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Sample records for methyl-dna immunoprecipitation combined

  1. Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing

    PubMed Central

    2010-01-01

    Background Cancer cells undergo massive alterations to their DNA methylation patterns that result in aberrant gene expression and malignant phenotypes. However, the mechanisms that underlie methylome changes are not well understood nor is the genomic distribution of DNA methylation changes well characterized. Results Here, we performed methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) to obtain whole-genome DNA methylation profiles for eight human breast cancer cell (BCC) lines and for normal human mammary epithelial cells (HMEC). The MeDIP-seq analysis generated non-biased DNA methylation maps by covering almost the entire genome with sufficient depth and resolution. The most prominent feature of the BCC lines compared to HMEC was a massively reduced methylation level particularly in CpG-poor regions. While hypomethylation did not appear to be associated with particular genomic features, hypermethylation preferentially occurred at CpG-rich gene-related regions independently of the distance from transcription start sites. We also investigated methylome alterations during epithelial-to-mesenchymal transition (EMT) in MCF7 cells. EMT induction was associated with specific alterations to the methylation patterns of gene-related CpG-rich regions, although overall methylation levels were not significantly altered. Moreover, approximately 40% of the epithelial cell-specific methylation patterns in gene-related regions were altered to those typical of mesenchymal cells, suggesting a cell-type specific regulation of DNA methylation. Conclusions This study provides the most comprehensive analysis to date of the methylome of human mammary cell lines and has produced novel insights into the mechanisms of methylome alteration during tumorigenesis and the interdependence between DNA methylome alterations and morphological changes. PMID:20181289

  2. Genome-wide analysis of methylation in bovine clones by methylated DNA immunoprecipitation (MeDIP).

    PubMed

    Kiefer, Hélène

    2015-01-01

    Methylated DNA immunoprecipitation (MeDIP), when coupled to high-throughput sequencing or microarray hybridization, allows for the identification of methylated loci at a genome-wide scale. Genomic regions affected by incomplete reprogramming after nuclear transfer can potentially be delineated by comparing the MeDIP profiles of bovine clones and non-clones. This chapter presents a MeDIP protocol largely inspired from Mohn and colleagues (Mohn et al., Methods Mol Biol 507:55-64, 2009), with PCR primers specific for cattle, and when possible, overviews of experimental designs adapted to the comparison between clones and non-clones.

  3. The Methylated DNA Immunoprecipitation [MeDIP] to Investigate the Epigenetic Remodeling in Cell Fate Determination and Cancer Development.

    PubMed

    Masciarelli, Silvia; Bellissimo, Teresa; Iosue, Ilaria; Fazi, Francesco

    2016-01-01

    Epigenetic mechanisms such as DNA methylation, posttranslational modifications of histone proteins, remodeling of nucleosomes, and the expression of noncoding RNAs contribute to the regulation of gene expression for the cell fate determination and tissue development. The disruption of these epigenetic mechanisms, in conjunction with genetic alterations, is a decisive element for cancer development and progression. The cancer phenotype is characterized by global DNA hypomethylation and gene-specific hypermethylation. The methylated DNA immunoprecipitation [MeDIP] is a useful approach currently used to clarify the functional consequences of DNA methylation on cell fate determination and cancer development.

  4. Clinical and public health research using methylated DNA Immunoprecipitation (MeDIP): A comparison of commercially available kits to examine differential DNA methylation across the genome

    PubMed Central

    Brebi-Mieville, Priscilla; Ili-Gangas, Carmen; Leal-Rojas, Pamela; Noordhuis, Maartje; Soudry, Ethan; Perez, Jimena; Roa, Juan Carlos; Sidransky, David; Guerrero-Preston, Rafael

    2012-01-01

    The methylated DNA immunoprecipitation method (MeDIP) is a genome-wide, high-resolution approach that detects DNA methylation with oligonucleotide tiling arrays or high throughput sequencing platforms. A simplified high-throughput MeDIP assay will enable translational research studies in clinics and populations, which will greatly enhance our understanding of the human methylome. We compared three commercial kits, MagMeDIP Kit TM (Diagenode), Methylated-DNA IP Kit (Zymo Research) and Methylamp™ Methylated DNA Capture Kit (Epigentek), in order to identify which one has better reliability and sensitivity for genomic DNA enrichment. Each kit was used to enrich two samples, one from fresh tissue and one from a cell line, with two different DNA amounts. The enrichment efficiency of each kit was evaluated by agarose gel band intensity after Nco I digestion and by reaction yield of methylated DNA. A successful enrichment is expected to have a 1:4 to 10:1 conversion ratio and a yield of 80% or higher. We also evaluated the hybridization efficiency to genome-wide methylation arrays in a separate cohort of tissue samples. We observed that the MagMeDIP kit had the highest yield for the two DNA amounts and for both the tissue and cell line samples, as well as for the positive control. In addition, the DNA was successfully enriched from a 1:4 to 10:1 ratio. Therefore, the MagMeDIP kit is a useful research tool that will enable clinical and public health genome-wide DNA methylation studies. PMID:22207357

  5. Sensitive and selective amplification of methylated DNA sequences using helper-dependent chain reaction in combination with a methylation-dependent restriction enzymes.

    PubMed

    Rand, Keith N; Young, Graeme P; Ho, Thu; Molloy, Peter L

    2013-01-01

    We have developed a novel technique for specific amplification of rare methylated DNA fragments in a high background of unmethylated sequences that avoids the need of bisulphite conversion. The methylation-dependent restriction enzyme GlaI is used to selectively cut methylated DNA. Then targeted fragments are tagged using specially designed 'helper' oligonucleotides that are also used to maintain selection in subsequent amplification cycles in a process called 'helper-dependent chain reaction'. The process uses disabled primers called 'drivers' that can only prime on each cycle if the helpers recognize specific sequences within the target amplicon. In this way, selection for the sequence of interest is maintained throughout the amplification, preventing amplification of unwanted sequences. Here we show how the method can be applied to methylated Septin 9, a promising biomarker for early diagnosis of colorectal cancer. The GlaI digestion and subsequent amplification can all be done in a single tube. A detection sensitivity of 0.1% methylated DNA in a background of unmethylated DNA was achieved, which was similar to the well-established Heavy Methyl method that requires bisulphite-treated DNA.

  6. Chromatin Immunoprecipitation.

    PubMed

    Wiehle, Laura; Breiling, Achim

    2016-01-01

    Chromatin immunoprecipitation (ChIP) is a valuable method to investigate protein-DNA interactions in vivo. Since its discovery it has been indispensable to identify binding sites and patterns of a variety of DNA-interacting proteins, such as transcription factors and regulators, modified histones, and epigenetic modifiers. The Polycomb repressors were the first proteins that have been mapped using this technique, which provided the mechanistic basis for the understanding of their biological function. Cross-linked (XChIP) or native (NChIP) chromatin from tissues or cultured cells is fragmented and the protein of interest is immunoprecipitated using a specific antibody. The co-precipitated DNA is then purified and subjected to analysis by region-specific PCR, DNA microarray (ChIP-on-chip), or next-generation sequencing (ChIP-seq). The assay can therefore produce information about the localization of the analyzed protein at specific candidate loci or throughout the entire genome. In this chapter, we provide a detailed protocol of the basic standard ChIP assay and some remarks about variations. PMID:27659971

  7. Combining Ultracentrifugation and Peptide Termini Group-specific Immunoprecipitation for Multiplex Plasma Protein Analysis

    PubMed Central

    Volk, Sonja; Schreiber, Thomas D.; Eisen, David; Wiese, Calvin; Planatscher, Hannes; Pynn, Christopher J.; Stoll, Dieter; Templin, Markus F.; Joos, Thomas O.; Pötz, Oliver

    2012-01-01

    Blood plasma is a valuable source of potential biomarkers. However, its complexity and the huge dynamic concentration range of its constituents complicate its analysis. To tackle this problem, an immunoprecipitation strategy was employed using antibodies directed against short terminal epitope tags (triple X proteomics antibodies), which allow the enrichment of groups of signature peptides derived from trypsin-digested plasma. Isolated signature peptides are subsequently detected using MALDI-TOF/TOF mass spectrometry. Sensitivity of the immunoaffinity approach was, however, compromised by the presence of contaminant peaks derived from the peptides of nontargeted high abundant proteins. A closer analysis of the enrichment strategy revealed nonspecific peptide binding to the solid phase affinity matrix as the major source of the contaminating peptides. We therefore implemented a sucrose density gradient ultracentrifugation separation step into the procedure. This yielded a 99% depletion of contaminating peptides from a sucrose fraction containing 70% of the peptide-antibody complexes and enabled the detection of the previously undetected low abundance protein filamin-A. Assessment of this novel approach using 15 different triple X proteomics antibodies demonstrated a more consistent detection of a greater number of targeted peptides and a significant reduction in the intensity of nonspecific peptides. Ultracentrifugation coupled with immunoaffinity MS approaches presents a powerful tool for multiplexed plasma protein analysis without the requirement for demanding liquid chromatography separation techniques. PMID:22527512

  8. Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel.

    PubMed

    Cipriany, Benjamin R; Murphy, Patrick J; Hagarman, James A; Cerf, Aline; Latulippe, David; Levy, Stephen L; Benítez, Jaime J; Tan, Christine P; Topolancik, Juraj; Soloway, Paul D; Craighead, Harold G

    2012-05-29

    Epigenetic modifications, such as DNA and histone methylation, are responsible for regulatory pathways that affect disease. Current epigenetic analyses use bisulfite conversion to identify DNA methylation and chromatin immunoprecipitation to collect molecules bearing a specific histone modification. In this work, we present a proof-of-principle demonstration for a new method using a nanofluidic device that combines real-time detection and automated sorting of individual molecules based on their epigenetic state. This device evaluates the fluorescence from labeled epigenetic modifications to actuate sorting. This technology has demonstrated up to 98% accuracy in molecule sorting and has achieved postsorting sample recovery on femtogram quantities of genetic material. We have applied it to sort methylated DNA molecules using simultaneous, multicolor fluorescence to identify methyl binding domain protein-1 (MBD1) bound to full-duplex DNA. The functionality enabled by this nanofluidic platform now provides a workflow for color-multiplexed detection, sorting, and recovery of single molecules toward subsequent DNA sequencing.

  9. RIP: RNA Immunoprecipitation.

    PubMed

    Gagliardi, Miriam; Matarazzo, Maria R

    2016-01-01

    The relevance of RNA-protein interactions in modulating mRNA and noncoding RNA function is increasingly appreciated and several methods have been recently developed to map them. The RNA immunoprecipitation (RIP) is a powerful method to study the physical association between individual proteins and RNA molecules in vivo. The basic principles of RIP are very similar to those of chromatin immunoprecipitation (ChIP), a largely used tool in the epigenetic field, but with some important caveats. The approach is based on the use of a specific antibody raised against the protein of interest to pull down the RNA-binding protein (RBP) and target-RNA complexes. Any RNA that is associated with this protein complex will also be isolated and can be further analyzed by polymerase chain reaction-based methods, hybridization, or sequencing.Several variants of this technique exist and can be divided into two main classes: native and cross-linked RNA immunoprecipitation. The native RIP allows to reveal the identity of RNAs directly bound by the protein and their abundance in the immunoprecipitated sample, while cross-linked RIP leads to precisely map the direct and indirect binding site of the RBP of interest to the RNA molecule.In this chapter both the protocols applied to mammalian cells are described taking into account the caveats and considerations required for designing, performing, and interpreting the results of these experiments. PMID:27659976

  10. Combination of immunoprecipitation (IP)-ATP_Glo kinase assay and melanogenesis for the assessment of potent and safe PAK1-blockers in cell culture.

    PubMed

    Nguyen, Binh Cao Quan; Be Tu, Pham Thi; Tawata, Shinkichi; Maruta, Hiroshi

    2015-08-01

    Cucurbitacin I (CBI) is a triterpene from a bitter melon called Goya grown in Okinawa, Japan, and directly inhibits both the Tyr-kinase JAK2 and the G protein RAC, leading to the inactivation of PAK1 (RAC/CDC42-activated kinase 1). Bio 30, a propolis produced in New Zealand, contains CAPE (caffeic acid phenethyl ester) as the major anti-cancer ingredient which directly down-regulates RAC, leading to the inactivation of PAK1. Since PAK1 is essential for the growth of RAS cancer cells such as A549 cell line which carry an oncogenic K-RAS mutant, and the melanogenesis in skin cells, here using these PAK1-blockers as model compounds, we introduce a new approach to the quick assessment of PAK1-blockers in cell culture. First, combining the immuno-precipitation (IP) of PAK1 from cell lysate and the in vitro ATP_Glo kinase assay kit (called "Macaroni-Western" assay), we confirmed that both CBI and Bio 30 inactivate PAK1 in A549 lung cancer cells in 24 h, and inhibit their PAK1-dependent growth in 72 h. Furthermore, we verified that CBI inhibits the PAK1/PAK4-dependent melanogenesis in melanoma cells by far more than 50%, while Bio 30 inhibits the melanogenesis only by 50%, with only a merginal effect on their growth per se. Since the "Macaroni-Western" kinase assay and melanogenesis are both rather simple and quick, the combination of these two cell culture assays would be highly useful for selecting both "potent" (highly cell-permeable) and "safe" (non-toxic) natural or synthetic PAK1-blockers. PMID:26370527

  11. Combination of immunoprecipitation (IP)-ATP_Glo kinase assay and melanogenesis for the assessment of potent and safe PAK1-blockers in cell culture.

    PubMed

    Nguyen, Binh Cao Quan; Be Tu, Pham Thi; Tawata, Shinkichi; Maruta, Hiroshi

    2015-08-01

    Cucurbitacin I (CBI) is a triterpene from a bitter melon called Goya grown in Okinawa, Japan, and directly inhibits both the Tyr-kinase JAK2 and the G protein RAC, leading to the inactivation of PAK1 (RAC/CDC42-activated kinase 1). Bio 30, a propolis produced in New Zealand, contains CAPE (caffeic acid phenethyl ester) as the major anti-cancer ingredient which directly down-regulates RAC, leading to the inactivation of PAK1. Since PAK1 is essential for the growth of RAS cancer cells such as A549 cell line which carry an oncogenic K-RAS mutant, and the melanogenesis in skin cells, here using these PAK1-blockers as model compounds, we introduce a new approach to the quick assessment of PAK1-blockers in cell culture. First, combining the immuno-precipitation (IP) of PAK1 from cell lysate and the in vitro ATP_Glo kinase assay kit (called "Macaroni-Western" assay), we confirmed that both CBI and Bio 30 inactivate PAK1 in A549 lung cancer cells in 24 h, and inhibit their PAK1-dependent growth in 72 h. Furthermore, we verified that CBI inhibits the PAK1/PAK4-dependent melanogenesis in melanoma cells by far more than 50%, while Bio 30 inhibits the melanogenesis only by 50%, with only a merginal effect on their growth per se. Since the "Macaroni-Western" kinase assay and melanogenesis are both rather simple and quick, the combination of these two cell culture assays would be highly useful for selecting both "potent" (highly cell-permeable) and "safe" (non-toxic) natural or synthetic PAK1-blockers.

  12. Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel

    PubMed Central

    Cipriany, Benjamin R.; Murphy, Patrick J.; Hagarman, James A.; Cerf, Aline; Latulippe, David; Levy, Stephen L.; Benítez, Jaime J.; Tan, Christine P.; Topolancik, Juraj; Soloway, Paul D.; Craighead, Harold G.

    2012-01-01

    Epigenetic modifications, such as DNA and histone methylation, are responsible for regulatory pathways that affect disease. Current epigenetic analyses use bisulfite conversion to identify DNA methylation and chromatin immunoprecipitation to collect molecules bearing a specific histone modification. In this work, we present a proof-of-principle demonstration for a new method using a nanofluidic device that combines real-time detection and automated sorting of individual molecules based on their epigenetic state. This device evaluates the fluorescence from labeled epigenetic modifications to actuate sorting. This technology has demonstrated up to 98% accuracy in molecule sorting and has achieved postsorting sample recovery on femtogram quantities of genetic material. We have applied it to sort methylated DNA molecules using simultaneous, multicolor fluorescence to identify methyl binding domain protein-1 (MBD1) bound to full-duplex DNA. The functionality enabled by this nanofluidic platform now provides a workflow for color-multiplexed detection, sorting, and recovery of single molecules toward subsequent DNA sequencing. PMID:22586076

  13. Structural basis for Klf4 recognition of methylated DNA.

    PubMed

    Liu, Yiwei; Olanrewaju, Yusuf Olatunde; Zheng, Yu; Hashimoto, Hideharu; Blumenthal, Robert M; Zhang, Xing; Cheng, Xiaodong

    2014-04-01

    Transcription factor Krüppel-like factor 4 (Klf4), one of the factors directing cellular reprogramming, recognizes the CpG dinucleotide (whether methylated or unmodified) within a specific G/C-rich sequence. The binding affinity of the mouse Klf4 DNA-binding domain for methylated DNA is only slightly stronger than that for an unmodified oligonucleotide. The structure of the C-terminal three Krüppel-like zinc fingers (ZnFs) of mouse Klf4, in complex with fully methylated DNA, was determined at 1.85 Å resolution. An arginine and a glutamate interact with the methyl group. By comparison with two other recently characterized structures of ZnF protein complexes with methylated DNA, we propose a common principle of recognition of methylated CpG by C2H2 ZnF proteins, which involves a spatially conserved Arg-Glu pair. PMID:24520114

  14. A Microfluidic Device with Integrated Sonication and Immunoprecipitation for Sensitive Epigenetic Assays.

    PubMed

    Cao, Zhenning; Lu, Chang

    2016-02-01

    Epigenetic studies increasingly require analysis of a small number of cells that are of one specific type and derived from patients or animals. In this report, we demonstrate a simple microfluidic device that integrates sonication and immunoprecipitation (IP) for epigenetic assays, such as chromatin immunoprecipitation (ChIP) and methylated DNA immunoprecipitation (MeDIP). By incorporating an ultrasonic transducer with a microfluidic chamber, we implemented microscale sonication for both shearing chromatin/DNA and mixing/washing of IP beads. Such integration allowed highly sensitive tests starting with 100 cross-linked cells for ChIP or 500 pg of genomic DNA for MeDIP (compared to 10(6)-10(7) cells for ChIP and 1-10 μg of DNA for MeDIP in conventional assays). The entire on-chip process of sonication and IP took only 1 h. Our tool will be useful for highly sensitive epigenetic studies based on a small quantity of sample.

  15. Protein tagging for chromatin immunoprecipitation from Arabidopsis.

    PubMed

    de Folter, Stefan

    2011-01-01

    A powerful method to identify binding sites in target genes is chromatin immunoprecipitation (ChIP), which allows the purification of in vivo formed complexes of a DNA-binding protein and associated DNA. Briefly, the method involves the fixation of plant tissue and the isolation of the total protein-DNA mixture, followed by an immunoprecipitation step with an antibody directed against the protein of interest and, subsequently, the DNA can be purified. Finally, the DNA can be analyzed by PCR for the enrichment of specific regions. A drawback of ChIP is that for each protein another antibody is needed. To overcome this, a generic strategy is possible using tags fused to the protein of interest. In this case, only antibody is needed against the tag. This protocol describes the tagging of proteins and how to perform ChIP. PMID:20931382

  16. Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation.

    PubMed

    He, Yan; Wang, Minghui; Sun, Qi; Pawlowski, Wojciech P

    2016-01-01

    Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi. PMID:27511175

  17. Machupo virus polypeptides: identification by immunoprecipitation.

    PubMed

    Lukashevich, I S; Lemeshko, N N

    1985-01-01

    The most abundant protein in purified Machupo virions (Corvallo strain) labelled with 14C-Protein hydrolysate is a 64 K polypeptide which is associated with virion RNAs. Another structural polypeptide, 37 K, solubilized by nonionic detergent seems to be a major surface glycoprotein. In addition to this, a 78 K polypeptide and a minor 50 K polypeptide have been detected. In Machupo virus infected cells three virus-specific polypeptides similar in size to those described for structural polypeptides were immunoprecipitated with anti-Machupo virus serum. The most abundant virus-specific polypeptide was nonglycosylated (64 K, NP), and the others were glycosylated polypeptides (78 K and 37 K). The synthesis of NP and 78 K polypeptides was recognized at the beginning of a log phase of virus replication. Pulse-chase experiments as well as experiments with an arginine analogue, canavanine (to block proteolytic processing) suggest that 78 K is a precursor for structural glycoproteins of Machupo virions.

  18. Protein composition of immunoprecipitated synaptic ribbons

    PubMed Central

    Kantardzhieva, A.; Peppi, M.; Lane, W.S.; Sewell, W.F.

    2012-01-01

    The synaptic ribbon is an electron-dense structure found in hair cells and photoreceptors. The ribbon is surrounded by neurotransmitter-filled vesicles and considered to play a role in vesicle release. We generated an objective, quantitative analysis of the protein composition of the ribbon complex using a mass spectrometry-based proteomics analysis. Our use of affinity-purified ribbons and control IgG immunoprecipitations ensure that the identified proteins are indeed associated with the ribbon complex. The use of mouse tissue, where the proteome is complete, generated a comprehensive analysis of the candidates. We identified 30 proteins (comprising 56 isoforms and subunits) associated with the ribbon complex. The ribbon complex primarily comprises proteins found in conventional synapses, which we categorized into 6 functional groups: vesicle handling (38.5%), scaffold (7.3%), cytoskeletal molecules (20.6%), phosphorylation enzymes (10.6%), molecular chaperones (8.2%), and transmembrane proteins from the presynaptic membrane firmly attached to the ribbon (11.3%). The 3 CtBP isoforms represent the major protein in the ribbon whether calculated by molar amount (30%) or by mass (20%). The relatively high quantity of phosphorylation enzymes suggests a very active and regulated structure. The ribbon appears to comprise a concentrated cluster of proteins dealing with vesicle creation, retention and distribution, and consequent exocytosis. PMID:22103298

  19. Chromatin immunoprecipitation analysis of Xenopus embryos.

    PubMed

    Akkers, Robert C; Jacobi, Ulrike G; Veenstra, Gert Jan C

    2012-01-01

    Chromatin immunoprecipitation (ChIP) is a powerful technique to study epigenetic regulation and transcription factor binding events in the nucleus. It is based on immune-affinity capture of epitopes that have been cross-linked to genomic DNA in vivo. A readout of the extent to which the epitope is associated with particular genomic regions can be obtained by quantitative PCR (ChIP-qPCR), microarray hybridization (ChIP-chip), or deep sequencing (ChIP-seq). ChIP can be used for molecular and quantitative analyses of histone modifications, transcription factors, and elongating RNA polymerase II at specific loci. It can also be applied to assess the cellular state of transcriptional activation or repression as a predictor of the cells' capabilities and potential. Another possibility is to employ ChIP to characterize genomes, as histone modifications and binding events occur at specific and highly characteristic genomic elements and locations. This chapter provides a step-by-step protocol of ChIP using early Xenopus embryos and discusses potential pitfalls and other issues relevant for successful probing of protein-genome interactions by ChIP-qPCR and ChIP-seq. PMID:22956095

  20. Immunoprecipitation of the parathyroid hormone receptor

    SciTech Connect

    Wright, B.S.; Tyler, G.A.; O'Brien, R.; Caporale, L.H.; Rosenblatt, M.

    1987-01-01

    An /sup 125/I-labeled synthetic analog of bovine parathyroid hormone, (8-norleucine,18-norleucine,34-tyrosine)PTH-(1-34) amide ((Nle)PTH-(1-34)-NH/sub 2/), purified by high-pressure liquid chromatography (HPLC), was employed to label the parathyroid hormone (PTH) receptor in cell lines derived from PTH target tissues: the ROS 17/2.8 rat osteosarcoma of bone and the CV1 and COS monkey kidney lines. After incubation of the radioligand with intact cultured cells, the hormone was covalently attached to receptors by using either a photoaffinity technique or chemical (affinity) crosslinking. In each case, covalent labeling was specific, as evidenced by a reduction of labeling when excess competing nonradioactive ligand was present. After covalent attachment of radioligand, membranes were prepared form the cells and solubilized in the nonionic detergent Nonidet P-40 or octyl glucoside. Analysis of the immunoprecipitate on NaDod-SO/sub 4//polyacrylamide gel electrophoresis followed by autoradiography revealed the presence of a doublet of apparent molecular mass 69-70 kDa. Specifically labeled bands of approximate molecular mass 95 and 28 kDa were also observed. The anti-PTH IgG was affinity purified by passage over a PTH-Sepharose column and used to made an immunoaffinity column. These studies suggest that the use of an anti-PTH antiserum that binds receptor-bound hormone is likely to be a useful step in the further physicochemical characterization and purification of the PTH receptor.

  1. Spectroscopic studies of STZ-induced methylated-DNA in both in vivo and in vitro conditions

    NASA Astrophysics Data System (ADS)

    Bathaie, S. Z.; Sedghgoo, F.; Jafarnejad, A.; Farzami, B.; Khayatian, M.

    2008-12-01

    Alkylating agents after formation of DNA adduct not only posses their harmful role on living cells but also can transfer this information to the next generation. Different techniques have been introduced to study the alkylated DNA, most of which are specific and designed for investigation of specific target DNA. But the exact differences between spectroscopic and functional properties of alkylated DNA are not seen in the literature. In the present study DNA was methylated using streptozotocin (STZ) by both in vitro and in vivo protocols, then methylated-DNA was investigated by various techniques. Our results show that (1) the binding of ethidium bromide as an intercalating dye decreases to methylated-DNA in comparison with normal DNA, (2) CD spectra of methylated-DNA show changes including a decrease in the positive band at 275 nm and a shift from 258 nm crossover to a longer wavelength, which is caused by reduction of water around it, due to the presence of additional hydrophobic methyl groups, (3) the stability of methylated-DNA against DTAB as a denaturant is decreased and (4) the enzyme-like activity of methylated-DNA in an electron transfer reaction is reduced. In conclusion, additional methyl groups not only protrude water around DNA, but also cause the loss of hydrogen bonding, loosening of conformation, preventing desired interactions and thus normal function of DNA.

  2. Immunoprecipitation and Characterization of Membrane Protein Complexes from Yeast

    ERIC Educational Resources Information Center

    Parra-Belky, Karlett; McCulloch, Kathryn; Wick, Nicole; Shircliff, Rebecca; Croft, Nicolas; Margalef, Katrina; Brown, Jamie; Crabill, Todd; Jankord, Ryan; Waldo, Eric

    2005-01-01

    In this undergraduate biochemistry laboratory experiment, the vacuolar ATPase protein complex is purified from yeast cell extracts by doing immunoprecipitations under nondenaturing conditions. Immunoprecipitations are performed using monoclonal antibodies to facilitate data interpretation, and subunits are separated on the basis of their molecular…

  3. Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates.

    PubMed

    Long, Hannah K; Sims, David; Heger, Andreas; Blackledge, Neil P; Kutter, Claudia; Wright, Megan L; Grützner, Frank; Odom, Duncan T; Patient, Roger; Ponting, Chris P; Klose, Robert J

    2013-01-01

    Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation on chromatin. In cold-blooded vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution. DOI:http://dx.doi.org/10.7554/eLife.00348.001. PMID:23467541

  4. Chromatin immunoprecipitation and microarray-based analysis of protein location

    PubMed Central

    Lee, Tong Ihn; Johnstone, Sarah E; Young, Richard A

    2010-01-01

    Genome-wide location analysis, also known as ChIP-Chip, combines chromatin immunoprecipitation and DNA microarray analysis to identify protein-DNA interactions that occur in living cells. Protein-DNA interactions are captured in vivo by chemical crosslinking. Cell lysis, DNA fragmentation and immunoaffinity purification of the desired protein will co-purify DNA fragments that are associated with that protein. The enriched DNA population is then labeled, combined with a differentially labeled reference sample and applied to DNA microarrays to detect enriched signals. Various computational and bioinformatic approaches are then applied to normalize the enriched and reference channels, to connect signals to the portions of the genome that are represented on the DNA microarrays, to provide confidence metrics and to generate maps of protein-genome occupancy. Here, we describe the experimental protocols that we use from crosslinking of cells to hybridization of labeled material, together with insights into the aspects of these protocols that influence the results. These protocols require approximately 1 week to complete once sufficient numbers of cells have been obtained, and have been used to produce robust, high-quality ChIP-chip results in many different cell and tissue types. PMID:17406303

  5. Methylated DNA-binding protein is present in various mammalian cell types

    SciTech Connect

    Supakar, P.C.; Weist, D.; Zhang, D.; Inamdar, N.; Zhang, Xianyang; Khan, R.; Ehrlich, M. ); Ehrlich, K.C. )

    1988-08-25

    A DNA-binding protein from human placenta, methylated DNA-binding protein (MDBP), binds to certain DNA sequences only when they contain 5-methylcytosine (m{sup 5}C) residues at specific positions. The authors found a very similar DNA-binding activity in nuclear extracts of rat tissues, calf thymus, human embryonal carcinoma cells, HeLa cells, and mouse LTK cells. Like human placental MDBP, the analogous DNA-binding proteins from the above mammalian cell lines formed a number of different low-electrophoretic-mobility complexes with a 14-bp MDBP-specific oligonucleotide duplex. All of these complexes exhibited the same DNA methylation specificity and DNA sequence specificity. Although MDBP activity was found in various mammalian cell types, it was not detected in extracts of cultured mosquito cells and so may be associated only with cells with vertebrate-type DNA methylation.

  6. Identification of an archaeal mercury regulon by chromatin immunoprecipitation.

    PubMed

    Rudrappa, Deepak; Yao, Andrew I; White, Derrick; Pavlik, Benjamin J; Singh, Raghuveer; Facciotti, Marc T; Blum, Paul

    2015-12-01

    Mercury is a heavy metal and toxic to all forms of life. Metal exposure can invoke a response to improve survival. In archaea, several components of a mercury response system have been identified, but it is not known whether metal transport is a member of this system. To identify such missing components, a peptide-tagged MerR transcription factor was used to localize enriched chromosome regions by chromosome immunoprecipitation combined with DNA sequence analysis. Such regions could serve as secondary regulatory binding sites to control the expression of additional genes associated with mercury detoxification. Among the 31 highly enriched loci, a subset of five was pursued as potential candidates based on their current annotations. Quantitative reverse transcription-PCR analysis of these regions with and without mercury treatment in WT and mutant strains lacking merR indicated significant regulatory responses under these conditions. Of these, a Family 5 extracellular solute-binding protein and the MarR transcription factor shown previously to control responses to oxidation were most strongly affected. Inactivation of the solute-binding protein by gene disruption increased the resistance of mutant cells to mercury challenge. Inductively coupled plasma-MS analysis of the mutant cell line following metal challenge indicated there was less intracellular mercury compared with the isogenic WT strain. Together, these regulated genes comprise new members of the archaeal MerR regulon and reveal a cascade of transcriptional control not previously demonstrated in this model organism.

