnostic accuracy for the prediction of AVS status, thus raising possibility of molecular screening markers for this disorder. Using epigenetic analysis we were able to identify genes significantly involved in the pathogenesis of AVS.

  9. Genome-Wide DNA Methylation Analysis and Epigenetic Variations Associated with Congenital Aortic Valve Stenosis (AVS).

    Science.gov (United States)

    Radhakrishna, Uppala; Albayrak, Samet; Alpay-Savasan, Zeynep; Zeb, Amna; Turkoglu, Onur; Sobolewski, Paul; Bahado-Singh, Ray O

    2016-01-01

    Congenital heart defect (CHD) is the most common cause of death from congenital anomaly. Among several candidate epigenetic mechanisms, DNA methylation may play an important role in the etiology of CHDs. We conducted a genome-wide DNA methylation analysis using an Illumina Infinium 450k human methylation assay in a cohort of 24 newborns who had aortic valve stenosis (AVS), with gestational-age matched controls. The study identified significantly-altered CpG methylation at 59 sites in 52 genes in AVS subjects as compared to controls (either hypermethylated or demethylated). Gene Ontology analysis identified biological processes and functions for these genes including positive regulation of receptor-mediated endocytosis. Consistent with prior clinical data, the molecular function categories as determined using DAVID identified low-density lipoprotein receptor binding, lipoprotein receptor binding and identical protein binding to be over-represented in the AVS group. A significant epigenetic change in the APOA5 and PCSK9 genes known to be involved in AVS was also observed. A large number CpG methylation sites individually demonstrated good to excellent diagnostic accuracy for the prediction of AVS status, thus raising possibility of molecular screening markers for this disorder. Using epigenetic analysis we were able to identify genes significantly involved in the pathogenesis of AVS.

  10. Fluorescence-labeled methylation-sensitive amplified fragment length polymorphism (FL-MS-AFLP) analysis for quantitative determination of DNA methylation and demethylation status.

    Science.gov (United States)

    Kageyama, Shinji; Shinmura, Kazuya; Yamamoto, Hiroko; Goto, Masanori; Suzuki, Koichi; Tanioka, Fumihiko; Tsuneyoshi, Toshihiro; Sugimura, Haruhiko

    2008-04-01

    The PCR-based DNA fingerprinting method called the methylation-sensitive amplified fragment length polymorphism (MS-AFLP) analysis is used for genome-wide scanning of methylation status. In this study, we developed a method of fluorescence-labeled MS-AFLP (FL-MS-AFLP) analysis by applying a fluorescence-labeled primer and fluorescence-detecting electrophoresis apparatus to the existing method of MS-AFLP analysis. The FL-MS-AFLP analysis enables quantitative evaluation of more than 350 random CpG loci per run. It was shown to allow evaluation of the differences in methylation level of blood DNA of gastric cancer patients and evaluation of hypermethylation and hypomethylation in DNA from gastric cancer tissue in comparison with adjacent non-cancerous tissue.

  11. Analysis of DNA Methylation of Gracilariopsis lemaneiformis Under Temperature Stress Using the Methylation Sensitive Amplification Polymorphism (MSAP) Technique

    Science.gov (United States)

    Peng, Chong; Sui, Zhenghong; Zhou, Wei; Hu, Yiyi; Mi, Ping; Jiang, Minjie; Li, Xiaodong; Ruan, Xudong

    2018-06-01

    Gracilariopsis lemaneiformis is an economically important agarophyte, which contains high quality gel and shows a high growth rate. Wild population of G. lemaneiformis displayed resident divergence, though with a low genetic diversity as was revealed by amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) analyses. In addition, different strains of G. lemaneiformis are diverse in morphology. The highly inconsistence between genetic background and physiological characteristics recommends strongly to the regulation at epigenetic level. In this study, the DNA methylation change in G. lemaneiformis among different generation branches and under different temperature stresses was assessed using methylation sensitive amplified polymorphism (MSAP) technique. It was shown that DNA methylation level among different generation branches was diverse. The full and total methylated DNA level was the lowest in the second generation branch and the highest in the third generation. The total methylation level was 61.11%, 60.88% and 64.12% at 15°C, 22°C and 26°C, respectively. Compared with the control group (22°C), the fully methylated and totally methylated ratios were increased in both experiment groups (15°C and 26°C). All of the cytosine methylation/demethylation transform (CMDT) was further analyzed. High temperature treatment could induce more CMDT than low temperature treatment did.

  12. Genome-wide methylation analysis identifies differentially methylated CpG loci associated with severe obesity in childhood.

    Science.gov (United States)

    Huang, R C; Garratt, E S; Pan, H; Wu, Y; Davis, E A; Barton, S J; Burdge, G C; Godfrey, K M; Holbrook, J D; Lillycrop, K A

    2015-01-01

    Childhood obesity is a major public health issue. Here we investigated whether differential DNA methylation was associated with childhood obesity. We studied DNA methylation profiles in whole blood from 78 obese children (mean BMI Z-score: 2.6) and 71 age- and sex-matched controls (mean BMI Z-score: 0.1). DNA samples from obese and control groups were pooled and analyzed using the Infinium HumanMethylation450 BeadChip array. Comparison of the methylation profiles between obese and control subjects revealed 129 differentially methylated CpG (DMCpG) loci associated with 80 unique genes that had a greater than 10% difference in methylation (P-value obesity were validated using sodium bisulfite pyrosequencing across loci within the FYN, PIWIL4, and TAOK3 genes in individual subjects. Three CpG loci within FYN were hypermethylated in obese individuals (all P obesity was associated with lower methylation of CpG loci within PIWIL4 (P = 0.003) and TAOK3 (P = 0.001). After building logistic regression models, we determined that a 1% increase in methylation in TAOK3, multiplicatively decreased the odds of being obese by 0.91 (95% CI: 0.86 - 0.97), and an increase of 1% methylation in FYN CpG3, multiplicatively increased the odds of being obese by 1.03 (95% CI: 0.99 - 1.07). In conclusion, these findings provide evidence that childhood obesity is associated with specific DNA methylation changes in whole blood, which may have utility as biomarkers of obesity risk.

  13. Morphological analysis and DNA methylation in Conyza bonariensis L. cronquist (Asteraceae phenotypes

    Directory of Open Access Journals (Sweden)

    Juliana Maria de Paula

    2017-08-01

    Full Text Available ABSTRACT The species Conyza bonariensis (L. cause losses in agriculture due to their invasive capacity and resistance to herbicides like glyphosate. The species of this genus exhibit phenotypic plasticity, which complicates their identification and characterization. Thus, experiments were performed with 2 extreme C. bonariensis phenotypes (called broad leaf and narrow leaf in greenhouse conditions and in the laboratory, in order to verify if the morphological differences among these phenotypes are a genetic character or result from environmental effects. In addition to the comparative morphological analysis, assessment of DNA methylation profile was performed to detect the occurrence, or not, of differences in the epigenetic level. The morphological characteristics evaluated were length, width, shape, margin and leaves indument; plant height and stem indument; the number of capitula, flowers and seeds. The Methylation Sensitive Amplified Polymorphism technique was used to investigate the methylation levels. The morphological differences of phenotypes supposed to be C. bonariensis are probably genetic in origin and not the result of environmental effects, since, after 6 crop cycles in a greenhouse under the same environmental conditions, these phenotypes remained with the same morphological characteristics and seed production in relation to the original phenotypes found in the collection site. The different phenotypes did not show differences corresponding to DNA methylation patterns that could indicate an epigenetic effect as the cause of the differences between the 2 phenotypes. The results of morphological analysis and methylation probably indicate that maybe they are individuals of populations from different taxa not registered yet in the literature.

  14. Analysis of DNA methylation level by methylation-sensitive amplification polymorphism in half smooth tongue sole ( Cynoglossus semilaevis) subjected to salinity stress

    Science.gov (United States)

    Li, Siping; He, Feng; Wen, Haishen; Li, Jifang; Si, Yufeng; Liu, Mingyuan; He, Huiwen; Huang, Zhengju

    2017-04-01

    Increasingly arisen environmental constraints may contribute to heritable phenotypic variation including methylation changes, which can help the animals with development, growth and survival. In this study, we assessed the DNA methylation levels in three tissues (gonad, kidney and gill) of half smooth tongue sole under the salinity stress. The methylation-sensitive amplification polymorphism (MSAP) technique was applied to illustrate the regulation of epigenetic mechanism in environmental stimuli. Fish were subjected to 15 salinity treatment for 7 and 60 days, respectively. A total of 11259 fragments were amplified with 8 pairs of selective primers. The levels of methylated DNA in different tissues of females and males without salinity stress were analyzed, which were 32.76% and 47.32% in gonad; 38.13% and 37.69% in kidney; 37.58% and 34.96% in gill, respectively. In addition, the significant difference was observed in gonad between females and males, indicating that discrepant regulation in gonadal development and differentiation may involve sex-related genes. Further analysis showed that total and hemi-methylation were significantly decreased under 15 salinity for 7 days, probably resulting in up-regulating salt-tolerance genes expression to adjust salt changing. With the adjustment for 60 days, total and hemi-methylation prominently went back to its normal levels to obtain equilibrium. Particularly, full methylation levels were steady along with salinity stress to maintain the stability of gene expression. Additionally, the data showed that gonads in females and gills in males were superior in adaptability. As a result, DNA methylation regulates tissue- specific epiloci, and may respond to salinity stress by regulating gene expression to maintain animal survival and activity.

  15. Genome‐wide DNA methylation analysis identifies MEGF10 as a novel epigenetically repressed candidate tumor suppressor gene in neuroblastoma

    Science.gov (United States)

    Charlet, Jessica; Tomari, Ayumi; Dallosso, Anthony R.; Szemes, Marianna; Kaselova, Martina; Curry, Thomas J.; Almutairi, Bader; Etchevers, Heather C.; McConville, Carmel; Malik, Karim T. A.

    2016-01-01

    Neuroblastoma is a childhood cancer in which many children still have poor outcomes, emphasising the need to better understand its pathogenesis. Despite recent genome‐wide mutation analyses, many primary neuroblastomas do not contain recognizable driver mutations, implicating alternate molecular pathologies such as epigenetic alterations. To discover genes that become epigenetically deregulated during neuroblastoma tumorigenesis, we took the novel approach of comparing neuroblastomas to neural crest precursor cells, using genome‐wide DNA methylation analysis. We identified 93 genes that were significantly differentially methylated of which 26 (28%) were hypermethylated and 67 (72%) were hypomethylated. Concentrating on hypermethylated genes to identify candidate tumor suppressor loci, we found the cell engulfment and adhesion factor gene MEGF10 to be epigenetically repressed by DNA hypermethylation or by H3K27/K9 methylation in neuroblastoma cell lines. MEGF10 showed significantly down‐regulated expression in neuroblastoma tumor samples; furthermore patients with the lowest‐expressing tumors had reduced relapse‐free survival. Our functional studies showed that knock‐down of MEGF10 expression in neuroblastoma cell lines promoted cell growth, consistent with MEGF10 acting as a clinically relevant, epigenetically deregulated neuroblastoma tumor suppressor gene. © 2016 The Authors. Molecular Carcinogenesis Published by Wiley Periodicals, Inc. PMID:27862318

  16. Quantitative DNA methylation analysis improves epigenotype-phenotype correlations in Beckwith-Wiedemann syndrome

    Science.gov (United States)

    Calvello, Mariarosaria; Tabano, Silvia; Colapietro, Patrizia; Maitz, Silvia; Pansa, Alessandra; Augello, Claudia; Lalatta, Faustina; Gentilin, Barbara; Spreafico, Filippo; Calzari, Luciano; Perotti, Daniela; Larizza, Lidia; Russo, Silvia; Selicorni, Angelo; Sirchia, Silvia M; Miozzo, Monica

    2013-01-01

    Beckwith-Wiedemann syndrome (BWS) is a rare disorder characterized by overgrowth and predisposition to embryonal tumors. BWS is caused by various epigenetic and/or genetic alterations that dysregulate the imprinted genes on chromosome region 11p15.5. Molecular analysis is required to reinforce the clinical diagnosis of BWS and to identify BWS patients with cancer susceptibility. This is particularly crucial prenatally because most signs of BWS cannot be recognized in utero. We established a reliable molecular assay by pyrosequencing to quantitatively evaluate the methylation profiles of ICR1 and ICR2. We explored epigenotype-phenotype correlations in 19 patients that fulfilled the clinical diagnostic criteria for BWS, 22 patients with suspected BWS, and three fetuses with omphalocele. Abnormal methylation was observed in one prenatal case and 19 postnatal cases, including seven suspected BWS. Seven cases showed ICR1 hypermethylation, five cases showed ICR2 hypomethylation, and eight cases showed abnormal methylation of ICR1 and ICR2 indicating paternal uniparental disomy (UPD). More cases of ICR1 alterations and UPD were found than expected. This is likely due to the sensitivity of this approach, which can detect slight deviations in methylation from normal levels. There was a significant correlation (p < 0.001) between the percentage of ICR1 methylation and BWS features: severe hypermethylation (range: 75–86%) was associated with macroglossia, macrosomia, and visceromegaly, whereas mild hypermethylation (range: 55–59%) was associated with umbilical hernia and diastasis recti. Evaluation of ICR1 and ICR2 methylation by pyrosequencing in BWS can improve epigenotype-phenotype correlations, detection of methylation alterations in suspected cases, and identification of UPD. PMID:23917791

  17. Comparison of Periodized and Non-Periodized Resistance Training on Maximal Strength: A Meta-Analysis.

    Science.gov (United States)

    Williams, Tyler D; Tolusso, Danilo V; Fedewa, Michael V; Esco, Michael R

    2017-10-01

    Periodization is a logical method of organizing training into sequential phases and cyclical time periods in order to increase the potential for achieving specific performance goals while minimizing the potential for overtraining. Periodized resistance training plans are proposed to be superior to non-periodized training plans for enhancing maximal strength. The primary aim of this study was to examine the previous literature comparing periodized resistance training plans to non-periodized resistance training plans and determine a quantitative estimate of effect on maximal strength. All studies included in the meta-analysis met the following inclusion criteria: (1) peer-reviewed publication; (2) published in English; (3) comparison of a periodized resistance training group to a non-periodized resistance training group; (4) maximal strength measured by 1-repetition maximum (1RM) squat, bench press, or leg press. Data were extracted and independently coded by two authors. Random-effects models were used to aggregate a mean effect size (ES), 95% confidence intervals (CIs) and potential moderators. The cumulative results of 81 effects gathered from 18 studies published between 1988 and 2015 indicated that the magnitude of improvement in 1RM following periodized resistance training was greater than non-periodized resistance training (ES = 0.43, 95% CI 0.27-0.58; P training status (β = -0.59; P = 0.0305), study length (β = 0.03; P = 0.0067), and training frequency (β = 0.46; P = 0.0123) were associated with a change in 1RM. These results indicate that undulating programs were more favorable for strength gains. Improvements in 1RM were greater among untrained participants. Additionally, higher training frequency and longer study length were associated with larger improvements in 1RM. These results suggest that periodized resistance training plans have a moderate effect on 1RM compared to non-periodized training plans. Variation in training stimuli

  18. Integrated analysis of dynamic FET PET/CT parameters, histology, and methylation profiling of 44 gliomas.

    Science.gov (United States)

    Röhrich, Manuel; Huang, Kristin; Schrimpf, Daniel; Albert, Nathalie L; Hielscher, Thomas; von Deimling, Andreas; Schüller, Ulrich; Dimitrakopoulou-Strauss, Antonia; Haberkorn, Uwe

    2018-05-07

    Dynamic 18 F-FET PET/CT is a powerful tool for the diagnosis of gliomas. 18 F-FET PET time-activity curves (TAC) allow differentiation between histological low-grade gliomas (LGG) and high-grade gliomas (HGG). Molecular methods such as epigenetic profiling are of rising importance for glioma grading and subclassification. Here, we analysed dynamic 18 F-FET PET data, and the histological and epigenetic features of 44 gliomas. Dynamic 18 F-FET PET was performed in 44 patients with newly diagnosed, untreated glioma: 10 WHO grade II glioma, 13 WHO grade III glioma and 21 glioblastoma (GBM). All patients underwent stereotactic biopsy or tumour resection after 18 F-FET PET imaging. As well as histological analysis of tissue samples, DNA was subjected to epigenetic analysis using the Illumina 850 K methylation array. TACs, standardized uptake values corrected for background uptake in healthy tissue (SUVmax/BG), time to peak (TTP) and kinetic modelling parameters were correlated with histological diagnoses and with epigenetic signatures. Multivariate analyses were performed to evaluate the diagnostic accuracy of 18 F-FET PET in relation to the tumour groups identified by histological and methylation-based analysis. Epigenetic profiling led to substantial tumour reclassification, with six grade II/III gliomas reclassified as GBM. Overlap of HGG-typical TACs and LGG-typical TACs was dramatically reduced when tumours were clustered on the basis of their methylation profile. SUVmax/BG values of GBM were higher than those of LGGs following both histological diagnosis and methylation-based diagnosis. The differences in TTP between GBMs and grade II/III gliomas were greater following methylation-based diagnosis than following histological diagnosis. Kinetic modeling showed that relative K1 and fractal dimension (FD) values significantly differed in histology- and methylation-based GBM and grade II/III glioma between those diagnosed histologically and those diagnosed by

  19. Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue

    Directory of Open Access Journals (Sweden)

    Woodfine Kathryn

    2011-01-01

    -line and the somatic DMRs. Conclusions Our validated pyrosequencing methylation assays can be widely used as a tool to investigate DNA methylation levels of imprinted genes in clinical samples. This first comprehensive analysis of normal methylation levels in adult somatic tissues at human imprinted regions confirm that, despite intra-individual variability and tissue specific expression, imprinted genes faithfully maintain their DNA methylation in healthy adult tissue. DNA methylation levels of a selection of imprinted genes are, therefore, a valuable indicator for epigenetic stability.

  20. Photometric Analysis and Period Investigation of the EW Type ...

    Indian Academy of Sciences (India)

    Photometric Analysis and Period Investigation of the EW Type. Eclipsing ... binary with the less massive secondary component filling the inner Roche lobe. ..... Cox 2000) assuming that the primary component is a normal main sequence star.

  1. A parallel and sensitive software tool for methylation analysis on multicore platforms.

    Science.gov (United States)

    Tárraga, Joaquín; Pérez, Mariano; Orduña, Juan M; Duato, José; Medina, Ignacio; Dopazo, Joaquín

    2015-10-01

    DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed. We present a new software tool, called HPG-Methyl, which efficiently maps bisulphite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows-Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPG-Methyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulphite reads. Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymous@clariano.uv.es (password 'anonymous'). juan.orduna@uv.es or jdopazo@cipf.es. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  2. Diagnostic value of WIF1 methylation for colorectal cancer: a meta-analysis

    OpenAIRE

    Hu, Haochang; Li, Bin; Zhou, Cong; Ying, Xiuru; Chen, Min; Huang, Tianyi; Chen, Yuehong; Ji, Huihui; Pan, Ranran; Wang, Tiangong; Jiang, Danjie; Chen, Yanfei; Yang, Yong; Duan, Shiwei

    2018-01-01

    As a common antagonist of Wnt/β-catenin signaling, Wnt inhibitory factor 1 (WIF1) plays an important role in the tumor progression. The aim of our meta-analysis was to summarize the diagnostic value of WIF1 methylation in colorectal cancer (CRC). Eligible studies were retrieved by a systemic search among PubMed, Embase, CNKI, and Wanfang literature databases. The diagnostic value of WIF1 methylation for CRC was assessed by the summary receiver operating characteristics (SROC) test. Our meta-a...

  3. msap: a tool for the statistical analysis of methylation-sensitive amplified polymorphism data.

    Science.gov (United States)

    Pérez-Figueroa, A

    2013-05-01

    In this study msap, an R package which analyses methylation-sensitive amplified polymorphism (MSAP or MS-AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user-friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user-defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN (http://cran.r-project.org/) and its own webpage (http://msap.r-forge.R-project.org/). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses. © 2013 Blackwell Publishing Ltd.

  4. Carbohydrate analysis of hemicelluloses by gas chromatography-mass spectrometry of acteylated methyl glycosides

    DEFF Research Database (Denmark)

    Sárossy, Zsuzsa; Plackett, David; Egsgaard, Helge

    2012-01-01

    A method based on gas chromatography–mass spectrometry analysis of acetylated methyl glycosides was developed in order to analyze monosaccharides obtained from various hemicelluloses. The derivatives of monosaccharide standards, arabinose, glucose, and xylose were studied in detail and 13C...

  5. Determination of DNA methylation associated with Acer rubrum (red maple) adaptation to metals: analysis of global DNA modifications and methylation-sensitive amplified polymorphism.

    Science.gov (United States)

    Kim, Nam-Soo; Im, Min-Ji; Nkongolo, Kabwe

    2016-08-01

    Red maple (Acer rubum), a common deciduous tree species in Northern Ontario, has shown resistance to soil metal contamination. Previous reports have indicated that this plant does not accumulate metals in its tissue. However, low level of nickel and copper corresponding to the bioavailable levels in contaminated soils in Northern Ontario causes severe physiological damages. No differentiation between metal-contaminated and uncontaminated populations has been reported based on genetic analyses. The main objective of this study was to assess whether DNA methylation is involved in A. rubrum adaptation to soil metal contamination. Global cytosine and methylation-sensitive amplified polymorphism (MSAP) analyses were carried out in A. rubrum populations from metal-contaminated and uncontaminated sites. The global modified cytosine ratios in genomic DNA revealed a significant decrease in cytosine methylation in genotypes from a metal-contaminated site compared to uncontaminated populations. Other genotypes from a different metal-contaminated site within the same region appear to be recalcitrant to metal-induced DNA alterations even ≥30 years of tree life exposure to nickel and copper. MSAP analysis showed a high level of polymorphisms in both uncontaminated (77%) and metal-contaminated (72%) populations. Overall, 205 CCGG loci were identified in which 127 were methylated in either outer or inner cytosine. No differentiation among populations was established based on several genetic parameters tested. The variations for nonmethylated and methylated loci were compared by analysis of molecular variance (AMOVA). For methylated loci, molecular variance among and within populations was 1.5% and 13.2%, respectively. These values were low (0.6% for among populations and 5.8% for within populations) for unmethylated loci. Metal contamination is seen to affect methylation of cytosine residues in CCGG motifs in the A. rubrum populations that were analyzed.

  6. Differential Thermal Analysis and Dielectric Studies on 2-Methyl-2-Nitro-Propane under High Pressure

    Science.gov (United States)

    Büsing, D.; Jenau, M.; Reuter, J.; Würflinger, A.; Tamarit, J. Li.

    1995-05-01

    Differential thermal analysis and dielectric studies under pressures up to 300 MPa and temperatures of about 200 to 350 K have been performed on 2-methyl-2-nitro-propane (TBN). TBN displays an orientationally disordered phase (ODIC), solid I, and two non-plastic phases, solids II and III. The coexistence region of the plastic phase I increases with increasing pressure, whereas the low-temperature phase II apparently vanishes at a triple point I, II, III, above 300 MPa. The static permittivity increases on freezing, characterizing the solid I as an ODIC phase. In the frame of the Kirkwood-Onsager-Fröhlich theory the g-factor is about unity, discounting specific dielectric correlations. The dielectric behaviour of TBN is similar to previously studied related compounds, such as 2-chloro-2-methyl-propane or 2-brome- 2-methyl-propane

  7. DAPK1 Promoter Methylation and Cervical Cancer Risk: A Systematic Review and a Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Antonella Agodi

    Full Text Available The Death-Associated Protein Kinase 1 (DAPK1 gene has been frequently investigated in cervical cancer (CC. The aim of the present study was to carry out a systematic review and a meta-analysis in order to evaluate DAPK1 promoter methylation as an epigenetic marker for CC risk.A systematic literature search was carried out. The Cochrane software package Review Manager 5.2 was used. The fixed-effects or random-effects models, according to heterogeneity across studies, were used to calculate odds ratios (ORs and 95% Confidence Intervals (CIs. Furthermore, subgroup analyses were conducted by histological type, assays used to evaluate DAPK1 promoter methylation, and control sample source.A total of 20 papers, published between 2001 and 2014, on 1929 samples, were included in the meta-analysis. DAPK1 promoter methylation was associated with an increased CC risk based on the random effects model (OR: 21.20; 95%CI = 11.14-40.35. Omitting the most heterogeneous study, the between study heterogeneity decreased and the association increased (OR: 24.13; 95% CI = 15.83-36.78. The association was also confirmed in all the subgroups analyses.A significant strong association between DAPK1 promoter methylation and CC was shown and confirmed independently by histological tumor type, method used to evaluate methylation and source of control samples. Methylation markers may have value in early detection of CC precursor lesions, provide added reassurances of safety for women who are candidates for less frequent screens, and predict outcomes of women infected with human papilloma virus.

  8. The application of methylation specific electrophoresis (MSE) to DNA methylation analysis of the 5' CpG island of mucin in cancer cells

    International Nuclear Information System (INIS)

    Yokoyama, Seiya; Yonezawa, Suguru; Kitamoto, Sho; Yamada, Norishige; Houjou, Izumi; Sugai, Tamotsu; Nakamura, Shin-ichi; Arisaka, Yoshifumi; Takaori, Kyoichi; Higashi, Michiyo

    2012-01-01

    Methylation of CpG sites in genomic DNA plays an important role in gene regulation and especially in gene silencing. We have reported mechanisms of epigenetic regulation for expression of mucins, which are markers of malignancy potential and early detection of human neoplasms. Epigenetic changes in promoter regions appear to be the first step in expression of mucins. Thus, detection of promoter methylation status is important for early diagnosis of cancer, monitoring of tumor behavior, and evaluating the response of tumors to targeted therapy. However, conventional analytical methods for DNA methylation require a large amount of DNA and have low sensitivity. Here, we report a modified version of the bisulfite-DGGE (denaturing gradient gel electrophoresis) using a nested PCR approach. We designated this method as methylation specific electrophoresis (MSE). The MSE method is comprised of the following steps: (a) bisulfite treatment of genomic DNA, (b) amplification of the target DNA by a nested PCR approach and (c) applying to DGGE. To examine whether the MSE method is able to analyze DNA methylation of mucin genes in various samples, we apply it to DNA obtained from state cell lines, ethanol-fixed colonic crypts and human pancreatic juices. The MSE method greatly decreases the amount of input DNA. The lower detection limit for distinguishing different methylation status is < 0.1% and the detectable minimum amount of DNA is 20 pg, which can be obtained from only a few cells. We also show that MSE can be used for analysis of challenging samples such as human isolated colonic crypts or human pancreatic juices, from which only a small amount of DNA can be extracted. The MSE method can provide a qualitative information of methylated sequence profile. The MSE method allows sensitive and specific analysis of the DNA methylation pattern of almost any block of multiple CpG sites. The MSE method can be applied to analysis of DNA methylation status in many different clinical

  9. DNA Methylation Analysis of HTR2A Regulatory Region in Leukocytes of Autistic Subjects.

    Science.gov (United States)

    Hranilovic, Dubravka; Blazevic, Sofia; Stefulj, Jasminka; Zill, Peter

    2016-02-01

    Disturbed brain and peripheral serotonin homeostasis is often found in subjects with autism spectrum disorder (ASD). The role of the serotonin receptor 2A (HTR2A) in the regulation of central and peripheral serotonin homeostasis, as well as its altered expression in autistic subjects, have implicated the HTR2A gene as a major candidate for the serotonin disturbance seen in autism. Several studies, yielding so far inconclusive results, have attempted to associate autism with a functional SNP -1438 G/A (rs6311) in the HTR2A promoter region, while possible contribution of epigenetic mechanisms, such as DNA methylation, to HTR2A dysregulation in autism has not yet been investigated. In this study, we compared the mean DNA methylation within the regulatory region of the HTR2A gene between autistic and control subjects. DNA methylation was analysed in peripheral blood leukocytes using bisulfite conversion and sequencing of the HTR2A region containing rs6311 polymorphism. Autistic subjects of rs6311 AG genotype displayed higher mean methylation levels within the analysed region than the corresponding controls (P epigenetic mechanisms might contribute to HTR2A dysregulation observed in individuals with ASD. © 2015 International Society for Autism Research, Wiley Periodicals, Inc.

  10. High Specificity of Quantitative Methylation-Specific PCR Analysis for MGMT Promoter Hypermethylation Detection in Gliomas

    Directory of Open Access Journals (Sweden)

    Paola Parrella

    2009-01-01

    Full Text Available Normal brain tissue from 28 individuals and 50 glioma samples were analyzed by real-time Quantitative Methylation-Specific PCR (QMSP. Data from this analysis were compared with results obtained on the same samples by MSP. QMSP analysis demonstrated a statistically significant difference in both methylation level (P=.000009 Mann Whitney Test and frequencies (P=.0000007, Z-test in tumour samples as compared with normal brain tissues. Although QMSP and MSP showed similar sensitivity, the specificity of QMSP analysis was significantly higher (93%; CI95%: 84%–100% as compared with MSP (64%; 95%CI: 46%–82%. Our results suggest that QMSP analysis may represent a powerful tool to identify glioma patients that will benefit from alkylating agents chemotherapy.

  11. Stratified randomization controls better for batch effects in 450K methylation analysis: A cautionary tale

    Directory of Open Access Journals (Sweden)

    Olive D. Buhule

    2014-10-01

    Full Text Available Background: Batch effects in DNA methylation microarray experiments can lead to spurious results if not properly handled during the plating of samples. Methods: Two pilot studies examining the association of DNA methylation patterns across the genome with obesity in Samoan men were investigated for chip- and row-specific batch effects. For each study, the DNA of 46 obese men and 46 lean men were assayed using Illumina's Infinium HumanMethylation450 BeadChip. In the first study (Sample One, samples from obese and lean subjects were examined on separate chips. In the second study (Sample Two, the samples were balanced on the chips by lean/obese status, age group, and census region. We used methylumi, watermelon, and limma R packages, as well as ComBat, to analyze the data. Principal component analysis and linear regression were respectively employed to identify the top principal components and to test for their association with the batches and lean/obese status. To identify differentially methylated positions (DMPs between obese and lean males at each locus, we used a moderated t-test.Results: Chip effects were effectively removed from Sample Two but not Sample One. In addition, dramatic differences were observed between the two sets of DMP results. After removing'' batch effects with ComBat, Sample One had 94,191 probes differentially methylated at a q-value threshold of 0.05 while Sample Two had zero differentially methylated probes. The disparate results from Sample One and Sample Two likely arise due to the confounding of lean/obese status with chip and row batch effects.Conclusion: Even the best possible statistical adjustments for batch effects may not completely remove them. Proper study design is vital for guarding against spurious findings due to such effects.

  12. Fourier analysis in dynamic non periodic phenomena in nuclear medicine

    International Nuclear Information System (INIS)

    Constantinesco, A.; Lallot, C.

    1984-01-01

    The success of Fourier analysis in assessing cardiac function has led us to investigate other possible uses of this technique. We show that phase analysis applied to dynamic non periodic activity changes gives useful parametric functional images. The phase image is comparable to a transit time image, the amplitude image is comparable to the maximum variations of activity and the mean image corresponds to a normalized sum of images. Exemples of this powerful application of Fourier analysis are discussed [fr

  13. Integrated analysis of epigenomic and genomic changes by DNA methylation dependent mechanisms provides potential novel biomarkers for prostate cancer.

    Science.gov (United States)

    White-Al Habeeb, Nicole M A; Ho, Linh T; Olkhov-Mitsel, Ekaterina; Kron, Ken; Pethe, Vaijayanti; Lehman, Melanie; Jovanovic, Lidija; Fleshner, Neil; van der Kwast, Theodorus; Nelson, Colleen C; Bapat, Bharati

    2014-09-15

    Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated two PCa cell lines, 22Rv1 and DU-145 with the demethylating agent 5-Aza 2'-deoxycitidine (DAC) and global methylation status was analyzed by performing methylation-sensitive restriction enzyme based differential methylation hybridization strategy followed by genome-wide CpG methylation array profiling. In addition, we examined gene expression changes using a custom microarray. Gene Set Enrichment Analysis (GSEA) identified the most significantly dysregulated pathways. In addition, we assessed methylation status of candidate genes that showed reduced CpG methylation and increased gene expression after DAC treatment, in Gleason score (GS) 8 vs. GS6 patients using three independent cohorts of patients; the publically available The Cancer Genome Atlas (TCGA) dataset, and two separate patient cohorts. Our analysis, by integrating methylation and gene expression in PCa cell lines, combined with patient tumor data, identified novel potential biomarkers for PCa patients. These markers may help elucidate the pathogenesis of PCa and represent potential prognostic markers for PCa patients.

  14. Sensitivity analysis of periodic errors in heterodyne interferometry

    International Nuclear Information System (INIS)

    Ganguly, Vasishta; Kim, Nam Ho; Kim, Hyo Soo; Schmitz, Tony

    2011-01-01

    Periodic errors in heterodyne displacement measuring interferometry occur due to frequency mixing in the interferometer. These nonlinearities are typically characterized as first- and second-order periodic errors which cause a cyclical (non-cumulative) variation in the reported displacement about the true value. This study implements an existing analytical periodic error model in order to identify sensitivities of the first- and second-order periodic errors to the input parameters, including rotational misalignments of the polarizing beam splitter and mixing polarizer, non-orthogonality of the two laser frequencies, ellipticity in the polarizations of the two laser beams, and different transmission coefficients in the polarizing beam splitter. A local sensitivity analysis is first conducted to examine the sensitivities of the periodic errors with respect to each input parameter about the nominal input values. Next, a variance-based approach is used to study the global sensitivities of the periodic errors by calculating the Sobol' sensitivity indices using Monte Carlo simulation. The effect of variation in the input uncertainty on the computed sensitivity indices is examined. It is seen that the first-order periodic error is highly sensitive to non-orthogonality of the two linearly polarized laser frequencies, while the second-order error is most sensitive to the rotational misalignment between the laser beams and the polarizing beam splitter. A particle swarm optimization technique is finally used to predict the possible setup imperfections based on experimentally generated values for periodic errors

  15. Sensitivity analysis of periodic errors in heterodyne interferometry

    Science.gov (United States)

    Ganguly, Vasishta; Kim, Nam Ho; Kim, Hyo Soo; Schmitz, Tony

    2011-03-01

    Periodic errors in heterodyne displacement measuring interferometry occur due to frequency mixing in the interferometer. These nonlinearities are typically characterized as first- and second-order periodic errors which cause a cyclical (non-cumulative) variation in the reported displacement about the true value. This study implements an existing analytical periodic error model in order to identify sensitivities of the first- and second-order periodic errors to the input parameters, including rotational misalignments of the polarizing beam splitter and mixing polarizer, non-orthogonality of the two laser frequencies, ellipticity in the polarizations of the two laser beams, and different transmission coefficients in the polarizing beam splitter. A local sensitivity analysis is first conducted to examine the sensitivities of the periodic errors with respect to each input parameter about the nominal input values. Next, a variance-based approach is used to study the global sensitivities of the periodic errors by calculating the Sobol' sensitivity indices using Monte Carlo simulation. The effect of variation in the input uncertainty on the computed sensitivity indices is examined. It is seen that the first-order periodic error is highly sensitive to non-orthogonality of the two linearly polarized laser frequencies, while the second-order error is most sensitive to the rotational misalignment between the laser beams and the polarizing beam splitter. A particle swarm optimization technique is finally used to predict the possible setup imperfections based on experimentally generated values for periodic errors.

  16. MLH1 Promoter Methylation and Prediction/Prognosis of Gastric Cancer: A Systematic Review and Meta and Bioinformatic Analysis.

    Science.gov (United States)

    Shen, Shixuan; Chen, Xiaohui; Li, Hao; Sun, Liping; Yuan, Yuan

    2018-01-01

    Background: The promoter methylation of MLH1 gene and gastric cancer (GC)has been investigated previously. To get a more credible conclusion, we performed a systematic review and meta and bioinformatic analysis to clarify the role of MLH1 methylation in the prediction and prognosis of GC. Methods: Eligible studies were targeted after searching the PubMed, Web of Science, Embase, BIOSIS, CNKI and Wanfang Data to collect the information of MLH1 methylation and GC. The link strength between the two was estimated by odds ratio with its 95% confidence interval. The Newcastle-Ottawa scale was used for quantity assessment . Subgroup and sensitivity analysis were conducted to explore sources of heterogeneity. The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were employed for bioinformatics analysis on the correlation between MLH1 methylation and GC risk, clinicopathological behavior as well as prognosis. Results: 2365 GC and 1563 controls were included in the meta-analysis. The pooled OR of MLH1 methylation in GC was 4.895 (95% CI: 3.149-7.611, PMLH1 methylation enhanced GC risk but might not related with GC clinicopathological features and prognosis. Conclusion: MLH1 methylation is an alive biomarker for the prediction of GC and it might not affect GC behavior. Further study could be conducted to verify the impact of MLH1 methylation on GC prognosis.

  17. Anti-N-Methyl-d-Aspartate receptor (NMDAR) encephalitis during pregnancy: Clinical analysis of reported cases.

    Science.gov (United States)

    Shi, Yan-Chao; Chen, Xiu-Ju; Zhang, Hong-Mei; Wang, Zhen; Du, Da-Yong

    2017-06-01

    To analyze the clinical features of 13 pregnant patients with anti-N-Methyl-d-Aspartate receptor (NMDAR) encephalitis. Retrospective review of thirteen reported cases was conducted for anti-NMDAR encephalitis patients during pregnancy. The clinical data were collected from papers published in PubMed prior to 16 February 2016. Statistical analysis of the data was performed, which encompasses the patients' age, past medical history, onset of symptoms, concomitant with ovarian teratomas, immunotherapy, outcomes of mothers and newborns. Thirteen cases were reported in 11 articles with a median age of 23 (interquartile range, 19-27) years old. There were eight cases in which the onset periods of gestation happened in the first trimester and five cases in the second trimester. Among 13 cases, five patients had a past medical history, one concomitant with autoimmune Graves' hyperthyroidism, one with bilateral ovarian teratomas removed history, one with anti-NMDAR encephalitis five years before pregnancy and two with psychiatric symptoms. Five patients were found with ovarian teratomas. Seven patients responded to first-line immunotherapy whereas all of two patients responded to second-line immunotherapy when the first-line immunotherapy failed. Following up all the 13 patients, most experienced a substantial recovery, except one had spasticity and dystonia in one hand, and one died of a superimposed infection. Three fetuses were miscarried or aborted in total. Most newborns were healthy, except two cases (2/10) with abnormal neurologic signs. Clinical analysis of the data indicates that most patients respond to first-line immunotherapy. A second-line immunotherapy is effective when first-line immunotherapy fails. It has also been found that most mothers and newborns can have good outcomes. Copyright © 2017. Published by Elsevier B.V.

  18. Correlation of pathologic features with CpG island methylator phenotype (CIMP) by quantitative DNA methylation analysis in colorectal carcinoma.

    Science.gov (United States)

    Ogino, Shuji; Odze, Robert D; Kawasaki, Takako; Brahmandam, Mohan; Kirkner, Gregory J; Laird, Peter W; Loda, Massimo; Fuchs, Charles S

    2006-09-01

    Extensive gene promoter methylation in colorectal carcinoma has been termed the CpG island methylator phenotype (CIMP). Previous studies on CIMP used primarily methylation-specific polymerase chain reaction (PCR), which, unfortunately, may detect low levels of methylation that has little or no biological significance. Utilizing quantitative real-time PCR (MethyLight), we measured DNA methylation in a panel of 5 CIMP-specific gene promoters (CACNA1G, CDKN2A (p16), CRABP1, MLH1, and NEUROG1) in 459 colorectal carcinomas obtained from 2 large prospective cohort studies. CIMP was defined as tumors that showed methylation in >or=4/5 promoters. CIMP was significantly associated with the presence of mucinous or signet ring cell morphology, marked Crohn's-like lymphoid reaction, tumor infiltrating lymphocytes, marked peritumoral lymphocytic reaction, tumor necrosis, tumor cell sheeting, and poor differentiation. All these features have previously been associated with microsatellite instability (MSI). Therefore, we divided the 459 colorectal carcinomas into 6 subtypes, namely, MSI-high (MSI-H)/CIMP, MSI-H/non-CIMP, MSI-low (MSI-L)/CIMP, MSI-L/non-CIMP, microsatellite stable/CIMP, and micro satellite sstable/non-CIMP. Compared with MSI-H/non-CIMP, MSI-H/CIMP was associated with marked tumor infiltrating lymphocytes, tumor necrosis, sheeting, and poor differentiation (all PCIMP, MSI-L/CIMP was associated with tumors that had CIMP. Both MSI and CIMP appear to play a role in the pathogenesis of specific morphologic patterns of colorectal carcinoma.

  19. Mutation and Methylation Analysis of the Chromodomain-Helicase-DNA Binding 5 Gene in Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Kylie L. Gorringe

    2008-11-01

    Full Text Available Chromodomain, helicase, DNA binding 5 (CHD5 is a member of a subclass of the chromatin remodeling Swi/Snf proteins and has recently been proposed as a tumor suppressor in a diverse range of human cancers. We analyzed all 41 coding exons of CHD5 for somatic mutations in 123 primary ovarian cancers as well as 60 primary breast cancers using high-resolution melt analysis. We also examined methylation of the CHD5 promoter in 48 ovarian cancer samples by methylation-specific single-stranded conformation polymorphism and bisulfite sequencing. In contrast to previous studies, no mutations were identified in the breast cancers, but somatic heterozygous missense mutations were identified in 3 of 123 ovarian cancers. We identified promoter methylation in 3 of 45 samples with normal CHD5 and in 2 of 3 samples with CHD5 mutation, suggesting these tumors may have biallelic inactivation of CHD5. Hemizygous copy number loss at CHD5 occurred in 6 of 85 samples as assessed by single nucleotide polymorphism array. Tumors with CHD5 mutation or methylation were more likely to have mutation of KRAS or BRAF (P = .04. The aggregate frequency of CHD5 haploinsufficiency or inactivation is 16.2% in ovarian cancer. Thus, CHD5 may play a role as a tumor suppressor gene in ovarian cancer; however, it is likely that there is another target of the frequent copy number neutral loss of heterozygosity observed at 1p36.

  20. Periodic radio variability in NRAO 530: phase dispersion minimization analysis

    International Nuclear Information System (INIS)

    Lu Junchao; Lin Jiming; Qiu Hongbing; Wang Junyi; An Tao

    2012-01-01

    A periodicity analysis of the radio light curves of the blazar NRAO 530 at 14.5, 8.0, and 4.8 GHz is presented employing an improved phase dispersion minimization technique. The result, which shows two persistent periodic components of ∼ 6 and ∼ 10 yr at all three frequencies, is consistent with the results obtained with the Lomb-Scargle periodogram and weighted wavelet Z-transform algorithms. The reliability of the derived periodicities is confirmed by the Monte Carlo numerical simulations which show a high statistical confidence. (Quasi-)Periodic fluctuations of the radio luminosity of NRAO 530 might be associated with the oscillations of the accretion disk triggered by hydrodynamic instabilities of the accreted flow. (research papers)

  1. DNA methylation map in circulating leukocytes mirrors subcutaneous adipose tissue methylation pattern: a genome-wide analysis from non-obese and obese patients

    Science.gov (United States)

    Crujeiras, A. B.; Diaz-Lagares, A.; Sandoval, J.; Milagro, F. I.; Navas-Carretero, S.; Carreira, M. C.; Gomez, A.; Hervas, D.; Monteiro, M. P.; Casanueva, F. F.; Esteller, M.; Martinez, J. A.

    2017-01-01

    The characterization of the epigenetic changes within the obesity-related adipose tissue will provide new insights to understand this metabolic disorder, but adipose tissue is not easy to sample in population-based studies. We aimed to evaluate the capacity of circulating leukocytes to reflect the adipose tissue-specific DNA methylation status of obesity susceptibility. DNA samples isolated from subcutaneous adipose tissue and circulating leukocytes were hybridized in the Infinium HumanMethylation 450 BeadChip. Data were compared between samples from obese (n = 45) and non-obese (n = 8–10) patients by Wilcoxon-rank test, unadjusted for cell type distributions. A global hypomethylation of the differentially methylated CpG sites (DMCpGs) was observed in the obese subcutaneous adipose tissue and leukocytes. The overlap analysis yielded a number of genes mapped by the common DMCpGs that were identified to reflect the obesity state in the leukocytes. Specifically, the methylation levels of FGFRL1, NCAPH2, PNKD and SMAD3 exhibited excellent and statistically significant efficiencies in the discrimination of obesity from non-obesity status (AUC > 0.80; p obesity-related adipose tissue pathogenesis through peripheral blood analysis, an easily accessible and minimally invasive biological material instead of adipose tissue. PMID:28211912

  2. Stability Analysis for Multi-Parameter Linear Periodic Systems

    DEFF Research Database (Denmark)

    Seyranian, A.P.; Solem, Frederik; Pedersen, Pauli

    1999-01-01

    This paper is devoted to stability analysis of general linear periodic systems depending on real parameters. The Floquet method and perturbation technique are the basis of the development. We start out with the first and higher-order derivatives of the Floquet matrix with respect to problem...

  3. ChAMP: updated methylation analysis pipeline for Illumina BeadChips.

    Science.gov (United States)

    Tian, Yuan; Morris, Tiffany J; Webster, Amy P; Yang, Zhen; Beck, Stephan; Feber, Andrew; Teschendorff, Andrew E

    2017-12-15

    The Illumina Infinium HumanMethylationEPIC BeadChip is the new platform for high-throughput DNA methylation analysis, effectively doubling the coverage compared to the older 450 K array. Here we present a significantly updated and improved version of the Bioconductor package ChAMP, which can be used to analyze EPIC and 450k data. Many enhanced functionalities have been added, including correction for cell-type heterogeneity, network analysis and a series of interactive graphical user interfaces. ChAMP is a BioC package available from https://bioconductor.org/packages/release/bioc/html/ChAMP.html. a.teschendorff@ucl.ac.uk or s.beck@ucl.ac.uk or a.feber@ucl.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  4. Analysis of chemical signatures of alkaliphiles using fatty acid methyl ester analysis

    Directory of Open Access Journals (Sweden)

    Basha Sreenivasulu

    2017-01-01

    Full Text Available Background: Fatty acids occur in nearly all living organisms as the important predominant constituents of lipids. While all fatty acids have essentially the same chemical nature, they are an extremely diverse group of compounds. Materials and Methods: To test the hypothesis, fatty acids of alkaliphiles isolates, Bacillus subtilis SVUNM4, Bacillus licheniformis SVUNM8, Bacillus methylotrohicus SVUNM9, and Paenibacillus dendritiformis SVUNM11, were characterized compared using gas chromatography-mass spectrometry (GC-MS analysis. Results: The content of investigated ten fatty acids, 1, 2-benzenedicarboxylic acid butyl 2-methylpropyl ester, phthalic acid, isobutyl 2-pentyl ester, dibutyl phthalate, cyclotrisiloxane, hexamethyl, cyclotetrasiloxane, octamethyl, dodecamethyl, heptasiloxane 1,1,3,3,5,5,7,7,9,9,11,11,13,13-etradecamethyl, 7,15-dihydroxydehydroabietic acid, methyl ester, di (trimethylsilyl ether, hentriacontane, 2-thiopheneacetic acid, undec-2-enyl ester, obviously varied among four species, suggesting each species has its own fatty acid pattern. Conclusions: These findings demonstrated that GC-MS-based fatty acid profiling analysis provides the reliable platform to classify these four species, which is helpful for ensuring their biotechnological interest and novel chemotaxonomic.

  5. DNA Methylation Analysis of the Angiotensin Converting Enzyme (ACE) Gene in Major Depression

    Science.gov (United States)

    Zill, Peter; Baghai, Thomas C.; Schüle, Cornelius; Born, Christoph; Früstück, Clemens; Büttner, Andreas; Eisenmenger, Wolfgang; Varallo-Bedarida, Gabriella; Rupprecht, Rainer; Möller, Hans-Jürgen; Bondy, Brigitta

    2012-01-01

    Background The angiotensin converting enzyme (ACE) has been repeatedly discussed as susceptibility factor for major depression (MD) and the bi-directional relation between MD and cardiovascular disorders (CVD). In this context, functional polymorphisms of the ACE gene have been linked to depression, to antidepressant treatment response, to ACE serum concentrations, as well as to hypertension, myocardial infarction and CVD risk markers. The mostly investigated ACE Ins/Del polymorphism accounts for ∼40%–50% of the ACE serum concentration variance, the remaining half is probably determined by other genetic, environmental or epigenetic factors, but these are poorly understood. Materials and Methods The main aim of the present study was the analysis of the DNA methylation pattern in the regulatory region of the ACE gene in peripheral leukocytes of 81 MD patients and 81 healthy controls. Results We detected intensive DNA methylation within a recently described, functional important region of the ACE gene promoter including hypermethylation in depressed patients (p = 0.008) and a significant inverse correlation between the ACE serum concentration and ACE promoter methylation frequency in the total sample (p = 0.02). Furthermore, a significant inverse correlation between the concentrations of the inflammatory CVD risk markers ICAM-1, E-selectin and P-selectin and the degree of ACE promoter methylation in MD patients could be demonstrated (p = 0.01 - 0.04). Conclusion The results of the present study suggest that aberrations in ACE promoter DNA methylation may be an underlying cause of MD and probably a common pathogenic factor for the bi-directional relationship between MD and cardiovascular disorders. PMID:22808171

  6. DNA methylation analysis of the angiotensin converting enzyme (ACE gene in major depression.

    Directory of Open Access Journals (Sweden)

    Peter Zill

    Full Text Available BACKGROUND: The angiotensin converting enzyme (ACE has been repeatedly discussed as susceptibility factor for major depression (MD and the bi-directional relation between MD and cardiovascular disorders (CVD. In this context, functional polymorphisms of the ACE gene have been linked to depression, to antidepressant treatment response, to ACE serum concentrations, as well as to hypertension, myocardial infarction and CVD risk markers. The mostly investigated ACE Ins/Del polymorphism accounts for ~40%-50% of the ACE serum concentration variance, the remaining half is probably determined by other genetic, environmental or epigenetic factors, but these are poorly understood. MATERIALS AND METHODS: The main aim of the present study was the analysis of the DNA methylation pattern in the regulatory region of the ACE gene in peripheral leukocytes of 81 MD patients and 81 healthy controls. RESULTS: We detected intensive DNA methylation within a recently described, functional important region of the ACE gene promoter including hypermethylation in depressed patients (p = 0.008 and a significant inverse correlation between the ACE serum concentration and ACE promoter methylation frequency in the total sample (p = 0.02. Furthermore, a significant inverse correlation between the concentrations of the inflammatory CVD risk markers ICAM-1, E-selectin and P-selectin and the degree of ACE promoter methylation in MD patients could be demonstrated (p = 0.01 - 0.04. CONCLUSION: The results of the present study suggest that aberrations in ACE promoter DNA methylation may be an underlying cause of MD and probably a common pathogenic factor for the bi-directional relationship between MD and cardiovascular disorders.

  7. Targeted DNA Methylation Analysis by High Throughput Sequencing in Porcine Peri-attachment Embryos

    OpenAIRE

    MORRILL, Benson H.; COX, Lindsay; WARD, Anika; HEYWOOD, Sierra; PRATHER, Randall S.; ISOM, S. Clay

    2013-01-01

    Abstract The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples. Fourteen discrete genomic regions were amplified by PCR using bisulfite-converted genomic DNA derived from day 14 in vivo-derived (IVV) and parthenogenetic (PA) porcine embryos as template DNA. Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx plat...

  8. Reliability analysis of structures under periodic proof tests in service

    Science.gov (United States)

    Yang, J.-N.

    1976-01-01

    A reliability analysis of structures subjected to random service loads and periodic proof tests treats gust loads and maneuver loads as random processes. Crack initiation, crack propagation, and strength degradation are treated as the fatigue process. The time to fatigue crack initiation and ultimate strength are random variables. Residual strength decreases during crack propagation, so that failure rate increases with time. When a structure fails under periodic proof testing, a new structure is built and proof-tested. The probability of structural failure in service is derived from treatment of all the random variables, strength degradations, service loads, proof tests, and the renewal of failed structures. Some numerical examples are worked out.

  9. Periodic tests: a human factors analysis of documentary aspects

    International Nuclear Information System (INIS)

    Perinet, Romuald; Rousseau, Jean-Marie

    2007-01-01

    Periodic tests are technical inspections aimed at verifying the availability of the safety-related systems during operation. The French licensee, Electricite de France (EDF), manages periodic tests according to procedures, methods of examination and a frequency, which were defined when the systems were designed. These requirements are defined by national authorities of EDF in a reference document composed of rules of testing and tables containing the reference values to be respected. This reference document is analyzed and transformed by each 'Centre Nucleaire de Production d'Electricite' (CNPE) into station-specific operating ranges of periodic tests. In 2003, the IRSN noted that significant events for safety (ESS) involving periodic tests represented more than 20% of ESS between 2000 and 2002. Thus, 340 ESS were related to non-compliance with the conditions of the test and errors in the implementation of the procedures. A first analysis showed that almost 26% of all ESSs from 2000 to 2002 were related to periodic tests. For many of them, the national reference document and the operating ranges of tests were involved. In this context, the 'Direction Generale de la Surete Nucleaire' (DGSNR), requested the 'Institut de Radioprotection et de Surete Nucleaire' (IRSN) to examine the process of definition and implementation of the periodic tests. The IRSN analyzed about thirty French Licensee event reports occurring during the considered period (2000-2002). The IRSN also interviewed the main persons responsible for the processes and observed the performance of 3 periodic tests. The results of this analysis were presented to a group of experts ('Groupe Permanent') charged with delivering advice to the DGSNR about the origin of the problems identified and the improvements to be implemented. The main conclusions of the IRSN addressed the quality of the prescriptive documents. In this context, EDF decided to carry out a thorough analysis of the whole process. The first

  10. The Combined Effect of Methyl- and Ethyl-Paraben on Lifespan and Preadult Development Period of Drosophila melanogaster (Diptera: Drosophilidae).

    Science.gov (United States)

    Chen, Qi; Pan, Chenguang; Li, Yajuan; Zhang, Min; Gu, Wei

    2016-01-01

    Parabens are widely used as preservative substances in foods, pharmaceuticals, industrial products, and cosmetics. But several studies have cautioned that parabens have estrogenic or endocrine-disrupting properties. Drosophila melanogaster is an ideal model in vivo to detect the toxic effects of chemistry. The study was designed to assess the potential additive toxic effects of methylparaben (MP) and ethylparaben (EP) mixture (MP + EP) on lifespan and preadult development period in D. melanogaster The data revealed that the MP + EP can reduce the longevity of flies compared with the control group, consistent with a significant reduction in malondialdehyde levels and an increase in superoxide dismutase activities. Furthermore, MP + EP may have a greater toxic effect on longevity of flies than separate using with the same concentration. Additionally, parabens had a nonmonotonic dose-response effect on D. melanogaster preadult development period, showing that MP + EP delayed preadult development period compared with control group while individual MP or EP significantly shortened (P melanogaster. © The Author 2016. Published by Oxford University Press on behalf of the Entomological Society of America.

  11. [GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value].

    Science.gov (United States)

    Skorodumova, L O; Babalyan, K A; Sultanov, R; Vasiliev, A O; Govorov, A V; Pushkar, D Y; Prilepskaya, E A; Danilenko, S A; Generozov, E V; Larin, A K; Kostryukova, E S; Sharova, E I

    2016-11-01

    There is a clear need in molecular markers for prostate cancer (PC) risk stratification. Alteration of DNA methylation is one of processes that occur during ÐÑ progression. Methylation-sensitive PCR with high resolution melting curve analysis (MS-HRM) can be used for gene methylation analysis in routine laboratory practice. This method requires very small amounts of DNA for analysis. Numerous results have been accumulated on DNA methylation in PC samples analyzed by the Infinium HumanMethylation450 BeadChip (HM450). However, the consistency of MS-HRM results with chip hybridization results has not been examined yet. The aim of this study was to assess the consistency of results of GSTP1, APC and RASSF1 gene methylation analysis in ÐÑ biopsy samples obtained by MS-HRM and chip hybridization. The methylation levels of each gene determined by MS-HRM were statistically different in the group of PC tissue samples and the samples without signs of tumor growth. Chip hybridization data analysis confirmed the results obtained with the MS-HRM. Differences in methylation levels between tumor tissue and histologically intact tissue of each sample determined by MS-HRM and chip hybridization, were consistent with each other. Thus, we showed that the assessment of GSTP1, APC and RASSF1 gene methylation analysis using MS-HRM is suitable for the design of laboratory assays that will differentiate the PC tissue from the tissue without signs of tumor growth.

  12. CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers.

    Science.gov (United States)

    Gu, Fei; Doderer, Mark S; Huang, Yi-Wen; Roa, Juan C; Goodfellow, Paul J; Kizer, E Lynette; Huang, Tim H M; Chen, Yidong

    2013-01-01

    DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. Also, experimental and computational technologies make it possible to find the functional relationship between cancer-specific methylation patterns and their clinicopathological parameters. Cancer methylome system (CMS) is a web-based database application designed for the visualization, comparison and statistical analysis of human cancer-specific DNA methylation. Methylation intensities were obtained from MBDCap-sequencing, pre-processed and stored in the database. 191 patient samples (169 tumor and 22 normal specimen) and 41 breast cancer cell-lines are deposited in the database, comprising about 6.6 billion uniquely mapped sequence reads. This provides comprehensive and genome-wide epigenetic portraits of human breast cancer and endometrial cancer to date. Two views are proposed for users to better understand methylation structure at the genomic level or systemic methylation alteration at the gene level. In addition, a variety of annotation tracks are provided to cover genomic information. CMS includes important analytic functions for interpretation of methylation data, such as the detection of differentially methylated regions, statistical calculation of global methylation intensities, multiple gene sets of biologically significant categories, interactivity with UCSC via custom-track data. We also present examples of discoveries utilizing the framework. CMS provides visualization and analytic functions for cancer methylome datasets. A comprehensive collection of datasets, a variety of embedded analytic functions and extensive applications with biological and translational significance make this system powerful and unique in cancer methylation research. CMS is freely accessible

  13. Stability Analysis of Periodic Systems by Truncated Point Mappings

    Science.gov (United States)

    Guttalu, R. S.; Flashner, H.

    1996-01-01

    An approach is presented deriving analytical stability and bifurcation conditions for systems with periodically varying coefficients. The method is based on a point mapping(period to period mapping) representation of the system's dynamics. An algorithm is employed to obtain an analytical expression for the point mapping and its dependence on the system's parameters. The algorithm is devised to derive the coefficients of a multinominal expansion of the point mapping up to an arbitrary order in terms of the state variables and of the parameters. Analytical stability and bifurcation condition are then formulated and expressed as functional relations between the parameters. To demonstrate the application of the method, the parametric stability of Mathieu's equation and of a two-degree of freedom system are investigated. The results obtained by the proposed approach are compared to those obtained by perturbation analysis and by direct integration which we considered to the "exact solution". It is shown that, unlike perturbation analysis, the proposed method provides very accurate solution even for large valuesof the parameters. If an expansion of the point mapping in terms of a small parameter is performed the method is equivalent to perturbation analysis. Moreover, it is demonstrated that the method can be easily applied to multiple-degree-of-freedom systems using the same framework. This feature is an important advantage since most of the existing analysis methods apply mainly to single-degree-of-freedom systems and their extension to higher dimensions is difficult and computationally cumbersome.

  14. Exercise-associated DNA methylation change in skeletal muscle and the importance of imprinted genes: a bioinformatics meta-analysis.