  7. Identification of Associated Proteins by Immunoprecipitation and Mass Spectrometry Analysis.

    PubMed

    Cao, Xiumei; Yan, Jianshe

    2016-01-01

    Protein-protein interactions play central roles in intercellular and intracellular signal transduction. Impairment of protein-protein interactions causes many diseases such as cancer, cardiomyopathies, diabetes, microbial infections, and genetic and neurodegenerative disorders. Immunoprecipitation is a technique in which a target protein of interest bound by an antibody is used to pull down the protein complex out of cell lysates, which can be identified by mass spectrometry. Here, we describe the protocol to immunoprecipitate and identify the components of the protein complexes of ElmoE in Dictyostelium discoideum cells. PMID:27271899

  8. Development of a mutant strain of Escherichia coli for molecular cloning of highly methylated DNA

    SciTech Connect

    Bishr, M.A.

    1991-01-01

    A mutant strain of Escherichia coli designated as GR219 that allows efficient molecular cloning of highly methylated bean DNA has been developed by UV light mutation of the parent LE392 str[sup r] strain. This mutant strain, like the parent, is streptomycin resistant and is biologically contained, because it requires thymidine for growth. Both the wild type and the mutant strain have lambda phage receptors so both can be utilized for construction of genomic libraries using the phase as a vector. The efficiency of transformation of the parent and the mutant strain with a recombinant plasmid containing bean DNA was compared to the efficiency of transformation of the PLK-F[prime] strain, which has a deletion of mcrA and mcrB genes and, therefore, allows transformation with methylated bean DNA. It has been found that the GR219 strain has the highest efficiency of transformation, while the PLK-F[prime] strain shows less, and the parent LE392 str[sup r] strain the least efficiency of transformation. These results indicate that strains of E. coli with mcrA and mcrB genes can recognize and degrade highly methylated DNA. However, other undefined factors affected by the altered gene(s) in the GR219 strain are also involved in the recognition and degradation of any cloned foreign DNA.

  9. Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

    PubMed Central

    Fang, Jian; Cheng, Jingdong; Wang, Jiaolong; Zhang, Qiao; Liu, Mengjie; Gong, Rui; Wang, Ping; Zhang, Xiaodan; Feng, Yangyang; Lan, Wenxian; Gong, Zhou; Tang, Chun; Wong, Jiemin; Yang, Huirong; Cao, Chunyang; Xu, Yanhui

    2016-01-01

    UHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD–PHD. The Spacer also facilitates UHRF1–DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD–PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1. PMID:27045799

  10. Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

    NASA Astrophysics Data System (ADS)

    Fang, Jian; Cheng, Jingdong; Wang, Jiaolong; Zhang, Qiao; Liu, Mengjie; Gong, Rui; Wang, Ping; Zhang, Xiaodan; Feng, Yangyang; Lan, Wenxian; Gong, Zhou; Tang, Chun; Wong, Jiemin; Yang, Huirong; Cao, Chunyang; Xu, Yanhui

    2016-04-01

    UHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD-PHD. The Spacer also facilitates UHRF1-DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD-PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1.

  11. Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition.

    PubMed

    Fang, Jian; Cheng, Jingdong; Wang, Jiaolong; Zhang, Qiao; Liu, Mengjie; Gong, Rui; Wang, Ping; Zhang, Xiaodan; Feng, Yangyang; Lan, Wenxian; Gong, Zhou; Tang, Chun; Wong, Jiemin; Yang, Huirong; Cao, Chunyang; Xu, Yanhui

    2016-01-01

    UHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD-PHD. The Spacer also facilitates UHRF1-DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD-PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1.

  12. Differential sensitivity to methylated DNA by ETS-family transcription factors is intrinsically encoded in their DNA-binding domains

    PubMed Central

    Stephens, Dominique C.; Poon, Gregory M. K.

    2016-01-01

    Transactivation by the ETS family of transcription factors, whose members share structurally conserved DNA-binding domains, is variably sensitive to methylation of their target genes. The mechanism by which DNA methylation controls ETS proteins remains poorly understood. Uncertainly also pervades the effects of hemi-methylated DNA, which occurs following DNA replication and in response to hypomethylating agents, on site recognition by ETS proteins. To address these questions, we measured the affinities of two sequence-divergent ETS homologs, PU.1 and Ets-1, to DNA sites harboring a hemi- and fully methylated CpG dinucleotide. While the two proteins bound unmethylated DNA with indistinguishable affinity, their affinities to methylated DNA are markedly heterogeneous and exhibit major energetic coupling between the two CpG methylcytosines. Analysis of simulated DNA and existing co-crystal structures revealed that hemi-methylation induced non-local backbone and groove geometries that were not conserved in the fully methylated state. Indirect readout of these perturbations was differentially achieved by the two ETS homologs, with the distinctive interfacial hydration in PU.1/DNA binding moderating the inhibitory effects of DNA methylation on binding. This data established a biophysical basis for the pioneering properties associated with PU.1, which robustly bound fully methylated DNA, but not Ets-1, which was substantially inhibited. PMID:27270080

  13. Interpreting results of coulometry and immunoprecipitation in diagnosing iron disorders.

    PubMed

    Rettmer, R L; Labbé, R F; Huebers, H A; Brown, W P; Josephson, B M; Finch, C A

    1987-07-01

    Concentration of iron in plasma, total iron-binding capacity (TIBC), and transferrin saturation are often determined by standard spectrophotometric methods, but iron concentration may be quantified by immunoprecipitation or, electrochemically, by controlled-potential coulometry. Because these iron assays do not all measure the same form(s) of iron, we studied subjects in various states of iron nutriture: normal adults, iron-deficient patients, thalassemia patients with unsaturated transferrin or oversaturated transferrin, and patients with idiopathic hemochromatosis. The spectrophotometric and coulometric methods detected essentially all non-heme iron in plasma; results correlated well but showed a negative bias toward the coulometric method. Results by an immunoprecipitation procedure, which measures only transferrin-bound iron, correlated well with those obtained coulometrically but were slightly higher than the latter. The characteristics of the various methods for iron must be understood by the clinical laboratory if diagnosis of iron disorders is to be accurate.

  14. Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.

    SciTech Connect

    Avvakumov, George V.; Walker, John R.; Xue, Sheng; Li, Yanjun; Duan, Shili; Bronner, Christian; Arrowsmith, Cheryl H.; Dhe-Paganon, Sirano

    2008-11-17

    Epigenetic inheritance in mammals is characterized by high-fidelity replication of CpG methylation patterns during development. UHRF1 (also known as ICBP90 in humans and Np95 in mouse) is an E3 ligase important for the maintenance of global and local DNA methylation in vivo. The preferential affinity of UHRF1 for hemi-methylated DNA over symmetrically methylated DNA by means of its SET and RING-associated (SRA) domain and its association with the maintenance DNA methyltransferase 1 (DNMT1) suggests a role in replication of the epigenetic code. Here we report the 1.7 {angstrom} crystal structure of the apo SRA domain of human UHRF1 and a 2.2 {angstrom} structure of its complex with hemi-methylated DNA, revealing a previously unknown reading mechanism for methylated CpG sites (mCpG). The SRA-DNA complex has several notable structural features including a binding pocket that accommodates the 5-methylcytosine that is flipped out of the duplex DNA. Two specialized loops reach through the resulting gap in the DNA from both the major and the minor grooves to read the other three bases of the CpG duplex. The major groove loop confers both specificity for the CpG dinucleotide and discrimination against methylation of deoxycytidine of the complementary strand. The structure, along with mutagenesis data, suggests how UHRF1 acts as a key factor for DNMT1 maintenance methylation through recognition of a fundamental unit of epigenetic inheritance, mCpG.

  15. Chromatin Preparation and Chromatin Immuno-precipitation from Drosophila Embryos.

    PubMed

    Löser, Eva; Latreille, Daniel; Iovino, Nicola

    2016-01-01

    This protocol provides specific details on how to perform Chromatin immunoprecipitation (ChIP) from Drosophila embryos. ChIP allows the matching of proteins or histone modifications to specific genomic regions. Formaldehyde-cross-linked chromatin is isolated and antibodies against the target of interest are used to determine whether the target is associated with a specific DNA sequence. This can be performed in spatial and temporal manner and it can provide information about the genome-wide localization of a given protein or histone modification if coupled with deep sequencing technology (ChIP-Seq). PMID:27659972

  16. Sequence analysis of chromatin immunoprecipitation data for transcription factors

    PubMed Central

    Fraenkel, Ernest

    2013-01-01

    Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis, and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such analyses, and recommend strategies for effective motif discovery from these data. PMID:20827592

  17. Isolation of proteins and protein complexes by immunoprecipitation.

    PubMed

    Kaboord, Barbara; Perr, Maria

    2008-01-01

    Immunoprecipitation (IP) uses the specificity of antibodies to isolate target proteins (antigens) out of complex sample mixtures. Three different approaches for performing IP will be discussed; traditional (classical) method, oriented affinity method and direct affinity method. The traditional method of incubating the IP antibody with the sample and sequentially binding to Protein A or G agarose beads (resin) facilitates the most efficient target antigen recovery. However, this approach results in the target protein becoming contaminated with the IP antibody that can interfere with downstream analyses. The orientated affinity method uses Protein A or G beads to serve as an anchor to which the IP antibody is crosslinked thereby preventing the antibody from co-eluting with the target protein. Similarly, the direct affinity method also immobilizes the IP antibody except in this case it is directly attached to a chemically activated support. Both methods prevent co-elution of the IP antibody enabling reuse of the immunomatrix. All three approaches have unique advantages and can also be used for co-immunoprecipitation to study protein:protein interactions and investigate the functional proteome.

  18. Immunoprecipitation of membrane proteins of cultured human sarcoma cells.

    PubMed

    Grófová, M; Forchhammer, J; Lizonová, A; Popovic, M

    1981-01-01

    Human sarcoma associated antigens (HSAA) have previously been identified by indirect immune fluorescence in human sarcoma cells in culture using sera from patients bearing different types of sarcoma. To further characterize these HSAA, surface proteins of cultured cells were labeled with 125Iodine, [3H]-glucosamine and [35S]-methionine and solubilized. After immunoprecipitation labeled proteins were detected in immune complexes by SDS polyacrylamide gel electrophoresis and autoradiography, which allowed comparison with antigens described by other groups. A surface protein (Mr 96 000) was precipitated with sera from sarcoma bearing patients, and two glycoproteins (Mr 115 000 and 85 000) were preferentially precipitated with antisera from rabbits immunized with membranes from two human sarcoma cell lines. At least two of these proteins were found in each of five human sarcoma cell lines studied (U-4SS, U-3930S, U-20S, B-5GT and B-6FS). None of the proteins were precipitated with three human control sera, and only occasionally a faint band was observed in immunoprecipitates from control cells (B-25F, B-41B, B-42FC, U-2S, and U-393S with the immune sera. These proteins are probably some of the antigens responsible for the immune fluorescence observed in determination of HSAA. However, purification of the proteins and competition experiments are needed before this can be finally established.

  19. UV-RNA Immunoprecipitation (UV-RIP) Protocol in Neurons.

    PubMed

    Schaukowitch, Katie; Joo, Jae-Yeol; Kim, Tae-Kyung

    2017-01-01

    With the many advances in genome-wide sequencing, it has been discovered that much more of the genome is transcribed into RNA than previously appreciated. These nonprotein-coding RNAs (ncRNAs) come in many different forms, and they have been shown to have a variety of functions within the cell, influencing processes such as gene expression, mRNA splicing, and transport, just as a few examples. As we delve deeper into studying their mechanisms of action, it becomes important to understand how they play these roles, in particular by understanding what proteins these ncRNAs interact with. This protocol describes one technique that can be used to study this, ultra-violet light cross-linking RNA immunoprecipitation (UV-RIP), which uses an antibody to pull down a specific protein of interest and then detects RNA that is bound to it. This technique utilizes UV light to cross-link the cells, which takes advantage of the fact that UV light will only cross-link proteins and nucleic acids that are directly interacting. This approach can provide key mechanistic insight into the function of these newly identified ncRNAs. PMID:27662868

  20. Searching for biomarkers: humoral response profiling with luciferase immunoprecipitation systems.

    PubMed

    Burbelo, Peter D; Ching, Kathryn H; Bren, Kathleen E; Iadarola, Michael J

    2011-06-01

    B-cell-mediated humoral responses are triggered in many human diseases, including autoimmune diseases, cancer, and neurologic and infectious diseases. However, the full exploitation of the information contained within a patient's antibody repertoire for diagnosis, monitoring and even disease prediction has been limited due to the poor diagnostic performance of many immunoassay formats. We have developed luciferase immunoprecipitation systems (LIPS) that harnesses light-emitting proteins to generate high-definition antibody profiles that are optimal for both diagnostics and biomarker discovery. Here, we describe the results and implications from a range of LIPS-antibody profiling studies performed in our laboratory. These include highly sensitive diagnostics for domestic and global pathogens, insights into infection-related diseases, discovery of new biomarkers for human diseases, subcategorization of symptoms and identification of pathogenic autoantibodies against self-proteins. These investigations highlight the types of humoral response profiles associated with different diseases, provide new information related to disease pathogenesis and offer a framework for incorporating LIPS antibody profiling into global health initiatives and disease monitoring. PMID:21679112

  1. Biochemical Analysis of Genome Functions Using Locus-Specific Chromatin Immunoprecipitation Technologies

    PubMed Central

    Fujita, Toshitsugu; Fujii, Hodaka

    2016-01-01

    To isolate specific genomic regions that retain their molecular interactions, allowing direct identification of chromatin-bound molecules, we developed two locus-specific chromatin immunoprecipitation (locus-specific ChIP) technologies, insertional ChIP (iChIP) and engineered DNA-binding molecule-mediated ChIP (enChIP) using the clustered regularly interspaced short palindromic repeats (CRISPR) system or transcription activator-like (TAL) proteins. Essentially, a locus-specific ChIP consists of locus-tagging and affinity purification and can be combined with downstream analyses to identify molecules associated with the target genomic regions. In this review, we discuss the applications of locus-specific ChIP to analyze the genome functions, including transcription and epigenetic regulation. PMID:26819551

  2. Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

    PubMed

    Blinka, Steven; Reimer, Michael H; Pulakanti, Kirthi; Pinello, Luca; Yuan, Guo-Cheng; Rao, Sridhar

    2017-01-01

    Recent work has shown that RNA polymerase II-mediated transcription at distal cis-regulatory elements serves as a mark of highly active enhancers. Production of noncoding RNAs at enhancers, termed eRNAs, correlates with higher expression of genes that the enhancer interacts with; hence, eRNAs provide a new tool to model gene activity in normal and disease tissues. Moreover, this unique class of noncoding RNA has diverse roles in transcriptional regulation. Transcribed enhancers can be identified by a common signature of epigenetic marks by overlaying a series of genome-wide chromatin immunoprecipitation and RNA sequencing datasets. A computational approach to filter non-enhancer elements and other classes of noncoding RNAs is essential to not cloud downstream analysis. Here we present a protocol that combines wet and dry bench methods to accurately identify transcribed enhancers genome-wide as well as an experimental procedure to validate these datasets. PMID:27662872

  3. Tagging of MADS domain proteins for chromatin immunoprecipitation

    PubMed Central

    de Folter, Stefan; Urbanus, Susan L; van Zuijlen, Lisette GC; Kaufmann, Kerstin; Angenent, Gerco C

    2007-01-01

    Background Most transcription factors fulfill their role in complexes and regulate their target genes upon binding to DNA motifs located in upstream regions or introns. To date, knowledge about transcription factor target genes and their corresponding transcription factor binding sites are still very limited. Two related methods that allow in vivo identification of transcription factor binding sites are chromatin immunoprecipitation (ChIP) and chromatin affinity purification (ChAP). For ChAP, the protein of interest is tagged with a peptide or protein, which can be used for affinity purification of the protein-DNA complex and hence, the identification of the target gene. Results Here, we present the results of experiments aiming at the development of a generic tagging approach for the Arabidopsis MADS domain proteins AGAMOUS, SEPALLATA3, and FRUITFULL. For this, Arabidopsis wild type plants were transformed with constructs containing a MADS-box gene fused to either a double Strep-tag® II-FLAG-tag, a triple HA-tag, or an eGFP-tag, all under the control of the constitutive double 35S Cauliflower Mosaic Virus (CaMV) promoter. Strikingly, in all cases, the number of transformants with loss-of-function phenotypes was much larger than those with an overexpression phenotype. Using endogenous promoters in stead of the 35S CaMV resulted in a dramatic reduction in the frequency of loss-of-function phenotypes. Furthermore, pleiotropic defects occasionally caused by an overexpression strategy can be overcome by using the native promoter of the gene. Finally, a ChAP result is presented using GFP antibody on plants carrying a genomic fragment of a MADS-box gene fused to GFP. Conclusion This study revealed that MADS-box proteins are very sensitive to fusions with small peptide tags and GFP tags. Furthermore, for the expression of chimeric versions of MADS-box genes it is favorable to use the entire genomic region in frame to the tag of choice. Interestingly, though unexpected

  4. The Human Proteins MBD5 and MBD6 Associate with Heterochromatin but They Do Not Bind Methylated DNA

    PubMed Central

    Laget, Sophie; Joulie, Michael; Le Masson, Florent; Sasai, Nobuhiro; Christians, Elisabeth; Pradhan, Sriharsa; Roberts, Richard J.; Defossez, Pierre-Antoine

    2010-01-01

    Background MBD5 and MBD6 are two uncharacterized mammalian proteins that contain a putative Methyl-Binding Domain (MBD). In the proteins MBD1, MBD2, MBD4, and MeCP2, this domain allows the specific recognition of DNA containing methylated cytosine; as a consequence, the proteins serve as interpreters of DNA methylation, an essential epigenetic mark. It is unknown whether MBD5 or MBD6 also bind methylated DNA; this question has interest for basic research, but also practical consequences for human health, as MBD5 deletions are the likely cause of certain cases of mental retardation. Principal Findings Here we report the first functional characterization of MBD5 and MBD6. We have observed that the proteins colocalize with heterochromatin in cultured cells, and that this localization requires the integrity of their MBD. However, heterochromatic localization is maintained in cells with severely decreased levels of DNA methylation. In vitro, neither MBD5 nor MBD6 binds any of the methylated sequences DNA that were tested. Conclusions Our data suggest that MBD5 and MBD6 are unlikely to be methyl-binding proteins, yet they may contribute to the formation or function of heterochromatin. One isoform of MBD5 is highly expressed in oocytes, which suggests a possible role in epigenetic reprogramming after fertilization. PMID:20700456

  5. Human age estimation from blood using mRNA, DNA methylation, DNA rearrangement, and telomere length.

    PubMed

    Zubakov, Dmitry; Liu, Fan; Kokmeijer, Iris; Choi, Ying; van Meurs, Joyce B J; van IJcken, Wilfred F J; Uitterlinden, André G; Hofman, Albert; Broer, Linda; van Duijn, Cornelia M; Lewin, Jörn; Kayser, Manfred

    2016-09-01

    Establishing the age of unknown persons, or persons with unknown age, can provide important leads in police investigations, disaster victim identification, fraud cases, and in other legal affairs. Previous methods mostly relied on morphological features available from teeth or skeletal parts. The development of molecular methods for age estimation allowing to use human specimens that possess no morphological age information, such as bloodstains, is extremely valuable as this type of samples is commonly found at crime scenes. Recently, we introduced a DNA-based approach for human age estimation from blood based on the quantification of T-cell specific DNA rearrangements (sjTRECs), which achieves accurate assignment of blood DNA samples to one of four 20-year-interval age categories. Aiming at improving the accuracy of molecular age estimation from blood, we investigated different types of biomarkers. We started out by systematic genome-wide surveys for new age-informative mRNA and DNA methylation markers in blood from the same young and old individuals using microarray technologies. The obtained candidate markers were validated in independent samples covering a wide age range using alternative technologies together with previously proposed DNA methylation, sjTREC, and telomere length markers. Cross-validated multiple regression analysis was applied for estimating and validating the age predictive power of various sets of biomarkers within and across different marker types. We found that DNA methylation markers outperformed mRNA, sjTREC, and telomere length in age predictive power. The best performing model included 8 DNA methylation markers derived from 3 CpG islands reaching a high level of accuracy (cross-validated R(2)=0.88, SE±6.97 years, mean absolute deviation 5.07 years). However, our data also suggest that mRNA markers can provide independent age information: a model using a combined set of 5 DNA methylation markers and one mRNA marker could provide

  6. Human age estimation from blood using mRNA, DNA methylation, DNA rearrangement, and telomere length.

    PubMed

    Zubakov, Dmitry; Liu, Fan; Kokmeijer, Iris; Choi, Ying; van Meurs, Joyce B J; van IJcken, Wilfred F J; Uitterlinden, André G; Hofman, Albert; Broer, Linda; van Duijn, Cornelia M; Lewin, Jörn; Kayser, Manfred

    2016-09-01

    Establishing the age of unknown persons, or persons with unknown age, can provide important leads in police investigations, disaster victim identification, fraud cases, and in other legal affairs. Previous methods mostly relied on morphological features available from teeth or skeletal parts. The development of molecular methods for age estimation allowing to use human specimens that possess no morphological age information, such as bloodstains, is extremely valuable as this type of samples is commonly found at crime scenes. Recently, we introduced a DNA-based approach for human age estimation from blood based on the quantification of T-cell specific DNA rearrangements (sjTRECs), which achieves accurate assignment of blood DNA samples to one of four 20-year-interval age categories. Aiming at improving the accuracy of molecular age estimation from blood, we investigated different types of biomarkers. We started out by systematic genome-wide surveys for new age-informative mRNA and DNA methylation markers in blood from the same young and old individuals using microarray technologies. The obtained candidate markers were validated in independent samples covering a wide age range using alternative technologies together with previously proposed DNA methylation, sjTREC, and telomere length markers. Cross-validated multiple regression analysis was applied for estimating and validating the age predictive power of various sets of biomarkers within and across different marker types. We found that DNA methylation markers outperformed mRNA, sjTREC, and telomere length in age predictive power. The best performing model included 8 DNA methylation markers derived from 3 CpG islands reaching a high level of accuracy (cross-validated R(2)=0.88, SE±6.97 years, mean absolute deviation 5.07 years). However, our data also suggest that mRNA markers can provide independent age information: a model using a combined set of 5 DNA methylation markers and one mRNA marker could provide

  7. Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts

    PubMed Central

    Lohse, Matthew B.; Kongsomboonvech, Pisiwat; Madrigal, Maria; Hernday, Aaron D.; Nobile, Clarissa J.

    2016-01-01

    Chromatin immunoprecipitation experiments are critical to investigating the interactions between DNA and a wide range of nuclear proteins within a cell or biological sample. In this chapter we outline an optimized protocol for genome-wide chromatin immunoprecipitation that has been used successfully for several distinct morphological forms of numerous yeast species, and include an optimized method for amplification of chromatin immunoprecipitated DNA samples and hybridization to a high-density oligonucleotide tiling microarray. We also provide detailed suggestions on how to analyze the complex data obtained from these experiments. PMID:26483022

  8. Isotope coded protein labeling coupled immunoprecipitation (ICPL-IP): a novel approach for quantitative protein complex analysis from native tissue.

    PubMed

    Vogt, Andreas; Fuerholzner, Bettina; Kinkl, Norbert; Boldt, Karsten; Ueffing, Marius

    2013-05-01

    High confidence definition of protein interactions is an important objective toward the understanding of biological systems. Isotope labeling in combination with affinity-based isolation of protein complexes has increased in accuracy and reproducibility, yet, larger organisms--including humans--are hardly accessible to metabolic labeling and thus, a major limitation has been its restriction to small animals, cell lines, and yeast. As composition as well as the stoichiometry of protein complexes can significantly differ in primary tissues, there is a great demand for methods capable to combine the selectivity of affinity-based isolation as well as the accuracy and reproducibility of isotope-based labeling with its application toward analysis of protein interactions from intact tissue. Toward this goal, we combined isotope coded protein labeling (ICPL)(1) with immunoprecipitation (IP) and quantitative mass spectrometry (MS). ICPL-IP allows sensitive and accurate analysis of protein interactions from primary tissue. We applied ICPL-IP to immuno-isolate protein complexes from bovine retinal tissue. Protein complexes of immunoprecipitated β-tubulin, a highly abundant protein with known interactors as well as the lowly expressed small GTPase RhoA were analyzed. The results of both analyses demonstrate sensitive and selective identification of known as well as new protein interactions by our method.

  9. Autoantibodies to IA-2 in insulin-dependent diabetes mellitus. Measurements with a new immunoprecipitation assay.

    PubMed

    Masuda, M; Powell, M; Chen, S; Beer, C; Fichna, P; Rees Smith, B; Furmaniak, J

    2000-01-20

    An immunoprecipitation assay for autoantibodies (Abs) to the human islet cell antigen IA-2 has been developed using 125I-labelled recombinant IA-2 expressed in E. coli. With this assay IA-2 Abs were detected in 103/217 (47%) of IDDM patients of different ages and with different disease duration. IA-2 Ab prevalence was higher in younger patients (at the age of 15 years or below) with the recent onset IDDM (64/113; 57%) compared to patients above the age of 15 years (11/25; 44%). One of 40 (2.5%) Graves' disease patients and five of 204 (2.5%) of NIDDM patients were also positive. IA-2 Abs were not detected in sera from patients with Hashimoto's thyroiditis (n=32), myasthenia gravis (n=20) or systemic lupus erythematosus (n=10). IA-2 Ab measurements based on 125I-labelled IA-2 showed a good correlation with the results of an immunoprecipitation assay based on 35S-labelled IA-2 produced in the in vitro transcription/translation system (r=0.78; n=113; p<0.001). Out of 217 IDDM sera which were tested for IA-2 Abs, 140 (65%) were positive for Abs to glutamic acid decarboxylase (GAD) and 166 (76%) were positive for Abs to IA-2 and/or Abs to GAD. In addition, Abs to IA-2, to GAD and to insulin were analysed in sera from recent onset IDDM patients who had not been treated with insulin (n=117). In all, 76/117 (65%) of these sera were positive for GAD Abs, 66/117 (56%) for IA-2 Abs, 45/117 (38%) for insulin Abs. However, 98/117 (84%) were positive for at least one of the three Abs confirming earlier observations on the complementarity of Ab testing in IDDM. Overall, the IA-2 Ab assay based on 125I-labelled recombinant IA-2 showed good sensitivity, precision and specificity which, combined with an easy and convenient protocol, makes it attractive for routine use.

  10. Combined analysis of DNA methylome and transcriptome reveal novel candidate genes with susceptibility to bovine Staphylococcus aureus subclinical mastitis

    PubMed Central

    Song, Minyan; He, Yanghua; Zhou, Huangkai; Zhang, Yi; Li, Xizhi; Yu, Ying

    2016-01-01

    Subclinical mastitis is a widely spread disease of lactating cows. Its major pathogen is Staphylococcus aureus (S. aureus). In this study, we performed genome-wide integrative analysis of DNA methylation and transcriptional expression to identify candidate genes and pathways relevant to bovine S. aureus subclinical mastitis. The genome-scale DNA methylation profiles of peripheral blood lymphocytes in cows with S. aureus subclinical mastitis (SA group) and healthy controls (CK) were generated by methylated DNA immunoprecipitation combined with microarrays. We identified 1078 differentially methylated genes in SA cows compared with the controls. By integrating DNA methylation and transcriptome data, 58 differentially methylated genes were shared with differently expressed genes, in which 20.7% distinctly hypermethylated genes showed down-regulated expression in SA versus CK, whereas 14.3% dramatically hypomethylated genes showed up-regulated expression. Integrated pathway analysis suggested that these genes were related to inflammation, ErbB signalling pathway and mismatch repair. Further functional analysis revealed that three genes, NRG1, MST1 and NAT9, were strongly correlated with the progression of S. aureus subclinical mastitis and could be used as powerful biomarkers for the improvement of bovine mastitis resistance. Our studies lay the groundwork for epigenetic modification and mechanistic studies on susceptibility of bovine mastitis. PMID:27411928

  11. Combined analysis of DNA methylome and transcriptome reveal novel candidate genes with susceptibility to bovine Staphylococcus aureus subclinical mastitis.

    PubMed

    Song, Minyan; He, Yanghua; Zhou, Huangkai; Zhang, Yi; Li, Xizhi; Yu, Ying

    2016-01-01

    Subclinical mastitis is a widely spread disease of lactating cows. Its major pathogen is Staphylococcus aureus (S. aureus). In this study, we performed genome-wide integrative analysis of DNA methylation and transcriptional expression to identify candidate genes and pathways relevant to bovine S. aureus subclinical mastitis. The genome-scale DNA methylation profiles of peripheral blood lymphocytes in cows with S. aureus subclinical mastitis (SA group) and healthy controls (CK) were generated by methylated DNA immunoprecipitation combined with microarrays. We identified 1078 differentially methylated genes in SA cows compared with the controls. By integrating DNA methylation and transcriptome data, 58 differentially methylated genes were shared with differently expressed genes, in which 20.7% distinctly hypermethylated genes showed down-regulated expression in SA versus CK, whereas 14.3% dramatically hypomethylated genes showed up-regulated expression. Integrated pathway analysis suggested that these genes were related to inflammation, ErbB signalling pathway and mismatch repair. Further functional analysis revealed that three genes, NRG1, MST1 and NAT9, were strongly correlated with the progression of S. aureus subclinical mastitis and could be used as powerful biomarkers for the improvement of bovine mastitis resistance. Our studies lay the groundwork for epigenetic modification and mechanistic studies on susceptibility of bovine mastitis.

  12. Immunoprecipitation of Plasma Membrane Receptor-Like Kinases for Identification of Phosphorylation Sites and Associated Proteins.