    Science.gov (United States)

    Brown, William M

    2015-12-01

    Epigenetics is the study of processes--beyond DNA sequence alteration--producing heritable characteristics. For example, DNA methylation modifies gene expression without altering the nucleotide sequence. A well-studied DNA methylation-based phenomenon is genomic imprinting (ie, genotype-independent parent-of-origin effects). We aimed to elucidate: (1) the effect of exercise on DNA methylation and (2) the role of imprinted genes in skeletal muscle gene networks (ie, gene group functional profiling analyses). Gene ontology (ie, gene product elucidation)/meta-analysis. 26 skeletal muscle and 86 imprinted genes were subjected to g:Profiler ontology analysis. Meta-analysis assessed exercise-associated DNA methylation change. g:Profiler found four muscle gene networks with imprinted loci. Meta-analysis identified 16 articles (387 genes/1580 individuals) associated with exercise. Age, method, sample size, sex and tissue variation could elevate effect size bias. Only skeletal muscle gene networks including imprinted genes were reported. Exercise-associated effect sizes were calculated by gene. Age, method, sample size, sex and tissue variation were moderators. Six imprinted loci (RB1, MEG3, UBE3A, PLAGL1, SGCE, INS) were important for muscle gene networks, while meta-analysis uncovered five exercise-associated imprinted loci (KCNQ1, MEG3, GRB10, L3MBTL1, PLAGL1). DNA methylation decreased with exercise (60% of loci). Exercise-associated DNA methylation change was stronger among older people (ie, age accounted for 30% of the variation). Among older people, genes exhibiting DNA methylation decreases were part of a microRNA-regulated gene network functioning to suppress cancer. Imprinted genes were identified in skeletal muscle gene networks and exercise-associated DNA methylation change. Exercise-associated DNA methylation modification could rewind the 'epigenetic clock' as we age. CRD42014009800. Published by the BMJ Publishing Group Limited. For permission to use (where

  15. Gas chromatography-vacuum ultraviolet spectroscopy for analysis of fatty acid methyl esters.

    Science.gov (United States)

    Fan, Hui; Smuts, Jonathan; Bai, Ling; Walsh, Phillip; Armstrong, Daniel W; Schug, Kevin A

    2016-03-01

    A new vacuum ultraviolet (VUV) detector for gas chromatography was recently developed and applied to fatty acid methyl ester (FAME) analysis. VUV detection features full spectral acquisition in a wavelength range of 115-240nm, where virtually all chemical species absorb. VUV absorption spectra of 37 FAMEs, including saturated, monounsaturated, and polyunsaturated types were recorded. Unsaturated FAMEs show significantly different gas phase absorption profiles than saturated ones, and these classes can be easily distinguished with the VUV detector. Another advantage includes differentiating cis/trans-isomeric FAMEs (e.g. oleic acid methyl ester and linoleic acid methyl ester isomers) and the ability to use VUV data analysis software for deconvolution of co-eluting signals. As a universal detector, VUV also provides high specificity, sensitivity, and a fast data acquisition rate, making it a powerful tool for fatty acid screening when combined with gas chromatography. The fatty acid profile of several food oil samples (olive, canola, vegetable, corn, sunflower and peanut oils) were analyzed in this study to demonstrate applicability to real world samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. DNA methylation analysis of allotetraploid hybrids of red crucian carp (Carassius auratus red var. and common carp (Cyprinus carpio L..

    Directory of Open Access Journals (Sweden)

    Jun Xiao

    Full Text Available Hybridization and polyploidization may lead to divergence in adaptation and boost speciation in angiosperms and some lower animals. Epigenetic change plays a significant role in the formation and adaptation of polyploidy. Studies of the effects of methylation on genomic recombination and gene expression in allopolyploid plants have achieved good progress. However, relevant advances in polyploid animals have been relatively slower. In the present study, we used the bisexual, fertile, genetically stable allotetraploid generated by hybridization of Carassius auratus red var. and Cyprinus carpio L. to investigate cytosine methylation level using methylation-sensitive amplification polymorphism (MSAP analysis. We observed 38.31% of the methylation changes in the allotetraploid compared with the parents at 355 randomly selected CCGG sites. In terms of methylation status, these results indicate that the level of methylation modification in the allotetraploid may have increased relative to that in the parents. We also found that the major methylation changes were hypermethylation on some genomic fragments and genes related to metabolism or cell cycle regulation. These results provide circumstantial evidence that DNA methylation might be related to the gene expression and phenotype variation in allotetraploid hybrids. Our study partly fulfils the need for epigenetic research in polyploid animals, and provides evidence for the epigenetic regulation of allopolyploids.

  17. Analysis of methylation profiling data of hyperplasia and primary and metastatic endometrial cancers.

    Science.gov (United States)

    Wu, Xihai; Miao, Jilan; Jiang, Jingyan; Liu, Fangmei

    2017-10-01

    Endometrial cancer is a prevalent cancer, and its metastasis causes low survival rate. This study aims to utilize DNA methylation data to investigate the mechanism of the development and metastasis of endometrial cancer. Methylation profiling data were down-loaded from Gene Expression Omnibus, including 8 hyperplasias, 33 primary and 53 metastatic endometrial cancers. COHCAP package and annotation files were utilized to identify differentially methylated genes (DMGs) and CpG islands between the three different endometrial diseases. STRING database and Cytoscape were used to analyze and visualize protein-protein interactions (PPIs) between DMGs. CytoNCA plugin was utilized to identify key nodes in PPI network. A total of 610, 1076, and 501 DMGs were identified between primary endometrial cancer and hyperplasia, metastatic endometrial cancer and hyperplasia, as well as metastatic and primary endometrial cancers, respectively. For the three DMG sets, 53 common hypermethylated DMGs (e.g. PAX6 and INSR) and 6 common hypomethylated DMGs (e.g. PRDM8, KLHL14, and DUSP6) were found. For primary-hyperplasia DMG set and metastasis-hyperplasia DMG set, 527 common DMGs were found. For these common DMGs, a PPI network involving 692 PPIs was constructed. For DMGs between metastatic and primary endometrial cancers, a PPI network involving 673 PPIs was established, with PAX6 and INSR in the top 20 DMGs in both networks. PRDM8, KLHL14, and DUSP6 had hypomethylated CpG islands. DMGs comparison, PPI network analysis, and analysis of differentially methylated CpG islands indicated that PAX6, INSR, PRDM8, KLHL14, and DUSP6 might participate in the development and metastasis of endometrial cancer. Copyright © 2017. Published by Elsevier B.V.

  18. In vitro analysis of integrated global high-resolution DNA methylation profiling with genomic imbalance and gene expression in osteosarcoma.

    Directory of Open Access Journals (Sweden)

    Bekim Sadikovic

    Full Text Available Genetic and epigenetic changes contribute to deregulation of gene expression and development of human cancer. Changes in DNA methylation are key epigenetic factors regulating gene expression and genomic stability. Recent progress in microarray technologies resulted in developments of high resolution platforms for profiling of genetic, epigenetic and gene expression changes. OS is a pediatric bone tumor with characteristically high level of numerical and structural chromosomal changes. Furthermore, little is known about DNA methylation changes in OS. Our objective was to develop an integrative approach for analysis of high-resolution epigenomic, genomic, and gene expression profiles in order to identify functional epi/genomic differences between OS cell lines and normal human osteoblasts. A combination of Affymetrix Promoter Tilling Arrays for DNA methylation, Agilent array-CGH platform for genomic imbalance and Affymetrix Gene 1.0 platform for gene expression analysis was used. As a result, an integrative high-resolution approach for interrogation of genome-wide tumour-specific changes in DNA methylation was developed. This approach was used to provide the first genomic DNA methylation maps, and to identify and validate genes with aberrant DNA methylation in OS cell lines. This first integrative analysis of global cancer-related changes in DNA methylation, genomic imbalance, and gene expression has provided comprehensive evidence of the cumulative roles of epigenetic and genetic mechanisms in deregulation of gene expression networks.

  19. Mortality in Danish women: age, period and cohort analysis

    DEFF Research Database (Denmark)

    Lindahl-Jacobsen, Rune

    smokers throughout their adult life, suggesting that these smoking habits may be an important factor for their increased mortality. Study aim 3 The analysis of causes of death suggested an increased risk for deaths associated with the respiratory system and from causes traditionally associated....... Conclusion This study has shown that examination of total mortality trends in relation to age, period and cohort is a powerful exploratory tool for understanding changes in mortality and thus life expectancy. The analysis of differences in mortality trends among women in Denmark, Norway and Sweden...

  20. Genome-wide DNA methylation analysis in jejunum of Sus scrofa with intrauterine growth restriction.

    Science.gov (United States)

    Hu, Yue; Hu, Liang; Gong, Desheng; Lu, Hanlin; Xuan, Yue; Wang, Ru; Wu, De; Chen, Daiwen; Zhang, Keying; Gao, Fei; Che, Lianqiang

    2018-02-01

    Intrauterine growth restriction (IUGR) may elicit a series of postnatal body developmental and metabolic diseases due to their impaired growth and development in the mammalian embryo/fetus during pregnancy. In the present study, we hypothesized that IUGR may lead to abnormally regulated DNA methylation in the intestine, causing intestinal dysfunctions. We applied reduced representation bisulfite sequencing (RRBS) technology to study the jejunum tissues from four newborn IUGR piglets and their normal body weight (NBW) littermates. The results revealed extensively regional DNA methylation changes between IUGR/NBW pairs from different gilts, affecting dozens of genes. Hiseq-based bisulfite sequencing PCR (Hiseq-BSP) was used for validations of 19 genes with epigenetic abnormality, confirming three genes (AIFM1, MTMR1, and TWIST2) in extra samples. Furthermore, integrated analysis of these 19 genes with proteome data indicated that there were three main genes (BCAP31, IRAK1, and AIFM1) interacting with important immunity- or metabolism-related proteins, which could explain the potential intestinal dysfunctions of IUGR piglets. We conclude that IUGR can lead to disparate DNA methylation in the intestine and these changes may affect several important biological processes such as cell apoptosis, cell differentiation, and immunity, which provides more clues linking IUGR and its long-term complications.

  1. HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data

    Directory of Open Access Journals (Sweden)

    Mancuso Francesco M

    2011-12-01

    Full Text Available Abstract Background The study of the human DNA methylome has gained particular interest in the last few years. Researchers can nowadays investigate the potential role of DNA methylation in common disorders by taking advantage of new high-throughput technologies. Among these, Illumina Infinium assays can interrogate the methylation levels of hundreds of thousands of CpG sites, offering an ideal solution for genome-wide methylation profiling. However, like for other high-throughput technologies, the main bottleneck remains at the stage of data analysis rather than data production. Findings We have developed HumMeth27QCReport, an R package devoted to researchers wanting to quickly analyse their Illumina Infinium methylation arrays. This package automates quality control steps by generating a report including sample-independent and sample-dependent quality plots, and performs primary analysis of raw methylation calls by computing data normalization, statistics, and sample similarities. This package is available at CRAN repository, and can be integrated in any Galaxy instance through the implementation of ad-hoc scripts accessible at Galaxy Tool Shed. Conclusions Our package provides users of the Illumina Infinium Methylation assays with a simplified, automated, open-source quality control and primary analysis of their methylation data. Moreover, to enhance its use by experimental researchers, the tool is being distributed along with the scripts necessary for its implementation in the Galaxy workbench. Finally, although it was originally developed for HumanMethylation27, we proved its compatibility with data generated with the HumanMethylation450 Bead Chip.

  2. Radical-Scavenging Activity of Thiols, Thiobarbituric Acid Derivatives and Phenolic Antioxidants Determined Using the Induction Period Method for Radical Polymerization of Methyl Methacrylate

    Directory of Open Access Journals (Sweden)

    Seiichiro Fujisawa

    2012-04-01

    Full Text Available The radical-scavenging activities of two thiols, eight (thiobarbituric acid derivatives and six chain-breaking phenolic antioxidants were investigated using the induction period method for polymerization of methyl methacrylate (MMA initiated by thermal decomposition of 2,2’-azobisisobutyronitrile (AIBN and monitored by differential scanning calorimetry (DSC. The induction period (IP for the thiols 2-mercaptoethanol (ME and 2-mercapto-1-methylimidazole (MMI was about half that for phenolic antioxidants. Except for the potent inhibitor 5,5-dimethyl-2-thiobarbituric acid (3, the IP for thiobarbituric acid derivatives was about one tenth of that for phenolic antioxidants. The IP for 1,3,5-trimethyl-2-thiobarbituric acid (1 and 5-allyl-1, 3-dimethyl-2-thiobarbituric acid (7 was less than that of the control, possibly due to inhibition by a small amount of atmospheric oxygen in the DSC container. The ratio of the chain inhibition to that of chain propagation (CI/CP for the thiols and thiobarbituric acid compounds except for 1, 3 and 7 was about 10 times greater or greater than that for phenolic compounds. A kinetic chain length (KCL about 10% greater than that of the control was observed for 1, suggesting that 1 had chain transfer reactivity in the polymerization of MMA. The average molecular weight of polymers formed from thiobarbituric acid derivatives is discussed.

  3. Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus.

    Directory of Open Access Journals (Sweden)

    Christopher G Bell

    2010-11-01

    Full Text Available Recent multi-dimensional approaches to the study of complex disease have revealed powerful insights into how genetic and epigenetic factors may underlie their aetiopathogenesis. We examined genotype-epigenotype interactions in the context of Type 2 Diabetes (T2D, focussing on known regions of genomic susceptibility. We assayed DNA methylation in 60 females, stratified according to disease susceptibility haplotype using previously identified association loci. CpG methylation was assessed using methylated DNA immunoprecipitation on a targeted array (MeDIP-chip and absolute methylation values were estimated using a Bayesian algorithm (BATMAN. Absolute methylation levels were quantified across LD blocks, and we identified increased DNA methylation on the FTO obesity susceptibility haplotype, tagged by the rs8050136 risk allele A (p = 9.40×10(-4, permutation p = 1.0×10(-3. Further analysis across the 46 kb LD block using sliding windows localised the most significant difference to be within a 7.7 kb region (p = 1.13×10(-7. Sequence level analysis, followed by pyrosequencing validation, revealed that the methylation difference was driven by the co-ordinated phase of CpG-creating SNPs across the risk haplotype. This 7.7 kb region of haplotype-specific methylation (HSM, encapsulates a Highly Conserved Non-Coding Element (HCNE that has previously been validated as a long-range enhancer, supported by the histone H3K4me1 enhancer signature. This study demonstrates that integration of Genome-Wide Association (GWA SNP and epigenomic DNA methylation data can identify potential novel genotype-epigenotype interactions within disease-associated loci, thus providing a novel route to aid unravelling common complex diseases.

  4. EG-13GENOME-WIDE METHYLATION ANALYSIS IDENTIFIES GENOMIC DNA DEMETHYLATION DURING MALIGNANT PROGRESSION OF GLIOMAS

    Science.gov (United States)

    Saito, Kuniaki; Mukasa, Akitake; Nagae, Genta; Aihara, Koki; Otani, Ryohei; Takayanagi, Shunsaku; Omata, Mayu; Tanaka, Shota; Shibahara, Junji; Takahashi, Miwako; Momose, Toshimitsu; Shimamura, Teppei; Miyano, Satoru; Narita, Yoshitaka; Ueki, Keisuke; Nishikawa, Ryo; Nagane, Motoo; Aburatani, Hiroyuki; Saito, Nobuhito

    2014-01-01

    Low-grade gliomas often undergo malignant progression, and these transformations are a leading cause of death in patients with low-grade gliomas. However, the molecular mechanisms underlying malignant tumor progression are still not well understood. Recent evidence indicates that epigenetic deregulation is an important cause of gliomagenesis; therefore, we examined the impact of epigenetic changes during malignant progression of low-grade gliomas. Specifically, we used the Illumina Infinium Human Methylation 450K BeadChip to perform genome-wide DNA methylation analysis of 120 gliomas and four normal brains. This study sample included 25 matched-pairs of initial low-grade gliomas and recurrent tumors (temporal heterogeneity) and 20 of the 25 recurring tumors recurred as malignant progressions, and one matched-pair of newly emerging malignant lesions and pre-existing lesions (spatial heterogeneity). Analyses of methylation profiles demonstrated that most low-grade gliomas in our sample (43/51; 84%) had a CpG island methylator phenotype (G-CIMP). Remarkably, approximately 50% of secondary glioblastomas that had progressed from low-grade tumors with the G-CIMP status exhibited a characteristic partial demethylation of genomic DNA during malignant progression, but other recurrent gliomas showed no apparent change in DNA methylation pattern. Interestingly, we found that most loci that were demethylated during malignant progression were located outside of CpG islands. The information of histone modifications patterns in normal human astrocytes and embryonal stem cells also showed that the ratio of active marks at the site corresponding to DNA demethylated loci in G-CIMP-demethylated tumors was significantly lower; this finding indicated that most demethylated loci in G-CIMP-demethylated tumors were likely transcriptionally inactive. A small number of the genes that were upregulated and had demethylated CpG islands were associated with cell cycle-related pathway. In

  5. Determination of trace elements in poly(methyl methacrylate) by neutron activation analysis

    International Nuclear Information System (INIS)

    Kobayashi, M.

    1979-01-01

    The results are reported of the neutron activation analysis of poly(methyl methacrylate) polymerized with a redox system of chromium (II) acetate and p-chlorobenzyl peroxide in dimethylformamide at 30 0 C. Since the polymer was originally synthesized in experiments for kinetic studies, the results indicate an arbitrary background of purity of polymers obtained in a laboratory. Samples were irradiated for 28m and gamma spectra detected trace amounts of chlorine, aluminum, vanadium, magnesium, manganese, potassium, copper, zinc, sodium, bromine, lanthanum, gold, and chromium. 2 figures, 1 table

  6. Periodic safety review of the HTR-10 safety analysis

    International Nuclear Information System (INIS)

    Chen Fubing; Zheng Yanhua; Shi Lei; Li Fu

    2015-01-01

    Designed by the Institute of Nuclear and New Energy Technology (INET) of Tsinghua University, the 10 MW High Temperature Gas-cooled Reactor-Test Module (HTR-10) is the first modular High Temperature Gas-cooled Reactor (HTGR) in China. According to the nuclear safety regulations of China, the periodic safety review (PSR) of the HTR-10 was initiated by INET after approved by the National Nuclear Safety Administration (NNSA) of China. Safety analysis of the HTR-10 is one of the key safety factors of the PSR. In this paper, the main contents in the review of safety analysis are summarized; meanwhile, the internal evaluation on the review results is presented by INET. (authors)

  7. Statistical analysis of first period of operation of FTU Tokamak

    International Nuclear Information System (INIS)

    Crisanti, F.; Apruzzese, G.; Frigione, D.; Kroegler, H.; Lovisetto, L.; Mazzitelli, G.; Podda, S.

    1996-09-01

    On the FTU Tokamak the plasma physics operations started on the 20/4/90. The first plasma had a plasma current Ip=0.75 MA for about a second. The experimental phase lasted until 7/7/94, when a long shut-down begun for installing the toroidal limiter in the inner side of the vacuum vessel. In these four years of operations plasma experiments have been successfully exploited, e.g. experiments of single and multiple pellet injections; full current drive up to Ip=300 KA was obtained by using waves at the frequency of the Lower Hybrid; analysis of ohmic plasma parameters with different materials (from the low Z silicon to high Z tungsten) as plasma facing element was performed. In this work a statistical analysis of the full period of operation is presented. Moreover, a comparison with the statistical data from other Tokamaks is attempted

  8. Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using restriction fragment length polymorphism.

    Science.gov (United States)

    Boyko, Alex; Kovalchuk, Igor

    2010-01-01

    Restriction fragment length polymorphism (RFLP) is a difference in DNA sequences of organisms belonging to the same species. RFLPs are typically detected as DNA fragments of different lengths after digestion with various restriction endonucleases. The comparison of RFLPs allows investigators to analyze the frequency of occurrence of mutations, such as point mutations, deletions, insertions, and gross chromosomal rearrangements, in the progeny of stressed plants. The assay involves restriction enzyme digestion of DNA followed by hybridization of digested DNA using a radioactively or enzymatically labeled probe. Since DNA can be digested with methylation sensitive enzymes, the assay can also be used to analyze a methylation pattern of a particular locus. Here, we describe RFLP analysis using methylation-insensitive and methylation-sensitive enzymes.

  9. Association between aberrant APC promoter methylation and breast cancer pathogenesis: a meta-analysis of 35 observational studies.

    Science.gov (United States)

    Zhou, Dan; Tang, Weiwei; Wang, Wenyi; Pan, Xiaoyan; An, Han-Xiang; Zhang, Yun

    2016-01-01

    Background. Adenomatous polyposis coli (APC) is widely known as an antagonist of the Wnt signaling pathway via the inactivation of β-catenin. An increasing number of studies have reported that APC methylation contributes to the predisposition to breast cancer (BC). However, recent studies have yielded conflicting results. Methods. Herein, we systematically carried out a meta-analysis to assess the correlation between APC methylation and BC risk. Based on searches of the Cochrane Library, PubMed, Web of Science and Embase databases, the odds ratio (OR) with 95% confidence interval (CI) values were pooled and summarized. Results. A total of 31 articles involving 35 observational studies with 2,483 cases and 1,218 controls met the inclusion criteria. The results demonstrated that the frequency of APC methylation was significantly higher in BC cases than controls under a random effect model (OR = 8.92, 95% CI [5.12-15.52]). Subgroup analysis further confirmed the reliable results, regardless of the sample types detected, methylation detection methods applied and different regions included. Interestingly, our results also showed that the frequency of APC methylation was significantly lower in early-stage BC patients than late-stage ones (OR = 0.62, 95% CI [0.42-0.93]). Conclusion. APC methylation might play an indispensable role in the pathogenesis of BC and could be regarded as a potential biomarker for the diagnosis of BC.

  10. Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer.

    Science.gov (United States)

    McInnes, Tyler; Zou, Donghui; Rao, Dasari S; Munro, Francesca M; Phillips, Vicky L; McCall, John L; Black, Michael A; Reeve, Anthony E; Guilford, Parry J

    2017-03-28

    Aberrant DNA methylation profiles are a characteristic of all known cancer types, epitomized by the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). Hypermethylation has been observed at CpG islands throughout the genome, but it is unclear which factors determine whether an individual island becomes methylated in cancer. DNA methylation in CRC was analysed using the Illumina HumanMethylation450K array. Differentially methylated loci were identified using Significance Analysis of Microarrays (SAM) and the Wilcoxon Signed Rank (WSR) test. Unsupervised hierarchical clustering was used to identify methylation subtypes in CRC. In this study we characterized the DNA methylation profiles of 94 CRC tissues and their matched normal counterparts. Consistent with previous studies, unsupervized hierarchical clustering of genome-wide methylation data identified three subtypes within the tumour samples, designated CIMP-H, CIMP-L and CIMP-N, that showed high, low and very low methylation levels, respectively. Differential methylation between normal and tumour samples was analysed at the individual CpG level, and at the gene level. The distribution of hypermethylation in CIMP-N tumours showed high inter-tumour variability and appeared to be highly stochastic in nature, whereas CIMP-H tumours exhibited consistent hypermethylation at a subset of genes, in addition to a highly variable background of hypermethylated genes. EYA4, TFPI2 and TLX1 were hypermethylated in more than 90% of all tumours examined. One-hundred thirty-two genes were hypermethylated in 100% of CIMP-H tumours studied and these were highly enriched for functions relating to skeletal system development (Bonferroni adjusted p value =2.88E-15), segment specification (adjusted p value =9.62E-11), embryonic development (adjusted p value =1.52E-04), mesoderm development (adjusted p value =1.14E-20), and ectoderm development (adjusted p value =7.94E-16). Our genome-wide characterization of DNA

  11. Diagnostic value of WIF1 methylation for colorectal cancer: a meta-analysis

    Science.gov (United States)

    Chen, Min; Huang, Tianyi; Chen, Yuehong; Ji, Huihui; Pan, Ranran; Wang, Tiangong; Jiang, Danjie; Chen, Yanfei; Yang, Yong; Duan, Shiwei

    2018-01-01

    As a common antagonist of Wnt/β-catenin signaling, Wnt inhibitory factor 1 (WIF1) plays an important role in the tumor progression. The aim of our meta-analysis was to summarize the diagnostic value of WIF1 methylation in colorectal cancer (CRC). Eligible studies were retrieved by a systemic search among PubMed, Embase, CNKI, and Wanfang literature databases. The diagnostic value of WIF1 methylation for CRC was assessed by the summary receiver operating characteristics (SROC) test. Our meta-analysis of 12 studies between 1420 CRC samples and 946 control samples showed that WIF1 hypermethylation was significantly associated with CRC (P < 0.001, OR = 30.10, 95% CI = 19.48-46.50). WIF1 hypermethylation, as a diagnostic biomarker for CRC, has a pooled sensitivity of 0.40 (95% CI: 0.37-0.42), a pooled specificity of 0.95 (95% CI: 0.93-0.96), a pooled positive-likelihood ratio (PLR) of 8.65 (95% CI, 4.47-16.73), and a pooled negative-likelihood ratio (NLR) of 0.41 (95% CI, 0.30-0.55), a diagnostic odds ratio (DOR) of 26.86 (95% CI: 15.73-45.89), and an area under the curve (AUC) of 0.9115. In conclusion, our study established that WIF1 hypermethylation might be a promising diagnostic biomarker for CRC. PMID:29435185

  12. Epigenetic Variation in Monozygotic Twins: A Genome-Wide Analysis of DNA Methylation in Buccal Cells

    NARCIS (Netherlands)

    van Dongen, J.; Ehli, E.A.; Slieker, R.C.; Bartels, M.; Weber, Z.M.; Davies, G.E.; Slagboom, P.E.; Heijmans, B.T.; Boomsma, D.I.

    2014-01-01

    DNA methylation is one of the most extensively studied epigenetic marks in humans. Yet, it is largely unknown what causes variation in DNA methylation between individuals. The comparison of DNA methylation profiles of monozygotic (MZ) twins offers a unique experimental design to examine the extent

  13. Environmental analysis of the life cycle emissions of 2-methyl tetrahydrofuran solvent manufactured from renewable resources.

    Science.gov (United States)

    Slater, C Stewart; Savelski, Mariano J; Hitchcock, David; Cavanagh, Eduardo J

    2016-01-01

    An environmental analysis has been conducted to determine the cradle to gate life cycle emissions to manufacture the green solvent, 2-methyl tetrahydrofuran. The solvent is considered a greener chemical since it can be manufactured from renewable resources with a lower life cycle footprint. Analyses have been performed using different methods to show greenness in both its production and industrial use. This solvent can potentially be substituted for other ether and chlorinated solvents commonly used in organometallic and biphasic reactions steps in pharmaceutical and fine chemical syntheses. The 2-methyl tetrahydrofuran made from renewable agricultural by-products is marketed by Penn A Kem under the name ecoMeTHF™. The starting material, 2-furfuraldehyde (furfural), is produced from corn cob waste by converting the available pentosans by acid hydrolysis. An evaluation of each step in the process was necessary to determine the overall life cycle and specific CO2 emissions for each raw material/intermediate produced. Allocation of credits for CO2 from the incineration of solvents made from renewable feedstocks significantly reduced the overall carbon footprint. Using this approach, the overall life cycle emissions for production of 1 kg of ecoMeTHF™ were determined to be 0.191 kg, including 0.150 kg of CO2. Life cycle emissions generated from raw material manufacture represents the majority of the overall environmental impact. Our evaluation shows that using 2-methyl tetrahydrofuran in an industrial scenario results in a 97% reduction in emissions, when compared to typically used solvents such as tetrahydrofuran, made through a conventional chemical route.

  14. Content analysis of 150 years of British periodicals.

    Science.gov (United States)

    Lansdall-Welfare, Thomas; Sudhahar, Saatviga; Thompson, James; Lewis, Justin; Cristianini, Nello

    2017-01-24

    Previous studies have shown that it is possible to detect macroscopic patterns of cultural change over periods of centuries by analyzing large textual time series, specifically digitized books. This method promises to empower scholars with a quantitative and data-driven tool to study culture and society, but its power has been limited by the use of data from books and simple analytics based essentially on word counts. This study addresses these problems by assembling a vast corpus of regional newspapers from the United Kingdom, incorporating very fine-grained geographical and temporal information that is not available for books. The corpus spans 150 years and is formed by millions of articles, representing 14% of all British regional outlets of the period. Simple content analysis of this corpus allowed us to detect specific events, like wars, epidemics, coronations, or conclaves, with high accuracy, whereas the use of more refined techniques from artificial intelligence enabled us to move beyond counting words by detecting references to named entities. These techniques allowed us to observe both a systematic underrepresentation and a steady increase of women in the news during the 20th century and the change of geographic focus for various concepts. We also estimate the dates when electricity overtook steam and trains overtook horses as a means of transportation, both around the year 1900, along with observing other cultural transitions. We believe that these data-driven approaches can complement the traditional method of close reading in detecting trends of continuity and change in historical corpora.

  15. ANALYSIS OF CONSUMPTION EXPENDITURE IN ROMANIA, PERIOD 2009-2015

    Directory of Open Access Journals (Sweden)

    BÂLDAN FLORENTINA CRISTINA

    2017-06-01

    Full Text Available The paper „Analysis of consumption expenditure in Romania, period 2009-2015” is highlighting a very important phenomenon for the Romanian economy, consumption. The financial and economic crisis determined a change in the income repartition for the basic products and services. The most influent stimulus at which the Romanian consumers are deciding a product acquisition is the price, therefore they were migrating to product segments with low prices, the quality of life being on a decreasing trend. The level of alimentary products consumption depends in a big extent on the macroeconomic policies, that through numerous leverages is influencing the population consumption behavior. From these leverages we may document the income policy, loan policy, monetary and exchange rate policies, social assistance policy, etc.

  16. Methyl-Analyzer--whole genome DNA methylation profiling.

    Science.gov (United States)

    Xin, Yurong; Ge, Yongchao; Haghighi, Fatemeh G

    2011-08-15

    Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-MAPS is an enzymatic-based method that uses both methylation-sensitive and -dependent enzymes covering >80% of CpG dinucleotides within mammalian genomes. It combines enzymatic-based approaches with high-throughput next-generation sequencing technology to provide whole genome DNA methylation profiles. Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution. Methyl-Analyzer is available at http://github.com/epigenomics/methylmaps. Sample dataset is available for download at http://epigenomicspub.columbia.edu/methylanalyzer_data.html. fgh3@columbia.edu Supplementary data are available at Bioinformatics online.

  17. DNA methylation analysis as novel tool for quality control in regenerative medicine.

    Science.gov (United States)

    Rapko, Stephen; Baron, Udo; Hoffmüller, Ulrich; Model, Fabian; Wolfe, Leslie; Olek, Sven

    2007-09-01

    Cell-based regenerative medicine, including tissue engineering, is a novel approach to reconstituting tissues that do not spontaneously heal, such as damaged cartilage, and to curing diseases caused by malfunctioning cells. Typically, manufacturing processes to generate cartilage for replacement therapies involve isolation and expansion of cells from cartilage biopsies. A challenge in the field is potential contamination by other cell types (e.g., fibroblast-like cells), which can overgrow the desired cells during culturing and may ultimately compromise clinical efficacy. No standard analytical system has been absolutely effective in ensuring the identity of these cell-based products. Therefore, we tested deoxyribonucleic acid methylation analysis as a quality assessment tool, applying it to Genzyme's Carticel product, a chondrocyte implant that the Food and Drug Administration has approved. We identified 7 potent discriminators by assaying candidate genomic regions derived from methylation discovery approaches and literature searches regarding a functional role of genes in chondrocyte biology. Using a support vector machine, we trained an optimal cell type classifier that was absolutely effective in discriminating chondrocytes from synovial membrane derived cells, the major potential contaminant of chondrocyte cultures. The abundant marker availability and high quality of this assay format also suggest it as a potential quality control test for other cell types grown or manipulated in vitro.

  18. Value of PAX1 Methylation Analysis by MS-HRM in the Triage of Atypical Squamous Cells of Undetermined Significance.

    Science.gov (United States)

    Li, Shi-Rong; Wang, Zhen-Ming; Wang, Yu-Hui; Wang, Xi-Bo; Zhao, Jian-Qiang; Xue, Hai-Bin; Jiang, Fu-Guo

    2015-01-01

    Detection of cervical high grade lesions in patients with atypical squamous cells of undetermined significance (ASCUS) is still a challenge. Our study tested the efficacy of the paired boxed gene 1 (PAX1) methylation analysis by methylation-sensitive high-resolution melting (MS-HRM) in the detection of high grade lesions in ASCUS and compared performance with the hybrid capture 2 (HC2) human papillomavirus (HPV) test. A total of 463 consecutive ASCUS women from primary screening were selected. Their cervical scrapings were collected and assessed by PAX1 methylation analysis (MS-HRM) and high-risk HPV-DNA test (HC2). All patients with ASCUS were admitted to colposcopy and cervical biopsies. The Chi- square test was used to test the differences of PAX1 methylation or HPV infection between groups. The specificity, sensitivity, and accuracy for detecting CIN2 + lesions were: 95.6%, 82.4%, and 94.6%, respectively, for the PAX1 MS-HRM test; and 59.7%, 64.7%, and 60.0% for the HC2 HPV test. The PAX1 methylation analysis by MS-HRM demonstrated a better performance than the high-risk HPV-DNA test for the detection of high grade lesions (CIN2 +) in ASCUS cases. This approach could screen out the majority of low grade cases of ASCUS, and thus reduce the referral rate to colposcopy.

  19. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)—A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes

    OpenAIRE

    Karolina Chwialkowska; Urszula Korotko; Joanna Kosinska; Iwona Szarejko; Miroslaw Kwasniewski

    2017-01-01

    Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing ...

  20. GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data.

    Science.gov (United States)

    Rahmani, Elior; Yedidim, Reut; Shenhav, Liat; Schweiger, Regev; Weissbrod, Omer; Zaitlen, Noah; Halperin, Eran

    2017-06-15

    GLINT is a user-friendly command-line toolset for fast analysis of genome-wide DNA methylation data generated using the Illumina human methylation arrays. GLINT, which does not require any programming proficiency, allows an easy execution of Epigenome-Wide Association Study analysis pipeline under different models while accounting for known confounders in methylation data. GLINT is a command-line software, freely available at https://github.com/cozygene/glint/releases . It requires Python 2.7 and several freely available Python packages. Further information and documentation as well as a quick start tutorial are available at http://glint-epigenetics.readthedocs.io . elior.rahmani@gmail.com or ehalperin@cs.ucla.edu. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  1. Prenatal stress, fearfulness, and the epigenome: Exploratory analysis of sex differences in DNA methylation of the glucocorticoid receptor gene.

    Directory of Open Access Journals (Sweden)

    Brendan Dale Ostlund

    2016-07-01

    Full Text Available Exposure to stress in utero is a risk factor for the development of problem behavior in the offspring, though precise pathways are unknown. We examined whether DNA methylation of the glucocorticoid receptor gene, NR3C1, was associated with experiences of stress by an expectant mother and fearfulness in her infant. Mothers reported on prenatal stress and infant temperament when infants were 5 months old (n = 68. Buccal cells for methylation analysis were collected from each infant. Prenatal stress was not related to infant fearfulness or NR3C1 methylation in the sample as a whole. Exploratory sex-specific analysis revealed a trend-level association between prenatal stress and increased methylation of NR3C1 exon 1F for female, but not male, infants. In addition, increased methylation was significantly associated with greater fearfulness for females. Results suggest an experience-dependent pathway to fearfulness for female infants via epigenetic modification of the glucocorticoid receptor gene. Future studies should examine prenatal stress in a comprehensive fashion while considering sex differences in epigenetic processes underlying infant temperament.

  2. Identification of Differentially Expressed Genes Induced by Aberrant Methylation in Oral Squamous Cell Carcinomas Using Integrated Bioinformatic Analysis

    Directory of Open Access Journals (Sweden)

    Xiaoqi Zhang

    2018-06-01

    Full Text Available Oral squamous cell carcinoma (OSCC is a malignant disease. Methylation plays a key role in the etiology and pathogenesis of OSCC. The goal of this study was to identify aberrantly methylated differentially expressed genes (DEGs in OSCCs, and to explore the underlying mechanisms of tumorigenesis by using integrated bioinformatic analysis. Gene expression profiles (GSE30784 and GSE38532 were analyzed using the R software to obtain aberrantly methylated DEGs. Functional enrichment analysis of screened genes was performed using the DAVID software. Protein–protein interaction (PPI networks were constructed using the STRING database. The cBioPortal software was used to exhibit the alterations of genes. Lastly, we validated the results with the Cancer Genome Atlas (TCGA data. Twenty-eight upregulated hypomethylated genes and 24 downregulated hypermethylated genes were identified. These genes were enriched in the biological process of regulation in immune response, and were mainly involved in the PI3K-AKT and EMT pathways. Additionally, three upregulated hypomethylated oncogenes and four downregulated hypermethylated tumor suppressor genes (TSGs were identified. In conclusion, our study indicated possible aberrantly methylated DEGs and pathways in OSCCs, which could improve the understanding of the underlying molecular mechanisms. Aberrantly methylated oncogenes and TSGs may also serve as biomarkers and therapeutic targets for the precise diagnosis and treatment of OSCCs in the future.

  3. COMBUSTION ANALYSIS OF ALGAL OIL METHYL ESTER IN A DIRECT INJECTION COMPRESSION IGNITION ENGINE

    Directory of Open Access Journals (Sweden)

    HARIRAM V.

    2013-02-01

    Full Text Available Algal oil methyl ester was derived from microalgae (Spirulina sp. The microalga was cultivated in BG 11 media composition in a photobioreactor. Upon harvesting, the biomass was filtered and dried. The algal oil was obtained by a two step solvent extraction method using hexane and ether solvent. Cyclohexane was added to biomass to expel the remaining algal oil. By this method 92% of algal oil is obtained. Transesterification process was carried out to produce AOME by adding sodium hydroxide and methanol. The AOME was blended with straight diesel in 5%, 10% and 15% blend ratio. Combustion parameters were analyzed on a Kirloskar single cylinder direct injection compression ignition engine. The cylinder pressure characteristics, the rate of pressure rise, heat release analysis, performance and emissions were studied for straight diesel and the blends of AOME’s. AOME 15% blend exhibits significant variation in cylinder pressure and rate of heat release.

  4. Classification of bacteria by simultaneous methylation-solid phase microextraction and gas chromatography/mass spectrometry analysis of fatty acid methyl esters.

    Science.gov (United States)

    Lu, Yao; Harrington, Peter B

    2010-08-01

    Direct methylation and solid-phase microextraction (SPME) were used as a sample preparation technique for classification of bacteria based on fatty acid methyl ester (FAME) profiles. Methanolic tetramethylammonium hydroxide was applied as a dual-function reagent to saponify and derivatize whole-cell bacterial fatty acids into FAMEs in one step, and SPME was used to extract the bacterial FAMEs from the headspace. Compared with traditional alkaline saponification and sample preparation using liquid-liquid extraction, the method presented in this work avoids using comparatively large amounts of inorganic and organic solvents and greatly decreases the sample preparation time as well. Characteristic gas chromatography/mass spectrometry (GC/MS) of FAME profiles was achieved for six bacterial species. The difference between Gram-positive and Gram-negative bacteria was clearly visualized with the application of principal component analysis of the GC/MS data of bacterial FAMEs. A cross-validation study using ten bootstrap Latin partitions and the fuzzy rule building expert system demonstrated 87 +/- 3% correct classification efficiency.

  5. Analysis of DNA Methylation in Young People: Limited Evidence for an Association Between Victimization Stress and Epigenetic Variation in Blood.

    Science.gov (United States)

    Marzi, Sarah J; Sugden, Karen; Arseneault, Louise; Belsky, Daniel W; Burrage, Joe; Corcoran, David L; Danese, Andrea; Fisher, Helen L; Hannon, Eilis; Moffitt, Terrie E; Odgers, Candice L; Pariante, Carmine; Poulton, Richie; Williams, Benjamin S; Wong, Chloe C Y; Mill, Jonathan; Caspi, Avshalom

    2018-01-12

    DNA methylation has been proposed as an epigenetic mechanism by which early-life experiences become "embedded" in the genome and alter transcriptional processes to compromise health. The authors sought to investigate whether early-life victimization stress is associated with genome-wide DNA methylation. The authors tested the hypothesis that victimization is associated with DNA methylation in the Environmental Risk (E-Risk) Longitudinal Study, a nationally representative 1994-1995 birth cohort of 2,232 twins born in England and Wales and assessed at ages 5, 7, 10, 12, and 18 years. Multiple forms of victimization were ascertained in childhood and adolescence (including physical, sexual, and emotional abuse; neglect; exposure to intimate-partner violence; bullying; cyber-victimization; and crime). Epigenome-wide analyses of polyvictimization across childhood and adolescence revealed few significant associations with DNA methylation in peripheral blood at age 18, but these analyses were confounded by tobacco smoking and/or did not survive co-twin control tests. Secondary analyses of specific forms of victimization revealed sparse associations with DNA methylation that did not replicate across different operationalizations of the same putative victimization experience. Hypothesis-driven analyses of six candidate genes in the stress response (NR3C1, FKBP5, BDNF, AVP, CRHR1, SLC6A4) did not reveal predicted associations with DNA methylation in probes annotated to these genes. Findings from this epidemiological analysis of the epigenetic effects of early-life stress do not support the hypothesis of robust changes in DNA methylation in victimized young people. We need to come to terms with the possibility that epigenetic epidemiology is not yet well matched to experimental, nonhuman models in uncovering the biological embedding of stress.

  6. Utility of MLH1 methylation analysis in the clinical evaluation of Lynch Syndrome in women with endometrial cancer.

    Science.gov (United States)

    Bruegl, Amanda S; Djordjevic, Bojana; Urbauer, Diana L; Westin, Shannon N; Soliman, Pamela T; Lu, Karen H; Luthra, Rajyalakshmi; Broaddus, Russell R

    2014-01-01

    Clinical screening criteria, such as young age of endometrial cancer diagnosis and family history of signature cancers, have traditionally been used to identify women with Lynch Syndrome, which is caused by mutation of a DNA mismatch repair gene. Immunohistochemistry and microsatellite instability analysis have evolved as important screening tools to evaluate endometrial cancer patients for Lynch Syndrome. A complicating factor is that 15-20% of sporadic endometrial cancers have immunohistochemical loss of the DNA mismatch repair protein MLH1 and high levels of microsatellite instability due to methylation of MLH1. The PCR-based MLH1 methylation assay potentially resolves this issue, yet many clinical laboratories do not perform this assay. The objective of this study was to determine if clinical and pathologic features help to distinguish sporadic endometrial carcinomas with MLH1 loss secondary to MLH1 methylation from Lynch Syndrome-associated endometrial carcinomas with MLH1 loss and absence of MLH1 methylation. Of 337 endometrial carcinomas examined, 54 had immunohistochemical loss of MLH1. 40/54 had MLH1 methylation and were designated as sporadic, while 14/54 lacked MLH1 methylation and were designated as Lynch Syndrome. Diabetes and deep myometrial invasion were associated with Lynch Syndrome; no other clinical or pathological variable distinguished the 2 groups. Combining Society of Gynecologic Oncology screening criteria with these 2 features accurately captured all Lynch Syndrome cases, but with low specificity. In summary, no single clinical/pathologic feature or screening criteria tool accurately identified all Lynch Syndrome-associated endometrial carcinomas, highlighting the importance of the MLH1 methylation assay in the clinical evaluation of these patients.

  7. MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.

    Science.gov (United States)

    Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K; Conneely, Karen N

    2012-03-01

    Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data.

  8. Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

    Directory of Open Access Journals (Sweden)

    He Zhou

    2016-08-01

    Full Text Available In this study, we selected natural polyploidy loach (diploid, triploid and tetraploid and hybrid F1 generation obverse cross (4 × 2 and inverse cross (2 × 4 by diploids and tetraploids as the research model. The MSAP (methylation-sensitive amplified polymorphism reaction system was established by our laboratory to explore methylation levels and pattern diversification features at the whole genome level of the polyploidy loach. The results showed that the total methylation and full methylation rates decreased on increased ploidy individuals; moreover, the hemimethylation rate showed no consistent pattern. Compared with diploid loach, the methylation patterns of tetraploid sites changed 68.17%, and the methylation patterns of triploid sites changed 73.05%. The proportion of hypermethylation genes is significantly higher than the proportion of demethylation genes. The methylation level of reciprocal cross F1 generation is lower than the male diploid and higher than the female tetraploid. The hemimethylation and total methylation rate of the cross hybrid F1 generation is significantly higher than the orthogonal F1 generation (p < 0.01. After readjusting, the methylation pattern of genome DNA of reciprocal hybrids changed 69.59% and 72.83%, respectively.

  9. Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

    Science.gov (United States)

    Zhou, He; Ma, Tian-Yu; Zhang, Rui; Xu, Qi-Zheng; Shen, Fu; Qin, Yan-Jie; Xu, Wen; Wang, Yuan; Li, Ya-Juan

    2016-01-01

    In this study, we selected natural polyploidy loach (diploid, triploid and tetraploid) and hybrid F1 generation obverse cross (4 × 2) and inverse cross (2 × 4) by diploids and tetraploids as the research model. The MSAP (methylation-sensitive amplified polymorphism) reaction system was established by our laboratory to explore methylation levels and pattern diversification features at the whole genome level of the polyploidy loach. The results showed that the total methylation and full methylation rates decreased on increased ploidy individuals; moreover, the hemimethylation rate showed no consistent pattern. Compared with diploid loach, the methylation patterns of tetraploid sites changed 68.17%, and the methylation patterns of triploid sites changed 73.05%. The proportion of hypermethylation genes is significantly higher than the proportion of demethylation genes. The methylation level of reciprocal cross F1 generation is lower than the male diploid and higher than the female tetraploid. The hemimethylation and total methylation rate of the cross hybrid F1 generation is significantly higher than the orthogonal F1 generation (p < 0.01). After readjusting, the methylation pattern of genome DNA of reciprocal hybrids changed 69.59% and 72.83%, respectively. PMID:27556458

  10. Methylation-Sensitive Amplification Length Polymorphism (MS-AFLP) Microarrays for Epigenetic Analysis of Human Genomes.

    Science.gov (United States)

    Alonso, Sergio; Suzuki, Koichi; Yamamoto, Fumiichiro; Perucho, Manuel

    2018-01-01

    Somatic, and in a minor scale also germ line, epigenetic aberrations are fundamental to carcinogenesis, cancer progression, and tumor phenotype. DNA methylation is the most extensively studied and arguably the best understood epigenetic mechanisms that become altered in cancer. Both somatic loss of methylation (hypomethylation) and gain of methylation (hypermethylation) are found in the genome of malignant cells. In general, the cancer cell epigenome is globally hypomethylated, while some regions-typically gene-associated CpG islands-become hypermethylated. Given the profound impact that DNA methylation exerts on the transcriptional profile and genomic stability of cancer cells, its characterization is essential to fully understand the complexity of cancer biology, improve tumor classification, and ultimately advance cancer patient management and treatment. A plethora of methods have been devised to analyze and quantify DNA methylation alterations. Several of the early-developed methods relied on the use of methylation-sensitive restriction enzymes, whose activity depends on the methylation status of their recognition sequences. Among these techniques, methylation-sensitive amplification length polymorphism (MS-AFLP) was developed in the early 2000s, and successfully adapted from its original gel electrophoresis fingerprinting format to a microarray format that notably increased its throughput and allowed the quantification of the methylation changes. This array-based platform interrogates over 9500 independent loci putatively amplified by the MS-AFLP technique, corresponding to the NotI sites mapped throughout the human genome.

  11. Analysis of the state of posttranslational calmodulin methylation in developing pea plants

    International Nuclear Information System (INIS)

    Oh, Sukheung; Roberts, D.M.

    1990-01-01

    A specific calmodulin-N-methyltransferase was used in a radiometric assay to analyze the degree of methylation of lysine-115 in pea (Pisum sativum) plants. Calmodulin was isolated from dissected segments of developing roots of young etiolated and green pea plants and was tested for its ability to be methylated by incubation with the calmodulin methyltransferase in the presence of [ 3 H]methyl-S-adenosylmethionine. By this approach, the presence of unmethylated calmodulins were demonstrated in pea tissues, and the levels of methylation varied depending on the developmental state of the tissue tested. Calmodulin methylation levels were lower in apical root segments of both etiolated and green plants, and in the young lateral roots compared with the mature, differentiated root tissues. The incorporation of methyl groups into these calmodulin samples appears to be specific for position 115 since site-directed mutants of calmodulin with substitutions at this position competitively inhibited methyl group incorporation. The present findings, combined with previous data showing differences in the ability of methylated and unmethylated calmodulins to activate pea NAD kinase raise the possibility that posttranslational methylation of calmodulin could be another mechanism for regulating calmodulin activity

  12. Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples.

    Science.gov (United States)

    Kalmár, Alexandra; Péterfia, Bálint; Hollósi, Péter; Wichmann, Barnabás; Bodor, András; Patai, Árpád V; Schöller, Andrea; Krenács, Tibor; Tulassay, Zsolt; Molnár, Béla

    2015-09-01

    We aimed to test the applicability of formalin-fixed and paraffin-embedded (FFPE) tissue samples for gene specific DNA methylation analysis after using two commercially available DNA isolation kits. Genomic DNA was isolated from 5 colorectal adenocarcinomas and 5 normal adjacent tissues from "recent", collected within 6 months, and "archived", collected more than 5 years ago, FFPE tissues using either High Pure FFPET DNA Isolation kit or QIAamp DNA FFPE Tissue kit. DNA methylation analysis of MAL, SFRP1 and SFRP2 genes, known to be hypermethylated in CRC, was performed using methylation-sensitive high resolution melting (MS-HRM) analysis and sequencing. QIAamp (Q) method resulted in slightly higher recovery in archived (HP: 1.22 ± 3.18 μg DNA; Q: 3.00 ± 4.04 μg DNA) and significantly (p < 0.05) higher recovery in recent samples compared to High Pure method (HP) (HP: 4.10 ± 2.91 μg DNA; Q: 11.51 ± 7.50 μg DNA). Both OD260/280 and OD260/230 ratios were lower, but still high in the High Pure isolated archived and recent samples compared to those isolated with QIAamp. Identical DNA methylation patterns were detected for all 3 genes tested by MS-HRM with both isolation kits in the recent group. However, despite of higher DNA recovery in QIAamp slightly more reproducible methylation results were obtained from High Pure isolated archived samples. Sequencing confirmed DNA hypermethylation in CRCs. In conclusion, reproducible DNA methylation patterns were obtained from recent samples using both isolation kits. However, long term storage may affect the reliability of the results leading to moderate differences between the efficiency of isolation kits.

  13. CADM1, MAL and miR124-2 methylation analysis in cervical scrapes to detect cervical and endometrial cancer

    NARCIS (Netherlands)

    De Strooper, Lise M. A.; van Zummeren, Marjolein; Steenbergen, Renske D. M.; Bleeker, Maaike C. G.; Hesselink, Albertus T.; Schuurs-Wisman, G. Bea A.; Snijders, Peter J. F.; Heideman, Danielle A. M.; Meijer, Chris J. L. M.

    2014-01-01

    Aims Gene promoter hypermethylation is recognised as an essential early step in carcinogenesis, indicating important application areas for DNA methylation analysis in early cancer detection. The current study was set out to assess the performance of CADM1, MAL and miR124-2 methylation analysis in

  14. Field responses of predaceous arthropods to methyl salicylate: a meta-analysis and case study in cranberries

    Science.gov (United States)

    Methyl salicylate (MeSA) is an herbivore-induced plant volatile (HIPV) that has shown potential in attracting natural enemies. Here, we conducted a meta-analysis to evaluate the magnitude of natural enemy response to MeSA in the field, and tested its attractiveness to insect predators in commercial...

  15. Region of interest methylation analysis: a comparison of MSP with MS-HRM and direct BSP.

    Science.gov (United States)

    Akika, Reem; Awada, Zainab; Mogharbil, Nahed; Zgheib, Nathalie K

    2017-07-01

    The aim of this study was to compare and contrast three DNA methylation methods of a specific region of interest (ROI): methylation-specific PCR (MSP), methylation-sensitive high resolution melting (MS-HRM) and direct bisulfite sequencing (BSP). The methylation of a CpG area in the promoter region of Estrogen receptor alpha (ESR1) was evaluated by these three methods with samples and standards of different methylation percentages. MSP data were neither reproducible nor sensitive, and the assay was not specific due to non-specific binding of primers. MS-HRM was highly reproducible and a step forward into categorizing the methylation status of the samples as percent ranges. Direct BSP was the most informative method regarding methylation percentage of each CpG site. Though not perfect, it was reproducible and sensitive. We recommend the use of either method depending on the research question and target amplicon, and provided that the designed primers and expected amplicons are within recommendations. If the research question targets a limited number of CpG sites and simple yes/no results are enough, MSP may be attempted. For short amplicons that are crowded with CpG sites and of single melting domain, MS-HRM may be the method of choice though it only indicates the overall methylation percentage of the entire amplicon. Although the assay is highly reproducible, being semi-quantitative makes it of lesser interest to study ROI methylation of samples with little methylation differences. Direct BSP is a step forward as it gives information about the methylation percentage at each CpG site.

  16. [Analysis of the character of film decomposition of methyl methacrylate (MMA) coated urea by infrared spectrum].

    Science.gov (United States)

    Li, Dong-po; Wu, Zhi-jie; Liang, Cheng-hua; Chen, Li-jun; Zhang, Yu-lan; Nie, Yan-xi

    2012-03-01

    The degradability characteristics of film with 4 kinds of methyl methacrylate coated urea amended with inhibitors were analyzed by FITR, which was purposed to supply theoretical basis for applying the FITR analysis method to film decomposition and methyl methacrylate coated urea fertilizers on farming. The result showed that the chemical component, molecule structure and material form of the membrane were not changed because of adding different inhibitors to urea. the main peaks of expressing film degradation process were brought by the -C-H of CH3 & CH2, -OH, C-O, C-C, C-O-C, C=O, C=C flexing vibrancy in asymmetry and symmetry in 3 479-3 195, 2 993--2 873, 1 741-1 564, 1 461-925 and 850-650 cm(-1). The peak value changed from smooth to tip, and from width to narrow caused by chemical structural transform of film The infrared spectrum of 4 kinds of fertilizers was not different remarkably before 60 days, and the film was slowly degraded. But degradation of the film was expedited after 60 days, it was most quickened at 120 day, and the decomposition rate of film was decreased at 310 day. The substantiality change of film in main molecule structure of 4 kinds of fertilizers didn't happen in 310 days. The main component of film materials was degraded most slowly in brown soil. The speed of film degradation wasn't heavily impacted by different inhibitors. The characteristic of film degradation may be monitored entirely by infrared spectrum. The degradation dynamic, chemical structure change, degradation speed difference of the film could be represented through infrared spectrum.

  17. The correlation between uptake of methyl green and Feulgen staining intensity of cell nuclei. An image analysis study

    DEFF Research Database (Denmark)

    Lyon, H; Schulte, E; Hoyer, P E

    1989-01-01

    were stored in the computer, making it possible to measure the same cells in the Feulgen-restained sections. Image analysis gave results which invalidate the sequential methods as opposed to the simultaneous method. Mean optical densities were significantly increased for both dyes with the simultaneous...... method after formaldehyde fixation as compared to Carnoy fixation. The quantitative correlation of Methyl Green and DNA in the simultaneous technique was found to parallel exactly that of the Feulgen stain. In conclusion, the simultaneous Methyl Green-Pyronin technique is recommended while the sequential......Paraffin sections of rat tissue fixed in either formaldehyde solution (3.6% w/v) or in Carnoy's fluid were stained using standardized Methyl Green-Pyronin procedures with the dyes used either simultaneously or in sequence. The sections were evaluated for the uptake of the two dyes by cell nuclei...

  18. The Relationship between FHIT Gene Promoter Methylation and Lung Cancer Risk: 
a Meta-analysis

    Directory of Open Access Journals (Sweden)

    Yichang SUN

    2014-03-01

    Full Text Available Background and objective Tumor-suppressor gene promoter DNA methylation in tumor cells is associated with its reduced expression. FHIT (fragile histindine triad was one of the important tumor suppressor genes which was found hypermethylated in the promoter region in most of tumors. The aim of this study is to evaluate the relationship between FIHT gene promother methylation and lung cancer risk by meta-analysis. Methods By searching Pubmed, CNKI and Wanfang, the open published articles related to FHIT gene promoter methylation and lung carcinoma risk were collected. The odds ratio (OR and range of FHIT gene of cancer tissue of lung cancer patients compared with normal lung tissue, plasma and the bronchial lavage fluid were pooled by statistical software Stata 11.0. Results Eleven studies were finally included in this meta-analysis. The median methylation rate were Pmedian=40.0% (0-68.3%, Pmedian=8.7% (0-35.0%, Pmedian=33.3% (17.1%-38.3% and Pmedian=35.9% (31.1%-50.8% in cancer tissue, NLT, BALF and plasm respectively. The pooled results showed the methylation rate in tumor tissue was much higer than that of NLT OR=5.82 (95%CI: 3.74-9.06, P0.05 and plasma OR=1.41 (95%CI: 0.90-2.20, P>0.05. Conclusion Hypermethylation of FHIT gene promoter region was found more frequent in cancer tissue than that of NLT which may demonstrated association between lung cancer risk and FHIT gene promoter methylation.

  19. Thermodynamic analysis of a variable compression ratio diesel engine running with palm oil methyl ester

    International Nuclear Information System (INIS)

    Debnath, Biplab K.; Sahoo, Niranjan; Saha, Ujjwal K.

    2013-01-01

    Highlights: ► Energy and exergy analysis of palm oil methyl ester (POME) run diesel engine. ► Engine was run at various compression ratios (CRs) and injection timings (ITs). ► POME can recover around 26% of the energy supplied by the fuel. ► CR rise and IT change cause shaft energy per unit fuel supply to increase. ► CR of 18 and IT of 20°BTDC reduce more entropy generation. - Abstract: The present work is set to explore the effect of compression ratio (CR) and injection timing (IT) on energy and exergy potential of a palm oil methyl ester (POME) run diesel engine. Experiments are carried out in a single cylinder, direct injection, water cooled variable compression ratio diesel engine at a constant peed of 1500 rpm under a full load of 4.24 bar brake mean effective pressure (BMEP). The study involves four different CRs of 16, 17, 17.5 and 18; and three different ITs of 20°, 23° and 28°BTDC. Here, the CR of 17.5 and IT of 23°BTDC are the standard ones. The energy analysis performed for the experimental data includes shaft power, energy input through fuel, output by cooling water and exhaust, uncounted loss per unit time. Side by side, the effects of varying CR and IT on peak pressure, peak heat release rate, brake thermal efficiency and exhaust gas temperature are also studied. The exergy analysis is carried out for availability input, shaft, cooling water and exhaust availability, availability destruction and entropy generation. It shows that higher values of CR increase the shaft availability and cooling water availability, however, they decrease the exhaust flow availability. The retardation and advancement of IT give similar results. The exergy analysis also shows that with the increase of CR, the injection retardation and advancement increase the shaft availability and exergy efficiency, while it reduces the exergy destruction. The entropy generation is also reduced for the similar CR and IT modifications.

  20. Methylation-sensitive amplification polymorphism analysis of fat and muscle tissues in pigs.

    Science.gov (United States)

    Ma, J D; Li, M Z; Zhou, S L; Zhou, C W; Li, X W

    2012-09-26

    DNA methylation may be involved in regulating the expression of protein-coding genes, resulting in different fat and muscle phenotypes. Using a methylation-sensitive amplified polymorphism approach, we obtained 7423 bands by selective amplification of genomic DNA from six different fat depots and two heterogeneous muscle types from Duroc/Landrace/Yorkshire cross-bred pigs. The degrees of DNA methylation, determined by the percentages of hemi- and fully methylated sites relative to the total number of CCGG sites, were similar in male and female pigs for each specific tissue [χ(2) test; P (two-tailed) > 0.05]. Gender bias was therefore ignored. There were significant differences in the degree of DNA methylation among the eight tissue types [χ(2) test; P(total) (two-tailed) = 0.009]. However, similar degrees of methylation were observed among the six fat depots [χ(2) test; P(fat) (two-tailed) = 0.24 > 0.05]and between the two muscle types [χ(2) test; P(muscle) (two-tailed) = 0.76 > 0.05]. We conclude that the degree of DNA methylation differs between porcine fat and muscle tissue, but that the methylation status of a particular tissue type is similar, despite being deposited at different body sites.

  1. Synthesis of tritium labelled methyl vinyl ketone and its use in copolymer analysis

    International Nuclear Information System (INIS)

    Burfield, D.R.; Savariar, C.M.

    1980-01-01

    The synthesis of tritiated methyl vinyl ketone by base catalysed exchange and its use in determining the ketone content of styrene/methyl vinyl ketone copolymers are reported. Methods of assay are described in detail and the general applicability of the method is discussed. (author)

  2. Epigenetic Variation in Monozygotic Twins: A Genome-Wide Analysis of DNA Methylation in Buccal Cells

    Directory of Open Access Journals (Sweden)

    Jenny van Dongen

    2014-05-01

    Full Text Available DNA methylation is one of the most extensively studied epigenetic marks in humans. Yet, it is largely unknown what causes variation in DNA methylation between individuals. The comparison of DNA methylation profiles of monozygotic (MZ twins offers a unique experimental design to examine the extent to which such variation is related to individual-specific environmental influences and stochastic events or to familial factors (DNA sequence and shared environment. We measured genome-wide DNA methylation in buccal samples from ten MZ pairs (age 8–19 using the Illumina 450k array and examined twin correlations for methylation level at 420,921 CpGs after QC. After selecting CpGs showing the most variation in the methylation level between subjects, the mean genome-wide correlation (rho was 0.54. The correlation was higher, on average, for CpGs within CpG islands (CGIs, compared to CGI shores, shelves and non-CGI regions, particularly at hypomethylated CpGs. This finding suggests that individual-specific environmental and stochastic influences account for more variation in DNA methylation in CpG-poor regions. Our findings also indicate that it is worthwhile to examine heritable and shared environmental influences on buccal DNA methylation in larger studies that also include dizygotic twins.

  3. Genome-wide DNA methylation analysis of the porcine hypothalamus-pituitary-ovary axis

    DEFF Research Database (Denmark)

    Yuan, Xiao Long; Zhang, Zhe; Li, Bin

    2017-01-01

    Previous studies have suggested that DNA methylation in both CpG and CpH (where H = C, T or A) contexts plays a critical role in biological functions of different tissues. However, the genome-wide DNA methylation patterns of porcine hypothalamus-pituitary-ovary (HPO) tissues remain virtually unex...

  4. Concordance analysis of methylation biomarkers detection in self-collected and physician-collected samples in cervical neoplasm

    International Nuclear Information System (INIS)

    Chang, Cheng-Chang; Huang, Rui-Lan; Liao, Yu-Ping; Su, Po-Hsuan; Hsu, Yaw-Wen; Wang, Hui-Chen; Tien, Chau-Yang; Yu, Mu-Hsien; Lin, Ya-Wen; Lai, Hung-Cheng

    2015-01-01

    Non-attendance at gynecological clinics is a major limitation of cervical cancer screening and self-collection of samples may improve this situation. Although HPV testing of self-collected vaginal samples is acceptable, the specificity is inadequate. The current focus is increasing self-collection of vaginal samples to minimize clinic visits. In this study, we analyzed the concordance and clinical performance of DNA methylation biomarker (PAX1, SOX1, and ZNF582) detection in self-collected vaginal samples and physician-collected cervical samples for the identification of cervical neoplasm. We enrolled 136 cases with paired methylation data identified from abnormal Pap smears (n = 126) and normal controls (n = 10) regardless of HPV status at gynecological clinics. The study group comprised 37 cervical intraepithelial neoplasm I (CIN1), 23 cervical intraepithelial neoplasm II (CIN2), 16 cervical intraepithelial neoplasm III (CIN3), 30 carcinoma in situ (CIS), 13 squamous cell carcinomas (SCCs) and seven adenocarcinomas (ACs)/adenosquamous carcinomas (ASCs). PAX1, SOX1 and ZNF582 methylation in study samples was assessed by real-time quantitative methylation-specific polymerase chain reaction analysis. We generated methylation index cutoff values for the detection of CIN3+ in physician-collected cervical samples for analysis of the self-collected group. Concordance between the physician-collected and self-collected groups was evaluated by Cohen’s Kappa. Sensitivity, specificity and area under curve (AUC) were calculated for detection of CIN3+ lesions. Finally, we produced an optimal cutoff value with the best sensitivity from the self-collected groups. We generated a methylation index cutoff value from physician-collected samples for detection of CIN3+. There were no significant differences in sensitivity, specificity of PAX1, SOX1 and ZNF582 between the self-collected and physician-collected groups. The methylation status of all three genes in the normal control

  5. Integrated analysis of DNA methylation and gene expression reveals specific signaling pathways associated with platinum resistance in ovarian cancer

    Directory of Open Access Journals (Sweden)

    Chung Jae

    2009-06-01

    Full Text Available Abstract Background Cisplatin and carboplatin are the primary first-line therapies for the treatment of ovarian cancer. However, resistance to these platinum-based drugs occurs in the large majority of initially responsive tumors, resulting in fully chemoresistant, fatal disease. Although the precise mechanism(s underlying the development of platinum resistance in late-stage ovarian cancer patients currently remains unknown, CpG-island (CGI methylation, a phenomenon strongly associated with aberrant gene silencing and ovarian tumorigenesis, may contribute to this devastating condition. Methods To model the onset of drug resistance, and investigate DNA methylation and gene expression alterations associated with platinum resistance, we treated clonally derived, drug-sensitive A2780 epithelial ovarian cancer cells with increasing concentrations of cisplatin. After several cycles of drug selection, the isogenic drug-sensitive and -resistant pairs were subjected to global CGI methylation and mRNA expression microarray analyses. To identify chemoresistance-associated, biological pathways likely impacted by DNA methylation, promoter CGI methylation and mRNA expression profiles were integrated and subjected to pathway enrichment analysis. Results Promoter CGI methylation revealed a positive association (Spearman correlation of 0.99 between the total number of hypermethylated CGIs and GI50 values (i.e., increased drug resistance following successive cisplatin treatment cycles. In accord with that result, chemoresistance was reversible by DNA methylation inhibitors. Pathway enrichment analysis revealed hypermethylation-mediated repression of cell adhesion and tight junction pathways and hypomethylation-mediated activation of the cell growth-promoting pathways PI3K/Akt, TGF-beta, and cell cycle progression, which may contribute to the onset of chemoresistance in ovarian cancer cells. Conclusion Selective epigenetic disruption of distinct biological

  6. Isobolographic Analysis for Mixture Effects of Mesosulfuron-Methyl+Iodosulfuron with Pinoxaden in Wheat (Triticum aestivum

    Directory of Open Access Journals (Sweden)

    masoud kargar

    2017-03-01

    with an 8002 flat fan nozzle tip delivering 200 L ha-1 at 2 bar spray pressure. Four weeks after spraying, the plants of the experimental units were harvested and oven-dried at 75°C for 48 h, then weighed. The greenhouse temperature varied from 18–25 °C during the day and 14–21°C at night. Field trial was conducted in completely randomized block design with three replications at Research Farm of Agricultural Faculty of Ferdowsi University of Mashhad, Iran in 2014. Because the appropriate ED50 obtained in the greenhouse therefor he recommended doses were used for field trial. Minitab 16.0 software was used for variance analysis and Mean comparison also for regression analysis, R software was applied. Results and Discussion: Greenhouse experiment results showed that pure application of mesosulfuron-methyl+iodosulfuron and pinoxaden herbicide was effective on wild oat and littleseed canarygrass. The results of mixing experiments on wild oat and littleseed canarygrass showed that mixture of mesosulfuron-methyl+iodosulfuron with pinoxaden had additive effect of both species. ED50 of different ratios of the two herbicides showed that maximum efficacy (maximum intensity effect in decreasing dry weight of wild oat was related to ratio 100: 0 mesosulfuron-methyl+iodosulfuron and pinoxaden with ED50= 2.16 and minimum efficacy (minimum intensity effect was related to ratio 75:25 mesosulfuron-methyl+iodosulfuron and pinoxaden with ED50= 4.22. The results of the field almost were consistent with the results of the greenhouse so that the different ratios no significant difference was observed in both species of wild oat and littleseed canarygrass. All herbicide treatments resulted in at least 85.4% and 86.86% reduction biomass and population of wild oat. Except control treatments, all tank mixing ratios of mesosulfuron-methyl+iodosulfuron and pinoxaden weren’t significantly different. On the other hand, jointed effects of the two herbicides on wild oat in field experiment

  7. Time analysis in astronomy: Tools for periodicity searches

    International Nuclear Information System (INIS)

    Buccheri, R.; Sacco, B.

    1985-01-01

    The authors discuss periodicity searches in radio and gamma-ray astronomy with special considerations for pulsar searches. The basic methodologies of fast Fourier transform, Rayleigh test, and epoch folding are reviewed with the main objective to compare cost and sensitivities in different applications. It is found that FFT procedures are convenient in unbiased searches for periodicity in radio astronomy, while in spark chamber gamma-ray astronomy, where the measurements are spread over a long integration time, unbiased searches are very difficult with the existing computing facilities and analyses with a-priori knowledge on the period values to look for are better done using the Rayleigh test with harmonics folding (Z /sub n/ test)

  8. Genomewide analysis indicates that queen larvae have lower methylation levels in the honey bee ( Apis mellifera)

    Science.gov (United States)

    Shi, Yuan Yuan; Yan, Wei Yu; Huang, Zachary Y.; Wang, Zi Long; Wu, Xiao Bo; Zeng, Zhi Jiang

    2013-02-01

    The honey bee is a social insect characterized by caste differentiation, by which a young larva can develop into either a queen or a worker. Despite possessing the same genome, queen and workers display marked differences in reproductive capacity, physiology, and behavior. Recent studies have shown that DNA methylation plays important roles in caste differentiation. To further explore the roles of DNA methylation in this process, we analyzed DNA methylome profiles of both queen larvae (QL) and worker larvae (WL) of different ages (2, 4, and 6 day old), by using methylated DNA immunoprecipitation-sequencing (meDIP-seq) technique. The global DNA methylation levels varied between the larvae of two castes. DNA methylation increased from 2-day- to 4-day-old QL and then decreased in 6-day-old larvae. In WL, methylation levels increased with age. The methylcytosines in both larvae were enriched in introns, followed by coding sequence (CDS) regions, CpG islands, 2 kbp downstream and upstream of genes, and 5' and 3' untranslated regions (UTRs). The number of differentially methylated genes (DMGs) in 2-, 4-, and 6-day-old QL and WL was 725, 3,013, and 5,049, respectively. Compared to 4- and 6-day-old WL, a large number of genes in QL were downmethylated, which were involved in many processes including development, reproduction, and metabolic regulation. In addition, some DMGs were concerned with caste differentiation.

  9. Bifurcation analysis of delay-induced periodic oscillations

    NARCIS (Netherlands)

    Green, K.

    2010-01-01

    In this paper we consider a generic differential equation with a cubic nonlinearity and delay. This system, in the absence of delay, is known to undergo an oscillatory instability. The addition of the delay is shown to result in the creation of a number of periodic solutions with constant amplitude

  10. Comprehensive analysis of genome-wide DNA methylation across human polycystic ovary syndrome ovary granulosa cell.

    Science.gov (United States)

    Xu, Jiawei; Bao, Xiao; Peng, Zhaofeng; Wang, Linlin; Du, Linqing; Niu, Wenbin; Sun, Yingpu

    2016-05-10

    Polycystic ovary syndrome (PCOS) affects approximately 7% of the reproductive-age women. A growing body of evidence indicated that epigenetic mechanisms contributed to the development of PCOS. The role of DNA modification in human PCOS ovary granulosa cell is still unknown in PCOS progression. Global DNA methylation and hydroxymethylation were detected between PCOS' and controls' granulosa cell. Genome-wide DNA methylation was profiled to investigate the putative function of DNA methylaiton. Selected genes expressions were analyzed between PCOS' and controls' granulosa cell. Our results showed that the granulosa cell global DNA methylation of PCOS patients was significant higher than the controls'. The global DNA hydroxymethylation showed low level and no statistical difference between PCOS and control. 6936 differentially methylated CpG sites were identified between control and PCOS-obesity. 12245 differential methylated CpG sites were detected between control and PCOS-nonobesity group. 5202 methylated CpG sites were significantly differential between PCOS-obesity and PCOS-nonobesity group. Our results showed that DNA methylation not hydroxymethylation altered genome-wide in PCOS granulosa cell. The different methylation genes were enriched in development protein, transcription factor activity, alternative splicing, sequence-specific DNA binding and embryonic morphogenesis. YWHAQ, NCF2, DHRS9 and SCNA were up-regulation in PCOS-obesity patients with no significance different between control and PCOS-nonobesity patients, which may be activated by lower DNA methylaiton. Global and genome-wide DNA methylation alteration may contribute to different genes expression and PCOS clinical pathology.

  11. Analysis of Periodic Errors for Synthesized-Reference-Wave Holography

    Directory of Open Access Journals (Sweden)

    V. Schejbal

    2009-12-01

    Full Text Available Synthesized-reference-wave holographic techniques offer relatively simple and cost-effective measurement of antenna radiation characteristics and reconstruction of complex aperture fields using near-field intensity-pattern measurement. These methods allow utilization of advantages of methods for probe compensations for amplitude and phasing near-field measurements for the planar and cylindrical scanning including accuracy analyses. The paper analyzes periodic errors, which can be created during scanning, using both theoretical results and numerical simulations.

  12. DNA Methylation in Newborns and Maternal Smoking in Pregnancy : Genome-wide Consortium Meta-analysis

    NARCIS (Netherlands)

    Joubert, Bonnie R.; Felix, Janine F.; Yousefi, Paul; Bakulski, Kelly M.; Just, Allan C.; Breton, Carrie; Reese, Sarah E.; Markunas, Christina A.; Richmond, Rebecca C.; Xu, Chengjian; Kupers, Leanne K.; Oh, Sam S.; Hoyo, Cathrine; Gruzieva, Olena; Soderhal, Cilla; Salas, Lucas A.; Baiz, Nour; Zhang, Hongmei; Lepeule, Johanna; Ruiz, Carlos; Ligthart, Symen; Wang, Tianyuan; Taylor, Jack A.; Duijts, Liesbeth; Sharp, Gemma C.; Jankipersadsing, Soesma A.; Nilsen, Roy M.; Vaez, Ahmad; Fallin, M. Daniele; Hu, Donglei; Litonjua, Augusto A.; Fuemmeler, Bernard F.; Huen, Karen; Kere, Juha; Kull, Inger; Munthe-Kaas, Monica Cheng; Gehring, Ulrike; Bustamante, Mariona; Saurel-Coubizolles, Marie Jose; Quraishi, Bilal M.; Ren, Jie; Tost, Jorg; Gonzalez, Juan R.; Peters, Marjolein J.; Haberg, Siri E.; Xu, Zongli; van Meurs, Joyce B.; Gaunt, Tom R.; Kerkhof, Marjan; Corpeleijn, Eva; Feinberg, Andrew P.; Eng, Celeste; Baccarelli, Andrea A.; Neelon, Sara E. Benjamin; Bradman, Asa; Merid, Simon Kebede; Bergstrom, Anna; Herceg, Zdenko; Hernandez-Vargas, Hector; Brunekreef, Bert; Pinart, Mariona; Heude, Barbara; Ewart, Susan; Yao, Jin; Lemonnier, Nathanael; Franco, Oscar H.; Wu, Michael C.; Hofman, Albert; McArdle, Wendy; Van der Vlies, Pieter; Falahi, Fahimeh; Gillman, Matthew W.; Barcellos, Lisa F.; Kumar, Ashish; Wickman, Magnus; Guerra, Stefano; Charles, Marie-Aline; Holloway, John; Auffray, Charles; Tiemeier, Henning W.; Smith, George Davey; Postma, Dirkje; Hivert, Marie-France; Eskenazi, Brenda; Vrijheid, Martine; Arshad, Hasan; Anto, Josep M.; Dehghan, Abbas; Karmaus, Wilfried; Annesi-Maesano, Isabella; Sunyer, Jordi; Ghantous, Akram; Pershagen, Goran; Hollands, Nina; Murphy, Susan K.; DeMeo, Dawn L.; Burchard, Esteban G.; Ladd-Acosta, Christine; Snieder, Harold; Nystad, Wenche; Koppelman, Gerard H.; Relton, Caroline L.; Jaddoe, Vincent W. V.; Wilcox, Allen; Melen, Erik; London, Stephanie J.

    2016-01-01

    Epigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences. The

  13. Analysis of methylated patterns and quality-related genes in tobacco (Nicotiana tabacum) cultivars.

    Science.gov (United States)

    Jiao, Junna; Jia, Yanlong; Lv, Zhuangwei; Sun, Chuanfei; Gao, Lijie; Yan, Xiaoxiao; Cui, Liusu; Tang, Zongxiang; Yan, Benju

    2014-08-01

    Methylation-sensitive amplified polymorphism was used in this study to investigate epigenetic information of four tobacco cultivars: Yunyan 85, NC89, K326, and Yunyan 87. The DNA fragments with methylated information were cloned by reamplified PCR and sequenced. The results of Blast alignments showed that the genes with methylation information included chitinase, nitrate reductase, chloroplast DNA, mitochondrial DNA, ornithine decarboxylase, ribulose carboxylase, and promoter sequences. Homologous comparison in three cloned gene sequences (nitrate reductase, ornithine decarboxylase, and ribulose decarboxylase) indicated that geographic factors had significant influence on the whole genome methylation. Introns also contained different information in different tobacco cultivars. These findings suggest that synthetic mechanisms for tobacco aromatic components could be affected by different environmental factors leading to variation of noncoding regions in the genome, which finally results in different fragrance and taste in different tobacco cultivars.

  14. H19DMR methylation analysis in patients with Beckwith-Wiedemann syndrome and isolated hemihyperplasia

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    Marcus Vinícius de Matos Gomes

    2005-01-01

    Full Text Available Beckwith-Wiedemann syndrome (BWS is a congenital overgrowth disorder of complex and heterogeneous etiology involving alterations in genomic imprinting. The cause of isolated hemihyperplasia (IHH is unknown but might be due to partial or incomplete expression of BWS because both these conditions share predisposition for the same types of neoplasias. We investigated the methylation pattern of the putative imprinting control region H19DMR using peripheral blood from 12 patients, six with clinical features of BWS and six with IHH. All the patients had normal karyotypes and paternal uniparental disomy (UPD was excluded in 10 informative cases. The normal H19DMR methylation pattern was found in eight informative patients, indicating that H19DMR methylation was not related to their condition. We suggest that the absence of neoplasias in the BWS and IHH patients studied might be related to the absence of UPD and to the presence of normal H19DMR methylation.

  15. Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Lee, Jung-Rok; Dahl, Christina

    2017-01-01

    specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection...

  16. Quantitative promoter methylation analysis of multiple cancer-related genes in renal cell tumors

    Directory of Open Access Journals (Sweden)

    Oliveira Jorge

    2007-07-01

    Full Text Available Abstract Background Aberrant promoter hypermethylation of cancer-associated genes occurs frequently during carcinogenesis and may serve as a cancer biomarker. In this study we aimed at defining a quantitative gene promoter methylation panel that might identify the most prevalent types of renal cell tumors. Methods A panel of 18 gene promoters was assessed by quantitative methylation-specific PCR (QMSP in 85 primarily resected renal tumors representing the four major histologic subtypes (52 clear cell (ccRCC, 13 papillary (pRCC, 10 chromophobe (chRCC, and 10 oncocytomas and 62 paired normal tissue samples. After genomic DNA isolation and sodium bisulfite modification, methylation levels were determined and correlated with standard clinicopathological parameters. Results Significant differences in methylation levels among the four subtypes of renal tumors were found for CDH1 (p = 0.0007, PTGS2 (p = 0.002, and RASSF1A (p = 0.0001. CDH1 hypermethylation levels were significantly higher in ccRCC compared to chRCC and oncocytoma (p = 0.00016 and p = 0.0034, respectively, whereas PTGS2 methylation levels were significantly higher in ccRCC compared to pRCC (p = 0.004. RASSF1A methylation levels were significantly higher in pRCC than in normal tissue (p = 0.035. In pRCC, CDH1 and RASSF1A methylation levels were inversely correlated with tumor stage (p = 0.031 and nuclear grade (p = 0.022, respectively. Conclusion The major subtypes of renal epithelial neoplasms display differential aberrant CDH1, PTGS2, and RASSF1A promoter methylation levels. This gene panel might contribute to a more accurate discrimination among common renal tumors, improving preoperative assessment and therapeutic decision-making in patients harboring suspicious renal masses.

  17. Quantitative promoter methylation analysis of multiple cancer-related genes in renal cell tumors

    International Nuclear Information System (INIS)

    Costa, Vera L; Henrique, Rui; Ribeiro, Franclim R; Pinto, Mafalda; Oliveira, Jorge; Lobo, Francisco; Teixeira, Manuel R; Jerónimo, Carmen

    2007-01-01

    Aberrant promoter hypermethylation of cancer-associated genes occurs frequently during carcinogenesis and may serve as a cancer biomarker. In this study we aimed at defining a quantitative gene promoter methylation panel that might identify the most prevalent types of renal cell tumors. A panel of 18 gene promoters was assessed by quantitative methylation-specific PCR (QMSP) in 85 primarily resected renal tumors representing the four major histologic subtypes (52 clear cell (ccRCC), 13 papillary (pRCC), 10 chromophobe (chRCC), and 10 oncocytomas) and 62 paired normal tissue samples. After genomic DNA isolation and sodium bisulfite modification, methylation levels were determined and correlated with standard clinicopathological parameters. Significant differences in methylation levels among the four subtypes of renal tumors were found for CDH1 (p = 0.0007), PTGS2 (p = 0.002), and RASSF1A (p = 0.0001). CDH1 hypermethylation levels were significantly higher in ccRCC compared to chRCC and oncocytoma (p = 0.00016 and p = 0.0034, respectively), whereas PTGS2 methylation levels were significantly higher in ccRCC compared to pRCC (p = 0.004). RASSF1A methylation levels were significantly higher in pRCC than in normal tissue (p = 0.035). In pRCC, CDH1 and RASSF1A methylation levels were inversely correlated with tumor stage (p = 0.031) and nuclear grade (p = 0.022), respectively. The major subtypes of renal epithelial neoplasms display differential aberrant CDH1, PTGS2, and RASSF1A promoter methylation levels. This gene panel might contribute to a more accurate discrimination among common renal tumors, improving preoperative assessment and therapeutic decision-making in patients harboring suspicious renal masses

  18. Epigenome-wide analysis of DNA methylation reveals a rectal cancer-specific epigenomic signature

    Czech Academy of Sciences Publication Activity Database

    Vymetálková, Veronika; Vodička, Pavel; Pardini, Barbara; Rosa, F.; Levý, M.; Schneiderová, M.; Liška, V.; Vodičková, Ludmila; Nilsson, T.K.; Farkas, S. A.

    2016-01-01

    Roč. 8, č. 9 (2016), s. 1193-1207 ISSN 1750-1911 R&D Projects: GA MZd(CZ) NT13424; GA MZd(CZ) NV15-27580A; GA ČR(CZ) GA15-08239S; GA MŠk(CZ) LD14050 Institutional support: RVO:68378041 Keywords : DNA methylation * Illumina Human Methylation 450 BeadChip * rectal cancer Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.541, year: 2016

  19. The Variation Analysis of DNA Methylation in Wheat Carrying Gametocidal Chromosome 3C from Aegilops triuncialis.

    Science.gov (United States)

    Wang, Dan; Zhao, Jieyu; Bai, Yan; Ao, You; Guo, Changhong

    2017-08-10

    Gametocidal (Gc) chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP) technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent. The results indicated that the overall levels of cytosine methylation of two studied Gc addition lines (CS-3C and CS-3C3C, 48.68% and 48.65%, respectively) were significantly increased when compared to common wheat CS (41.31%) and no matter fully methylated or hemimethylated rates enhanced in Gc addition lines. A set of 30 isolated fragments that showed different DNA methylation or demethylation patterns between the three lines were sequenced and the results indicated that 8 fragments showed significant homology to known sequences, of which three were homologous to MITE transposon (Miniature inverted-repeat transposable elements), LTR-retrotransposon WIS-1p and retrotransposon Gypsy , respectively. Overall, our results showed that DNA methylation could play a role in the Gc action.

  20. The Variation Analysis of DNA Methylation in Wheat Carrying Gametocidal Chromosome 3C from Aegilops triuncialis

    Directory of Open Access Journals (Sweden)

    Dan Wang

    2017-08-01

    Full Text Available Gametocidal (Gc chromosomes can ensure their preferential transmission by killing the gametes without themselves through causing chromosome breakage and therefore have been exploited as an effective tool for genetic breeding. However, to date very little is known about the molecular mechanism of Gc action. In this study, we used methylation-sensitive amplified polymorphism (MSAP technique to assess the extent and pattern of cytosine methylation alterations at the whole genome level between two lines of wheat Gc addition line and their common wheat parent. The results indicated that the overall levels of cytosine methylation of two studied Gc addition lines (CS–3C and CS–3C3C, 48.68% and 48.65%, respectively were significantly increased when compared to common wheat CS (41.31% and no matter fully methylated or hemimethylated rates enhanced in Gc addition lines. A set of 30 isolated fragments that showed different DNA methylation or demethylation patterns between the three lines were sequenced and the results indicated that 8 fragments showed significant homology to known sequences, of which three were homologous to MITE transposon (Miniature inverted–repeat transposable elements, LTR-retrotransposon WIS-1p and retrotransposon Gypsy, respectively. Overall, our results showed that DNA methylation could play a role in the Gc action.

  1. Three dimensional analysis of histone methylation patterns in normal and tumor cell nuclei

    Directory of Open Access Journals (Sweden)

    M Cremer

    2009-06-01

    Full Text Available Histone modifications represent an important epigenetic mechanism for the organization of higher order chromatin structure and gene regulation. Methylation of position-specific lysine residues in the histone H3 and H4 amino termini has been linked with the formation of constitutive and facultative heterochromatin as well as with specifically repressed single gene loci. Using an antibody, directed against dimethylated lysine 9 of histone H3 and several other lysine methylation sites, we visualized the nuclear distribution pattern of chromatin flagged by these methylated lysines in 3D preserved nuclei of normal and malignant cell types. Optical confocal serial sections were used for a quantitative evaluation. We demonstrate distinct differences of these histone methylation patterns among nuclei of different cell types after exit of the cell cycle. Changes in the pattern formation were also observed during the cell cycle. Our data suggest an important role of methylated histones in the reestablishment of higher order chromatin arrangements during telophase/early G1. Cell type specific histone methylation patterns are possibly causally involved in the formation of cell type specific heterochromatin compartments, composed of (pericentromeric regions and chromosomal subregions from neighboring chromosome territories, which contain silent genes.

  2. High-throughput DNA methylation analysis in anorexia nervosa confirms TNXB hypermethylation.

    Science.gov (United States)

    Kesselmeier, Miriam; Pütter, Carolin; Volckmar, Anna-Lena; Baurecht, Hansjörg; Grallert, Harald; Illig, Thomas; Ismail, Khadeeja; Ollikainen, Miina; Silén, Yasmina; Keski-Rahkonen, Anna; Bulik, Cynthia M; Collier, David A; Zeggini, Eleftheria; Hebebrand, Johannes; Scherag, André; Hinney, Anke

    2018-04-01

    Patients with anorexia nervosa (AN) are ideally suited to identify differentially methylated genes in response to starvation. We examined high-throughput DNA methylation derived from whole blood of 47 females with AN, 47 lean females without AN and 100 population-based females to compare AN with both controls. To account for different cell type compositions, we applied two reference-free methods (FastLMM-EWASher, RefFreeEWAS) and searched for consensus CpG sites identified by both methods. We used a validation sample of five monozygotic AN-discordant twin pairs. Fifty-one consensus sites were identified in AN vs. lean and 81 in AN vs. population-based comparisons. These sites have not been reported in AN methylation analyses, but for the latter comparison 54/81 sites showed directionally consistent differential methylation effects in the AN-discordant twins. For a single nucleotide polymorphism rs923768 in CSGALNACT1 a nearby site was nominally associated with AN. At the gene level, we confirmed hypermethylated sites at TNXB. We found support for a locus at NR1H3 in the AN vs. lean control comparison, but the methylation direction was opposite to the one previously reported. We confirm genes like TNXB previously described to comprise differentially methylated sites, and highlight further sites that might be specifically involved in AN starvation processes.

  3. Unstable Periodic Orbit Analysis of Histograms of Chaotic Time Series

    International Nuclear Information System (INIS)

    Zoldi, S.M.

    1998-01-01

    Using the Lorenz equations, we have investigated whether unstable periodic orbits (UPOs) associated with a strange attractor may predict the occurrence of the robust sharp peaks in histograms of some experimental chaotic time series. Histograms with sharp peaks occur for the Lorenz parameter value r=60.0 but not for r=28.0 , and the sharp peaks for r=60.0 do not correspond to a histogram derived from any single UPO. However, we show that histograms derived from the time series of a non-Axiom-A chaotic system can be accurately predicted by an escape-time weighting of UPO histograms. copyright 1998 The American Physical Society

  4. Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC and its application for DNA methylation analysis

    Directory of Open Access Journals (Sweden)

    Ottaviani Diego

    2008-05-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome. Methods To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP, methylated DNA immunoprecipitation (MeDIP, array comparative genomic hybridization (aCGH and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls. Results Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs. Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation. Conclusion A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics.

  5. Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments

    Science.gov (United States)

    2014-01-01

    Background Whole-genome bisulfite sequencing currently provides the highest-precision view of the epigenome, with quantitative information about populations of cells down to single nucleotide resolution. Several studies have demonstrated the value of this precision: meaningful features that correlate strongly with biological functions can be found associated with only a few CpG sites. Understanding the role of DNA methylation, and more broadly the role of DNA accessibility, requires that methylation differences between populations of cells are identified with extreme precision and in complex experimental designs. Results In this work we investigated the use of beta-binomial regression as a general approach for modeling whole-genome bisulfite data to identify differentially methylated sites and genomic intervals. Conclusions The regression-based analysis can handle medium- and large-scale experiments where it becomes critical to accurately model variation in methylation levels between replicates and account for influence of various experimental factors like cell types or batch effects. PMID:24962134

  6. Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample.

    Directory of Open Access Journals (Sweden)

    Katsuhiko Nosho

    Full Text Available The CpG island methylator phenotype (CIMP is a distinct phenotype associated with microsatellite instability (MSI and BRAF mutation in colon cancer. Recent investigations have selected 5 promoters (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1 as surrogate markers for CIMP-high. However, no study has comprehensively evaluated an expanded set of methylation markers (including these 5 markers using a large number of tumors, or deciphered the complex clinical and molecular associations with CIMP-high determined by the validated marker panel. METHOLODOLOGY/PRINCIPAL FINDINGS: DNA methylation at 16 CpG islands [the above 5 plus CDKN2A (p16, CHFR, CRABP1, HIC1, IGFBP3, MGMT, MINT1, MINT31, MLH1, p14 (CDKN2A/ARF and WRN] was quantified in 904 colorectal cancers by real-time PCR (MethyLight. In unsupervised hierarchical clustering analysis, the 5 markers (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1, CDKN2A, CRABP1, MINT31, MLH1, p14 and WRN were generally clustered with each other and with MSI and BRAF mutation. KRAS mutation was not clustered with any methylation marker, suggesting its association with a random methylation pattern in CIMP-low tumors. Utilizing the validated CIMP marker panel (including the 5 markers, multivariate logistic regression demonstrated that CIMP-high was independently associated with older age, proximal location, poor differentiation, MSI-high, BRAF mutation, and inversely with LINE-1 hypomethylation and beta-catenin (CTNNB1 activation. Mucinous feature, signet ring cells, and p53-negativity were associated with CIMP-high in only univariate analysis. In stratified analyses, the relations of CIMP-high with poor differentiation, KRAS mutation and LINE-1 hypomethylation significantly differed according to MSI status.Our study provides valuable data for standardization of the use of CIMP-high-specific methylation markers. CIMP-high is independently associated with clinical and key molecular features in colorectal cancer. Our data also

  7. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants.

    Science.gov (United States)

    How-Kit, Alexandre; Daunay, Antoine; Mazaleyrat, Nicolas; Busato, Florence; Daviaud, Christian; Teyssier, Emeline; Deleuze, Jean-François; Gallusci, Philippe; Tost, Jörg

    2015-07-01

    Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing.

  8. Computational analysis of acoustic transmission through periodically perforated interfaces

    Directory of Open Access Journals (Sweden)

    Rohan E.

    2009-06-01

    Full Text Available The objective of the paper is to demonstrate the homogenization approach applied to modelling the acoustic transmission on perforated interfaces embedded in the acoustic fluid. We assume a layer, with periodically perforated obstacles, separating two half-spaces filled with the fluid. The homogenization method provides limit transmission conditions which can be prescribed at the homogenized surface representing the "limit" interface. The conditions describe relationship between jump of the acoustic pressures and the transversal acoustic velocity, on introducing the "in-layer pressure" which describes wave propagation in the tangent directions with respect to the interface.This approach may serve as a relevant tool for optimal design of devices aimed at attenuation of the acoustic waves, such as the engine exhaust mufflers or other structures fitted with sieves and grillages. We present numerical examples of wave propagation in a muffler-like structure illustrating viability of the approach when complex 3D geometries of the interface perforation are considered.

  9. Analysis of decision procedures for a sequence of inventory periods

    International Nuclear Information System (INIS)

    Avenhaus, R.

    1982-07-01

    Optimal test procedures for a sequence of inventory periods will be discussed. Starting with a game theoretical description of the conflict situation between the plant operator and the inspector, the objectives of the inspector as well as the general decision theoretical problem will be formulated. In the first part the objective of 'secure' detection will be emphasized which means that only at the end of the reference time a decision is taken by the inspector. In the second part the objective of 'timely' detection will be emphasized which will lead to sequential test procedures. At the end of the paper all procedures will be summarized, and in view of the multitude of procedures available at the moment some comments about future work will be given. (orig./HP) [de

  10. Identification of Differentially Methylated Sites with Weak Methylation Effects

    Directory of Open Access Journals (Sweden)

    Hong Tran

    2018-02-01

    Full Text Available Deoxyribonucleic acid (DNA methylation is an epigenetic alteration crucial for regulating stress responses. Identifying large-scale DNA methylation at single nucleotide resolution is made possible by whole genome bisulfite sequencing. An essential task following the generation of bisulfite sequencing data is to detect differentially methylated cytosines (DMCs among treatments. Most statistical methods for DMC detection do not consider the dependency of methylation patterns across the genome, thus possibly inflating type I error. Furthermore, small sample sizes and weak methylation effects among different phenotype categories make it difficult for these statistical methods to accurately detect DMCs. To address these issues, the wavelet-based functional mixed model (WFMM was introduced to detect DMCs. To further examine the performance of WFMM in detecting weak differential methylation events, we used both simulated and empirical data and compare WFMM performance to a popular DMC detection tool methylKit. Analyses of simulated data that replicated the effects of the herbicide glyphosate on DNA methylation in Arabidopsis thaliana show that WFMM results in higher sensitivity and specificity in detecting DMCs compared to methylKit, especially when the methylation differences among phenotype groups are small. Moreover, the performance of WFMM is robust with respect to small sample sizes, making it particularly attractive considering the current high costs of bisulfite sequencing. Analysis of empirical Arabidopsis thaliana data under varying glyphosate dosages, and the analysis of monozygotic (MZ twins who have different pain sensitivities—both datasets have weak methylation effects of <1%—show that WFMM can identify more relevant DMCs related to the phenotype of interest than methylKit. Differentially methylated regions (DMRs are genomic regions with different DNA methylation status across biological samples. DMRs and DMCs are essentially the same

  11. Prognostic value of three different methods of MGMT promoter methylation analysis in a prospective trial on newly diagnosed glioblastoma.

    Directory of Open Access Journals (Sweden)

    Arne Christians

    Full Text Available Hypermethylation in the promoter region of the MGMT gene encoding the DNA repair protein O(6-methylguanine-DNA methyltransferase is among the most important prognostic factors for patients with glioblastoma and predicts response to treatment with alkylating agents like temozolomide. Hence, the MGMT status is widely determined in most clinical trials and frequently requested in routine diagnostics of glioblastoma. Since various different techniques are available for MGMT promoter methylation analysis, a generally accepted consensus as to the most suitable diagnostic method remains an unmet need. Here, we assessed methylation-specific polymerase chain reaction (MSP as a qualitative and semi-quantitative method, pyrosequencing (PSQ as a quantitative method, and methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA as a semi-quantitative method in a series of 35 formalin-fixed, paraffin-embedded glioblastoma tissues derived from patients treated in a prospective clinical phase II trial that tested up-front chemoradiotherapy with dose-intensified temozolomide (UKT-05. Our goal was to determine which of these three diagnostic methods provides the most accurate prediction of progression-free survival (PFS. The MGMT promoter methylation status was assessable by each method in almost all cases (n = 33/35 for MSP; n = 35/35 for PSQ; n = 34/35 for MS-MLPA. We were able to calculate significant cut-points for the continuous methylation signals at each CpG site analysed by PSQ (range, 11.5 to 44.9% and at one CpG site assessed by MS-MLPA (3.6% indicating that a dichotomisation of continuous methylation data as a prerequisite for comparative survival analyses is feasible. Our results show that, unlike MS-MLPA, MSP and PSQ provide a significant improvement of predicting PFS compared with established clinical prognostic factors alone (likelihood ratio tests: p<0.001. Conclusively, taking into consideration prognostic value

  12. Genome-wide DNA methylation analysis of transient neonatal diabetes type 1 patients with mutations in ZFP57.

    Science.gov (United States)

    Bak, Mads; Boonen, Susanne E; Dahl, Christina; Hahnemann, Johanne M D; Mackay, Deborah J D G; Tümer, Zeynep; Grønskov, Karen; Temple, I Karen; Guldberg, Per; Tommerup, Niels

    2016-04-14

    Transient neonatal diabetes mellitus 1 (TNDM1) is a rare imprinting disorder characterized by intrautering growth retardation and diabetes mellitus usually presenting within the first six weeks of life and resolves by the age of 18 months. However, patients have an increased risk of developing diabetes mellitus type 2 later in life. Transient neonatal diabetes mellitus 1 is caused by overexpression of the maternally imprinted genes PLAGL1 and HYMAI on chromosome 6q24. One of the mechanisms leading to overexpression of the locus is hypomethylation of the maternal allele of PLAGL1 and HYMAI. A subset of patients with maternal hypomethylation at PLAGL1 have hypomethylation at additional imprinted loci throughout the genome, including GRB10, ZIM2 (PEG3), MEST (PEG1), KCNQ1OT1 and NESPAS (GNAS-AS1). About half of the TNDM1 patients carry mutations in ZFP57, a transcription factor involved in establishment and maintenance of methylation of imprinted loci. Our objective was to investigate whether additional regions are aberrantly methylated in ZFP57 mutation carriers. Genome-wide DNA methylation analysis was performed on four individuals with homozygous or compound heterozygous ZFP57 mutations, three relatives with heterozygous ZFP57 mutations and five controls. Methylation status of selected regions showing aberrant methylation in the patients was verified using bisulfite-sequencing. We found large variability among the patients concerning the number and identity of the differentially methylated regions, but more than 60 regions were aberrantly methylated in two or more patients and a novel region within PPP1R13L was found to be hypomethylated in all the patients. The hypomethylated regions in common between the patients are enriched for the ZFP57 DNA binding motif. We have expanded the epimutational spectrum of TNDM1 associated with ZFP57 mutations and found one novel region within PPP1R13L which is hypomethylated in all TNDM1 patients included in this study. Functional

  13. Genome-Wide Analysis of DNA Methylation before-and after Exercise in the Thoroughbred Horse with MeDIP-Seq

    Science.gov (United States)

    Gim, Jeong-An; Hong, Chang Pyo; Kim, Dae-Soo; Moon, Jae-Woo; Choi, Yuri; Eo, Jungwoo; Kwon, Yun-Jeong; Lee, Ja-Rang; Jung, Yi-Deun; Bae, Jin-Han; Choi, Bong-Hwan; Ko, Junsu; Song, Sanghoon; Ahn, Kung; Ha, Hong-Seok; Yang, Young Mok; Lee, Hak-Kyo; Park, Kyung-Do; Do, Kyoung-Tag; Han, Kyudong; Yi, Joo Mi; Cha, Hee-Jae; Ayarpadikannan, Selvam; Cho, Byung-Wook; Bhak, Jong; Kim, Heui-Soo

    2015-01-01

    Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethylated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits. PMID:25666347

  14. Analysis of periodically patterned metallic nanostructures for infrared absorber

    Science.gov (United States)

    Peng, Sha; Yuan, Ying; Long, Huabao; Liu, Runhan; Wei, Dong; Zhang, Xinyu; Wang, Haiwei; Xie, Changsheng

    2018-02-01

    With rapid advancement of infrared detecting technology in both military and civil domains, the photo-electronic performances of near-infrared detectors have been widely concerned. Currently, near-infrared detectors demonstrate some problems such as low sensitivity, low detectivity, and relatively small array scale. The current studies show that surface plasmons (SPs) stimulated over the surface of metallic nanostructures by incident light can be used to break the diffraction limit and thus concentrate light into sub-wavelength scale, so as to indicate a method to develop a new type of infrared absorber or detector with very large array. In this paper, we present the design and characterization of periodically patterned metallic nanostructures that combine nanometer thickness aluminum film with silicon wafer. Numerical computations show that there are some valleys caused by surface plasmons in the reflection spectrum in the infrared region, and both red shift and blue shift of the reflection spectrum were observed through changing the nanostructural parameters such as angle α and diameters D. Moreover, the strong E-field intensity is located at the sharp corner of the nano-structures.

  15. Integrative analysis of gene expression and DNA methylation using unsupervised feature extraction for detecting candidate cancer biomarkers.

    Science.gov (United States)

    Moon, Myungjin; Nakai, Kenta

    2018-04-01

    Currently, cancer biomarker discovery is one of the important research topics worldwide. In particular, detecting significant genes related to cancer is an important task for early diagnosis and treatment of cancer. Conventional studies mostly focus on genes that are differentially expressed in different states of cancer; however, noise in gene expression datasets and insufficient information in limited datasets impede precise analysis of novel candidate biomarkers. In this study, we propose an integrative analysis of gene expression and DNA methylation using normalization and unsupervised feature extractions to identify candidate biomarkers of cancer using renal cell carcinoma RNA-seq datasets. Gene expression and DNA methylation datasets are normalized by Box-Cox transformation and integrated into a one-dimensional dataset that retains the major characteristics of the original datasets by unsupervised feature extraction methods, and differentially expressed genes are selected from the integrated dataset. Use of the integrated dataset demonstrated improved performance as compared with conventional approaches that utilize gene expression or DNA methylation datasets alone. Validation based on the literature showed that a considerable number of top-ranked genes from the integrated dataset have known relationships with cancer, implying that novel candidate biomarkers can also be acquired from the proposed analysis method. Furthermore, we expect that the proposed method can be expanded for applications involving various types of multi-omics datasets.

  16. Analysis of Greek small coinage from the classic period

    Science.gov (United States)

    Šmit, Ž.; Šemrov, A.

    2018-02-01

    A series of 25 Greek coins from the 6th to 4th centuries BC was studied by PIXE for their trace element composition, with an aim to discover the origin of their silver ore. The procedure revealed a counterfeited coin, and then concentrated on distinguishing the coins minted from the ore of Laurion on the Attica peninsula and the coins minted from other sources. Linear discriminant analysis based on the impurities and alloying elements of copper, gold, lead and bismuth revealed that discrimination is indeed possible according to a single canonical variable.

  17. QUALIS PERIODIC EVALUATION: ANALYSIS OF QUALIS UPGRADE IN MEDICINE III.

    Science.gov (United States)

    Jukemura, José; Diniz, Márcio Augusto

    2015-01-01

    To evaluate the preliminary results related to journals up-grade that was used by Medicine III, through opportunity offered by Capes to all agency areas programs. Were used area document of Medicine I, II and III, besides other relevant topics available online at Capes site, between 2009 and 2013. The research was focused to answer two questions: 1) the stratification of Qualis is similar in the three areas of medicine? and 2) the evolution of Qualis in Medicine III was higher? Medicine III showed an increase in its Qualis classification and is publishing in journals with higher impact factors, virtually the same as the Medicine I and II. The area showed the strongest growth in recent three-year periods. Avaliar os resultados preliminares sobre a Medicina III do up-grade oportunizado pela Capes para todas as áreas. Foram utilizados os documentos de áreas e os relevantes ao tema disponíveis online no site da Capes entre 2009 e 2013. Procurou-se focar a pesquisa em dois aspectos para responder duas perguntas: 1) a estratificação do Qualis é semelhante nas três áreas da medicina? e 2) a evolução do Qualis da Medicina III foi maior? A Medicina III apresentou evolução em sua classificação Qualis e está publicando em revistas com maior fator de impacto e é praticamente igual ao da Medicina I e II. A área foi a que apresentou maior evolução nestes últimos triênios.

  18. Diffusional analysis of the adsorption of methyl iodide on silver exchanged mordenite

    International Nuclear Information System (INIS)

    Jubin, R.T.; Counce, R.M.

    1997-01-01

    The removal of organic iodides from off-gas streams is an important step in controlling the release of radioactive iodine to the environment during the treatment of radioactive wastes or the processing of some irradiated materials. Nine-well accepted mass transfer models were evaluated for their ability to adequately explain the observed CH 3 I uptake behavior onto the Ag degrees Z. Linear and multidimensional regression techniques were used to estimate the diffusion constants and other model parameters, which then permitted the selection of an appropriate mass transfer model. Although a number of studies have been conducted to evaluate the loading of both elemental and methyl iodide on silver-exchanged mordenite, these studies focused primarily on the macro scale (deep bed) while evaluating the material under a broad range of process conditions and contaminants for total bed loading at the time of breakthrough. A few studies evaluated equilibrium or maximum loading. Thus, to date, only bulk loading data exist for the adsorption of CH 3 I onto Ag degrees Z. Hence this is believed to be the first study to quantify the controlling mass transfer mechanisms of this process, It can be concluded from the analysis of the experimental data obtained by the open-quotes single-pelletclose quotes type experiments and for the process conditions used in this study that the overall mass transfer rate associated with the adsorption of CH 3 I onto Ag degrees Z is affected by both micropore and macropore diffusion. The macropore diffusion rate was significantly faster than the micropore diffusion, resulting in a two-step adsorption behavior which was adequately modeled by a bimodal pore distribution model. The micropore diffusivity was determined to be on the order of 2 x 10 -14 cm 2 /s. The system was also shown to be isothermal under all conditions of this study. 21 refs., 6 figs., 8 tabs

  19. Metabolomics analysis and biosynthesis of rosmarinic acid in Agastache rugosa Kuntze treated with methyl jasmonate.

    Directory of Open Access Journals (Sweden)

    Yeon Bok Kim

    Full Text Available This study investigated the effect of methyl jasmonate (MeJA on metabolic profiles and rosmarinic acid (RA biosynthesis in cell cultures of Agastache rugosa Kuntze. Transcript levels of phenylpropanoid biosynthetic genes, i.e., ArPAL, Ar4CL, and ArC4H, maximally increased 4.5-fold, 3.4-fold, and 3.5-fold, respectively, compared with the untreated controls, and the culture contained relatively high amounts of RA after exposure of cells to 50 µM MeJA. RA levels were 2.1-, 4.7-, and 3.9-fold higher after exposure to 10, 50, and 100 µM MeJA, respectively, than those in untreated controls. In addition, the transcript levels of genes attained maximum levels at different time points after the initial exposure. The transcript levels of ArC4H and Ar4CL were transiently induced by MeJA, and reached a maximum of up to 8-fold at 3 hr and 6 hr, respectively. The relationships between primary metabolites and phenolic acids in cell cultures of A. rugosa treated with MeJA were analyzed by gas chromatography coupled with time-of-flight mass spectrometry. In total, 45 metabolites, including 41 primary metabolites and 4 phenolic acids, were identified from A. rugosa. Metabolite profiles were subjected to partial least square-discriminate analysis to evaluate the effects of MeJA. The results indicate that both phenolic acids and precursors for the phenylpropanoid biosynthetic pathway, such as aromatic amino acids and shikimate, were induced as a response to MeJA treatment. Therefore, MeJA appears to have an important impact on RA accumulation, and the increased RA accumulation in the treated cells might be due to activation of the phenylpropanoid genes ArPAL, ArC4H, and Ar4CL.

  20. Diffusional analysis of the adsorption of methyl iodide on silver exchanged mordenite

    Energy Technology Data Exchange (ETDEWEB)

    Jubin, R.T. [Oak Ridge National Lab., TN (United States); Counce, R.M. [Univ. of Tennessee, Knoxville, TN (United States)

    1997-08-01

    The removal of organic iodides from off-gas streams is an important step in controlling the release of radioactive iodine to the environment during the treatment of radioactive wastes or the processing of some irradiated materials. Nine-well accepted mass transfer models were evaluated for their ability to adequately explain the observed CH{sub 3}I uptake behavior onto the Ag{degrees}Z. Linear and multidimensional regression techniques were used to estimate the diffusion constants and other model parameters, which then permitted the selection of an appropriate mass transfer model. Although a number of studies have been conducted to evaluate the loading of both elemental and methyl iodide on silver-exchanged mordenite, these studies focused primarily on the macro scale (deep bed) while evaluating the material under a broad range of process conditions and contaminants for total bed loading at the time of breakthrough. A few studies evaluated equilibrium or maximum loading. Thus, to date, only bulk loading data exist for the adsorption of CH{sub 3}I onto Ag{degrees}Z. Hence this is believed to be the first study to quantify the controlling mass transfer mechanisms of this process, It can be concluded from the analysis of the experimental data obtained by the {open_quotes}single-pellet{close_quotes} type experiments and for the process conditions used in this study that the overall mass transfer rate associated with the adsorption of CH{sub 3}I onto Ag{degrees}Z is affected by both micropore and macropore diffusion. The macropore diffusion rate was significantly faster than the micropore diffusion, resulting in a two-step adsorption behavior which was adequately modeled by a bimodal pore distribution model. The micropore diffusivity was determined to be on the order of 2 x 10{sup -14} cm{sup 2}/s. The system was also shown to be isothermal under all conditions of this study. 21 refs., 6 figs., 8 tabs.

  1. Robust joint score tests in the application of DNA methylation data analysis.

    Science.gov (United States)

    Li, Xuan; Fu, Yuejiao; Wang, Xiaogang; Qiu, Weiliang

    2018-05-18

    Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential methylation level. Anh and Wang (2013) proposed a joint score test (AW) to simultaneously detect for differential methylation and differential variability. However, AW's method seems to be quite conservative and has not been fully compared with existing joint tests. We proposed three improved joint score tests, namely iAW.Lev, iAW.BF, and iAW.TM, and have made extensive comparisons with the joint likelihood ratio test (jointLRT), the Kolmogorov-Smirnov (KS) test, and the AW test. Systematic simulation studies showed that: 1) the three improved tests performed better (i.e., having larger power, while keeping nominal Type I error rates) than the other three tests for data with outliers and having different variances between cases and controls; 2) for data from normal distributions, the three improved tests had slightly lower power than jointLRT and AW. The analyses of two Illumina HumanMethylation27 data sets GSE37020 and GSE20080 and one Illumina Infinium MethylationEPIC data set GSE107080 demonstrated that three improved tests had higher true validation rates than those from jointLRT, KS, and AW. The three proposed joint score tests are robust against the violation of normality assumption and presence of outlying observations in comparison with other three existing tests. Among the three proposed tests, iAW.BF seems to be the most robust and effective one for all simulated scenarios and also in real data analyses.

  2. Comparative analysis of vitamin status of schoolchildren in recreational period

    Directory of Open Access Journals (Sweden)

    L.V. Podrigalo

    2013-10-01

    Full Text Available It is a comparative analysis of the characteristics of the vitamin status of schoolchildren during the summer recreation of 90th years of the last century and now. The study involved 167 schoolchildren aged 11-14 years. With the help of questionnaires developed by the authors assessed the severity of symptoms of vitamin deficiency, the prevalence of vitamin supplementation, frequency and volume of consumption of fruits and vegetables. It is confirmed that the saturation is the state of the vitamin in children is the best compared with data from 20 years ago, the state of multi-vitamin deficiency is replaced mono-vitamin deficit. The results, data evaluation and the availability of additional fortification of the diet of fruit and vegetables support the need for measures aimed at improving vitamin status. Using the questionnaire method is most appropriate for monitoring the vitamin status of schoolchildren.

  3. Protein methylation in pea chloroplasts

    International Nuclear Information System (INIS)

    Niemi, K.J.; Adler, J.; Selman, B.R.

    1990-01-01

    The methylation of chloroplast proteins has been investigated by incubating intact pea (Pisum sativum) chloroplasts with [ 3 H-methyl]-S-adenosylmethionine. Incubation in the light increases the amount of methylation in both the thylakoid and stromal fractions. Numerous thylakoid proteins serve as substrates for the methyltransfer reactions. Three of these thylakoid proteins are methylated to a significantly greater extent in the light than in the dark. The primary stromal polypeptide methylated is the large subunit of ribulose bisphosphate carboxylase/oxygenase. One other stromal polypeptide is also methylated much more in the light than in the dark. Two distinct types of protein methylation occur. One methylinkage is stable to basic conditions whereas a second type is base labile. The base-stable linkage is indicative of N-methylation of amino acid residues while base-lability is suggestive of carboxymethylation of amino acid residues. Labeling in the light increases the percentage of methylation that is base labile in the thylakoid fraction while no difference is observed in the amount of base-labile methylations in light-labeled and dark-labeled stromal proteins. Also suggestive of carboxymethylation is the detection of volatile [ 3 H]methyl radioactivity which increases during the labeling period and is greater in chloroplasts labeled in the light as opposed to being labeled in the dark; this implies in vivo turnover of the [ 3 H]methyl group

  4. Improved reproducibility in genome-wide DNA methylation analysis for PAXgene® fixed samples compared to restored FFPE DNA

    DEFF Research Database (Denmark)

    Andersen, Gitte Brinch; Hager, Henrik; Hansen, Lise Lotte

    2014-01-01

    Chip. Quantitative DNA methylation analysis demonstrated that the methylation profile in PAXgene-fixed tissues showed, in comparison with restored FFPE samples, a higher concordance with the profile detected in frozen samples. We demonstrate, for the first time, that DNA from PAXgene conserved tissue performs better......Formalin fixation has been the standard method for conservation of clinical specimens for decades. However, a major drawback is the high degradation of nucleic acids, which complicates its use in genome-wide analyses. Unbiased identification of biomarkers, however, requires genome-wide studies......, precluding the use of the valuable archives of specimens with long-term follow-up data. Therefore, restoration protocols for DNA from formalin-fixed and paraffin-embedded (FFPE) samples have been developed, although they are cost-intensive and time-consuming. An alternative to FFPE and snap...

  5. PAX1 methylation analysis by MS-HRM is useful in triage of high-grade squamous intraepithelial lesions.

    Science.gov (United States)

    Wang, Zhen-Ming

    2014-01-01

    This study is aimed to investigate the role of paired boxed gene 1 (PAX1) methylation analysis by methylation- sensitive high-resolution melting (MS-HRM) in the detection of high grade lesions in atypical squamous cells cannot exclude high-grade squamous intraepithelial lesion (ASC-H) and compared its performance with the Hybrid Capture 2 (HC2) human papillomavirus (HPV) test. In our study, 130 cases with a diagnosis of ASC-H from the cervical cytological screening by Thinprep cytologic test (TCT) technique were selected for triage. Their cervical scrapings were collected and evaluated by using PAX1 methylation analysis (MS-HRM) and high-risk HPV DNA test (HC2), followed by colposcopy and cervical biopsy. Chi-square test were used to test the differences of PAX1 methylation or HPV infection between groups. In the detection of CIN2+, the sensitivity, specificity, the PPV, NPV and the accuracy of PAX1 MS-HRM assay and high-risk HPV (HR-HPV) tests were respectively 80.6% vs 67.7%, 94.9% vs 54.5%, 83.3%, vs 31.8%, 94.0% vs 84.4%, and 91.5% vs 57.7%. The PAX1 MS-HRM assay proved superior to HR-HPV testing in the detection of high grade lesions (CIN2+) in ASC-H. This approach could screen out the majority of high grade lesion cases of ASC-H, and thus could reduce the referral rate to colposcopy.

  6. DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis

    NARCIS (Netherlands)

    B.R. Joubert (Bonnie); J.F. Felix (Janine); P. Yousefi (Paul); K.M. Bakulski (Kelly M.); A.C. Just (Allan C.); C. Breton (Carrie); S.E. Reese (Sarah E.); C.A. Markunas (Christina A.); R.C. Richmond (Rebecca C.); C.-J. Xu (Cheng-Jian); L.K. Küpers (Leanne); S.S. Oh (Sam S.); C. Hoyo (Cathrine); O. Gruzieva (Olena); C. Söderhäll (Cilla); L.A. Salas (Lucas A.); N. Baïz (Nour); H. Zhang (Hongmei); J. Lepeule (Johanna); C. Ruiz (Carlos); S. Ligthart (Symen); T. Wang (Tianyuan); J.A. Taylor (Jack A.); L. Duijts (Liesbeth); G.C. Sharp (Gemma C.); S.A. Jankipersadsing (Soesma A.); R.M. Nilsen (Roy M.); A. Vaez (Ahmad); M.D. Fallin (M. Daniele); D. Hu (Donglei); A. Litonjua (Augusto); B.F. Fuemmeler (Bernard F.); K. Huen (Karen); J. Kere (Juha); C.A. Kull (Christian); M.C. Munthe-Kaas (Monica Cheng); U. Gehring (Ulrike); M. Bustamante (Mariona); M.J. Saurel-Coubizolles (Marie José); B.M. Quraishi (Bilal M.); J. Ren (Jie); J. Tost (Jörg); J.R. Gonzalez (Juan R.); M.J. Peters (Marjolein); S.E. Håberg (Siri E); Z. Xu (Zongli); J.B.J. van Meurs (Joyce); T.R. Gaunt (Tom); M. Kerkhof (Marjan); W.E. Corpeleijn (Willemijn); A.P. Feinberg (Andrew P.); C. Eng (Celeste); A.A. Baccarelli (Andrea A.); S.E. Benjamin Neelon (Sara E.); A. Bradman (Asa); S.K. Merid (Simon Kebede); A. Bergström (Anna); Z. Herceg (Zdenko); H. Hernandez-Vargas (Hector); B. Brunekreef (Bert); M. Pinart (Mariona); B. Heude (Barbara); S. Ewart (Susan); J. Yao (Jin); N. Lemonnier (Nathanaël); O.H. Franco (Oscar); M.C. Wu (Michael); A. Hofman (Albert); W.L. McArdle (Wendy); P. van der Vlies (P.); F. Falahi (Fahimeh); M.W. Gillman (Matthew W.); L.F. Barcellos (Lisa); A. Kumar (Ashish); M. Wickman (Magnus); S. Guerra (S.); M.-A. Charles (Marie-Aline); J. Holloway (John); C. Auffray (C.); H.W. Tiemeier (Henning); G.D. Smith; D.S. Postma (Dirkje); M.-F. Hivert (Marie-France); B. Eskenazi (Brenda); M. Vrijheid (Martine); H. Arshad (Hasan); J.M. Antó (Josep M.); A. Dehghan (Abbas); W. Karmaus (Wilfried); I. Annesi-Maesano; J. Sunyer (Jordi); A. Ghantous (Akram); G. Pershagen (Göran); N. Holland (Nina); S.K. Murphy (Susan K.); D.L. Demeo (Dawn L.); E.G. Burchard (Esteban); C. Ladd-Acosta (Christine); H. Snieder (Harold); W. Nystad (Wenche); G.H. Koppelman (Gerard); C.L. Relton (Caroline); V.W.V. Jaddoe (Vincent); A.J. Wilcox (Allen); E. Melén (Erik); S.J. London (Stephanie J.)

    2016-01-01

    textabstractEpigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences.

  7. Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas

    DEFF Research Database (Denmark)

    Beltrami, Caroline Moraes; Dos Reis, Mariana Bisarro; Barros-Filho, Mateus Camargo

    2017-01-01

    and positive correlation, respectively. Genes showing negative correlation underlined FGF and retinoic acid signaling as critical canonical pathways disrupted by DNA methylation in PTC. BRAF mutation was detected in 68% (28 of 41) of the tumors, which presented a higher level of demethylation (95...

  8. INHALATION EXPOSURE TO METHYL TERT-BUTYL ETHER (MTBE) AND DIBROMOCHLOROMETHANE (DBCM) USING CONTINUOUS BREATH ANALYSIS

    Science.gov (United States)

    The oxygenate methyl tert-butyl ether (MTBE) has been added to gasoline to help meet national ambient air quality standards in those parts of the U.S. that are non-compliant for carbon monoxide. Although MTBE has provided important health benefits in terms of reduced haza...

  9. MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.

    Science.gov (United States)

    Pandey, Ram Vinay; Pulverer, Walter; Kallmeyer, Rainer; Beikircher, Gabriel; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

    2016-01-01

    Bisulfite (BS) conversion-based and methylation-sensitive restriction enzyme (MSRE)-based PCR methods have been the most commonly used techniques for locus-specific DNA methylation analysis. However, both methods have advantages and limitations. Thus, an integrated approach would be extremely useful to quantify the DNA methylation status successfully with great sensitivity and specificity. Designing specific and optimized primers for target regions is the most critical and challenging step in obtaining the adequate DNA methylation results using PCR-based methods. Currently, no integrated, optimized, and high-throughput methylation-specific primer design software methods are available for both BS- and MSRE-based methods. Therefore an integrated, powerful, and easy-to-use methylation-specific primer design pipeline with great accuracy and success rate will be very useful. We have developed a new web-based pipeline, called MSP-HTPrimer, to design primers pairs for MSP, BSP, pyrosequencing, COBRA, and MSRE assays on both genomic strands. First, our pipeline converts all target sequences into bisulfite-treated templates for both forward and reverse strand and designs all possible primer pairs, followed by filtering for single nucleotide polymorphisms (SNPs) and known repeat regions. Next, each primer pairs are annotated with the upstream and downstream RefSeq genes, CpG island, and cut sites (for COBRA and MSRE). Finally, MSP-HTPrimer selects specific primers from both strands based on custom and user-defined hierarchical selection criteria. MSP-HTPrimer produces a primer pair summary output table in TXT and HTML format for display and UCSC custom tracks for resulting primer pairs in GTF format. MSP-HTPrimer is an integrated, web-based, and high-throughput pipeline and has no limitation on the number and size of target sequences and designs MSP, BSP, pyrosequencing, COBRA, and MSRE assays. It is the only pipeline, which automatically designs primers on both genomic

  10. DNA methylation analysis in rat kidney epithelial cells exposed to 3-MCPD and glycidol.

    Science.gov (United States)

    Senyildiz, Mine; Alpertunga, Buket; Ozden, Sibel

    2017-10-01

    3-Monochloropropane-1,2-diol (3-MCPD) is a well-known food processing contaminant that has been regarded as a rat carcinogen, which is known to induce Leydig-cell and mammary gland tumors in males, as well as kidney tumors in both genders. 3-MCPD is highly suspected to be a non-genotoxic carcinogen. 2,3-Epoxy-1-propanol (glycidol) can be formed via dehalogenation from 3-MCPD. We aimed to investigate the cytotoxic effects of 3-MCPD and glycidol, then to demonstrate the possible epigenetic mechanisms with global and gene-specific DNA methylation in rat kidney epithelial cells (NRK-52E). IC 50 value of 3-MCPD was determined as 48 mM and 41.39 mM, whereas IC 50 value of glycidol was 1.67 mM and 1.13 mM by MTT and NRU test, respectively. Decreased global DNA methylation at the concentrations of 100 μM and 1000 μM for 3-MCPD and 100 μM and 500 μM for glycidol were observed after 48 h exposure by using 5-methylcytosine (5-mC) ELISA kit. Methylation changes were detected in promoter regions of c-myc and Rassf1a in 3-MCPD and glycidol treated NRK-52E cells by using methylation-specific PCR (MSP), whereas changes on gene expression of c-myc and Rassf1a were observed by using real-time PCR. However, e-cadherin, p16, VHL and p15 genes were unmethylated in their CpG promoter regions in response to treatment with 3-MCPD and glycidol. Alterations in DNA methylation might be key events in the toxicity of 3-MCPD and glycidol.