    PubMed

    Kadota, Yasuhiro; Macho, Alberto P; Zipfel, Cyril

    2016-01-01

    Membrane proteins are difficult to study for numerous reasons. The surface of membrane proteins is relatively hydrophobic and sometimes very unstable, additionally requiring detergents for their extraction from the membrane. This leads to challenges at all levels, including expression, solubilization, purification, identification of associated proteins, and the identification of post-translational modifications. However, recent advances in immunoprecipitation technology allow to isolate membrane proteins efficiently, facilitating the study of protein-protein interactions, the identification of novel associated proteins, and to identify post-translational modifications, such as phosphorylation. Here, we describe an optimized immunoprecipitation protocol for plant plasma membrane receptor-like kinases. PMID:26577786

  13. Detection of xenoestrogens in serum after immunoprecipitation of endogenous steroidal estrogens.

    PubMed Central

    Natarajan, Kala; Overstreet, James W; Rogers, Jane M; Denison, Michael S; Chen, Jiangang; Lohstroh, Peter N; McConnell, Daniel S; Lasley, Bill L

    2002-01-01

    In this article we report a simple and efficient method for detecting nonsteroidal estrogens in a biologic sample. This method uses polyclonal antibodies to estradiol (E2) to immunoprecipitate these major biologically active steroidal estrogens, leaving behind the nonsteroidal estrogens, which are then detected in a cell-based transcriptional activation bioassay for estrogen receptor agonist. The immunoprecipitation method efficiently removed 99% of radiolabeled E2 and estrone (E1) from human serum. In experiments in which supraphysiologic concentrations of E2 and E1 to human serum, all of the immunoreactive estrogens were still removed by the immunoprecipitation protocol. We carried out an in vivo validation study of this method in which we treated female macaques with the xenoestrogen nonylphenol (NP), during the late follicular phase of the menstrual cycle. We used blood samples collected before and after treatment to evaluate and characterize endogenous and exogenous serum estrogens. An immunoassay for E2 did not detect the NP in treated monkeys. The cell-based bioassay also did not detect the estrogenic activity of NP because of its saturation by the endogenous serum steroidal estrogens. However, when steroidal estrogens were removed by immunoprecipitation, we detected the estrogenic activity of NP in the bioassay. Thus, this approach is appropriate for detecting exogenous, nonsteroidal estrogens in serum samples. PMID:12153760

  14. Clinical and histological findings associated with autoantibodies detected by RNA immunoprecipitation in inflammatory myopathies.

    PubMed

    Suzuki, Shigeaki; Yonekawa, Takahiro; Kuwana, Masataka; Hayashi, Yukiko K; Okazaki, Yuka; Kawaguchi, Yasushi; Suzuki, Norihiro; Nishino, Ichizo

    2014-09-15

    Of 207 adult patients with idiopathic inflammatory myopathies, detection of autoantibodies by RNA immunoprecipitation showed that 99 patients (48%) were antibody-positive. We divided these 99 into five subgroups: anti-signal recognition particle (SRP), anti-aminoacyl transfer RNA synthetase, anti-Ku, anti-U1RNP, and anti-SSA/B. Younger age at onset, severe weakness, muscle atrophy, elevated creatine kinase, and necrosis in muscle fibers without inflammatory cell infiltration were found significantly more frequently among the patients with anti-SRP antibodies (n=41) compared to the antibody-negative patients (n=108). Autoantibody detection by RNA immunoprecipitation can provide useful information associated with clinical and histological findings.

  15. Immunoprecipitation of Cullin-RING Ligases (CRLs) in Arabidopsis thaliana Seedlings.

    PubMed

    Franciosini, Anna; Serino, Giovanna

    2016-01-01

    CRL (Cullin-RING ubiquitin ligase) is the major class of plant E3 ubiquitin ligases. Immunoprecipitation-based methods are useful techniques for revealing interactions among Cullin-RING Ligase (CRL) subunits or between CRLs and other proteins, as well as for detecting poly-ubiquitin modifications of the CRLs themselves. Here, we describe two immunoprecipitation (IP) procedures suitable for CRLs in Arabidopsis: a procedure for IP analysis of CRL subunits and their interactors and a second procedure for in vivo ubiquitination analysis of the CRLs. Both protocols can be divided into two major steps: (1) preparation of cell extracts without disruption of protein interactions and (2) affinity purification of the protein complexes and subsequent detection. We provide a thorough description of all the steps, as well as advice on how to choose proper buffers for these analyses. We also suggest a series of negative controls that can be used to verify the specificity of the procedure. PMID:27424742

  16. Chapter 15. Co-immunoprecipitation techniques for assessing RNA-protein interactions in vivo.

    PubMed

    Conrad, Nicholas K

    2008-01-01

    From the moment a nascent transcript emerges from an RNA polymerase until its ultimate destruction, an RNA is bound by proteins that govern its fate. Thus, in order to understand posttranscriptional regulation of gene expression, it is essential to ascertain which proteins bind a given RNA in vivo. This chapter describes three immunoprecipitation-based assays designed to query the in vivo makeup of RNA-protein complexes. Two of these, UV cross-linking and RNA immunoprecipitation (RIP), include cross-linking steps that trap complexes formed in vivo. A third, a cell mixing experiment, verifies that an interaction occurs in vivo by controlling for RNA-protein association subsequent to cell lysis. Using these protocols, this chapter presents evidence that the abundant nuclear RNA-binding protein hnRNP C interacts with the Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA in vivo. PMID:19215765

  17. Identification of the immunoproteome of the meningococcus by cell surface immunoprecipitation and MS.

    PubMed

    Newcombe, Jane; Mendum, Tom A; Ren, Chuan-peng; McFadden, Johnjoe

    2014-02-01

    Most healthy adults are protected from meningococcal disease by the presence of naturally acquired anti-meningococcal antibodies; however, the identity of the target antigens of this protective immunity remains unclear, particularly for protection against serogroup B disease. To identify the protein targets of natural protective immunity we developed an immunoprecipitation and proteomics approach to define the immunoproteome of the meningococcus. Sera from 10 healthy individuals showing serum bactericidal activity against both a meningococcal C strain (L91543) and the B strain MC58, together with commercially available pooled human sera, were used as probe antisera. Immunoprecipitation was performed with each serum sample and live cells from both meningococcal strains. Immunoprecipitated proteins were identified by MS. Analysis of the immunoproteome from each serum demonstrated both pan-reactive antigens that were recognized by most sera as well as subject-specific antigens. Most antigens were found in both meningococcal strains, but a few were strain-specific. Many of the immunoprecipitated proteins have been characterized previously as surface antigens, including adhesins and proteases, several of which have been recognized as vaccine candidate antigens, e.g. factor H-binding protein, NadA and neisserial heparin-binding antigen. The data demonstrate clearly the presence of meningococcal antibodies in healthy individuals with no history of meningococcal infection and a wide diversity of immune responses. The identification of the immunoreactive proteins of the meningococcus provides a basis for understanding the role of each antigen in the natural immunity associated with carriage and may help to design vaccination strategies. PMID:24275101

  18. Pr-specific phytochrome phosphorylation in vitro by a protein kinase present in anti-phytochrome maize immunoprecipitates

    NASA Technical Reports Server (NTRS)

    Biermann, B. J.; Pao, L. I.; Feldman, L. J.

    1994-01-01

    Protein kinase activity has repeatedly been found to co-purify with the plant photoreceptor phytochrome, suggesting that light signals received by phytochrome may be transduced or modulated through protein phosphorylation. In this study immunoprecipitation techniques were used to characterize protein kinase activity associated with phytochrome from maize (Zea mays L.). A protein kinase that specifically phosphorylated phytochrome was present in washed anti-phytochrome immunoprecipitates of etiolated coleoptile proteins. No other substrate tested was phosphorylated by this kinase. Adding salts or detergents to disrupt low-affinity protein interactions reduced background phosphorylation in immunoprecipitates without affecting phytochrome phosphorylation, indicating that the protein kinase catalytic activity is either intrinsic to the phytochrome molecule or associated with it by high-affinity interactions. Red irradiation (of coleoptiles or extracts) sufficient to approach photoconversion saturation reduced phosphorylation of immunoprecipitated phytochrome. Subsequent far-red irradiation reversed the red-light effect. Phytochrome phosphorylation was stimulated about 10-fold by a co-immunoprecipitated factor. The stimulatory factor was highest in immunoprecipitates when Mg2+ was present in immunoprecipitation reactions but remained in the supernatant in the absence of Mg2+. These observations provide strong support for the hypothesis that phytochrome-associated protein kinase modulates light responses in vivo. Since only phytochrome was found to be phosphorylated, the co-immunoprecipitated protein kinase may function to regulate receptor activity.

  19. Chromatin immunoprecipitation and deep sequencing in Xenopus tropicalis and Xenopus laevis

    PubMed Central

    Wills, Andrea E.; Gupta, Rakhi; Chuong, Edward; Baker, Julie C.

    2014-01-01

    Chromatin immunoprecipitation and deep sequencing (ChIP-SEQ) represents a powerful tool for identifying the genomic targets of transcription factors, chromatin remodeling factors, and histone modifications. The frogs Xenopus laevis and Xenopus tropicalis have historically been outstanding model systems for embryology and cell biology, with emerging utility as highly accessible embryos for genome-wide studies. Here we focus on the particular strengths and limitations of Xenopus cell biology and genomics as they apply to ChIP-SEQ, and outline a methodology for ChIP-SEQ in both species, providing detailed strategies for sample preparation, antibody selection, quality control, sequencing library preparation, and basic analysis. PMID:24064036

  20. Protocol: methodology for chromatin immunoprecipitation (ChIP) in Chlamydomonas reinhardtii

    PubMed Central

    2011-01-01

    We report on a detailed chromatin immunoprecipitation (ChIP) protocol for the unicellular green alga Chlamydomonas reinhardtii. The protocol is suitable for the analysis of nucleosome occupancy, histone modifications and transcription factor binding sites at the level of mononucleosomes for targeted and genome-wide studies. We describe the optimization of conditions for crosslinking, chromatin fragmentation and antibody titer determination and provide recommendations and an example for the normalization of ChIP results as determined by real-time PCR. PMID:22050920

  1. Quantitation of haptens by homogeneous immunoprecipitation. 2. Centrifugal analysis for tobramycin, phenobarbital, and theophylline in serum.

    PubMed

    Wu, J W; Bunyagidj, C; Hoskin, S; Riebe, S M; Aucker, J; White, K; O'Neill, S P

    1983-08-01

    Our homogeneous immunoprecipitation inhibition assay (Clin. Chem. 28:659-661, 1982) is applied here to tobramycin, phenobarbital, and theophylline. Only 10-50 microL of test sample is needed. No sample treatment, dilution, or extraction is required. A test serum sample is simultaneously mixed with a drug conjugate and its specific antiserum in a centrifugal analyzer. The subsequent reaction and the measurement are completed in 3 min. Within-run and between-run CVs for clinically relevant concentrations were well below 10%. Results for patients' samples correlated well with those by enzyme immunoassay.

  2. Characterization of human platelet glycoprotein antigens giving rise to individual immunoprecipitates in crossed-immunoelectrophoresis

    SciTech Connect

    Kunicki, T.J.; Nurden, A.T.; Pidard, D.; Russell, N.R.; Caen, J.P.

    1981-12-01

    Washed human platelets were labeled with 125I by the lactoperoxidase-catalyzed method and solubilized in 1% Triton X-100. The soluble proteins were analyzed by crossed-immunoelectrophoresis in 1% agarose, employing a rabbit antibody raised against whole human platelets. Analysis of autoradiograms developed from dried agarose gels led to the establishment of a normal reference pattern that was consistent for platelets obtained from more than 50 normal individuals. Six platelet membrane glycoprotein antigens contained in four distinguishable precipitates were identified. Each identification was based on direct sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of 125I-antigens contained in individually excised precipitates. These platelet antigens include major membrane glycoproteins previously designated la, lb, lla, llb, llla, and lllb. Glycoproteins llb and llla were shown to be contained in a single immunoprecipitate, while glycoproteins la and lla were routinely detected in a single different immunoprecipitate. Analysis of soluble proteins from platelets of five patients with Glanzmann's thrombasthenia demonstrated either a complete absence or a marked reduction of only one radiolabeled precipitate, that containing membrane glycoproteins llb and llla. Platelet samples from two patients with Bernard-Soulier syndrome were devoid of a different precipitate, that containing membrane glycoprotein lb.

  3. N-DSK gamma-chain binds to immunoprecipitated GP IIb-IIIa

    SciTech Connect

    Thorsen, L.I.; Hessel, B.; Brosstad, F.; Gogstad, G.; Solum, N.O.

    1987-08-01

    The CNBr-split N-terminal disulphide knot of the fibrinogen molecule (N-DSK) binds to ADP-stimulated gel-filtered platelets and immunoprecipitated fibrinogen receptor. To investigate which part of the N-DSK molecule that is involved in this binding, the glycoprotein IIb-IIIa complex (the fibrinogen receptor) was immunoprecipitated in crossed immunoelectrophoresis of Triton X-100 extracts of platelets against rabbit antibodies to whole platelet proteins. The immunoelectrophoresis plates were incubated with solubilized, carboxymethylated /sup 125/I-labelled A alpha -, B beta - or gamma-chains of N-DSK, and investigated for binding by autoradiography. The N-DSK gamma-chain, but not the A alpha - or B beta -chains demonstrated binding to the GP IIb-IIIa complex. These results show that the fibrinogen molecule contains a third sequence of amino acids, in addition to the two previously reported ones that can be involved in binding of fibrinogen to the fibrinogen receptor on the platelets.

  4. A chromatin immunoprecipitation (ChIP) protocol for use in whole human adipose tissue.

    PubMed

    Haim, Yulia; Tarnovscki, Tanya; Bashari, Dana; Rudich, Assaf

    2013-11-01

    Chromatin immunoprecipitation (ChIP) has become a central method when studying in vivo protein-DNA interactions, with the major challenge being the hope to capture "authentic" interactions. While ChIP protocols have been optimized for use with specific cell types and tissues including adipose tissue-derived cells, a working ChIP protocol addressing the challenges imposed by fresh whole human adipose tissue has not been described. Utilizing human paired omental and subcutaneous adipose tissue obtained during elective abdominal surgeries, we have carefully identified and optimized individual steps in the ChIP protocol employed directly on fresh tissue fragments. We describe a complete working protocol for using ChIP on whole adipose tissue fragments. Specific steps required adaptation of the ChIP protocol to human whole adipose tissue. In particular, a cross-linking step was performed directly on fresh small tissue fragments. Nuclei were isolated before releasing chromatin, allowing better management of fat content; a sonication protocol to obtain fragmented chromatin was optimized. We also demonstrate the high sensitivity of immunoprecipitated chromatin from adipose tissue to freezing. In conclusion, we describe the development of a ChIP protocol optimized for use in studying whole human adipose tissue, providing solutions for the unique challenges imposed by this tissue. Unraveling protein-DNA interaction in whole human adipose tissue will likely contribute to elucidating molecular pathways contributing to common human diseases such as obesity and type 2 diabetes.

  5. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles.

    PubMed

    Cejas, Paloma; Li, Lewyn; O'Neill, Nicholas K; Duarte, Melissa; Rao, Prakash; Bowden, Michaela; Zhou, Chensheng W; Mendiola, Marta; Burgos, Emilio; Feliu, Jaime; Moreno-Rubio, Juan; Guadalajara, Héctor; Moreno, Víctor; García-Olmo, Damián; Bellmunt, Joaquim; Mullane, Stephanie; Hirsch, Michelle; Sweeney, Christopher J; Richardson, Andrea; Liu, X Shirley; Brown, Myles; Shivdasani, Ramesh A; Long, Henry W

    2016-06-01

    Extensive cross-linking introduced during routine tissue fixation of clinical pathology specimens severely hampers chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) analysis from archived tissue samples. This limits the ability to study the epigenomes of valuable, clinically annotated tissue resources. Here we describe fixed-tissue chromatin immunoprecipitation sequencing (FiT-seq), a method that enables reliable extraction of soluble chromatin from formalin-fixed paraffin-embedded (FFPE) tissue samples for accurate detection of histone marks. We demonstrate that FiT-seq data from FFPE specimens are concordant with ChIP-seq data from fresh-frozen samples of the same tumors. By using multiple histone marks, we generate chromatin-state maps and identify cis-regulatory elements in clinical samples from various tumor types that can readily allow us to distinguish between cancers by the tissue of origin. Tumor-specific enhancers and superenhancers that are elucidated by FiT-seq analysis correlate with known oncogenic drivers in different tissues and can assist in the understanding of how chromatin states affect gene regulation. PMID:27111282

  6. Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo.

    PubMed

    Komar, Dorota N; Mouriz, Alfonso; Jarillo, José A; Piñeiro, Manuel

    2016-01-14

    Intricate gene regulatory networks orchestrate biological processes and developmental transitions in plants. Selective transcriptional activation and silencing of genes mediate the response of plants to environmental signals and developmental cues. Therefore, insights into the mechanisms that control plant gene expression are essential to gain a deep understanding of how biological processes are regulated in plants. The chromatin immunoprecipitation (ChIP) technique described here is a procedure to identify the DNA-binding sites of proteins in genes or genomic regions of the model species Arabidopsis thaliana. The interactions with DNA of proteins of interest such as transcription factors, chromatin proteins or posttranslationally modified versions of histones can be efficiently analyzed with the ChIP protocol. This method is based on the fixation of protein-DNA interactions in vivo, random fragmentation of chromatin, immunoprecipitation of protein-DNA complexes with specific antibodies, and quantification of the DNA associated with the protein of interest by PCR techniques. The use of this methodology in Arabidopsis has contributed significantly to unveil transcriptional regulatory mechanisms that control a variety of plant biological processes. This approach allowed the identification of the binding sites of the Arabidopsis chromatin protein EBS to regulatory regions of the master gene of flowering FT. The impact of this protein in the accumulation of particular histone marks in the genomic region of FT was also revealed through ChIP analysis.

  7. A Yeast Display Immunoprecipitation Method for Efficient Isolation and Characterization of Antigens

    PubMed Central

    Cho, Yong Ku; Chen, Irene; Wei, Xin; Li, Lingjun; Shusta, Eric V.

    2009-01-01

    Yeast antibody display has found a wide variety of applications including antibody affinity maturation, epitope mapping, and library screening. Here we report a yeast display immunoprecipitation (YDIP) technique that employs yeast cells displaying single-chain antibody fragments (scFv) on their surface as affinity capture reagents to isolate and characterize antigens. We show that displayed single-chain antibody fragments are active in a variety of detergent solutions commonly used for immunoprecipitation and that the antigen-antibody interaction can be accurately quantified by YDIP coupled with flow cytometry. The YDIP method has also been optimized so that it is compatible with commonly used protein characterization tools such as Western blotting, silver staining, and mass spectrometry. From complex protein mixtures, we have used YDIP to isolate, analyze and sequence both soluble and plasma membrane antigens using tandem mass spectrometry. In the case of the membrane antigen, YDIP coupled with tandem mass spectrometry was successful in identifying neural cell adhesion molecule (NCAM) as the antigen for an antibody previously selected as binding to the plasma membranes of endothelial cells. The presented method therefore has potential to facilitate antibody-antigen characterization. PMID:19041873

  8. The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA.

    PubMed

    Berkyurek, Ahmet Can; Suetake, Isao; Arita, Kyohei; Takeshita, Kohei; Nakagawa, Atsushi; Shirakawa, Masahiro; Tajima, Shoji

    2014-01-01

    Dnmt1 is responsible for the maintenance DNA methylation during replication to propagate methylation patterns to the next generation. The replication foci targeting sequence (RFTS), which plugs the catalytic pocket, is necessary for recruitment of Dnmt1 to the replication site. In the present study we found that the DNA methylation activity of Dnmt1 was DNA length-dependent and scarcely methylated 12-bp short hemi-methylated DNA. Contrarily, the RFTS-deleted Dnmt1 and Dnmt1 mutants that destroyed the hydrogen bonds between the RFTS and catalytic domain showed significant DNA methylation activity even toward 12-bp hemi-methylated DNA. The DNA methylation activity of the RFTS-deleted Dnmt1 toward 12-bp hemi-methylated DNA was strongly inhibited on the addition of RFTS, but to a lesser extent by Dnmt1 harboring the mutations that impair the hydrogen bond formation. The SRA domain of Uhrf1, which is a prerequisite factor for maintenance methylation and selectively binds to hemi-methylated DNA, stimulated the DNA methylation activity of Dnmt1. The SRA to Dnmt1 concentration ratio was the determinant for the maximum stimulation. In addition, a mutant SRA, which had lost the DNA binding activity but was able to bind to Dnmt1, stimulated the DNA methylation activity of Dnmt1. The results indicate that the DNA methylation activity of Dnmt1 was stimulated on the direct interaction of the SRA and Dnmt1. The SRA facilitated acceptance of the 12-bp fluorocytosine-containing DNA by the catalytic center. We propose that the SRA removes the RFTS plug from the catalytic pocket to facilitate DNA acceptance by the catalytic center.

  9. The DNA Methyltransferase Dnmt1 Directly Interacts with the SET and RING Finger-associated (SRA) Domain of the Multifunctional Protein Uhrf1 to Facilitate Accession of the Catalytic Center to Hemi-methylated DNA*

    PubMed Central

    Berkyurek, Ahmet Can; Suetake, Isao; Arita, Kyohei; Takeshita, Kohei; Nakagawa, Atsushi; Shirakawa, Masahiro; Tajima, Shoji

    2014-01-01

    Dnmt1 is responsible for the maintenance DNA methylation during replication to propagate methylation patterns to the next generation. The replication foci targeting sequence (RFTS), which plugs the catalytic pocket, is necessary for recruitment of Dnmt1 to the replication site. In the present study we found that the DNA methylation activity of Dnmt1 was DNA length-dependent and scarcely methylated 12-bp short hemi-methylated DNA. Contrarily, the RFTS-deleted Dnmt1 and Dnmt1 mutants that destroyed the hydrogen bonds between the RFTS and catalytic domain showed significant DNA methylation activity even toward 12-bp hemi-methylated DNA. The DNA methylation activity of the RFTS-deleted Dnmt1 toward 12-bp hemi-methylated DNA was strongly inhibited on the addition of RFTS, but to a lesser extent by Dnmt1 harboring the mutations that impair the hydrogen bond formation. The SRA domain of Uhrf1, which is a prerequisite factor for maintenance methylation and selectively binds to hemi-methylated DNA, stimulated the DNA methylation activity of Dnmt1. The SRA to Dnmt1 concentration ratio was the determinant for the maximum stimulation. In addition, a mutant SRA, which had lost the DNA binding activity but was able to bind to Dnmt1, stimulated the DNA methylation activity of Dnmt1. The results indicate that the DNA methylation activity of Dnmt1 was stimulated on the direct interaction of the SRA and Dnmt1. The SRA facilitated acceptance of the 12-bp fluorocytosine-containing DNA by the catalytic center. We propose that the SRA removes the RFTS plug from the catalytic pocket to facilitate DNA acceptance by the catalytic center. PMID:24253042

  10. Effective Identification of Akt Interacting Proteins by Two-Step Chemical Crosslinking, Co-Immunoprecipitation and Mass Spectrometry

    PubMed Central

    Huang, Bill X.; Kim, Hee-Yong

    2013-01-01

    Akt is a critical protein for cell survival and known to interact with various proteins. However, Akt binding partners that modulate or regulate Akt activation have not been fully elucidated. Identification of Akt-interacting proteins has been customarily achieved by co-immunoprecipitation combined with western blot and/or MS analysis. An intrinsic problem of the method is loss of interacting proteins during procedures to remove non-specific proteins. Moreover, antibody contamination often interferes with the detection of less abundant proteins. Here, we developed a novel two-step chemical crosslinking strategy to overcome these problems which resulted in a dramatic improvement in identifying Akt interacting partners. Akt antibody was first immobilized on protein A/G beads using disuccinimidyl suberate and allowed to bind to cellular Akt along with its interacting proteins. Subsequently, dithiobis[succinimidylpropionate], a cleavable crosslinker, was introduced to produce stable complexes between Akt and binding partners prior to the SDS-PAGE and nanoLC-MS/MS analysis. This approach enabled identification of ten Akt partners from cell lysates containing as low as 1.5 mg proteins, including two new potential Akt interacting partners. None of these but one protein was detectable without crosslinking procedures. The present method provides a sensitive and effective tool to probe Akt-interacting proteins. This strategy should also prove useful for other protein interactions, particularly those involving less abundant or weakly associating partners. PMID:23613850

  11. Optimization of a method for chromatin immunoprecipitation assays in the marine invertebrate chordate Ciona

    PubMed Central

    Aihara, Hitoshi; Katikala, Lavanya; Zeller, Robert W.; Di Gregorio, Anna; Nibu, Yutaka

    2013-01-01

    Chromatin immunoprecipitation (ChIP) assays allow the efficient characterization of the in vivo occupancy of genomic regions by DNA-binding proteins, and thus facilitate the prediction of cis-regulatory sequences in silico and guide their validation in vivo. For these reasons, these assays and their permutations (e.g., ChIP-on-chip, ChIP-Sequencing) are currently being extended to several non-mainstream model organisms, as the availability of specific antibodies increases. Here we describe the development of a polyclonal antibody against the Brachyury protein of the marine invertebrate chordate Ciona intestinalis and provide a detailed ChIP protocol that should be easily adaptable to other marine organisms. PMID:23592257

  12. A systematic immunoprecipitation approach reinforces the concept of common conformational alterations in amyotrophic lateral sclerosis-linked SOD1 mutants.

    PubMed

    Fujisawa, Takao; Yamaguchi, Namiko; Kadowaki, Hisae; Tsukamoto, Yuka; Tsuburaya, Naomi; Tsubota, Atsushi; Takahashi, Hiromitsu; Naguro, Isao; Takahashi, Yuji; Goto, Jun; Tsuji, Shoji; Nishitoh, Hideki; Homma, Kengo; Ichijo, Hidenori

    2015-10-01

    Mutations in the Cu, Zn superoxide dismutase (SOD1) gene are one of the causative agents of amyotrophic lateral sclerosis (ALS). Although more than 100 different mutations in SOD1 have been identified, it is unclear whether all the mutations are pathogenic or just single nucleotide polymorphisms (SNPs) unrelated to the disease. Our previous systematic analysis found that all pathogenic SOD1 mutants (SOD1(mut)) have a common property, namely, an association with Derlin-1, a component of the endoplasmic reticulum-associated degradation machinery. For the proposed mechanism, we found that most pathogenic SOD1(mut) have a constitutively exposed Derlin-1-binding region (DBR), which is concealed in wild-type SOD1 (SOD1(WT)). Moreover, we generated MS785, a monoclonal antibody against DBR. MS785 distinguished most ALS-causative SOD1(mut) from both SOD1(WT) and non-toxic SOD1(mut). However, MS785 could not recognize SOD1(mut) that has mutations in the MS785 epitope region. Here, we developed a new diagnostic antibody, which could compensate for this shortcoming of MS785. We hypothesized that in ALS-causative SOD1(mut), the DBR-neighboring region [SOD1(30-40)] may also be exposed. We then generated MS27, a monoclonal antibody against SOD1(30-40). We found that MS27 could distinguish SOD1(WT) from the pathogenic SOD1(mut), which has mutations in the MS785 epitope region. Moreover, all pathogenic SOD1(mut), without exception, were immunoprecipitated with a combination of MS785 and MS27. The MS785-MS27 combination could be developed as a novel mechanism-based biomarker for the diagnosis of ALS.

  13. Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging.

    PubMed

    Tatavosian, Roubina; Zhen, Chao Yu; Duc, Huy Nguyen; Balas, Maggie M; Johnson, Aaron M; Ren, Xiaojun

    2015-11-20

    Epigenetic complexes play an essential role in regulating chromatin structure, but information about their assembly stoichiometry on chromatin within cells is poorly understood. The cellular assembly stoichiometry is critical for appreciating the initiation, propagation, and maintenance of epigenetic inheritance during normal development and in cancer. By combining genetic engineering, chromatin biochemistry, and single-molecule fluorescence imaging, we developed a novel and sensitive approach termed single-molecule chromatin immunoprecipitation imaging (Sm-ChIPi) to enable investigation of the cellular assembly stoichiometry of epigenetic complexes on chromatin. Sm-ChIPi was validated by using chromatin complexes with known stoichiometry. The stoichiometry of subunits within a polycomb complex and the assembly stoichiometry of polycomb complexes on chromatin have been extensively studied but reached divergent views. Moreover, the cellular assembly stoichiometry of polycomb complexes on chromatin remains unexplored. Using Sm-ChIPi, we demonstrated that within mouse embryonic stem cells, one polycomb repressive complex (PRC) 1 associates with multiple nucleosomes, whereas two PRC2s can bind to a single nucleosome. Furthermore, we obtained direct physical evidence that the nucleoplasmic PRC1 is monomeric, whereas PRC2 can dimerize in the nucleoplasm. We showed that ES cell differentiation induces selective alteration of the assembly stoichiometry of Cbx2 on chromatin but not other PRC1 components. We additionally showed that the PRC2-mediated trimethylation of H3K27 is not required for the assembly stoichiometry of PRC1 on chromatin. Thus, these findings uncover that PRC1 and PRC2 employ distinct mechanisms to assemble on chromatin, and the novel Sm-ChIPi technique could provide single-molecule insight into other epigenetic complexes.

  14. Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging.

    PubMed

    Tatavosian, Roubina; Zhen, Chao Yu; Duc, Huy Nguyen; Balas, Maggie M; Johnson, Aaron M; Ren, Xiaojun

    2015-11-20

    Epigenetic complexes play an essential role in regulating chromatin structure, but information about their assembly stoichiometry on chromatin within cells is poorly understood. The cellular assembly stoichiometry is critical for appreciating the initiation, propagation, and maintenance of epigenetic inheritance during normal development and in cancer. By combining genetic engineering, chromatin biochemistry, and single-molecule fluorescence imaging, we developed a novel and sensitive approach termed single-molecule chromatin immunoprecipitation imaging (Sm-ChIPi) to enable investigation of the cellular assembly stoichiometry of epigenetic complexes on chromatin. Sm-ChIPi was validated by using chromatin complexes with known stoichiometry. The stoichiometry of subunits within a polycomb complex and the assembly stoichiometry of polycomb complexes on chromatin have been extensively studied but reached divergent views. Moreover, the cellular assembly stoichiometry of polycomb complexes on chromatin remains unexplored. Using Sm-ChIPi, we demonstrated that within mouse embryonic stem cells, one polycomb repressive complex (PRC) 1 associates with multiple nucleosomes, whereas two PRC2s can bind to a single nucleosome. Furthermore, we obtained direct physical evidence that the nucleoplasmic PRC1 is monomeric, whereas PRC2 can dimerize in the nucleoplasm. We showed that ES cell differentiation induces selective alteration of the assembly stoichiometry of Cbx2 on chromatin but not other PRC1 components. We additionally showed that the PRC2-mediated trimethylation of H3K27 is not required for the assembly stoichiometry of PRC1 on chromatin. Thus, these findings uncover that PRC1 and PRC2 employ distinct mechanisms to assemble on chromatin, and the novel Sm-ChIPi technique could provide single-molecule insight into other epigenetic complexes. PMID:26381410

  15. Probing flagellar promoter occupancy in wild-type and mutant Caulobacter crescentus by chromatin immunoprecipitation.