  11. DNA Methylation Analysis of BRD1 Promoter Regions and the Schizophrenia rs138880 Risk Allele.

    Directory of Open Access Journals (Sweden)

    Mads Dyrvig

    Full Text Available The bromodomain containing 1 gene, BRD1 is essential for embryogenesis and CNS development. It encodes a protein that participates in histone modifying complexes and thereby regulates the expression of a large number of genes. Genetic variants in the BRD1 locus show association with schizophrenia and bipolar disorder and risk alleles in the promoter region correlate with reduced BRD1 expression. Insights into the transcriptional regulation of BRD1 and the pathogenic mechanisms associated with BRD1 risk variants, however, remain sparse. By studying transcripts in human HeLa and SH-SY5Y cells we provide evidence for differences in relative expression of BRD1 transcripts with three alternative 5' UTRs (exon 1C, 1B, and 1A. We further show that expression of these transcript variants covaries negatively with DNA methylation proportions in their upstream promoter regions suggesting that promoter usage might be regulated by DNA methylation. In line with findings that the risk allele of the rs138880 SNP in the BRD1 promoter region correlates with reduced BRD1 expression, we find that it is also associated with moderate regional BRD1 promoter hypermethylation in both adipose tissue and blood. Importantly, we demonstrate by inspecting available DNA methylation and expression data that these regions undergo changes in methylation during fetal brain development and that differences in their methylation proportions in fetal compared to postnatal frontal cortex correlate significantly with BRD1 expression. These findings suggest that BRD1 may be dysregulated in both the developing and mature brain of risk allele carriers. Finally, we demonstrate that commonly used mood stabilizers Lithium, Valproate, and Carbamazepine affect the expression of BRD1 in SH-SY5Y cells. Altogether this study indicates a link between genetic risk and epigenetic dysregulation of BRD1 which raises interesting perspectives for targeting the mechanisms pharmacologically.

  12. Analysis of RTEL1 and PCDHGB6 promoter methylation in circulating-free DNA of lung cancer patients using liquid biopsy: A pilot study.

    Science.gov (United States)

    Powrózek, Tomasz; Krawczyk, Paweł; Kuźnar-Kamińska, Barbara; Batura-Gabryel, Halina; Milanowski, Janusz

    2016-08-01

    Analysis of epigenetic alterations such as methylation of circulating-free DNA (cf-DNA) expression significantly broadened perspectives of lung cancer (LC) screening. Moreover, methylation of tumor suppressor genes may be analyzed with non-invasive manner in patients' blood samples (liquid biopsy), what underline necessity of detailed investigation of tumor cf-DNA. The purpose of current study was to assess methylation of RTEL1 and PCDHGB6 promoter regions in cf-DNA of 70 LC patients and 80 healthy individuals using qMSP-PCR technique. Methylation status of both genes has not been investigated in cf-DNA of LC patients before. PCDHGB6 promoter methylation was found in 41.4% of LC patients and in 1.3% of healthy individuals, whereas promoter of RTEL1 was found methylated in 51.4% of LC patients and in 8.8% of healthy individuals. Combined analysis of two markers improved test sensitivity up to 62.9% and specificity up to 90% with area under the curve (AUC) in receiver operating curve (ROC) of 0.755. The evaluation of RTEL1 and PCDHGB6 promoter methylation may be an useful tool for non-invasive diagnosis of LC in liquid biopsy.

  13. Genome-wide CpG island methylation analysis implicates novel genes in the pathogenesis of renal cell carcinoma

    OpenAIRE

    Ricketts, Christopher J.; Morris, Mark R.; Gentle, Dean; Brown, Michael; Wake, Naomi; Woodward, Emma R.; Clarke, Noel; Latif, Farida; Maher, Eamonn R.

    2012-01-01

    In order to identify novel candidate tumor suppressor genes (TSGs) implicated in renal cell carcinoma (RCC), we performed genome-wide methylation profiling of RCC using the HumanMethylation27 BeadChips to assess methylation at >14,000 genes. Two hundred and twenty hypermethylated probes representing 205 loci/genes were identified in genomic CpG islands. A subset of TSGs investigated in detail exhibited frequent tumor methylation, promoter methylation associated transcriptional silencing an...

  14. Analysis of deuterium relaxation-derived methyl axis order parameters and correlation with local structure

    International Nuclear Information System (INIS)

    Mittermaier, Anthony; Kay, Lewis E.; Forman-Kay, Julie D.

    1999-01-01

    Methyl axis (S2axis) and backbone NH (S2NH) order parameters derived from eight proteins have been analyzed. Similar distribution profiles for Ala S2axis and S2NH order parameters were observed. A good correlation between the two S2axis values of Val and Leu methyl groups is noted, although differences between order parameters can arise. The relation of S2axis or S2NH to solvent accessibility and packing density has also been investigated. Correlations are weak, likely reflecting the importance of collective, non-local motions in proteins. The lack of correlation between these simple structural parameters and dynamics emphasizes the importance of motional studies to fully characterize proteins

  15. Longitudinal Analysis of DNA Methylation in CD34+ Hematopoietic Progenitors in Myelodysplastic Syndrome

    DEFF Research Database (Denmark)

    Wong, Yan Fung; Micklem, Chris N; Taguchi, Masataka

    2014-01-01

    Myelodysplastic syndrome (MDS) is a disorder of hematopoietic stem cells (HSCs) that is often treated with DNA methyltransferase 1 (DNMT1) inhibitors (5-azacytidine [AZA], 5-aza-2'-deoxycytidine), suggesting a role for DNA methylation in disease progression. How DNMT inhibition retards disease...... regulators not expressed within the hematopoietic compartment and was distinct from that observed between healthy hematopoietic cell types. After AZA treatment, we observed only limited DNA demethylation at sites that varied between patients. This suggests that a subset of the stem cell population...... is resistant to AZA and provides a basis for disease relapse. Using gene expression data from patient samples and an in vitro AZA treatment study, we identified differentially methylated genes that can be activated following treatment and that remain silent in the CD34+ stem cell compartment of high-risk MDS...

  16. Crystal structure, conformational analysis, and molecular dynamics of tetra-0-methyl-(+)-catechin

    Science.gov (United States)

    Frank R. Fronczek; Richard W. Hemingway; G. Wayne McGraw; Jan P. Steynberg; Carin A. Helfer; Wayne L. Mattice

    1993-01-01

    The structure of tetra-O-methyl-(+)-catechin has been determined in the crystalline state. Two independent molecules, denoted structure A and structure B, exist in the unit cell. Crystals are triclinic, space group P1, a=4.8125(2) Ǻ, b=12.9148(8) Ǻ, c=13.8862(11) Ǻ, α=86.962(6)°, β=89.120(5)°, γ=...

  17. GC-MS ANALYSIS OF THE FATTY ACID METHYL ESTER IN JAPANESE QUAIL FAT

    Directory of Open Access Journals (Sweden)

    Ion Dragalin

    2015-12-01

    Full Text Available The accumulated as production waste fat from Faraon quail breeds has been investigated for the first time by using GC-MS technique, preventively converting it via methanolysis to fatty acid methyl esters. The test results, regarding the content of unsaturated fatty acids having a favorable to human body cis-configuration (77.8%, confirm their nutritional value and the possibility of using this fat in cosmetic, pharmaceutical and food industries.

  18. Mediation analysis of alcohol consumption, DNA methylation, and epithelial ovarian cancer.

    Science.gov (United States)

    Wu, Dongyan; Yang, Haitao; Winham, Stacey J; Natanzon, Yanina; Koestler, Devin C; Luo, Tiane; Fridley, Brooke L; Goode, Ellen L; Zhang, Yanbo; Cui, Yuehua

    2018-03-01

    Epigenetic factors and consumption of alcohol, which suppresses DNA methylation, may influence the development and progression of epithelial ovarian cancer (EOC). However, there is a lack of understanding whether these factors interact to affect the EOC risk. In this study, we aimed to gain insight into this relationship by identifying leukocyte-derived DNA methylation markers acting as potential mediators of alcohol-associated EOC. We implemented a causal inference test (CIT) and the VanderWeele and Vansteelandt multiple mediator model to examine CpG sites that mediate the association between alcohol consumption and EOC risk. We modified one step of the CIT by adopting a high-dimensional inference procedure. The data were based on 196 cases and 202 age-matched controls from the Mayo Clinic Ovarian Cancer Case-Control Study. Implementation of the CIT test revealed two CpG sites (cg09358725, cg11016563), which represent potential mediators of the relationship between alcohol consumption and EOC case-control status. Implementation of the VanderWeele and Vansteelandt multiple mediator model further revealed that these two CpGs were the key mediators. Decreased methylation at both CpGs was more common in cases who drank alcohol at the time of enrollment vs. those who did not. cg11016563 resides in TRPC6 which has been previously shown to be overexpressed in EOC. These findings suggest two CpGs may serve as novel biomarkers for EOC susceptibility.

  19. Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of DNA methylation and gene expression profiling.

    Science.gov (United States)

    Zhang, Lei; Ma, Shiyun; Wang, Huailiang; Su, Hang; Su, Ke; Li, Longjie

    2017-11-15

    The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes. In addition, we used RT-PCR and MSP to verify the expression levels and methylation status of these crucial genes in 20 synovial biopsy samples obtained from 10 RA model mice and 10 normal mice. BCL11B, CCDC88C, FCRLA and APOL6 were both up-regulated and hypomethylated in RA according to integrated analysis, RT-PCR and MSP verification. Four crucial genes (BCL11B, CCDC88C, FCRLA and APOL6) identified and analyzed in this study might be closely connected with the pathogenesis of RA. Copyright © 2017. Published by Elsevier B.V.

  20. PHENOTYPIC CHARACTERISATION AND GENETIC ANALYSIS OF MUTANTS OF ASPERGILLUS NIDULANS RESISTANT TO THE FUNGICIDE TOLCLOFOS-METHYL

    Directory of Open Access Journals (Sweden)

    A CHIBANI

    2000-12-01

    Full Text Available Spontaneous mutants of Aspergillus nidulans were recovered from 0,55.10+7  conidia incubated on synthetic medium supplemented with 100 mg tolclofos-methyl/ml. They differed considerably in morphology, growth rate, and level of resistance to two other fungicides. All mutants tested were cross-resistant to quintozene and vinclozolin; they produced fewer conidia than their wild-type parent. Some mutants required fungicides for maximum growth. Genetic analysis revealed that the mutants carried mutations in one gene located on linkage group III.

  1. Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep

    Directory of Open Access Journals (Sweden)

    Yang Cao

    2017-11-01

    Full Text Available Objective The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods Six samples (three in each group were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs between the two groups. Results 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypo-methylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3, acyl-CoA synthetase long chain family member 1 (ACSL1, ryanodine receptor 1 (RYR1, acyl-CoA oxidase 2 (ACOX2, peroxisome proliferator activated receptor-gamma2 (PPARG2, netrin 1 (NTN1, ras and rab interactor 2 (RIN2, microtubule associated protein RP/EB family member 1 (MAPRE1, ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2, myomesin 1 (MYOM1, zinc finger, DHHC type containing 13 (ZDHHC13, and SH3 and PX domains 2B (SH3PXD2B. The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3

  2. Is methylation analysis of SFRP2, TFPI2, NDRG4, and BMP3 promoters suitable for colorectal cancer screening in the Korean population?

    Directory of Open Access Journals (Sweden)

    Soo-Kyung Park

    2017-10-01

    Full Text Available Background/Aims: Colorectal cancer (CRC screening using stool DNA was recently found to yield good detection rates. A multi-target stool DNA test (Cologuard®, Exact Sciences, including methylated genes has been recently approved by the U.S. Food and Drug Administration. The aim of this study was to validate these aberrantly methylated genes as stool-based DNA markers for detecting CRC and colorectal advanced adenoma (AA in the Korean population.Methods: A single-center study was conducted in 36 patients with AA; 35 patients with CRC; and 40 endoscopically diagnosed healthy controls using CRC screening colonoscopy. The methylation status of the SFRP2, TFPI2, NDRG4, and BMP3 promoters was investigated blindly using bisulfate-modified stool DNA obtained from 111 participants. Methylation status was investigated by methylation-specific polymerase chain reaction.Results: Methylated SFRP2, TFPI2, NDRG4, and BMP3 promoters were detected in 60.0%, 31.4%, 68.8%, and 40.0% of CRC samples and in 27.8%, 27.8%, 27.8%, and 33.3% of AA samples, respectively. The sensitivities obtained using 4 markers to detect CRC and AA were 94.3% and 72.2%, respectively. The specificity was 55.0%.Conclusions: Our results demonstrate that the SFRP2, TFPI2, NDRG4, and BMP3 promoter methylation analysis of stool sample DNA showed high sensitivity but low specificity for detecting CRC and AA. Because of the low specificity, 4 methylated markers might not be sufficient for CRC screening in the Korean population. Further large-scale studies are required to validate the methylation of these markers in the Asian population and to find new markers for the Asian population.

  3. High resolution melt curve analysis based on methylation status for human semen identification.

    Science.gov (United States)

    Fachet, Caitlyn; Quarino, Lawrence; Karnas, K Joy

    2017-03-01

    A high resolution melt curve assay to differentiate semen from blood, saliva, urine, and vaginal fluid based on methylation status at the Dapper Isoform 1 (DACT1) gene was developed. Stains made from blood, saliva, urine, semen, and vaginal fluid were obtained from volunteers and DNA was isolated using either organic extraction (saliva, urine, and vaginal fluid) or Chelex ® 100 extraction (blood and semen). Extracts were then subjected to bisulfite modification in order to convert unmethylated cytosines to uracil, consequently creating sequences whose amplicons have melt curves that vary depending on their initial methylation status. When primers designed to amplify the promoter region of the DACT1 gene were used, DNA from semen samples was distinguishable from other fluids by a having a statistically significant lower melting temperature. The assay was found to be sperm-significant since semen from a vasectomized man produced a melting temperature similar to the non-semen body fluids. Blood and semen stains stored up to 5 months and tested at various intervals showed little variation in melt temperature indicating the methylation status was stable during the course of the study. The assay is a more viable method for forensic science practice than most molecular-based methods for body fluid stain identification since it is time efficient and utilizes instrumentation common to forensic biology laboratories. In addition, the assay is advantageous over traditional presumptive chemical methods for body fluid identification since results are confirmatory and the assay offers the possibility of multiplexing which may test for multiple body fluids simultaneously.

  4. Genome-scale analysis of aberrant DNA methylation in colorectal cancer

    Science.gov (United States)

    Hinoue, Toshinori; Weisenberger, Daniel J.; Lange, Christopher P.E.; Shen, Hui; Byun, Hyang-Min; Van Den Berg, David; Malik, Simeen; Pan, Fei; Noushmehr, Houtan; van Dijk, Cornelis M.; Tollenaar, Rob A.E.M.; Laird, Peter W.

    2012-01-01

    Colorectal cancer (CRC) is a heterogeneous disease in which unique subtypes are characterized by distinct genetic and epigenetic alterations. Here we performed comprehensive genome-scale DNA methylation profiling of 125 colorectal tumors and 29 adjacent normal tissues. We identified four DNA methylation–based subgroups of CRC using model-based cluster analyses. Each subtype shows characteristic genetic and clinical features, indicating that they represent biologically distinct subgroups. A CIMP-high (CIMP-H) subgroup, which exhibits an exceptionally high frequency of cancer-specific DNA hypermethylation, is strongly associated with MLH1 DNA hypermethylation and the BRAFV600E mutation. A CIMP-low (CIMP-L) subgroup is enriched for KRAS mutations and characterized by DNA hypermethylation of a subset of CIMP-H-associated markers rather than a unique group of CpG islands. Non-CIMP tumors are separated into two distinct clusters. One non-CIMP subgroup is distinguished by a significantly higher frequency of TP53 mutations and frequent occurrence in the distal colon, while the tumors that belong to the fourth group exhibit a low frequency of both cancer-specific DNA hypermethylation and gene mutations and are significantly enriched for rectal tumors. Furthermore, we identified 112 genes that were down-regulated more than twofold in CIMP-H tumors together with promoter DNA hypermethylation. These represent ∼7% of genes that acquired promoter DNA methylation in CIMP-H tumors. Intriguingly, 48/112 genes were also transcriptionally down-regulated in non-CIMP subgroups, but this was not attributable to promoter DNA hypermethylation. Together, we identified four distinct DNA methylation subgroups of CRC and provided novel insight regarding the role of CIMP-specific DNA hypermethylation in gene silencing. PMID:21659424

  5. Evaluation of CP sil 8 film thickness for the capillary GC analysis of methyl mercury

    DEFF Research Database (Denmark)

    Petersen, Jens Højslev; Drabæk, Iver

    1992-01-01

    Different commercially available CP-Sil 8 CB capillary columns have been tested with a mixed standard containing methyl mercury chloride, ethyl mercury chloride and a stable nonpolar chlorinated hydrocarbon. The aim of the study was to see whether the columns tested could be used without special...... available insert for on-column injections on wide bore columns, and a 5.35 mum thick stationary phase. It was concluded that this CP Sil 8 CB column gave good results although minor interactions between the organo-mercury compounds and the column could be seen....

  6. Midterm Periodicity Analysis of the Mount Wilson Magnetic Indices Using the Synchrosqueezing Transform

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Song; Wang, Feng; Deng, Hui; Yang, Yunfei [Yunnan Key Laboratory of Computer Technology Application/Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650500 (China); Yu, Lan, E-mail: ynkmfs@escience.cn [Department of Mechanical and Electrical Engineering, Yunnan Land and Resources Vocational College, Kunming 650217 (China)

    2017-08-10

    A novel time–frequency technique, called the synchrosqueezing transform (SST), is used to investigate the midterm periodic variations of magnetic fields on the solar surface. The Magnetic Plage Strength Index (MPSI) and the Mount Wilson Sunspot Index (MWSI), measured daily by the Mount Wilson Observatory between 1970 January 19 and 2012 January 22, are selected. Short-, mid, and longer-term periodicities are represented and decomposed by the SST with hardly any mode mixing. This demonstrates that the SST is a useful time–frequency analysis technique to characterize the periodic modes of helioseismic data. Apart from the fundamental modes of the annual periodicity, ∼27 day rotational cycle and ∼11 year solar cycle, the SST reveals several midterm periodicities in the two magnetic activity indices, specifically, ∼157 days (i.e., Rieger-type periodicity), and ∼1.3 and 1.7 years. The periodic modes, with 116.4 and 276.2 day periodicity in the MPSI, 108.5 and 251.6 day periodicity in the MWSI, and 157.7 day periodicity in the two indices, are in better accord with those significant periodicities derived from the Rossby waves theoretical model. This study suggests that the modes are caused by Rossby waves. For the 1.30 and 1.71 year periodicity of the MPSI, and the 1.33 and 1.67 year periodicity of the MWSI, our analysis infers that they are related to those periodicities with the same timescale in the interior of the Sun and in the high atmospheric layers.

  7. Analysis of the association between CIMP and BRAF in colorectal cancer by DNA methylation profiling.

    Directory of Open Access Journals (Sweden)

    Toshinori Hinoue

    Full Text Available A CpG island methylator phenotype (CIMP is displayed by a distinct subset of colorectal cancers with a high frequency of DNA hypermethylation in a specific group of CpG islands. Recent studies have shown that an activating mutation of BRAF (BRAF(V600E is tightly associated with CIMP, raising the question of whether BRAF(V600E plays a causal role in the development of CIMP or whether CIMP provides a favorable environment for the acquisition of BRAF(V600E. We employed Illumina GoldenGate DNA methylation technology, which interrogates 1,505 CpG sites in 807 different genes, to further study this association. We first examined whether expression of BRAF(V600E causes DNA hypermethylation by stably expressing BRAF(V600E in the CIMP-negative, BRAF wild-type COLO 320DM colorectal cancer cell line. We determined 100 CIMP-associated CpG sites and examined changes in DNA methylation in eight stably transfected clones over multiple passages. We found that BRAF(V600E is not sufficient to induce CIMP in our system. Secondly, considering the alternative possibility, we identified genes whose DNA hypermethylation was closely linked to BRAF(V600E and CIMP in 235 primary colorectal tumors. Interestingly, genes that showed the most significant link include those that mediate various signaling pathways implicated in colorectal tumorigenesis, such as BMP3 and BMP6 (BMP signaling, EPHA3, KIT, and FLT1 (receptor tyrosine kinases and SMO (Hedgehog signaling. Furthermore, we identified CIMP-dependent DNA hypermethylation of IGFBP7, which has been shown to mediate BRAF(V600E-induced cellular senescence and apoptosis. Promoter DNA hypermethylation of IGFBP7 was associated with silencing of the gene. CIMP-specific inactivation of BRAF(V600E-induced senescence and apoptosis pathways by IGFBP7 DNA hypermethylation might create a favorable context for the acquisition of BRAF(V600E in CIMP+ colorectal cancer. Our data will be useful for future investigations toward

  8. Analysis of the association between CIMP and BRAF in colorectal cancer by DNA methylation profiling.

    Science.gov (United States)

    Hinoue, Toshinori; Weisenberger, Daniel J; Pan, Fei; Campan, Mihaela; Kim, Myungjin; Young, Joanne; Whitehall, Vicki L; Leggett, Barbara A; Laird, Peter W

    2009-12-21

    A CpG island methylator phenotype (CIMP) is displayed by a distinct subset of colorectal cancers with a high frequency of DNA hypermethylation in a specific group of CpG islands. Recent studies have shown that an activating mutation of BRAF (BRAF(V600E)) is tightly associated with CIMP, raising the question of whether BRAF(V600E) plays a causal role in the development of CIMP or whether CIMP provides a favorable environment for the acquisition of BRAF(V600E). We employed Illumina GoldenGate DNA methylation technology, which interrogates 1,505 CpG sites in 807 different genes, to further study this association. We first examined whether expression of BRAF(V600E) causes DNA hypermethylation by stably expressing BRAF(V600E) in the CIMP-negative, BRAF wild-type COLO 320DM colorectal cancer cell line. We determined 100 CIMP-associated CpG sites and examined changes in DNA methylation in eight stably transfected clones over multiple passages. We found that BRAF(V600E) is not sufficient to induce CIMP in our system. Secondly, considering the alternative possibility, we identified genes whose DNA hypermethylation was closely linked to BRAF(V600E) and CIMP in 235 primary colorectal tumors. Interestingly, genes that showed the most significant link include those that mediate various signaling pathways implicated in colorectal tumorigenesis, such as BMP3 and BMP6 (BMP signaling), EPHA3, KIT, and FLT1 (receptor tyrosine kinases) and SMO (Hedgehog signaling). Furthermore, we identified CIMP-dependent DNA hypermethylation of IGFBP7, which has been shown to mediate BRAF(V600E)-induced cellular senescence and apoptosis. Promoter DNA hypermethylation of IGFBP7 was associated with silencing of the gene. CIMP-specific inactivation of BRAF(V600E)-induced senescence and apoptosis pathways by IGFBP7 DNA hypermethylation might create a favorable context for the acquisition of BRAF(V600E) in CIMP+ colorectal cancer. Our data will be useful for future investigations toward understanding

  9. DNA methylation analysis of paediatric low-grade astrocytomas identifies a tumour-specific hypomethylation signature in pilocytic astrocytomas.

    Science.gov (United States)

    Jeyapalan, Jennie N; Doctor, Gabriel T; Jones, Tania A; Alberman, Samuel N; Tep, Alexander; Haria, Chirag M; Schwalbe, Edward C; Morley, Isabel C F; Hill, Alfred A; LeCain, Magdalena; Ottaviani, Diego; Clifford, Steven C; Qaddoumi, Ibrahim; Tatevossian, Ruth G; Ellison, David W; Sheer, Denise

    2016-05-27

    Low-grade gliomas (LGGs) account for about a third of all brain tumours in children. We conducted a detailed study of DNA methylation and gene expression to improve our understanding of the biology of pilocytic and diffuse astrocytomas. Pilocytic astrocytomas were found to have a distinctive signature at 315 CpG sites, of which 312 were hypomethylated and 3 were hypermethylated. Genomic analysis revealed that 182 of these sites are within annotated enhancers. The signature was not present in diffuse astrocytomas, or in published profiles of other brain tumours and normal brain tissue. The AP-1 transcription factor was predicted to bind within 200 bp of a subset of the 315 differentially methylated CpG sites; the AP-1 factors, FOS and FOSL1 were found to be up-regulated in pilocytic astrocytomas. We also analysed splice variants of the AP-1 target gene, CCND1, which encodes cell cycle regulator cyclin D1. CCND1a was found to be highly expressed in both pilocytic and diffuse astrocytomas, but diffuse astrocytomas have far higher expression of the oncogenic variant, CCND1b. These findings highlight novel genetic and epigenetic differences between pilocytic and diffuse astrocytoma, in addition to well-described alterations involving BRAF, MYB and FGFR1.

  10. Rotational Spectrum and Conformational Analysis of N-Methyl-2-Aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters

    Directory of Open Access Journals (Sweden)

    Camilla Calabrese

    2018-02-01

    Full Text Available We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol's family, and include 2-amino-1-phenylethanol, 2-methylamino-1-phenylethanol, noradrenaline, adrenaline 2-aminoethanol, and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6–18 and 59.6–74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was performed, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.

  11. Rotational Spectrum and Conformational Analysis of N-methyl-2-aminoethanol: Insights into the Shape of Adrenergic Neurotransmitters

    Science.gov (United States)

    Calabrese, Camilla; Maris, Assimo; Evangelisti, Luca; Piras, Anna; Parravicini, Valentina; Melandri, Sonia

    2018-02-01

    Abstract We describe an experimental and quantum chemical study for the accurate determination of the conformational space of small molecular systems governed by intramolecular non-covalent interactions. The model systems investigated belong to the biological relevant aminoalcohol’s family, and include 2-aminophenylethanol, 2-methylaminophenylethanol, noradrenaline, adrenaline 2-aminoethanol and N-methyl-2-aminoethanol. For the latter molecule, the rotational spectrum in the 6-18 and 59.6-74.4 GHz ranges was recorded in the isolated conditions of a free jet expansion. Based on the analysis of the rotational spectra, two different conformational species and 11 isotopologues were observed and their spectroscopic constants, including 14N-nuclear hyperfine coupling constants and methyl internal rotation barriers, were determined. From the experimental data a structural determination was obtained, which was also used to benchmark accurate quantum chemical calculations on the whole conformational space. Atom in molecules and non-covalent interactions theories allowed the characterization of the position of the intramolecular non-covalent interactions and the energies involved, highlighting the subtle balance responsible of the stabilization of all the molecular systems.

  12. Structure and conformational analysis of spiroketals from 6-O-methyl-9(E-hydroxyiminoerythronolide A

    Directory of Open Access Journals (Sweden)

    Ana Čikoš

    2015-08-01

    Full Text Available Three novel spiroketals were prepared by a one-pot transformation of 6-O-methyl-9(E-hydroxyiminoerythronolide A. We present the formation of a [4.5]spiroketal moiety within the macrolide lactone ring, but also the unexpected formation of a 10-C=11-C double bond and spontaneous change of stereochemistry at position 8-C. As a result, a thermodynamically stable structure was obtained. The structures of two new diastereomeric, unsaturated spiroketals, their configurations and conformations, were determined by means of NMR spectroscopy and molecular modelling. The reaction kinetics and mechanistic aspects of this transformation are discussed. These rearrangements provide a facile synthesis of novel macrolide scaffolds.

  13. Distinct functions of Period2 and Period3 in the mouse circadian system revealed by in vitro analysis.

    Directory of Open Access Journals (Sweden)

    Julie S Pendergast

    2010-01-01

    Full Text Available The mammalian circadian system, which is composed of a master pacemaker in the suprachiasmatic nuclei (SCN as well as other oscillators in the brain and peripheral tissues, controls daily rhythms of behavior and physiology. Lesions of the SCN abolish circadian rhythms of locomotor activity and transplants of fetal SCN tissue restore rhythmic behavior with the periodicity of the donor's genotype, suggesting that the SCN determines the period of the circadian behavioral rhythm. According to the model of timekeeping in the SCN, the Period (Per genes are important elements of the transcriptional/translational feedback loops that generate the endogenous circadian rhythm. Previous studies have investigated the functions of the Per genes by examining locomotor activity in mice lacking functional PERIOD proteins. Variable behavioral phenotypes were observed depending on the line and genetic background of the mice. In the current study we assessed both wheel-running activity and Per1-promoter-driven luciferase expression (Per1-luc in cultured SCN, pituitary, and lung explants from Per2(-/- and Per3(-/- mice congenic with the C57BL/6J strain. We found that the Per2(-/- phenotype is enhanced in vitro compared to in vivo, such that the period of Per1-luc expression in Per2(-/- SCN explants is 1.5 hours shorter than in Per2+/+ SCN, while the free-running period of wheel-running activity is only 11 minutes shorter in Per2(-/- compared to Per2+/+ mice. In contrast, circadian rhythms in SCN explants from Per3(-/- mice do not differ from Per3+/+ mice. Instead, the period and phase of Per1-luc expression are significantly altered in Per3(-/- pituitary and lung explants compared to Per3+/+ mice. Taken together these data suggest that the function of each Per gene may differ between tissues. Per2 appears to be important for period determination in the SCN, while Per3 participates in timekeeping in the pituitary and lung.

  14. An Analysis of Periodic Components in BL Lac Object S5 0716 +714 with MUSIC Method

    Science.gov (United States)

    Tang, J.

    2012-01-01

    Multiple signal classification (MUSIC) algorithms are introduced to the estimation of the period of variation of BL Lac objects.The principle of MUSIC spectral analysis method and theoretical analysis of the resolution of frequency spectrum using analog signals are included. From a lot of literatures, we have collected a lot of effective observation data of BL Lac object S5 0716 + 714 in V, R, I bands from 1994 to 2008. The light variation periods of S5 0716 +714 are obtained by means of the MUSIC spectral analysis method and periodogram spectral analysis method. There exist two major periods: (3.33±0.08) years and (1.24±0.01) years for all bands. The estimation of the period of variation of the algorithm based on the MUSIC spectral analysis method is compared with that of the algorithm based on the periodogram spectral analysis method. It is a super-resolution algorithm with small data length, and could be used to detect the period of variation of weak signals.

  15. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  16. CFD Analysis on the Periodic Element of a Printed Circuit Heat Exchanger

    International Nuclear Information System (INIS)

    Tak, Nam-il; Kim, Min-Hwan; Lee, Won-Jae

    2007-01-01

    A typical printed circuit heat exchanger (PCHE) is composed of a large number of flow channels with lateral corrugations. In an effort to investigate fundamental thermo-fluid characteristics of a PCHE with corrugated channels, computational fluid dynamics (CFD) analyses were previously made in. One pair of flow channels (i.e., cold and hot channels) with the entire flow path was considered for the computational domain in the previous studies. Although only one pair of flow channels with coarse meshes was used, computational loads were found to be very high to simulate the entire flow path of the PCHE. Fortunately a recent study has shown that a simplified CFD methodology with a stream wise periodic assumption (called periodic CFD analysis) is feasible for a CFD evaluation of the thermo-fluid performance of compact heat exchangers. Since the periodic CFD analysis focuses on the periodic element of a flow channel, the required computing resources are dramatically reduced. In the present paper, the periodic CFD analysis has been applied to the periodic element of the PCHE. The results are compared with those of the full elements which have an entire flow path. Based on the periodic approach the effects of the corrugation parameters on the thermo-fluid performance of the PCHE are investigated

  17. miRNAting control of DNA methylation

    Indian Academy of Sciences (India)

    miRNAting control of DNA methylation. ASHWANI ... function and biological process ... Enrichment analysis of the genes methylated by DRM2 for molecular function and biological ... 39(3), June 2014, 365–380, © Indian Academy of Sciences.

  18. Intrauterine Reprogramming of the Polycystic Ovary Syndrome: Evidence from a Pilot Study of Cord Blood Global Methylation Analysis

    Directory of Open Access Journals (Sweden)

    Luca Lambertini

    2017-12-01

    Full Text Available Polycystic ovary syndrome (PCOS affects 5–15% of women. PCOS is a heterogeneous disorder displaying endocrine, metabolic, and reproductive dysfunction and cardiovascular risk manifestations. Evidence of heritability exists, but only a portion of the genetic transmission has been identified by genome-wide association studies and linkage studies, suggesting epigenetic phenomena may play a role. Evidence implicates intrauterine influences in the genesis of PCOS. This was a pilot study that aimed at identifying an epigenetic PCOS reprogramming signature by profiling the methylation of the DNA extracted from umbilical cord blood (UCB from 12 subjects undergoing in vitro fertilization. Six subjects were anovulatory PCOS women diagnosed by Rotterdam criteria and six ovulatory non-PCOS women matched for age and body mass index. UCB was collected at delivery of the placenta; the DNA was extracted and submitted to methylation analysis. A differential methylation picture of prevalent hypomethylation affecting 918 genes was detected. Of these, 595 genes (64.8% carried single or multiple hypomethylated CpG dinucleotides and 323 genes (35.2% single or multiple hypermethylated CpG dinucleotides. The Ingenuity Pathway Analysis (IPA online platform enlisted 908 of the 918 input genes and clustered 794 of them into 21 gene networks. Key features of the primary networks scored by IPA included carbohydrate and lipid metabolism, neurotransmitter signaling, cardiovascular system development and function, glycosaminoglycan signaling regulation and control of amino acid biosynthesis. Central to the network activities were genes controlling hormonal regulation (ESR1, mitochondrial activity (APP, PARK2, and glucose metabolism (INS. Regulatory pathways such as G-protein coupled receptor signaling, inositol metabolism, and inflammatory response were also highlighted. These data suggested the existence of a putative “PCOS epigenomic superpathway” with three main

  19. Is the prognostic significance of O6-methylguanine- DNA methyltransferase promoter methylation equally important in glioblastomas of patients from different continents? A systematic review with meta-analysis.

    Science.gov (United States)

    Meng, Wei; Jiang, Yangyang; Ma, Jie

    2017-01-01

    O6-methylguanine-DNA methyltransferase (MGMT) is an independent predictor of therapeutic response and potential prognosis in patients with glioblastoma multiforme (GBM). However, its significance of clinical prognosis in different continents still needs to be explored. To explore the effects of MGMT promoter methylation on both progression-free survival (PFS) and overall survival (OS) among GBM patients from different continents, a systematic review of published studies was conducted. A total of 5103 patients from 53 studies were involved in the systematic review and the total percentage of MGMT promoter methylation was 45.53%. Of these studies, 16 studies performed univariate analyses and 17 performed multivariate analyses of MGMT promoter methylation on PFS. The pooled hazard ratio (HR) estimated for PFS was 0.55 (95% CI 0.50, 0.60) by univariate analysis and 0.43 (95% CI 0.38, 0.48) by multivariate analysis. The effect of MGMT promoter methylation on OS was explored in 30 studies by univariate analysis and in 30 studies by multivariate analysis. The combined HR was 0.48 (95% CI 0.44, 0.52) and 0.42 (95% CI 0.38, 0.45), respectively. In each subgroup divided by areas, the prognostic significance still remained highly significant. The proportion of methylation in each group was in inverse proportion to the corresponding HR in the univariate and multivariate analyses of PFS. However, from the perspective of OS, compared with data from Europe and the US, higher methylation rates in Asia did not bring better returns.

  20. Nonlinear analysis of field distribution in electric motor with periodicity conditions

    Energy Technology Data Exchange (ETDEWEB)

    Stabrowski, M M; Sikora, J

    1981-01-01

    Numerical analysis of electromagnetic field distribution in linear motion tubular electric motor has been performed with the aid of finite element method. Two Fortran programmes for the solution of DBBF and BF large linear symmetric equation systems have been developed for purposes of this analysis. A new iterative algorithm, taking into account iron nonlinearity and periodicity conditions, has been introduced. Final results of the analysis in the form of induction diagrammes and motor driving force are directly useful for motor designers.

  1. Periodic precipitation a microcomputer analysis of transport and reaction processes in diffusion media, with software development

    CERN Document Server

    Henisch, H K

    1991-01-01

    Containing illustrations, worked examples, graphs and tables, this book deals with periodic precipitation (also known as Liesegang Ring formation) in terms of mathematical models and their logical consequences, and is entirely concerned with microcomputer analysis and software development. Three distinctive periodic precipitation mechanisms are included: binary diffusion-reaction; solubility modulation, and competitive particle growth. The book provides didactic illustrations of a valuable investigational procedure, in the form of hypothetical experimentation by microcomputer. The development

  2. Experimental analysis on thermally coated diesel engine with neem oil methyl ester and its blends

    Science.gov (United States)

    Karthickeyan, V.

    2018-01-01

    Depletion of fossil fuel has created a threat to the nation's energy policy, which in turn led to the development of new source renewable of energy. Biodiesel was considered as the most promising alternative to the traditional fossil fuel. In the present study, raw neem oil was considered as a principle source for the production of biodiesel and converted into Neem Oil Methyl Ester (NOME) using two stage transesterification process. The chemical compositions of NOME was analysed using Fourier Transform Infra-Red Spectroscopy (FTIR) and Gas Chromatography- Mass Spectrometry (GC-MS). Baseline readings were recorded with diesel, 25NOME (25% NOME with 75% diesel) and 50NOME (50% NOME with 50% diesel) in a direct injection, four stroke, water cooled diesel engine. Thermal Barrier Coating (TBC) was considered as a better technique for emission reduction in direct injection diesel engine. In the present study, Partially Stabilized Zirconia (PSZ) was used as a TBC material to coat the combustion chamber components like cylinder head, piston head and intake and exhaust valves. In coated engine, 25NOME showed better brake thermal efficiency and declined brake specific fuel consumption than 50NOME. Decreased exhaust emissions like CO, HC and smoke were observed with 25NOME in coated engine except NOx. [Figure not available: see fulltext.

  3. DNA methylation-based measures of biological age: meta-analysis predicting time to death

    Science.gov (United States)

    Chen, Brian H.; Marioni, Riccardo E.; Colicino, Elena; Peters, Marjolein J.; Ward-Caviness, Cavin K.; Tsai, Pei-Chien; Roetker, Nicholas S.; Just, Allan C.; Demerath, Ellen W.; Guan, Weihua; Bressler, Jan; Fornage, Myriam; Studenski, Stephanie; Vandiver, Amy R.; Moore, Ann Zenobia; Tanaka, Toshiko; Kiel, Douglas P.; Liang, Liming; Vokonas, Pantel; Schwartz, Joel; Lunetta, Kathryn L.; Murabito, Joanne M.; Bandinelli, Stefania; Hernandez, Dena G.; Melzer, David; Nalls, Michael; Pilling, Luke C.; Price, Timothy R.; Singleton, Andrew B.; Gieger, Christian; Holle, Rolf; Kretschmer, Anja; Kronenberg, Florian; Kunze, Sonja; Linseisen, Jakob; Meisinger, Christine; Rathmann, Wolfgang; Waldenberger, Melanie; Visscher, Peter M.; Shah, Sonia; Wray, Naomi R.; McRae, Allan F.; Franco, Oscar H.; Hofman, Albert; Uitterlinden, André G.; Absher, Devin; Assimes, Themistocles; Levine, Morgan E.; Lu, Ake T.; Tsao, Philip S.; Hou, Lifang; Manson, JoAnn E.; Carty, Cara L.; LaCroix, Andrea Z.; Reiner, Alexander P.; Spector, Tim D.; Feinberg, Andrew P.; Levy, Daniel; Baccarelli, Andrea; van Meurs, Joyce; Bell, Jordana T.; Peters, Annette; Deary, Ian J.; Pankow, James S.; Ferrucci, Luigi; Horvath, Steve

    2016-01-01

    Estimates of biological age based on DNA methylation patterns, often referred to as “epigenetic age”, “DNAm age”, have been shown to be robust biomarkers of age in humans. We previously demonstrated that independent of chronological age, epigenetic age assessed in blood predicted all-cause mortality in four human cohorts. Here, we expanded our original observation to 13 different cohorts for a total sample size of 13,089 individuals, including three racial/ethnic groups. In addition, we examined whether incorporating information on blood cell composition into the epigenetic age metrics improves their predictive power for mortality. All considered measures of epigenetic age acceleration were predictive of mortality (p≤8.2×10−9), independent of chronological age, even after adjusting for additional risk factors (p<5.4×10−4), and within the racial/ethnic groups that we examined (non-Hispanic whites, Hispanics, African Americans). Epigenetic age estimates that incorporated information on blood cell composition led to the smallest p-values for time to death (p=7.5×10−43). Overall, this study a) strengthens the evidence that epigenetic age predicts all-cause mortality above and beyond chronological age and traditional risk factors, and b) demonstrates that epigenetic age estimates that incorporate information on blood cell counts lead to highly significant associations with all-cause mortality. PMID:27690265

  4. Pharmacokinetics for regulatory risk analysis: the case of 1,1,1-trichloroethane (methyl chloroform).

    Science.gov (United States)

    Bogen, K T; Hall, L C

    1989-08-01

    A methodology for using physiologically based pharmacokinetic (PBPK) models to derive predicted safe concentrations of noncarcinogens in drinking water for humans based on experimentally determined no observed adverse effect levels (NOAELs) in animals is presented and applied to the case of 1,1,1-trichloroethane (methyl chloroform, MC). For each toxic endpoint and lowest corresponding NOAEL identified for MC, we considered a set of toxicologically plausible options regarding the presumed toxic agent and the metric for effective dose to target tissue. A four-compartment PBPK model for rodents was used to estimate corresponding effective doses to the animals used to obtain the experimental NOAELs. A five-compartment PBPK model was then applied, in conjunction with a multiroute (inhalation, ingestion and dermal) human-exposure scenario, to calculate alternative concentrations of MC in drinking water predicted to result in corresponding effective doses to the same target tissues in humans. In the case of MC, the PBPK approach to interspecies and interroute extrapolation of toxicity data resulted in lower drinking water concentrations predicted to be nontoxic to humans than corresponding concentrations obtained using a traditional method for determining safe levels.

  5. Integrated multidimensional and comprehensive 2D GC analysis of fatty acid methyl esters.

    Science.gov (United States)

    Zeng, Annie Xu; Chin, Sung-Tong; Marriott, Philip J

    2013-03-01

    Fatty acid methyl ester (FAME) profiling in complex fish oil and milk fat samples was studied using integrated comprehensive 2D GC (GC × GC) and multidimensional GC (MDGC). Using GC × GC, FAME compounds--cis- and trans-isomers, and essential fatty acid isomers--ranging from C18 to C22 in fish oil and C18 in milk fat were clearly displayed in contour plot format according to structural properties and patterns, further identified based on authentic standards. Incompletely resolved regions were subjected to MDGC, with Cn (n = 18, 20) zones transferred to a (2)D column. Elution behavior of C18 FAME on various (2)D column phases (ionic liquids IL111, IL100, IL76, and modified PEG) was evaluated. Individual isolated Cn zones demonstrated about four-fold increased peak capacities. The IL100 provided superior separation, good peak shape, and utilization of elution space. For milk fat-derived FAME, the (2)D chromatogram revealed at least three peaks corresponding to C18:1, more than six peaks for cis/trans-C18:2 isomers, and two peaks for C18:3. More than 17 peaks were obtained for the C20 region of fish oil-derived FAMEs using MDGC, compared with ten peaks using GC × GC. The MDGC strategy is useful for improved FAME isomer separation and confirmation. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Analysis of self-broadened pure rotational and rovibrational lines of methyl chloride at room temperature

    Science.gov (United States)

    Bray, C.; Jacquemart, D.; Lacome, N.; Guinet, M.; Cuisset, A.; Eliet, S.; Hindle, F.; Mouret, G.; Rohart, F.; Buldyreva, J.

    2013-02-01

    Rovibrational absorption spectra of methyl chloride in the spectral region between 2800 and 3200 cm-1 were recorded with a high-resolution Fourier transform spectrometer. A multispectrum fitting procedure was used to analyze 527 transitions of the ν1 band and to retrieve the self-broadening coefficients for various J- and K-values with an estimated accuracy around 8%. Pure rotational transitions of CH3Cl in the submillimeter/terahertz region (0.2-1.4 THz) were also investigated using two complementary techniques of frequency-multiplication and continuous-wave photomixing. Forty-three pure rotational self-broadening coefficients were extracted with the accuracy between 3 and 5%. The whole set of measured values was used to model the J- and K-rotational dependences of the self-broadening coefficients by second-order polynomials. In addition, semi-classical calculations were performed, based on the real symmetric-top geometry of the active molecule, an intermolecular potential model including not only the dominant electrostatic but also the short-range forces, as well as on an exact classical treatment of the relative translational motion of the colliding partners. Comparison of all experimental and theoretical results shows similar rotational dependences and no significant vibrational dependence, so that extrapolations to other spectral regions should be straightforward.

  7. Thermal explosion analysis of methyl ethyl ketone peroxide by non-isothermal and isothermal calorimetric applications

    International Nuclear Information System (INIS)

    Chi, Jen-Hao; Wu, Sheng-Hung; Shu, Chi-Min

    2009-01-01

    In the past, process incidents attributed to organic peroxides (OPs) that involved near misses, over-pressures, runaway reactions, and thermal explosions occurred because of poor training, human error, incorrect kinetic assumptions, insufficient change management, and inadequate chemical knowledge in the manufacturing process. Calorimetric applications were employed broadly to test organic peroxides on a small-scale because of their thermal hazards, such as exothermic behavior and self-accelerating decomposition in the laboratory. In essence, methyl ethyl ketone peroxide (MEKPO) is highly reactive and exothermically unstable. In recent years, it has undergone many thermal explosions and runaway reaction incidents in the manufacturing process. Differential scanning calorimetry (DSC), vent sizing package 2 (VSP2), and thermal activity monitor (TAM) were employed to analyze thermokinetic parameters and safety index. The intent of the analyses was to facilitate the use of various auto-alarm equipments to detect over-pressure, over-temperature, and hazardous materials leaks for a wide spectrum of operations. Results indicated that MEKPO decomposition is detected at low temperatures (30-40 deg. C), and the rate of decomposition was shown to exponentially increase with temperature and pressure. Determining time to maximum rate (TMR), self-accelerating decomposition temperature (SADT), maximum temperature (T max ), exothermic onset temperature (T 0 ), and heat of decomposition (ΔH d ) was essential for identifying early-stage runaway reactions effectively for industries.

  8. Lifetime Analysis of Rubber Gasket Composed of Methyl Vinyl Silicone Rubber with Low-Temperature Resistance

    Directory of Open Access Journals (Sweden)

    Young-Doo Kwon

    2015-01-01

    Full Text Available Most machines and instruments constantly require elastomeric materials like rubber for the purposes of shock absorption, noise attenuation, and sealing. The material properties and accurate lifetime prediction of rubber are closely related to the quality of machines, especially their durability and reliability. The properties of rubber-like elastomers are influenced by ambient conditions, such as temperature, environment, and mechanical load. Moreover, the initial properties of rubber gaskets must be sustained under working conditions to satisfy their required function. Because of its technical merits, as well as its low cost, the highly accelerated life test (HALT is used by many researchers to predict the long-term lifetime of rubber materials. Methyl vinyl silicone rubber (VMQ has recently been adopted to improve the lifetime of automobile radiator gaskets. A four-parameter method of determining the recovery ability of the gaskets was recently published, and two revised methods of obtaining the recovery were proposed for polyacrylate (ACM rubber. The recovery rate curves for VMQ were acquired using the successive zooming genetic algorithm (SZGA. The gasket lifetime for the target recovery (60% of a compressed gasket was computed somewhat differently depending on the selected regression model.

  9. Argonaute pull-down and RISC analysis using 2'-O-methylated oligonucleotides affinity matrices.

    Science.gov (United States)

    Jannot, Guillaume; Vasquez-Rifo, Alejandro; Simard, Martin J

    2011-01-01

    During the last decade, several novel small non-coding RNA pathways have been unveiled, which reach out to many biological processes. Common to all these pathways is the binding of a small RNA molecule to a protein member of the Argonaute family, which forms a minimal core complex called the RNA-induced silencing complex or RISC. The RISC targets mRNAs in a sequence-specific manner, either to induce mRNA cleavage through the intrinsic activity of the Argonaute protein or to abrogate protein synthesis by a mechanism that is still under investigation. We describe here, in details, a method for the affinity chromatography of the let-7 RISC starting from extracts of the nematode Caenorhabditis elegans. Our method exploits the sequence specificity of the RISC and makes use of biotinylated and 2'-O-methylated oligonucleotides to trap and pull-down small RNAs and their associated proteins. Importantly, this technique may easily be adapted to target other small RNAs expressed in different cell types or model organisms. This method provides a useful strategy to identify the proteins associated with the RISC, and hence gain insight in the functions of small RNAs.

  10. Case–control study of HLA-G promoter methylation status, HPV infection and cervical neoplasia in Curitiba, Brazil: a pilot analysis

    International Nuclear Information System (INIS)

    Gillio-Tos, Anna; Carvalho, Newton S; Maestri, Carlos A; Lacerda, Hadriano M; Zugna, Daniela; Richiardi, Lorenzo; Merletti, Franco; Bicalho, Maria da Graça; Fiano, Valentina; Grasso, Chiara; Tarallo, Valentina; De Marco, Laura; Trevisan, Morena; Xavier, MarinaBarbaradeSousa; Slowik, Renata

    2012-01-01

    The causal association between persistent human papillomavirus (HPV) infection and cervical cancer has been established, but the mechanisms that favor HPV persistence in cervical cells are still unknown. The diminished capability of the immune system to control and resolve HPV infection is one of several hypotheses. The tolerogenic protein HLA-G has shown aberrant expression in a variety of cancers, which has been suggested as a mechanism for tumor escape from immunosurveillance. In the present study we evaluate the role of epigenetic modification (promoter de-methylation) of the HLA-G gene on susceptibility to HPV infection and development of high-grade cervical lesions. A case–control study was carried out in Curitiba, Brazil, between February and June 2010. A total of 789 women aged 15–47 years were recruited: 510 controls with normal cervical cytology, and 279 cases with histologically confirmed cervical intraepithelial neoplasia grade 2 (CIN2, N = 150) or grade 3 (CIN3, N = 129). All women were administered a questionnaire by interview, which collected information on demographic and lifestyle factors, and a cervical sample was collected. HPV DNA detection was performed by GP5+/GP6+ primer-mediated PCR. HPV-positive samples were genotyped by multiplex PCR. A pilot analysis of HLA-G promoter methylation was carried out in a subset of the study population (96 cases and 76 controls) by pyrosequencing. HLA-G methylation and HPV infection status of cases and controls were compared, and confounding factors were computed by t Student and non-parametric Wilcoxon tests. Comparison of HLA-G methylation between cases and controls was assessed by the Bonferroni correction. The association of HLA-G methylation with CIN2/3 was evaluated by logistic regression. HPV prevalence was 19.6% in controls and 94.3% in CIN2/3 cases. HPV16, 31, 33, 35 and 18 were the most prevalent types. Methylation analysis of seven CpGs in the HLA-G promoter did not reveal any spontaneous de-methylation

  11. Proteomic analysis of JAZ interacting proteins under methyl jasmonate treatment in finger millet.

    Science.gov (United States)

    Sen, Saswati; Kundu, Sangeeta; Dutta, Samir Kr

    2016-11-01

    Jasmonic acid (JA) signaling pathway in plants is activated against various developmental processes as well as biotic and abiotic stresses. The Jasmonate ZIM-domain (JAZ) protein family, the key regulator of plant JA signaling pathway, also participates in phytohormone crosstalk. This is the first study revealing the in vivo interactions of finger millet (Eleusine coracana (L.) Gaertn.) JAZ protein (EcJAZ) under methyl jasmonate (MJ) treatment. The aim of the study was to explore not only the JA signaling pathway but also the phytohormone signaling crosstalk of finger millet, a highly important future crop. From the MJ-treated finger millet seedlings, the EcJAZ interacting proteins were purified by affinity chromatography with the EcJAZ-matrix. Twenty-one proteins of varying functionalities were successfully identified by MALDI-TOF-TOF Mass spectrometry. Apart from the previously identified JAZ binding proteins, most prominently, EcJAZ was found to interact with transcription factors like NAC, GATA and also with Cold responsive protein (COR), etc. that might have extended the range of functionalities of JAZ proteins. Moreover, to evaluate the interactions of EcJAZ in the JA-co-receptor complex, we generated ten in-silico models containing the EcJAZ degron and the COI1-SKP1 of five monocot cereals viz., rice, wheat, maize, Sorghum and Setaria with JA-Ile or coronatine. Our results indicated that the EcJAZ protein of finger millet could act as the signaling hub for the JA and other phytohormone signaling pathways, in response to a diverse set of stressors and developmental cues to provide survival fitness to the plant. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  12. Anti-N-methyl-D-aspartate receptor encephalitis: analysis of three cases

    Directory of Open Access Journals (Sweden)

    Hui SU

    2015-07-01

    Full Text Available Objective To study clinical features, diagnosis, therapy response and prognosis of anti-N-methyl-D-aspartate receptor (anti-NMDAR encephalitis.  Methods Three cases with anti-NMDAR encephalitis were reported. The clinical features, laboratory examinations, imaging, EEG and therapy response of 3 cases were retrospectively analyzed, and also related literatures were reviewed.  Results Two patients were young male and one patient was old female. Main symptoms included psychiatric symptoms in 3 cases (mania in 2 male patients and stupor in the female patient, epilepsy in 2 cases and respiratory failure in one case. The results of MRI examination revealed normal, while EEG examination showed abnormal in all cases. No tumor was detected in any of these patients. Lumbar puncture revealed normal cerebrospinal fluid (CSF pressure (3 cases, elevated white blood cell (WBC, 3 cases and protein quantification (one case. All cases were confirmed to have the disease by detection of anti-NMDAR antibodies in serum and CSF. One male patient got better after receiving immunotherapy with methylprednisolone and intravenous immunoglobulin (IVIg, but psychiatric symptoms were left over. Another male patient had no response to the above treatment. But the female patient was improved without immunotherapy. All 3 cases were followed up for one year after being discharged. One male patient died by accident because of mental disorders. Another male patient showed no sign of relief. The female patient got mild personality and memory change.  Conclusions Anti-NMDAR encephalitis is a new type of autoimmune encephalitis. It is characterized by fever, memory deficits, seizures, disturbance of consciousness, and autonomic dysfunction in males and females of all ages. This type of encephalitis is often associated with teratoma, and has a good response to immunotherapy. There is a certain correlation between progression and prognosis. DOI: 10.3969/j.issn.1672-6731.2015.07.013

  13. Preparation of acryloyl β-cyclodextrin-silica hybrid monolithic column and its application in pipette tip solid-phase extraction and HPLC analysis of methyl parathion and fenthion.

    Science.gov (United States)

    Chen, Ling; Dang, Xueping; Ai, Youhong; Chen, Huaixia

    2018-05-07

    An acryloyl β-cyclodextrin-silica hybrid monolithic column for pipette tip solid-phase extraction and high-performance liquid chromatography determination of methyl parathion and fenthion have been prepared through a sol-gel polymerization method. The synthesis conditions, including the volume of cross-linker and the ratio of inorganic solution to organic solution, were optimized. The prepared monolithic column was characterized by thermogravimetric analysis, scanning electron microscopy and Fourier transform infrared spectroscopy. The eluent type, volume and flow rate, sample volume, flow rate, acidity and ionic strength were optimized in detail. Under the optimized conditions, a simple and sensitive pipette tip solid-phase extraction with high-performance liquid chromatography method was developed for the determination of methyl parathion and fenthion in lettuce. The method yielded a linear calibration curve in the concentration ranges of 15-400 μg/kg for methyl parathion and 20-400 μg/kg for fenthion with correlation coefficients of above 0.9957. The limits of detection were 4.5 μg/kg for methyl parathion and 6.0 μg/kg for fenthion, respectively. The recoveries of methyl parathion and fenthion spiked in lettuce ranged from 96.0 to 104.2% with relative standard deviations less than 8.4%. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  14. Transcriptomics analysis of interactive effects of benzene, trichloroethylene and methyl mercury within binary and ternary mixtures on the liver and kidney following subchronic exposure in the rat

    NARCIS (Netherlands)

    Hendriksen, P.J.M.; Freidig, A.P.; Jonker, D.; Thissen, U.; Bogaards, J.J.P.; Mumtaz, M.M.; Groten, J.P.; Stierum, R.H.

    2007-01-01

    The present research aimed to study the interaction of three chemicals, methyl mercury, benzene and trichloroethylene, on mRNA expression alterations in rat liver and kidney measured by microarray analysis. These compounds were selected based on presumed different modes of action. The chemicals were

  15. Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM.

    Science.gov (United States)

    Kristensen, Lasse S; Wojdacz, Tomasz K; Thestrup, Britta B; Wiuf, Carsten; Hager, Henrik; Hansen, Lise Lotte

    2009-12-21

    The High Resolution Melting (HRM) technology has recently been introduced as a rapid and robust analysis tool for the detection of DNA methylation. The methylation status of multiple tumor suppressor genes may serve as biomarkers for early cancer diagnostics, for prediction of prognosis and for prediction of response to treatment. Therefore, it is important that methodologies for detection of DNA methylation continue to evolve. Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM. Here, we have assessed the quality of DNA extracted from up to 30 years old Formalin Fixed Paraffin Embedded (FFPE) tissue for DNA methylation analysis using SMART-MSP and MS-HRM. The quality assessment was performed on DNA extracted from 54 Non-Small Cell Lung Cancer (NSCLC) samples derived from FFPE tissue, collected over 30 years and grouped into five years intervals. For each sample, the methylation levels of the CDKN2A (p16) and RARB promoters were estimated using SMART-MSP and MS-HRM assays designed to assess the methylation status of the same CpG positions. This allowed for a direct comparison of the methylation levels estimated by the two methods for each sample. CDKN2A promoter methylation levels were successfully determined by SMART-MSP and MS-HRM in all 54 samples. Identical methylation estimates were obtained by the two methods in 46 of the samples. The methylation levels of the RARB promoter were successfully determined by SMART-MSP in all samples. When using MS-HRM to assess RARB methylation five samples failed to amplify and 15 samples showed a melting profile characteristic for heterogeneous methylation. Twenty-seven of the remaining 34 samples, for which the methylation level could be estimated, gave the same result as observed when using SMART-MSP. MS-HRM and SMART-MSP can be successfully used for single locus

  16. Comparison of Fatty Acid Methyl Ester Analysis with the Use of API 20E and NFT Strips for Identification of Aquatic Bacteria

    OpenAIRE

    Brown, B. J.; Leff, L. G.

    1996-01-01

    Aquatic bacteria grown on MacConkey agar and modified nutrient agar were identified by using API 20E and NFT strips and fatty acid methyl ester (FAME) analysis. Identifications agreed at the species level 35.7% of the time when API 20E strips and FAME analysis were used and in 4.3% of the cases when API NFT strips and FAME analysis were used. These techniques require further development before extended use in ecological studies.

  17. Mining pathway associations for disease-related pathway activity analysis based on gene expression and methylation data.

    Science.gov (United States)

    Lee, Hyeonjeong; Shin, Miyoung

    2017-01-01

    The problem of discovering genetic markers as disease signatures is of great significance for the successful diagnosis, treatment, and prognosis of complex diseases. Even if many earlier studies worked on identifying disease markers from a variety of biological resources, they mostly focused on the markers of genes or gene-sets (i.e., pathways). However, these markers may not be enough to explain biological interactions between genetic variables that are related to diseases. Thus, in this study, our aim is to investigate distinctive associations among active pathways (i.e., pathway-sets) shown each in case and control samples which can be observed from gene expression and/or methylation data. The pathway-sets are obtained by identifying a set of associated pathways that are often active together over a significant number of class samples. For this purpose, gene expression or methylation profiles are first analyzed to identify significant (active) pathways via gene-set enrichment analysis. Then, regarding these active pathways, an association rule mining approach is applied to examine interesting pathway-sets in each class of samples (case or control). By doing so, the sets of associated pathways often working together in activity profiles are finally chosen as our distinctive signature of each class. The identified pathway-sets are aggregated into a pathway activity network (PAN), which facilitates the visualization of differential pathway associations between case and control samples. From our experiments with two publicly available datasets, we could find interesting PAN structures as the distinctive signatures of breast cancer and uterine leiomyoma cancer, respectively. Our pathway-set markers were shown to be superior or very comparable to other genetic markers (such as genes or gene-sets) in disease classification. Furthermore, the PAN structure, which can be constructed from the identified markers of pathway-sets, could provide deeper insights into

  18. Combined Analysis of COX-2 and p53 Expressions Reveals Synergistic Inverse Correlations with Microsatellite Instability and CpG Island Methylator Phenotype in Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Shuji Ogino

    2006-06-01

    Full Text Available Cyclooxygenase-2 (COX-2 overexpression and mutations of p53 (a known COX-2 regulator are inversely associated with microsatellite instability—high (MSI-H and CpG island methylator phenotype (CIMP, characterized by extensive promoter methylation, is associated with MSI-H. However, no studies have comprehensively examined interrelations between COX-2, p53, MSI, and CIMP. Using MethyLight, we measured DNA methylation in five CIMP-specific gene promoters [CACNA1G, CDKN2A (p16/INK4A, CRABP1, MLH1, and NEUROG1] in relatively unbiased samples of 751 colorectal cancer cases obtained from two large prospective cohorts; 115 (15% tumors were CIMP-high (≥ 4 of 5 methylated promoters, 251 (33% were CIMP-low (1 to 3 methylated promoters, and the remaining 385 (51% were CIMP-0 (no methylated promoters. CIMP-high tumors were much less frequent in COX-2+/p53+ tumors (4.6% than in COX-2+/p53- tumors (19%; P < .0001, COX-2-/p53+ tumors (17%; P = .04, and COX-2-/p53- tumors (28%; P < .0001. In addition, COX-2+/p53+ tumors were significantly less common in MSI-H CIMP-high tumors (9.7% than in non-MSI-H CIMP-low/CIMP-0 tumors (44–47%; P < .0001. In conclusion, COX-2 and p53 alterations were synergistically inversely correlated with both MSI-H and CIMP-high. Our data suggest that a combined analysis of COX-2 and p53 may be more useful for the molecular classification of colorectal cancer than either COX-2 or p53 analysis alone.

  19. QNB: differential RNA methylation analysis for count-based small-sample sequencing data with a quad-negative binomial model.

    Science.gov (United States)

    Liu, Lian; Zhang, Shao-Wu; Huang, Yufei; Meng, Jia

    2017-08-31

    As a newly emerged research area, RNA epigenetics has drawn increasing attention recently for the participation of RNA methylation and other modifications in a number of crucial biological processes. Thanks to high throughput sequencing techniques, such as, MeRIP-Seq, transcriptome-wide RNA methylation profile is now available in the form of count-based data, with which it is often of interests to study the dynamics at epitranscriptomic layer. However, the sample size of RNA methylation experiment is usually very small due to its costs; and additionally, there usually exist a large number of genes whose methylation level cannot be accurately estimated due to their low expression level, making differential RNA methylation analysis a difficult task. We present QNB, a statistical approach for differential RNA methylation analysis with count-based small-sample sequencing data. Compared with previous approaches such as DRME model based on a statistical test covering the IP samples only with 2 negative binomial distributions, QNB is based on 4 independent negative binomial distributions with their variances and means linked by local regressions, and in the way, the input control samples are also properly taken care of. In addition, different from DRME approach, which relies only the input control sample only for estimating the background, QNB uses a more robust estimator for gene expression by combining information from both input and IP samples, which could largely improve the testing performance for very lowly expressed genes. QNB showed improved performance on both simulated and real MeRIP-Seq datasets when compared with competing algorithms. And the QNB model is also applicable to other datasets related RNA modifications, including but not limited to RNA bisulfite sequencing, m 1 A-Seq, Par-CLIP, RIP-Seq, etc.

  20. Genome-wide placental DNA methylation analysis of severely growth-discordant monochorionic twins reveals novel epigenetic targets for intrauterine growth restriction.

    Science.gov (United States)

    Roifman, Maian; Choufani, Sanaa; Turinsky, Andrei L; Drewlo, Sascha; Keating, Sarah; Brudno, Michael; Kingdom, John; Weksberg, Rosanna

    2016-01-01

    Intrauterine growth restriction (IUGR), which refers to reduced fetal growth in the context of placental insufficiency, is etiologically heterogeneous. IUGR is associated not only with perinatal morbidity and mortality but also with adult-onset disorders, such as cardiovascular disease and diabetes, posing a major health burden. Placental epigenetic dysregulation has been proposed as one mechanism that causes IUGR; however, the spectrum of epigenetic pathophysiological mechanisms leading to IUGR remains to be elucidated. Monozygotic monochorionic twins are particularly affected by IUGR, in the setting of severe discordant growth. Because monozygotic twins have the same genotype at conception and a shared maternal environment, they provide an ideal model system for studying epigenetic dysregulation of the placenta. We compared genome-wide placental DNA methylation patterns of severely growth-discordant twins to identify novel candidate genes for IUGR. Snap-frozen placental samples for eight severely growth-discordant monozygotic monochorionic twin pairs were obtained at delivery from each twin. A high-resolution DNA methylation array platform was used to identify methylation differences between IUGR and normal twins. Our analysis revealed differentially methylated regions in the promoters of eight genes: DECR1, ZNF300, DNAJA4, CCL28, LEPR, HSPA1A/L, GSTO1, and GNE. The largest methylation differences between the two groups were in the promoters of DECR1 and ZNF300. The significance of these group differences was independently validated by bisulfite pyrosequencing, implicating aberrations in fatty acid beta oxidation and transcriptional regulation, respectively. Further analysis of the array data identified methylation changes most prominently affecting the Wnt and cadherin pathways in the IUGR cohort. Our results suggest that IUGR in monozygotic twins is associated with impairments in lipid metabolism and transcriptional regulation as well as cadherin and Wnt

  1. Microarray-Based Analysis of Methylation of 1st Trimester Trisomic Placentas from Down Syndrome, Edwards Syndrome and Patau Syndrome

    DEFF Research Database (Denmark)

    Hatt, Lotte; Aagaard, Mads M; Bach, Cathrine

    2016-01-01

    Methylation-based non-invasive prenatal testing of fetal aneuploidies is an alternative method that could possibly improve fetal aneuploidy diagnosis, especially for trisomy 13 (T13) and trisomy 18(T18). Our aim was to study the methylation landscape in placenta DNA from trisomy 13, 18 and 21 pre...

  2. Disability in Mexico: a comparative analysis between descriptive models and historical periods using a timeline

    Directory of Open Access Journals (Sweden)

    Hugo Sandoval

    2017-07-01

    Full Text Available Some interpretations frequently argue that three Disability Models (DM (Charity, Medical/Rehabilitation, and Social correspond to historical periods in terms of chronological succession. These views permeate a priori within major official documents on the subject in Mexico. This paper intends to test whether this association is plausible by applying a timeline method. A document search was made with inclusion and exclusion criteria in databases to select representative studies with which to depict milestones in the timelines for each period. The following is demonstrated: 1 models should be considered as categories of analysis and not as historical periods, in that the prevalence of elements of the three models is present to date, and 2 the association between disability models and historical periods results in teleological interpretations of the history of disability in Mexico.

  3. Hybrid FDTD Analysis for Periodic On-Chip Terahertz (THZ) Structures

    Energy Technology Data Exchange (ETDEWEB)

    Hussein, Yasser A.; Spencer, James E.; /SLAC

    2005-06-07

    We present electromagnetic analysis and radiation efficiency calculations for on-chip terahertz (THz) structures based on a hybrid, finite-difference, time-domain (HFDTD) technique. The method employs the FDTD technique to calculate S-parameters for one cell of a periodic structure. The transmission ABCD matrix is then estimated and multiplied by itself n times to obtain the n-cell periodic structure ABCD parameters that are then converted back to S-parameters. Validation of the method is carried out by comparing the results of the hybrid technique with FDTD calculations of the entire periodic structure as well as with HFSS which all agree quite well. This procedure reduces the CPU-time and allows efficient design and optimization of periodic THz radiation sources. Future research will involve coupling of Maxwell's equations with a more detailed, physics-based transport model for higher-order effects.

  4. The marriage boom and marriage bust in the United States: An age-period-cohort analysis.

    Science.gov (United States)

    Schellekens, Jona

    2017-03-01

    In the 1950s and 1960s there was an unprecedented marriage boom in the United States. This was followed in the 1970s by a marriage bust. Some argue that both phenomena are cohort effects, while others argue that they are period effects. The study reported here tested the major period and cohort theories of the marriage boom and bust, by estimating an age-period-cohort model of first marriage for the years 1925-79 using census microdata. The results of the analysis indicate that the marriage boom was mostly a period effect, although there were also cohort influences. More specifically, the hypothesis that the marriage boom was mostly a response to rising wages is shown to be consistent with the data. However, much of the marriage bust can be accounted for by unidentified cohort influences, at least until 1980.

  5. Methods for the Quasi-Periodic Variability Analysis in Blazars Y. Liu ...

    Indian Academy of Sciences (India)

    the variability analysis in blazars in optical and radio bands, to search for possible quasi-periodic signals. 2. Power spectral density (PSD). In statistical signal processing and physics, the power spectral density (PSD) is a positive real function of a frequency variable associated with a stationary stochas- tic process. Intuitively ...

  6. Long Term Periodicity Analysis of OJ 287 at Optical V Waveband Jie ...

    Indian Academy of Sciences (India)

    these spectrum estimation methods in the periodicity analysis on real observational data. We select the blazar OJ 287 for our experiments. In addition to make certain comparative studies, we studied the properties and differences of the methods. We organize the paper as follows: the light curves and data of OJ 287 are ...

  7. Robust periodic steady state analysis of autonomous oscillators based on generalized eigenvalues

    NARCIS (Netherlands)

    Mirzavand, R.; Maten, ter E.J.W.; Beelen, T.G.J.; Schilders, W.H.A.; Abdipour, A.

    2011-01-01

    In this paper, we present a new gauge technique for the Newton Raphson method to solve the periodic steady state (PSS) analysis of free-running oscillators in the time domain. To find the frequency a new equation is added to the system of equations. Our equation combines a generalized eigenvector

  8. Robust periodic steady state analysis of autonomous oscillators based on generalized eigenvalues

    NARCIS (Netherlands)

    Mirzavand, R.; Maten, ter E.J.W.; Beelen, T.G.J.; Schilders, W.H.A.; Abdipour, A.; Michielsen, B.; Poirier, J.R.

    2012-01-01

    In this paper, we present a new gauge technique for the Newton Raphson method to solve the periodic steady state (PSS) analysis of free-running oscillators in the time domain. To find the frequency a new equation is added to the system of equations. Our equation combines a generalized eigenvector

  9. pETM: a penalized Exponential Tilt Model for analysis of correlated high-dimensional DNA methylation data.

    Science.gov (United States)

    Sun, Hokeun; Wang, Ya; Chen, Yong; Li, Yun; Wang, Shuang

    2017-06-15

    DNA methylation plays an important role in many biological processes and cancer progression. Recent studies have found that there are also differences in methylation variations in different groups other than differences in methylation means. Several methods have been developed that consider both mean and variance signals in order to improve statistical power of detecting differentially methylated loci. Moreover, as methylation levels of neighboring CpG sites are known to be strongly correlated, methods that incorporate correlations have also been developed. We previously developed a network-based penalized logistic regression for correlated methylation data, but only focusing on mean signals. We have also developed a generalized exponential tilt model that captures both mean and variance signals but only examining one CpG site at a time. In this article, we proposed a penalized Exponential Tilt Model (pETM) using network-based regularization that captures both mean and variance signals in DNA methylation data and takes into account the correlations among nearby CpG sites. By combining the strength of the two models we previously developed, we demonstrated the superior power and better performance of the pETM method through simulations and the applications to the 450K DNA methylation array data of the four breast invasive carcinoma cancer subtypes from The Cancer Genome Atlas (TCGA) project. The developed pETM method identifies many cancer-related methylation loci that were missed by our previously developed method that considers correlations among nearby methylation loci but not variance signals. The R package 'pETM' is publicly available through CRAN: http://cran.r-project.org . sw2206@columbia.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  10. [Biodegradation of methyl tert-butyl ether by stabilized immobilized Methylibium petroleiphilum PM1 cells and its biodegradation kinetics analysis].

    Science.gov (United States)

    Cheng, Zhuo-wei; Fu, Ling-xiao; Jiang, Yi-feng; Chen, Jian-meng; Zhang, Rong

    2011-05-01

    Methylibium petroleiphilum PM1, which is capable of degrading methyl tert-butyl ether (MTBE) , was immobilized in calcium alginate gel beads. Several methods were explored to increase the strength of these gel beads. The central composite design analysis indicated that the introduction of 0.2 mol x L(-1) Ca2+ into the crosslinking solution, 1.38 mmol x L(-1) Ca2+ into the growth medium and 0.1% polyethyleneimine (PEI) as the chemical crosslinking agent could increase the stability of the Ca-alginate gel beads with no loss of biodegradation activity. The stabilized immobilized cells could be used 400 h continuously with no breakage and no bioactivity loss. Examination of scanning electron microscope demonstrated that a membrane surrounding the gel beads was formed and the cells could grow and breed well in the stabilized calcium alginate gel beads. Kinetic analysis of the gel bead-degradation indicated that the rate-limiting step was biochemical process instead of intraparticle diffusion process. The diameter of 3 mm affected the biodegradability less while high concentration of PEI induced much more serious mass transfer restraint.

  11. Characterisation of capillary ionic liquid columns for gas chromatography-mass spectrometry analysis of fatty acid methyl esters.

    Science.gov (United States)

    Zeng, Annie Xu; Chin, Sung-Tong; Nolvachai, Yada; Kulsing, Chadin; Sidisky, Leonard M; Marriott, Philip J

    2013-11-25

    Due to their distinct chemical properties, the application of ionic liquid (IL) compounds as gas chromatography (GC) stationary phases offer unique GC separation especially in the analysis of geometric and positional fatty acid methyl ester (FAME) isomers. Elution behaviour of FAME on several commercialised IL capillary columns including phosphonium based SLB-IL59, SLB-IL60, SLB-IL61 and SLB-IL76 and imidazolium based SLB-IL82, SLB-IL100, and SLB-IL111 as well as a general purpose column SLB-5ms, were evaluated in gas chromatography-mass spectrometry (GC-MS) analysis. The phases were further characterised by using a linear solvation energy relationship (LSER) approach according to the equivalent chain length (ECL) index of FAME. Among all tested IL columns, elution temperatures of saturated FAME increased as their McReynolds' polarity value decreased, except for IL60. ECL values increased markedly as the stationary phase polarity increased, particularly for the polyunsaturated FAME. The LSER study indicated a lowest l/e value at 0.864 for IL111, displaying phase selectivity towards unsaturated FAME, with higher peak capacity within a carbon number isomer group. s and e descriptors calculated from LSER were validated by excellent correlation with dipole moments and lowest unoccupied molecular orbital (LUMO) energies, with R(2) values of 0.99 and 0.92 respectively, calculated using GAUSSIAN. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Method detection limit determination and application of a convenient headspace analysis method for methyl tert-butyl ether in water.

    Science.gov (United States)

    O'Neill, Dennis T; Rochette, Elizabeth A; Ramsey, Philip J

    2002-11-15

    Methyl tert-butyl ether (MTBE) is a common groundwater contaminant, introduced to the environment by leaking petroleum storage tanks, urban runoff, and motorized watercraft. In this study. a simplified (static) headspace analysis method was adapted for determination of MTBE in water samples and soil water extracts. The MDL of the headspace method was calculated to be 2.0 microg L(-1) by the EPA single-concentration design method(1) and 1.2 microg L(-1) by a calibration method developed by Hubaux and Vos (Hubaux, A.; Vos, G. Anal. Chem. 1970,42, 849-855). The MDL calculated with the Hubaux and Vos method was favored because it considers both a true positive and a false positive. The static headspace method was applied to analysis of a tap water sample and a monitoring well sample from a gasoline service station, a river sample, and aqueous extracts from soil excavated during removal of a leaking underground storage tank (LUST). The water samples examined in this study had MTTBE concentrations ranging from 6 to 19 microg L(-1). Aqueous extracts of a soil sample taken from the LUST site had 8 microg L(-1) MTBE.

  13. Meta-analysis of the prognostic value of CpG island methylator phenotype in gastric cancer.

    Science.gov (United States)

    Powell, A G M T; Soul, S; Christian, A; Lewis, W G

    2018-01-01

    CpG island methylator phenotype (CIMP) has been identified as a distinct molecular subtype of gastric cancer, yet associations with survival are conflicting. A meta-analysis was performed to estimate the prognostic significance of CIMP. Embase, MEDLINE, PubMed, PubMed Central and Cochrane databases were searched systematically for studies related to the association between CIMP and survival in patients undergoing potentially curative resection for gastric cancer. A total of 918 patients from ten studies were included, and the median proportion of tumours with CIMP-high (CIMP-H) status was 40·9 (range 4·8-63) per cent. Gene panels for assessing CIMP status varied between the studies. Pooled analysis suggested that specimens exhibiting CIMP-H were associated with poorer 5-year survival (odds ratio (OR) for death 1·48, 95 per cent c.i. 1·10 to 1·99; P = 0·009). Significant heterogeneity was observed between studies (I 2 = 88 per cent, P CIMP-H tumours, revealed that CIMP-H was associated with both poor (OR for death 8·15, 4·65 to 14·28, P CIMP, which may explain the survival differences. © 2018 BJS Society Ltd Published by John Wiley & Sons Ltd.

  14. Preliminary individualized chemotherapy for malignant astrocytomas based on O6-methylguanine-deoxyribonucleic acid methyltransferase methylation analysis.

    Science.gov (United States)

    Watanabe, Takao; Katayama, Yoichi; Ogino, Akiyoshi; Ohta, Takashi; Yoshino, Atsuo; Fukushima, Takao

    2006-08-01

    O(6)-methylguanine-deoxyribonucleic acid methyltransferase gene (MGMT) methylation is apparently correlated with responsiveness to nitrosourea chemotherapy, suggesting this alkylating agent should be effective against MGMT-methylated tumors. MGMT appears not to be linked to platinum resistance, so platinum chemotherapy should be used for MGMT-unmethylated tumors. This study was a preliminary trial of individualized chemotherapy based on MGMT methylation status in a total of 20 patients with newly diagnosed malignant astrocytomas (9 anaplastic astrocytomas and 11 glioblastomas multiforme). The procarbazine, 1-(4-amino-2-methyl-5-pyrimidinyl)methyl-3-2(2-chloroethyl)-3-nitrosourea, and vincristine (PAV) regimen was administered to seven patients with MGMT-methylated tumors, and the carboplatin and etoposide (CE) regimen was administered to 13 patients with MGMT-unmethylated tumors. Objective response to the PAV therapy was noted in all three patients with measurable residual tumor (2 complete responses and 1 partial response). Five of the seven patients continued to be disease-free after initiation of the PAV therapy. Objective response to the CE therapy was seen in only one of seven patients with measurable residual tumor (1 partial response). Three of the 13 patients were free from progression, whereas the remaining 10 patients showed early progression. The PAV regimen is effective against MGMT-methylated malignant astrocytomas, but the CE regimen is not useful at the given dose and schedule in MGMT-unmethylated tumors.

  15. Multiple Criteria and Multiple Periods Performance Analysis: The Comparison of North African Railways

    Science.gov (United States)

    Sabri, Karim; Colson, Gérard E.; Mbangala, Augustin M.

    2008-10-01

    Multi-period differences of technical and financial performances are analysed by comparing five North African railways over the period (1990-2004). A first approach is based on the Malmquist DEA TFP index for measuring the total factors productivity change, decomposed into technical efficiency change and technological changes. A multiple criteria analysis is also performed using the PROMETHEE II method and the software ARGOS. These methods provide complementary detailed information, especially by discriminating the technological and management progresses by Malmquist and the two dimensions of performance by Promethee: that are the service to the community and the enterprises performances, often in conflict.

  16. Integrated genomic classification of melanocytic tumors of the central nervous system using mutation analysis, copy number alterations and DNA methylation profiling.

    Science.gov (United States)

    Griewank, Klaus; Koelsche, Christian; van de Nes, Johannes A P; Schrimpf, Daniel; Gessi, Marco; Möller, Inga; Sucker, Antje; Scolyer, Richard A; Buckland, Michael E; Murali, Rajmohan; Pietsch, Torsten; von Deimling, Andreas; Schadendorf, Dirk

    2018-06-11

    In the central nervous system, distinguishing primary leptomeningeal melanocytic tumors from melanoma metastases and predicting their biological behavior solely using histopathologic criteria can be challenging. We aimed to assess the diagnostic and prognostic value of integrated molecular analysis. Targeted next-generation-sequencing, array-based genome-wide methylation analysis and BAP1 immunohistochemistry was performed on the largest cohort of central nervous system melanocytic tumors analyzed to date, incl. 47 primary tumors of the central nervous system, 16 uveal melanomas. 13 cutaneous melanoma metastasis and 2 blue nevus-like melanomas. Gene mutation, DNA-methylation and copy-number profiles were correlated with clinicopathological features. Combining mutation, copy-number and DNA-methylation profiles clearly distinguished cutaneous melanoma metastases from other melanocytic tumors. Primary leptomeningeal melanocytic tumors, uveal melanomas and blue nevus-like melanoma showed common DNA-methylation, copy-number alteration and gene mutation signatures. Notably, tumors demonstrating chromosome 3 monosomy and BAP1 alterations formed a homogeneous subset within this group. Integrated molecular profiling aids in distinguishing primary from metastatic melanocytic tumors of the central nervous system. Primary leptomeningeal melanocytic tumors, uveal melanoma and blue nevus-like melanoma share molecular similarity with chromosome 3 and BAP1 alterations markers of poor prognosis. Copyright ©2018, American Association for Cancer Research.

  17. The return period analysis of natural disasters with statistical modeling of bivariate joint probability distribution.

    Science.gov (United States)

    Li, Ning; Liu, Xueqin; Xie, Wei; Wu, Jidong; Zhang, Peng

    2013-01-01

    New features of natural disasters have been observed over the last several years. The factors that influence the disasters' formation mechanisms, regularity of occurrence and main characteristics have been revealed to be more complicated and diverse in nature than previously thought. As the uncertainty involved increases, the variables need to be examined further. This article discusses the importance and the shortage of multivariate analysis of natural disasters and presents a method to estimate the joint probability of the return periods and perform a risk analysis. Severe dust storms from 1990 to 2008 in Inner Mongolia were used as a case study to test this new methodology, as they are normal and recurring climatic phenomena on Earth. Based on the 79 investigated events and according to the dust storm definition with bivariate, the joint probability distribution of severe dust storms was established using the observed data of maximum wind speed and duration. The joint return periods of severe dust storms were calculated, and the relevant risk was analyzed according to the joint probability. The copula function is able to simulate severe dust storm disasters accurately. The joint return periods generated are closer to those observed in reality than the univariate return periods and thus have more value in severe dust storm disaster mitigation, strategy making, program design, and improvement of risk management. This research may prove useful in risk-based decision making. The exploration of multivariate analysis methods can also lay the foundation for further applications in natural disaster risk analysis. © 2012 Society for Risk Analysis.

  18. Floods in Serbia in the 1999-2009 period: Hydrological analysis and flood protection measures

    Directory of Open Access Journals (Sweden)

    Milanović Ana

    2010-01-01

    Full Text Available The review on greatest floods recorded in Vojvodina and central Serbia within the period from 1999 to 2009 is given in this paper. For 13 hydrological stations, that recorded the greatest floods for the present period, probability of occurrence of these floods has been accomplished. Based on analysis of time series of discharge and water level maximum, performed by applying probability theory and mathematical statistics, and calculated theoretical probability distribution function of floods, probability of occurrence of flood has been obtained. Most often the best agreement with the empirical distribution function had a Log-Pearson III, Pearson III distribution. These results can be used for dimensioning of hydro-technical objects for flood protection. The most significant causes for floods recorded in this period were melting of snow and intensive rainfall. In this paper the current situation of flood protection and future development of flood protection measures were also presented. .

  19. Study on The Extended Range Weather Forecast of Low Frequency Signal Based on Period Analysis Method

    Science.gov (United States)

    Li, X.

    2016-12-01

    Although many studies have explored the MJO and its application for weather forecasting, low-frequency oscillation has been insufficiently studied for the extend range weather forecasting over middle and high latitudes. In China, low-frequency synoptic map is a useful tool for meteorological operation department to forecast extend range weather. It is therefore necessary to develop objective methods to serve the need for finding low-frequency signal, interpretation and application of this signal in the extend range weather forecasting. In this paper, method of Butterworth band pass filter was applied to get low-frequency height field at 500hPa from 1980 to 2014 by using NCEP/NCAR daily grid data. Then period analysis and optimal subset regression methods were used to process the low frequency data of 150 days before the first forecast day and extend the low frequency signal of 500hPa low-frequency high field to future 30 days in the global from June to August during 2011-2014. Finally, the results were test. The main results are as follows: (1) In general, the fitting effect of low frequency signals of 500hPa low-frequency height field by period analysis in the northern hemisphere was better than that in the southern hemisphere, and was better in the low latitudes than that in the high latitudes. The fitting accuracy gradually reduced with the increase of forecast time length, which tended to be stable during the late forecasting period. (2) The fitting effects over the 6 key regions in China showed that except filtering result over Xinjiang area in the first 10 days and 30 days, filtering results over the other 5 key regions throughout the whole period have passed reliability test with level more than 95%. (3) The center and scope of low and high low frequency systems can be fitted well by using the methods mentioned above, which is consist with the corresponding use of the low-frequency synoptic map for the prediction of the extended period. Application of the

  20. Analysis of the expression level and methylation of tumor protein p53, phosphatase and tensin homolog and mutS homolog 2 in N-methyl-N-nitrosourea-induced thymic lymphoma in C57BL/6 mice.

    Science.gov (United States)

    Huo, Xueyun; Li, Zhenkun; Zhang, Shuangyue; Li, Changlong; Guo, Meng; Lu, Jing; Lv, Jianyi; Du, Xiaoyan; Chen, Zhenwen

    2017-10-01

    Tumorigenesis is often caused by somatic mutation or epigenetic changes in genes that regulate aspects of cell death, proliferation and survival. Although the functions of multiple tumor suppressor genes have been well studied in isolation, how these genes cooperate during the progression of a single tumor remains unclear in numerous cases. The present study used N-methyl-N-nitrosourea (MNU), one of the most potent mutagenic nitrosourea compounds, to induce thymic lymphoma in C57BL/6J mice. Subsequently, the protein expression levels of phosphatase and tensin homolog (PTEN), transformation protein 53 and mutS homolog 2 (MSH2) were evaluated concomitantly in the thymus, liver, kidney and spleen of MNU-treated mice by western blotting. To determine whether changes in expression level were due to aberrant epigenetic regulation, the present study further examined the methylation status of each gene by MassARRAY analysis. During the tumorigenesis process of an MNU-induced single thymic lymphoma, the expression level of PTEN was revealed to be reduced in thymic lymphoma samples but not in normal or non-tumor thymus tissue samples. Furthermore, a marked reduction of P53 expression levels were demonstrated in thymic lymphomas and spleens with a metastatic tumor. Conversely, MSH2 upregulation was identified only in liver, kidney, and spleen samples that were infiltrated by thymic lymphoma cells. Furthermore, the present study revealed that a number of 5'-C-phosphate-G-3' sites located in the promoter of aberrantly expressed genes had significantly altered methylation statuses. These results improve the understanding of the course of mutagen-induced cancer, and highlight that epigenetic regulation may serve an important function in cancer.

  1. Anti-N-Methyl-d-Aspartate receptor (NMDAR encephalitis during pregnancy: Clinical analysis of reported cases

    Directory of Open Access Journals (Sweden)

    Yan-Chao Shi

    2017-06-01

    Conclusions: Clinical analysis of the data indicates that most patients respond to first-line immunotherapy. A second-line immunotherapy is effective when first-line immunotherapy fails. It has also been found that most mothers and newborns can have good outcomes.

  2. Three-layer poly(methyl methacrylate) microsystem for analysis of lysosomal enzymes for diagnostic purposes

    DEFF Research Database (Denmark)

    Kwapiszewski, Radoslaw; Kwapiszewska, Karina; Kutter, Jörg P

    2015-01-01

    by statistical analysis including construction of a Bland-Altman plot. The approach presented can be an alternative for the currently used diagnostic procedures. The method developed has a potential for the implementation into complex microfluidic devices thus becoming a powerful tool for a high...

  3. Structural analysis of acidic oligosaccharides derived from the methylated, acidic polysaccharide associated with coccoliths of Emiliania huxleyi (lohmann) kamptner

    NARCIS (Netherlands)

    Fichtinger-Schepman, A.M.J.; Kamerling, J.P.; Versluis, C.; Vliegenthart, J.F.G.

    1980-01-01

    A series of acidic oligosaccharides was obtained by graded, acid hydrolysis of the methylated, acidic polysaccharide associated with the coccoliths of the alga Emiliania huxleyi (Lohmann) Kamptner. After fractionation by ion-exchange chromatography, the structures of the oligosaccharides were

  4. Changes in adiposity levels in schoolchildren according to nutritional status: analysis over a 30-year period

    Directory of Open Access Journals (Sweden)

    Gerson Luis de Moraes Ferrari

    2013-05-01

    Full Text Available The aim of this study was to analyze changes in adiposity levels over a 30-year period in schoolchildren according to nutritional status. This study is part of Projeto Misto Longitudinal de Crescimento, Desenvolvimento e Aptidão Física de Ilhabela. 1.144 schoolchildren of both sexes, aged between 10 and 11 years, met the following inclusion criteria: (a have at least one complete evaluation in one of the analyzed periods; (b be in the prepubertal stage of sexual maturation;and (c be apparently healthy. Analyzed periods were 1978/1980 (Baseline,1988/1990 (10 years, 1998/2000 (20 years, 2008/2010 (30 years. Analyzed variables were: body mass (kg, height (cm and adiposity levels (mm. Children were classified into three categories: eutrophic, overweight and obese, according to nutritional status, using World Health Organization (WHO body mass index (BMI curves for age and sex. For a comparison between periods, Two-Factor Analysis of Variance and Bonferroni’s test were used. In both sexes, the most significant increase in adiposity levels occurred among the eutrophic group, followed by the overweight group and obese group. Results showed an increase in adiposity levels over a 30-year period, even with nutritional status control. It shows that individuals with a similar BMI may vary in proportion and distribution of subcutaneous adipose tissue.

  5. Changes in adiposity levels in schoolchildren according to nutritional status: analysis over a 30-year period

    Directory of Open Access Journals (Sweden)

    Gerson Luis de Moraes Ferrari

    2013-04-01

    Full Text Available DOI: http://dx.doi.org/10.5007/1980-0037.2013v15n4p405 The aim of this study was to analyze changes in adiposity levels over a 30-year period in schoolchildren according to nutritional status. This study is part of Projeto Misto Longitudinal de Crescimento, Desenvolvimento e Aptidão Física de Ilhabela. 1.144 schoolchildren of both sexes, aged between 10 and 11 years, met the following inclusion criteria: (a have at least one complete evaluation in one of the analyzed periods; (b be in the prepubertal stage of sexual maturation;and (c be apparently healthy. Analyzed periods were 1978/1980 (Baseline,1988/1990 (10 years, 1998/2000 (20 years, 2008/2010 (30 years. Analyzed variables were: body mass (kg, height (cm and adiposity levels (mm. Children were classified into three categories: eutrophic, overweight and obese, according to nutritional status, using World Health Organization (WHO body mass index (BMI curves for age and sex. For a comparison between periods, Two-Factor Analysis of Variance and Bonferroni’s test were used. In both sexes, the most significant increase in adiposity levels occurred among the eutrophic group, followed by the overweight group and obese group. Results showed an increase in adiposity levels over a 30-year period, even with nutritional status control. It shows that individuals with a similar BMI may vary in proportion and distribution of subcutaneous adipose tissue.

  6. Stress-strain state analysis and optimization of rod system under periodic pulse load

    Directory of Open Access Journals (Sweden)

    Grebenyuk Grigory

    2018-01-01

    Full Text Available The paper considers the problem of analysis and optimization of rod systems subjected to combined static and periodic pulse load. As a result of the study the analysis method was developed based on traditional approach to solving homogeneous matrix equations of state and a special algorithm for developing a particular solution. The influence of pulse parameters variations on stress-strain state of a rod system was analyzed. Algorithms for rod systems optimization were developed basing on strength recalculation and statement and solution of optimization problem as a problem of nonlinear mathematical programming. Recommendations are developed for efficient organization of process for optimization of rod systems under static and periodic pulse load.

  7. Model-based analysis of CO2 revalorization for di-methyl ether synthesis driven by solar catalytic reforming

    International Nuclear Information System (INIS)

    Luu, Minh Tri; Milani, Dia; Sharma, Manish; Zeaiter, Joseph; Abbas, Ali

    2016-01-01

    Highlights: • Solar energy applied for synthesis of di-methyl ether via dry methane reforming. • Concentrated solar energy at receiver reaction zone for syngas generation. • H 2 /CO molar ratio of ‘1’ is maintained via two alternative processing routes. • Assessed three days of operation under different insolation levels. • Improvements of 18.7%, 32.2% and 20% for methane, energy and CO 2 emission intensities. - Abstract: The application of solar energy is investigated for the synthesis of di-methyl ether (DME) in a solar irradiated dry methane reformer (DMR). Solar radiations are concentrated onto a receiver and distributed to the reaction zone to provide necessary energy for syngas (CO and H 2 ) generation. In order to maintain a H 2 /CO molar ratio of ‘1’, as required in DME synthesis, the produced syngas is processed via two alternative routes: solar reformer coupled in parallel with a non-solar reformer (SoR-NSoR) and solar reformer integrated with a water-gas shift reactor (SoR-WGS). It is found that steam methane reforming (SMR) is the most suitable methodology when coupled with a solar reformer due to high H 2 content in the SMR syngas. Further performance analysis is conducted by simulating three days of operation under different insolation levels (high, medium and low irradiations). The simulation results showed that the SoR-WGS configuration produces the highest improvements of 18.7%, 32.2% and 20% in terms of methane, energy and CO 2 emission intensity respectively. This enhanced process performance originates from the exothermic nature of the WGS process which helps in controlling the overall syngas composition, whereas the SoR-NSoR requires fossil based thermal energy to drive the NSoR process to similar control targets. This promising improvement of all metrics in SoR-WGS may stimulate in-depth techno-economic feasibility of this unique solar integration for DME and other synthetic fuels production.

  8. Kinetic Analysis of Hexose Conversion to Methyl Lactate by Sn Beta: Effects of Substrate Masking and of Water

    DEFF Research Database (Denmark)

    Tosi, Irene; Riisager, Anders; Taarning, Esben

    2018-01-01

    Simple sugars bear promise as substrates for the formation of fuels and chemicals using heterogeneous catalysts in alcoholic solvents. Sn-Beta is a particularly well suited catalyst for the cleavage, isomerization and dehydration of sugars into more valuable chemicals. In order to understand....... This release is the rate limiting step in the Sn-Beta catalysed methyl lactate process, but can be accelerated by the addition of small amounts of water at the expense of maximum methyl lactate yield....

  9. Genome-wide analysis of DNA methylation differences in muscle and fat from monozygotic twins discordant for type 2 diabetes

    DEFF Research Database (Denmark)

    Ribel-Madsen, Rasmus; Fraga, Mario F; Jacobsen, Stine

    2012-01-01

    Monozygotic twins discordant for type 2 diabetes constitute an ideal model to study environmental contributions to type 2 diabetic traits. We aimed to examine whether global DNA methylation differences exist in major glucose metabolic tissues from these twins.......Monozygotic twins discordant for type 2 diabetes constitute an ideal model to study environmental contributions to type 2 diabetic traits. We aimed to examine whether global DNA methylation differences exist in major glucose metabolic tissues from these twins....

  10. Epigenome-wide analysis links SMAD3 methylation at birth to asthma in children of asthmatic mothers.

    Science.gov (United States)

    DeVries, Avery; Wlasiuk, Gabriela; Miller, Susan J; Bosco, Anthony; Stern, Debra A; Lohman, I Carla; Rothers, Janet; Jones, Anya C; Nicodemus-Johnson, Jessie; Vasquez, Monica M; Curtin, John A; Simpson, Angela; Custovic, Adnan; Jackson, Daniel J; Gern, James E; Lemanske, Robert F; Guerra, Stefano; Wright, Anne L; Ober, Carole; Halonen, Marilyn; Vercelli, Donata

    2017-08-01

    The timing and mechanisms of asthma inception remain imprecisely defined. Although epigenetic mechanisms likely contribute to asthma pathogenesis, little is known about their role in asthma inception. We sought to assess whether the trajectory to asthma begins already at birth and whether epigenetic mechanisms, specifically DNA methylation, contribute to asthma inception. We used the Methylated CpG Island Recovery Assay chip to survey DNA methylation in cord blood mononuclear cells from 36 children (18 nonasthmatic and 18 asthmatic subjects by age 9 years) from the Infant Immune Study (IIS), an unselected birth cohort closely monitored for asthma for a decade. SMAD3 methylation in IIS (n = 60) and in 2 replication cohorts (the Manchester Asthma and Allergy Study [n = 30] and the Childhood Origins of Asthma Study [n = 28]) was analyzed by using bisulfite sequencing or Illumina 450K arrays. Cord blood mononuclear cell-derived IL-1β levels were measured by means of ELISA. Neonatal immune cells harbored 589 differentially methylated regions that distinguished IIS children who did and did not have asthma by age 9 years. In all 3 cohorts methylation in SMAD3, the most connected node within the network of asthma-associated, differentially methylated regions, was selectively increased in asthmatic children of asthmatic mothers and was associated with childhood asthma risk. Moreover, SMAD3 methylation in IIS neonates with maternal asthma was strongly and positively associated with neonatal production of IL-1β, an innate inflammatory mediator. The trajectory to childhood asthma begins at birth and involves epigenetic modifications in immunoregulatory and proinflammatory pathways. Maternal asthma influences epigenetic mechanisms that contribute to the inception of this trajectory. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  11. Chromatographic efficiency of polar capillary columns applied for the analysis of fatty acid methyl esters by gas chromatography.

    Science.gov (United States)

    Waktola, Habtewold D; Mjøs, Svein A

    2018-04-01

    The chromatographic efficiency that could be achieved in temperature-programmed gas chromatography was compared for four capillary columns that are typically applied for analysis of fatty acid methyl esters (FAME). Three different carrier gases, hydrogen, helium and nitrogen, were applied. For each experiment, the carrier gas velocities and the temperature rates were varied with a full 9 × 3 design, with nine levels on the carrier gas velocity and temperature rates of 1, 2 or 3°C/min. Response surface methodology was used to create models of chromatographic efficiency as a function of temperature rate and carrier gas velocity. The chromatographic efficiency was defined as the inverse of peak widths measured in retention index units. The final results were standardized so that the efficiencies that could be achieved within a certain time frame, defined by the retention time of the last compound in the chromatogram, could be compared. The results show that there were clear differences in the efficiencies that could be achieved with the different columns and that the efficiency decreased with increasing polarity of the stationary phase. The differences can be explained by higher resistance to mass transfer in the stationary phase in the most polar columns. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1.

    Science.gov (United States)

    Kane, Staci R; Chakicherla, Anu Y; Chain, Patrick S G; Schmidt, Radomir; Shin, Maria W; Legler, Tina C; Scow, Kate M; Larimer, Frank W; Lucas, Susan M; Richardson, Paul M; Hristova, Krassimira R

    2007-03-01

    Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C(5) to C(12)) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an approximately 4-Mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (approximately 99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.

  13. ToF-SIMS analysis of poly(L-lysine)-graft-poly(2-methyl-2-oxazoline) ultrathin adlayers.

    Science.gov (United States)

    Pidhatika, Bidhari; Chen, Yin; Coullerez, Geraldine; Al-Bataineh, Sameer; Textor, Marcus

    2014-02-01

    Understanding of the interfacial chemistry of ultrathin polymeric adlayers is fundamentally important in the context of establishing quantitative design rules for the fabrication of nonfouling surfaces in various applications such as biomaterials and medical devices. In this study, seven poly(L-lysine)-graft-poly(2-methyl-2-oxazoline) (PLL-PMOXA) copolymers with grafting density (number of PMOXA chains per lysine residue) 0.09, 0.14, 0.19, 0.33, 0.43, 0.56, and 0.77, respectively, were synthesized and characterized by means of nuclear magnetic resonance spectroscopy (NMR). The copolymers were then adsorbed on Nb2O5 surfaces. Optical waveguide lightmode spectroscopy method was used to monitor the surface adsorption in situ of these copolymers and provide information on adlayer masses that were then converted into PLL and PMOXA surface densities. To investigate the relationship between copolymer bulk architecture (as shown by NMR data) and surface coverage as well as surface architecture, time-of-flight secondary ion mass spectrometry (ToF-SIMS) analysis was performed. Furthermore, ToF-SIMS method combined with principal component analysis (PCA) was used to verify the protein resistant properties of PLL-PMOXA adlayers, by thorough characterization before and after adlayer exposure to human serum. ToF-SIMS analysis revealed that the chemical composition as well as the architecture of the different PLL-PMOXA adlayers indeed reflects the copolymer bulk composition. ToF-SIMS results also indicated a heterogeneous surface coverage of PLL-PMOXA adlayers with high grafting densities higher than 0.33. In the case of protein resistant surface, PCA results showed clear differences between protein resistant and nonprotein-resistant surfaces. Therefore, ToF-SIMS results combined with PCA confirmed that the PLL-PMOXA adlayer with brush architecture resists protein adsorption. However, low increases of some amino acid signals in ToF-SIMS spectra were detected after the adlayer has

  14. Age-period-cohort analysis of suicides among Japanese 1950-2003: a Bayesian cohort model analysis.

    Science.gov (United States)

    Ooe, Yosuke; Ohno, Yuko; Nakamura, Takashi

    2009-07-01

    The suicide rate in Japan is one of the highest in the world and presents us with a considerable challenge. Demographic statistics show that the number of suicides is on the rise, and at roughly 30,000 people per year have committed suicide since 1998. Suicide trends are not only related to economic boom and bust but also to certain generations and age groups. During the 1950s, there was a remarkably high suicide rate among people in their 20s, and this cohort was identical to that of the middle-age generation in the 1980s. It is important to separately understand both the trend of suicide rates and the numbers analyzed to determine the different factors that influence suicide. These include age, time period, cohort, interaction between age and time period, and changes in population composition. We performed an age-period-cohort analysis of annual trends of suicide rates by age group in Japan using a Bayesian cohort model. With the help of the Nakamura method, we have been able to break down the effects of age, time period, cohort, and the age-by-period interaction. The cohort comprised of people born in the 1930s demonstrated a relatively high suicide rate. Men currently in their 50s also belong to a high suicide rate cohort. Regarding the period effect, business cycles and by-period interaction effect, it became apparent that the high suicide rate among young adults in their early 20s around 1960 was slowing, especially among men. Instead, there was an obvious recent trend for men in their late 50s to have the highest suicide rate. This study confirmed that age-period-cohort analysis can describe these trends of suicide mortality of the Japanese.

  15. Periodicity Analysis of X-ray Light Curves of SS 433

    Science.gov (United States)

    Wang, Jun-yi; Lu, Xiang-long; Zhao, Qiu-wen; Dong, Dian-qiao; Lao, Bao-qiang; Lu, Yang; Wei, Yan-heng; Wu, Xiao-cong; An, Tao

    2017-01-01

    SS 433 is sofar the unique X-ray binary that has the simultaneously detected orbital period, super-orbital period, and nutation period, as well as a bidirectional spiral jet. The study on its X-ray light variability is helpful for understanding the dynamic process of the system, and the correlations between the different wavebands. In this paper, two time-series analysis techniques, i.e., the Lomb-Scargle periodogram and weighted wavelet Z-transform, are employed to search for the periods in the Swift/BAT (Burst Alert Telescope) (15-50 keV) and RXTE/ASM (Rose X-ray Timing Explorer/All Sky Monitor) (1.5-3, 3- 4, and 5-12 keV) light curves of SS 433, and the Monte Carlo simulation is performed for the obtained periodical components. For the 15-50 keV energy band, five significant periodical components are detected, which are P1(∼6.29 d), P2 (∼6.54 d), P3 (∼13.08 d), P4 (∼81.50 d), and P5 (∼162.30 d). For the 3-5 and 5-12 keV energy bands, the periodical components P3 (∼13 d) and P5 (∼162 d) are detected in both energy bands. However, for the 1.5-3 keV energy band, no significant periodic signal is detected. P5 is the strongest periodic signal in the power spectrum for all the energy bands of 3-5, 5-12, and 15-50 keV, and it is consistent with the previous result obtained from the study of optical light curves. Furthermore, in combination with the radio spiral jet of SS 433, it is suggested that the X-ray and optical variability of P5 (∼162 d) is probably related to the precession of its relativistic jet. The high correlation between the X-ray and optical light curves may also imply that the X-ray and optical radiations are of the same physical origin. P3 shows a good agreement with the orbital period (∼13.07 d) obtained by the previous study, and P2 and P4 are respectively the high-frequency harmonics of P3 and P5. P1 is detected only in the power spectrum of the 15-50 keV energy band, and it is consistent with the nutation period of the system. As

  16. Genome-Wide Analysis of DNA Methylation and Fine Particulate Matter Air Pollution in Three Study Populations: KORA F3, KORA F4, and the Normative Aging Study.

    Science.gov (United States)

    Panni, Tommaso; Mehta, Amar J; Schwartz, Joel D; Baccarelli, Andrea A; Just, Allan C; Wolf, Kathrin; Wahl, Simone; Cyrys, Josef; Kunze, Sonja; Strauch, Konstantin; Waldenberger, Melanie; Peters, Annette

    2016-07-01

    Epidemiological studies have reported associations between particulate matter (PM) concentrations and cancer and respiratory and cardiovascular diseases. DNA methylation has been identified as a possible link but so far it has only been analyzed in candidate sites. We studied the association between DNA methylation and short- and mid-term air pollution exposure using genome-wide data and identified potential biological pathways for additional investigation. We collected whole blood samples from three independent studies-KORA F3 (2004-2005) and F4 (2006-2008) in Germany, and the Normative Aging Study (1999-2007) in the United States-and measured genome-wide DNA methylation proportions with the Illumina 450k BeadChip. PM concentration was measured daily at fixed monitoring stations and three different trailing averages were considered and regressed against DNA methylation: 2-day, 7-day and 28-day. Meta-analysis was performed to pool the study-specific results. Random-effect meta-analysis revealed 12 CpG (cytosine-guanine dinucleotide) sites as associated with PM concentration (1 for 2-day average, 1 for 7-day, and 10 for 28-day) at a genome-wide Bonferroni significance level (p ≤ 7.5E-8); 9 out of these 12 sites expressed increased methylation. Through estimation of I2 for homogeneity assessment across the studies, 4 of these sites (annotated in NSMAF, C1orf212, MSGN1, NXN) showed p > 0.05 and I2 F4, and the Normative Aging Study. Environ Health Perspect 124:983-990; http://dx.doi.org/10.1289/ehp.1509966.

  17. A novel methylation derivatization method for δ(18)O analysis of individual carbohydrates by gas chromatography/pyrolysis-isotope ratio mass spectrometry.

    Science.gov (United States)

    Lehmann, Marco M; Fischer, Maria; Blees, Jan; Zech, Michael; Siegwolf, Rolf T W; Saurer, Matthias

    2016-01-15

    The oxygen isotope ratio (δ(18)O) of carbohydrates derived from animals, plants, sediments, and soils provides important information about biochemical and physiological processes, past environmental conditions, and geographical origins, which are otherwise not available. Nowadays, δ(18)O analyses are often performed on carbohydrate bulk material, while compound-specific δ(18)O analyses remain challenging and methods for a wide range of individual carbohydrates are rare. To improve the δ(18)O analysis of individual carbohydrates by gas chromatography/pyrolysis-isotope ratio mass spectrometry (GC/Pyr-IRMS) we developed a new methylation derivatization method. Carbohydrates were fully methylated within 24 h in an easy-to-handle one-pot reaction in acetonitrile, using silver oxide as proton acceptor, methyl iodide as methyl group carrier, and dimethyl sulfide as catalyst. The precision of the method ranged between 0.12 and 1.09‰ for the δ(18)O values of various individual carbohydrates of different classes (mono-, di-, and trisaccharides, alditols), with an accuracy of a similar order of magnitude, despite high variation in peak areas. Based on the δ(18)O values of the main isomers, important monosaccharides such as glucose and fructose could also be precisely analyzed for the first time. We tested the method on standard mixtures, honey samples, and leaf carbohydrates extracted from Pinus sylvestris, showing that the method is also applicable to different carbohydrate mixtures. The new methylation method shows unrivalled accuracy and precision for δ(18)O analysis of various individual carbohydrates; it is fast and easy-to-handle, and may therefore find wide-spread application. Copyright © 2015 John Wiley & Sons, Ltd.

  18. Analysis of annealed thin polymer films prepared from dichloro(methyl)phenylsilane by plasma polymerization

    Czech Academy of Sciences Publication Activity Database

    Cech, V.; Horvath, P.; Trchová, M.; Zemek, Josef; Matějková, Jiřina

    2001-01-01

    Roč. 82, - (2001), s. 2106-2112 ISSN 0021-8995 R&D Projects: GA ČR GV106/98/K013; GA ČR GA104/00/0708 Institutional research plan: CEZ:AV0Z1010914 Keywords : plasma polymerization * thin films * thermogravimetric analysis ( TSA ) * FTIR * ESCA/XPS Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.992, year: 2001

  19. [Analysis of tissue-specific differentially methylated genes with differential gene expression in non-small cell lung cancer].

    Science.gov (United States)

    Yin, L G; Zou, Z Q; Zhao, H Y; Zhang, C L; Shen, J G; Qi, L; Qi, M; Xue, Z Q

    2014-01-01

    Adenocarcinoma (ADC) and squamous cell carcinomas (SCC) are two subtypes of non-small cell lung carcinomas which are regarded as the leading cause of cancer-related malignancy worldwide. The aim of this study is to detect the differentially methylated loci (DMLs) and differentially methylated genes (DMGs) of these two tumor sets, and then to illustrate the different expression level of specific methylated genes. Using TCGA database and Illumina HumanMethylation 27 arrays, we first screened the DMGs and DMLs in tumor samples. Then, we explored the BiologicalProcess terms of hypermethylated and hypomethylated genes using Functional Gene Ontology (GO) catalogues. Hypermethylation intensively occurred in CpG-island, whereas hypomethylation was located in non-CpG-island. Most SCC and ADC hypermethylated genes involved GO function of DNA dependenit regulation of transcription, and hypomethylated genes mainly 'enriched in the term of immune responses. Additionally, the expression level of specific differentially methylated genesis distinctbetween ADC and SCC. It is concluded that ADC and SCC have different methylated status that might play an important role in carcinogenesis.

  20. Analysis of the ecological parameters of the diesel engine powered with biodiesel fuel containing methyl esters from Camelina sativa oil

    Directory of Open Access Journals (Sweden)

    S. Lebedevas

    2010-03-01

    Full Text Available The article explores the possibilities of using fatty acid methyl esters derived from the oil of a new species of oily plant Camelina sativa not demanding on soil. The performed research on the physical and chemical properties of pure methyl esters from Camelina sativa show that biofuels do not meet requirements for the biodiesel fuel standard (LST EN 14214:2009 of a high iodine value and high content of linoleic acid methyl ester, so they must be mixed with methyl esters produced from pork lard the content of which in the mixture must be not less than 32%. This article presents the results of tests on combustion emission obtained when three-cylinder diesel engine VALMET 320 DMG was fuelled with a mixture containing 30% of this new kind of fuel with fossil diesel fuel comparing with emissions obtained when the engine was fuelled with a fuel mixture containing 30% of conventional biodiesel fuel (rapeseed oil methyl esters with fossil diesel fuel. The obtained results show that using both types of fuel, no significant differences in CO and NOx concentrations were observed throughout the tested load range. When operating on fuels containing methyl esters from Camelina sativa, HC emissions decreased by 10 to 12% and the smokeness of exhaust gas by 12 to 25%.

  1. Analysis of Nonlinear Periodic and Aperiodic Media: Application to Optical Logic Gates

    Science.gov (United States)

    Yu, Yisheng

    This dissertation is about the analysis of nonlinear periodic and aperiodic media and their application to the design of intensity controlled all optical logic gates: AND, OR, and NOT. A coupled nonlinear differential equation that characterizes the electromagnetic wave propagation in a nonlinear periodic (and aperiodic) medium has been derived from the first principle. The equations are general enough that it reflects the effect of transverse modal fields and can be used to analyze both co-propagating and counter propagating waves. A numerical technique based on the finite differences method and absorbing boundary condition has been developed to solve the coupled differential equations here. The numerical method is simple and accurate. Unlike the method based on characteristics that has been reported in the literature, this method does not involve integration and step sizes of time and space coordinates are decoupled. The decoupling provides independent choice for time and space step sizes. The concept of "gap soliton" has also been re-examined. The dissertation consists of four manuscripts. Manuscript I reports on the design of all optical logic gates: AND, OR, and NOT based on the bistability property of nonlinear periodic and aperiodic waveguiding structures. The functioning of the logic gates has been shown by analysis. The numerical technique that has been developed to solve the nonlinear differential equations are addressed in manuscript II. The effect of transverse modal fields on the bistable property of nonlinear periodic medium is reported in manuscript III. The concept of "gap soliton" that are generated in a nonlinear periodic medium has been re-examined. The details on the finding of the re-examination are discussed in manuscript IV.

  2. Analysis of electromagnetic scattering by nearly periodic structures: an LDRD report.

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, William Arthur; Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Wilton, Donald R. (University of Houston, Houston, TX); Basilio, Lorena I.; Peters, David William; Capolino, F. (University of Houston, Houston, TX)

    2006-10-01

    In this LDRD we examine techniques to analyze the electromagnetic scattering from structures that are nearly periodic. Nearly periodic could mean that one of the structure's unit cells is different from all the others--a defect. It could also mean that the structure is truncated, or butted up against another periodic structure to form a seam. Straightforward electromagnetic analysis of these nearly periodic structures requires us to grid the entire structure, which would overwhelm today's computers and the computers in the foreseeable future. In this report we will examine various approximations that allow us to continue to exploit some aspects of the structure's periodicity and thereby reduce the number of unknowns required for analysis. We will use the Green's Function Interpolation with a Fast Fourier Transform (GIFFT) to examine isolated defects both in the form of a source dipole over a meta-material slab and as a rotated dipole in a finite array of dipoles. We will look at the numerically exact solution of a one-dimensional seam. In order to solve a two-dimensional seam, we formulate an efficient way to calculate the Green's function of a 1d array of point sources. We next formulate ways of calculating the far-field due to a seam and due to array truncation based on both array theory and high-frequency asymptotic methods. We compare the high-frequency and GIFFT results. Finally, we use GIFFT to solve a simple, two-dimensional seam problem.

  3. Biodegradation of methyl red by Bacillus sp. strain UN2: decolorization capacity, metabolites characterization, and enzyme analysis.

    Science.gov (United States)

    Zhao, Ming; Sun, Peng-Fei; Du, Lin-Na; Wang, Guan; Jia, Xiao-Ming; Zhao, Yu-Hua

    2014-05-01

    Azo dyes are recalcitrant and refractory pollutants that constitute a significant menace to the environment. The present study is focused on exploring the capability of Bacillus sp. strain UN2 for application in methyl red (MR) degradation. Effects of physicochemical parameters (pH of medium, temperature, initial concentration of dye, and composition of the medium) were studied in detail. The suitable pH and temperature range for MR degradation by strain UN2 were respectively 7.0-9.0 and 30-40 °C, and the optimal pH value and temperature were respectively 8.0 and 35 °C. Mg(2+) and Mn(2+) (1 mM) were found to significantly accelerate the MR removal rate, while the enhancement by either Fe(3+) or Fe(2+) was slight. Under the optimal degradation conditions, strain UN2 exhibited greater than 98 % degradation of the toxic azo dye MR (100 ppm) within 30 min. Analysis of samples from decolorized culture flasks confirmed biodegradation of MR into two prime metabolites: N,N'dimethyl-p-phenyle-nediamine and 2-aminobenzoic acid. A study of the enzymes responsible for the biodegradation of MR, in the control and cells obtained during (10 min) and after (30 min) degradation, showed a significant increase in the activities of azoreductase, laccase, and NADH-DCIP reductase. Furthermore, a phytotoxicity analysis demonstrated that the germination inhibition was almost eliminated for both the plants Triticum aestivum and Sorghum bicolor by MR metabolites at 100 mg/L concentration, yet the germination inhibition of parent dye was significant. Consequently, the high efficiency of MR degradation enables this strain to be a potential candidate for bioremediation of wastewater containing MR.

  4. Utility of 2-Pyridine Aldoxime Methyl Chloride (2-PAM) for Acute Organophosphate Poisoning: A Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Blumenberg, Adam; Benabbas, Roshanak; deSouza, Ian S; Conigliaro, Alyssa; Paladino, Lorenzo; Warman, Elliot; Sinert, Richard; Wiener, Sage W

    2018-03-01

    Organophosphates (OP) account for the majority of pesticide-related unintentional or intentional poisonings in lower- and middle-income countries. The therapeutic role of atropine is well-established for patients with acute OP poisoning. The benefit of adding 2-pyridine aldoxime methyl chloride (2-PAM), however, is controversial. We performed a systematic review and meta-analysis of available randomized controlled trials (RCT) to compare 2-PAM plus atropine in comparison to atropine alone for acute OP poisoning. We searched PubMed, EMBASE, and SCOPUS up to March 2017. The Cochrane review handbook was used to assess the risk of bias. Data were abstracted and risk ratios (RR) were calculated for mortality, rate of intubation, duration of intubation, intermediate syndrome, and complications such as hospital-acquired infections, dysrhythmias, and pulmonary edema. We found five studies comprising 586 patients with varying risks of bias. The risk of death (RR = 1.5, 95% CI 0.9-2.5); intubation (RR = 1.3, 95% CI 1.0-1.6); intermediate syndrome (RR = 1.6, 95% CI 1.0-2.6); complications (RR = 1.2, 95% CI 0.8-1.8); and the duration of intubation (mean difference 0.0, 95% CI - 1.6-1.6) were not significantly different between the atropine plus 2-PAM and atropine alone. Based on our meta-analysis of the available RCTs, 2-PAM was not shown to improve outcomes in patients with acute OP poisoning.

  5. Application of the Periodic Average System Model in Dam Deformation Analysis

    Directory of Open Access Journals (Sweden)

    Yueqian Shen

    2015-01-01

    Full Text Available Dams are among the most important hydraulic engineering facilities used for water supply, flood control, and hydroelectric power. Monitoring of dams is crucial since deformation might have occurred. How to obtain the deformation information and then judge the safe conditions is the key and difficult problem in dam deformation monitoring field. This paper proposes the periodic average system model and creates the concept of “settlement activity” based on the dam deformation issue. Long-term deformation monitoring data is carried out in a pumped-storage power station, this model combined with settlement activity is used to make the single point deformation analysis, and then the whole settlement activity profile is drawn by clustering analysis. Considering the cumulative settlement value of every point, the dam deformation trend is analyzed in an intuitive effect way. The analysis mode of combined single point with multipoints is realized. The results show that the key deformation information of the dam can be easily grasped by the application of the periodic average system model combined with the distribution diagram of settlement activity. And, above all, the ideas of this research provide an effective method for dam deformation analysis.

  6. Molecular characterization of HOXC8 gene and methylation status analysis of its exon 1 associated with the length of cashmere fiber in Liaoning cashmere goat.

    Science.gov (United States)

    Bai, Wen L; Wang, Jiao J; Yin, Rong H; Dang, Yun L; Wang, Ze Y; Zhu, Yu B; Cong, Yu Y; Deng, Liang; Guo, Dan; Wang, Shi Q; Yang, Shu H; Xue, Hui L

    2017-02-01

    Homeobox protein Hox-C8 (HOXC8) is a member of Hox family. It is expressed in the dermal papilla of the skin and is thought to be associated with the hair inductive capacity of dermal papilla cells. In the present study, we isolated and characterized a full-length open reading frame of HOXC8 cDNA from the skin tissue of Liaoning cashmere goat, as well as, established a phylogenetic relationship of goat HOXC8 with that of other species. Also, we investigated the effect of methylation status of HOXC8 exon 1 at anagen secondary hair follicle on the cashmere fiber traits in Liaoning cashmere goat. The sequence analysis indicated that the obtained cDNA was 1134-bp in length containing a complete ORF of 729-bp. It encoded a peptide of 242 amino acid residues in length. The structural analysis indicated that goat HOXC8 contained a typical homeobox domain. The phylogenetic analysis revealed that Capra hircus HOXC8 had a closer genetic relationship with that of Ovis aries, followed by Bos Taurus and Bubalus bubalis. The methylation analysis suggested that the methylation degree of HOXC8 exon 1 in anagen secondary hair follicle might be involved in regulating the growth of cashmere fiber in Liaoning cashmere goat. Our results provide new evidence for understanding the molecular structural and evolutionary characteristics of HOXC8 in Liaoning cashmere goat, as well as, for further insight into the role of methylation degree of HOXC8 exon 1 regulates the growth of cashmere fiber in goat.