    PubMed

    Davis, Nicole J; Viollier, Patrick H

    2011-06-01

    In the asymmetric predivisional cell of Caulobacter crescentus, TipF and TipN mark the cellular pole for future flagellar development. TipF is essential for motility and contains a cyclic-di-GMP phosphodiesterase-like (EAL) domain that is necessary for proper function. TipN is localized to the flagellar pole before TipF and is essential for the proper placement of the flagellum in C. crescentus. Using β-galactosidase promoter-probe assays and quantitative chromatin immunoprecipitation, we investigated the influence of the C. crescentus flagellar assembly regulator TipF on flagellar gene transcription. We compared the transcriptional activity of class II-fliF-lacZ, class III-flgE-lacZ, and class IV-fljL-lacZ fusions in a ΔtipF mutant with that of other flagellar mutants and the wild-type strain. We subsequently verified the in vivo occupancy of the fliF, flgE, and fljL flagellar promoters by the flagellar regulators CtrA, FlbD, and FliX in addition to RNA polymerase. We deduce that TipF contributes to proper expression of flagellar genes in C. crescentus by acting both within and outside of the canonical flagellar gene expression hierarchy.

  16. Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data

    PubMed Central

    Kawakami, Eiryo; Nakaoka, Shinji; Ohta, Tazro; Kitano, Hiroaki

    2016-01-01

    Predicting responsible transcription regulators on the basis of transcriptome data is one of the most promising computational approaches to understanding cellular processes and characteristics. Here, we present a novel method employing vast amounts of chromatin immunoprecipitation (ChIP) experimental data to address this issue. Global high-throughput ChIP data was collected to construct a comprehensive database, containing 8 578 738 binding interactions of 454 transcription regulators. To incorporate information about heterogeneous frequencies of transcription factor (TF)-binding events, we developed a flexible framework for gene set analysis employing the weighted t-test procedure, namely weighted parametric gene set analysis (wPGSA). Using transcriptome data as an input, wPGSA predicts the activities of transcription regulators responsible for observed gene expression. Validation of wPGSA with published transcriptome data, including that from over-expressed TFs, showed that the method can predict activities of various TFs, regardless of cell type and conditions, with results totally consistent with biological observations. We also applied wPGSA to other published transcriptome data and identified potential key regulators of cell reprogramming and influenza virus pathogenesis, generating compelling hypotheses regarding underlying regulatory mechanisms. This flexible framework will contribute to uncovering the dynamic and robust architectures of biological regulation, by incorporating high-throughput experimental data in the form of weights. PMID:27131787

  17. Analysis of TGFβ1 and IL-10 transcriptional regulation in CTCL cells by chromatin immunoprecipitation.

    PubMed

    Chang, Tzu-Pei; Kim, Myra; Vancurova, Ivana

    2014-01-01

    The immunosuppressive cytokines transforming growth factor β1 (TGFβ1) and interleukin-10 (IL-10) regulate a variety of biological processes including differentiation, proliferation, tissue repair, tumorigenesis, inflammation, and host defense. Aberrant expression of TGFβ1 and IL-10 has been associated with many types of autoimmune and inflammatory disorders, as well as with many types of cancer and leukemia. Patients with cutaneous T cell lymphoma (CTCL) have high levels of malignant CD4+ T cells expressing IL-10 and TGFβ1 that suppress the immune system and diminish the antitumor responses. The transcriptional regulation of TGFβ1 and IL-10 expression is orchestrated by several transcription factors, including NFκB. However, while the transcriptional regulation of pro-inflammatory and anti-apoptotic genes by NFκB has been studied extensively, much less is known about the NFκB regulation of immunosuppressive genes. In this chapter, we describe a protocol that uses chromatin immunoprecipitation (ChIP) to analyze the transcriptional regulation of TGFβ1 and IL-10 by measuring recruitment of NFκB p65, p50, c-Rel, Rel-B, and p52 subunits to TGFβ1 and IL-10 promoters in human CTCL Hut-78 cells. PMID:24908319

  18. Immunoprecipitation and characterization of a binding protein specific for the peptide, intestinal trefoil factor.

    PubMed

    Chinery, R; Cox, H M

    1995-01-01

    Recombinant rat intestinal trefoil factor (rITF) and human spasmolytic polypeptide (hSP) were irreversibly cross-linked to specific binding sites in solubilized rat intestinal epithelial membranes and human adenocarcinoma cells. Analysis of the immunoprecipitates by immunoblotting identified a cross-linked protein complex of approximately 45 kDa, which under reducing conditions appeared as a approximately 28-kDa band and the latter displayed ligand-stimulated phosphorylation of a tyrosine, but not a threonine or serine, residue in the binding complex. [125I]rITF was used to localize binding sites by autoradiography of frozen sections from rat gastrointestinal tissues. A high density of specific [125I]rITF binding sites was present within gastric, colonic, and jejunal mucosal glands. Unlabeled hSP partially inhibited [125I]rITF binding at a concentration of 1 microM when compared with the same concentration of unlabeled rITF. These studies support earlier observations for the existence of trefoil binding sites in the gastrointestinal tract and further suggest that hSP has affinity for the mucosal rITF binding site.

  19. A DNA immunoprecipitation assay used in quantitative detection of in vitro DNA-protein complex binding.

    PubMed

    Kim, Min Young; Chae, Ji Hyung; Oh, Chang-Ho; Kim, Chul Geun

    2013-10-15

    To begin gene transcription, several transcription factors must bind to specific DNA sequences to form a complex via DNA-protein interactions. We established an in vitro method for specific and sensitive analyses of DNA-protein interactions based on a DNA immunoprecipitation (DIP) method. We verified the accuracy and efficiency of the DIP assay in quantitatively measuring DNA-protein binding using transcription factor CP2c as a model. With our DIP assay, we could detect specific interactions within a DNA-CP2c complex, with reproducible and quantitative binding values. In addition, we were able to effectively measure the changes in DNA-CP2c binding by the addition of a small molecule, FQI1 (factor quinolinone inhibitor 1), previously identified as a specific inhibitor of this binding. To identify a new regulator of DNA-CP2c binding, we analyzed several CP2c binding peptides and found that only one class of peptide severely inhibits DNA-CP2c binding. These data show that our DIP assay is very useful in quantitatively detecting the binding dynamics of DNA-protein complex. Because DNA-protein interaction is very dynamic in different cellular environments, our assay can be applied to the detection of active transcription factors, including promoter occupancy in normal and disease conditions. Moreover, it may be used to develop a targeted regulator of specific DNA-protein interaction.

  20. Analysis of TGFβ1 and IL-10 transcriptional regulation in CTCL cells by chromatin immunoprecipitation.

    PubMed

    Chang, Tzu-Pei; Kim, Myra; Vancurova, Ivana

    2014-01-01

    The immunosuppressive cytokines transforming growth factor β1 (TGFβ1) and interleukin-10 (IL-10) regulate a variety of biological processes including differentiation, proliferation, tissue repair, tumorigenesis, inflammation, and host defense. Aberrant expression of TGFβ1 and IL-10 has been associated with many types of autoimmune and inflammatory disorders, as well as with many types of cancer and leukemia. Patients with cutaneous T cell lymphoma (CTCL) have high levels of malignant CD4+ T cells expressing IL-10 and TGFβ1 that suppress the immune system and diminish the antitumor responses. The transcriptional regulation of TGFβ1 and IL-10 expression is orchestrated by several transcription factors, including NFκB. However, while the transcriptional regulation of pro-inflammatory and anti-apoptotic genes by NFκB has been studied extensively, much less is known about the NFκB regulation of immunosuppressive genes. In this chapter, we describe a protocol that uses chromatin immunoprecipitation (ChIP) to analyze the transcriptional regulation of TGFβ1 and IL-10 by measuring recruitment of NFκB p65, p50, c-Rel, Rel-B, and p52 subunits to TGFβ1 and IL-10 promoters in human CTCL Hut-78 cells.

  1. Characterizing RNA-protein interaction using cross-linking and metabolite supplemented nuclear RNA-immunoprecipitation.

    PubMed

    Au, Phil Chi Khang; Helliwell, Chris; Wang, Ming-Bo

    2014-05-01

    RNA-immunoprecipitation (RNA-IP) is a method used to isolate and identify RNA molecules specifically associated with an RNA-binding protein. Non-coding RNAs are emerging as key regulators of many biological and developmental pathways and RNA-IP has become an important tool in studying their function(s). While RNA-IP is successfully used to determine protein-RNA interaction, specific details regarding the level of this association and the metabolic requirement of this interaction which can influence the success of RNA-IP remain unclear. Here, we investigate the conditions required for efficient nuclear RNA-IP using Arabidopsis AGO4 (Argonaute 4) and siRNA binding as the study model. We showed that formaldehyde cross-linking, but not UV cross-linking, allowed for efficient pull-down of 24-nt siRNAs, suggesting that AGO4-siRNA interaction involves other protein(s). We also showed that, while formaldehyde cross-linking could also be performed on purified nuclei, ATP supplementation to the nuclei isolation buffer was needed to efficiently pull down 24-nt siRNAs. This result indicates that ATP is required for efficient siRNA loading onto AGO4. As most of the known RNA-mediated regulatory processes occur in the nucleus, our findings on cross-linking conditions and metabolite requirement for successful AGO4 nuclear RNA-IP provide a valuable insight and future consideration when studying the function of protein-RNA interactions in plants.

  2. Physicochemical characterization of C3b receptors isolated from human erythrocytes by immunoprecipitation.

    PubMed Central

    Gerdes, J; Stein, H

    1980-01-01

    A high yield of active C3b receptors was obtained by solubilizing human erythrocyte membranes with 2 M KBr, whereas other solubilization agents yielded no, or significantly less activity. Gel filtration of the KBr lysates revealed that the apparent molecular wieght of biologically active C3b receptor molecules was greater than 1 x 10(6). Immunoprecipitates prepared with radio-iodinated KBr lysates and anti-C3 receptor sera (AC3RS) were subjected to sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) or sodium dodecyl gel filtration. Unreduced SDS-PAGE and gel filtration profiles showed three predominant peaks with apparent mol. wts of 1--1.3 x 10(6), 80,000 and 60,000. Whereas the high mol. wt component decreased only slightly after reduction, the 80,000 and 60,000 mol. wt components disappeared and two new peaks with apparent mol. wts of 38,000 and 18,000 appeared in SDS-PAGE profiles. Although the high mol. wt component present in reduced SDS-PAGE profiles was detectable in some of the control experiments, none of the other peaks could be precipitated with control sera, and these components could be demonstrated only when KBr lysates of C3b receptor-positive erythrocytes and AC3RS that were able to inhibit ligand binding of the C3b receptors were used for precipitation. These findings suggest that (a) the C3b receptor of human erythrocytes in its biologically active state is a macromolecule with an apparent mol. wt higher than 1 x 10(6) and (b) the protein moiety consists predominantly of non-covalently linked protein molecules with apparent mol wts of 80,000 and 60,000. These protein molecules are composed of disulphide-bridged polypeptide chains with apparent mol. wts of 38,000 and 18,000. PMID:7461716

  3. Identification of Lysine Acetylation in Mycobacterium abscessus Using LC-MS/MS after Immunoprecipitation.

    PubMed

    Guo, Jintao; Wang, Changwei; Han, Yi; Liu, Zhiyong; Wu, Tian; Liu, Yan; Liu, Yang; Tan, Yaoju; Cai, Xinshan; Cao, Yuanyuan; Wang, Bangxing; Zhang, Buchang; Liu, Chunping; Tan, Shouyong; Zhang, Tianyu

    2016-08-01

    Mycobacterium abscessus (MAB), which manifests in the pulmonary system, is one of the neglected causes of nontuberculous mycobacteria (NTM) infection. Treatment against MAB is difficult, characterized by its intrinsic antibiotic drug resistance. Lysine acetylation can alter the physiochemical property of proteins in living organisms. This study aimed to determine if this protein post-translational modification (PTM) exists in a clinical isolate M. abscessus GZ002. We used the antiacetyl-lysine immunoprecipitation to enrich the low-abundant PTM proteins, followed by the LC-MS/MS analysis. The lysine acetylome of M. abscessus GZ002 was determined. There were 459 lysine acetylation sites found in 289 acetylated proteins. Lysine acetylation occurred in 5.87% of the M. abscessus GZ002 proteome, and at least 25% of them were growth essential. Aerobic respiration and carbohydrate metabolic pathways of M. abscessus GZ002 were enriched with lysine acetylation. Through bioinformatics analysis, we identified four major acetyl motif logos (K(ac)Y, K(ac)F, K(ac)H, and DK(ac)). Further comparison of the reported M. tuberculosis (MTB) acetylomes and that of MAB GZ002 revealed several common features between these two species. The lysine residues of several antibiotic-resistance, virulence, and persistence-related proteins were acetylated in both MAB GZ002 and MTB. There were 51 identical acetylation sites in 37 proteins found in common between MAB GZ002 and MTB. Overall, we demonstrate a profile of lysine acetylation in MAB GZ002 proteome that shares similarities with MTB. Interventions that target at these conserved sections may be valuable as anti-NTM or anti-TB therapies. PMID:27323652

  4. Evaluation of myc E-box phylogenetic footprints in glycolytic genes by chromatin immunoprecipitation assays.

    PubMed

    Kim, Jung-whan; Zeller, Karen I; Wang, Yunyue; Jegga, Anil G; Aronow, Bruce J; O'Donnell, Kathryn A; Dang, Chi V

    2004-07-01

    Prediction of gene regulatory sequences using phylogenetic footprinting has advanced considerably but lacks experimental validation. Here, we report whether transcription factor binding sites predicted by dot plotting or web-based Trafac analysis could be validated by chromatin immunoprecipitation assays. MYC overexpression enhances glycolysis without hypoxia and hence may contribute to altered tumor metabolism. Because the full spectrum of glycolytic genes directly regulated by Myc is not known, we chose Myc as a model transcription factor to determine whether it binds target glycolytic genes that have conserved canonical Myc binding sites or E boxes (5'-CACGTG-3'). Conserved canonical E boxes in ENO1, HK2, and LDHA occur in 31- to 111-bp islands with high interspecies sequence identity (>65%). Trafac analysis revealed another region in ENO1 that corresponds to a murine region with a noncanonical E box. Myc bound all these conserved regions well in the human P493-6 B lymphocytes. We also determined whether Myc could bind nonconserved canonical E boxes found in the remaining human glycolytic genes. Myc bound PFKM, but it did not significantly bind GPI, PGK1, and PKM2. Binding to BPGM, PGAM2, and PKLR was not detected. Both GAPD and TPI1 do not have conserved E boxes but are induced and bound by Myc through regions with noncanonical E boxes. Our results indicate that Myc binds well to conserved canonical E boxes, but not nonconserved E boxes. However, the binding of Myc to unpredicted genomic regions with noncanonical E boxes reveals a limitation of phylogenetic footprinting. In aggregate, these observations indicate that Myc is an important regulator of glycolytic genes, suggesting that MYC plays a key role in a switch to glycolytic metabolism during cell proliferation or tumorigenesis.

  5. Immunoprecipitation of Native Botulinum Neurotoxin Complexes from Clostridium botulinum Subtype A Strains

    PubMed Central

    Lin, Guangyun; Tepp, William H.; Bradshaw, Marite; Fredrick, Chase M.

    2014-01-01

    Botulinum neurotoxins (BoNTs) naturally exist as components of protein complexes containing nontoxic proteins. The nontoxic proteins impart stability of BoNTs in the gastrointestinal tract and during purification and handling. The two primary neurotoxin complexes (TCs) are (i) TC1, consisting of BoNT, nontoxin-nonhemagglutinin (NTNH), and hemagglutinins (HAs), and (ii) TC2, consisting of BoNT and NTNH (and possibly OrfX proteins). In this study, BoNT/A subtypes A1, A2, A3, and A5 were examined for the compositions of their TCs in culture extracts using immunoprecipitation (IP). IP analyses showed that BoNT/A1 and BoNT/A5 form TC1s, while BoNT/A2 and BoNT/A3 form TC2s. A Clostridium botulinum host strain expressing recombinant BoNT/A4 (normally present as a TC2) from an extrachromosomal plasmid formed a TC1 with complexing proteins from the host strain, indicating that the HAs and NTNH encoded on the chromosome associated with the plasmid-encoded BoNT/A4. Strain NCTC 2916 (A1/silent B1), which carries both an ha silent bont/b cluster and an orfX bont/a1 cluster, was also examined. IP analysis revealed that NCTC 2916 formed only a TC2 containing BoNT/A1 and its associated NTNH. No association between BoNT/A1 and the nontoxic proteins from the silent bont/b cluster was detected, although the HAs were expressed as determined by Western blotting analysis. Additionally, NTNH and HAs from the silent bont/b cluster did not form a complex in NCTC 2916. The stabilities of the two types of TC differed at various pHs and with addition of KCl and NaCl. TC1 complexes were more stable than TC2 complexes. Mouse serum stabilized TC2, while TC1 was unaffected. PMID:25362065

  6. Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP)

    PubMed Central

    Fujita, Toshitsugu; Asano, Yoshinori; Ohtsuka, Junko; Takada, Yoko; Saito, Kazunobu; Ohki, Rieko; Fujii, Hodaka

    2013-01-01

    Biochemical analysis of molecular interactions in specific genomic regions requires their isolation while retaining molecular interactions in vivo. Here, we report isolation of telomeres by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using a transcription activator-like (TAL) protein recognizing telomere repeats. Telomeres recognized by the tagged TAL protein were immunoprecipitated with an antibody against the tag and subjected to identification of telomere-binding molecules. enChIP-mass spectrometry (enChIP-MS) targeting telomeres identified known and novel telomere-binding proteins. The data have been deposited to the ProteomeXchange with identifier PXD000461. In addition, we showed that RNA associated with telomeres could be isolated by enChIP. Identified telomere-binding molecules may play important roles in telomere biology. enChIP using TAL proteins would be a useful tool for biochemical analysis of specific genomic regions of interest. PMID:24201379

  7. Proteomics Analysis of Cellular Proteins Co-Immunoprecipitated with Nucleoprotein of Influenza A Virus (H7N9).

    PubMed

    Sun, Ningning; Sun, Wanchun; Li, Shuiming; Yang, Jingbo; Yang, Longfei; Quan, Guihua; Gao, Xiang; Wang, Zijian; Cheng, Xin; Li, Zehui; Peng, Qisheng; Liu, Ning

    2015-01-01

    Avian influenza A viruses are serious veterinary pathogens that normally circulate among avian populations, causing substantial economic impacts. Some strains of avian influenza A viruses, such as H5N1, H9N2, and recently reported H7N9, have been occasionally found to adapt to humans from other species. In order to replicate efficiently in the new host, influenza viruses have to interact with a variety of host factors. In the present study, H7N9 nucleoprotein was transfected into human HEK293T cells, followed by immunoprecipitated and analyzed by proteomics approaches. A series of host proteins co-immunoprecipitated were identified with high confidence, some of which were found to be acetylated at their lysine residues. Bioinformatics analysis revealed that spliceosome might be the most relevant pathway involved in host response to nucleoprotein expression, increasing our emerging knowledge of host proteins that might be involved in influenza virus replication activities. PMID:26528969

  8. Application of the chromatin immunoprecipitation method to identify in vivo protein-DNA associations in fission yeast.

    PubMed

    Takahashi, K; Saitoh, S; Yanagida, M

    2000-10-31

    The chromatin immunoprecipitation (ChIP) method provides an ideal tool for detecting direct or indirect interactions between proteins of interest and DNAs with known sequences. Here, we introduce the ChIP protocol used in our laboratory to identify in vivo protein-DNA association in the fission yeast Schizosaccharomyces pombe. The cytological and genetic merits of the fission yeast for studying control of the eukaryotic cell cycle and chromosome dynamics are reinforced by application of this ChIP method.

  9. Isolation of a thyroid hormone-responsive gene by immunoprecipitation of thyroid hormone receptor-DNA complexes.

    PubMed Central

    Bigler, J; Eisenman, R N

    1994-01-01

    Thyroid hormone (T3) receptor (TR) is a ligand-dependent transcription factor that acts through specific binding sites in the promoter region of target genes. In order to identify new genes that are regulated by T3, we used anti-TR antiserum to immunoprecipitate TR-DNA complexes from GH4 cell nuclei that had previously been treated with a restriction enzyme. Screening of the immunopurified, cloned DNA for TR binding sites by electrophoretic mobility shift assay yielded 53 positive clones. A subset of these clones was specifically immunoprecipitated with anti-TR antiserum and may therefore represent biologically significant binding sites. One of these clones, clone 122, was characterized in detail. It includes sequences highly related to the NICER long terminal repeat-like element and contains three TR binding sites as determined by DNase I footprinting. Two of the clone 122 TR binding sites are located upstream of the TATA box, and one is located downstream. The TR binding site downstream from the promoter was necessary and sufficient to confer T3-dependent regulation in transient transfection experiments. Expression of a reporter construct under the control of the clone 122 promoter region was activated by TR in the absence of ligand and returned to basal levels after T3 addition. Clone 122 sequences hybridize to at least two different mRNAs of approximately 6 and 10 kb from GH4 cells. The levels of both of these mRNAs increased upon removal of T3. Our studies suggest that specific immunoprecipitation of chromatin allows identification of binding sites and target genes for transcription factors. Images PMID:7935476

  10. Immunoprecipitation of Amyloid Fibrils by the Use of an Antibody that Recognizes a Generic Epitope Common to Amyloid Fibrils

    PubMed Central

    Greiner, Erin R.; Kelly, Jeffery W.; Palhano, Fernando L.

    2014-01-01

    Amyloid fibrils are associated with many maladies, including Alzheimer’s disease (AD). The isolation of amyloids from natural materials is very challenging because the extreme structural stability of amyloid fibrils makes it difficult to apply conventional protein science protocols to their purification. A protocol to isolate and detect amyloids is desired for the diagnosis of amyloid diseases and for the identification of new functional amyloids. Our aim was to develop a protocol to purify amyloid from organisms, based on the particular characteristics of the amyloid fold, such as its resistance to proteolysis and its capacity to be recognized by specific conformational antibodies. We used a two-step strategy with proteolytic digestion as the first step followed by immunoprecipitation using the amyloid conformational antibody LOC. We tested the efficacy of this method using as models amyloid fibrils produced in vitro, tissue extracts from C. elegans that overexpress Aβ peptide, and cerebrospinal fluid (CSF) from patients diagnosed with AD. We were able to immunoprecipitate Aβ1–40 amyloid fibrils, produced in vitro and then added to complex biological extracts, but not α-synuclein and gelsolin fibrils. This method was useful for isolating amyloid fibrils from tissue homogenates from a C. elegans AD model, especially from aged worms. Although we were able to capture picogram quantities of Aβ1–40 amyloid fibrils produced in vitro when added to complex biological solutions, we could not detect any Aβ amyloid aggregates in CSF from AD patients. Our results show that although immunoprecipitation using the LOC antibody is useful for isolating Aβ1–40 amyloid fibrils, it fails to capture fibrils of other amyloidogenic proteins, such as α-synuclein and gelsolin. Additional research might be needed to improve the affinity of these amyloid conformational antibodies for an array of amyloid fibrils without compromising their selectivity before application of this

  11. Investigation of histone H4 hyperacetylation dynamics in the 5S rRNA genes family by chromatin immunoprecipitation assay.

    PubMed

    Burlibașa, Liliana; Suciu, Ilinca

    2015-12-01

    Oogenesis is a critical event in the formation of female gamete, whose role in development is to transfer genomic information to the next generation. During this process, the gene expression pattern changes dramatically concomitant with genome remodelling, while genomic information is stably maintained. The aim of the present study was to investigate the presence of H4 acetylation of the oocyte and somatic 5S rRNA genes in Triturus cristatus, using chromatin immunoprecipitation assay (ChIP). Our findings suggest that some epigenetic mechanisms such as histone acetylation could be involved in the transcriptional regulation of 5S rRNA gene families.

  12. Binding of 125I-labelled fibrin(ogen) fragments to platelets and to immunoprecipitated glycoprotein IIb-IIIa complex

    SciTech Connect

    Thorsen, L.I.; Brosstad, F.; Gogstad, G.; Sletten, K.; Solum, N.O.

    1986-06-01

    To further investigate which parts of the fibrinogen molecule that are responsible for its binding to the fibrinogen receptor on human platelets, the following approaches were made: The glycoprotein IIb-IIIa complex (the putative fibrinogen receptor) was immunoprecipitated in crossed immunoelectrophoresis of Triton X-100-extracts of platelets against antibodies to whole platelet proteins. Subsequently, the immunoplates were incubated with /sup 125/I-labelled, plasmin- or CNBr-cleaved fibrinogen fragments (pre-X,X,Y,D,Degta,Efg,N-DSK) or fibrin fragments (E1,N-dsk), characterized by partial sequenation. The immunoplates were exposed to X-ray films, and binding of the fragments to the glycoprotein IIb-IIIa complex was examined. The findings were compared to the results obtained from studies on binding of the same fragments to intact gel-filtered platelets after ADP-stimulation. The following conclusions were made: All fragments except Efg and Degta bound to the immunoprecipitated GPIIb-IIIa complex as well as to ADP-stimulated platelets suggesting that at least two sequences in the E domain and one in each of the D domains of fibrinogen are involved in binding to the platelet receptor. The GPIIb-IIIa complex is the only surface-located platelet antigen that binds fibrinogen and the aforementioned fragments. The binding of the fragments to the receptor is dependent on divalent cations.

  13. Sensitive detection of C-reactive protein in serum by immunoprecipitation-microchip capillary gel electrophoresis.

    PubMed

    Herwig, Ela; Marchetti-Deschmann, Martina; Wenz, Christian; Rüfer, Andreas; Redl, Heinz; Bahrami, Soheyl; Allmaier, Günter

    2015-06-01

    Sepsis represents a significant cause of mortality in intensive care units. Early diagnosis of sepsis is essential to increase the survival rate of patients. Among others, C-reactive protein (CRP) is commonly used as a sepsis marker. In this work we introduce immune precipitation combined with microchip capillary gel electrophoresis (IP-MCGE) for the detection and quantification of CRP in serum samples. First high-abundance proteins (HSA, IgG) are removed from serum samples using affinity spin cartridges, and then the remaining proteins are labeled with a fluorescence dye and incubated with an anti-CRP antibody, and the antigen/antibody complex is precipitated with protein G-coated magnetic beads. After precipitation the complex is eluted from the beads and loaded onto the MCGE system. CRP could be reliably detected and quantified, with a detection limit of 25 ng/μl in serum samples and 126 pg/μl in matrix-free samples. The overall sensitivity (LOQ = 75 ng/μl, R(2) = 0.9668) of the method is lower than that of some specially developed methods (e.g., immune radiometric assay) but is comparable to those of clinically accepted ELISA methods. The straightforward sample preparation (not prone to mistakes), reduced sample and reagent volumes (including the antibodies), and high throughput (10 samples/3 h) are advantages and therefore IP-MCGE bears potential for point-of-care diagnosis. PMID:25778394

  14. Sensitive detection of C-reactive protein in serum by immunoprecipitation-microchip capillary gel electrophoresis.

    PubMed

    Herwig, Ela; Marchetti-Deschmann, Martina; Wenz, Christian; Rüfer, Andreas; Redl, Heinz; Bahrami, Soheyl; Allmaier, Günter

    2015-06-01

    Sepsis represents a significant cause of mortality in intensive care units. Early diagnosis of sepsis is essential to increase the survival rate of patients. Among others, C-reactive protein (CRP) is commonly used as a sepsis marker. In this work we introduce immune precipitation combined with microchip capillary gel electrophoresis (IP-MCGE) for the detection and quantification of CRP in serum samples. First high-abundance proteins (HSA, IgG) are removed from serum samples using affinity spin cartridges, and then the remaining proteins are labeled with a fluorescence dye and incubated with an anti-CRP antibody, and the antigen/antibody complex is precipitated with protein G-coated magnetic beads. After precipitation the complex is eluted from the beads and loaded onto the MCGE system. CRP could be reliably detected and quantified, with a detection limit of 25 ng/μl in serum samples and 126 pg/μl in matrix-free samples. The overall sensitivity (LOQ = 75 ng/μl, R(2) = 0.9668) of the method is lower than that of some specially developed methods (e.g., immune radiometric assay) but is comparable to those of clinically accepted ELISA methods. The straightforward sample preparation (not prone to mistakes), reduced sample and reagent volumes (including the antibodies), and high throughput (10 samples/3 h) are advantages and therefore IP-MCGE bears potential for point-of-care diagnosis.

  15. DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures.

    PubMed

    Thomson, John P; Fawkes, Angie; Ottaviano, Raffaele; Hunter, Jennifer M; Shukla, Ruchi; Mjoseng, Heidi K; Clark, Richard; Coutts, Audrey; Murphy, Lee; Meehan, Richard R

    2015-05-14

    Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets.

  16. Detection of genes expressed in Bordetella bronchiseptica colonizing rat trachea by in vivo expressed-tag immunoprecipitation method.

    PubMed

    Abe, Hiroyuki; Kamitani, Shigeki; Fukui-Miyazaki, Aya; Shinzawa, Naoaki; Nakamura, Keiji; Horiguchi, Yasuhiko

    2015-05-01

    Analyses of bacterial genes expressed in response to the host environment provide clues to understanding the host-pathogen interactions that lead to the establishment of infection. In this study, a novel method named In Vivo Expressed-Tag ImmunoPrecipitation (IVET-PI) was developed for detecting genes expressed in bacteria that are recovered in a small numbers from host tissues. IVET-IP was designed to overcome some drawbacks of previous similar methods. We applied IVET-IP to Bordetella bronchiseptica colonizing rat trachea and identified 173 genes that were expressed in the bacteria over the entire course of an infection. These gene products included two transcriptional factors that are involved in the expression of filamentous hemagglutinin, adenylate cyclase toxin, and major virulence factors for the bordetellae. We consider that this method might provide novel insight into the course of Bordetella infection. PMID:25683445

  17. The brain as immunoprecipitator of serum autoantibodies against N-Methyl-D-aspartate receptor subunit NR1.

    PubMed

    Castillo-Gomez, Esther; Kästner, Anne; Steiner, Johann; Schneider, Anja; Hettling, Bilke; Poggi, Giulia; Ostehr, Kristin; Uhr, Manfred; Asif, Abdul R; Matzke, Mike; Schmidt, Ulrike; Pfander, Viktoria; Hammer, Christian; Schulz, Thomas F; Binder, Lutz; Stöcker, Winfried; Weber, Frank; Ehrenreich, Hannelore

    2016-01-01

    Autoantibodies (AB) against N-methyl-D-aspartate receptor subunit NR1 (NMDAR1) are highly seroprevalent in health and disease. Symptomatic relevance may arise upon compromised blood-brain barrier (BBB). However, it remained unknown whether circulating NMDAR1 AB appear in the cerebrospinal fluid (CSF). Of n = 271 subjects with CSF-serum pairs, 26 were NMDAR1 AB seropositive, but only 1 was CSF positive. Contrariwise, tetanus AB (non-brain-binding) were present in serum and CSF of all subjects, with CSF levels higher upon BBB dysfunction. Translational mouse experiments proved the hypothesis that the brain acts as an 'immunoprecipitator'; simultaneous injection of NMDAR1 AB and the non-brain-binding green fluorescent protein AB resulted in high detectability of the former in brain and the latter in CSF. PMID:26505629

  18. Detection of genes expressed in Bordetella bronchiseptica colonizing rat trachea by in vivo expressed-tag immunoprecipitation method.