  7. QSAR Analysis of 2-Amino or 2-Methyl-1-Substituted Benzimidazoles Against Pseudomonas aeruginosa

    Science.gov (United States)

    Podunavac-Kuzmanović, Sanja O.; Cvetković, Dragoljub D.; Barna, Dijana J.

    2009-01-01

    A set of benzimidazole derivatives were tested for their inhibitory activities against the Gram-negative bacterium Pseudomonas aeruginosa and minimum inhibitory concentrations were determined for all the compounds. Quantitative structure activity relationship (QSAR) analysis was applied to fourteen of the abovementioned derivatives using a combination of various physicochemical, steric, electronic, and structural molecular descriptors. A multiple linear regression (MLR) procedure was used to model the relationships between molecular descriptors and the antibacterial activity of the benzimidazole derivatives. The stepwise regression method was used to derive the most significant models as a calibration model for predicting the inhibitory activity of this class of molecules. The best QSAR models were further validated by a leave one out technique as well as by the calculation of statistical parameters for the established theoretical models. To confirm the predictive power of the models, an external set of molecules was used. High agreement between experimental and predicted inhibitory values, obtained in the validation procedure, indicated the good quality of the derived QSAR models. PMID:19468332

  8. Semiclassical analysis of long-wavelength multiphoton processes: The periodically driven harmonic oscillator

    International Nuclear Information System (INIS)

    Fox, Ronald F.; Vela-Arevalo, Luz V.

    2002-01-01

    The problem of multiphoton processes for intense, long-wavelength irradiation of atomic and molecular electrons is presented. The recently developed method of quasiadiabatic time evolution is used to obtain a nonperturbative analysis. When applied to the standard vector potential coupling, an exact auxiliary equation is obtained that is in the electric dipole coupling form. This is achieved through application of the Goeppert-Mayer gauge. While the analysis to this point is general and aimed at microwave irradiation of Rydberg atoms, a Floquet analysis of the auxiliary equation is presented for the special case of the periodically driven harmonic oscillator. Closed form expressions for a complete set of Floquet states are obtained. These are used to demonstrate that for the oscillator case there are no multiphoton resonances

  9. Corrective shoeing in horses: analysis of the adaptation period to the new condition imposed

    Directory of Open Access Journals (Sweden)

    Raquel M. Albernaz

    2012-10-01

    Full Text Available Corrective shoeing is a method commonly used to alter the locomotion pattern in animals or as therapy for various disorders of the locomotive system of horses. However, to date, there have been no scientific studies discussing the period during which animals adapt to this type of intervention. The goal of this study was to evaluate the horseshoe adaptation period with the toe or heel elevated by six degrees at 0, 48, and 96 hours after each type of shoeing. For this analysis, the horses were recorded while walking on a treadmill. Stride length and gait qualitative analyzes were performed using Dvideow software. The level of significance adopted was 5%. In the present study, there was no significant difference between the evaluation times; elevating the toe or heel by six degrees do not generates discomfort during locomotion, therefore, horses are able to return to a regular exercise or training routine immediately after shoeing.

  10. Canonical integration and analysis of periodic maps using non-standard analysis and life methods

    Energy Technology Data Exchange (ETDEWEB)

    Forest, E.; Berz, M.

    1988-06-01

    We describe a method and a way of thinking which is ideally suited for the study of systems represented by canonical integrators. Starting with the continuous description provided by the Hamiltonians, we replace it by a succession of preferably canonical maps. The power series representation of these maps can be extracted with a computer implementation of the tools of Non-Standard Analysis and analyzed by the same tools. For a nearly integrable system, we can define a Floquet ring in a way consistent with our needs. Using the finite time maps, the Floquet ring is defined only at the locations s/sub i/ where one perturbs or observes the phase space. At most the total number of locations is equal to the total number of steps of our integrator. We can also produce pseudo-Hamiltonians which describe the motion induced by these maps. 15 refs., 1 fig.

  11. Age-period-cohort analysis of tuberculosis notifications in Hong Kong from 1961 to 2005.

    Science.gov (United States)

    Wu, P; Cowling, B J; Schooling, C M; Wong, I O L; Johnston, J M; Leung, C-C; Tam, C-M; Leung, G M

    2008-04-01

    Despite its wealth, excellent vital indices and robust health care infrastructure, Hong Kong has a relatively high incidence of tuberculosis (TB) (85.4 per 100 000). Hong Kong residents have also experienced a very rapid and recent epidemiological transition; the population largely originated from migration by southern Chinese in the mid 20th century. Given the potentially long latency period of TB infection, an investigation was undertaken to determine the extent to which TB incidence rates reflect the population history and the impact of public health interventions. An age-period-cohort model was used to break down the Hong Kong TB notification rates from 1961 to 2005 into the effects of age, calendar period and birth cohort. Analysis by age showed a consistent pattern across all the cohorts by year of birth, with a peak in the relative risk of TB at 20-24 years of age. Analysis by year of birth showed an increase in the relative risk of TB from 1880 to 1900, stable risk until 1910, then a linear rate of decline from 1910 with an inflection point at 1990 for a steeper rate of decline. Period effects yielded only one inflection during the calendar years 1971-5. Economic development, social change and the World Health Organisation's short-course directly observed therapy (DOTS) strategy have contributed to TB control in Hong Kong. The linear cohort effect until 1990 suggests that a relatively high, but slowly falling, incidence of TB in Hong Kong will continue into the next few decades.

  12. Temporal diagnostic analysis of the SWAT model to detect dominant periods of poor model performance

    Science.gov (United States)

    Guse, Björn; Reusser, Dominik E.; Fohrer, Nicola

    2013-04-01

    Hydrological models generally include thresholds and non-linearities, such as snow-rain-temperature thresholds, non-linear reservoirs, infiltration thresholds and the like. When relating observed variables to modelling results, formal methods often calculate performance metrics over long periods, reporting model performance with only few numbers. Such approaches are not well suited to compare dominating processes between reality and model and to better understand when thresholds and non-linearities are driving model results. We present a combination of two temporally resolved model diagnostic tools to answer when a model is performing (not so) well and what the dominant processes are during these periods. We look at the temporal dynamics of parameter sensitivities and model performance to answer this question. For this, the eco-hydrological SWAT model is applied in the Treene lowland catchment in Northern Germany. As a first step, temporal dynamics of parameter sensitivities are analyzed using the Fourier Amplitude Sensitivity test (FAST). The sensitivities of the eight model parameters investigated show strong temporal variations. High sensitivities were detected for two groundwater (GW_DELAY, ALPHA_BF) and one evaporation parameters (ESCO) most of the time. The periods of high parameter sensitivity can be related to different phases of the hydrograph with dominances of the groundwater parameters in the recession phases and of ESCO in baseflow and resaturation periods. Surface runoff parameters show high parameter sensitivities in phases of a precipitation event in combination with high soil water contents. The dominant parameters give indication for the controlling processes during a given period for the hydrological catchment. The second step included the temporal analysis of model performance. For each time step, model performance was characterized with a "finger print" consisting of a large set of performance measures. These finger prints were clustered into

  13. Stochastic analysis of a novel nonautonomous periodic SIRI epidemic system with random disturbances

    Science.gov (United States)

    Zhang, Weiwei; Meng, Xinzhu

    2018-02-01

    In this paper, a new stochastic nonautonomous SIRI epidemic model is formulated. Given that the incidence rates of diseases may change with the environment, we propose a novel type of transmission function. The main aim of this paper is to obtain the thresholds of the stochastic SIRI epidemic model. To this end, we investigate the dynamics of the stochastic system and establish the conditions for extinction and persistence in mean of the disease by constructing some suitable Lyapunov functions and using stochastic analysis technique. Furthermore, we show that the stochastic system has at least one nontrivial positive periodic solution. Finally, numerical simulations are introduced to illustrate our results.

  14. Enumeration and stability analysis of simple periodic orbits in β-Fermi Pasta Ulam lattice

    International Nuclear Information System (INIS)

    Sonone, Rupali L.; Jain, Sudhir R.

    2014-01-01

    We study the well-known one-dimensional problem of N particles with a nonlinear interaction. The special case of quadratic and quartic interaction potential among nearest neighbours is the β-Fermi-Pasta-Ulam model. We enumerate and classify the simple periodic orbits for this system and find the stability zones, employing Floquet theory. Such stability analysis is crucial to understand the transition of FPU lattice from recurrences to globally chaotic behavior, energy transport in lower dimensional system, dynamics of optical lattices and also its impact on shape parameter of bio-polymers such as DNA and RNA

  15. Enumeration and stability analysis of simple periodic orbits in β-Fermi Pasta Ulam lattice

    Energy Technology Data Exchange (ETDEWEB)

    Sonone, Rupali L., E-mail: vaidehisonone@gmail.com; Jain, Sudhir R., E-mail: vaidehisonone@gmail.com [Department of Physics, University of Pune, Pune-411007, India and Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai - 400085 (India)

    2014-04-24

    We study the well-known one-dimensional problem of N particles with a nonlinear interaction. The special case of quadratic and quartic interaction potential among nearest neighbours is the β-Fermi-Pasta-Ulam model. We enumerate and classify the simple periodic orbits for this system and find the stability zones, employing Floquet theory. Such stability analysis is crucial to understand the transition of FPU lattice from recurrences to globally chaotic behavior, energy transport in lower dimensional system, dynamics of optical lattices and also its impact on shape parameter of bio-polymers such as DNA and RNA.

  16. Application of wavelet analysis in determining the periodicity of global warming

    Science.gov (United States)

    Feng, Xiao

    2018-04-01

    In the last two decades of the last century, the global average temperature has risen by 0.48 ° C over 100 years ago. Since then, global warming has become a hot topic. Global warming will have complex and potential impacts on humans and the Earth. However, the negative impacts far outweigh the positive impacts. The most obvious external manifestation of global warming is temperature. Therefore, this study uses wavelet analysis study the characteristics of temperature time series, solve the periodicity of the sequence, find out the trend of temperature change and predict the extent of global warming in the future, so as to take the necessary precautionary measures.

  17. Quantitative analysis of adenosine A1 receptors in human brain using positron emission tomography and [1 -methyl-11C]8-dicyclopropylmethyl-1-methyl-3-propylxanthine

    International Nuclear Information System (INIS)

    Kimura, Yuichi; Ishii, Kenji; Fukumitsu, Nobuyoshi; Oda, Keiichi; Sasaki, Toru; Kawamura, Kazunori; Ishiwata, Kiichi

    2004-01-01

    Fully quantitative analysis of the adenosine A 1 receptor (A1R) in the brain with 11 C-MPDX and positron emission tomography is reported. The kinetics is described using a two-tissue three-compartment model, and estimated binding potentials correspond well with the estimates made by Logan plot. The image of the binding potential of the MPDX is physiologically reasonable. We conclude that MPDX is applicable to the visualization of the A1Rs in the brain with Logan plot

  18. Prognostic value of CpG island methylator phenotype among colorectal cancer patients: a systematic review and meta-analysis.

    Science.gov (United States)

    Juo, Y Y; Johnston, F M; Zhang, D Y; Juo, H H; Wang, H; Pappou, E P; Yu, T; Easwaran, H; Baylin, S; van Engeland, M; Ahuja, N

    2014-12-01

    Divergent findings regarding the prognostic value of CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) patients exist in current literature. We aim to review data from published studies in order to examine the association between CIMP and CRC prognosis. A comprehensive search for studies reporting disease-free survival (DFS), overall survival (OS), or cancer-specific mortality of CRC patients stratified by CIMP is carried out. Study findings are summarized descriptively and quantitatively, using adjusted hazard ratios (HRs) as summary statistics. Thirty-three studies reporting survival in 10 635 patients are included for review. Nineteen studies provide data suitable for meta-analysis. The definition of CIMP regarding gene panel, marker threshold, and laboratory method varies across studies. Pooled analysis shows that CIMP is significantly associated with shorter DFS (pooled HR estimate 1.45; 95% confidence interval (CI) 1.07-1.97, Q = 3.95, I(2) = 0%) and OS (pooled HR estimate 1.43; 95% CI 1.18-1.73, Q = 4.03, I(2) = 0%) among CRC patients irrespective of microsatellite instability (MSI) status. Subgroup analysis of microsatellite stable (MSS) CRC patients also shows significant association between shorter OS (pooled HR estimate 1.37; 95% CI 1.12-1.68, Q = 4.45, I(2) = 33%) and CIMP. Seven studies have explored CIMP's value as a predictive factor on stage II and III CRC patient's DFS after receiving adjuvant 5-fluorouracil (5-FU) therapy: of these, four studies showed that adjuvant chemotherapy conferred a DFS benefit among CIMP(+) patients, one concluded to the contrary, and two found no significant correlation. Insufficient data was present for statistical synthesis of CIMP's predictive value among CRC patients receiving adjuvant 5-FU therapy. CIMP is independently associated with significantly worse prognosis in CRC patients. However, CIMP's value as a predictive factor in assessing whether adjuvant 5-FU therapy will confer additional survival

  19. Statistical analysis of incidents reported in the Greek Petrochemical Industry for the period 1997-2003

    International Nuclear Information System (INIS)

    Konstandinidou, Myrto; Nivolianitou, Zoe; Markatos, Nikolaos; Kiranoudis, Chris

    2006-01-01

    This paper makes an analysis of all reported accidents and incidents in the Greek Petrochemical Industry for the period spanning from 1997 to 2003. The work performed is related to the analysis of important parameters of the incidents, their inclusion in a database adequately designed for the purposes of this analysis and an importance assessment of this reporting scheme. Indeed, various stakeholders have highlighted the importance of a reporting system for industrial accidents and incidents. The European Union has established for this purpose the Major Accident Reporting System (MARS) for the reporting of major accidents in the Member States. However, major accidents are not the only measure that can characterize the safety status of an establishment; neither are the former the only events from which important lessons can be learned. Near misses, industrial incidents without major consequences, as well as occupational accidents could equally supply with important findings the interested analyst, while statistical analysis of these incidents could give significant insight in the understanding and the prevention of similar incidents or major accidents in the future. This analysis could be more significant, if each industrial sector was separately analyzed, as the authors do for the petrochemical sector in the present article

  20. Bibliometric Analysis of the Journal Kemija u industriji for the Period 2000–2009

    Directory of Open Access Journals (Sweden)

    Macan, B.

    2011-02-01

    Full Text Available This paper deals with a bibliometric analysis of journal Kemija u industriji for the period 2000–2009. The results of the analysis show that the journal is still dealing with the problem of publishing scientific papers, which was also detected in a previous similar analysis (M. Jokia et al. (2002. Furthermore, in 82.1 % of categorized papers at least one author is from Croatia, while in 88.4 % at least one author is from neighboring countries (Croatia and other ex-Yugoslavia countries. This data reveals the strong national and regional orientation of the journal, which can be related with the language of publishing (mostly Croatian – 76.4 %, as well as with one of the basic functions of the journal according to its mission, which is to develop and improve chemistry and engineering terminology and nomenclature in the Croatian language. Journal citation analysis is based on the citation data gathered from the bibliographic and citation databases Scopus and Web of Science (WoS. Still, according to the specific bibliometric journal indicators(Impact Factor (IF, SCImago Journal Rank (SJR and Source Normalized Impact per Paper (SNIP, the analysis shows that Kemija u industriji could find its place among other related world journals.

  1. Isolation and Expression analysis of OsPME1, encoding for a putative Pectin Methyl Esterase from Oryza sativa (subsp. indica).

    Science.gov (United States)

    Kanneganti, Vydehi; Gupta, Aditya Kumar

    2009-04-01

    Pectin Methyl Esterases (PMEs) play an essential role during plant development by affecting the mechanical properties of the plant cell walls. Recent studies indicated that PMEs play important role in pollen tube development. In this study, we isolated a 1.3 kb cDNA clone from rice panicle cDNA library. It contained a 1038 bp of open reading frame (ORF) encoding for a putative pectin methyl esterase of 345 aminoacids with a 20 aminoacid signal peptide and was hence designated as OsPME1 (Oryza sativaPectin Methyl Esterase 1). It contained the structural arrangement GXYXE and GXXDFIF, found in the active groups of all PMEs. OsPME1 gene product shared varying identities, ranging from 52 % to 33 % with PMEs from other plant species belonging to Brassicaceae, Fabaceae, Amaranthaceae and Funariaceae. Southern blot analysis indicated that PME1 exists as a single copy in the rice genome. Expression pattern analysis revealed that OsPME1 is expressed only in pollen grains, during the later stages of their development and was also regulated by various abiotic stress treatments and phytohormones. Functional characterization of this pollen specific PME from rice would enable us to understand its role in pollen development.

  2. A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits

    DEFF Research Database (Denmark)

    Volkov, Petr; Olsson, Anders H; Gillberg, Linn

    2016-01-01

    Little is known about the extent to which interactions between genetics and epigenetics may affect the risk of complex metabolic diseases and/or their intermediary phenotypes. We performed a genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human adipose tissue of 119 men, w...... and epigenetic variation in both cis and trans positions influencing gene expression in adipose tissue and in vivo (dys)metabolic traits associated with the development of obesity and diabetes.......Little is known about the extent to which interactions between genetics and epigenetics may affect the risk of complex metabolic diseases and/or their intermediary phenotypes. We performed a genome-wide DNA methylation quantitative trait locus (mQTL) analysis in human adipose tissue of 119 men......, where 592,794 single nucleotide polymorphisms (SNPs) were related to DNA methylation of 477,891 CpG sites, covering 99% of RefSeq genes. SNPs in significant mQTLs were further related to gene expression in adipose tissue and obesity related traits. We found 101,911 SNP-CpG pairs (mQTLs) in cis and 5...

  3. Fourier mode analysis of slab-geometry transport iterations in spatially periodic media

    International Nuclear Information System (INIS)

    Larsen, E W; Zika, M R

    1999-01-01

    We describe a Fourier analysis of the diffusion-synthetic acceleration (DSA) and transport-synthetic acceleration (TSA) iteration schemes for a spatially periodic, but otherwise arbitrarily heterogeneous, medium. Both DSA and TSA converge more slowly in a heterogeneous medium than in a homogeneous medium composed of the volume-averaged scattering ratio. In the limit of a homogeneous medium, our heterogeneous analysis contains eigenvalues of multiplicity two at ''resonant'' wave numbers. In the presence of material heterogeneities, error modes corresponding to these resonant wave numbers are ''excited'' more than other error modes. For DSA and TSA, the iteration spectral radius may occur at these resonant wave numbers, in which case the material heterogeneities most strongly affect iterative performance

  4. A general symplectic method for the response analysis of infinitely periodic structures subjected to random excitations

    Directory of Open Access Journals (Sweden)

    You-Wei Zhang

    Full Text Available A general symplectic method for the random response analysis of infinitely periodic structures subjected to stationary/non-stationary random excitations is developed using symplectic mathematics in conjunction with variable separation and the pseudo-excitation method (PEM. Starting from the equation of motion for a single loaded substructure, symplectic analysis is firstly used to eliminate the dependent degrees of the freedom through condensation. A Fourier expansion of the condensed equation of motion is then applied to separate the variables of time and wave number, thus enabling the necessary recurrence scheme to be developed. The random response is finally determined by implementing PEM. The proposed method is justified by comparison with results available in the literature and is then applied to a more complicated time-dependent coupled system.

  5. Application of Recurrence Analysis to the period doubling cascade of a confined buoyant flow

    International Nuclear Information System (INIS)

    Angeli, D; Corticelli, M A; Fichera, A; Pagano, A

    2017-01-01

    Recurrence Analysis (RA) is a promising and flexible tool to identify the behaviour of nonlinear dynamical systems. The potentialities of such a technique are explored in the present work, for the study of transitions to chaos of buoyant flow in enclosures. The case of a hot cylindrical source centred in a square enclosure, is considered here, for which an extensive database of results has been collected in recent years. For a specific value of the system aspect ratio, a sequence of period doublings has been identified, leading to the onset of chaos. RA is applied here to analyse the different flow regimes along the route to chaos. The qualitative visual identification of patterns and the statistics given by the quantitative analysis suggest that this kind of tool is well suited to the study of transitional flows in thermo-fluid dynamics. (paper)

  6. Analysis of premature births for the period from 2009. to 2013. in Health Center Kosovska Mitrovica

    Directory of Open Access Journals (Sweden)

    Adžić V.

    2015-01-01

    Full Text Available Delivery before 37th week of gestation is defined as preterm, independently of body mass of babies, according to the World Health Organization. Premature birth is the current problem in the world due to the high risk of neonatal morbidity and mortality and incompletely clear etiology. In our country the frequency of preterm delivery is 6%. We have retrospectively analyzed early deliveries in Health Center Kosovska Mitrovica in the period from 2009 to 2013. In this five-year period, there were totaly 3398 deliveries, of which 148 or 4.35 % were preterm delivery. The aim of this study was to investigate the incidence of premature birth in the five-year period in relation to: the total number of births in a given period, the age of the patients, the manner of completion of delivery, gestational week of pregnancy, parity and the most common causes that led to the PTP. In the analysis we have included the body weight and Apgar score of premature infants. We have used protocols of births, maternal history of disease, neonatal protocols and lists of newborns. Most of them were multiparas (41.2 %,56.7 % of pregnant women were aged of 21-30 years and pregnancy in 79.9 % of cases ended with 33 to 37 ng. Vaginal deliveries were completed in 84.4% of premature births, and caesarean in 15.6%. Twin pregnancies with preterm deliveries were represented in 10.2%. The most common weight of premature infants ranged from 2000 to 2500 grams (48.6 %. The most common causes that led to the PTP were PPROM (22.9 %, unknown causes (27. 1 %, multiple pregnancy (18.2 %, genital infection (8.7 %, cervical incompetence (6.7 %, IUGR (5.4%, PIH (4.2%, placental abruption and placenta previa (2.1 % and other (4.7% .

  7. Extreme value analysis of meterological parameters observed at Narora during the period 1989-2001

    International Nuclear Information System (INIS)

    Varakhedkar, V.K.; Dube, B.; Gurg, R.P.

    2002-08-01

    The design of engineering structures requires an understanding of extreme weather conditions that may occur at the site of interest, which is very essential, so that the structures can be designed to withstand weather stresses. In this report an analysis of extreme values of meteorological parameters observed at Narora for the period 1989- 2001 is described. The parameters considered are maximum and minimum air temperature, minimum relative humidity, maximum wind speed, maximum rainfall in a day and month, and annual rainfall. The extreme value analysis reveals that the variables such as annual maximum air temperature, minimum relative humidity and monthly maximum rainfall obey Fisher -Tippet Type -I extreme value distribution where as annual minimum air temperature, maximum hourly wind speed, daily maximum rainfall and maximum and minimum annual rainfall, obey Fisher -Tippet Type -2 extreme value distribution function. Various distribution function parameters for each variable are determined. Extreme values corresponding to return periods of 50 years and 100 years are worked out. These derived extreme values are particularly useful for arriving at suitable design values to ensure the safety of any civil structure in Narora area with respect to stresses due to weather conditions. (author)

  8. Narrow band quantitative and multivariate electroencephalogram analysis of peri-adolescent period.

    Science.gov (United States)

    Martinez, E I Rodríguez; Barriga-Paulino, C I; Zapata, M I; Chinchilla, C; López-Jiménez, A M; Gómez, C M

    2012-08-24

    The peri-adolescent period is a crucial developmental moment of transition from childhood to emergent adulthood. The present report analyses the differences in Power Spectrum (PS) of the Electroencephalogram (EEG) between late childhood (24 children between 8 and 13 years old) and young adulthood (24 young adults between 18 and 23 years old). The narrow band analysis of the Electroencephalogram was computed in the frequency range of 0-20 Hz. The analysis of mean and variance suggested that six frequency ranges presented a different rate of maturation at these ages, namely: low delta, delta-theta, low alpha, high alpha, low beta and high beta. For most of these bands the maturation seems to occur later in anterior sites than posterior sites. Correlational analysis showed a lower pattern of correlation between different frequencies in children than in young adults, suggesting a certain asynchrony in the maturation of different rhythms. The topographical analysis revealed similar topographies of the different rhythms in children and young adults. Principal Component Analysis (PCA) demonstrated the same internal structure for the Electroencephalogram of both age groups. Principal Component Analysis allowed to separate four subcomponents in the alpha range. All these subcomponents peaked at a lower frequency in children than in young adults. The present approaches complement and solve some of the incertitudes when the classical brain broad rhythm analysis is applied. Children have a higher absolute power than young adults for frequency ranges between 0-20 Hz, the correlation of Power Spectrum (PS) with age and the variance age comparison showed that there are six ranges of frequencies that can distinguish the level of EEG maturation in children and adults. The establishment of maturational order of different frequencies and its possible maturational interdependence would require a complete series including all the different ages.

  9. Stable carbon and hydrogen isotope analysis of methyl tert-butyl ether and tert-amyl methyl ether by purge and trap-gas chromatography-isotope ratio mass spectrometry: method evaluation and application.

    Science.gov (United States)

    Kujawinski, Dorothea M; Stephan, Manuel; Jochmann, Maik A; Krajenke, Karen; Haas, Joe; Schmidt, Torsten C

    2010-01-01

    In order to monitor the behaviour of contaminants in the aqueous environment effective enrichment techniques often have to be employed due to their low concentrations. In this work a robust and sensitive purge and trap-gas chromatography-isotope ratio mass spectrometry method for carbon and hydrogen isotope analysis of fuel oxygenates in water is presented. The method evaluation included the determination of method detection limits, accuracy and reproducibility of deltaD and delta(13)C values. Lowest concentrations at which reliable delta(13)C values could be determined were 5 microg L(-1) and 28 microg L(-1) for TAME and MTBE, respectively. Stable deltaD values for MTBE and TAME could be achieved for concentrations as low as 25 and 50 microg L(-1). Good long-term reproducibility of delta(13)C and deltaD values was obtained for all target compounds. But deltaD values varying more than 5 per thousand were observed using different thermal conversion tubes. Thus, a correction of deltaD values in the analysis of groundwater samples was necessary to guarantee comparability of the results. The applicability of this method was shown by the analysis of groundwater samples from a gasoline contaminated site. By two dimensional isotope analysis two locations within this site were identified at which anaerobic and aerobic degradation of methyl tert-butyl ether occurred.

  10. Identification of exotic genetic components and DNA methylation pattern analysis of three cotton introgression lines from Gossypium bickii.

    Science.gov (United States)

    He, Shou-Pu; Sun, Jun-Ling; Zhang, Chao; Du, Xiong-Ming

    2011-01-01

    The impact of alien DNA fragments on plant genome has been studied in many species. However, little is known about the introgression lines of Gossypium. To study the consequences of introgression in Gossypium, we investigated 2000 genomic and 800 epigenetic sites in three typical cotton introgression lines, as well as their cultivar (Gossypium hirsutum) and wild parents (Gossypium bickii), by amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP). The results demonstrate that an average of 0.5% of exotic DNA segments from wild cotton is transmitted into the genome of each introgression line, with the addition of other forms of genetic variation. In total, an average of 0.7% of genetic variation sites is identified in introgression lines. Simultaneously, the overall cytosine methylation level in each introgression line is very close to that of the upland cotton parent (an average of 22.6%). Further dividing patterns reveal that both hypomethylation and hypermethylation occurred in introgression lines in comparison with the upland cotton parent. Sequencing of nine methylation polymorphism fragments showed that most (7 of 9) of the methylation alternations occurred in the noncoding sequences. The molecular evidence of introgression from wild cotton into introgression lines in our study is identified by AFLP. Moreover, the causes of petal variation in introgression lines are discussed.

  11. Characterization of spirochetal isolates from arthropods collected in South Moravia, Czech Republic, using fatty acid methyl esters analysis

    Czech Academy of Sciences Publication Activity Database

    Čechová, L.; Durnová, E.; Šikutová, Silvie; Halouzka, Jiří; Němec, M.

    2004-01-01

    Roč. 808, č. 2 (2004), s. 249-254 ISSN 1570-0232 R&D Projects: GA ČR GA206/03/0726 Institutional research plan: CEZ:AV0Z6093917 Keywords : spirochetes * arthropods * fatty acid methyl esters Subject RIV: EE - Microbiology, Virology Impact factor: 2.176, year: 2004

  12. Epigenome-wide meta-analysis of methylation in children related to prenatal NO2 air pollution exposure

    NARCIS (Netherlands)

    Gruzieva, O.; Xu, C.J.; Breton, C.V.; Annesi-Maesano, I.; Antó, J.M.; Auffray, C.; Ballereau, S.; Bellander, T.; Bousquet, J.; Bustamante, M.; Charles, M.A.; de Kluizenaar, Y.; Den Dekker, H.T.; Duijts, L.; Felix, J.F.; Gehring, U.; Guxens, M.; Jaddoe, V.V.W.; Jankipersadsing, S.A.; Merid, S.K.; Kere, J.; Kumar, A.; Lemonnier, N.; Lepeule, J.; Nystad, W.; Page, C.M.; Panasevich, S.; Postma, D.; Slama, R.; Sunyer, J.; Söderhäll, C.; Yao, J.; London, S.J.; Pershagen, G.; Koppelman, G.H.; Melén, E.

    2017-01-01

    Background: Prenatal exposure to air pollution is considered to be associated with adverse effects on child health. This may partly be mediated by mechanisms related to DNA methylation. Objectives: We investigated associations between exposure to air pollution, using nitrogen dioxide (NO2) as

  13. Convergence analysis of the rebalance methods in multiplying finite slab having periodic boundary conditions

    International Nuclear Information System (INIS)

    Hong, Ser Gi; Lee, Young Ouk; Song, Jae Seung

    2009-01-01

    This paper analyzes the convergence of the rebalance iteration methods for the discrete ordinates transport equation in the multiplying finite slab problem. The finite slab is assumed to be homogeneous and it has the periodic boundary conditions. A general formulation is used to include three well-known rebalance methods of the linearized form in a unified way. The rebalance iteration methods considered in this paper are the CMR (Coarse-Mesh Rebalance), the CMFD (Coarse-Mesh Finite Difference), and p-CMFD (Partial Current-Based Coarse Mesh Finite Difference) methods which have been popularly used in the reactor physics. The convergence analysis is performed with the well-known Fourier analysis through a linearization. The analyses are applied for one-group problems. The theoretical analysis shows that there are one fundamental mode and N-1 Eigen-modes which determine the convergence if the finite slab is divided into N uniform meshes. The numerical tests show that the Fourier convergence analysis provides the reasonable estimate of the numerical spectral radii for the model problems and the spectral radius for the finite slab approaches the one for the infinite slab as the thickness of the slab increases. (author)

  14. De novo DNA methylation during monkey pre-implantation embryogenesis.

    Science.gov (United States)

    Gao, Fei; Niu, Yuyu; Sun, Yi Eve; Lu, Hanlin; Chen, Yongchang; Li, Siguang; Kang, Yu; Luo, Yuping; Si, Chenyang; Yu, Juehua; Li, Chang; Sun, Nianqin; Si, Wei; Wang, Hong; Ji, Weizhi; Tan, Tao

    2017-04-01

    Critical epigenetic regulation of primate embryogenesis entails DNA methylome changes. Here we report genome-wide composition, patterning, and stage-specific dynamics of DNA methylation in pre-implantation rhesus monkey embryos as well as male and female gametes studied using an optimized tagmentation-based whole-genome bisulfite sequencing method. We show that upon fertilization, both paternal and maternal genomes undergo active DNA demethylation, and genome-wide de novo DNA methylation is also initiated in the same period. By the 8-cell stage, remethylation becomes more pronounced than demethylation, resulting in an increase in global DNA methylation. Promoters of genes associated with oxidative phosphorylation are preferentially remethylated at the 8-cell stage, suggesting that this mode of energy metabolism may not be favored. Unlike in rodents, X chromosome inactivation is not observed during monkey pre-implantation development. Our study provides the first comprehensive illustration of the 'wax and wane' phases of DNA methylation dynamics. Most importantly, our DNA methyltransferase loss-of-function analysis indicates that DNA methylation influences early monkey embryogenesis.

  15. Interactive remote data processing using Pixelize Wavelet Filtration (PWF-method) and PeriodMap analysis

    Science.gov (United States)

    Sych, Robert; Nakariakov, Valery; Anfinogentov, Sergey

    Wavelet analysis is suitable for investigating waves and oscillating in solar atmosphere, which are limited in both time and frequency. We have developed an algorithms to detect this waves by use the Pixelize Wavelet Filtration (PWF-method). This method allows to obtain information about the presence of propagating and non-propagating waves in the data observation (cube images), and localize them precisely in time as well in space. We tested the algorithm and found that the results of coronal waves detection are consistent with those obtained by visual inspection. For fast exploration of the data cube, in addition, we applied early-developed Period- Map analysis. This method based on the Fast Fourier Transform and allows on initial stage quickly to look for "hot" regions with the peak harmonic oscillations and determine spatial distribution at the significant harmonics. We propose the detection procedure of coronal waves separate on two parts: at the first part, we apply the PeriodMap analysis (fast preparation) and than, at the second part, use information about spatial distribution of oscillation sources to apply the PWF-method (slow preparation). There are two possible algorithms working with the data: in automatic and hands-on operation mode. Firstly we use multiply PWF analysis as a preparation narrowband maps at frequency subbands multiply two and/or harmonic PWF analysis for separate harmonics in a spectrum. Secondly we manually select necessary spectral subband and temporal interval and than construct narrowband maps. For practical implementation of the proposed methods, we have developed the remote data processing system at Institute of Solar-Terrestrial Physics, Irkutsk. The system based on the data processing server - http://pwf.iszf.irk.ru. The main aim of this resource is calculation in remote access through the local and/or global network (Internet) narrowband maps of wave's sources both in whole spectral band and at significant harmonics. In addition

  16. MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status

    NARCIS (Netherlands)

    P. Bady (Pierre); D. Sciuscio (Davide); A.C. Diserens; J. Bloch (Jocelyne); M.J. van den Bent (Martin); C. Marosi (Christine); P-Y. Dietrich (Pierre Yves); M. Weller (Michael); L. Mariani (Luigi); F.L. Heppner (Frank ); D.R. Mcdonald (David ); D. Lacombe (Denis); R. Stupp (Roger); M. Delorenzi (Mauro); M.E. Hegi (Monika)

    2012-01-01

    textabstractThe methylation status of the O6-methylguanine- DNA methyltransferase (MGMT) gene is an important predictive biomarker for benefit from alkylating agent therapy in glioblastoma. Recent studies in anaplastic glioma suggest a prognostic value for MGMT methylation. Investigation of

  17. On-Chip Evaluation of DNA Methylation with Electrochemical Combined Bisulfite Restriction Analysis Utilizing a Carbon Film Containing a Nanocrystalline Structure.

    Science.gov (United States)

    Kurita, Ryoji; Yanagisawa, Hiroyuki; Kamata, Tomoyuki; Kato, Dai; Niwa, Osamu

    2017-06-06

    This paper reports an on-chip electrochemical assessment of the DNA methylation status in genomic DNA on a conductive nanocarbon film electrode realized with combined bisulfite restriction analysis (COBRA). The film electrode consists of sp 2 and sp 3 hybrid bonds and is fabricated with an unbalanced magnetron (UBM) sputtering method. First, we studied the effect of the sp 2 /sp 3 ratio of the UBM nanocarbon film electrode with p-aminophenol, which is a major electro-active product of the labeling enzyme from p-aminophenol phosphate. The signal current for p-aminophenol increases as the sp 2 content in the UBM nanocarbon film electrode increases because of the π-π interaction between aromatic p-aminophenol and the graphene-like sp 2 structure. Furthermore, the capacitative current at the UBM nanocarbon film electrode was successfully reduced by about 1 order of magnitude thanks to the angstrom-level surface flatness. Therefore, a high signal-to-noise ratio was achieved compared with that of conventional electrodes. Then, after performing an ELISA-like hybridization assay with a restriction enzyme, we undertook an electrochemical evaluation of the cytosine methylation status in DNA by measuring the oxidation current derived from p-aminophenol. When the target cytosine in the analyte sequence is methylated (unmethylated), the restriction enzyme of HpyCH4IV is able (unable) to cleave the sequence, that is, the detection probe cannot (can) hybridize. We succeeded in estimating the methylation ratio at a site-specific CpG site from the peak current of a cyclic voltammogram obtained from a PCR product solution ranging from 0.01 to 1 nM.

  18. Aggregate analysis of regulatory authority assessors' comments to improve the quality of periodic safety update reports.

    Science.gov (United States)

    Jullian, Sandra; Jaskiewicz, Lukasz; Pfannkuche, Hans-Jürgen; Parker, Jeremy; Lalande-Luesink, Isabelle; Lewis, David J; Close, Philippe

    2015-09-01

    Marketing authorization holders (MAHs) are expected to provide high-quality periodic safety update reports (PSURs) on their pharmaceutical products to health authorities (HAs). We present a novel instrument aiming at improving quality of PSURs based on standardized analysis of PSUR assessment reports (ARs) received from the European Union HAs across products and therapeutic areas. All HA comments were classified into one of three categories: "Request for regulatory actions," "Request for medical and scientific information," or "Data deficiencies." The comments were graded according to their impact on patients' safety, the drug's benefit-risk profile, and the MAH's pharmacovigilance system. A total of 476 comments were identified through the analysis of 63 PSUR HA ARs received in 2013 and 2014; 47 (10%) were classified as "Requests for regulatory actions," 309 (65%) as "Requests for medical and scientific information," and 118 (25%) comments were related to "Data deficiencies." The most frequent comments were requests for labeling changes (35 HA comments in 19 ARs). The aggregate analysis revealed commonly raised issues and prompted changes of the MAH's procedures related to the preparation of PSURs. The authors believe that this novel instrument based on the evaluation of PSUR HA ARs serves as a valuable mechanism to enhance the quality of PSURs and decisions about optimization of the use of the products and, therefore, contributes to improve further the MAH's pharmacovigilance system and patient safety. Copyright © 2015 John Wiley & Sons, Ltd.

  19. Microstructural Analysis of Carbonyl Signal in the 13C NMR Spectra of Methyl Methacrylate - n-Butyl Acrylate Copolymer

    International Nuclear Information System (INIS)

    Bujak, P.; Matlengiewicz, M.

    2005-01-01

    Microstructural information on acrylic copolymers, i.e. distribution of the comonomers along the macromolecular chain and their stereochemical arrangement (tacticity) can be derived from 13 C NMR, analyzing the splitting of their carbonyl signal. In the 100 MHz 13 C NMR spectrum of poly(methyl methacrylate-co-n-butyl acrylate), PMMA-nBA, the carbonyl signal at 174-178,5 ppm is clearly split into the lines of configurational-compositional pentads. This splitting is slightly different in different solvents, hence, recording of the same sample in different solvents may reveal differences important to correct assignment of individual sequences, since their probabilities (intensities) remain the same, while the chemical shift can vary in different solvents. If we would like to perform a complete analysis at this level we have to determine the distribution of 272 individual pentads. The outermost lines in the carbonyl signal of the copolymer can be assigned to the sequences of pure composition by simple comparison with the spectra of respective homopolymers. The rest of the inner lines cannot be easily attributed, therefore, a series of copolymer samples of different composition were synthesized in order to observe the different heterosequences, since depending on copolymer composition, different signals representing individual sequences, assume different relative intensities. To confirm the correctness of proposed attribution a simulation of the carbonyl signal can be performed. It is therefore necessary to know the intensities and positions of individual signals, representing individual compositional-configurational pentads. Calculation of the intensity of the lines can be performed assuming Bernoullian and/or Markov statistics, separately for compositional and configurational sequences and verifying the overall distribution of the individual probabilities. The position of the individual lines cannot be straightforwardly determined, therefore, we have adopted an

  20. Quantum mechanical analysis of fractal conductance fluctuations: a picture using self-similar periodic orbits

    International Nuclear Information System (INIS)

    Ogura, Tatsuo; Miyamoto, Masanori; Budiyono, Agung; Nakamura, Katsuhiro

    2007-01-01

    Fractal magnetoconductance fluctuations are often observed in experiments on ballistic quantum dots. Although the analysis of the exact self-affine fractal has been given by the semiclassical theory using self-similar periodic orbits in systems with a soft-walled potential with a saddle, there has been no corresponding quantum mechanical investigation. We numerically calculate the quantum conductance with use of the recursive Green's function method applied to open cavities characterized by a Henon-Heiles type potential. The conductance fluctuations show exact self-affinity just as in some of the experimental observations. The enlargement factor for the horizontal axis can be explained by the scaling factor of the area of self-similar periodic orbits, and therefore be attributed to the curvature of the saddle in the cavity potential. The fractal dimension obtained through the box counting method agrees with those evaluated with use of the Hurst exponent, and coincides with the semiclassical prediction. We further investigate the variation of the fractal dimension by changing the control parameters between the classical and quantum domains. (fast track communication)

  1. Financial Performance Analysis of BIST Tourism Companies with TOPSIS for 2011-2015 Period

    Directory of Open Access Journals (Sweden)

    Mahmut ERDOĞAN

    2018-01-01

    Full Text Available The main aim of this paper is to investigate of financial performance of 13 tourism firms quoted on BIST with TOPSIS method by exploitation of financial ratios for the 2011-2015 period. Basically, to determine financial power of the tourism firms financial ratios have measured and then general corporate performance scores estimated by TOPSIS method. Algorithm of the TOPSIS method is repeated and ranking orders of firms are calculated for each year. However, companies’ yearly performances are outlined and an average ranking is stated for 6 years. Lastly, tourism corporations have ranked with these scores. The result of this paper shows that financial performance of tourism companies point instability out during the all period. According to the results of analysis Net Turizm, Tekart Turizm, and Marmaris Altinyunus have the best performance in 2011 respectively, but Metemtur has the worst. On the other hand, surprisingly, Metemtur has the best financial efficiency and Martı Otel has the worst performance in 2015. However, Net Turizm and Marmaris Altinyunus have been continuing their financial stability and Metemtur is very volatile company in given term.

  2. A Busy period analysis for the state dependent M/M/1/K queue

    NARCIS (Netherlands)

    Al Hanbali, Ahmad; Boxma, Onno

    2010-01-01

    In this paper, we study the transient behavior of a state dependent M/M/1/K queue during the busy period. We derive in closed-form the joint transform of the length of the busy period, the number of customers served during the busy period, and the number of losses during the busy period. For two

  3. EVALUATION OF PRODUCTION IN SEASONALITY PERIODS: ANALYSIS OF THE CONSTRUCTION INDUSTRY IN BRAZIL

    Directory of Open Access Journals (Sweden)

    Marcos William Kaspchak Machado

    2013-06-01

    Full Text Available The present work has as an objective to evaluate the impacts of production seasonality in seasonality periods in the Brazilian construction industry. The adopted methodology was based on the qualitative and quantitative approaches of the aspects inherent to the seasonality factors in the construction industry and its possible causes. Besides that, literature data were collected in year report books and devices provided by institutions of the sector. The results demonstrated the importance of production management mechanisms to optimize the use of productive factors through cost analysis, which are fundamental to understand the operational flux of resources used in the operational media. Obtaining this information, connected to market indicators helped in the decision making process related to the development of prospective scenarios which will give support to the decision making strategy aiming to stabilize the production levels.

  4. Detecting periodic oscillations in astronomy data: revisiting wavelet analysis with coloured and white noise

    Science.gov (United States)

    Xu, Chang

    2017-04-01

    The intrinsic random variability of an astronomical source hampers the detection of possible periodicities that we are interested in. We find that a simple first-order autoregressive [AR(1)] process gives a poor fit to the power decay in the observed spectrum for astrophysical sources and geodetic observations. Thus, appropriate background noise models have to be chosen for significance tests to distinguish real features from the intrinsic variability of the source. Here we recall the wavelet analysis with significance and confidence testing but extend it with the generalized Gauss Markov stochastic model as the null hypothesis, which includes AR(1) and a power law as special cases. We exemplify this discussion with real data, such as sunspot number data, geomagnetic indices, X-ray observations, as well as a Global Positioning System (GPS) position time series.

  5. Life-cycle cost and payback period analysis for commercial unitary air conditioners

    Energy Technology Data Exchange (ETDEWEB)

    Rosenquist, Greg; Coughlin, Katie; Dale, Larry; McMahon, James; Meyers, Steve

    2004-03-31

    This report describes an analysis of the economic impacts of possible energy efficiency standards for commercial unitary air conditioners and heat pumps on individual customers in terms of two metrics: life-cycle cost (LCC) and payback period (PBP). For each of the two equipment classes considered, the 11.5 EER provides the largest mean LCC savings. The results show how the savings vary among customers facing different electricity prices and other conditions. At 11.5 EER, at least 80% of the users achieve a positive LCC savings. At 12.0 EER, the maximum efficiency analyzed, mean LCC savings are lower but still positive. For the {ge} $65,000 Btu/h to <135,000 Btu/h equipment class, 59% of users achieve a positive LCC savings. For the $135,000 Btu/h to <240,000 Btu/h equipment class, 91% of users achieve a positive LCC savings.

  6. Use of the spectral analysis for estimating the intensity of a weak periodic source

    International Nuclear Information System (INIS)

    Marseguerra, M.

    1989-01-01

    This paper deals with the possibility of exploiting spectral methods for the analysis of counting experiments in which one has to estimate the intensity of a weak periodic source of particles buried in a high background. The general theoretical expressions here obtained for the auto- and cross-spectra are applied to three kinds of simulated experiments. In all cases it turns out that the source intensity can acutally be estimated with a standard deviation comparable with that obtained in classical experiments in which the source can be moved out. Thus the spectral methods represent an interesting technique nowadays easy to implement on low-cost computers which could also be used in many research fields by suitably redesigning classical experiments. The convenience of using these methods in the field of nuclear safeguards is presently investigated in our Institute. (orig.)

  7. Analysis of European ozone trends in the period 1995-2014

    Science.gov (United States)

    Yan, Yingying; Pozzer, Andrea; Ojha, Narendra; Lin, Jintai; Lelieveld, Jos

    2018-04-01

    Surface-based measurements from the EMEP and Airbase networks are used to estimate the changes in surface ozone levels during the 1995-2014 period over Europe. We find significant ozone enhancements (0.20-0.59 µg m-3 yr-1 for the annual means; P-value climate model EMAC, the importance of anthropogenic emissions changes in determining these changes over background sites are investigated. The EMAC model is found to successfully capture the observed temporal variability in mean ozone concentrations, as well as the contrast in the trends of 95th and 5th percentile ozone over Europe. Sensitivity simulations and statistical analysis show that a decrease in European anthropogenic emissions had contrasting effects on surface ozone trends between the 95th and 5th percentile levels and that background ozone levels have been influenced by hemispheric transport, while climate variability generally regulated the inter-annual variations of surface ozone in Europe.

  8. Band structure analysis of a thin plate with periodic arrangements of slender beams

    Science.gov (United States)

    Serrano, Ó.; Zaera, R.; Fernández-Sáez, J.

    2018-04-01

    This work analyzes the wave propagation in structures composed of a periodic arrangement of vertical beams rigidly joined to a plate substrate. Three different configurations for the distribution of the beams have been analyzed: square, triangular, and hexagonal. A dimensional analysis of the problem indicates the presence of three dimensionless groups of parameters controlling the response of the system. The main features of the wave propagation have been found using numerical procedures based on the Finite Element Method, through the application of the Bloch's theorem for the corresponding primitive unit cells. Illustrative examples of the effect of the different dimensionless parameters on the dynamic behavior of the system are presented, providing information relevant for design.

  9. Whole-genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus.

    Science.gov (United States)

    Zhu, Honglin; Mi, Wentao; Luo, Hui; Chen, Tao; Liu, Shengxi; Raman, Indu; Zuo, Xiaoxia; Li, Quan-Zhen

    2016-07-13

    Recent achievement in genetics and epigenetics has led to the exploration of the pathogenesis of systemic lupus erythematosus (SLE). Identification of differentially expressed genes and their regulatory mechanism(s) at whole-genome level will provide a comprehensive understanding of the development of SLE and its devastating complications, lupus nephritis (LN). We performed whole-genome transcription and DNA methylation analysis in PBMC of 30 SLE patients, including 15 with LN (SLE LN(+)) and 15 without LN (SLE LN(-)), and 25 normal controls (NC) using HumanHT-12 Beadchips and Illumina Human Methy450 chips. The serum proinflammatory cytokines were quantified using Bio-plex Human Cytokine 27-plex assay. Differentially expressed genes and differentially methylated CpG were analyzed with GenomeStudio, R, and SAM software. The association between DNA methylation and gene expression were tested. Gene interaction pathways of the differentially expressed genes were analyzed by IPA software. We identified 552 upregulated genes and 550 downregulated genes in PBMC of SLE. Integration of DNA methylation and gene expression profiling showed that 334 upregulated genes were hypomethylated, and 479 downregulated genes were hypermethylated. Pathway analysis on the differential genes in SLE revealed significant enrichment in interferon (IFN) signaling and toll-like receptor (TLR) signaling pathways. Nine IFN- and seven TLR-related genes were identified and displayed step-wise increase in SLE LN(-) and SLE LN(+). Hypomethylated CpG sites were detected on these genes. The gene expressions for MX1, GPR84, and E2F2 were increased in SLE LN(+) as compared to SLE LN(-) patients. The serum levels of inflammatory cytokines, including IL17A, IP-10, bFGF, TNF-α, IL-6, IL-15, GM-CSF, IL-1RA, IL-5, and IL-12p70, were significantly elevated in SLE compared with NC. The levels of IL-15 and IL1RA correlated with their mRNA expression. The upregulation of IL-15 may be regulated by hypomethylated

  10. Periodic analysis of solar activity and its link with the Arctic oscillation phenomenon

    Energy Technology Data Exchange (ETDEWEB)

    Qu, Weizheng; Li, Chun; Du, Ling; Huang, Fei [Ocean University of China, 14-1' -601, 2117 Jinshui Road, Qingdao 266100 (China); Li, Yanfang, E-mail: quweizhe@ouc.edu.cn [Yantai Institute of Coastal Zone Research Chinese Academy of Sciences (China)

    2014-12-01

    Based on spectrum analysis, we provide the arithmetic expressions of the quasi 11 yr cycle, 110 yr century cycle of relative sunspot numbers, and quasi 22 yr cycle of solar magnetic field polarity. Based on a comparative analysis of the monthly average geopotential height, geopotential height anomaly, and temperature anomaly of the northern hemisphere at locations with an air pressure of 500 HPa during the positive and negative phases of AO (Arctic Oscillation), one can see that the abnormal warming period in the Arctic region corresponds to the negative phase of AO, while the anomalous cold period corresponds to its positive phase. This shows that the abnormal change in the Arctic region is an important factor in determining the anomalies of AO. In accordance with the analysis performed using the successive filtering method, one can see that the AO phenomenon occurring in January shows a clear quasi 88 yr century cycle and quasi 22 yr decadal cycle, which are closely related to solar activities. The results of our comparative analysis show that there is a close inverse relationship between the solar activities (especially the solar magnetic field index changes) and the changes in the 22 yr cycle of the AO occurring in January, and that the two trends are basically opposite of each other. That is to say, in most cases after the solar magnetic index MI rises from the lowest value, the solar magnetic field turns from north to south, and the high-energy particle flow entering the Earth's magnetosphere increases to heat the polar atmosphere, thus causing the AO to drop from the highest value; after the solar magnetic index MI drops from the highest value, the solar magnetic field turns from south to north, and the solar high-energy particle flow passes through the top of the Earth's magnetosphere rather than entering it to heat the polar atmosphere. Thus the polar temperature drops, causing the AO to rise from the lowest value. In summary, the variance

  11. Fate of the organophosphorus insecticide methoxy-14 C-Azinphos-methyl in baladi egyptian goats

    International Nuclear Information System (INIS)

    Hamdy, N.A.; Fakhr, I.M.I.; Abdalla, E.A.M.; Fouzy, A.S.M.; Hassan, M.N.A.

    1998-01-01

    Consecutive feeding of lactating goats with methoxy- 14 C-azinphos-methyl fo 4 days at dietary levels of 25 mg and 50 mg/goat per day resulted in the presence 0 the insecticide residues in milk 0.028ppm, 0.068ppm respectively at the end of the administration period. The residue levels were marckedly reduced after a withdrawa period of one week and completely disappeared after two weeks. Analysis of milk an urine residues showed similar metabolites in addition to a very small amount of the parent compound in the milk only. The major part of the residues consisted of mon demethylatedl azinophos-methyl, dimethyl phosphorohthioic, dimethyl phosphoro dithioic acids, dimethyl and mono-methyl phosphates. The animals remaine symptoms-frce during the experimental period

  12. Morphological study and thermal analysis of surface modified α-FeOOH via in situ polymerization of methyl methacrylate

    International Nuclear Information System (INIS)

    Han Yaoxing; Ma Xinsheng; Cao Hongming; Zhang Haiying; Wu Qiufang

    2004-01-01

    Considering the interfacial characteristics of goethite (α-FeOOH, iron oxide yellow), the in situ polymerization of methyl methacrylate was employed to modify the surfaces of α-FeOOH pigments in aqueous slurry. The scanning electron micrographs indicated that the poly(methyl methacrylate) anchored on the surfaces of the particle homogeneously. From this study, it was found that one of the key requirements in the synthesis of the α-FeOOH-PMMA composite was to enhance interfacial compatibility between inorganic particles and organic monomer. Moreover, polymer-treated α-FeOOH particles were easily dispersed in organic medium to form a stable colloid and the heat resistance of α-FeOOH particles was improved

  13. Analysis of rRNA gene methylation in Arabidopsis thaliana by CHEF-Conventional 2D gel electrophoresis

    Science.gov (United States)

    Mohannath, Gireesha; Pikaard, Craig S.

    2017-01-01

    Summary Contour-clamped homogenous electric field (CHEF) gel electrophoresis, a variant of Pulsed-field gel electrophoresis (PFGE), is a powerful technique for resolving large fragments of DNA (10 kb to 9 Mb). CHEF has many applications including the physical mapping of chromosomes, artificial chromosomes and sub-chromosomal DNA fragments, etc. Here we describe the use of CHEF and two-dimensional gel electrophoresis to analyze rRNA gene methylation patterns within the two ~ 4 million base pair nucleolus organizer regions (NORs) of Arabidopsis thaliana. The method involves CHEF gel electrophoresis of agarose-embedded DNA following restriction endonuclease digestion to cut the NORs into large but resolvable segments, followed by digestion with methylation-sensitive restriction endonucleases and conventional (or CHEF) gel electrophoresis, in a second dimension. Resulting products are then detected by Southern blotting or PCR analyses capable of discriminating rRNA gene subtypes. PMID:27576719

  14. Methylation analysis of histone H4K12ac-associated promoters in sperm of healthy donors and subfertile patients

    Czech Academy of Sciences Publication Activity Database

    Vieweg, M.; Dvořáková-Hortová, Kateřina; Dudková, B.; Waliszewski, P.; Otte, M.; Oels, B.; Hajimohammad, A.; Schorsch, M.; Schuppe, H.M.; Weidner, W.; Steger, K.; Paradowska-Dogan, A.

    2015-01-01

    Roč. 7, č. 31 (2015) ISSN 1868-7083 R&D Projects: GA ČR(CZ) GA14-05547S; GA MŠk(CZ) CZ1.05/1.1.00/02.0109 Institutional support: RVO:86652036 Keywords : H4K12ac in spermatozoa * μChIP * promoter methylation * pyrosequencing * subfertility Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.327, year: 2015

  15. MGMT methylation analysis of glioblastoma on the Infinium methylation BeadChip identifies two distinct CpG regions associated with gene silencing and outcome, yielding a prediction model for comparisons across datasets, tumor grades, and CIMP-status.

    Science.gov (United States)

    Bady, Pierre; Sciuscio, Davide; Diserens, Annie-Claire; Bloch, Jocelyne; van den Bent, Martin J; Marosi, Christine; Dietrich, Pierre-Yves; Weller, Michael; Mariani, Luigi; Heppner, Frank L; Mcdonald, David R; Lacombe, Denis; Stupp, Roger; Delorenzi, Mauro; Hegi, Monika E

    2012-10-01

    The methylation status of the O(6)-methylguanine-DNA methyltransferase (MGMT) gene is an important predictive biomarker for benefit from alkylating agent therapy in glioblastoma. Recent studies in anaplastic glioma suggest a prognostic value for MGMT methylation. Investigation of pathogenetic and epigenetic features of this intriguingly distinct behavior requires accurate MGMT classification to assess high throughput molecular databases. Promoter methylation-mediated gene silencing is strongly dependent on the location of the methylated CpGs, complicating classification. Using the HumanMethylation450 (HM-450K) BeadChip interrogating 176 CpGs annotated for the MGMT gene, with 14 located in the promoter, two distinct regions in the CpG island of the promoter were identified with high importance for gene silencing and outcome prediction. A logistic regression model (MGMT-STP27) comprising probes cg12434587 [corrected] and cg12981137 provided good classification properties and prognostic value (kappa = 0.85; log-rank p CIMP) positive tumors was found in glioblastomas from The Cancer Genome Atlas than in low grade and anaplastic glioma cohorts, while in CIMP-negative gliomas MGMT was classified as methylated in approximately 50 % regardless of tumor grade. The proposed MGMT-STP27 prediction model allows mining of datasets derived on the HM-450K or HM-27K BeadChip to explore effects of distinct epigenetic context of MGMT methylation suspected to modulate treatment resistance in different tumor types.

  16. Methyl-Donor and Cofactor Nutrient Intakes in the First 2–3 Years and Global DNA Methylation at Age 4: A Prospective Cohort Study

    Science.gov (United States)

    Taylor, Rachael M.; Smith, Roger; Collins, Clare E.; Mossman, David; Wong-Brown, Michelle W.; Chan, Eng-Cheng; Evans, Tiffany-Jane; Attia, John R.; Smith, Tenele; Butler, Trent

    2018-01-01

    Background: During the early postnatal period, the impact of nutrition on DNA methylation has not been well studied in humans. The aim was to quantify the relationship between one-carbon metabolism nutrient intake during the first three years of life and global DNA methylation levels at four years. Design: Childhood dietary intake was assessed using infant feeding questionnaires, food frequency questionnaires, 4-day weighed food records and 24-h food records. The dietary records were used to estimate the intake of methionine, folate, vitamins B2, B6 and B12 and choline. The accumulative nutrient intake specific rank from three months to three years of age was used for analysis. Global DNA methylation (%5-methyl cytosines (%5-mC)) was measured in buccal cells at four years of age, using an enzyme-linked immunosorbent assay (ELISA) commercial kit. Linear regression models were used to quantify the statistical relationships. Results: Data were collected from 73 children recruited from the Women and their Children’s Health (WATCH) study. No association was found between one-carbon metabolism nutrient intake and global DNA methylation levels (P 0.05). Global DNA methylation levels in males were significantly higher than in females (median %5-mC: 1.82 vs. 1.03, males and females respectively, (P 0.05)). Conclusion: No association was found between the intake of one-carbon metabolism nutrients during the early postnatal period and global DNA methylation levels at age four years. Higher global DNA methylation levels in males warrants further investigation. PMID:29495543

  17. Methyl-Donor and Cofactor Nutrient Intakes in the First 2–3 Years and Global DNA Methylation at Age 4: A Prospective Cohort Study

    Directory of Open Access Journals (Sweden)

    Rachael M. Taylor

    2018-02-01

    Full Text Available Background: During the early postnatal period, the impact of nutrition on DNA methylation has not been well studied in humans. The aim was to quantify the relationship between one-carbon metabolism nutrient intake during the first three years of life and global DNA methylation levels at four years. Design: Childhood dietary intake was assessed using infant feeding questionnaires, food frequency questionnaires, 4-day weighed food records and 24-h food records. The dietary records were used to estimate the intake of methionine, folate, vitamins B2, B6 and B12 and choline. The accumulative nutrient intake specific rank from three months to three years of age was used for analysis. Global DNA methylation (%5-methyl cytosines (%5-mC was measured in buccal cells at four years of age, using an enzyme-linked immunosorbent assay (ELISA commercial kit. Linear regression models were used to quantify the statistical relationships. Results: Data were collected from 73 children recruited from the Women and their Children’s Health (WATCH study. No association was found between one-carbon metabolism nutrient intake and global DNA methylation levels (P > 0.05. Global DNA methylation levels in males were significantly higher than in females (median %5-mC: 1.82 vs. 1.03, males and females respectively, (P < 0.05. Conclusion: No association was found between the intake of one-carbon metabolism nutrients during the early postnatal period and global DNA methylation levels at age four years. Higher global DNA methylation levels in males warrants further investigation.

  18. Educational expansion and the education gradient in health: A hierarchical age-period-cohort analysis.

    Science.gov (United States)

    Delaruelle, Katrijn; Buffel, Veerle; Bracke, Piet

    2015-11-01

    Researchers have recently been investigating the temporal variation in the educational gradient in health. While there is abundant literature concerning age trajectories, theoretical knowledge about cohort differences is relatively limited. Therefore, in analogy with the life course perspective, we introduce two contrasting cohort-specific hypotheses. The diminishing health returns hypothesis predicts a decrease in educational disparities in health across cohorts. By contrast, the cohort accretion hypothesis suggests that the education-health gap will be more pronounced among younger cohorts. To shed light on this, we perform a hierarchical age-period-cohort analysis (HAPC), using data from a subsample of individuals between 25 and 85 years of age (N = 232,573) from 32 countries in the European Social Survey (six waves: 2002-2012). The analysis leads to three important conclusions. First, we observe a widening health gap between different educational levels over the life course. Second, we find that these educational differences in the age trajectories of health seem to strengthen with each successive birth cohort. However, the two age-related effects disappear when we control for employment status, household income, and family characteristics. Last, when adjusting for these mediators, we reveal evidence to support the diminishing health returns hypothesis, implying that it is primarily the direct association between education and health that decreases across cohorts. This finding raises concerns about potential barriers to education being a vehicle for empowerment and the promotion of health. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Analysis of the genetic structure of allopatric populations of Lutzomyia umbratilis using the period clock gene.

    Science.gov (United States)

    de Souza Freitas, Moises Thiago; Ríos-Velasquez, Claudia Maria; da Silva, Lidiane Gomes; Costa, César Raimundo Lima; Marcelino, Abigail; Leal-Balbino, Tereza Cristina; Balbino, Valdir de Queiroz; Pessoa, Felipe Arley Costa

    2016-02-01

    In South America, Lutzomyia umbratilis is the main vector of Leishmania guyanensis, one of the species involved in the transmission of American tegumentary leishmaniasis. In Brazil, L. umbratilis has been recorded in the Amazon region, and an isolated population has been identified in the state of Pernambuco, Northeastern region. This study assessed the phylogeographic structure of three allopatric Brazilian populations of L. umbratilis. Samples of L. umbratilis were collected from Rio Preto da Eva (north of the Amazon River, Amazonas), from Manacapuru (south of the Amazon River), and from the isolated population in Recife, Pernambuco state. These samples were processed to obtain sequences of the period gene. Phylogenetic analysis revealed the presence of two distinct monophyletic clades: one clade comprised of the Recife and Rio Preto da Eva samples, and one clade comprised of the Manacapuru samples. Comparing the Manacapuru population with the Recife and Rio Preto da Eva populations revealed high indices of interpopulational divergence. Phylogenetic analysis indicated that geographical distance and environmental differences have not modified the ancestral relationship shared by the Recife and Rio Preto da Eva populations. Genetic similarities suggest that, in evolutionary terms, these populations are more closely related to each other than to the Manacapuru population. These results confirm the existence of an L. umbratilis species complex composed of at least two incipient species. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Greenhouse gas emissions in Europe: a retrospective trend analysis for the period 1990-2008

    Energy Technology Data Exchange (ETDEWEB)

    Borgan, A.; Gugele, B.; Haider, S. (Umweltbundesamt, Vienna (Austria)) (and others)

    2011-10-15

    This report presents a retrospective overview of the greenhouse gas (GHG) emission trends in Europe from 1990 to 2008, with a particular focus on the underpinning drivers and the influence of EU policies. The analysis is based on the combination of decomposition analyses to identify the respective influence of each identified driver and an overview of the main EU policies and their likely effects on these drivers. The period covered by the analysis stops in 2008. As a result, the analysis avoids the effects of the recent economic crisis on GHG emissions. This reinforces the conclusion on long-term emission drivers. The report covers the EU-27 and presents results for the other EEA member countries (Iceland, Liechtenstein, Norway, Switzerland and Turkey) and Croatia (EU candidate country together with Turkey) as far as data is available. The results can be summarized as: 1) Overall GHG emission trends. EU GHG emissions were reduced between 1990 and 2008. Most of the reductions took place in the 1990s, but emissions have also been decreasing every year from 2003 until the last year considered in this report, 2008. 2) Predominant drivers. For the most part, the GHG emission trends observed in the EU between 1990 and 2008 resulted from economic factors. However, EU policies, some of which were not directly targeting GHG emissions, as well as national policies by some front runner countries, also played a role in these trends. 3) Impacts of EU policies. Between 2000 and 2008, emission trends were more directly targeted by a range of energy and climate policies, e.g. the implementation of the European Climate Change programme. However, the steady increase in energy demand during this period - particularly electricity - outweighed the considerable EU-wide savings generated by energy efficiency improvements and the development of renewable energy. 4) Co-benefits. Taking example from the positive benefits on GHG emissions that resulted from the implementation of non

  1. Stochastic sensitivity analysis of periodic attractors in non-autonomous nonlinear dynamical systems based on stroboscopic map

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Kong-Ming, E-mail: kmguo@xidian.edu.cn [School of Electromechanical Engineering, Xidian University, P.O. Box 187, Xi' an 710071 (China); Jiang, Jun, E-mail: jun.jiang@mail.xjtu.edu.cn [State Key Laboratory for Strength and Vibration, Xi' an Jiaotong University, Xi' an 710049 (China)

    2014-07-04

    To apply stochastic sensitivity function method, which can estimate the probabilistic distribution of stochastic attractors, to non-autonomous dynamical systems, a 1/N-period stroboscopic map for a periodic motion is constructed in order to discretize the continuous cycle into a discrete one. In this way, the sensitivity analysis of a cycle for discrete map can be utilized and a numerical algorithm for the stochastic sensitivity analysis of periodic solutions of non-autonomous nonlinear dynamical systems under stochastic disturbances is devised. An external excited Duffing oscillator and a parametric excited laser system are studied as examples to show the validity of the proposed method. - Highlights: • A method to analyze sensitivity of stochastic periodic attractors in non-autonomous dynamical systems is proposed. • Probabilistic distribution around periodic attractors in an external excited Φ{sup 6} Duffing system is obtained. • Probabilistic distribution around a periodic attractor in a parametric excited laser system is determined.

  2. The association, clinicopathological significance, and diagnostic value of CDH1 promoter methylation in head and neck squamous cell carcinoma: a meta-analysis of 23 studies

    Directory of Open Access Journals (Sweden)

    Shen ZS

    2016-10-01

    Full Text Available Zhisen Shen,1 Chongchang Zhou,1,2 Jinyun Li,2 Hongxia Deng,1 Qun Li,1 Jian Wang3 1Department of Otorhinolaryngology-Head and Neck Surgery, Lihuili Hospital, Ningbo University, 2Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, 3Department of Otorhinolaryngology-Head and Neck Surgery, Ningbo Yinzhou People’s Hospital, Ningbo, Zhejiang, People’s Republic of China Abstract: Epithelial cadherin (encoded by the CDH1 gene is a tumor suppressor glycoprotein that plays a role in the invasion and metastasis of human cancers. As previous studies regarding the association between CDH1 promoter methylation and head and neck squamous cell carcinoma (HNSCC have yielded inconsistent conclusions, a meta-analysis was performed. A systematic literature review was undertaken from four databases: PubMed, Embase, Google Scholar, and Web of Science. Finally, a total of 23 studies (including 1,727 cases of HNSCC and 555 normal controls were included in the present study. Our results showed that the frequency of CDH1 promoter methylation in HNSCC was statistically greater than in controls (odds ratio [OR] =5.94, 95% confidence interval [CI]: 3.36–10.51, P<0.001. In reported cases of HNSCC, CDH1 promoter methylation was statistically associated with tumor stage (OR =0.46, 95% CI: 0.27–0.78, P=0.004 and a history of alcohol consumption (OR =6.04, 95% CI: 2.41–15.14, P<0.001. Moreover, the sensitivity, specificity, and area under the curve of the summary receiver operator characteristic for the included studies were 0.50 (95% CI: 0.4–0.61, 0.89 (95% CI: 0.79–0.95, and 0.74 (95% CI: 0.70–0.78, respectively. In conclusion, our meta-analyses indicated that CDH1 promoter methylation was associated with HNSCC risk, and may be utilized as a valuable diagnostic biomarker for HNSCC. Keywords: CDH1, methylation, diagnosis, head and neck squamous cell carcinoma, HNSCC 

  3. An international contrast of rates of placental abruption: an age-period-cohort analysis.

    Directory of Open Access Journals (Sweden)

    Cande V Ananth

    Full Text Available Although rare, placental abruption is implicated in disproportionately high rates of perinatal morbidity and mortality. Understanding geographic and temporal variations may provide insights into possible amenable factors of abruption. We examined abruption frequencies by maternal age, delivery year, and maternal birth cohorts over three decades across seven countries.Women that delivered in the US (n = 863,879; 1979-10, Canada (4 provinces, n = 5,407,463; 1982-11, Sweden (n = 3,266,742; 1978-10, Denmark (n = 1,773,895; 1978-08, Norway (n = 1,780,271, 1978-09, Finland (n = 1,411,867; 1987-10, and Spain (n = 6,151,508; 1999-12 were analyzed. Abruption diagnosis was based on ICD coding. Rates were modeled using Poisson regression within the framework of an age-period-cohort analysis, and multi-level models to examine the contribution of smoking in four countries.Abruption rates varied across the seven countries (3-10 per 1000, Maternal age showed a consistent J-shaped pattern with increased rates at the extremes of the age distribution. In comparison to births in 2000, births after 2000 in European countries had lower abruption rates; in the US there was an increase in rate up to 2000 and a plateau thereafter. No birth cohort effects were evident. Changes in smoking prevalence partially explained the period effect in the US (P = 0.01 and Sweden (P<0.01.There is a strong maternal age effect on abruption. While the abruption rate has plateaued since 2000 in the US, all other countries show declining rates. These findings suggest considerable variation in abruption frequencies across countries; differences in the distribution of risk factors, especially smoking, may help guide policy to reduce abruption rates.

  4. An international contrast of rates of placental abruption: an age-period-cohort analysis.

    Science.gov (United States)

    Ananth, Cande V; Keyes, Katherine M; Hamilton, Ava; Gissler, Mika; Wu, Chunsen; Liu, Shiliang; Luque-Fernandez, Miguel Angel; Skjærven, Rolv; Williams, Michelle A; Tikkanen, Minna; Cnattingius, Sven

    2015-01-01

    Although rare, placental abruption is implicated in disproportionately high rates of perinatal morbidity and mortality. Understanding geographic and temporal variations may provide insights into possible amenable factors of abruption. We examined abruption frequencies by maternal age, delivery year, and maternal birth cohorts over three decades across seven countries. Women that delivered in the US (n = 863,879; 1979-10), Canada (4 provinces, n = 5,407,463; 1982-11), Sweden (n = 3,266,742; 1978-10), Denmark (n = 1,773,895; 1978-08), Norway (n = 1,780,271, 1978-09), Finland (n = 1,411,867; 1987-10), and Spain (n = 6,151,508; 1999-12) were analyzed. Abruption diagnosis was based on ICD coding. Rates were modeled using Poisson regression within the framework of an age-period-cohort analysis, and multi-level models to examine the contribution of smoking in four countries. Abruption rates varied across the seven countries (3-10 per 1000), Maternal age showed a consistent J-shaped pattern with increased rates at the extremes of the age distribution. In comparison to births in 2000, births after 2000 in European countries had lower abruption rates; in the US there was an increase in rate up to 2000 and a plateau thereafter. No birth cohort effects were evident. Changes in smoking prevalence partially explained the period effect in the US (P = 0.01) and Sweden (Prate has plateaued since 2000 in the US, all other countries show declining rates. These findings suggest considerable variation in abruption frequencies across countries; differences in the distribution of risk factors, especially smoking, may help guide policy to reduce abruption rates.

  5. Studies on molecular structure, vibrational spectra and molecular docking analysis of 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate

    Science.gov (United States)

    Suresh, D. M.; Amalanathan, M.; Hubert Joe, I.; Bena Jothy, V.; Diao, Yun-Peng

    2014-09-01

    The molecular structure, vibrational analysis and molecular docking analysis of the 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate (MDDNAB) molecule have been carried out using FT-IR and FT-Raman spectroscopic techniques and DFT method. The equilibrium geometry, harmonic vibrational wave numbers, various bonding features have been computed using density functional method. The calculated molecular geometry has been compared with experimental data. The detailed interpretation of the vibrational spectra has been carried out by using VEDA program. The hyper-conjugative interactions and charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The simulated FT-IR and FT-Raman spectra satisfactorily coincide with the experimental spectra. The PES and charge analysis have been made. The molecular docking was done to identify the binding energy and the Hydrogen bonding with the cancer protein molecule.

  6. ANOVA Analysis of Student Daily Test Scores in Multi-Day Test Periods

    Science.gov (United States)

    Mouritsen, Matthew L.; Davis, Jefferson T.; Jones, Steven C.

    2016-01-01

    Instructors are often concerned when giving multiple-day tests because students taking the test later in the exam period may have an advantage over students taking the test early in the exam period due to information leakage. However, exam scores seemed to decline as students took the same test later in a multi-day exam period (Mouritsen and…

  7. Simultaneous analysis of Grazing Incidence X-Ray reflectivity and X-ray standing waves from periodic multilayer systems

    NARCIS (Netherlands)

    Yakunin, S.N.; Makhotkin, Igor Alexandrovich; Chuyev, M.A.; Seregin, A.Y.; Pashayev, E.M.; Louis, Eric; van de Kruijs, Robbert Wilhelmus Elisabeth; Bijkerk, Frederik; Kovalchuk, M.V.

    2012-01-01

    Structural analysis of periodic multilayers with small period thickness (~4 nm) is a challenging task, especially when thicknesses of intermixed interfaces become comparable to individual layer thicknesses. In general, angular dependent X-ray fluorescence measurements, excited by the X-ray standing

  8. Poly(styrene-co-N-methacryloyl-l-phenylalanine methyl ester)-functionalized magnetic nanoparticles as sorbents for the analysis of sodium benzoate in beverages.

    Science.gov (United States)

    Ji, Shilei; Li, Nan; Qi, Li; Wang, Minglin

    2017-01-01

    In this study, poly(styrene-co-N-methacryloyl-l-phenylalanine methyl ester)-functionalized magnetic nanoparticles were constructed and used as magnetic solid-phase extraction sorbents for analysis of food preservatives in beverages. To prepare the poly(amino acid)-based sorbents, N-methacryloyl-l-phenylalanine methyl ester, and styrene served as the functional monomers and modified onto the magnetic nanoparticles via free radical polymerization. Interestingly, compared with propylparaben and potassium sorbate, the proposed poly(amino acid)-based sorbents showed a good selectivity to sodium benzoate. The adsorption capacity of the sorbents to sodium benzoate was 6.08 ± 0.31 mg/g. Moreover, the fast adsorption equilibrium could be reached within 5 min. Further, the resultant poly(amino acid)-based sorbents were applied in the analysis of sodium benzoate in real beverage samples. The results proved that the proposed magnetic solid-phase extraction sorbents have a great potential for the analysis of preservatives in food samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. The comparative analysis of results of surgical treatment of myasthenia in the remote periods of disease

    Directory of Open Access Journals (Sweden)

    L. Zaslavsky

    2016-01-01

    Full Text Available Based on long-term follow-up to perform comparative analysis of long-term results of surgical treatment of myasthenia. A retrospective analysis of long-term results of surgical treatment of 146 patients with myasthenia has been carried out. We used the modified Keynes classification to estimate the severity of myasthenia and to summarize the data relating to therapy volume and treatment results. In dependence on the type of thymus lesion patients were divided into two groups. Thymus hyperplasia was verified at — 106 (72.6 % patients, tumor lesion of the thymus gland (thymoma — at 40 (27.4 % ones. The results were estimated in the following periods after thymectomy: 1—2 years, 3—4 years, 5—6 years, 7 — 9 years, 10—14 years, and over 15 years. Short- and longterm results of surgical treatment of myasthenia for the patients without tumor lesions of the thymus gland were significantly better. Positive effects of surgical treatment of myasthenia in patients with hyperplasia are observed after 1 year of surgery (p = 0.0023, and the best results are observed after 5 — 6 year of the disease, then after 7 — 9 year one notes some deterioration of state (p = 0.026. In the myasthenia patients with thymoma one notes the similar trends in dynamics of state, but in general, the results are significantly (p = 0.042 badly than in the group of the patients with hyperplasia. Starting from the first year after operation treatment the patients with myasthenia with thymus hyperplasia have statistically significant (p = 0.048 decrease of average doses of glucocorticoids, and anticholinesterase drugs. The statistically best treatment results were noted for the patients operated at the first year of the disease. Positive result of surgical treatment of myasthenia is noted both in the short- and long-term period and at thymomas. In the group of patients with thymoma one has noted significantly badly results in comparison with group of hyperplasia. It is

  10. Mental health consultations in the perinatal period: a cost-analysis of Medicare services provided to women during a period of intense mental health reform in Australia.

    Science.gov (United States)

    Chambers, Georgina M; Randall, Sean; Mihalopoulos, Cathrine; Reilly, Nicole; Sullivan, Elizabeth A; Highet, Nicole; Morgan, Vera A; Croft, Maxine L; Chatterton, Mary Lou; Austin, Marie-Paule

    2017-12-05

    Objective To quantify total provider fees, benefits paid by the Australian Government and out-of-pocket patients' costs of mental health Medicare Benefits Schedule (MBS) consultations provided to women in the perinatal period (pregnancy to end of the first postnatal year). Method A retrospective study of MBS utilisation and costs (in 2011-12 A$) for women giving birth between 2006 and 2010 by state, provider-type, and geographic remoteness was undertaken. Results The cost of mental health consultations during the perinatal period was A$17.5million for women giving birth in 2007, rising to A$29million in 2010. Almost 9% of women giving birth in 2007 had a mental health consultation compared with more than 14% in 2010. An increase in women accessing consultations, along with an increase in the average number of consultations received, were the main drivers of the increased cost, with costs per service remaining stable. There was a shift to non-specialist care and bulk billing rates increased from 44% to 52% over the study period. In 2010, the average total cost (provider fees) per woman accessing mental health consultations during the perinatal period was A$689, and the average cost per service was A$133. Compared with women residing in regional and remote areas, women residing in major cities where more likely to access consultations, and these were more likely to be with a psychiatrist rather than an allied health professional or general practitioner. Conclusion Increased access to mental health consultations has coincided with the introduction of recent mental health initiatives, however disparities exist based on geographic location. This detailed cost analysis identifies inequities of access to perinatal mental health services in regional and remote areas and provides important data for economic and policy analysis of future mental health initiatives. What is known about the topic? The mental healthcare landscape in Australia has changed significantly over the

  11. A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray

    Directory of Open Access Journals (Sweden)

    Qiao Yingjuan

    2008-01-01

    Full Text Available Abstract Background DNA methylation based techniques are important tools in both clinical diagnostics and therapeutics. But most of these methods only analyze a few CpG sites in a target region. Indeed, difference of site-specific methylation may also lead to a change of methylation density in many cases, and it has been found that the density of methylation is more important than methylation of single CpG site for gene silencing. Results We have developed a novel approach for quantitative analysis of CpG methylation density on the basis of microarray-based hybridization and incorporation of Cy5-dCTP into the Cy3 labeled target DNA by using Taq DNA Polymerase on microarray. The quantification is achieved by measuring Cy5/Cy3 signal ratio which is proportional to methylation density. This methylation-sensitive technique, termed RMEAM (regional methylation elongation assay on microarray, provides several advantages over existing methods used for methylation analysis. It can determine an exact methylation density of the given region, and has potential of high throughput. We demonstrate a use of this method in determining the methylation density of the promoter region of the tumor-related gene MLH1, TERT and MGMT in colorectal carcinoma patients. Conclusion This technique allows for quantitative analysis of regional methylation density, which is the representative of all allelic methylation patterns in the sample. The results show that this technique has the characteristics of simplicity, rapidness, specificity and high-throughput.

  12. Scattering analysis of periodic structures using finite-difference time-domain

    CERN Document Server

    ElMahgoub, Khaled; Elsherbeni, Atef Z

    2012-01-01

    Periodic structures are of great importance in electromagnetics due to their wide range of applications such as frequency selective surfaces (FSS), electromagnetic band gap (EBG) structures, periodic absorbers, meta-materials, and many others. The aim of this book is to develop efficient computational algorithms to analyze the scattering properties of various electromagnetic periodic structures using the finite-difference time-domain periodic boundary condition (FDTD/PBC) method. A new FDTD/PBC-based algorithm is introduced to analyze general skewed grid periodic structures while another algor

  13. Bifurcation analysis of the logistic map via two periodic impulsive forces

    International Nuclear Information System (INIS)

    Jiang Hai-Bo; Li Tao; Zeng Xiao-Liang; Zhang Li-Ping

    2014-01-01

    The complex dynamics of the logistic map via two periodic impulsive forces is investigated in this paper. The influences of the system parameter and the impulsive forces on the dynamics of the system are studied respectively. With the parameter varying, the system produces the phenomenon such as periodic solutions, chaotic solutions, and chaotic crisis. Furthermore, the system can evolve to chaos by a cascading of period-doubling bifurcations. The Poincaré map of the logistic map via two periodic impulsive forces is constructed and its bifurcation is analyzed. Finally, the Floquet theory is extended to explore the bifurcation mechanism for the periodic solutions of this non-smooth map. (general)

  14. Cross platform analysis of methylation, miRNA and stem cell gene expression data in germ cell tumors highlights characteristic differences by tumor histology

    International Nuclear Information System (INIS)

    Poynter, Jenny N.; Bestrashniy, Jessica R. B. M.; Silverstein, Kevin A. T.; Hooten, Anthony J.; Lees, Christopher; Ross, Julie A.; Tolar, Jakub

    2015-01-01

    Alterations in methylation patterns, miRNA expression, and stem cell protein expression occur in germ cell tumors (GCTs). Our goal is to integrate molecular data across platforms to identify molecular signatures in the three main histologic subtypes of Type I and Type II GCTs (yolk sac tumor (YST), germinoma, and teratoma). We included 39 GCTs and 7 paired adjacent tissue samples in the current analysis. Molecular data available for analysis include DNA methylation data (Illumina GoldenGate Cancer Methylation Panel I), miRNA expression (NanoString nCounter miRNA platform), and stem cell factor expression (SABiosciences Human Embryonic Stem Cell Array). We evaluated the cross platform correlations of the data features using the Maximum Information Coefficient (MIC). In analyses of individual datasets, differences were observed by tumor histology. Germinomas had higher expression of transcription factors maintaining stemness, while YSTs had higher expression of cytokines, endoderm and endothelial markers. We also observed differences in miRNA expression, with miR-371-5p, miR-122, miR-302a, miR-302d, and miR-373 showing elevated expression in one or more histologic subtypes. Using the MIC, we identified correlations across the data features, including six major hubs with higher expression in YST (LEFTY1, LEFTY2, miR302b, miR302a, miR 126, and miR 122) compared with other GCT. While prognosis for GCTs is overall favorable, many patients experience resistance to chemotherapy, relapse and/or long term adverse health effects following treatment. Targeted therapies, based on integrated analyses of molecular tumor data such as that presented here, may provide a way to secure high cure rates while reducing unintended health consequences

  15. Climate impact on airborne particulate matter concentrations in California using seven year analysis periods

    Directory of Open Access Journals (Sweden)

    A. Mahmud

    2010-11-01

    Full Text Available The effect of global climate change on the annual average concentration of fine particulate matter (PM2.5 in California was studied using a climate-air quality modeling system composed of global through regional models. Output from the NCAR/DOE Parallel Climate Model (PCM generated under the "business as usual" global emissions scenario was downscaled using the Weather Research and Forecasting (WRF model followed by air quality simulations using the UCD/CIT airshed model. The system represents major atmospheric processes acting on gas and particle phase species including meteorological effects on emissions, advection, dispersion, chemical reaction rates, gas-particle conversion, and dry/wet deposition. The air quality simulations were carried out for the entire state of California with a resolution of 8-km for the years 2000–2006 (present climate with present emissions and 2047–2053 (future climate with present emissions. Each of these 7-year analysis periods was analyzed using a total of 1008 simulated days to span a climatologically relevant time period with a practical computational burden. The 7-year windows were chosen to properly account for annual variability with the added benefit that the air quality predictions under the present climate could be compared to actual measurements. The climate-air quality modeling system successfully predicted the spatial pattern of present climate PM2.5 concentrations in California but the absolute magnitude of the annual average PM2.5 concentrations were under-predicted by ~4–39% in the major air basins. The majority of this under-prediction was caused by excess ventilation predicted by PCM-WRF that should be present to the same degree in the current and future time periods so that the net bias introduced into the comparison is minimized.

    Surface temperature, relative humidity (RH, rain rate, and wind speed were predicted to increase in the future climate

  16. Maternal intake of methyl-group donors affects DNA methylation of metabolic genes in infants.

    Science.gov (United States)

    Pauwels, Sara; Ghosh, Manosij; Duca, Radu Corneliu; Bekaert, Bram; Freson, Kathleen; Huybrechts, Inge; Langie, Sabine A S; Koppen, Gudrun; Devlieger, Roland; Godderis, Lode

    2017-01-01

    Maternal nutrition during pregnancy and infant nutrition in the early postnatal period (lactation) are critically involved in the development and health of the newborn infant. The Maternal Nutrition and Offspring's Epigenome (MANOE) study was set up to assess the effect of maternal methyl-group donor intake (choline, betaine, folate, methionine) on infant DNA methylation. Maternal intake of dietary methyl-group donors was assessed using a food-frequency questionnaire (FFQ). Before and during pregnancy, we evaluated maternal methyl-group donor intake through diet and supplementation (folic acid) in relation to gene-specific ( IGF2 DMR, DNMT1 , LEP , RXRA ) buccal epithelial cell DNA methylation in 6 months old infants ( n  = 114) via pyrosequencing. In the early postnatal period, we determined the effect of maternal choline intake during lactation (in mothers who breast-fed for at least 3 months) on gene-specific buccal DNA methylation ( n  = 65). Maternal dietary and supplemental intake of methyl-group donors (folate, betaine, folic acid), only in the periconception period, was associated with buccal cell DNA methylation in genes related to growth ( IGF2 DMR), metabolism ( RXRA ), and appetite control ( LEP ). A negative association was found between maternal folate and folic acid intake before pregnancy and infant LEP (slope = -1.233, 95% CI -2.342; -0.125, p  = 0.0298) and IGF2 DMR methylation (slope = -0.706, 95% CI -1.242; -0.107, p  = 0.0101), respectively. Positive associations were observed for maternal betaine (slope = 0.875, 95% CI 0.118; 1.633, p  = 0.0241) and folate (slope = 0.685, 95% CI 0.245; 1.125, p  = 0.0027) intake before pregnancy and RXRA methylation. Buccal DNMT1 methylation in the infant was negatively associated with maternal methyl-group donor intake in the first and second trimester of pregnancy and negatively in the third trimester. We found no clear association between maternal choline intake

  17. Methylation in hepatocellular carcinoma

    Directory of Open Access Journals (Sweden)

    Regina M. Santella

    2007-02-01

    epigenetic aberrations as DNA isolated from an individual's tumor. The process by which tumor DNA is released into circulating blood is unclear but may result from accelerated necrosis, apoptosis or other processes. p53 mutation and p16 promoter hypermethylation have been detected in paired tumor and plasma of HCC cases. More recently, we investigated promoter hypermethylation in DNA isolated from the serum of HCC patients who provided repeated blood samples prior to diagnosis and controls enrolled in a cancer screen program in Taiwan. Among cases, aberrant methylation was found in serum DNA one to nine years before clinical HCC diagnosis. RASSF1A had the highest frequency of hypermethylation with 70% of cases having at least one positive sample compared to 44% for p16 and 22% for p15. For the controls, promoter hypermethylation was found in 6 and 4% of subjects for RASSF1A and p16, respectively; none had methylation of p15. An ROC curve that included clinical risk factors (age, HBsAg status, anti-HCV status, smoking, alcohol status and hypermethylation biomarkers gave an overall predictive accuracy of 89% with sensitivity and specificity 84% and 94%, respectively. The analysis of epigenetic changes on RASSF1A, p16 and p15 tumor suppressor genes in serum DNA may be a valuable biomarkers for early detection in populations at high risk of HCC. In addition, the area of global hypomethylation remains largely unexplored in HCC.

  18. Analysis of a yearly multi-round, multi-period, multi-product transmission rights auction

    International Nuclear Information System (INIS)

    Ziogos, N.P.; Bakirtzis, A.G.

    2008-01-01

    A yearly multi-round, multi-period, multi-product transmission rights (TR) auction issuing both point-to-point Financial Transmission Rights (FTRs) and Flow-Gate Rights (FGRs) is studied in this paper. In each round the TR market participants (buyers or sellers) submit their bid or offer prices based on past energy market performance. A Locational Marginal Pricing (LMP) based energy market is assumed. The TR market participants' bid or offer prices reflect their expectation of the average annual LMP differences between withdrawal and injections points for FTRs and of the transmission link capacity prices for FGRs. The TR auction is performed in four rounds; in each round 25% of the entire system capability is awarded. TRs that are awarded in one round are modeled as fixed injections in subsequent rounds. Market participants that have acquired TRs in one round can sell them in subsequent rounds. A market participant can submit bids or offers for on-peak, off-peak or 24-h TRs. A three-area, nine-bus test system with six TR market participants is used for the analysis of the TR auction. (author)

  19. A parametric analysis of periodic and coupled heat and mass diffusion in desiccant wheels

    International Nuclear Information System (INIS)

    Nóbrega, Carlos E.L.

    2014-01-01

    Solid sorbents are frequently adopted for gas component separation in the chemical industry. Over the last decades, solid sorbents have also been applied for the benefit of indoor air quality and humidity control in modern building design. Adsorptive rotors have been designed for the removal of water vapor, CO and VOCs from indoor environments. Although the adsorption of water vapor by a specific adsorbent (particularly silica-gel) has been extensively studied, a non-dimensional parametric analysis of humidity adsorption on a nonspecific hygroscopic material appears to be an original contribution to the literature. Accordingly, a mathematical model using non-dimensional parameters is built from energy and mass balances applied to elementary control volumes. The periodic nature of the cyclic adsorption/desorption processes requires an iterative solution, which is carried out by comparing temperature and mass distributions at the onset to the distributions by the end of the cycle. - Highlights: • Fully non-dimensional model of heat and mass transfer in a hygroscopic channel. • Investigation of mass and energy diffusion through the hygroscopic layer. • Analytic modeling of the heat of adsorption

  20. Evaluating the efficiency of a zakat institution over a period of time using data envelopment analysis

    Science.gov (United States)

    Krishnan, Anath Rau; Hamzah, Ahmad Aizuddin

    2017-08-01

    It is crucial for a zakat institution to evaluate and understand how efficiently they have operated in the past, thus ideal strategies could be developed for future improvement. However, evaluating the efficiency of a zakat institution is actually a challenging process as it involves the presence of multiple inputs or/and outputs. This paper proposes a step-by-step procedure comprising two data envelopment analysis models, namely dual Charnes-Cooper-Rhodes and slack-based model to quantitatively measure the overall efficiency of a zakat institution over a period of time. The applicability of the proposed procedure was demonstrated by evaluating the efficiency of Pusat Zakat Sabah, Malaysia from the year of 2007 up to 2015 by treating each year as a decision making unit. Two inputs (i.e. number of staff and number of branches) and two outputs (i.e. total collection and total distribution) were used to measure the overall efficiency achieved each year. The causes of inefficiency and strategy for future improvement were discussed based on the results.

  1. Bibliometric analysis of scientific literature on intestinal parasites in Argentina during the period 1985-2014.

    Science.gov (United States)

    Basualdo, Juan A; Grenóvero, María S; Bertucci, Evangelina; Molina, Nora B

    2016-01-01

    The study of scientific production is a good indicator of the progress in research and knowledge generation. Bibliometrics is a scientific discipline that uses a set of indicators to quantitatively express the bibliographic characteristics of scientific publications. The scientific literature on the epidemiology of intestinal parasites in Argentina is scattered in numerous sources, hindering access and visibility to the scientific community. Our purpose was to perform a quantitative, bibliometric study of the scientific literature on intestinal parasites in humans in Argentina published in the period 1985-2014. This bibliometric analysis showed an increase in the number of articles on intestinal parasites in humans in Argentina published over the past 30 years. Those articles showed a collaboration index similar to that of the literature, with a high index of institutionality for national institutions and a very low one for international collaboration. The original articles were published in scientific journals in the American Continent, Europe and Asia. The use of bibliometric indicators can provide a solid tool for the diagnosis and survey of the research on epidemiology of intestinal parasites and contributes to the dissemination and visibility of information on the scientific production developed in Argentina. Copyright © 2016 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  2. Rainfall Data Analysis and Study of Meteorological Draught in Iraq for the Period 1970-2010

    Directory of Open Access Journals (Sweden)

    Taymoor A. Awchi

    2018-01-01

    Full Text Available This work aimed to analyze and evaluate the metrological draught in Iraq. Monthly rainfalldata were collected from 22 meteorological stations scattered all over Iraq for the period 1970-2010. Various statistical tests have been performed to examine the data accuracy, e.g.Consistency test, Trend analysis, as well as homogeneity test. The Standard Precipitation Index(SPI and Theory of Runs are used to analyze the metrological draught and evaluating thedraught characteristics. SPI values have been estimated for 12-month time scale, from Januaryto December. To analyze the drought characteristics, the accumulative deficit, drought durationand intensity for each station have been estimated. The results showed that the rainfall dataseries considered in the study are all consistent with negative trends except Hilla station, random except Haditha and Samawah stations and homogeneous. It was shown that the study area has been suffered from sequent drought events through nearly half of the years considered in the study, and the worst were in 1997-2001 and 2007-2010 in which extreme droughts were dominated several parts of study area.

  3. The environmental radioactivity data analysis at the inr platform in the post-chernobyl period

    International Nuclear Information System (INIS)

    Tudor, G.; Valeca, M.; Iordache, R.

    2016-01-01

    As a result of the Chernobyl accident, large quantities of radioactive substances were released into the atmosphere and were transported long distances, covering virtually the whole Europe, including Romania. This paper presents the analysis of the environment radioactivity data around the INR site, in the post-Chernobyl period in different types of samples. The purpose of this study was to evaluate the evolution of Chernobyl originated radionuclides concentration in Mioveni-Pitesti area. The selected indicator was Cs-137, which was monitored on a regular basis. From the post-Chernobyl annual reports, were collected the average values for Cs-137 activity in environmental samples. The concentration was determined for eleven sampling locations (soil and vegetation samples) distributed on 10 km distance around INR site, and the determination was made using gamma spectrometry. The data reveals significant variations of the Cs-137 activity. These variations may be generated by various disturbances that detach material from the soil and air, therefore allowing the substance to travel long distances from its origin. (authors)

  4. The joint return period analysis of natural disasters based on monitoring and statistical modeling of multidimensional hazard factors

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xueqin [State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Beijing 100875 (China); National Marine Environmental Monitoring Center, State Oceanic Administration, Dalian 116023 (China); School of Social Development and Public Policy, Beijing Normal University, Beijing 100875 (China); Li, Ning [State Key Laboratory of Earth Surface Processes and Resource Ecology, Beijing Normal University, Beijing 100875 (China); Yuan, Shuai, E-mail: syuan@nmemc.org.cn [National Marine Environmental Monitoring Center, State Oceanic Administration, Dalian 116023 (China); Xu, Ning; Shi, Wenqin; Chen, Weibin [National Marine Environmental Monitoring Center, State Oceanic Administration, Dalian 116023 (China)

    2015-12-15

    As a random event, a natural disaster has the complex occurrence mechanism. The comprehensive analysis of multiple hazard factors is important in disaster risk assessment. In order to improve the accuracy of risk analysis and forecasting, the formation mechanism of a disaster should be considered in the analysis and calculation of multi-factors. Based on the consideration of the importance and deficiencies of multivariate analysis of dust storm disasters, 91 severe dust storm disasters in Inner Mongolia from 1990 to 2013 were selected as study cases in the paper. Main hazard factors from 500-hPa atmospheric circulation system, near-surface meteorological system, and underlying surface conditions were selected to simulate and calculate the multidimensional joint return periods. After comparing the simulation results with actual dust storm events in 54 years, we found that the two-dimensional Frank Copula function showed the better fitting results at the lower tail of hazard factors and that three-dimensional Frank Copula function displayed the better fitting results at the middle and upper tails of hazard factors. However, for dust storm disasters with the short return period, three-dimensional joint return period simulation shows no obvious advantage. If the return period is longer than 10 years, it shows significant advantages in extreme value fitting. Therefore, we suggest the multivariate analysis method may be adopted in forecasting and risk analysis of serious disasters with the longer return period, such as earthquake and tsunami. Furthermore, the exploration of this method laid the foundation for the prediction and warning of other nature disasters. - Highlights: • A method to estimate the multidimensional joint return periods is presented. • 2D function allows better fitting results at the lower tail of hazard factors. • Three-dimensional simulation has obvious advantages in extreme value fitting. • Joint return periods are closer to the reality

  5. The joint return period analysis of natural disasters based on monitoring and statistical modeling of multidimensional hazard factors

    International Nuclear Information System (INIS)

    Liu, Xueqin; Li, Ning; Yuan, Shuai; Xu, Ning; Shi, Wenqin; Chen, Weibin

    2015-01-01

    As a random event, a natural disaster has the complex occurrence mechanism. The comprehensive analysis of multiple hazard factors is important in disaster risk assessment. In order to improve the accuracy of risk analysis and forecasting, the formation mechanism of a disaster should be considered in the analysis and calculation of multi-factors. Based on the consideration of the importance and deficiencies of multivariate analysis of dust storm disasters, 91 severe dust storm disasters in Inner Mongolia from 1990 to 2013 were selected as study cases in the paper. Main hazard factors from 500-hPa atmospheric circulation system, near-surface meteorological system, and underlying surface conditions were selected to simulate and calculate the multidimensional joint return periods. After comparing the simulation results with actual dust storm events in 54 years, we found that the two-dimensional Frank Copula function showed the better fitting results at the lower tail of hazard factors and that three-dimensional Frank Copula function displayed the better fitting results at the middle and upper tails of hazard factors. However, for dust storm disasters with the short return period, three-dimensional joint return period simulation shows no obvious advantage. If the return period is longer than 10 years, it shows significant advantages in extreme value fitting. Therefore, we suggest the multivariate analysis method may be adopted in forecasting and risk analysis of serious disasters with the longer return period, such as earthquake and tsunami. Furthermore, the exploration of this method laid the foundation for the prediction and warning of other nature disasters. - Highlights: • A method to estimate the multidimensional joint return periods is presented. • 2D function allows better fitting results at the lower tail of hazard factors. • Three-dimensional simulation has obvious advantages in extreme value fitting. • Joint return periods are closer to the reality

  6. Dissociation dynamics of methylal

    Energy Technology Data Exchange (ETDEWEB)

    Beaud, P; Frey, H -M; Gerber, T; Mischler, B; Radi, P P; Tzannis, A -P [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1999-08-01

    The dissociation of methylal is investigated using mass spectrometry, combined with a pyrolytic radical source and femtosecond pump probe experiments. Based on preliminary results two reaction paths of methylal dissociation are proposed and discussed. (author) 4 fig., 3 refs.

  7. DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes.

    Directory of Open Access Journals (Sweden)

    Dimos Gaidatzis

    2014-02-01

    Full Text Available For the most part metazoan genomes are highly methylated and harbor only small regions with low or absent methylation. In contrast, partially methylated domains (PMDs, recently discovered in a variety of cell lines and tissues, do not fit this paradigm as they show partial methylation for large portions (20%-40% of the genome. While in PMDs methylation levels are reduced on average, we found that at single CpG resolution, they show extensive variability along the genome outside of CpG islands and DNase I hypersensitive sites (DHS. Methylation levels range from 0% to 100% in a roughly uniform fashion with only little similarity between neighboring CpGs. A comparison of various PMD-containing methylomes showed that these seemingly disordered states of methylation are strongly conserved across cell types for virtually every PMD. Comparative sequence analysis suggests that DNA sequence is a major determinant of these methylation states. This is further substantiated by a purely sequence based model which can predict 31% (R(2 of the variation in methylation. The model revealed CpG density as the main driving feature promoting methylation, opposite to what has been shown for CpG islands, followed by various dinucleotides immediately flanking the CpG and a minor contribution from sequence preferences reflecting nucleosome positioning. Taken together we provide a reinterpretation for the nucleotide-specific methylation levels observed in PMDs, demonstrate their conservation across tissues and suggest that they are mainly determined by specific DNA sequence features.

  8. Experimental vapor pressures (from 1 Pa to 100 kPa) of six saturated Fatty Acid Methyl Esters (FAMEs): Methyl hexanoate, methyl octanoate, methyl decanoate, methyl dodecanoate, methyl tetradecanoate and methyl hexadecanoate

    International Nuclear Information System (INIS)

    Sahraoui, Lakhdar; Khimeche, Kamel; Dahmani, Abdallah; Mokbel, Ilham; Jose, Jacques

    2016-01-01

    Highlight: • Vapor-liquid equilibria, Enthalpy of Vaporization, saturated Fatty Acid Methyl Ester. - Abstract: Vapor pressures of six saturated Fatty Acid Methyl Esters (FAMEs), methyl hexanoate (or methyl caproate), methyl octanoate (or methyl caprylate), Methyl decanoate (or methyl caprate), methyl dodecanoate (or methyl laurate), methyl tetradecanoate (or methyl myristate), and methyl hexadecanoate (or methyl palmitate) were measured from 1 Pa to 100 kPa and at temperature range between 262 and 453 K using a static apparatus. The experimental data (P-T) were compared with the available literature data.

  9. Prognostic value of CpG island methylator phenotype among hepatocellular carcinoma patients: A systematic review and meta-analysis.

    Science.gov (United States)

    Wang, Qian; Wang, Gang; Liu, Chaoxu; He, Xianli

    2018-04-24

    CpG island methylator phenotype (CIMP), characterized by multiple genes are concurrently methylated, has been reported to be associated with the prognosis of colorectal cancer. However, current studies have not explored the relationship between CIMP status with hepatocellular carcinoma (HCC) clinicopathological features. To assess these associations, we performed a comprehensive search of PubMed, EMBASE, and the Web of Science to identify all eligible studies. Publication bias was tested using Begg's and Egger's test. Seven studies that involved 568 HCC patients (379 CIMP+ and 189 CIMP-) were eligible for inclusion in our study. CIMP+ in HCC was significantly associated with distant metastasis (OR = 4.28, 95% CI = 2.57-7.10, P 300 ng/ml) than those with CIMP- (OR = 2.63, 95% CI = 1.79,3.89, P CIMP+ was associated with an unfavorable overall survival (OS) (HR = 3.02, 95% CI = 1.60-5.70, P CIMP is independently associated with significantly worse prognosis in HCC patients. Examination of CIMP status may be useful for identifying patients who are at higher risk for disease progression. Copyright © 2018 IJS Publishing Group Ltd. Published by Elsevier Ltd. All rights reserved.

  10. Meta-analysis of promoter methylation in eight tumor-suppressor genes and its association with the risk of thyroid cancer.

    Directory of Open Access Journals (Sweden)

    Fatemeh Khatami

    Full Text Available Promoter methylation in a number of tumor-suppressor genes (TSGs can play crucial roles in the development of thyroid carcinogenesis. The focus of the current meta-analysis was to determine the impact of promoter methylation of eight selected candidate TSGs on thyroid cancer and to identify the most important molecules in this carcinogenesis pathway. A comprehensive search was performed using Pub Med, Scopus, and ISI Web of Knowledge databases, and eligible studies were included. The methodological quality of the included studies was evaluated according to the Newcastle Ottawa scale table and pooled odds ratios (ORs; 95% confidence intervals (CIs were used to estimate the strength of the associations with Stata 12.0 software. Egger's and Begg's tests were applied to detect publication bias, in addition to the "Metatrim" method. A total of 55 articles were selected, and 135 genes with altered promoter methylation were found. Finally, we included eight TSGs that were found in more than four studies (RASSF1, TSHR, PTEN, SLC5A, DAPK, P16, RARβ2, and CDH1. The order of the pooled ORs for these eight TSGs from more to less significant was CDH1 (OR = 6.73, SLC5 (OR = 6.15, RASSF1 (OR = 4.16, PTEN (OR = 3.61, DAPK (OR = 3.51, P16 (OR = 3.31, TSHR (OR = 2.93, and RARβ2 (OR = 1.50. Analyses of publication bias and sensitivity confirmed that there was very little bias. Thus, our findings showed that CDH1 and SCL5A8 genes were associated with the risk of thyroid tumor genesis.

  11. Studies of pirimiphos-methyl residues in stored rice, using 14C-pirimiphos-methyl

    International Nuclear Information System (INIS)

    Varca, L.M.; Sanchez, T.E.; Gambalan, N.; Magallona, E.D.

    1990-01-01

    The distribution and persistence of pirimiphos-methyl on rice (hulled and unhulled) stored over a period of 6 months at 30 deg. C and about 11% moisture were studied using 14 C labelled insecticide. The procedures used for preparing the labelled formulation, applying the insecticide and for the handling and analysis of the grain samples were similar to those described for fenvalerate, see Varca, Sanchez and Magallona, ''Isotopic tracer aided studies of fenvalerate residues in stored products'', these Proceedings. After applying the pirimiphos-methyl, a concentration equal to 0.87 ppm was found on the hulled rice immediately after application; this concentration declined to 0.60 ppm after 6 months of storage. Over 28% of the residue was present in the seed in the methanol extractable form, and 38% was found on the surface at the end of the storage period. For the unhulled rice, most of the residue was retained in the hull with no decrease in the overall level during the storage period. (author)

  12. A Busy period analysis of the level dependent PH/PH/1/K queue

    NARCIS (Netherlands)

    Al Hanbali, Ahmad

    2011-01-01

    In this paper, we study the transient behavior of a level dependent single server queuing system with a waiting room of finite size during the busy period. The focus is on the level dependent PH/PH/1/K queue. We derive in closed form the joint transform of the length of the busy period, the number

  13. Analysis of obese patients' medical conditions in the pre and postoperative periods of bariatric surgery.

    Science.gov (United States)

    Rêgo, Anderson DA Silva; Zulin, Aline; Scolari, Sandro; Marcon, Sônia Silva; Radovanovic, Cremilde Aparecida Trindade

    2017-01-01

    to compare the clinical conditions of obese patients in the pre and postoperative period of bariatric surgery. we carried out a descriptive, retrospective, quantitative study by consulting the charts of 134 patients who underwent bariatric surgery in the period from 2009 to 2014. We collected the data between September and November 2015. We performed a descriptive statistical analysis and comparative analysis of anthropometric, metabolic, biochemical and clinical variables, considering six months before and after surgery. the majority of the patients were female (91.8%), with a higher prevalence (35%) in the age group 18-29 years old, complete high-school education (65.6%) and grade III obesity (60.4%). Six months after surgery, weight and lipid profile reduction were significant in both genders, but the impact on biochemical, anthropometric, metabolic and clinical parameters was significant only in female subjects, with a reduction in morbidities associated with obesity, such as arterial hypertension, diabetes mellitus, dyslipidemia and metabolic syndrome and in the use of drugs to control them. bariatric surgery was effective in weight loss, with improvements in anthropometric, metabolic and biochemical parameters and in the reduction of morbidities associated with obesity. comparar as condições clínicas de pacientes obesos em período pré e pós-operatório de cirurgia bariátrica. estudo descritivo, retrospectivo, de abordagem quantitativa, por meio de consulta ao prontuário de 134 pacientes submetidos à cirurgia bariátrica no período de 2009 a 2014. Os dados foram coletados entre os meses de setembro e novembro de 2015. Foi realizada análise estatística descritiva e comparativa das variáveis antropométricas, metabólicas, bioquímicas e clínicas, considerando seis meses antes e após a cirurgia. a maioria dos pacientes era do sexo feminino (91,8%), com maior prevalência (35%) na faixa etária de 18 aos 29 anos, com ensino médio completo (65

  14. Meta-analysis of CDKN2A methylation to find its role in prostate cancer development and progression, and also to find the effect of CDKN2A expression on disease-free survival (PRISMA).

    Science.gov (United States)

    Cao, Zipei; Wei, Lijuan; Zhu, Weizhi; Yao, Xuping

    2018-03-01

    Reduction of cyclin-dependent kinase inhibitor 2A (CDKN2A) (p16 and p14) expression through DNA methylation has been reported in prostate cancer (PCa). This meta-analysis was conducted to assess the difference of p16 and p14 methylation between PCa and different histological types of nonmalignant controls and the correlation of p16 or p14 methylation with clinicopathological features of PCa. According to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement criteria, articles were searched in PubMed, Embase, EBSCO, Wanfang, and CNKI databases. The strength of correlation was calculated by the pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs). Trial sequential analysis (TSA) was used to estimate the required population information for significant results. A total of 20 studies published from 1997 to 2017 were identified in this meta-analysis, including 1140 PCa patients and 530 cases without cancer. Only p16 methylation in PCa was significantly higher than in benign prostatic lesions (OR = 4.72, P = .011), but had a similar level in PCa and adjacent tissues or high-grade prostatic intraepithelial neoplasias (HGPIN). TSA revealed that this analysis on p16 methylation is a false positive result in cancer versus benign prostatic lesions (the estimated required information size of 5116 participants). p16 methylation was not correlated with PCa in the urine and blood. Besides, p16 methylation was not linked to clinical stage, prostate-specific antigen (PSA) level, and Gleason score (GS) of patients with PCa. p14 methylation was not correlated with PCa in tissue and urine samples. No correlation was observed between p14 methylation and clinical stage or GS. CDKN2A mutation and copy number alteration were not associated with prognosis of PCa in overall survival and disease-free survival. CDKN2A expression was not correlated with the prognosis of PCa in overall survival (492 cases) (P > .1

  15. Colorectal Cancer "Methylator Phenotype": Fact or Artifact?

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    Charles Anacleto

    2005-04-01

    Full Text Available It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI. We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.

  16. Analysis of the Chinese martial periodicals edited during the Republican Era

    Directory of Open Access Journals (Sweden)

    William Acevedo

    2012-07-01

    Full Text Available The present article studies the periodicals and magazines published during the Chinese Republican period (1912-1949. The main sources for this work are the index and thirty volumes of the Republican Era Collection of National Arts Periodicals (Mingguo Guoshu Qi Kan Wenxian Jicheng, edited by Shi Yong Xing in 2008. Besides basic data about the 45 publications included in the collection such as title, editor, publication information and period of existence; this article emphasises the historical context in which these publications appeared as well as their efforts to help China becoming a nation recognized at the world stage. As an example of the wealth of information contained in these periodicals regarding Chinese martial arts, we have analyzed the terminology that was used to define them, the publications’ contribution to exalt nationalism up to their influence in strengthening of China’s citizens and military.

  17. Comprehensive analysis of CpG island methylator phenotype (CIMP)-high, -low, and -negative colorectal cancers based on protein marker expression and molecular features.

    Science.gov (United States)

    Zlobec, Inti; Bihl, Michel; Foerster, Anja; Rufle, Alex; Lugli, Alessandro

    2011-11-01

    CpG island methylator phenotype (CIMP) is being investigated for its role in the molecular and prognostic classification of colorectal cancer patients but is also emerging as a factor with the potential to influence clinical decision-making. We report a comprehensive analysis of clinico-pathological and molecular features (KRAS, BRAF and microsatellite instability, MSI) as well as of selected tumour- and host-related protein markers characterizing CIMP-high (CIMP-H), -low, and -negative colorectal cancers. Immunohistochemical analysis for 48 protein markers and molecular analysis of CIMP (CIMP-H: ≥ 4/5 methylated genes), MSI (MSI-H: ≥ 2 instable genes), KRAS, and BRAF were performed on 337 colorectal cancers. Simple and multiple regression analysis and receiver operating characteristic (ROC) curve analysis were performed. CIMP-H was found in 24 cases (7.1%) and linked (p CIMP-low or -negative cases. Of the 48 protein markers, decreased levels of RKIP (p = 0.0056), EphB2 (p = 0.0045), CK20 (p = 0.002), and Cdx2 (p CIMP-H, independently of MSI status. In addition to the expected clinico-pathological and molecular associations, CIMP-H colorectal cancers are characterized by a loss of protein markers associated with differentiation, and metastasis suppression, and have increased CD8+ T-lymphocytes regardless of MSI status. In particular, Cdx2 loss seems to strongly predict CIMP-H in both microsatellite-stable (MSS) and MSI-H colorectal cancers. Cdx2 is proposed as a surrogate marker for CIMP-H. Copyright © 2011 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  18. Modeling spatiotemporal dynamics of DNA methylation

    DEFF Research Database (Denmark)

    Lövkvist, Cecilia Elisabet

    into how epigenetic marks are distributed in the human genome. In the first part of the thesis, we investigate DNA methylation and maintenance of methylation patterns throughout cell division. We argue that collaborative models, those where the methylation of CpG sites depends on the methylation status...... into the game more explicitly in another type of model that speaks out the duality of the two aspects. Using statistical analysis of experimental data, this thesis further explores a link between DNA methylation and nucleosome occupancy. By comparing the patterns on promoters to regions with similar Cp...... division. The patterns of epigentic marks depend on enzymes that ensure their maintenance and introduction. Using theoretical models, this thesis proposes new mechanisms for how enzymes operate to maintain patterns of epigenetic marks. Through analysis of experimental data this work gives new insight...

  19. A Genome-Wide mQTL Analysis in Human Adipose Tissue Identifies Genetic Variants Associated with DNA Methylation, Gene Expression and Metabolic Traits.

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    Petr Volkov

    Full Text Available Little is known about the extent to which interactions between genetics and epigenetics may affect the risk of complex metabolic diseases and/or their intermediary phenotypes. We performed a genome-wide DNA methylation quantitative trait locus (mQTL analysis in human adipose tissue of 119 men, where 592,794 single nucleotide polymorphisms (SNPs were related to DNA methylation of 477,891 CpG sites, covering 99% of RefSeq genes. SNPs in significant mQTLs were further related to gene expression in adipose tissue and obesity related traits. We found 101,911 SNP-CpG pairs (mQTLs in cis and 5,342 SNP-CpG pairs in trans showing significant associations between genotype and DNA methylation in adipose tissue after correction for multiple testing, where cis is defined as distance less than 500 kb between a SNP and CpG site. These mQTLs include reported obesity, lipid and type 2 diabetes loci, e.g. ADCY3/POMC, APOA5, CETP, FADS2, GCKR, SORT1 and LEPR. Significant mQTLs were overrepresented in intergenic regions meanwhile underrepresented in promoter regions and CpG islands. We further identified 635 SNPs in significant cis-mQTLs associated with expression of 86 genes in adipose tissue including CHRNA5, G6PC2, GPX7, RPL27A, THNSL2 and ZFP57. SNPs in significant mQTLs were also associated with body mass index (BMI, lipid traits and glucose and insulin levels in our study cohort and public available consortia data. Importantly, the Causal Inference Test (CIT demonstrates how genetic variants mediate their effects on metabolic traits (e.g. BMI, cholesterol, high-density lipoprotein (HDL, hemoglobin A1c (HbA1c and homeostatic model assessment of insulin resistance (HOMA-IR via altered DNA methylation in human adipose tissue. This study identifies genome-wide interactions between genetic and epigenetic variation in both cis and trans positions influencing gene expression in adipose tissue and in vivo (dysmetabolic traits associated with the development of

  20. STR analysis of human DNA from maggots fed on decomposing bodies: Assessment of the time period for successful analysis

    Directory of Open Access Journals (Sweden)

    Daniel Gachuiri Njau

    2016-09-01

    Full Text Available Frequently, forensic entomology is applied in the use of insect maggots for the identification of specimens or remains of humans. Maggot crop analysis could be valuable in criminal investigations when maggots are found at a crime scene and a corpse is absent. Human short tandem repeat (STR has previously been used to support the association of maggots to a specific corpse but not in the period at which the body has been decomposing. The aim of this research was to assess the time period for successful STR analyses of human DNA from third instar maggots (Protophormia terraenovae obtained from decomposing human corpses as well as to investigate the human DNA turnover and degradation in the maggot crop after they are removed from food and/or are fed on a beef (a new/different food source. Results showed that the amount of human DNA recovered from maggots decreased with time in all cases. For maggots fed on beef, the human DNA could only be recovered up to day two and up to day four for the starved maggots. STR analyses of human DNA from maggots’ crop content using 16 loci generated profiles that matched those of reference samples although some of the alleles were not amplifiable therefore generating partial profiles for the samples starved for 4 days and those fed on beef. This may be due to nuclease activity present in the gut of larvae that may have caused degradation of DNA and consequently reduction in DNA yield. It was possible to identify the decomposing body using STRs as markers.

  1. Comparative analysis of DNA methylation polymorphism in drought sensitive (HPKC2) and tolerant (HPK4) genotypes of horse Gram (Macrotyloma uniflorum).

    Science.gov (United States)

    Bhardwaj, Jyoti; Mahajan, Monika; Yadav, Sudesh Kumar

    2013-08-01

    DNA methylation is known as an epigenetic modification that affects gene expression in plants. Variation in CpG methylation behavior was studied in two natural horse gram (Macrotyloma uniflorum [Lam.] Verdc.) genotypes, HPKC2 (drought-sensitive) and HPK4 (drought-tolerant). The methylation pattern in both genotypes was studied through methylation-sensitive amplified polymorphism. The results revealed that methylation was higher in HPKC2 (10.1%) than in HPK4 (8.6%). Sequencing demonstrated sequence homology with the DRE binding factor (cbf1), the POZ/BTB protein, and the Ty1-copia retrotransposon among some of the polymorphic fragments showing alteration in methylation behavior. Differences in DNA methylation patterns could explain the differential drought tolerance and the epigenetic signature of these two horse gram genotypes.

  2. Tracking the Correlation Between CpG Island Methylator Phenotype and Other Molecular Features and Clinicopathological Features in Human Colorectal Cancers: A Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Zong, Liang; Abe, Masanobu; Ji, Jiafu; Zhu, Wei-Guo; Yu, Duonan

    2016-03-10

    The controversy of CpG island methylator phenotype (CIMP) in colorectal cancers (CRCs) persists, despite many studies that have been conducted on its correlation with molecular and clinicopathological features. To drive a more precise estimate of the strength of this postulated relationship, a meta-analysis was performed. A comprehensive search for studies reporting molecular and clinicopathological features of CRCs stratified by CIMP was performed within the PubMed, EMBASE, and Cochrane Library. CIMP was defined by either one of the three panels of gene-specific CIMP markers (Weisenberger panel, classic panel, or a mixture panel of the previous two) or the genome-wide DNA methylation profile. The associations of CIMP with outcome parameters were estimated using odds ratio (OR) or weighted mean difference (WMD) or hazard ratios (HRs) with 95% confidence interval (CI) for each study using a fixed effects or random effects model. A total of 29 studies involving 9,393 CRC patients were included for analysis. We observed more BRAF mutations (OR 34.87; 95% CI, 22.49-54.06) and microsatellite instability (MSI) (OR 12.85 95% CI, 8.84-18.68) in CIMP-positive vs. -negative CRCs, whereas KRAS mutations were less frequent (OR 0.47; 95% CI, 0.30-0.75). Subgroup analysis showed that only the genome-wide methylation profile-defined CIMP subset encompassed all BRAF-mutated CRCs. As expected, CIMP-positive CRCs displayed significant associations with female (OR 0.64; 95% CI, 0.56-0.72), older age at diagnosis (WMD 2.77; 95% CI, 1.15-4.38), proximal location (OR 6.91; 95% CI, 5.17-9.23), mucinous histology (OR 3.81; 95% CI, 2.93-4.95), and poor differentiation (OR 4.22; 95% CI, 2.52-7.08). Although CIMP did not show a correlation with tumor stage (OR 1.10; 95% CI, 0.82-1.46), it was associated with shorter overall survival (HR 1.73; 95% CI, 1.27-2.37). The meta-analysis highlights that CIMP-positive CRCs take their own molecular feature, especially overlapping with BRAF mutations

  3. Evaluating genome-wide DNA methylation changes in mice by Methylation Specific Digital Karyotyping

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    Maruoka Shuichiro

    2008-12-01

    Full Text Available Abstract Background The study of genome-wide DNA methylation changes has become more accessible with the development of various array-based technologies though when studying species other than human the choice of applications are limited and not always within reach. In this study, we adapted and tested the applicability of Methylation Specific Digital Karyotyping (MSDK, a non-array based method, for the prospective analysis of epigenetic changes after perinatal nutritional modifications in a mouse model of allergic airway disease. MSDK is a sequenced based method that allows a comprehensive and unbiased methylation profiling. The method generates 21 base pairs long sequence tags derived from specific locations in the genome. The resulting tag frequencies determine in a quantitative manner the methylation level of the corresponding loci. Results Genomic DNA from whole lung was isolated and subjected to MSDK analysis using the methylation-sensitive enzyme Not I as the mapping enzyme and Nla III as the fragmenting enzyme. In a pair wise comparison of the generated mouse MSDK libraries we identified 158 loci that are significantly differentially methylated (P-value = 0.05 after perinatal dietary changes in our mouse model. Quantitative methylation specific PCR and sequence analysis of bisulfate modified genomic DNA confirmed changes in methylation at specific loci. Differences in genomic MSDK tag counts for a selected set of genes, correlated well with changes in transcription levels as measured by real-time PCR. Furthermore serial analysis of gene expression profiling demonstrated a dramatic difference in expressed transcripts in mice exposed to perinatal nutritional changes. Conclusion The genome-wide methylation survey applied in this study allowed for an unbiased methylation profiling revealing subtle changes in DNA methylation in mice maternally exposed to dietary changes in methyl-donor content. The MSDK method is applicable for mouse models

  4. Analysis on optimization of the critical path for civil construction period of Fangjiashan nuclear island constructed under EPC mode

    International Nuclear Information System (INIS)

    Liu Yongqing; Wu Youcong; Qiu Jinhong

    2011-01-01

    Based on the actual situation of nuclear island civil construction in Fangjiashan nuclear power plant and combined with the arrangement of the construction schedule, the analysis on optimization of the critical path for civil construction period is conducted. The result shows that on the premise of not increasing the contract price and the total engineering cost based on the original 57-month construction period, the construction period can be shorten to 21 month through strengthening the schedule control, keeping the critical work in a reasonable duration and rearranging the link between programmers. In addition, in view of the economic analysis, if we increase the mechanical engagement and adopt special method, the 2-month construction period can be even shortened to 20 months. (authors)

  5. Marker evaluation for differentiation of blood and menstrual fluid by methylation-sensitive SNaPshot analysis.

    Science.gov (United States)

    Holtkötter, Hannah; Schwender, Kristina; Wiegand, Peter; Pfeiffer, Heidi; Vennemann, Marielle

    2018-03-01

    The differentiation of blood and menstrual fluid is especially important in cases of alleged sexual assault. While the identification of blood is relatively straightforward, the identification of menstrual fluid in trace evidence has been shown to be more challenging. This may be due to the complex nature of menstrual fluid that leads to intra- and inter-individual differences in composition. Nevertheless, recent advances in DNA methylation profiling have revealed promising markers for the differentiation of the two body fluids and furthermore, markers to distinguish menstrual fluid from vaginal fluid. A literature study was performed and in total, 11 markers were evaluated in this study of which seven could be validated for menstrual fluid and blood identification purposes. Marker "BLU2" (chr16:29757334) was identified as most suitable for differentiation of blood and menstrual fluid.