    PubMed

    Abe, Hiroyuki; Kamitani, Shigeki; Fukui-Miyazaki, Aya; Shinzawa, Naoaki; Nakamura, Keiji; Horiguchi, Yasuhiko

    2015-05-01

    Analyses of bacterial genes expressed in response to the host environment provide clues to understanding the host-pathogen interactions that lead to the establishment of infection. In this study, a novel method named In Vivo Expressed-Tag ImmunoPrecipitation (IVET-PI) was developed for detecting genes expressed in bacteria that are recovered in a small numbers from host tissues. IVET-IP was designed to overcome some drawbacks of previous similar methods. We applied IVET-IP to Bordetella bronchiseptica colonizing rat trachea and identified 173 genes that were expressed in the bacteria over the entire course of an infection. These gene products included two transcriptional factors that are involved in the expression of filamentous hemagglutinin, adenylate cyclase toxin, and major virulence factors for the bordetellae. We consider that this method might provide novel insight into the course of Bordetella infection.

  19. Development of a Luciferase Immunoprecipitation System Assay To Detect IgG Antibodies against Human Respiratory Syncytial Virus Nucleoprotein

    PubMed Central

    Kumari, Sangeeta; Crim, Roberta Lynne; Kulkarni, Ashwin; Audet, Susette A.; Mdluli, Thembi; Murata, Haruhiko

    2014-01-01

    The nucleoprotein of respiratory syncytial virus (RSV-N) is immunogenic and elicits an IgG response following infection. The RSV-N gene was cloned into a mammalian expression vector, pREN2, and the expressed luciferase-tagged protein (Ruc-N) detected anti-RSV-N-specific IgG antibodies using a high-throughput immunoprecipitation method (the luciferase immunoprecipitation system [LIPS]-NRSV assay). The specificity of the assay was evaluated using monoclonal antibodies (MAbs) and monospecific pre- and postimmunization rabbit antisera. Blood serum samples from chimpanzees and humans with proven/probable RSV infection were also tested. The pre- and postimmunization serum samples from rabbits given human metapneumovirus (HMPV) or measles virus were negative when tested by the LIPS-NRSV assay, while antisera obtained after immunization with either the RSV-A or RSV-B strain gave positive signals in a dose-dependent manner. RSV-N MAb 858-3 gave a positive signal in the LIPS-NRSV assay, while MAbs against other paramyxovirus nucleoproteins or RSV-F or RSV-G did not. Serum samples from chimpanzees simultaneously immunized with vaccinia-RSV-F and vaccinia-RSV-G recombinant viruses were negative in the LIPS-NRSV assay; however, anti-RSV-N IgG responses were detected following subsequent RSV challenge. Seven of the 12 infants who were seronegative at 9 months of age had detectable anti-RSV-N antibodies when they were retested at 15 to 18 months of age. The LIPS-NRSV assay detects specific anti-RSV-N IgG responses that may be used as a biomarker of RSV infection. PMID:24403526

  20. Novel in vivo targets of ΔNp63 in keratinocytes identified by a modified chromatin immunoprecipitation approach

    PubMed Central

    Birkaya, Barbara; Ortt, Kori; Sinha, Satrajit

    2007-01-01

    Background p63 is a transcription factor that plays an important role in skin epidermal development and differentiation. The p63 gene encodes for two major protein isoforms, those containing an amino-terminal trans-activation domain (TAp63) and those lacking this domain (ΔNp63). Both the TA and ΔN transcripts are also alternatively spliced at the 3' end producing proteins with unique C-termini that are designated as α, β and γ isoforms. Recent research has suggested that ΔNp63 is the predominant isoform expressed and active in keratinocytes. Results To better elucidate the biological role of p63 in regulating gene expression in keratinocytes we performed chromatin immunoprecipitation (ChIP) experiments with ΔNp63-specific antibodies. We included an additional step in the ChIP procedure to enrich for ΔNp63 targets by screening the library of immunoprecipitated DNA for its ability to bind recombinant GST-ΔNp63. Cloning of ΔNp63-ChIP-derived DNA fragments identified more than 60 potential ΔNp63 target loci that were located close to or embedded within known or predicted genes. Identity of these target genes suggests that they may participate in a myriad of cellular processes including transcriptional regulation, signaling and metabolism. Here we confirm the binding of ΔNp63 to several of these genomic loci both by EMSA and replicate ChIP assays. Finally we show that the expression of many of these target genes is altered when ΔNp63 levels in keratinocytes are reduced by siRNA, further confirming that these are bona fide targets. Conclusion This unbiased genomic approach has allowed us to uncover functional targets of ΔNp63 and serves as the initial step in further analysis of the transcriptional regulatory mechanisms that are governed by p63 in keratinocytes. PMID:17521434

  1. Crystallization and preliminary X-ray analysis of the type IV restriction endonuclease ScoMcrA from Streptomyces coelicolor, which cleaves both Dcm-methylated DNA and phosphorothioated DNA.

    PubMed

    Liu, Guang; Zhang, Zhenyi; Zhao, Gong; Deng, Zixin; Wu, Geng; He, Xinyi

    2015-01-01

    ScoMcrA is a type IV modification-dependent restriction endonuclease found in the model strain Streptomyces coelicolor. Unlike type I, II and III restriction endonucleases, which cleave unmodified DNA, type IV restriction endonucleases cleave modified DNA, including methylated, hydroxymethylated, glucosyl-hydroxymethylated and phosphorothioated DNA. ScoMcrA targets both Dcm-methylated DNA and phosphorothioated DNA, and makes double-strand breaks 16-28 nt away from the modified nucleotides or the phosphorothioate links. However, the mechanism by which ScoMcrA recognizes these two entirely different types of modification remains unclear. In this study, the ScoMcrA protein was overexpressed, purified and crystallized. The crystals diffracted to 3.35 Å resolution and belonged to space group P2(1)2(1)2(1). The unit-cell parameters were determined to be a=130.19, b=139.36, c=281.01 Å, α=β=γ=90°. These results will facilitate the detailed structural analysis of ScoMcrA and further elucidation of its biochemical mechanism.

  2. High-efficiency solid-phase capture using glass beads bonded to microcentrifuge tubes: immunoprecipitation of proteins from cell extracts and assessment of ras activation.

    PubMed

    Chen, Jeffrey C; von Lintig, Friederike C; Jones, Stephen B; Huvar, Ivana; Boss, Gerry R

    2002-03-15

    We have bonded glass microbeads (425-600 microm diameter) to the inner walls of polypropylene microcentrifuge tubes. In addition to increasing the surface area of the tubes manyfold, the beads provide surface Si groups which can be reacted with a silane compound such as aminopropyltriethoxysilane, yielding a free amino group. The amino group is reacted with another cross-linking reagent, for example, the homobifunctional compound dimethyl suberimidate, which can form a covalent bond with amine groups of proteins. After binding protein A or G to the dimethyl suberimidate, the beads were used to immunoprecipitate proteins from cell extracts; we show that the protein A/G-coated glass beads yield similar amounts of immunoprecipitated proteins as a standard method using protein A- or G-agarose beads, but with fewer contaminating proteins. In addition, we show that when immunoprecipitating Ras from cell extracts and measuring the amounts of Ras-bound GTP and GDP, the new method yielded higher guanine nucleotide levels than protein G-agarose beads, suggesting that it caused less denaturation of Ras. Because the glass beads are bonded to the walls of the tubes, the immunoprecipitates can be washed rapidly and efficiently, and we show that 20-30 tubes can be washed in 1/10 the time required to wash immunoprecipitates on protein A- or G-agarose beads.

  3. Chromatin immunoprecipitation and multiplex sequencing (ChIP-Seq) to identify global transcription factor binding sites in the nematode Caenorhabditis elegans.

    PubMed

    Brdlik, Cathleen M; Niu, Wei; Snyder, Michael

    2014-01-01

    The global identification of transcription factor (TF) binding sites is a critical step in the elucidation of the functional elements of the genome. Several methods have been developed that map TF binding in human cells, yeast, and other model organisms. These methods make use of chromatin immunoprecipitation, or ChIP, and take advantage of the fact that formaldehyde fixation of living cells can be used to cross-link DNA sequences to the TFs that bind them in vivo. In ChIP, the cross-linked TF-DNA complexes are sheared by sonication, size fractionated, and incubated with antibody specific to the TF of interest to generate a library of TF-bound DNA sequences. ChIP-chip was the first technology developed to globally identify TF-bound DNA sequences and involves subsequent hybridization of the ChIP DNA to oligonucleotide microarrays. However, ChIP-chip proved to be costly, labor-intensive, and limited by the fixed number of probes available on the microarray chip. ChIP-Seq combines ChIP with massively parallel high-throughput sequencing (see Explanatory Chapter: Next Generation Sequencing) and has demonstrated vast improvement over ChIP-chip with respect to time and cost, signal-to-noise ratio, and resolution. In particular, multiplex sequencing can be used to achieve a higher throughput in ChIP-Seq analyses involving organisms with genomes of lower complexity than that of human (Lefrançois et al., 2009) and thereby reduce the cost and amount of time needed for each result. The multiplex ChIP-Seq method described in this section has been developed for Caenorhabditis elegans, but is easily adaptable for other organisms.

  4. Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans

    PubMed Central

    Mukhopadhyay, Arnab; Deplancke, Bart; Walhout, Albertha J M; Tissenbaum, Heidi A

    2009-01-01

    In order to determine how signaling pathways differentially regulate gene expression, it is necessary to identify the interactions between transcription factors (TFs) and their cognate cis-regulatory DNA elements. Here, we have outlined a chromatin immunoprecipitation (ChIP) protocol for use in whole Caenorhabditis elegans extracts. We discuss optimization of the procedure, including growth and harvesting of the worms, formaldehyde fixation, TF immunoprecipitation and analysis of bound sequences through real-time PCR. It takes ∼10–12 d to obtain the worm culture for ChIP; the ChIP procedure is spaced out over a period of 2.5 d with two overnight incubations. PMID:18388953

  5. Characterization of the Escherichia coli σS core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis

    PubMed Central

    Peano, Clelia; Wolf, Johannes; Demol, Julien; Rossi, Elio; Petiti, Luca; De Bellis, Gianluca; Geiselmann, Johannes; Egli, Thomas; Lacour, Stephan; Landini, Paolo

    2015-01-01

    In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with σ factors, accessory subunits able to direct RNA polymerase “core enzyme” (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the σS-associated RNA polymerase form (EσS) during transition from exponential to stationary phase. We identified 63 binding sites for EσS overlapping known or putative promoters, often located upstream of genes (encoding either ORFs or non-coding RNAs) showing at least some degree of dependence on the σS-encoding rpoS gene. EσS binding did not always correlate with an increase in transcription level, suggesting that, at some σS-dependent promoters, EσS might remain poised in a pre-initiation state upon binding. A large fraction of EσS-binding sites corresponded to promoters recognized by RNA polymerase associated with σ70 or other σ factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, EσS appears to contribute significantly to transcription of genes encoding proteins involved in LPS biosynthesis and in cell surface composition. Finally, our results highlight a direct role of EσS in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC. PMID:26020590

  6. Specific detection of peste des petits ruminants virus antibodies in sheep and goat sera by the luciferase immunoprecipitation system.

    PubMed

    Berguido, Francisco J; Bodjo, Sanne Charles; Loitsch, Angelika; Diallo, Adama

    2016-01-01

    Peste des petits ruminants (PPR) is a contagious and often fatal transboundary animal disease affecting mostly sheep, goats and wild small ruminants. This disease is endemic in most of Africa, the Middle, Near East, and large parts of Asia. The causal agent is peste des petits ruminants virus (PPRV), which belongs to the genus Morbillivirus in the family Paramyxoviridae. This genus also includes measles virus (MV), canine distemper virus (CDV) and rinderpest virus (RPV). All are closely related viruses with serological cross reactivity. In this study, we have developed a Luciferase Immunoprecipitation System (LIPS) for the rapid detection of antibodies against PPRV in serum samples and for specific differentiation from antibodies against RPV. PPR and rinderpest (RP) serum samples were assayed by PPR-LIPS and two commercially available PPR cELISA tests. The PPR-LIPS showed high sensitivity and specificity for the samples tested and showed no cross reactivity with RPV unlike the commercial PPR cELISA tests which did cross react with RPV. Based on the results shown in this study, PPR-LIPS is presented as a good candidate for the specific serosurveillance of PPR.

  7. MOBE-ChIP: a large-scale chromatin immunoprecipitation assay for cell type-specific studies.

    PubMed

    Lau, On Sun; Bergmann, Dominique C

    2015-10-01

    Cell type-specific transcriptional regulators play critical roles in the generation and maintenance of multicellularity. As they are often expressed at low levels, in vivo DNA-binding studies of these regulators by standard chromatin immunoprecipitation (ChIP) assays are technically challenging. We describe here an optimized ChIP protocol termed Maximized Objects for Better Enrichment (MOBE)-ChIP, which enhances the sensitivity of ChIP assays for detecting cell type-specific signals. The protocol, which is based on the disproportional increase of target signals over background at higher scales, uses substantially greater volume of starting materials than conventional ChIPs to achieve high signal enrichment. This technique can capture weak binding events that are ambiguous in standard ChIP assays, and is useful both in gene-specific and whole-genome analysis. This protocol has been optimized for Arabidopsis, but should be applicable to other model systems with minor modifications. The full procedure can be completed within 3 days.

  8. Specific detection of peste des petits ruminants virus antibodies in sheep and goat sera by the luciferase immunoprecipitation system.

    PubMed

    Berguido, Francisco J; Bodjo, Sanne Charles; Loitsch, Angelika; Diallo, Adama

    2016-01-01

    Peste des petits ruminants (PPR) is a contagious and often fatal transboundary animal disease affecting mostly sheep, goats and wild small ruminants. This disease is endemic in most of Africa, the Middle, Near East, and large parts of Asia. The causal agent is peste des petits ruminants virus (PPRV), which belongs to the genus Morbillivirus in the family Paramyxoviridae. This genus also includes measles virus (MV), canine distemper virus (CDV) and rinderpest virus (RPV). All are closely related viruses with serological cross reactivity. In this study, we have developed a Luciferase Immunoprecipitation System (LIPS) for the rapid detection of antibodies against PPRV in serum samples and for specific differentiation from antibodies against RPV. PPR and rinderpest (RP) serum samples were assayed by PPR-LIPS and two commercially available PPR cELISA tests. The PPR-LIPS showed high sensitivity and specificity for the samples tested and showed no cross reactivity with RPV unlike the commercial PPR cELISA tests which did cross react with RPV. Based on the results shown in this study, PPR-LIPS is presented as a good candidate for the specific serosurveillance of PPR. PMID:26506137

  9. Identification of cross-reactive promastigote cell surface antigens of some leishmanial stocks by 125I labeling and immunoprecipitation.

    PubMed Central

    Gardiner, P R; Jaffe, C L; Dwyer, D M

    1984-01-01

    Externally oriented surface membrane constituents of promastigotes from several Leishmania species were radiolabeled with 125I. Autoradiographs of cell surface-labeled and sodium dodecyl sulfate-polyacrylamide gel electrophoresis-separated proteins of the stocks revealed distinctive patterns of bands in the molecular weight range of 6,000 to 240,000. Immunoprecipitation of detergent extracts of the labeled promastigote stocks with anti-Leishmania donovani membrane serum demonstrated that each of the stocks contained some antigenically cross-reactive determinants. The electrophoretic patterns of these determinants serve both to distinguish the parasite stocks (by unique, species-specific patterns) and to indicate antigenic similarities in stocks thought to be different by other biochemical criteria. At least 12 cross-reactive cell surface antigens in two New World leishmanias are recognized by polyvalent anti-L. donovani serum, suggesting that these common leishmanial antigens may account for the documented serological cross-reactivities among various Leishmania species. In all stocks tested, an iodinated protein was identified which had a relative molecular weight of 65,000 under reducing conditions but which demonstrated an increase in relative mobility in sodium dodecyl sulfate-polyacrylamide gels under nonreducing conditions. Distinctive patterns of the antigens common to the several stocks were also demonstrated with the use of monoclonal antibodies. Images PMID:6363295

  10. Methylated DNA Binding Domain Protein 2 (MBD2) Coordinately Silences Gene Expression through Activation of the MicroRNA hsa-mir-496 Promoter in Breast Cancer Cell Line

    PubMed Central

    Alvarado, Sebastian; Wyglinski, Joanne; Suderman, Matthew; Andrews, Stephen A.; Szyf, Moshe

    2013-01-01

    Methylated DNA binding protein 2 (MBD2) binds methylated promoters and suppresses transcription in cis through recruitment of a chromatin modification repressor complex. We show here a new mechanism of action for MBD2: suppression of gene expression indirectly through activation of microRNA hsa-mir-496. Overexpression of MBD2 in breast epithelial cell line MCF-10A results in induced expression and demethylation of hsa-mir-496 while depletion of MBD2 in a human breast cancer cell lines MCF-7 and MDA-MB231 results in suppression of hsa-mir-496. Activation of hsa-mir-496 by MBD2 is associated with silencing of several of its target genes while depletion of MBD2 leads to induction of hsa-mir-496 target genes. Depletion of hsa-mir-496 by locked nucleic acid (LNA) antisense oligonucleotide leads to activation of these target genes in MBD2 overexpressing cells supporting that hsa-mir-496 is mediating in part the effects of MBD2 on gene expression. We demonstrate that MBD2 binds the promoter of hsa-mir-496 in MCF-10A, MCF-7 and MDA-MB-231 cells and that it activates an in vitro methylated hsa-mir-496 promoter driving a CG-less luciferase reporter in a transient transfection assay. The activation of hsa-mir-496 is associated with reduced methylation of the promoter. Taken together these results describe a novel cascade for gene regulation by DNA methylation whereby activation of a methylated microRNA by MBD2 that is associated with loss of methylation triggers repression of downstream targets. PMID:24204564

  11. Chromatin analyses of Zymoseptoria tritici: Methods for chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

    PubMed

    Soyer, Jessica L; Möller, Mareike; Schotanus, Klaas; Connolly, Lanelle R; Galazka, Jonathan M; Freitag, Michael; Stukenbrock, Eva H

    2015-06-01

    The presence or absence of specific transcription factors, chromatin remodeling machineries, chromatin modification enzymes, post-translational histone modifications and histone variants all play crucial roles in the regulation of pathogenicity genes. Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) provides an important tool to study genome-wide protein-DNA interactions to help understand gene regulation in the context of native chromatin. ChIP-seq is a convenient in vivo technique to identify, map and characterize occupancy of specific DNA fragments with proteins against which specific antibodies exist or which can be epitope-tagged in vivo. We optimized existing ChIP protocols for use in the wheat pathogen Zymoseptoria tritici and closely related sister species. Here, we provide a detailed method, underscoring which aspects of the technique are organism-specific. Library preparation for Illumina sequencing is described, as this is currently the most widely used ChIP-seq method. One approach for the analysis and visualization of representative sequence is described; improved tools for these analyses are constantly being developed. Using ChIP-seq with antibodies against H3K4me2, which is considered a mark for euchromatin or H3K9me3 and H3K27me3, which are considered marks for heterochromatin, the overall distribution of euchromatin and heterochromatin in the genome of Z. tritici can be determined. Our ChIP-seq protocol was also successfully applied to Z. tritici strains with high levels of melanization or aberrant colony morphology, and to different species of the genus (Z. ardabiliae and Z. pseudotritici), suggesting that our technique is robust. The methods described here provide a powerful framework to study new aspects of chromatin biology and gene regulation in this prominent wheat pathogen.

  12. Chromatin immunoprecipitation assays revealed CREB and serine 133 phospho-CREB binding to the CART gene proximal promoter

    PubMed Central

    Rogge, George A; Shen, Li-Ling; Kuhar, Michael J.

    2010-01-01

    Both over expression of cyclic AMP response element binding protein (CREB) in the nucleus accumbens (NAc), and intra-accumbal injection of cocaine- and amphetamine-regulated transcript (CART) peptides, have been shown to decrease cocaine reward. Also, over expression of CREB in the rat NAc increased CART mRNA and peptide levels, but it is not known if this was due to a direct action of P-CREB on the CART gene promoter. The goal of this study was to test if CREB and P-CREB bound directly to the CRE site in the CART promoter, using chromatin immunoprecipitation (ChIP) assays. ChIP assay with anti-CREB antibodies showed an enrichment of the CART promoter fragment containing the CRE region over IgG precipitated material, a non-specific control. Forskolin, which was known to increase CART mRNA levels in GH3 cells, was utilized to show that the drug increased levels of P-CREB protein and P-CREB binding to the CART promoter CRE-containing region. A region of the c-Fos promoter containing a CRE cis-regulatory element was previously shown to bind P-CREB, and it was used here as a positive control. These data suggest that the effects of CREB over expression on blunting cocaine reward could be, at least in part, attributed to the increased expression of the CART gene by direct interaction of P-CREB with the CART promoter CRE site, rather than by some indirect action. PMID:20451507

  13. P1 plasmid replication requires methylated DNA.

    PubMed Central

    Abeles, A L; Austin, S J

    1987-01-01

    Plasmids driven by the plasmid replication origin of bacteriophage P1 cannot be established in Escherichia coli strains that are defective for the DNA adenine methylase (dam). Using a composite plasmid that has two origins, we show that the P1 origin cannot function even in a plasmid that is already established in a dam strain. An in vitro replication system for the P1 origin was developed that uses as a substrate M13 replicative-form DNA containing the minimal P1 origin. The reaction mixture contains a crude extract of E. coli and purified P1 RepA protein. In addition to being RepA dependent, synthesis was shown to be dependent on methylation of the dam methylase-sensitive sites of the substrate DNA. As the P1 origin contains five such sites in a small region known to be critical for origin function, it can be concluded that methylation of these sites is a requirement for initiation. This suggests that the postreplicational methylation of the origin may control reinitiation and contribute to the accuracy of the highly stringent copy-number control of the origin in vivo. PMID:2826133

  14. Genomic response to Wnt signalling is highly context-dependent - Evidence from DNA microarray and chromatin immunoprecipitation screens of Wnt/TCF targets

    SciTech Connect

    Railo, Antti; Pajunen, Antti; Itaeranta, Petri; Naillat, Florence; Vuoristo, Jussi; Kilpelaeinen, Pekka; Vainio, Seppo

    2009-10-01

    Wnt proteins are important regulators of embryonic development, and dysregulated Wnt signalling is involved in the oncogenesis of several human cancers. Our knowledge of the downstream target genes is limited, however. We used a chromatin immunoprecipitation-based assay to isolate and characterize the actual gene segments through which Wnt-activatable transcription factors, TCFs, regulate transcription and an Affymetrix microarray analysis to study the global transcriptional response to the Wnt3a ligand. The anti-{beta}-catenin immunoprecipitation of DNA-protein complexes from mouse NIH3T3 fibroblasts expressing a fusion protein of {beta}-catenin and TCF7 resulted in the identification of 92 genes as putative TCF targets. GeneChip assays of gene expression performed on NIH3T3 cells and the rat pheochromocytoma cell line PC12 revealed 355 genes in NIH3T3 and 129 genes in the PC12 cells with marked changes in expression after Wnt3a stimulus. Only 2 Wnt-regulated genes were shared by both cell lines. Surprisingly, Disabled-2 was the only gene identified by the chromatin immunoprecipitation approach that displayed a marked change in expression in the GeneChip assay. Taken together, our approaches give an insight into the complex context-dependent nature of Wnt pathway transcriptional responses and identify Disabled-2 as a potential new direct target for Wnt signalling.

  15. Co-immunoprecipitation with Tau Isoform-specific Antibodies Reveals Distinct Protein Interactions and Highlights a Putative Role for 2N Tau in Disease*

    PubMed Central

    Liu, Chang; Song, Xiaomin; Nisbet, Rebecca

    2016-01-01

    Alternative splicing generates multiple isoforms of the microtubule-associated protein Tau, but little is known about their specific function. In the adult mouse brain, three Tau isoforms are expressed that contain either 0, 1, or 2 N-terminal inserts (0N, 1N, and 2N). We generated Tau isoform-specific antibodies and performed co-immunoprecipitations followed by tandem mass tag multiplexed quantitative mass spectrometry. We identified novel Tau-interacting proteins of which one-half comprised membrane-bound proteins, localized to the plasma membrane, mitochondria, and other organelles. Tau was also found to interact with proteins involved in presynaptic signal transduction. MetaCore analysis revealed one major Tau interaction cluster that contained 33 Tau pulldown proteins. To explore the pathways in which these proteins are involved, we conducted an ingenuity pathway analysis that revealed two significant overlapping pathways, “cell-to-cell signaling and interaction” and “neurological disease.” The functional enrichment tool DAVID showed that in particular the 2N Tau-interacting proteins were specifically associated with neurological disease. Finally, for a subset of Tau interactions (apolipoprotein A1 (apoA1), apoE, mitochondrial creatine kinase U-type, β-synuclein, synaptogyrin-3, synaptophysin, syntaxin 1B, synaptotagmin, and synapsin 1), we performed reverse co-immunoprecipitations, confirming the preferential interaction of specific isoforms. For example, apoA1 displayed a 5-fold preference for the interaction with 2N, whereas β-synuclein showed preference for 0N. Remarkably, a reverse immunoprecipitation with apoA1 detected only the 2N isoform. This highlights distinct protein interactions of the different Tau isoforms, suggesting that they execute different functions in brain tissue. PMID:26861879

  16. Immunoprecipitation and mass spectrometry identify non-cell autonomous Otx2 homeoprotein in the granular and supragranular layers of mouse visual cortex

    PubMed Central

    Kim, Namsuk; Acampora, Dario; Dingli, Florent; Loew, Damarys; Simeone, Antonio; Prochiantz, Alain; Di Nardo, Ariel A.

    2014-01-01

    Plasticity in the visual cerebral cortex is regulated by the internalization of Otx2 homeoprotein into parvalbumin neurons in cortical layers II/III and IV. However the Otx2 locus is not active in these neurons and the protein is imported from external sources, including the choroid plexus. Because Otx1 and Otx2 may have redundant functions, we wanted to verify if part of the staining in parvalbumin neurons corresponds to Otx1 transported from cortical layer V neurons. It is demonstrated here that Otx staining in layer IV cells is maintained in Otx1-null mice. The immunoprecipitation of extracts from finely dissected granular and supragranular cortex (layers I-IV) gave immunoblots with a band corresponding to Otx2 and not Otx1. Moreover, high-resolution mass spectrometry analysis after immunoprecipitation identifies two peptides within the Otx2 homeodomain. One of these peptides is specific for Otx2 and is not found in Otx1. These results unambiguously establish that the staining in parvalbumin neurons revealed with the anti-Otx2 antibodies used in our previous studies identifies non-cell autonomous Otx2. PMID:25165539

  17. Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies

    PubMed Central

    Gasper, William C.; Marinov, Georgi K.; Pauli-Behn, Florencia; Scott, Max T.; Newberry, Kimberly; DeSalvo, Gilberto; Ou, Susan; Myers, Richard M.; Vielmetter, Jost; Wold, Barbara J.

    2014-01-01

    Chromatin immunoprecipitation coupled with DNA sequencing (ChIP-seq) is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It identifies sites of transcription factor, cofactor and RNA polymerase occupancy, as well as the distribution of histone marks. Consortia such as the ENCyclopedia Of DNA Elements (ENCODE) have produced large datasets using manual protocols. However, future measurements of hundreds of additional factors in many cell types and physiological states call for higher throughput and consistency afforded by automation. Such automation advances, when provided by multiuser facilities, could also improve the quality and efficiency of individual small-scale projects. The immunoprecipitation process has become rate-limiting, and is a source of substantial variability when performed manually. Here we report a fully automated robotic ChIP (R-ChIP) pipeline that allows up to 96 reactions. A second bottleneck is the dearth of renewable ChIP-validated immune reagents, which do not yet exist for most mammalian transcription factors. We used R-ChIP to screen new mouse monoclonal antibodies raised against p300, a histone acetylase, well-known as a marker of active enhancers, for which ChIP-competent monoclonal reagents have been lacking. We identified, validated for ChIP-seq, and made publicly available a monoclonal reagent called ENCITp300-1. PMID:24919486

  18. Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis of the Penicillium chrysogenum Velvet Protein PcVelA Identifies Methyltransferase PcLlmA as a Novel Downstream Regulator of Fungal Development

    PubMed Central

    Becker, Kordula; Ziemons, Sandra; Lentz, Katharina; Freitag, Michael

    2016-01-01

    the molecular level. To address this issue, we performed ChIP-seq (chromatin immunoprecipitation in combination with next-generation sequencing) on and follow-up analysis of PcVelA, the core component of the velvet complex in P. chrysogenum. We demonstrate direct involvement of velvet in transcriptional control and present the putative methyltransferase PcLlmA as a new downstream factor and interaction partner of PcVelA. PMID:27570838

  19. Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis of the Penicillium chrysogenum Velvet Protein PcVelA Identifies Methyltransferase PcLlmA as a Novel Downstream Regulator of Fungal Development.

    PubMed

    Becker, Kordula; Ziemons, Sandra; Lentz, Katharina; Freitag, Michael; Kück, Ulrich

    2016-01-01

    molecular level. To address this issue, we performed ChIP-seq (chromatin immunoprecipitation in combination with next-generation sequencing) on and follow-up analysis of PcVelA, the core component of the velvet complex in P. chrysogenum. We demonstrate direct involvement of velvet in transcriptional control and present the putative methyltransferase PcLlmA as a new downstream factor and interaction partner of PcVelA. PMID:27570838

  20. Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis of the Penicillium chrysogenum Velvet Protein PcVelA Identifies Methyltransferase PcLlmA as a Novel Downstream Regulator of Fungal Development.

    PubMed

    Becker, Kordula; Ziemons, Sandra; Lentz, Katharina; Freitag, Michael; Kück, Ulrich

    2016-01-01

    molecular level. To address this issue, we performed ChIP-seq (chromatin immunoprecipitation in combination with next-generation sequencing) on and follow-up analysis of PcVelA, the core component of the velvet complex in P. chrysogenum. We demonstrate direct involvement of velvet in transcriptional control and present the putative methyltransferase PcLlmA as a new downstream factor and interaction partner of PcVelA.

  1. High-throughput sequencing of RNA isolated by cross-linking and immunoprecipitation (HITS-CLIP) to determine sites of binding of CstF-64 on nascent RNAs.

    PubMed

    Grozdanov, Petar N; Macdonald, Clinton C

    2014-01-01

    Genome-wide analysis of gene expression has changed the RNA world. Recent techniques leading to this revolution have been the use of cross-linking and immunoprecipitation (CLIP) combined with high-throughput sequencing (HITS-CLIP) to determine sites on nascent mRNAs to which RNA-binding proteins bind. Several researchers (including us) have been examining the role of RNA-binding proteins in polyadenylation, including the role of the 64,000 Mr component of the cleavage stimulation factor, CstF-64. In this chapter, we present our optimizations of the CLIP procedure for examination of CstF-64 binding to nascent pre-mRNAs expressed in testis. For CstF-64 CLIP, we use a well-characterized monoclonal antibody (3A7) that recognizes CstF-64. Rather than optimizing tricky but essential RNA fragment cloning schemes, we illustrate the use of the proprietary Illumina TruSeq Small RNA Sample Preparation kit for this step. Other techniques such as SDS-PAGE and the transfer to the nitrocellulose membrane techniques follow the original Illumina protocol (though we point out potential pitfalls). Finally, we discuss the options for high-throughput sequencing and some general suggestions for bioinformatic analysis of the data.

  2. Dynamic chromatin remodelling of ciliate macronuclear DNA as determined by an optimized chromatin immunoprecipitation (ChIP) method for Paramecium tetraurelia.

    PubMed

    Cheaib, Miriam; Simon, Martin

    2013-03-01

    We report the detailed evaluation of crucial parameters for chromatin immunoprecipitation (ChIP) of macronuclear DNA in the unicellular eukaryote Paramecium tetraurelia. Optimized parameters include crosslinking conditions, chromatin sonication and antibody titration thus providing a detailed protocol for successful ChIP in P. tetraurelia. As this ciliate is bacterivorous and RNAi by feeding represents a powerful tool for analysis of gene function, we moreover determined the effects of ingested nucleic acids by food bacteria. Feasibility of our protocol is demonstrated by characterisation of chromatin remodelling at promoters of cytosolic HSP70 isoforms during transcriptional activation under heat shock conditions by analyzing RNA abundance, nucleosome occupancy and levels of H3 lysine 9 acetylation.

  3. Detection of antibodies to varicella-zoster virus in recipients of the varicella vaccine by using a luciferase immunoprecipitation system assay.

    PubMed

    Cohen, Jeffrey I; Ali, Mir A; Bayat, Ahmad; Steinberg, Sharon P; Park, Hosun; Gershon, Anne A; Burbelo, Peter D

    2014-09-01

    A high-throughput test to detect varicella-zoster virus (VZV) antibodies in varicella vaccine recipients is not currently available. One of the most sensitive tests for detecting VZV antibodies after vaccination is the fluorescent antibody to membrane antigen (FAMA) test. Unfortunately, this test is labor-intensive, somewhat subjective to read, and not commercially available. Therefore, we developed a highly quantitative and high-throughput luciferase immunoprecipitation system (LIPS) assay to detect antibody to VZV glycoprotein E (gE). Tests of children who received the varicella vaccine showed that the gE LIPS assay had 90% sensitivity and 70% specificity, a viral capsid antigen enzyme-linked immunosorbent assay (ELISA) had 67% and 87% specificity, and a glycoprotein ELISA (not commercially available in the United States) had 94% sensitivity and 74% specificity compared with the FAMA test. The rates of antibody detection by the gE LIPS and glycoprotein ELISA were not statistically different. Therefore, the gE LIPS assay may be useful for detecting VZV antibodies in varicella vaccine recipients. (This study has been registered at ClinicalTrials.gov under registration no. NCT00921999.).

  4. Identification of C/EBPβ Target Genes in ALK+ Anaplastic Large Cell Lymphoma (ALCL) by Gene Expression Profiling and Chromatin Immunoprecipitation

    PubMed Central

    Bonzheim, Irina; Irmler, Martin; Klier-Richter, Margit; Steinhilber, Julia; Anastasov, Nataša; Schäfer, Sabine; Adam, Patrick; Beckers, Johannes; Raffeld, Mark; Fend, Falko; Quintanilla-Martinez, Leticia

    2013-01-01

    C/EBPβ (CCAAT enhancer binding protein) is a transcription factor that plays a crucial role in survival and transformation of ALK+ anaplastic large cell lymphoma (ALCL). The aim of this study was to identify the downstream targets of C/EBPβ responsible for ALK-mediated oncogenesis. C/EBPβ was knocked down in ALK+ ALCL cell lines with a C/EBPβ-shRNA, followed by gene expression profiling (GEP). GEP analysis revealed a reproducible signature of genes that were significantly regulated by C/EBPβ. Classification into biological categories revealed overrepresentation of genes involved in the immune response, apoptosis and cell proliferation. Transcriptional regulation by C/EBPβ was found in 6 of 11 (BCL2A1, G0S2, TRIB1, S100A9, DDX21 and DDIT4) genes investigated by chromatin immunoprecipitation. We demonstrated that BCL2A1, G0S2 and DDX21 play a crucial role in survival and proliferation of ALK+ ALCL cells. DDX21, a gene involved in rRNA biogenesis, was found differentially overexpressed in primary ALK+ ALCL cases. All three candidate genes were validated in primary ALCL cases by either immunohistochemistry or RT-qPCR. In conclusion, we identified and validated several key C/EBPβ-regulated genes with major impact on survival and cell growth in ALK+ ALCL, supporting the central role of C/EBPβ in ALK-mediated oncogenesis. PMID:23741337

  5. The antigens of the chick blastula: a comparison between the epiblast, primary hypoblast, yolk entoderm, and extraembryonic yolk by immunoprecipitation in agar.

    PubMed

    Wolk, M; Schlesinger, M; Eyal-Giladi, H

    1982-01-01

    Antisera to chicken embryo epiblast, primary hypoblast, extraembryonic yolk, and yolk entoderm were elicited in rabbits. Extracts from the different sources were tested for their immunoprecipitation by these antisera in immunoelectrophoresis and double diffusion in agar (Ouchterlony) tests. The main findings were as follows: 1) Antigens recovered in the soluble fractions of the cells of the full hypoblast stage (Eyal-Giladi and Kochav, Stage XIII) are immunologically identical to antigens from the extraembryonic yolk, 2) Similar patterns of precipitation lines were formed between the soluble fractions of both the epiblast and primary hypoblast, and the different antisera. The epiblast and the primary hypoblast differed in 1-2 precipitation lines only, 3) The most prominent antigenic differences between the primary hypoblast and the epiblast reside in the microsomal fraction as revealed by immunoelectrophoresis, and 4) For all four sources of antigens which were compared, it was found that the electrophoretic mobility of the antigens migrating closest to the catodic end is modified according to the ratio of solvent to solute during the preparation of the lyophilized antigen.

  6. Chromatin immunoprecipitation analysis of bortezomib-mediated inhibition of NFκB recruitment to IL-1β and TNFα gene promoters in human macrophages.

    PubMed

    Sanacora, Shannon; Chang, Tzu-Pei; Vancurova, Ivana

    2014-01-01

    Interleukin-1β (IL-1) and tumor necrosis factor-α (TNF) are important pro-inflammatory cytokines involved in the mediation of the immune response, inflammation, tissue repair, and tumor progression. Regulation of IL-1 and TNF expression is mediated at the level of transcription by the transcription factor NFκB. Inhibition of NFκB activity by the proteasome inhibitor bortezomib (BZ) has been used as a frontline therapy in multiple myeloma and other hematological malignancies. In this chapter, we describe a protocol that uses chromatin immunoprecipitation (ChIP) to analyze the NFκB recruitment to endogenous IL-1 and TNF promoters in BZ-treated human macrophages. Corresponding to the BZ-suppressed mRNA levels of IL-1 and TNF, we show that BZ inhibits p65 NFκB recruitment to IL-1 and TNF promoters. This study specifically uses U937 macrophages, but the protocol could be easily modified to analyze the regulation of NFκB recruitment in other cell types. PMID:24908318

  7. Chromatin immunoprecipitation analysis of bortezomib-mediated inhibition of NFκB recruitment to IL-1β and TNFα gene promoters in human macrophages.

    PubMed

    Sanacora, Shannon; Chang, Tzu-Pei; Vancurova, Ivana

    2014-01-01

    Interleukin-1β (IL-1) and tumor necrosis factor-α (TNF) are important pro-inflammatory cytokines involved in the mediation of the immune response, inflammation, tissue repair, and tumor progression. Regulation of IL-1 and TNF expression is mediated at the level of transcription by the transcription factor NFκB. Inhibition of NFκB activity by the proteasome inhibitor bortezomib (BZ) has been used as a frontline therapy in multiple myeloma and other hematological malignancies. In this chapter, we describe a protocol that uses chromatin immunoprecipitation (ChIP) to analyze the NFκB recruitment to endogenous IL-1 and TNF promoters in BZ-treated human macrophages. Corresponding to the BZ-suppressed mRNA levels of IL-1 and TNF, we show that BZ inhibits p65 NFκB recruitment to IL-1 and TNF promoters. This study specifically uses U937 macrophages, but the protocol could be easily modified to analyze the regulation of NFκB recruitment in other cell types.

  8. Detection of a rare BCR-ABL tyrosine kinase fusion protein in H929 multiple myeloma cells using immunoprecipitation (IP)-tandem mass spectrometry (MS/MS).

    PubMed

    Breitkopf, Susanne B; Yuan, Min; Pihan, German A; Asara, John M

    2012-10-01

    Hypothesis directed proteomics offers higher throughput over global analyses. We show that immunoprecipitation (IP)-tandem mass spectrometry (LC-MS/MS) in H929 multiple myeloma (MM) cancer cells led to the discovery of a rare and unexpected BCR-ABL fusion, informing a therapeutic intervention using imatinib (Gleevec). BCR-ABL is the driving mutation in chronic myeloid leukemia (CML) and is uncommon to other cancers. Three different IP-MS experiments central to cell signaling pathways were sufficient to discover a BCR-ABL fusion in H929 cells: phosphotyrosine (pY) peptide IP, p85 regulatory subunit of phosphoinositide-3-kinase (PI3K) IP, and the GRB2 adaptor IP. The pY peptides inform tyrosine kinase activity, p85 IP informs the activating adaptors and receptor tyrosine kinases (RTKs) involved in AKT activation and GRB2 IP identifies RTKs and adaptors leading to ERK activation. Integration of the bait-prey data from the three separate experiments identified the BCR-ABL protein complex, which was confirmed by biochemistry, cytogenetic methods, and DNA sequencing revealed the e14a2 fusion transcript. The tyrosine phosphatase SHP2 and the GAB2 adaptor protein, important for MAPK signaling, were common to all three IP-MS experiments. The comparative treatment of tyrosine kinase inhibitor (TKI) drugs revealed only imatinib, the standard of care in CML, was inhibitory to BCR-ABL leading to down-regulation of pERK and pS6K and inhibiting cell proliferation. These data suggest a model for directed proteomics from patient tumor samples for selecting the appropriate TKI drug(s) based on IP and LC-MS/MS. The data also suggest that MM patients, in addition to CML patients, may benefit from BCR-ABL diagnostic screening.

  9. Genome-Wide Mapping of the Distribution of CarD, RNAP σ(A), and RNAP β on the Mycobacterium smegmatis Chromosome using Chromatin Immunoprecipitation Sequencing.

    PubMed

    Landick, Robert; Krek, Azra; Glickman, Michael S; Socci, Nicholas D; Stallings, Christina L

    2014-12-01

    CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis (6). We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed Chromatin Immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σ(A) were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σ(A) would be predominantly enriched at promoters based on work in Escherichia coli (3), however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σ(A). The colocalization of σ(A) and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 (5) as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164).

  10. Genome-wide mapping of the distribution of CarD, RNAP σA, and RNAP β on the Mycobacterium smegmatis chromosome using chromatin immunoprecipitation sequencing

    PubMed Central

    Landick, Robert; Krek, Azra; Glickman, Michael S.; Socci, Nicholas D.; Stallings, Christina L.

    2014-01-01

    CarD is an essential mycobacterial protein that binds the RNA polymerase (RNAP) and affects the transcriptional profile of Mycobacterium smegmatis and Mycobacterium tuberculosis [6]. We predicted that CarD was directly regulating RNAP function but our prior experiments had not determined at what stage of transcription CarD was functioning and at which genes CarD interacted with the RNAP. To begin to address these open questions, we performed chromatin immunoprecipitation sequencing (ChIP-seq) to survey the distribution of CarD throughout the M. smegmatis chromosome. The distribution of RNAP subunits β and σA were also profiled. We expected that RNAP β would be present throughout transcribed regions and RNAP σA would be predominantly enriched at promoters based on work in Escherichia coli [3], however this had yet to be determined in mycobacteria. The ChIP-seq analyses revealed that CarD was never present on the genome in the absence of RNAP, was primarily associated with promoter regions, and was highly correlated with the distribution of RNAP σA. The colocalization of σA and CarD led us to propose that in vivo, CarD associates with RNAP initiation complexes at most promoters and is therefore a global regulator of transcription initiation. Here we describe in detail the data from the ChIP-seq experiments associated with the study published by Srivastava and colleagues in the Proceedings of the National Academy of Science in 2013 [5] as well as discuss the findings from this dataset in relation to both CarD and mycobacterial transcription as a whole. The ChIP-seq data have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE48164). PMID:25089258

  11. Adenosine A1( )receptors are selectively coupled to Gα(i-3) in postmortem human brain cortex: Guanosine-5'-O-(3-[(35)S]thio)triphosphate ([(35)S]GTPγS) binding/immunoprecipitation study.

    PubMed

    Odagaki, Yuji; Kinoshita, Masakazu; Ota, Toshio; Meana, J Javier; Callado, Luis F; García-Sevilla, Jesús A

    2015-10-01

    By means of guanosine-5'-O-(3-[(35)S]thio)triphosphate ([(35)S]GTPγS) binding assay combined with immunoprecipitation using anti-Gα subunit antibody, we recently reported 5-HT2A receptor- and M1 muscarinic acetylcholine receptor-mediated Gαq activation in rat cerebral cortical membranes (Odagaki et al., 2014). In the present study, this method has been applied to postmortem human brains, with focusing on adenosine receptor-mediated G-protein activation. In the exploratory experiments using a series of agonists and the antibodies specific to each Gα subtypes in the presence of low (10 nM) or high (50 μM) concentration of GDP, the most prominent increases in specific [(35)S]GTPγS binding in the membranes prepared from human prefrontal cortex were obtained for the combinations of adenosine (1mM)/anti-Gαi-3 in the presence of 50 μM GDP as well as 5-HT (100 μM)/anti-Gαq and carbachol (1mM)/anti-Gαq in the presence of 10nM GDP. Adenosine-induced activation of Gαi-3 emerged only when GDP concentrations were increased higher than 10 μM, and the following experiments were performed in the presence of 300 μM GDP. Adenosine increased specific [(35)S]GTPγS binding to Gαi-3 in a concentration-dependent manner to 251.4% of the basal unstimulated binding, with an EC50 of 1.77 μM. The involvement of adenosine A1 receptor was verified by the experiments using selective agonists and antagonists at adenosine A1 or A3 receptor. Among the α subunits of Gi/o class (Gαi-1, Gαi-2, Gαi-3, and Gαo.), only Gαi-3 was activated by 1mM adenosine, indicating that human brain adenosine A1 receptor is coupled preferentially, if not exclusively, to Gαi-3.

  12. Adenosine A1( )receptors are selectively coupled to Gα(i-3) in postmortem human brain cortex: Guanosine-5'-O-(3-[(35)S]thio)triphosphate ([(35)S]GTPγS) binding/immunoprecipitation study.

    PubMed

    Odagaki, Yuji; Kinoshita, Masakazu; Ota, Toshio; Meana, J Javier; Callado, Luis F; García-Sevilla, Jesús A

    2015-10-01

    By means of guanosine-5'-O-(3-[(35)S]thio)triphosphate ([(35)S]GTPγS) binding assay combined with immunoprecipitation using anti-Gα subunit antibody, we recently reported 5-HT2A receptor- and M1 muscarinic acetylcholine receptor-mediated Gαq activation in rat cerebral cortical membranes (Odagaki et al., 2014). In the present study, this method has been applied to postmortem human brains, with focusing on adenosine receptor-mediated G-protein activation. In the exploratory experiments using a series of agonists and the antibodies specific to each Gα subtypes in the presence of low (10 nM) or high (50 μM) concentration of GDP, the most prominent increases in specific [(35)S]GTPγS binding in the membranes prepared from human prefrontal cortex were obtained for the combinations of adenosine (1mM)/anti-Gαi-3 in the presence of 50 μM GDP as well as 5-HT (100 μM)/anti-Gαq and carbachol (1mM)/anti-Gαq in the presence of 10nM GDP. Adenosine-induced activation of Gαi-3 emerged only when GDP concentrations were increased higher than 10 μM, and the following experiments were performed in the presence of 300 μM GDP. Adenosine increased specific [(35)S]GTPγS binding to Gαi-3 in a concentration-dependent manner to 251.4% of the basal unstimulated binding, with an EC50 of 1.77 μM. The involvement of adenosine A1 receptor was verified by the experiments using selective agonists and antagonists at adenosine A1 or A3 receptor. Among the α subunits of Gi/o class (Gαi-1, Gαi-2, Gαi-3, and Gαo.), only Gαi-3 was activated by 1mM adenosine, indicating that human brain adenosine A1 receptor is coupled preferentially, if not exclusively, to Gαi-3. PMID:26213104

  13. PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins.

    PubMed

    Spitzer, Jessica; Hafner, Markus; Landthaler, Markus; Ascano, Manuel; Farazi, Thalia; Wardle, Greg; Nusbaum, Jeff; Khorshid, Mohsen; Burger, Lukas; Zavolan, Mihaela; Tuschl, Thomas

    2014-01-01

    We recently developed a protocol for the transcriptome-wide isolation of RNA recognition elements readily applicable to any protein or ribonucleoprotein complex directly contacting RNA (including RNA helicases, polymerases, or nucleases) expressed in cell culture models either naturally or ectopically (Hafner et al., 2010). Briefly, immunoprecipitation of the RNA-binding protein of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. In the course of lysate preparation and immunoprecipitation, the mRNAs are partially degraded using Ribonuclease T1. The isolated crosslinked RNA fragments are converted into a cDNA library and deep-sequenced using Solexa technology (see Explanatory Chapter: Next Generation Sequencing). By introducing photoreactive nucleosides that generate characteristic sequence changes upon crosslinking (see below), our protocol allows one to separate RNA segments bound by the protein of interest from the background un-crosslinked RNAs.

  14. PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a Step-By-Step Protocol to the Transcriptome-Wide Identification of Binding Sites of RNA-Binding Proteins

    PubMed Central

    Spitzer, Jessica; Hafner, Markus; Landthaler, Markus; Ascano, Manuel; Farazi, Thalia; Wardle, Greg; Nusbaum, Jeff; Khorshid, Mohsen; Burger, Lukas; Zavolan, Mihaela; Tuschl, Thomas

    2014-01-01

    We recently developed a protocol for the transcriptome-wide isolation of RNA recognition elements readily applicable to any protein or ribonucleoprotein complex directly contacting RNA (including RNA helicases, polymerases, or nucleases) expressed in cell culture models either naturally or ectopically (Hafner et al., 2010). Briefly, immunoprecipitation of the RNA-binding protein of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. In the course of lysate preparation and immunoprecipitation, the mRNAs are partially degraded using Ribonu-clease T1. The isolated crosslinked RNA fragments are converted into a cDNA library and deep-sequenced using Solexa technology (see Explanatory Chapter: Next Generation Sequencing). By introducing photoreactive nucleosides that generate characteristic sequence changes upon crosslinking (see below), our protocol allows one to separate RNA segments bound by the protein of interest from the background un-crosslinked RNAs. PMID:24581442

  15. COMBINES AND COMBINING.

    ERIC Educational Resources Information Center

    RIDENOUR, HARLAN E.

    THROUGH THE USE OF THIS MANUAL, VOCATIONAL AGRICULTURE STUDENTS WITH OCCUPATIONAL INTEREST IN GRAIN FARMING AND CUSTOM COMBINE OPERATION MAY GAIN KNOWLEDGE ABOUT THE BASIC DESIGN AND OPERATION OF COMBINES. DEVELOPMENT BY A STATE CURRICULUM MATERIALS DIRECTOR INCLUDED CONSULTATION WITH ENGINEERS, TRIAL, AND REVISION. OBJECTIVES ARE STATED IN TERMS…

  16. Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins

    PubMed Central

    Fujii, Hodaka; Fujita, Toshitsugu

    2015-01-01

    Comprehensive understanding of genome functions requires identification of molecules (proteins, RNAs, genomic regions, etc.) bound to specific genomic regions of interest in vivo. To perform biochemical and molecular biological analysis of specific genomic regions, we developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) to purify genomic regions of interest. In enChIP, specific genomic regions are tagged for biochemical purification using engineered DNA-binding molecules, such as transcription activator-like (TAL) proteins and a catalytically inactive form of the clustered regularly interspaced short palindromic repeats (CRISPR) system. enChIP is a comprehensive approach that emphasizes non-biased search using next-generation sequencing (NGS), microarrays, mass spectrometry (MS), and other methods. Moreover, this approach is not restricted to cultured cell lines and can be easily extended to organisms. In this review, we discuss applications of enChIP to elucidating the molecular mechanisms underlying genome functions. PMID:26370991

  17. Isolation of Specific Genomic Regions and Identification of Their Associated Molecules by Engineered DNA-Binding Molecule-Mediated Chromatin Immunoprecipitation (enChIP) Using the CRISPR System and TAL Proteins.

    PubMed

    Fujii, Hodaka; Fujita, Toshitsugu

    2015-09-09

    Comprehensive understanding of genome functions requires identification of molecules (proteins, RNAs, genomic regions, etc.) bound to specific genomic regions of interest in vivo. To perform biochemical and molecular biological analysis of specific genomic regions, we developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) to purify genomic regions of interest. In enChIP, specific genomic regions are tagged for biochemical purification using engineered DNA-binding molecules, such as transcription activator-like (TAL) proteins and a catalytically inactive form of the clustered regularly interspaced short palindromic repeats (CRISPR) system. enChIP is a comprehensive approach that emphasizes non-biased search using next-generation sequencing (NGS), microarrays, mass spectrometry (MS), and other methods. Moreover, this approach is not restricted to cultured cell lines and can be easily extended to organisms. In this review, we discuss applications of enChIP to elucidating the molecular mechanisms underlying genome functions.

  18. Quantitative Characterization of E-selectin Interaction with Native CD44 and P-selectin Glycoprotein Ligand-1 (PSGL-1) Using a Real Time Immunoprecipitation-based Binding Assay*

    PubMed Central

    AbuSamra, Dina B.; Al-Kilani, Alia; Hamdan, Samir M.; Sakashita, Kosuke; Gadhoum, Samah Z.; Merzaban, Jasmeen S.

    2015-01-01

    Selectins (E-, P-, and L-selectins) interact with glycoprotein ligands to mediate the essential tethering/rolling step in cell transport and delivery that captures migrating cells from the circulating flow. In this work, we developed a real time immunoprecipitation assay on a surface plasmon resonance chip that captures native glycoforms of two well known E-selectin ligands (CD44/hematopoietic cell E-/L-selectin ligand and P-selectin glycoprotein ligand-1) from hematopoietic cell extracts. Here we present a comprehensive characterization of their binding to E-selectin. We show that both ligands bind recombinant monomeric E-selectin transiently with fast on- and fast off-rates, whereas they bind dimeric E-selectin with remarkably slow on- and off-rates. This binding requires the sialyl Lewis x sugar moiety to be placed on both O- and N-glycans, and its association, but not dissociation, is sensitive to the salt concentration. Our results suggest a mechanism through which monomeric selectins mediate initial fast on and fast off kinetics to help capture cells out of the circulating shear flow; subsequently, tight binding by dimeric/oligomeric selectins is enabled to significantly slow rolling. PMID:26124272

  19. Combination Vaccines

    PubMed Central

    Skibinski, David AG; Baudner, Barbara C; Singh, Manmohan; O’Hagan, Derek T

    2011-01-01

    The combination of diphtheria, tetanus, and pertussis vaccines into a single product has been central to the protection of the pediatric population over the past 50 years. The addition of inactivated polio, Haemophilus influenzae, and hepatitis B vaccines into the combination has facilitated the introduction of these vaccines into recommended immunization schedules by reducing the number of injections required and has therefore increased immunization compliance. However, the development of these combinations encountered numerous challenges, including the reduced response to Haemophilus influenzae vaccine when given in combination; the need to consolidate the differences in the immunization schedule (hepatitis B); and the need to improve the safety profile of the diphtheria, tetanus, and pertussis combination. Here, we review these challenges and also discuss future prospects for combination vaccines. PMID:21572611

  20. Power combiner

    SciTech Connect

    Arnold, Mobius; Ives, Robert Lawrence

    2006-09-05

    A power combiner for the combining of symmetric and asymmetric traveling wave energy comprises a feed waveguide having an input port and a launching port, a reflector for reflecting launched wave energy, and a final waveguide for the collection and transport of launched wave energy. The power combiner has a launching port for symmetrical waves which comprises a cylindrical section coaxial to the feed waveguide, and a launching port for asymmetric waves which comprises a sawtooth rotated about a central axis.

  1. Chromatin immunoprecipitation analysis of the tobacco PR-1a- and the truncated CaMV 35S promoter reveals differences in salicylic acid-dependent TGA factor binding and histone acetylation.

    PubMed

    Butterbrodt, Thomas; Thurow, Corinna; Gatz, Christiane

    2006-07-01

    Salicylic acid (SA) is a plant signalling molecule needed for the induction of defence responses upon attack by a variety of pathogens. Truncation of the Cauliflower Mosaic Virus (CaMV) 35S promoter down to 90 bp has identified activation sequence-1 (as-1) as an autonomous SA-responsive cis element. The as-1-like elements are found in a number of SA-inducible promoters like e.g. the tobacco PR-1a promoter. They are recognized by basic/leucine zipper (bZIP) transcription factors of the TGA family. In tobacco leaves, TGA2.2 is the most abundant TGA factor. TGA2.2 is required for the expression of as-1-containing promoters. Here we unravel clear differences between the "truncated" CaMV 35S and the PR-1a promoter with respect to in vivo TGA binding and histone acetylation. Chromatin immunoprecipitation (ChIP) analysis revealed SA-inducible recruitment of tobacco TGA2.2 as well as SA-inducible histone acetylation at the PR-1a promoter. In contrast, no influence of SA on TGA2.2 binding and histone acetylation was detectable at the "truncated" CaMV 35S promoter. The finding of SA-independent TGA factor binding in the absence of additional flanking regulatory sequences suggests that transcriptional activation is not necessarily mediated by inducible DNA binding of TGA factors. Plants with severely reduced TGA2.2 protein levels also showed SA-induced histone acetylation at the PR-1a promoter indicating that regulatory events independent from TGA2.2 function are initiated at the PR-1a promoter.

  2. Genome-Wide Chromatin Immunoprecipitation Sequencing Analysis Shows that WhiB Is a Transcription Factor That Cocontrols Its Regulon with WhiA To Initiate Developmental Cell Division in Streptomyces

    PubMed Central

    Chandra, Govind; Bibb, Maureen J.; Findlay, Kim C.; Buttner, Mark J.

    2016-01-01

    ABSTRACT WhiB is the founding member of a family of proteins (the WhiB-like [Wbl] family) that carry a [4Fe-4S] iron-sulfur cluster and play key roles in diverse aspects of the biology of actinomycetes, including pathogenesis, antibiotic resistance, and the control of development. In Streptomyces, WhiB is essential for the process of developmentally controlled cell division that leads to sporulation. The biochemical function of Wbl proteins has been controversial; here, we set out to determine unambiguously if WhiB functions as a transcription factor using chromatin immunoprecipitation sequencing (ChIP-seq) in Streptomyces venezuelae. In the first demonstration of in vivo genome-wide Wbl binding, we showed that WhiB regulates the expression of key genes required for sporulation by binding upstream of ~240 transcription units. Strikingly, the WhiB regulon is identical to the previously characterized WhiA regulon, providing an explanation for the identical phenotypes of whiA and whiB mutants. Using ChIP-seq, we demonstrated that in vivo DNA binding by WhiA depends on WhiB and vice versa, showing that WhiA and WhiB function cooperatively to control expression of a common set of WhiAB target genes. Finally, we show that mutation of the cysteine residues that coordinate the [4Fe-4S] cluster in WhiB prevents DNA binding by both WhiB and WhiA in vivo. PMID:27094333

  3. Mechanism of insulin gene regulation by the pancreatic transcription factor Pdx-1: application of pre-mRNA analysis and chromatin immunoprecipitation to assess formation of functional transcriptional complexes.

    PubMed

    Iype, Tessy; Francis, Joshua; Garmey, James C; Schisler, Jonathan C; Nesher, Rafael; Weir, Gordon C; Becker, Thomas C; Newgard, Christopher B; Griffen, Steven C; Mirmira, Raghavendra G

    2005-04-29

    The homeodomain factor Pdx-1 regulates an array of genes in the developing and mature pancreas, but whether regulation of each specific gene occurs by a direct mechanism (binding to promoter elements and activating basal transcriptional machinery) or an indirect mechanism (via regulation of other genes) is unknown. To determine the mechanism underlying regulation of the insulin gene by Pdx-1, we performed a kinetic analysis of insulin transcription following adenovirus-mediated delivery of a small interfering RNA specific for pdx-1 into insulinoma cells and pancreatic islets to diminish endogenous Pdx-1 protein. insulin transcription was assessed by measuring both a long half-life insulin mRNA (mature mRNA) and a short half-life insulin pre-mRNA species by real-time reverse transcriptase-PCR. Following progressive knock-down of Pdx-1 levels, we observed coordinate decreases in pre-mRNA levels (to about 40% of normal levels at 72 h). In contrast, mature mRNA levels showed strikingly smaller and delayed declines, suggesting that the longer half-life of this species underestimates the contribution of Pdx-1 to insulin transcription. Chromatin immunoprecipitation assays revealed that the decrease in insulin transcription was associated with decreases in the occupancies of Pdx-1 and p300 at the proximal insulin promoter. Although there was no corresponding change in the recruitment of RNA polymerase II to the proximal promoter, its recruitment to the insulin coding region was significantly reduced. Our results suggest that Pdx-1 directly regulates insulin transcription through formation of a complex with transcriptional coactivators on the proximal insulin promoter. This complex leads to enhancement of elongation by the basal transcriptional machinery.