  6. CpG Methylation Analysis of HPV16 in Laser Capture Microdissected Archival Tissue and Whole Tissue Sections from High Grade Anal Squamous Intraepithelial Lesions: A Potential Disease Biomarker.

    Directory of Open Access Journals (Sweden)

    Monica Molano

    Full Text Available Incidence and mortality rates of anal cancer are increasing globally. More than 90% of anal squamous cell carcinomas (ASCC are associated with human papillomavirus (HPV. Studies on HPV-related anogenital lesions have shown that patterns of methylation of viral and cellular DNA targets could potentially be developed as disease biomarkers. Lesion-specific DNA isolated from formalin-fixed paraffin-embedded (FFPE tissues from existing or prospective patient cohorts may constitute a valuable resource for methylation analysis. However, low concentrations of DNA make these samples technically challenging to analyse using existing methods. We therefore set out to develop a sensitive and reproducible nested PCR-pyrosequencing based method to accurately quantify methylation at 10 CpG sites within the E2BS1, E2BS2,3,4 and Sp1 binding sites in the viral upstream regulatory region of HPV16 genome. Methylation analyses using primary and nested PCR-pyrosequencing on 52 FFPE tissue [26 paired whole tissue sections (WTS and laser capture microdissected (LCM tissues] from patients with anal squamous intraepithelial lesions was performed. Using nested PCR, methylation results were obtained for the E2BS1, E2BS2,3,4 and Sp1 binding sites in 86.4% of the WTS and 81.8% of the LCM samples. Methylation patterns were strongly correlated within median values of matched pairs of WTS and LCM sections, but overall methylation was higher in LCM samples at different CpG sites. High grade lesions showed low methylation levels in the E2BS1 and E2BS2 regions, with increased methylation detected in the E2BS,3,4/Sp1 regions, showing the highest methylation at CpG site 37. The method developed is highly sensitive in samples with low amounts of DNA and demonstrated to be suitable for archival samples. Our data shows a possible role of specific methylation in the HPV16 URR for detection of HSIL.

  7. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

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    Kiwako S Araki

    Full Text Available In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals. We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers. We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms

  8. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

    Science.gov (United States)

    Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

    2017-01-01

    In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for

  9. Live Cell Analysis and Mathematical Modeling Identify Determinants of Attenuation of Dengue Virus 2'-O-Methylation Mutant.

    Directory of Open Access Journals (Sweden)

    Bianca Schmid

    2015-12-01

    Full Text Available Dengue virus (DENV is the most common mosquito-transmitted virus infecting ~390 million people worldwide. In spite of this high medical relevance, neither a vaccine nor antiviral therapy is currently available. DENV elicits a strong interferon (IFN response in infected cells, but at the same time actively counteracts IFN production and signaling. Although the kinetics of activation of this innate antiviral defense and the timing of viral counteraction critically determine the magnitude of infection and thus disease, quantitative and kinetic analyses are lacking and it remains poorly understood how DENV spreads in IFN-competent cell systems. To dissect the dynamics of replication versus antiviral defense at the single cell level, we generated a fully viable reporter DENV and host cells with authentic reporters for IFN-stimulated antiviral genes. We find that IFN controls DENV infection in a kinetically determined manner that at the single cell level is highly heterogeneous and stochastic. Even at high-dose, IFN does not fully protect all cells in the culture and, therefore, viral spread occurs even in the face of antiviral protection of naïve cells by IFN. By contrast, a vaccine candidate DENV mutant, which lacks 2'-O-methylation of viral RNA is profoundly attenuated in IFN-competent cells. Through mathematical modeling of time-resolved data and validation experiments we show that the primary determinant for attenuation is the accelerated kinetics of IFN production. This rapid induction triggered by mutant DENV precedes establishment of IFN-resistance in infected cells, thus causing a massive reduction of virus production rate. In contrast, accelerated protection of naïve cells by paracrine IFN action has negligible impact. In conclusion, these results show that attenuation of the 2'-O-methylation DENV mutant is primarily determined by kinetics of autocrine IFN action on infected cells.

  10. Analysis of Personal Dosimetry for Nuclear Medicine Staff in Ten-Year Period

    International Nuclear Information System (INIS)

    Poropat, M.; Dodig, D.; Ciglar, M.; Tezak, S.

    2011-01-01

    The aim of this study was to assess the value of personal dosimetry for nuclear medicine personnel in our department in a ten-year period. We have analyzed personal doses for 80 employees in nuclear medicine in a ten year period that we divided into two five year periods (from 2000 to 2004 and from 2005 to 2009). The personnel was dived into 8 groups according to their working assignments due to different radiation exposure from various radioisotopes in different wards in nuclear medicine: nuclear medicine specialists, technologists in scintigraphy ward, personnel of physics ward, ward for radiochemistry and radioimmunology, clinical ward and ultrasound ward, cleaning personnel, administrative personnel. We have compared average dose per person in particular ward in two five year periods. All doses for all personnel were in the permissible limits prescribed by the authorities. Higher average dose per person in a first five year period was detected in two wards, scintigraphy ward and ward for radiochemistry and radioimmunology due to the nature of their working assignments (preparation and application of radiopharmaceuticals, contact with patients who have received radiopharmaceutical). The decrease in the average dose per person was noticed in a second five-year period, especially in the wards with personnel that had no prior education in ionizing radiation protection. The decrease of dose was from 7.5 % to 84.2 %. We think that the decrease of average dose per person in a second five-year period was not only the result of the increased personal protection measures but also the result of continuing education of nuclear medicine personnel that is obligatory by the Law for ionizing radiation protection from year 1999, and the results from a ten-year period show its positive effect on radiation protection. (author)

  11. Analysis of premature births for the period from 2009. to 2013. in Health Center Kosovska Mitrovica

    OpenAIRE

    Adžić V.; Galjak S.; Radojević G.; Relić G.

    2015-01-01

    Delivery before 37th week of gestation is defined as preterm, independently of body mass of babies, according to the World Health Organization. Premature birth is the current problem in the world due to the high risk of neonatal morbidity and mortality and incompletely clear etiology. In our country the frequency of preterm delivery is 6%. We have retrospectively analyzed early deliveries in Health Center Kosovska Mitrovica in the period from 2009 to 2013. In this five-year period, there were...

  12. Analysis of longer period variation of the Kuroshio Current intrusion into the Luzon Strait using rectified wavelet power spectra

    Science.gov (United States)

    Yuan, Yaochu; Yang, Chenghao; Tseng, Yu-heng; Zhu, Xiao-Hua; Wang, Huiqun; Chen, Hong

    2017-08-01

    Longer period variation of the Kuroshio into the Luzon Strait (LS) was identified using acoustic Doppler current profiler (ADCP) observations as well as pressure and temperature time series data recorded by two TDs (manufactured by the RBR Ltd.) at mooring station N2 (20°40.441‧N, 120°38.324‧E). The ADCP was deployed at depths of 50-300 m between July 7, 2009 and April 10, 2011, and the TDs at around 340 and 365 m between July 9, 2009 and July 9, 2011. Observations provide strong evidence of longer period variation of the Kuroshio into the LS using the Vector rotary spectra (VRS) and Rectified wavelet power spectra analysis (RWPSA). RWPSA of the observations allowed the identification of two types of dominant periods. The first type, with the strongest power spectral density (PSD), had a dominant period of 112 d and was found throughout the upper 300 m. For example, the maximum PSD for western and northern velocity components time series were 3800 and 3550 at 50 m, respectively. The maximum power spectral density decrease with deeper depths, i.e., the depth dependence of maximum PSD. The 112 d period was also identified in the pressure and temperature time series data, at 340 m and 365 m. Combined RWPSA with VRS and mechanism analysis, it is clear that the occurrence of the most dominant period of 112 d in the upper 300 m is related to the clockwise meandering of the Kuroshio into the LS, which is caused by westward propagating stronger anticyclonic eddies from the interior ocean due to the interaction of Rossby eddies with the Kuroshio. The second type of dominant period, for example a 40 d period, is related to the anticlockwise meandering of the Kuroshio. The final dominant period of 14 d coincides with the fortnightly spring-neap tidal period.

  13. An analysis of the radiation field characteristics for extremity dose assessment during maintenance periods at nuclear power plants in Korea

    International Nuclear Information System (INIS)

    Kim, H. G.; Kong, T. Y.

    2012-01-01

    Workers who maintain the water chambers of steam generators during maintenance periods in nuclear power plants (NPPs) have a higher likelihood of high radiation exposure, even if they are exposed for a short period of time. In particular, it is expected that the hands of workers would receive the highest radiation exposure as a consequence of hand contact with radioactive materials. In this study, a characteristic analysis of inhomogeneous radiation fields for contact operations was conducted using thermoluminescent dosemeters for the whole body and extremities during maintenance periods at Korean NPPs. It was observed that inhomogeneous radiation fields for contact operations at NPPs were dominated by high-energy photons. (authors)

  14. Period Prevalence and Reporting Rate of Needlestick Injuries to Nurses in Iran: A Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Rezaei, Satar; Hajizadeh, Mohammad; Zandian, Hamed; Fathi, Afshin; Nouri, Bijan

    2017-08-01

    The purpose of this systematic review and meta-analysis was to provide a precise estimate of the period prevalence of needlestick injuries (NSI) among nurses working in hospitals in Iran and the reporting rate of NSI to nurse managers. We searched both international (PubMed, Scopus and the Institute for Scientific Information) and Iranian (Scientific Information Database, Iranmedex and Magiran) scientific databases to find studies published from 2000 to 2016 of NSI among Iranian nurses. The following keywords in Persian and English were used: "needle-stick" or "needle stick" or "needlestick," with and without "injury" or "injuries," "prevalence" or "frequency," "nurses" or "nursing staff," and "Iran." In a sample of 21 articles with 6,480 participants, we estimated that the overall 1-year period prevalence of NSI was 44% (95% confidence interval [CI], 35-53%) among Iranian nurses. The overall 1-year period prevalence of reporting NSI to nurse managers was 42% (95% CI, 33-52%). In meta-regression analysis, sample size, mean age, years of experience, and gender ratio were not associated with prevalence of NSI or reporting rate. The year of data collection was positively associated with period prevalence of NSI (p managers. Results indicated a high NSI period prevalence and low NSI reporting rate among nurses in Iran. Thus, effective interventions are required in hospitals in Iran to reduce the prevalence and increase the reporting rate of NSI. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  15. An Analysis of Light Periods of BL Lac Object S5 0716+714 with the MUSIC Algorithm

    Science.gov (United States)

    Tang, Jie

    2012-07-01

    The multiple signal classification (MUSIC) algorithm is introduced to the estimation of light periods of BL Lac objects. The principle of the MUSIC algorithm is given, together with a testing on its spectral resolution by using a simulative signal. From a lot of literature, we have collected a large number of effective observational data of the BL Lac object S5 0716+714 in the three optical wavebands V, R, and I from 1994 to 2008. The light periods of S5 0716+714 are obtained by means of the MUSIC algorithm and average periodogram algorithm, respectively. It is found that there exist two major periodic components, one is the period of (3.33±0.08) yr, another is the period of (1.24±0.01) yr. The comparison of the performances of periodicity analysis of two algorithms indicates that the MUSIC algorithm has a smaller requirement on the sample length, as well as a good spectral resolution and anti-noise ability, to improve the accuracy of periodicity analysis in the case of short sample length.

  16. Asymptotic analysis of reaction-diffusion-advection problems: Fronts with periodic motion and blow-up

    Science.gov (United States)

    Nefedov, Nikolay

    2017-02-01

    This is an extended variant of the paper presented at MURPHYS-HSFS 2016 conference in Barcelona. We discuss further development of the asymptotic method of differential inequalities to investigate existence and stability of sharp internal layers (fronts) for nonlinear singularly perturbed periodic parabolic problems and initial boundary value problems with blow-up of fronts for reaction-diffusion-advection equations. In particular, we consider periodic solutions with internal layer in the case of balanced reaction. For the initial boundary value problems we prove the existence of fronts and give their asymptotic approximation including the new case of blowing-up fronts. This case we illustrate by the generalised Burgers equation.

  17. Qualitative analysis of an integro-differential equation model of periodic chemotherapy

    KAUST Repository

    Jain, Harsh Vardhan

    2012-12-01

    An existing model of tumor growth that accounts for cell cycle arrest and cell death induced by chemotherapy is extended to simulate the response to treatment of a tumor growing in vivo. The tumor is assumed to undergo logistic growth in the absence of therapy, and treatment is administered periodically rather than continuously. Necessary and sufficient conditions for the global stability of the cancer-free equilibrium are derived and conditions under which the system evolves to periodic solutions are determined. © 2012 Elsevier Ltd. All rights reserved.

  18. A novel asymptotic expansion homogenization analysis for 3-D composite with relieved periodicity in the thickness direction

    KAUST Repository

    Nasution, Muhammad Ridlo Erdata

    2014-06-01

    A new asymptotic expansion homogenization analysis is proposed to analyze 3-D composite in which thermomechanical and finite thickness effects are considered. Finite thickness effect is captured by relieving periodic boundary condition at the top and bottom of unit-cell surfaces. The mathematical treatment yields that only 2-D periodicity (i.e. in in-plane directions) is taken into account. A unit-cell representing the whole thickness of 3-D composite is built to facilitate the present method. The equivalent in-plane thermomechanical properties of 3-D orthogonal interlock composites are calculated by present method, and the results are compared with those obtained by standard homogenization method (with 3-D periodicity). Young\\'s modulus and Poisson\\'s ratio obtained by present method are also compared with experiments whereby a good agreement is particularly found for the Young\\'s modulus. Localization analysis is carried out to evaluate the stress responses within the unit-cell of 3-D composites for two cases: thermal and biaxial tensile loading. Standard finite element (FE) analysis is also performed to validate the stress responses obtained by localization analysis. It is found that present method results are in a good agreement with standard FE analysis. This fact emphasizes that relieving periodicity in the thickness direction is necessary to accurately simulate the real free-traction condition in 3-D composite. © 2014 Elsevier Ltd.

  19. A novel asymptotic expansion homogenization analysis for 3-D composite with relieved periodicity in the thickness direction

    KAUST Repository

    Nasution, Muhammad Ridlo Erdata; Watanabe, Naoyuki; Kondo, Atsushi; Yudhanto, Arief

    2014-01-01

    A new asymptotic expansion homogenization analysis is proposed to analyze 3-D composite in which thermomechanical and finite thickness effects are considered. Finite thickness effect is captured by relieving periodic boundary condition at the top and bottom of unit-cell surfaces. The mathematical treatment yields that only 2-D periodicity (i.e. in in-plane directions) is taken into account. A unit-cell representing the whole thickness of 3-D composite is built to facilitate the present method. The equivalent in-plane thermomechanical properties of 3-D orthogonal interlock composites are calculated by present method, and the results are compared with those obtained by standard homogenization method (with 3-D periodicity). Young's modulus and Poisson's ratio obtained by present method are also compared with experiments whereby a good agreement is particularly found for the Young's modulus. Localization analysis is carried out to evaluate the stress responses within the unit-cell of 3-D composites for two cases: thermal and biaxial tensile loading. Standard finite element (FE) analysis is also performed to validate the stress responses obtained by localization analysis. It is found that present method results are in a good agreement with standard FE analysis. This fact emphasizes that relieving periodicity in the thickness direction is necessary to accurately simulate the real free-traction condition in 3-D composite. © 2014 Elsevier Ltd.

  20. Analysis of irradiation processes for laser-induced periodic surface structures

    NARCIS (Netherlands)

    Eichstädt, J.; Huis In 't Veld, A.J.

    2013-01-01

    The influence of errors on the irradiation process for laser-induced periodic surface structures (LIPSS) was studied theoretically with energy density simulations. Therefore an irradiation model has been extended by a selection of technical variations. The influence of errors has been found in a

  1. Modeling and analysis of periodic orbits around a contact binary asteroid

    NARCIS (Netherlands)

    Feng, J.; Noomen, R.; Visser, P.N.A.M.; Yuan, J.

    2015-01-01

    The existence and characteristics of periodic orbits (POs) in the vicinity of a contact binary asteroid are investigated with an averaged spherical harmonics model. A contact binary asteroid consists of two components connected to each other, resulting in a highly bifurcated shape. Here, it is

  2. Uncertainty in return period analysis of combined sewer overflow effects using embedded Monte Carlo simulations

    NARCIS (Netherlands)

    Grum, M.; Aalderink, R.H.

    1999-01-01

    The rerun periods of detrimental effects ate often used as design criteria in urban storm water management. Considerable uncertainty is associated with the models used. This is either ignored or pooled with the inherent event to event variation such as rainfall depth It is here argued that

  3. Analysis of the electricity supply-demand balance for the winter period 2009-2010

    International Nuclear Information System (INIS)

    2009-10-01

    Every year, RTE conducts a prospective study of the balance between supply and demand for electricity for the coming winter period, covering the whole of mainland France. This period of the year is looked at closely, primarily due to the high levels of electricity demand seen during cold snaps. The study by RTE is used to identify periods where the supply-demand balance comes under strain; it explores the measures that can be taken by electricity market players and RTE to avoid any interruption in supply during peak demand periods in France. RTE is responsible for managing the balance between supply and demand for electricity in mainland France, in real time. To do this, it anticipates potential risks that may supply may come under strain - well in advance - and informs market players. If periods are identified where the supply-demand balance comes under strain, RTE works with the electricity generators to look at possible ways of altering the schedules for shutting down generating units, and takes account of the possibilities for demand response (load reduction) reported by suppliers. As a last resort, if these preemptive measures prove insufficient and the situation becomes critical, RTE alerts the government of the risk that supply will be interrupted, and takes action in real time to limit the impact on the power system. For temperatures close to seasonal norms, the forecast outlook for the electricity supply-demand balance appears significantly less favourable than last winter until the end of January. Imports could be required between mid-November 2009 and the end of January 2010, to cover electricity demand in France and satisfy the technical security margin stipulated by RTE. To do this, suppliers would have to look to the European markets, in addition to activating demand response (load reduction) possibilities with their customer portfolios. In the event of an intense and sustained spell of cold weather, the technical limit for imports into the French

  4. The emission analysis of an IDI diesel engine fueled with methyl ester of waste frying palm oil and its blends

    Energy Technology Data Exchange (ETDEWEB)

    Ozsezen, Ahmet Necati; Canakci, Mustafa [Department of Automotive Engineering Technology, Kocaeli University, 41380, Izmit (Turkey); Alternative Fuels R and D Center, Kocaeli University, 41275, Izmit (Turkey)

    2010-12-15

    In this study, the exhaust emissions of an unmodified diesel engine fueled with methyl ester of waste frying palm-oil (biodiesel) and its blends with petroleum based diesel fuel (PBDF) were investigated at the full load-variable speed condition. The relationships between the fuel properties and the air-fuel equivalence ratio, fuel line pressure, start of injection (SOI) timing, and ignition delay were also discussed to explain their effects on the emissions. The obtained test results were compared with the reference values which were determined by using PBDF. The results showed that when biodiesel was used in the test engine, the fuel line pressure increased while air-fuel equivalence ratio and ignition delay decreased. These behaviors affected the combustion phenomena of biodiesel which caused to reduction 57% in carbon monoxide (CO) emission, about 40% in unburned hydrocarbon (HC) emission and about 23% in smoke opacity when compared with PBDF. However, NO{sub x} and CO{sub 2} emissions of the biodiesel have showed different behaviors in terms of the engine speed. (author)

  5. Inductive effect of methyl group in a series of methylated indoles: A ...

    Indian Academy of Sciences (India)

    Vol. 125, No. 4, July 2013, pp. 905–912. c Indian Academy of Sciences. Inductive effect of methyl group in a series of methylated indoles: A graph theoretical analysis in the light of density functional theory and correlation with experimental charge transfer transition energies. AMIT S TIWARYa,∗ and ASOK K MUKHERJEEb.

  6. Legal Culture as the Determinant of Value Orientations in Youth in the Society of the Transition Period (Philosophical Analysis)

    Science.gov (United States)

    Kulzhanova, Zhuldizay T.; Kulzhanova, Gulbaram T.

    2016-01-01

    This research is devoted to the philosophical analysis of legal culture as a determinant of value orientations in the transition period society. The purpose of the study is to discover the essence and specificity of legal culture as a determinant of value orientations in a transition society from the philosophical perspective. In accordance with…

  7. Energy consumption and economic growth: an analysis for Rio Grande do Norte, Brazil, in the period 1980-1994

    International Nuclear Information System (INIS)

    Teixeira, Pedro Helio Gomes; Santos, Sara Macedo dos

    1999-01-01

    The aim of this work is to introduce and to analyze the energetic content of the gross domestic product of Rio Grande do Norte (a Brazilian state) economy in the period 1980-1994. Analysis plans, energy supply structure, energy consumption sectorial structure, and economic activity profile are presented. Just the qualitative evaluation is presented

  8. Analysis of scientific and technical production of IPEN-CNEN/SP in the period of 1984 to 1988

    International Nuclear Information System (INIS)

    Sugai, M.

    1989-01-01

    An analysis of scientific and technical production of Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP in the period of 1984 to 1988 is presented. It includes articles, dissertation, thesis, books, reports and papers presented in scientific meetings or published in the Publicacao IPEN series. (C.M.)

  9. Busy period analysis, rare events and transient behavior in fluid flow models

    Directory of Open Access Journals (Sweden)

    Søren Asmussen

    1994-01-01

    Full Text Available We consider a process {(Jt,Vt}t≥0 on E×[0,∞, such that {Jt} is a Markov process with finite state space E, and {Vt} has a linear drift ri on intervals where Jt=i and reflection at 0. Such a process arises as a fluid flow model of current interest in telecommunications engineering for the purpose of modeling ATM technology. We compute the mean of the busy period and related first passage times, show that the probability of buffer overflow within a busy cycle is approximately exponential, and give conditioned limit theorems for the busy cycle with implications for quick simulation. Further, various inequalities and approximations for transient behavior are given. Also explicit expressions for the Laplace transform of the busy period are found. Mathematically, the key tool is first passage probabilities and exponential change of measure for Markov additive processes.

  10. [Analysis of fatigue associated to periodic limb movement during sleep in former poliomyelitis patients].

    Science.gov (United States)

    Oliveira, A R; Correa, F I; Correa, J C F; Oliveira, L V F

    2012-01-01

    Following poliomyelitis, patients may experience sleep disorders stemming from periodic limb movement, leading to fatigue and compromised muscle function the following day. To establish the presence or absence of muscle fatigue in these patients using electromyography and relating the data to polysomnographic findings. An analytical cross-sectional study was carried out involving 19 individuals with motor sequelae in the lower limbs stemming from poliomyelitis. Quantitative tests for the assessment of neurophysiological aspects (knee-jerk/Achilles reflexes and peripheral muscle strength of rectus femoris) and a sleep study (standard, level I polysomnography) were administered. A statistically significant difference was detected (p fatigue associated to sleep disorder. Individuals with sequelae from poliomyelitis exhibit sleep disorders that may lead to muscle fatigue. Periodic limb movement may contribute to this phenomenon.

  11. Design and Analysis of a Triple Stop-band Filter Using Ratioed Periodical Defected Microstrip Structure

    Science.gov (United States)

    Jiang, Tao; Wang, Yanyan; Li, Yingsong

    2017-07-01

    In this paper, a triple stop-band filter with a ratioed periodical defected microstrip structure is proposed for wireless communication applications. The proposed ratioed periodical defected microstrip structures are spiral slots, which are embedded into a 50 Ω microstrip line to obtain multiple stop-bands. The performance of the proposed triple stop-band filter is investigated numerically and experimentally. Moreover, the equivalent circuit model of the proposed filter is also established and discussed. The results are given to verify that the proposed triple stop-band filter has three stop bands at 3.3 GHz, 5.2 GHz, 6.8 GHz to reject the unwanted signals, which is promising for integrating into UWB communication systems to efficiently prevent the potential interferences from unexpected narrowband signals such as WiMAX, WLAN and RFID communication systems.

  12. Periodicity analysis of tourist arrivals to Banda Aceh using smoothing SARIMA approach

    Science.gov (United States)

    Miftahuddin, Helida, Desri; Sofyan, Hizir

    2017-11-01

    Forecasting the number of tourist arrivals who enters a region is needed for tourism businesses, economic and industrial policies, so that the statistical modeling needs to be conducted. Banda Aceh is the capital of Aceh province more economic activity is driven by the services sector, one of which is the tourism sector. Therefore, the prediction of the number of tourist arrivals is needed to develop further policies. The identification results indicate that the data arrival of foreign tourists to Banda Aceh to contain the trend and seasonal nature. Allegedly, the number of arrivals is influenced by external factors, such as economics, politics, and the holiday season caused the structural break in the data. Trend patterns are detected by using polynomial regression with quadratic and cubic approaches, while seasonal is detected by a periodic regression polynomial with quadratic and cubic approach. To model the data that has seasonal effects, one of the statistical methods that can be used is SARIMA (Seasonal Autoregressive Integrated Moving Average). The results showed that the smoothing, a method to detect the trend pattern is cubic polynomial regression approach, with the modified model and the multiplicative periodicity of 12 months. The AIC value obtained was 70.52. While the method for detecting the seasonal pattern is a periodic regression polynomial cubic approach, with the modified model and the multiplicative periodicity of 12 months. The AIC value obtained was 73.37. Furthermore, the best model to predict the number of foreign tourist arrivals to Banda Aceh in 2017 to 2018 is SARIMA (0,1,1)(1,1,0) with MAPE is 26%.

  13. ANALYSIS OF RELIABILITY OF THE PERIODICALLY AND CONTINUOUSLY CONTROLLED QUEUING SYSTEM WITH TIME REDUNDANCY

    International Nuclear Information System (INIS)

    Mikadze, I.; Namchevadze, T.; Gobiani, I.

    2007-01-01

    There is proposed a generalized mathematical model of the queuing system with time redundancy without preliminary checking of the queuing system at transition from the free state into the engaged one. The model accounts for various failures of the queuing system detected by continuous instrument control, periodic control, control during recovery and the failures revealed immediately after accumulation of a certain number of failures. The generating function of queue length in both stationary and nonstationary modes was determined. (author)

  14. Analysis of Arab Abbasid and Modern Turkish Period Translation Activities With the Approach of Andre Lefevere

    OpenAIRE

    M. Zahit Can

    2015-01-01

    Translation on its own is not a happening phenomenon. Beyond doubt there have to be some reasons bringing it to light. These can be expressed in one or more than one generic terms such as geographical, historical, political, commercial, and social reasons. It is possible that within different historical period, geography, culture, religion and interactions of communities there are some commonalities inducing translation. Given that the common work of translation environments implying such div...

  15. Silk and Sakoku : a simulation analysis of industrial location in Edo period Japan

    OpenAIRE

    ATSUMI, Toshihiro

    2012-01-01

    Japan closed itself to international trade from the 17^ century to the mid-19^ century during the Edo period, known as the Sakoku. After the closure, industries dispersed from western coastal cities to inland areas in western and eastern Japan. This paper investigates how the Sakoku may have aff ected industrial locations within Japan by applying a footloose entrepreneur type geography model to an economy with agricultural raw materials in a continuous space setting. The simulations based on ...

  16. Mortality from Cardiovascular Diseases in the Elderly: Comparative Analysis of Two Five-year Periods

    Directory of Open Access Journals (Sweden)

    Grasiela Piuvezam

    2015-01-01

    Full Text Available Background:Cardiovascular diseases are the leading cause of death in Brazil. The better understanding of the spatial and temporal distribution of mortality from cardiovascular diseases in the Brazilian elderly population is essential to support more appropriate health actions for each region of the country.Objective:To describe and to compare geospatially the rates of mortality from cardiovascular disease in elderly individuals living in Brazil by gender in two 5-year periods: 1996 to 2000 and 2006 to 2010.Methods:This is an ecological study, for which rates of mortality were obtained from DATASUS and the population rates from the Brazilian Institute of Geography and Statistics (Instituto Brasileiro de Geografia e Estatística. An average mortality rate for cardiovascular disease in elderly by gender was calculated for each period. The spatial autocorrelation was evaluated by TerraView 4.2.0 through global Moran index and the formation of clusters by the index of local Moran-LISA.Results:There was an increase, in the second 5-year period, in the mortality rates in the Northeast and North regions, parallel to a decrease in the South, South-East and Midwest regions. Moreover, there was the formation of clusters with high mortality rates in the second period in Roraima among females, and in Ceará, Pernambuco and Roraima among males.Conclusion:The increase in mortality rates in the North and Northeast regions is probably related to the changing profile of mortality and improvement in the quality of information, a result of the increase in surveillance and health care measures in these regions.

  17. Characteristics Analysis of Joint Acoustic Echo and Noise Suppression in Periodic Drillstring Waveguide

    Directory of Open Access Journals (Sweden)

    Li Cheng

    2014-01-01

    Full Text Available A new method of wireless data telemetry used by oil industry uses compressional acoustic waves to transmit downhole information from the bottom hole to the surface. Unfortunately, acoustic echoes and drilling vibration noises in periodic drillstring are a major issue in transmission performance. A combined acoustic echo and noise suppression method based on wave motion characteristic in drillstring is adopted to enhance an upward-going transmitted acoustic signal. The presented scheme consists of a primary acoustic echo canceller using an array of two accelerometers for dealing with the downward-going noises and a secondary acoustic insulation structure for restraining the upward-going vibration noises. Furthermore, the secondary acoustic insulation structure exhibits a banded and dispersive spectral structure because of periodic groove configuration. By using a finite-differential algorithm for the one-dimensional propagation of longitudinal waves, acoustic receiving characteristics of transmitted signals are simulated with additive Gaussian noise in a periodic pipe structure of limited length to investigate the effects on transmission performance optimization. The results reveal that the proposed scheme can achieve a much lower error bit ratio over a specified acoustic isolation frequency range with a 30–40 dB reduction in the average noise level compared to traditional single-receiver scheme.

  18. Characterization of Escherichia coli isolates from different fecal sources by means of classification tree analysis of fatty acid methyl ester (FAME) profiles.

    Science.gov (United States)

    Seurinck, Sylvie; Deschepper, Ellen; Deboch, Bishaw; Verstraete, Willy; Siciliano, Steven

    2006-03-01

    Microbial source tracking (MST) methods need to be rapid, inexpensive and accurate. Unfortunately, many MST methods provide a wealth of information that is difficult to interpret by the regulators who use this information to make decisions. This paper describes the use of classification tree analysis to interpret the results of a MST method based on fatty acid methyl ester (FAME) profiles of Escherichia coli isolates, and to present results in a format readily interpretable by water quality managers. Raw sewage E. coli isolates and animal E. coli isolates from cow, dog, gull, and horse were isolated and their FAME profiles collected. Correct classification rates determined with leaveone-out cross-validation resulted in an overall low correct classification rate of 61%. A higher overall correct classification rate of 85% was obtained when the animal isolates were pooled together and compared to the raw sewage isolates. Bootstrap aggregation or adaptive resampling and combining of the FAME profile data increased correct classification rates substantially. Other MST methods may be better suited to differentiate between different fecal sources but classification tree analysis has enabled us to distinguish raw sewage from animal E. coli isolates, which previously had not been possible with other multivariate methods such as principal component analysis and cluster analysis.

  19. Methyl jasmonate-induced emission of biogenic volatiles is biphasic in cucumber: a high-resolution analysis of dose dependence.

    Science.gov (United States)

    Jiang, Yifan; Ye, Jiayan; Li, Shuai; Niinemets, Ülo

    2017-07-20

    Methyl jasmonate (MeJA) is a key airborne elicitor activating jasmonate-dependent signaling pathways, including induction of stress-related volatile emissions, but how the magnitude and timing of these emissions scale with MeJA dose is not known. Treatments with exogenous MeJA concentrations ranging from mild (0.2 mM) to lethal (50 mM) were used to investigate quantitative relationships among MeJA dose and the kinetics and magnitude of volatile release in Cucumis sativus by combining high-resolution measurements with a proton-transfer reaction time-of-flight mass spectrometer (PTR-TOF-MS) and GC-MS. The results highlighted biphasic kinetics of elicitation of volatiles. The early phase, peaking in 0.1-1 h after the MeJA treatment, was characterized by emissions of lipoxygenase (LOX) pathway volatiles and methanol. In the subsequent phase, starting in 6-12 h and reaching a maximum in 15-25 h after the treatment, secondary emissions of LOX compounds as well as emissions of monoterpenes and sesquiterpenes were elicited. For both phases, the maximum emission rates and total integrated emissions increased with applied MeJA concentration. Furthermore, the rates of induction and decay, and the duration of emission bursts were positively, and the timing of emission maxima were negatively associated with MeJA dose for LOX compounds and terpenoids, except for the duration of the first LOX burst. These results demonstrate major effects of MeJA dose on the kinetics and magnitude of volatile response, underscoring the importance of biotic stress severity in deciphering the downstream events of biological impacts. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  20. Correcting for binomial measurement error in predictors in regression with application to analysis of DNA methylation rates by bisulfite sequencing.

    Science.gov (United States)

    Buonaccorsi, John; Prochenka, Agnieszka; Thoresen, Magne; Ploski, Rafal

    2016-09-30

    Motivated by a genetic application, this paper addresses the problem of fitting regression models when the predictor is a proportion measured with error. While the problem of dealing with additive measurement error in fitting regression models has been extensively studied, the problem where the additive error is of a binomial nature has not been addressed. The measurement errors here are heteroscedastic for two reasons; dependence on the underlying true value and changing sampling effort over observations. While some of the previously developed methods for treating additive measurement error with heteroscedasticity can be used in this setting, other methods need modification. A new version of simulation extrapolation is developed, and we also explore a variation on the standard regression calibration method that uses a beta-binomial model based on the fact that the true value is a proportion. Although most of the methods introduced here can be used for fitting non-linear models, this paper will focus primarily on their use in fitting a linear model. While previous work has focused mainly on estimation of the coefficients, we will, with motivation from our example, also examine estimation of the variance around the regression line. In addressing these problems, we also discuss the appropriate manner in which to bootstrap for both inferences and bias assessment. The various methods are compared via simulation, and the results are illustrated using our motivating data, for which the goal is to relate the methylation rate of a blood sample to the age of the individual providing the sample. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  1. A projection-based model reduction strategy for the wave and vibration analysis of rotating periodic structures

    Science.gov (United States)

    Beli, D.; Mencik, J.-M.; Silva, P. B.; Arruda, J. R. F.

    2018-05-01

    The wave finite element method has proved to be an efficient and accurate numerical tool to perform the free and forced vibration analysis of linear reciprocal periodic structures, i.e. those conforming to symmetrical wave fields. In this paper, its use is extended to the analysis of rotating periodic structures, which, due to the gyroscopic effect, exhibit asymmetric wave propagation. A projection-based strategy which uses reduced symplectic wave basis is employed, which provides a well-conditioned eigenproblem for computing waves in rotating periodic structures. The proposed formulation is applied to the free and forced response analysis of homogeneous, multi-layered and phononic ring structures. In all test cases, the following features are highlighted: well-conditioned dispersion diagrams, good accuracy, and low computational time. The proposed strategy is particularly convenient in the simulation of rotating structures when parametric analysis for several rotational speeds is usually required, e.g. for calculating Campbell diagrams. This provides an efficient and flexible framework for the analysis of rotordynamic problems.

  2. Whole-genome methylation caller designed for methyl- DNA ...

    African Journals Online (AJOL)

    etchie

    2013-02-20

    Feb 20, 2013 ... Our method uses a single-CpG-resolution, whole-genome methylation ... Key words: Methyl-DNA immunoprecipitation, next-generation sequencing, ...... methylation is prevalent in embryonic stem cells andmaybe mediated.

  3. Analysis of cryopyrin-associated periodic syndromes (CAPS) in German children: epidemiological, clinical and genetic characteristics.

    Science.gov (United States)

    Lainka, E; Neudorf, U; Lohse, P; Timmann, C; Bielak, M; Stojanov, S; Huss, K; von Kries, R; Niehues, T

    2010-11-01

    Cryopyrin-associated periodic syndromes (CAPS) are rare disorders belonging to the group of hereditary periodic fever (HPF)syndromes. These auto-inflammatory diseases(AID) are characterized by recurrent episodes of inflammation with attacks of fever variably associated with serosal, synovial and / or cutaneous inflammation, usually in a self-limiting manner, and with a mostly monogenic origin. The aims were to determine the incidence of CAPS and the spectrum of mutations in the NLRP3 (formerly= CIAS1) gene and to describe the clinical manifestations. A prospective surveillance of children with CAPS was conducted in Germany during a time period of 3 years(2003-2006). Monthly inquiries were sent to 370 children's hospitals by the German Paediatric Surveillance Unit (Clinic-ESPED, n1) and to 2 laboratories (Laboratory-ESPED, n2). Inclusion criteria were children ≤ 16 years of age, disease-associated NLRP3 mutation, more than 3 self-limiting episodes of fever > 38.5 ° C, and increased inflammation markers. Clinical, epidemiological and genetic data were evaluated via questionnaires. 6 out of 14 patients were identified in Clinic-ESPED (n1) and 13 / 14 in Laboratory-ESPED(n2). Clinical and laboratory surveys overlapped in 5 of 14 cases. The incidence of CAPS in German children was estimated to be 3.43 per 10⁷ person-years. The patients carried 11 different NLRP3 mutations and were classified as MWS(n = 6), CINCA (n = 4), FCAS (n = 1) and undefined CAPS (n = 3). The incidence of CAPS in Germany is very low and corresponds to 2-7 newly diagnosed patients ≤ 16 years per year. © Georg Thieme Verlag KG Stuttgart · New York.

  4. Ventricular Effective Refraction Period and Ventricular Repolarization Analysis in Experimental Tachycardiomyopathy in Swine.

    Science.gov (United States)

    Noszczyk-Nowak, Agnieszka; Pasławska, Urszula; Gajek, Jacek; Janiszewski, Adrian; Pasławski, Robert; Zyśko, Dorota; Nicpoń, Józef

    2016-01-01

    Swine are recognized animal models of human cardiovascular diseases. However, little is known on the CHF-associated changes in the electrophysiological ventricular parameters of humans and animals. The aim of this study was to analyze changes in the durations of ventricular effective refraction period (VERP), QT and QTc intervals of pigs with chronic tachycardia-induced tachycardiomyopathy (TIC). The study was comprised of 28 adult pigs (8 females and 20 males) of the Polish Large White breed. A one-chamber pacemaker was implanted in each of the 28 pigs. Electrocardiographic, echocardiographic and electrophysiological studies were carried out prior to the pacemaker implantation and at subsequent 4-week intervals. All electrocardiographic, echocardiographic and short electrophysiological study measurements in all swine were done under general anesthesia (propofol) after premedication with midazolam, medetomidine, and ketamine. No significant changes in the duration of QT interval and corrected QT interval (QTc) were observed during consecutive weeks of the experiment. The duration of the QTc interval of female pigs was shown to be significantly longer than that of the males throughout the whole study period. Beginning from the 12th week of rapid ventricular pacing, a significant increase in duration of VERP was observed in both male and female pigs. Males and females did not differ significantly in terms of VERP duration determined throughout the whole study period. Ventricular pacing, stimulation with 2 and 3 premature impulses at progressively shorter coupling intervals and an imposed rhythm of 130 bpm or 150 bpm induced transient ventricular tachycardia in one female pig and four male pigs. One episode of permanent ventricular tachycardia was observed. The number of induced arrhythmias increased proportionally to the severity of heart failure and duration of the experiment. However, relatively aggressive protocols of stimulation were required in order to induce

  5. ROMANIAN PEASANTRY AND BULGARIAN AGRARIANISM IN THE INTERWAR PERIOD: BENCHMARKS FOR A COMPARATIVE ANALYSIS

    Directory of Open Access Journals (Sweden)

    Cornel POPESCU

    2014-05-01

    Full Text Available This article is a comparative study that attempts to highlight the similarities and differences between Bulgarian agrarianism and Romanian peasants during the Interwar period, the Second World War and period of transition towards the Leninist-Stalinist totalitarian regimes. The objectives of our approach are integrated within the boundaries of the main research directions and concrete levels, namely: the general context from the two countries, early agrarian/peasants’ movements, the political program, election results, the promotion of certain legislative measures, and the relationship with other political and institutional entities. Without trying to offer an exhaustive view or reveal new aspects in the strict sense of the term, our contribution confronts, in a coherent whole, a series of data and information on the basis of which one could make value judgments. These judgments might help to shape a global, comparative image. Among the main sources of the article we included the monographic works signed by Ioan Scurtu, Pamfil Șeicaru, Apostol Stan, Dimitrina Petrova, John D. Bell, R.J. Crampton, supplemented by data from several other publications (encyclopedias, syntheses etc.. One can identify several distinct stages within the period under review (1918-1947. The broad picture is that the Bulgarian agrarian group was more popular and better organized than its Romanian counterpart, but more inclined towards Leftism and authoritarianism, which led to its political isolation in 1923 and subsequent fragmentation, whilst the Romanian peasants’ movement managed, after 1924, to remain at the forefront of the political scene, showing an interest for dialogue and sometimes for compromise, first with The National Party, then with the authoritarian monarchy, but also with the Antonescu regime and, to a lesser extent, with the communist regime.

  6. Analysis of publications by the Nuclear Regulation Authority for the period 2000-2014

    International Nuclear Information System (INIS)

    Wallingre, G.V.; Carregado, M.A.; Barone, M.L.

    2015-01-01

    This paper analyzes the publication habits by the Nuclear Regulation Authority (ARN) of Argentina for the period 2000-2014, through indicators of volume, typology, language and co authorship. It makes focus on publications in academic journals and characterizes them by publication country, language and access, and at the same time measures their impact and visibility through their classification in the SJR (SCImago Journal Rank) and their Impact Factor. Finally, it makes an introduction of Open Access journals in which the ARN has published, and briefly describes this method of dissemination. (authors) [es

  7. Evaluating the optimum rest period prior to blood collection for fractionated plasma free metanephrines analysis

    LENUS (Irish Health Repository)

    Griffin, T.P.

    2016-05-01

    The high diagnostic accuracy of plasma metanephrines (PMets) in the di-agnosis of Phaeochromocytoma\\/Paraganglioma (PPGL) is well established. Considerable controversy exists regarding optimum sampling conditions for PMets. The use of reference intervals that do not compromise diagnostic sensitivity is recommended. However, the optimum rest period prior to sampling has yet to be clearly established. The aim of this study was to evaluate PMets concentrations in paired blood samples collected following 30 and 40 min seated-rest prior to sampling, in patients in whom it was clinically rea-sonable to suspect that PPGL may be present.

  8. Maintaining high precision of isotope ratio analysis over extended periods of time.

    Science.gov (United States)

    Brand, Willi A

    2009-06-01

    Stable isotope ratios are reliable and long lasting process tracers. In order to compare data from different locations or different sampling times at a high level of precision, a measurement strategy must include reliable traceability to an international stable isotope scale via a reference material (RM). Since these international RMs are available in low quantities only, we have developed our own analysis schemes involving laboratory working RM. In addition, quality assurance RMs are used to control the long-term performance of the delta-value assignments. The analysis schemes allow the construction of quality assurance performance charts over years of operation. In this contribution, the performance of three typical techniques established in IsoLab at the MPI-BGC in Jena is discussed. The techniques are (1) isotope ratio mass spectrometry with an elemental analyser for delta(15)N and delta(13)C analysis of bulk (organic) material, (2) high precision delta(13)C and delta(18)O analysis of CO(2) in clean-air samples, and (3) stable isotope analysis of water samples using a high-temperature reaction with carbon. In addition, reference strategies on a laser ablation system for high spatial resolution delta(13)C analysis in tree rings is exemplified briefly.

  9. A dynamical systems analysis of the kinematics of time-periodic vortex shedding past a circular cylinder

    Science.gov (United States)

    Ottino, Julio M.

    1991-01-01

    Computer flow simulation aided by dynamical systems analysis is used to investigate the kinematics of time-periodic vortex shedding past a two-dimensional circular cylinder in the context of the following general questions: (1) Is a dynamical systems viewpoint useful in the understanding of this and similar problems involving time-periodic shedding behind bluff bodies; and (2) Is it indeed possible, by adopting such a point of view, to complement previous analyses or to understand kinematical aspects of the vortex shedding process that somehow remained hidden in previous approaches. We argue that the answers to these questions are positive. Results are described.

  10. Comments to "Analysis of constant rate period of spray drying of slurry" by Liang et al., 2001

    DEFF Research Database (Denmark)

    Jørgensen, Kåre; Jensen, Anker Degn; Sloth, Jakob

    2006-01-01

    In the study by Liang et al. [2001. Analysis of constant rate period of spray drying of slurry. Chemical Engineering Science 56, 2205-2213] the Darcy flow of liquid through a pore system of primary particles to the surface of a slurry droplet was applied for the constant rate period. Steep primary...... particle concentration gradients inside -25 mu m droplets with a primary particle size of 0.2 mu m were observed. Unfortunately, the boundary condition at the droplet surface for the parabolic second-order PDE did not conserve the solid mass in the droplet, and the plots for the primary particle...

  11. Analysis and enhancement of flexural wave stop bands in 2D periodic plates

    Energy Technology Data Exchange (ETDEWEB)

    Song, Yubao [Laboratory of Science and Technology on Integrated Logistics Support, National University of Defense Technology, 410073 Changsha (China); The Marcus Wallenberg Laboratory for Sound and Vibration Research, KTH – The Royal Institute of Technology, SE-100 44 Stockholm (Sweden); Feng, Leping [The Marcus Wallenberg Laboratory for Sound and Vibration Research, KTH – The Royal Institute of Technology, SE-100 44 Stockholm (Sweden); Wen, Jihong, E-mail: wenjihong_nudt1@vip.sina.com [Laboratory of Science and Technology on Integrated Logistics Support, National University of Defense Technology, 410073 Changsha (China); Yu, Dianlong; Wen, Xisen [Laboratory of Science and Technology on Integrated Logistics Support, National University of Defense Technology, 410073 Changsha (China)

    2015-07-17

    The band structure and enhancement of flexural wave stop bands in a 2D periodic plate are investigated. A unified method for analysing and designing the stop band of the plates with various attached structures is proposed. The effect of attached structures is considered based on their equivalent parameters (added equivalent mass and equivalent moment of inertia). The influences of the equivalent parameters on the band structures are studied. Three cases are considered: adding pure equivalent mass, pure equivalent moment of inertia and the combination of these two. The stop bands are enhanced via the multi interaction between the host plate and the attached structure. The enhancement pattern is determined, and several ways to obtain a wider combined stop band are presented. The frequency response functions of corresponding finite periodic plates are calculated to verify the stop bands and their enhancement in a number of typical cases. - Highlights: • A unified method for studying the stop band of the plates with various simplified attached structures is proposed. • The enhancement of flexural wave stop bands in a 2D phononic plate is investigated. • The stop bands are widened via multi interaction between the host plate and the attached structure. • The enhancement pattern is determined and several ways to get a wider stop band are presented.

  12. Raman analysis of phonon modes in a short period AlN/GaN superlattice

    Science.gov (United States)

    Sarkar, Ketaki; Datta, Debopam; Gosztola, David J.; Shi, Fengyuan; Nicholls, Alan; Stroscio, Michael A.; Dutta, Mitra

    2018-03-01

    AlN/GaN-based optoelectronic devices have been the subject of intense research underlying the commercialization of efficient devices. Areas of considerable interest are the study of their lattice dynamics, phonon transport, and electron-phonon interactions specific to the interface of these heterostructures which results in additional optical phonon modes known as interface phonon modes. In this study, the framework of the dielectric continuum model (DCM) has been used to compare and analyze the optical phonon modes obtained from experimental Raman scattering measurements on AlN/GaN short-period superlattices. We have observed the localized E2(high), A1(LO) and the E1(TO) modes in superlattice measurements at frequencies shifted from their bulk values. To the best of our knowledge, the nanostructures used in these studies are among the smallest yielding useful Raman signatures for the interface modes. In addition, we have also identified an additional spread of interface phonon modes in the TO range resulting from the superlattice periodicity. The Raman signature contribution from the underlying AlxGa1-xN ternary has also been observed and analyzed. A temperature calibration was done based on Stokes/anti-Stokes ratio of A1(LO) using Raman spectroscopy in a broad operating temperature range. Good agreement between the experimental results and theoretically calculated calibration plot predicted using Bose-Einstein statistics was obtained.

  13. Analysis of Puerarin and Chemical Compositions Changes in Kudzu Root during Growth Period

    Directory of Open Access Journals (Sweden)

    Yiguo Zhao

    2014-01-01

    Full Text Available The kudzu root is one of the earliest medicinal plants listed in traditional Chinese medicine. In this paper, chemical compositions changes of kudzu roots from one year old to five years old were analyzed with respect to puerarin, acid-insoluble polysaccharides, acid-soluble polysaccharides, reducing sugar, protein, free amino acids, and lipid. In addition, the puerarin content was determined by high performance liquid chromatography (HPLC method. The results showed that acid-soluble polysaccharides content of kudzu root increased with each growth period. In contrast, the acid-insoluble polysaccharides decreased significantly. The contents of reducing sugar and puerarin in kudzu root decreased significantly during its growth period. Beyond that, the contents of protein, free amino acids, and lipid in kudzu root ranged from 31.8 to 45.8 g/kg, 2.21 to 4.33 g/kg, and 32.2 to 76.9 g/kg, respectively. The trend of protein content coincided with the total content of free amino acids, in contrast to lipid. This paper provides a set of data and the select of kudzu root for the processing and development of new products of kudzu root.

  14. Cost analysis of two-dimensional warranty for products with periodic preventive maintenance

    International Nuclear Information System (INIS)

    Huang, Yeu-Shiang; Gau, Wei-Yo; Ho, Jyh-Wen

    2015-01-01

    This study uses a bivariate approach, which simultaneously considers the time and usage of a repairable product, and takes into account periodic preventive maintenance to develop a two-dimensional warranty policy for the repairable product. The proposed model is based on the bivariate Weibull process to analyze the breakdown process of a repairable product simultaneously in terms of time and usage. A repairable product may be differently utilized by various customers. We consider two types of customers: (1) customers whose product warranty is terminated because the warranty time limit has reached first; (2) customers whose product warranty is terminated because the warranty usage limit has reached first, to perform cost analyses for determining an appropriate warranty policy. However, since it is often the case that the repairable product may be equally likely purchased by the two types of customers who are equivalently important to the product manufacturer; the optimal warranty policy would thus be the equilibrium solution of the cost analyses which pay the same attention to both types of customers in order to maximize the total profit of the manufacturer. - Highlights: • We use a bivariate method to model the breakdown process. • We consider a periodic PM schedule. • We obtain an optimal two-dimensional warranty policy considering various customers. • The optimal 2D warranty is an equilibrium which satisfies both seller and buyer

  15. The analysis and interpretation of very-long-period seismic signals on volcanoes

    Science.gov (United States)

    Sindija, Dinko; Neuberg, Jurgen; Smith, Patrick

    2017-04-01

    The study of very long period (VLP) seismic signals became possible with the widespread use of broadband instruments. VLP seismic signals are caused by transients of pressure in the volcanic edifice and have periods ranging from several seconds to several minutes. For the VLP events recorded in March 2012 and 2014 at Soufriere Hills Volcano, Montserrat, we model the ground displacement using several source time functions: a step function using Richards growth equation, Küpper wavelet, and a damped sine wave to which an instrument response is then applied. This way we get a synthetic velocity seismogram which is directly comparable to the data. After the full vector field of ground displacement is determined, we model the source mechanism to determine the relationship between the source mechanism and the observed VLP waveforms. Emphasis of the research is on how different VLP waveforms are related to the volcano environment and the instrumentation used and on the processing steps in this low frequency band to get most out of broadband instruments.

  16. [Analysis on acupuncture literature in Science Citation Index (SCI) periodicals in 2007].

    Science.gov (United States)

    Gao, Liang; Tian, Li-xin; Guo, Yi

    2009-06-01

    To grasp the international developing tendency of acupuncture research and provide some references for promoting acupuncture and moxibustion internationalization process, the articles about acupuncture in Science Citation Index (SCI) periodicals in 2007 were retrieved by adopting the retrieval tactics on line in combination with database searching. Results indicate that 257 articles about acupuncture had been retrived from the SCI Web databases. These articles were published in 125 journals respectively, most of which were Euramerican journals. Among these journals, the impact factor of the Journal of the American Medical Association (JAMA), 25. 547, is the highest one. It is shown that the impact factors of the SCI periodicals, in which acupuncture articles embodied are increased, the quality of these articles are improved obviously and the types of the articles are various in 2007, but there is obvious difference in the results of these studies due to the difference of experimental methods, the subjects of these experiments and acupuncture manipulations. Therefore, standardization of many problems arising from the researches on acupuncture is extremely imminent.

  17. Quantitative Analysis of Major Constituents in Green Tea with Different Plucking Periods and Their Antioxidant Activity

    Directory of Open Access Journals (Sweden)

    Lan-Sook Lee

    2014-07-01

    Full Text Available The objective of this study was to determine the relationship between the plucking periods and the major constituents and the antioxidant activity in green tea. Green tea was prepared from leaves plucked from the end of April 2013 to the end of May 2013 at intervals of one week or longer. The contents of theanine, theobromine, caffeine, catechin (C, and gallocatechin gallate (GCg were significantly decreased, whereas those of epicatechin (EC, epigallocatechin gallate (EGCg and epigallocatechin (EGC were significantly increased along with the period of tea leaf plucking. In addition, antioxidant activity of green tea and standard catechins was investigated using ABTS, FRAP and DPPH assays. The highest antioxidant activity was observed in relatively the oldest leaf, regardless of the assay methods used. Additionally, the order of antioxidant activity of standard catechins was as follows: EGCg ³ GCg ³ ECg > EGC ³ GC ³ EC ³ C. Moreover, the cis-catechins contents were the key factor affecting the antioxidant activity of green tea in all assays employed (ABTS, r = 0.731, p < 0.01; FRAP, r = 0.886, p < 0.01; DPPH, r = 0.778, p < 0.01.

  18. Maternal Alcohol Consumption During the Perinatal and Early Parenting Period: A Longitudinal Analysis.

    Science.gov (United States)

    Liu, Weiwei; Mumford, Elizabeth A; Petras, Hanno

    2016-02-01

    Despite potential health risks for women and children, one in five women report alcohol use during pregnancy and a significant proportion of those who quit during pregnancy return to drinking post-delivery. This study seeks to understand the longitudinal patterns of alcohol consumption before, during pregnancy and post-delivery, and the role of maternal characteristics for purposes of informing prevention design. General growth mixture models were used to describe the average developmental patterns of maternal weekly drinking quantity at six time points, from preconception through child entering kindergarten, as well as heterogeneity in these patterns among 9100 mothers from the Early Childhood Longitudinal Study representing the 2001 US national birth cohort. Four distinct classes of mothers were defined by their longitudinal alcohol consumption patterns: Low Probability Drinkers (50.3 %), Escalating Risk Drinkers (12.0 %), Escalating Low Risk Drinkers (27.4 %), and Early Parenting Quitters (10.2 %). Heterogeneous covariate associations were observed. For example, mothers who gave birth after age 36 were twice as likely to be Escalating Risk Drinkers and Escalating Low Risk Drinkers (vs Low Probability Drinkers), but not more likely to be Early Parenting Quitters, when compared to mothers who gave birth between the ages of 26 and 35. There is significant heterogeneity in maternal longitudinal alcohol use patterns during the perinatal period. Baseline maternal characteristics and behavior associated with these heterogeneous patterns provide valuable tools to identify potential risky drinkers during this critical time period and may be synthesized to tailor pre- and postnatal clinical counseling protocols.

  19. Optical resonance analysis of reflected long period fiber gratings with metal film overlay

    Science.gov (United States)

    Zhang, Guiju; Cao, Bing; Wang, Chinua; Zhao, Minfu

    2008-11-01

    We present the experimental results of a novel single-ended reflecting surface plasma resonance (SPR) based long period fiber grating (LPFG) sensor. A long period fiber grating sensing device is properly designed and fabricated with a pulsed CO2 laser writing system. Different nm-thick thin metal films are deposited on the fiber cladding and the fiber end facet for the excitation of surface plasma waves (SPWs) and the reflection of the transmission spectrum of the LPFG with doubled interaction between metal-dielectric interfaces of the fiber to enhance the SPW of the all-fiber SPR-LPFG sensing system. Different thin metal films with different thicknesses are investigated. The effect of the excited SPW transmission along the fiber cladding-metal interface with silver and aluminum films is observed. It is found that different thicknesses of the metal overlay show different resonant behaviors in terms of resonance peak situation, bandwidth and energy loss. Within a certain range, thinner metal film shows narrower bandwidth and deeper peak loss.

  20. Dynamic acetylation of all lysine 4-methylated histone H3 in the mouse nucleus: analysis at c-fos and c-jun.

    Directory of Open Access Journals (Sweden)

    Catherine A Hazzalin

    2005-12-01

    Full Text Available A major focus of current research into gene induction relates to chromatin and nucleosomal regulation, especially the significance of multiple histone modifications such as phosphorylation, acetylation, and methylation during this process. We have discovered a novel physiological characteristic of all lysine 4 (K4-methylated histone H3 in the mouse nucleus, distinguishing it from lysine 9-methylated H3. K4-methylated histone H3 is subject to continuous dynamic turnover of acetylation, whereas lysine 9-methylated H3 is not. We have previously reported dynamic histone H3 phosphorylation and acetylation as a key characteristic of the inducible proto-oncogenes c-fos and c-jun. We show here that dynamically acetylated histone H3 at these genes is also K4-methylated. Although all three modifications are proven to co-exist on the same nucleosome at these genes, phosphorylation and acetylation appear transiently during gene induction, whereas K4 methylation remains detectable throughout this process. Finally, we address the functional significance of the turnover of histone acetylation on the process of gene induction. We find that inhibition of turnover, despite causing enhanced histone acetylation at these genes, produces immediate inhibition of gene induction. These data show that all K4-methylated histone H3 is subject to the continuous action of HATs and HDACs, and indicates that at c-fos and c-jun, contrary to the predominant model, turnover and not stably enhanced acetylation is relevant for efficient gene induction.

  1. Methylation pathways in schizophrenia

    International Nuclear Information System (INIS)

    Sargent, T.W. III.

    1982-01-01

    Research on the biochemical causes of human psychosis concentrates on investigating whether schizophremia is linked to abnormalities in the metabolism of methyl carbon groups in the body. The metabolism of C-14 labeled methyl groups in methionine is studied in animals, normal subjects and patient volunteers

  2. Observed ozone exceedances in Italy: statistical analysis and modelling in the period 2002-2015

    Science.gov (United States)

    Falasca, Serena; Curci, Gabriele; Candeloro, Luca; Conte, Annamaria; Ippoliti, Carla

    2017-04-01

    Local ambient air quality is strongly influenced by anthropogenic emissions and meteorological conditions. The year 2015 is considered by NASA scientists as one of the hottest at the global scale since 1880. Furthermore, in Europe it was the first summer after the introduction of Euro6 regulation, the latest emission standard for passenger vehicles. The goal of this study is twofold: (1) the investigation of the impact o