  4. Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data

    PubMed Central

    Sharov, Alexei A; Masui, Shinji; Sharova, Lioudmila V; Piao, Yulan; Aiba, Kazuhiro; Matoba, Ryo; Xin, Li; Niwa, Hitoshi; Ko, Minoru SH

    2008-01-01

    Background Target genes of a transcription factor (TF) Pou5f1 (Oct3/4 or Oct4), which is essential for pluripotency maintenance and self-renewal of embryonic stem (ES) cells, have previously been identified based on their response to Pou5f1 manipulation and occurrence of Chromatin-immunoprecipitation (ChIP)-binding sites in promoters. However, many responding genes with binding sites may not be direct targets because response may be mediated by other genes and ChIP-binding site may not be functional in terms of transcription regulation. Results To reduce the number of false positives, we propose to separate responding genes into groups according to direction, magnitude, and time of response, and to apply the false discovery rate (FDR) criterion to each group individually. Using this novel algorithm with stringent statistical criteria (FDR < 0.2) to a compendium of published and new microarray data (3, 6, 12, and 24 hr after Pou5f1 suppression) and published ChIP data, we identified 420 tentative target genes (TTGs) for Pou5f1. The majority of TTGs (372) were down-regulated after Pou5f1 suppression, indicating that the Pou5f1 functions as an activator of gene expression when it binds to promoters. Interestingly, many activated genes are potent suppressors of transcription, which include polycomb genes, zinc finger TFs, chromatin remodeling factors, and suppressors of signaling. Similar analysis showed that Sox2 and Nanog also function mostly as transcription activators in cooperation with Pou5f1. Conclusion We have identified the most reliable sets of direct target genes for key pluripotency genes – Pou5f1, Sox2, and Nanog, and found that they predominantly function as activators of downstream gene expression. Thus, most genes related to cell differentiation are suppressed indirectly. PMID:18522731

  5. Combinations Therapies.

    PubMed

    Reinmuth, Niels; Reck, Martin

    2015-01-01

    Immunotherapy of cancer encompasses different strategies that elicit or enhance the immune response against tumors. The first results from clinical studies have provided promising data for the treatment of lung cancer patients with immunomodulating monotherapies. To improve the potential benefit of cancer immunotherapy, synergistic combinations of the various immunotherapy approaches or of different elements within each of the immunotherapy approaches are being explored. The rationale typically involves different but complementary mechanisms of action, eventually impinging on more than one immune system mechanism. As a prominent example, the simultaneous blockade of PD-1 and CTLA-4 is giving rise to therapeutic synergy, while still offering room for efficacy improvement. Moreover, combinations of immunomodulating agents with chemotherapy or targeted molecules are being tested. Animal models suggest that immunotherapies in combination with these various options offer evidence for synergistic effects and are likely to radically change cancer treatment paradigms. However, data obtained so far indicate that toxic side effects are also potentiated, which may even restrict the selection of patients that are suitable for these combinational approaches. Advancing the field of combinatorial immunotherapy will require changes in the way investigational agents are clinically developed as well as novel experimental end-points for efficacy evaluation. However, this combined therapeutic manipulation of both tumor and stromal cells may lead to a dramatic change in the therapeutic options of lung cancer patients in any disease stage that can only grossly be appreciated by the current studies. PMID:26384009

  6. Combination Light

    NASA Technical Reports Server (NTRS)

    1990-01-01

    The Rayovac TANDEM is an advanced technology combination work light and general purpose flashlight that incorporates several NASA technologies. The TANDEM functions as two lights in one. It features a long range spotlight and wide angle floodlight; simple one-hand electrical switching changes the beam from spot to flood. TANDEM developers made particular use of NASA's extensive research in ergonomics in the TANDEM's angled handle, convenient shape and different orientations. The shatterproof, water resistant plastic casing also draws on NASA technology, as does the shape and beam distance of the square diffused flood. TANDEM's heavy duty magnet that permits the light to be affixed to any metal object borrows from NASA research on rare earth magnets that combine strong magnetic capability with low cost. Developers used a NASA-developed ultrasonic welding technique in the light's interior.

  7. Combined inhibition of DNA methyltransferase and histone deacetylase restores caspase-8 expression and sensitizes SCLC cells to TRAIL.

    PubMed

    Kaminskyy, Vitaliy O; Surova, Olga V; Vaculova, Alena; Zhivotovsky, Boris

    2011-10-01

    Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a promising drug for the treatment of tumors; however, a number of cancer cells are resistant to this cytokine. Among the mechanisms of resistance of small cell lung carcinomas (SCLCs) to TRAIL is the lack of caspase-8 expression. Although methylation of the caspase-8 promoter has been suggested as the main mechanism of caspase-8 silencing, we showed that reduction of the enzymes involved in DNA methylation, DNA methyltransferases (DNMT) 1, 3a and 3b, was not sufficient to significantly restore caspase-8 expression in SCLC cells, signifying that other mechanisms are involved in caspase-8 silencing. We found that combination of the DNMT inhibitor decitabine with an inhibitor of histone deacetylase (HDAC) significantly increased caspase-8 expression in SCLC cells at the RNA and protein levels. Among all studied HDAC inhibitors, valproic acid (VPA) and CI-994 showed prolonged effects on histone acetylation, while combination with decitabine produced the most prominent effects on caspase-8 re-expression. Moreover, a significant reduction of survivin and cIAP-1 proteins level was observed after treatment with VPA. The combination of two drugs sensitized SCLC cells to TRAIL-induced apoptosis, involving mitochondrial apoptotic pathway and was accompanied by Bid cleavage, activation of Bax, and release of cytochrome c. Both initiator caspase-8 and -9 were required for the sensitization of SCLC cells to TRAIL. Thus, efficient restoration of caspase-8 expression in SCLC cells is achieved when a combination of DNMT and HDAC inhibitors is used, suggesting a combination of decitabine and VPA or CI-994 as a potential treatment for sensitization of SCLC cells lacking caspase-8 to TRAIL. PMID:21771726

  8. Next Generation Epigenetic Detection Technique: Identifying Methylated DNA using Graphene Nanopore

    NASA Astrophysics Data System (ADS)

    Ahmed, Towfiq; Haraldsen, Jason T.; Zhu, Jian-Xin; Balatsky, A. V.

    2014-03-01

    DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells.Unusual methylation on CPG islands are identified as the prime causes for silencing the tumor suppressant genes. Early detection of such methylation can diagnose the potentially harmful oncogenic evolution of cells, and provide a promising guideline for cancer prevention.We propose a detection technique and calculate the transport current through punctured graphene as the cytosine and methylated cytosine translocate through the nanopore. We also calculate the transport properties for uracil and cyano-cytosine to compare. Our calculations of transmission, current and tunneling conductance show distinct signatures in their spectrum for each molecular type. Our theoretical study provides a next generation detection technique for identifying DNA methylation using graphene based nanopore device. This work was supported by U.S. DOE Office of Basic Energy Sciences, and by VR 621-2012-2983 and ERC 321031-DM. This work was, in part, supported by the Center for Integrated Nanotechnologies, a U.S. DOE BES user facility.

  9. Methylated DNA collected by tampons--a new tool to detect endometrial cancer.

    PubMed

    Fiegl, Heidi; Gattringer, Conny; Widschwendter, Andreas; Schneitter, Alois; Ramoni, Angela; Sarlay, Daniela; Gaugg, Inge; Goebel, Georg; Müller, Hannes M; Mueller-Holzner, Elisabeth; Marth, Christian; Widschwendter, Martin

    2004-05-01

    This proof of principle study aimed to define a new and simple strategy for detection of endometrial cancer using epigenetic markers. We investigated DNA isolated from vaginal secretion collected from tampon for aberrant methylation of five genes (CDH13, HSPA2, MLH1, RASSF1A, and SOCS2) using MethyLight in 15 patients with endometrial cancer and 109 patients without endometrial cancer. All endometrial cancer patients revealed three or more methylated genes, whereas 91% (99 of 109) of the patients without endometrial cancer had no or fewer than three genes methylated in their vaginal secretion. The methods developed in this study provide the basis for a prospective clinical trial to screen asymptomatic women who are at high risk for endometrial cancer.

  10. Griffithsin and Carrageenan Combination To Target Herpes Simplex Virus 2 and Human Papillomavirus

    PubMed Central

    Levendosky, Keith; Mizenina, Olga; Martinelli, Elena; Jean-Pierre, Ninochka; Kizima, Larisa; Rodriguez, Aixa; Kleinbeck, Kyle; Bonnaire, Thierry; Robbiani, Melissa; Zydowsky, Thomas M.; O'Keefe, Barry R.

    2015-01-01

    Extensive preclinical evaluation of griffithsin (GRFT) has identified this lectin to be a promising broad-spectrum microbicide. We set out to explore the antiviral properties of a GRFT and carrageenan (CG) combination product against herpes simplex virus 2 (HSV-2) and human papillomavirus (HPV) as well as determine the mechanism of action (MOA) of GRFT against both viruses. We performed the experiments in different cell lines, using time-of-addition and temperature dependence experiments to differentiate inhibition of viral attachment from entry and viral receptor internalization. Surface plasmon resonance (SPR) was used to assess GRFT binding to viral glycoproteins, and immunoprecipitation and immunohistochemistry were used to identify the specific glycoprotein involved. We determined the antiviral activity of GRFT against HSV-2 to be a 50% effective concentration (EC50) of 230 nM and provide the first evidence that GRFT has moderate anti-HPV activity (EC50 = 0.429 to 1.39 μM). GRFT blocks the entry of HSV-2 and HPV into target cells but not the adsorption of HSV-2 and HPV onto target cells. The results of the SPR, immunoprecipitation, and immunohistochemistry analyses of HSV-2 combined suggest that GRFT may block viral entry by binding to HSV-2 glycoprotein D. Cell-based assays suggest anti-HPV activity through α6 integrin internalization. The GRFT-CG combination product but not GRFT or CG alone reduced HSV-2 vaginal infection in mice when given an hour before challenge (P = 0.0352). While GRFT significantly protected mice against vaginal HPV infection when dosed during and after HPV16 pseudovirus challenge (P < 0.026), greater CG-mediated protection was afforded by the GRFT-CG combination for up to 8 h (P < 0.0022). These findings support the development of the GRFT-CG combination as a broad-spectrum microbicide. PMID:26369967

  11. Antiepiligrin cicatricial pemphigoid of the larynx successfully treated with a combination of tetracycline and niacinamide.

    PubMed

    Sakamoto, Kikuo; Mori, Kazunori; Hashimoto, Takashi; Yancey, Kim B; Nakashima, Tadashi

    2002-12-01

    A case of antiepiligrin cicatricial pemphigoid that primarily involved the larynx and required a tracheostomy was studied. The diagnosis was based on the direct immunofluorescence findings of a biopsy specimen from the glottis, immunofluorescence using normal and 1M sodium chloride-split normal human skin as substrates, and immunoprecipitation. A dramatic clinical improvement was observed after the combined administration of tetracycline hydrochloride and niacinamide. The tracheal stoma could be shut after the narrow segment was cut by means of carbon dioxide laser therapy. The patient showed no respiratory difficulty during the 2-year follow-up period. The combined therapy of tetracycline and niacinamide is thus considered to be an effective treatment for various types of cicatricial pemphigoid.

  12. Combined environmental stresses

    NASA Technical Reports Server (NTRS)

    Murray, R. H.; Mccally, M.

    1973-01-01

    Tolerance levels, physiological effects, and performance degradation during simultaneous or sequential exposures to two environmental stresses, and also three or more simultaneous stresses are described. Environmental stress combinations are characterized by four descriptors: order of occurrence, duration of exposure, severity of exposure, and type of interaction. Combined stress data and facilities for combined stress study are briefly mentioned.

  13. Embodied Conceptual Combination

    PubMed Central

    Lynott, Dermot; Connell, Louise

    2010-01-01

    Conceptual combination research investigates the processes involved in creating new meaning from old referents. It is therefore essential that embodied theories of cognition are able to explain this constructive ability and predict the resultant behavior. However, by failing to take an embodied or grounded view of the conceptual system, existing theories of conceptual combination cannot account for the role of perceptual, motor, and affective information in conceptual combination. In the present paper, we propose the embodied conceptual combination (ECCo) model to address this oversight. In ECCo, conceptual combination is the result of the interaction of the linguistic and simulation systems, such that linguistic distributional information guides or facilitates the combination process, but the new concept is fundamentally a situated, simulated entity. So, for example, a cactus beetle is represented as a multimodal simulation that includes visual (e.g., the shiny appearance of a beetle) and haptic (e.g., the prickliness of the cactus) information, all situated in the broader location of a desert environment under a hot sun, and with (at least for some people) an element of creepy-crawly revulsion. The ECCo theory differentiates interpretations according to whether the constituent concepts are destructively, or non-destructively, combined in the situated simulation. We compare ECCo to other theories of conceptual combination, and discuss how it accounts for classic effects in the literature. PMID:21833267

  14. Effective Nutritional Supplement Combinations

    NASA Astrophysics Data System (ADS)

    Cooke, Matt; Cribb, Paul J.

    Few supplement combinations that are marketed to athletes are supported by scientific evidence of their effectiveness. Quite often, under the rigor of scientific investigation, the patented combination fails to provide any greater benefit than a group given the active (generic) ingredient. The focus of this chapter is supplement combinations and dosing strategies that are effective at promoting an acute physiological response that may improve/enhance exercise performance or influence chronic adaptations desired from training. In recent years, there has been a particular focus on two nutritional ergogenic aids—creatine monohydrate and protein/amino acids—in combination with specific nutrients in an effort to augment or add to their already established independent ergogenic effects. These combinations and others are discussed in this chapter.

  15. Optical Communications Channel Combiner

    NASA Technical Reports Server (NTRS)

    Quirk, Kevin J.; Quirk, Kevin J.; Nguyen, Danh H.; Nguyen, Huy

    2012-01-01

    NASA has identified deep-space optical communications links as an integral part of a unified space communication network in order to provide data rates in excess of 100 Mb/s. The distances and limited power inherent in a deep-space optical downlink necessitate the use of photon-counting detectors and a power-efficient modulation such as pulse position modulation (PPM). For the output of each photodetector, whether from a separate telescope or a portion of the detection area, a communication receiver estimates a log-likelihood ratio for each PPM slot. To realize the full effective aperture of these receivers, their outputs must be combined prior to information decoding. A channel combiner was developed to synchronize the log-likelihood ratio (LLR) sequences of multiple receivers, and then combines these into a single LLR sequence for information decoding. The channel combiner synchronizes the LLR sequences of up to three receivers and then combines these into a single LLR sequence for output. The channel combiner has three channel inputs, each of which takes as input a sequence of four-bit LLRs for each PPM slot in a codeword via a XAUI 10 Gb/s quad optical fiber interface. The cross-correlation between the channels LLR time series are calculated and used to synchronize the sequences prior to combining. The output of the channel combiner is a sequence of four-bit LLRs for each PPM slot in a codeword via a XAUI 10 Gb/s quad optical fiber interface. The unit is controlled through a 1 Gb/s Ethernet UDP/IP interface. A deep-space optical communication link has not yet been demonstrated. This ground-station channel combiner was developed to demonstrate this capability and is unique in its ability to process such a signal.

  16. [Advantages of fixed combinations].

    PubMed

    Lachkar, Y

    2008-07-01

    Fixed combinations are indicated in the treatment of glaucoma and ocular hypertension when monotherapy does not sufficiently reduce IOP. Fixed combinations show better efficacy than the instillation of each separate component and are at least equivalent to the administration of both components in a separate association. They simplify treatment, increase compliance and quality of life, and decrease exposure to preservatives. Although they are less aggressive for patients when a new drug needs to be added, the use of fixed combinations should not decrease the follow-up. PMID:18957922

  17. Hydrocodone Combination Products

    MedlinePlus

    ... Other hydrocodone combination products are used to relieve cough. Hydrocodone is in a class of medications called ... and nervous system respond to pain. Hydrocodone relieves cough by decreasing activity in the part of the ...

  18. Earth science: Deadly combination

    NASA Astrophysics Data System (ADS)

    Duncan, Robert

    2015-11-01

    New evidence suggests that seismic waves from the Chicxulub meteorite impact doubled the eruption rate of lavas on the opposite side of the planet -- a combination that led to the mass extinction at the end of the Cretaceous period.

  19. Bilateral combined laryngocele

    PubMed Central

    Suqati, Abrar A.; Alherabi, Ameen Z.; Marglani, Osama A.; Alaidarous, Tariq O.

    2016-01-01

    Laryngocele is an uncommon condition that represents a benign dilatation of the laryngeal saccule with air and/or fluid, arising in the region of the laryngeal ventricle. Laryngoceles, or laryngomucocele can be classified as internal, or combined. The aim of presenting this rare case of a bilateral combined laryngocele, are to emphasize the importance of diagnostic laryngoscopy in upper airway pathologies evaluation, increase awareness in the general otolaryngologist community, and to highlight the external surgical method. PMID:27464869

  20. Multifunctional Cu2−xTe Nanocubes Mediated Combination Therapy for Multi-Drug Resistant MDA MB 453

    PubMed Central

    Poulose, Aby Cheruvathoor; Veeranarayanan, Srivani; Mohamed, M. Sheikh; Aburto, Rebeca Romero; Mitcham, Trevor; Bouchard, Richard R.; Ajayan, Pulickel M.; Sakamoto, Yasushi; Maekawa, Toru; Kumar, D. Sakthi

    2016-01-01

    Hypermethylated cancer populations are hard to treat due to their enhanced chemo-resistance, characterized by aberrant methylated DNA subunits. Herein, we report on invoking response from such a cancer lineage to chemotherapy utilizing multifunctional copper telluride (Cu2−XTe) nanocubes (NCs) as photothermal and photodynamic agents, leading to significant anticancer activity. The NCs additionally possessed photoacoustic and X-ray contrast imaging abilities that could serve in image-guided therapeutic studies. PMID:27775048

  1. [Fixed-dose combination].

    PubMed

    Nagai, Yoshio

    2015-03-01

    Many patients with type 2 diabetes mellitus(T2DM) do not achieve satisfactory glycemic control by monotherapy alone, and often require multiple oral hypoglycemic agents (OHAs). Combining OHAs with complementary mechanisms of action is fundamental to the management of T2DM. Fixed-dose combination therapy(FDC) offers a method of simplifying complex regimens. Efficacy and tolerability appear to be similar between FDC and treatment with individual agents. In addition, FDC can enhance adherence and improved adherence may result in improved glycemic control. Four FDC agents are available in Japan: pioglitazone-glimepiride, pioglitazone-metformin, pioglitazone-alogliptin, and voglibose-mitiglinide. In this review, the advantages and disadvantages of these four combinations are identified and discussed. PMID:25812374

  2. Severe Combined Immunodeficiency Disorders.

    PubMed

    Chinn, Ivan K; Shearer, William T

    2015-11-01

    Severe combined immunodeficiency disorders represent pediatric emergencies due to absence of adaptive immune responses to infections. The conditions result from either intrinsic defects in T-cell development (ie, severe combined immunodeficiency disease [SCID]) or congenital athymia (eg, complete DiGeorge anomaly). Hematopoietic stem cell transplant provides the only clinically approved cure for SCID, although gene therapy research trials are showing significant promise. For greatest survival, patients should undergo transplant before 3.5 months of age and before the onset of infections. Newborn screening programs have yielded successful early identification and treatment of infants with SCID and congenital athymia in the United States. PMID:26454313

  3. ILSE combiner study

    SciTech Connect

    Hahn, K.

    1994-03-01

    In a heavy ion inertial fusion (HIF) driver, the beam energy and current are increased several orders of magnitude from the injector to the final focus system. At low and high energy stages of the driver, electrostatic and magnetic focusing transport channels, respectively, can be used. At the electric-to-magnetic transition point, the beams may be combined to reduce the transverse dimensions of the system, which could have significant impact on the driver cost. In a presently envisioned combiner, four beams are brought together transversely into a single transport channel. A matching section follows the combiner in order to provide a smooth transition to the subsequent magnetic transport channel. This report summarizes a conceptual design study of possible combiner configurations for the proposed Introduction Linac Systems Experiment (ILSE). The conceptual design study includes subjects such as the expected technical difficulties, predicted emittance growth, particle loss, effect of geometric and chromatic aberrations, and the sensitivity of emittance growth on the initial beam position and angle errors.

  4. Coherently combining antennas

    NASA Technical Reports Server (NTRS)

    Dybdal, Robert B. (Inventor); Curry, Samuel J. (Inventor)

    2009-01-01

    An apparatus includes antenna elements configured to receive a signal including pseudo-random code, and electronics configured to use the pseudo-random code to determine time delays of signals incident upon the antenna elements and to compensate the signals to coherently combine the antenna elements.

  5. Energy and combination systems

    SciTech Connect

    Hartsock, D.K.

    1995-08-01

    Energy and combination systems are outlined. The following topics are discussed: NO{sub x} control technologies; coal fired boilers; gas reburning (GR); NO{sub x} emissions using GR; integration of GR and selective noncatalytic reduction (SNCR); enhanced temperature windows; methanol injection; combi NO{sub x}; integrated GR technologies, reburning alternate fuels, reburning fuel types; and comparison of GR technologies.

  6. Introduction to combined cycles

    NASA Astrophysics Data System (ADS)

    Moore, M. J.

    Ideas and concepts underlying the technology of combined cycles including the scientific principles involved and the reasons these cycles are in fashion at the present time, are presented. A cycle is a steady flow process for conversion of heat energy into work, in which a working medium passes through a range of states, returning to its original state. Cycles for power production are the steam cycle, which is a closed cycle, and the gas turbine, which represents an open cycle. Combined cycle thermodynamic parameters, are discussed. The general arrangement of the plant is outlined and important features of their component parts described. The scope for future development is discussed. It is concluded that for the next few years the natural gas fired combined cycle will be the main type of plant installed for electricity generation and cogeneration. Whilst gas turbines may not increase substantially in unit size, there remains scope for further increase in firing temperature with consequent increase in cycle performance. However the larger global reserves of coal are providing an incentive to the development of plant for clean coal combustion using the inherent advantage of the combined cycle to attain high efficiencies.

  7. Sentence-Combining Practice

    ERIC Educational Resources Information Center

    Akin, Judy O'Neal

    1978-01-01

    Sample sentence-combining lessons developed to accompany the first-year A-LM German textbook are presented. The exercises are designed for language manipulation practice; they involve breaking down more complex sentences into simpler sentences and the subsequent recombination into complex sentences. All language skills, and particularly writing,…

  8. Interschool Production Training Combines

    ERIC Educational Resources Information Center

    Il'ina, L. A.; Fat'ianov, V. V.

    1977-01-01

    An educational program draws together students from several secondary schools in one region in a labor practicum which combines training shops, classroom work, and laboratory experience. Examples are presented of schools throughout the USSR which are training pupils to be computer and machine operators, construction workers, cooks, automotive…

  9. Combination hand rejuvenation procedures.

    PubMed

    Shamban, Ava T

    2009-01-01

    Although the hands age at the same rate as the face, the aging process differs and requires a combination treatment approach for optimal rejuvenation. Photoaging causes epidermal changes such as lentigines, actinic keratoses, fine wrinkles, and crepe-like textural change. Thinning of the dermis and subcutaneous fat occurs as a result of both ultraviolet light exposure and intrinsic aging. This process can lead to a skeletal appearance of the hands, with prominent veins and bulging tendons. The combination approach addresses all of these issues, employing lasers, intense pulsed light devices, fractional devices, fillers, peels, vein sclerotherapy, and an effective at-home skin care program as indicated for individual needs and concerns. PMID:19825471

  10. NASA combines two offices

    NASA Astrophysics Data System (ADS)

    The National Aeronautics and Space Administration has completed plans for combining its Office of Space Science and its Office of Space and Terrestrial Applications. The new organization was effective December 3.The new Office of Space Science and Applications will retain the programs and responsibilities of the two program offices with the exception of the Technology Utilization Program, which has been transferred to the Government/Industry Affairs Division of the Office of External Relations.

  11. Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1.

    PubMed

    Harrison, Joseph S; Cornett, Evan M; Goldfarb, Dennis; DaRosa, Paul A; Li, Zimeng M; Yan, Feng; Dickson, Bradley M; Guo, Angela H; Cantu, Daniel V; Kaustov, Lilia; Brown, Peter J; Arrowsmith, Cheryl H; Erie, Dorothy A; Major, Michael B; Klevit, Rachel E; Krajewski, Krzysztof; Kuhlman, Brian; Strahl, Brian D; Rothbart, Scott B

    2016-01-01

    The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. Collectively, our studies are the first demonstrations of a DNA-protein interaction and an epigenetic modification directly regulating E3 ubiquitin ligase activity. They also define an orchestrated epigenetic control mechanism involving modifications both to histones and DNA that facilitate UHRF1 chromatin targeting, H3 ubiquitylation, and DNA methylation inheritance. PMID:27595565

  12. Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1

    PubMed Central

    Harrison, Joseph S; Cornett, Evan M; Goldfarb, Dennis; DaRosa, Paul A; Li, Zimeng M; Yan, Feng; Dickson, Bradley M; Guo, Angela H; Cantu, Daniel V; Kaustov, Lilia; Brown, Peter J; Arrowsmith, Cheryl H; Erie, Dorothy A; Major, Michael B; Klevit, Rachel E; Krajewski, Krzysztof; Kuhlman, Brian; Strahl, Brian D; Rothbart, Scott B

    2016-01-01

    The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. Collectively, our studies are the first demonstrations of a DNA-protein interaction and an epigenetic modification directly regulating E3 ubiquitin ligase activity. They also define an orchestrated epigenetic control mechanism involving modifications both to histones and DNA that facilitate UHRF1 chromatin targeting, H3 ubiquitylation, and DNA methylation inheritance. DOI: http://dx.doi.org/10.7554/eLife.17101.001 PMID:27595565

  13. Combining modules for movement.

    PubMed

    Bizzi, E; Cheung, V C K; d'Avella, A; Saltiel, P; Tresch, M

    2008-01-01

    We review experiments supporting the hypothesis that the vertebrate motor system produces movements by combining a small number of units of motor output. Using a variety of approaches such as microstimulation of the spinal cord, NMDA iontophoresis, and an examination of natural behaviors in intact and deafferented animals we have provided evidence for a modular organization of the spinal cord. A module is a functional unit in the spinal cord that generates a specific motor output by imposing a specific pattern of muscle activation. Such an organization might help to simplify the production of movements by reducing the degrees of freedom that need to be specified.

  14. DNA Methylation Profiling of Embryonic Stem Cell Differentiation into the Three Germ Layers

    PubMed Central

    Isagawa, Takayuki; Nagae, Genta; Shiraki, Nobuaki; Fujita, Takanori; Sato, Noriko; Ishikawa, Shumpei; Kume, Shoen; Aburatani, Hiroyuki

    2011-01-01

    Embryogenesis is tightly regulated by multiple levels of epigenetic regulation such as DNA methylation, histone modification, and chromatin remodeling. DNA methylation patterns are erased in primordial germ cells and in the interval immediately following fertilization. Subsequent developmental reprogramming occurs by de novo methylation and demethylation. Variance in DNA methylation patterns between different cell types is not well understood. Here, using methylated DNA immunoprecipitation and tiling array technology, we have comprehensively analyzed DNA methylation patterns at proximal promoter regions in mouse embryonic stem (ES) cells, ES cell-derived early germ layers (ectoderm, endoderm and mesoderm) and four adult tissues (brain, liver, skeletal muscle and sperm). Most of the methylated regions are methylated across all three germ layers and in the three adult somatic tissues. This commonly methylated gene set is enriched in germ cell-associated genes that are generally transcriptionally inactive in somatic cells. We also compared DNA methylation patterns by global mapping of histone H3 lysine 4/27 trimethylation, and found that gain of DNA methylation correlates with loss of histone H3 lysine 4 trimethylation. Our combined findings indicate that differentiation of ES cells into the three germ layers is accompanied by an increased number of commonly methylated DNA regions and that these tissue-specific alterations in methylation occur for only a small number of genes. DNA methylation at the proximal promoter regions of commonly methylated genes thus appears to be an irreversible mark which functions to fix somatic lineage by repressing the transcription of germ cell-specific genes. PMID:22016810

  15. [Insulin combined with selenium inhibit p38MAPK/CBP pathway and suppresses cardiomyocyte apoptosis in rats with diabetic cardiomyopathy].

    PubMed

    Xu, Tianjiao; Liu, Yong; Deng, Yating; Meng, Jin; Li, Ping; Xu, Xiaoli; Zeng, Jurong

    2016-07-01

    Objective To investigate the effect of insulin in combination with selenium on p38-mitogen-activated protein kinase/CREB-binding protein (p38MAPK/CBP) pathway in rats with diabetic cardiomyopathy. Methods Fifty SD rats were randomly grouped into control group, diabetic cardiomyopathy (DCM) group, diabetic cardiomyopathy with insulin treatment (DCM-In) group, diabetic cardiomyopathy with selenium treatment (DCM-Se) group, and diabetic cardiomyopathy with insulin and selenium combination treatment (DCM-In-Se) group. Flow cytometry was used to analyze cell cycle. TUNEL staining was used to detect cardiomyocyte apoptosis. Western blotting was used to examine the levels of cyclin D1, cyclin E, Bax, Bcl-2, p38MAPK, p-p38MAPK, CBP and Ku70. Co-immunoprecipitation was used to examine the acetylation status of Ku70. Results Insulin in combination with selenium significantly inhibited cardiomyocyte apoptosis, increased Bcl-2 levels and decreased Bax, cyclin D1, cyclin E, p38MAPK, p-p38MAPK, CBP, Ku70 and acetylated Ku70 levels. Conclusion The combined treatment of insulin and selenium suppresses cardiomyocyte apoptosis by inhibiting p38MAPK/CBP pathway. PMID:27363274

  16. Stove-hearth combinations

    SciTech Connect

    Nesje, A.

    1980-08-26

    Stove-hearth combinations are described that are comprised of a combustion chamber having a pair of side walls supported on a base in opposing relation and joined by a rear wall. A cover or hood defines with the base and front edges of the side walls an opening to the chamber. Two doors are each hingedly associated with upper and lower pivot pins which when the door is in a closed position are disposed adjacent but outside a respective side wall front edge. Along upper and lower side edges of each side wall are formed parallel grooves adapted to be engaged slidably by the upper and lower pivot pins. As the door is opened from a stove to a hearth position the pivot pins are displaced along the grooves causing the door to be led gradually into a position along the outer side of its side wall.

  17. Combining environmental information.

    PubMed Central

    Piegorsch, W W

    1994-01-01

    Workshop proceedings and summary reports will appear in scientific periodicals and will also be available in various forms as technical reports from the NISS in Research Triangle Park, North Carolina. In particular, study papers from the workshop will be prepared that will serve as indicators of further research directions, as well as current summaries of the complex issue of combining environmental data. Potential applications and improvements in associated areas of scientific/statistical research include census sampling, geostatistics, and biological effect modeling. This workshop was an experiment in how to stimulate and foster research and collaborations across disciplinary lines. Its motivation derives, however, from ever-growing social, political, economic, and scientific needs; with such strong background, it is hoped that the workshop stimulus will be strong, compelling, and fruitful. Images p222-a PMID:7913438

  18. Newberry Combined Gravity 2016

    DOE Data Explorer

    Kelly Rose

    2016-01-22

    Newberry combined gravity from Zonge Int'l, processed for the EGS stimulation project at well 55-29. Includes data from both Davenport 2006 collection and for OSU/4D EGS monitoring 2012 collection. Locations are NAD83, UTM Zone 10 North, meters. Elevation is NAVD88. Gravity in milligals. Free air and observed gravity are included, along with simple Bouguer anomaly and terrain corrected Bouguer anomaly. SBA230 means simple Bouguer anomaly computed at 2.30 g/cc. CBA230 means terrain corrected Bouguer anomaly at 2.30 g/cc. This suite of densities are included (g/cc): 2.00, 2.10, 2.20, 2.30, 2.40, 2.50, 2.67.

  19. Biomass Gasification Combined Cycle

    SciTech Connect

    Judith A. Kieffer

    2000-07-01

    Gasification combined cycle continues to represent an important defining technology area for the forest products industry. The ''Forest Products Gasification Initiative'', organized under the Industry's Agenda 2020 technology vision and supported by the DOE ''Industries of the Future'' program, is well positioned to guide these technologies to commercial success within a five-to ten-year timeframe given supportive federal budgets and public policy. Commercial success will result in significant environmental and renewable energy goals that are shared by the Industry and the Nation. The Battelle/FERCO LIVG technology, which is the technology of choice for the application reported here, remains of high interest due to characteristics that make it well suited for integration with the infrastructure of a pulp production facility. The capital cost, operating economics and long-term demonstration of this technology area key input to future economically sustainable projects and must be verified by the 200 BDT/day demonstration facility currently operating in Burlington, Vermont. The New Bern application that was the initial objective of this project is not currently economically viable and will not be implemented at this time due to several changes at and around the mill which have occurred since the inception of the project in 1995. The analysis shows that for this technology, and likely other gasification technologies as well, the first few installations will require unique circumstances, or supportive public policies, or both to attract host sites and investors.

  20. Combining multiple altimeter missions

    NASA Astrophysics Data System (ADS)

    Jacobs, G. A.; Mitchell, J. L.

    1997-10-01

    Viewing altimeter data only at the points where separate altimeter missions' ground tracks cross provides a method to observe long time period sea surface height (SSH) variations and avoids many of the problems inherent in combining separate altimeter data sets through an independently determined geoid. TOPEX/POSEIDON (T/P) data over the time period from January 1, 1993, to December 31, 1995, form a mean SSH that is used as a reference by other altimeter data sets. A least squares analysis of the mean T/P SSH determines the portion of the Geographically Correlated Orbit Error (GCOE) that may be observed through crossover differences and removes this portion of the GCOE. The analysis removes errors of 0.86 cm RMS at 1 cycle per orbit revolution (cpr) and indicates negligible errors at higher frequencies. After the GCOE removal, the accuracy of the T/P reference mean is better than 1 cm RMS as measured by crossover differences. The GCOE contained in the Geosat-Exact Repeat Mission (ERM) and ERS 1 data with orbit solutions using the Joint Gravity Model (JGM) 3 is evaluated through an adjustment to the T/P reference mean surface. The Geosat-ERM data indicate a bias of about 28 cm averaged over the globe, and the ERS 1 bias is 44 cm. The T/P data used here is not corrected for the oscillator drift correction error so that the actual bias is less by about 13 cm. Both the Geosat-ERM and ERS 1 GCOE are mainly 1 cpr. GCOE estimates at frequencies above 1 cpr indicate little actual orbit error but are more correlated to instrument correction errors (particularly water vapor). Simultaneous T/P and ERS 1 SSH anomalies to the T/P mean indicate good correlation.

  1. Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis.

    PubMed

    Suda, Natsuno; Itoh, Takehiko; Nakato, Ryuichiro; Shirakawa, Daisuke; Bando, Masashige; Katou, Yuki; Kataoka, Kohsuke; Shirahige, Katsuhiko; Tickle, Cheryll; Tanaka, Mikiko

    2014-07-01

    Apoptosis is an important mechanism for sculpting morphology. However, the molecular cascades that control apoptosis in developing limb buds remain largely unclear. Here, we show that MafB was specifically expressed in apoptotic regions of chick limb buds, and MafB/cFos heterodimers repressed apoptosis, whereas MafB/cJun heterodimers promoted apoptosis for sculpting the shape of the limbs. Chromatin immunoprecipitation sequencing in chick limb buds identified potential target genes and regulatory elements controlled by Maf and Jun. Functional analyses revealed that expression of p63 and p73, key components known to arrest the cell cycle, was directly activated by MafB and cJun. Our data suggest that dimeric combinations of MafB, cFos and cJun in developing chick limb buds control the number of apoptotic cells, and that MafB/cJun heterodimers lead to apoptosis via activation of p63 and p73.

  2. Elucidating Novel Hepatitis C Virus–Host Interactions Using Combined Mass Spectrometry and Functional Genomics Approaches*

    PubMed Central

    Germain, Marie-Anne; Chatel-Chaix, Laurent; Gagné, Bridget; Bonneil, Éric; Thibault, Pierre; Pradezynski, Fabrine; de Chassey, Benoît; Meyniel-Schicklin, Laurène; Lotteau, Vincent; Baril, Martin; Lamarre, Daniel

    2014-01-01

    More than 170 million people worldwide are infected with the hepatitis C virus (HCV), for which future therapies are expected to rely upon a combination of oral antivirals. For a rapidly evolving virus like HCV, host-targeting antivirals are an attractive option. To decipher the role of novel HCV–host interactions, we used a proteomics approach combining immunoprecipitation of viral–host protein complexes coupled to mass spectrometry identification and functional genomics RNA interference screening of HCV partners. Here, we report the proteomics analyses of protein complexes associated with Core, NS2, NS3/4A, NS4B, NS5A, and NS5B proteins. We identified a stringent set of 98 human proteins interacting specifically with one of the viral proteins. The overlap with previous virus–host interaction studies demonstrates 24.5% shared HCV interactors overall (24/98), illustrating the reliability of the approach. The identified human proteins show enriched Gene Ontology terms associated with the endoplasmic reticulum, transport proteins with a major contribution of NS3/4A interactors, and transmembrane proteins for Core interactors. The interaction network emphasizes a high degree distribution, a high betweenness distribution, and high interconnectivity of targeted human proteins, in agreement with previous virus–host interactome studies. The set of HCV interactors also shows extensive enrichment for known targets of other viruses. The combined proteomic and gene silencing study revealed strong enrichment in modulators of HCV RNA replication, with the identification of 11 novel cofactors among our set of specific HCV partners. Finally, we report a novel immune evasion mechanism of NS3/4A protein based on its ability to affect nucleocytoplasmic transport of type I interferon-mediated signal transducer and activator of transcription 1 nuclear translocation. The study revealed highly stringent association between HCV interactors and their functional contribution to the

  3. Symbol Stream Combining Versus Baseband Combining for Telemetry Arraying

    NASA Technical Reports Server (NTRS)

    Divsalar, D.

    1983-01-01

    The objectives of this article are to investigate and analyze the problem of combining symbol streams from many Deep Space Network stations to enhance bit signal-to-noise ratio and to compare the performance of this combining technique with baseband combining. Symbol stream combining (SSC) has some advantages and some disadvantages over baseband combining (BBC). The SSC suffers almost no loss in combining the digital data and no loss due to the transmission of the digital data by microwave links between the stations. The BBC suffers 0.2 dB loss due to alignment and combining the IF signals and 0.2 dB loss due to transmission of signals by microwave links. On the other hand, the losses in the subcarrier demodulation assembly (SDA) and in the symbol synchronization assembly (SSA) for SSC are more than the losses in the SDA and SSA for BBC. It is shown that SSC outperforms BBC by about 0.35 dB (in terms of the required bit energy-to-noise spectral density for a bit error rate of 1,000) for an array of three DSN antennas, namely 64 m, 34m(T/R) and 34m(R).

  4. Revised Accounting for Business Combinations

    ERIC Educational Resources Information Center

    Wilson, Arlette C.; Key, Kimberly

    2008-01-01

    The Financial Accounting Standards Board (FASB) has recently issued Statement of Financial Accounting Standards No. 141 (Revised 2007) Business Combinations. The object of this Statement is to improve the relevance, representational faithfulness, and comparability of reported information about a business combination and its effects. This Statement…

  5. Combination Classes and Educational Achievement

    ERIC Educational Resources Information Center

    Thomas, Jaime L.

    2012-01-01

    Using the ECLS-K and considering first graders in single-grade and K-1 and 1-2 combination classes, I discuss the mechanisms underlying the combination-class effect and address the systematic school-, teacher-, and student-level differences that confound estimates of this effect. I find evidence for positive selection into 1-2 classes, but using a…

  6. Combination moisture and hydrogen getter

    DOEpatents

    Not Available

    1982-04-29

    A combination moisture and hydrogen getter comprises (a) a moisture getter comprising a readily oxidizable metal; and (b) a hydrogen getter comprising (i) a solid acetylenic compound and (ii) a hydrogenation catalyst. A method of scavenging moisture from a closed container uses the combination moisture and hydrogen getter to irreversibly chemically reduce the moisture and chemically bind the reusltant hydrogen.

  7. Combination moisture and hydrogen getter

    DOEpatents

    Harrah, Larry A.; Mead, Keith E.; Smith, Henry M.

    1983-01-01

    A combination moisture and hydrogen getter comprises (a) a moisture getter comprising a readily oxidizable metal; and (b) a hydrogen getter comprising (i) a solid acetylenic compound and (ii) a hydrogenation catalyst. A method of scavenging moisture from a closed container uses the combination moisture and hydrogen getter to irreversibly chemically reduce the moisture and chemically bind the resultant hydrogen.

  8. Combination moisture and hydrogen getter

    DOEpatents

    Harrah, L.A.; Mead, K.E.; Smith, H.M.

    1983-09-20

    A combination moisture and hydrogen getter comprises (a) a moisture getter comprising a readily oxidizable metal; and (b) a hydrogen getter comprising (1) a solid acetylenic compound and (2) a hydrogenation catalyst. A method of scavenging moisture from a closed container uses the combination moisture and hydrogen getter to irreversibly chemically reduce the moisture and chemically bind the resultant hydrogen.

  9. Combined deficiency of factor V and factor VIII is due to mutations in either LMAN1 or MCFD2

    PubMed Central

    Zhang, Bin; McGee, Beth; Yamaoka, Jennifer S.; Guglielmone, Hugo; Downes, Katharine A.; Minoldo, Salvador; Jarchum, Gustavo; Peyvandi, Flora; de Bosch, Norma B.; Ruiz-Saez, Arlette; Chatelain, Bernard; Olpinski, Marian; Bockenstedt, Paula; Sperl, Wolfgang; Kaufman, Randal J.; Nichols, William C.; Tuddenham, Edward G. D.; Ginsburg, David

    2006-01-01

    Mutations in LMAN1 (ERGIC-53) or MCFD2 cause combined deficiency of factor V and factor VIII (F5F8D). LMAN1 and MCFD2 form a protein complex that functions as a cargo receptor ferrying FV and FVIII from the endoplasmic reticulum to the Golgi. In this study, we analyzed 10 previously reported and 10 new F5F8D families. Mutations in the LMAN1 or MCFD2 genes accounted for 15 of these families, including 3 alleles resulting in no LMAN1 mRNA accumulation. Combined with our previous reports, we have identified LMAN1 or MCFD2 mutations as the causes of F5F8D in 71 of 76 families. Among the 5 families in which no mutations were identified, 3 were due to misdiagnosis, with the remaining 2 likely carrying LMAN1 or MCFD2 mutations that were missed by direct sequencing. Our results suggest that mutations in LMAN1 and MCFD2 may account for all cases of F5F8D. Immunoprecipitation and Western blot analysis detected a low level of LMAN1-MCFD2 complex in lymphoblasts derived from patients with missense mutations in LMAN1 (C475R) or MCFD2 (I136T), suggesting that complete loss of the complex may not be required for clinically significant reduction in FV and FVIII. PMID:16304051

  10. Thermodynamics of combined cycle plant

    NASA Astrophysics Data System (ADS)

    Crane, R. I.

    The fundamental thermodynamics of power plants including definitions of performance criteria and an introduction to exergy are reviewed, and treatments of simplified performance calculations for the components which form the major building blocks and a gas/steam combined cycle plant are given: the gas turbine, the heat recovery steam generator, and the remainder of the steam plant. Efficiency relationships and energy and exergy analyses of combined cycle plant are presented, with examples. Among the aspects considered are gas turbine performance characteristics and fuels, temperature differences for heat recovery, multiple steam pressures and reheat, supplementary firing and feed water heating. Attention is drawn to points of thermodynamic interest arising from applications of combined cycle plant to repowering of existing steam plant and to combined heat and power (cogeneration); some advances, including coal firing, are also introduced.

  11. New combinations in Odontostemma (Caryophyllaceae)

    PubMed Central

    Rabeler, Richard K.; Wagner, Warren L.

    2016-01-01

    Abstract Sixty-three new combinations in Odontostemma (Alsineae, Caryophyllaceae) are made to accommodate placement of all currently recognized taxa of Arenaria subg. Odontostemma within the genus Odontostemma. PMID:27489480

  12. Autonomous grain combine control system

    DOEpatents

    Hoskinson, Reed L.; Kenney, Kevin L.; Lucas, James R.; Prickel, Marvin A.

    2013-06-25

    A system for controlling a grain combine having a rotor/cylinder, a sieve, a fan, a concave, a feeder, a header, an engine, and a control system. The feeder of the grain combine is engaged and the header is lowered. A separator loss target, engine load target, and a sieve loss target are selected. Grain is harvested with the lowered header passing the grain through the engaged feeder. Separator loss, sieve loss, engine load and ground speed of the grain combine are continuously monitored during the harvesting. If the monitored separator loss exceeds the selected separator loss target, the speed of the rotor/cylinder, the concave setting, the engine load target, or a combination thereof is adjusted. If the monitored sieve loss exceeds the selected sieve loss target, the speed of the fan, the size of the sieve openings, or the engine load target is adjusted.

  13. New combinations in Neotropical Thelypteridaceae

    PubMed Central

    Salino, Alexandre; Almeida, Thaís E.; Smith, Alan R.

    2015-01-01

    Abstract 288 new combinations of Neotropical Thelypteridaceae taxa are proposed in order to recognize monophyletic genera, based on the results of the most recent molecular phylogeny of the family, as well as the morphological uniformity of characters for each genus. The new nomenclatural combinations correspond to 186 Amauropelta taxa, 77 species of Goniopteris, and 25 Steiropteris taxa. A key to all native Neotropical genera of the family is also presented. PMID:26752025

  14. Vaccine Potentiation by Combination Adjuvants

    PubMed Central

    Levast, Benoît; Awate, Sunita; Babiuk, Lorne; Mutwiri, George; Gerdts, Volker; van Drunen Littel-van den Hurk, Sylvia

    2014-01-01

    Adjuvants are crucial components of vaccines. They significantly improve vaccine efficacy by modulating, enhancing, or extending the immune response and at the same time reducing the amount of antigen needed. In contrast to previously licensed adjuvants, current successful adjuvant formulations often consist of several molecules, that when combined, act synergistically by activating a variety of immune mechanisms. These “combination adjuvants” are already registered with several vaccines, both in humans and animals, and novel combination adjuvants are in the pipeline. With improved knowledge of the type of immune responses needed to successfully induce disease protection by vaccination, combination adjuvants are particularly suited to not only enhance, but also direct the immune responses desired to be either Th1-, Th2- or Th17-biased. Indeed, in view of the variety of disease and population targets for vaccine development, a panel of adjuvants will be needed to address different disease targets and populations. Here, we will review well-known and new combination adjuvants already licensed or currently in development—including ISCOMs, liposomes, Adjuvant Systems Montanides, and triple adjuvant combinations—and summarize their performance in preclinical and clinical trials. Several of these combination adjuvants are promising having promoted improved and balanced immune responses. PMID:26344621

  15. [Combination therapy for invasive aspergillosis].

    PubMed

    Ruiz-Camps, Isabel

    2011-03-01

    The frequency of invasive fungal infections, and specifically invasive aspergillosis, has increased in the last few decades. Despite the development of new antifungal agents, these infections are associated with high mortality, ranging from 40% to 80%, depending on the patient and the localization of the infection. To reduce these figures, several therapeutic strategies have been proposed, including combination therapy. Most of the available data on the efficacy of these combinations are from experimental models, in vitro data and retrospective observational studies or studies with a small number of patients that have included both patients in first-line treatment and those receiving rescue therapy; in addition there are many patients with possible forms of aspergillosis and few with demonstrated or probable forms. To date, there is no evidence that combination therapy has significantly higher efficacy than monotherapy; however, combination therapy could be indicated in severe forms of aspergillosis, or forms with central nervous involvement or extensive pulmonary involvement with respiratory insufficiency, etc. Among the combinations, the association of an echinocandin--the group that includes micafungin--with voriconazole or liposomal amphotericin B seems to show synergy. These combinations are those most extensively studied in clinical trials and therefore, although the grade of evidence is low, are recommended by the various scientific societies. PMID:21420576

  16. Combination vaccines against diarrheal diseases

    PubMed Central

    Venkatesan, Malabi M; Van de Verg, Lillian L

    2015-01-01

    Abstract Diarrheal diseases remain a leading cause of global childhood mortality and morbidity. Several recent epidemiological studies highlight the rate of diarrheal diseases in different parts of the world and draw attention to the impact on childhood growth and survival. Despite the well-documented global burden of diarrheal diseases, currently there are no combination diarrheal vaccines, only licensed vaccines for rotavirus and cholera, and Salmonella typhi-based vaccines for typhoid fever. The recognition of the impact of diarrheal episodes on infant growth, as seen in resource-poor countries, has spurred action from governmental and non-governmental agencies to accelerate research toward affordable and effective vaccines against diarrheal diseases. Both travelers and children in endemic countries will benefit from a combination diarrheal vaccine, but it can be argued that the greater proportion of any positive impact will be on the public health status of the latter. The history of combination pediatric vaccines indicate that monovalent or single disease vaccines are typically licensed first prior to formulation in a combination vaccine, and that the combinations themselves undergo periodic revision in response to need for improvement in safety or potential for wider coverage of important pediatric pathogens. Nevertheless combination pediatric vaccines have proven to be an effective tool in limiting or eradicating communicable childhood diseases worldwide. The landscape of diarrheal vaccine candidates indicates that there now several in active development that offer options for potential testing of combinations to combat those bacterial and viral pathogens responsible for the heaviest disease burden—rotavirus, ETEC, Shigella, Campylobacter, V. cholera and Salmonella. PMID:25891647

  17. COMBINE Archive Specification Version 1.

    PubMed

    Bergmann, Frank T; Rodriguez, Nicolas; Le Novère, Nicolas

    2015-01-01

    Several standard formats have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. The Open Modeling EXchange format (OMEX) supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, an optional metadata file, and the files describing the model. The manifest is an XML file listing all files included in the archive and their type. The metadata file provides additional information about the archive and its content. Although any format can be used, we recommend an XML serialization of the Resource Description Framework. Together with the other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. PMID:26528559

  18. Genome-Wide DNA Methylation Changes between the Superficial and Deep Backfat Tissues of the Pig

    PubMed Central

    Li, Mingzhou; Wang, Tao; Wu, Honglong; Zhang, Jie; Zhou, Chaowei; Jiang, Anan; Li, Ruiqiang; Li, Xuewei

    2012-01-01

    Adipose tissue is not only a storage organ involved in fuel metabolism, but also an endocrine organ involved in the regulation of insulin sensitivity, thermogenesis, immunity, and inflammation. There are anatomical, cellular, molecular and physiological differences among adipose tissues deposited in different body sites. However, current understanding of the intrinsic differences between the sub-compartments of the subcutaneous adipose tissue remains rudimentary. Here, we analyzed the genome-wide DNA methylation differences between the porcine superficial and deep backfat tissues using methylated DNA immunoprecipitation combined with high-throughput sequencing. We show that the genes with differentially methylated regions in their promoter are mainly involved in the processes of “lipid metabolism” and “regulation of immune-related cytokines”. Compared with the deep backfat tissue, the promoters of genes related to the ‘positive regulation of cytokine production’ were significantly hypermethylated in the superficial backfat tissue, which reflects the intrinsic functional and metabolic differences between the sub-compartments of the subcutaneous adipose tissue. This study provides epigenetic evidence for functionally relevant methylation differences between different layers of porcine backfat tissues. PMID:22837681

  19. Isolation of Human Genomic DNA Sequences with Expanded Nucleobase Selectivity.

    PubMed

    Rathi, Preeti; Maurer, Sara; Kubik, Grzegorz; Summerer, Daniel

    2016-08-10

    We report the direct isolation of user-defined DNA sequences from the human genome with programmable selectivity for both canonical and epigenetic nucleobases. This is enabled by the use of engineered transcription-activator-like effectors (TALEs) as DNA major groove-binding probes in affinity enrichment. The approach provides the direct quantification of 5-methylcytosine (5mC) levels at single genomic nucleotide positions in a strand-specific manner. We demonstrate the simple, multiplexed typing of a variety of epigenetic cancer biomarker 5mC with custom TALE mixes. Compared to antibodies as the most widely used affinity probes for 5mC analysis, i.e., employed in the methylated DNA immunoprecipitation (MeDIP) protocol, TALEs provide superior sensitivity, resolution and technical ease. We engineer a range of size-reduced TALE repeats and establish full selectivity profiles for their binding to all five human cytosine nucleobases. These provide insights into their nucleobase recognition mechanisms and reveal the ability of TALEs to isolate genomic target sequences with selectivity for single 5-hydroxymethylcytosine and, in combination with sodium borohydride reduction, single 5-formylcytosine nucleobases. PMID:27429302

  20. Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice.

    PubMed

    Yan, Huihuang; Kikuchi, Shinji; Neumann, Pavel; Zhang, Wenli; Wu, Yufeng; Chen, Feng; Jiang, Jiming

    2010-08-01

    We conducted genome-wide mapping of cytosine methylation using methylcytosine immunoprecipitation combined with Illumina sequencing. The chromosomal distribution pattern of methylated DNA is similar to the heterochromatin distribution pattern on rice chromosomes. The DNA methylation patterns of rice genes are similar to those in Arabidopsis thaliana, including distinct methylation patterns asssociated with gene bodies and promoters. The DNA sequences in the core domains of rice Cen4, Cen5 and Cen8 showed elevated methylation levels compared with sequences in the pericentromeric regions. In addition, elevated methylation levels were associated with the DNA sequences in the CENH3-binding subdomains, compared with the sequences in the flanking H3 subdomains. In contrast, the centromeric domain of Cen11, which is composed exclusively of centromeric satellite DNA, is hypomethylated compared with the pericentromeric domains. Thus, the DNA sequences associated with functional centromeres can be either hypomethylated or hypermethylated. The methylation patterns of centromeric DNA appear to be correlated with the composition of the associated DNA sequences. We propose that both hypomethylation and hypermethylation of CENH3-associated DNA sequences can serve as epigenetic marks to distinguish where CENH3 deposition will occur within the surrounding H3 chromatin.

  1. Printed sectoral horn power combiner

    NASA Astrophysics Data System (ADS)

    Boccia, Luigi; Emanuele, Antonio; Shamsafar, Alireza; Arnieri, Emilio; Amendola, Giandomenico

    2015-02-01

    In this work, it is presented a new configuration of planar power combiner/divider based on an H-plane sectoral horn antenna. This component is proposed to realise the basic building blocks of printed power-combining amplifiers. It will be shown how the sectoral horn elements can be implemented on substrate integrated waveguide and multilayer printed circuit board technologies, thus obtaining a high integration level. In the following, the design procedure will be described reporting an example of an 11-stage power divider/combiner in C-band. A prototype has been fabricated, and the measured results compared with the numerical model. Experimental results are in good agreement with theoretical expectations showing a single-stage efficiency of about 90% and a bandwidth of 40%.

  2. Combined magnetic and gravity analysis

    NASA Technical Reports Server (NTRS)

    Hinze, W. J.; Braile, L. W.; Chandler, V. W.; Mazella, F. E.

    1975-01-01

    Efforts are made to identify methods of decreasing magnetic interpretation ambiguity by combined gravity and magnetic analysis, to evaluate these techniques in a preliminary manner, to consider the geologic and geophysical implications of correlation, and to recommend a course of action to evaluate methods of correlating gravity and magnetic anomalies. The major thrust of the study was a search and review of the literature. The literature of geophysics, geology, geography, and statistics was searched for articles dealing with spatial correlation of independent variables. An annotated bibliography referencing the Germane articles and books is presented. The methods of combined gravity and magnetic analysis techniques are identified and reviewed. A more comprehensive evaluation of two types of techniques is presented. Internal correspondence of anomaly amplitudes is examined and a combined analysis is done utilizing Poisson's theorem. The geologic and geophysical implications of gravity and magnetic correlation based on both theoretical and empirical relationships are discussed.

  3. Combined Endoscopic and Laparoscopic Surgery

    PubMed Central

    Garrett, Kelly A.; Lee, Sang W.

    2015-01-01

    Benign colon polyps are best treated endoscopically. Colon polyps that are not amenable for endoscopic removals either because they are too large or situated in anatomically difficult locations can pose a clinical dilemma. Traditionally the most common recommendation for these patients has been to offer a colon resection. Although the laparoscopic approach has improved short-term outcomes, morbidities associated with bowel resection are still significant. We may be over treating majority of these patients because of the remote possibility that these polyps may be harboring a cancer. A combined approach using both laparoscopy and colonoscopy (combined endoscopic and laparoscopic surgery) has been described as an alternative to bowel resection in select patients with polyps that cannot be removed endoscopically. Polyp removal using this combined approach may be an effective alternative in select patients. PMID:26491405

  4. Phenobarbital Mediates an Epigenetic Switch at the Constitutive Androstane Receptor (CAR) Target Gene Cyp2b10 in the Liver of B6C3F1 Mice

    PubMed Central

    Brasa, Sarah; Teo, Soon-Siong; Roloff, Tim-Christoph; Morawiec, Laurent; Zamurovic, Natasa; Vicart, Axel; Funhoff, Enrico; Couttet, Philippe; Schübeler, Dirk; Grenet, Olivier; Marlowe, Jennifer; Moggs, Jonathan; Terranova, Rémi

    2011-01-01

    Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent histone modifications) may take place at the earliest stages of carcinogenesis and their identification holds great promise for biomedical research. Here, we evaluate the sensitivity and specificity of genome-wide epigenomic and transcriptomic profiling in phenobarbital (PB)-treated B6C3F1 mice, a well-characterized rodent model of non-genotoxic liver carcinogenesis. Methylated DNA Immunoprecipitation (MeDIP)-coupled microarray profiling of 17,967 promoter regions and 4,566 intergenic CpG islands was combined with genome-wide mRNA expression profiling to identify liver tissue-specific PB-mediated DNA methylation and transcriptional alterations. Only a limited number of significant anti-correlations were observed between PB-induced transcriptional and promoter-based DNA methylation perturbations. However, the constitutive androstane receptor (CAR) target gene Cyp2b10 was found to be concomitantly hypomethylated and transcriptionally activated in a liver tissue-specific manner following PB treatment. Furthermore, analysis of active and repressive histone modifications using chromatin immunoprecipitation revealed a strong PB-mediated epigenetic switch at the Cyp2b10 promoter. Our data reveal that PB-induced transcriptional perturbations are not generally associated with broad changes in the DNA methylation status at proximal promoters and suggest that the drug-inducible CAR pathway regulates an epigenetic switch from repressive to active chromatin at the target gene Cyp2b10. This study demonstrates the utility of integrated epigenomic and transcriptomic profiling for elucidating early mechanisms and biomarkers of non-genotoxic carcinogenesis. PMID:21455306

  5. Combination throttle and shutoff valve

    NASA Technical Reports Server (NTRS)

    Carriker, J. W.

    1972-01-01

    Combination of translating sleeve throttle valve and conventional poppet valve provides capability of shutting off flow completely by poppet and sleeve control of the rate of flow. Integration of the two concepts can be accomplished without difficulty and in a manner that requires a minimum of development.

  6. Combined mediastinal and retroperitoneal fibrosis

    PubMed Central

    Salmon, H. W.

    1968-01-01

    A case of combined idiopathic mediastinal fibrosis and retroperitoneal fibrosis is described. It is possibly the twelfth case to be reported during life. A review of the literature reveals the `ubiquity' of localized collagenosis and the trend of opinion as regards aetiology and treatment. Images PMID:5654073

  7. Sentence Combining: A Literature Review.

    ERIC Educational Resources Information Center

    Phillips, Sylvia E.

    Sentence combining--a technique of putting strings of sentence kernels together in a variety of ways so that completed sentences possess greater syntactic maturity--is a method offering much promise in the teaching of writing and composition. The purpose of this document is to provide a literature review of this procedure. After defining the term…

  8. Combined amalgam and composite restorations.

    PubMed

    Abu-Hanna, Amer A; Mjör, Ivar A

    2004-01-01

    All indirect restorative techniques involving cast metals, ceramics or resin-based materials are expensive compared to directly placed restorations. A restorative technique is presented that combines the esthetic properties of directly bonded resin-based composite material and the wide range of indications for dental amalgam in stress-bearing areas.

  9. H gas turbine combined cycle

    SciTech Connect

    Corman, J.

    1995-10-01

    A major step has been taken in the development of the Next Power Generation System - {open_quotes}H{close_quotes} Technology Combined Cycle. This new gas turbine combined-cycle system increases thermal performance to the 60% level by increasing gas turbine operating temperature to 1430 C (2600 F) at a pressure ratio of 23 to 1. Although this represents a significant increase in operating temperature for the gas turbine, the potential for single digit NOx levels (based upon 15% O{sub 2}, in the exhaust) has been retained. The combined effect of performance increase and environmental control is achieved by an innovative closed loop steam cooling system which tightly integrates the gas turbine and steam turbine cycles. The {open_quotes}H{close_quotes} Gas Turbine Combined Cycle System meets the goals and objectives of the DOE Advanced Turbine System Program. The development and demonstration of this new system is being carried out as part of the Industrial/Government cooperative agreement under the ATS Program. This program will achieve first commercial operation of this new system before the end of the century.

  10. Combining Clozapine and Talk Therapies.

    ERIC Educational Resources Information Center

    Mulroy, Kevin

    Clozapine is an antipsychotic medication used in the treatment of schizophrenia. This paper reviews articles concerning clozapine therapy. It considers its benefits and dangers in various situations, and how it can be successfully combined with talk therapies. Studies are reviewed concerning patients in outpatient clinics, partial hospitalization…

  11. Combination Effects of Antimicrobial Peptides

    PubMed Central

    Yu, Guozhi; Baeder, Desiree Y.; Regoes, Roland R.

    2016-01-01

    Antimicrobial peptides (AMPs) are ancient and conserved across the tree of life. Their efficacy over evolutionary time has been largely attributed to their mechanisms of killing. Yet, the understanding of their pharmacodynamics both in vivo and in vitro is very limited. This is, however, crucial for applications of AMPs as drugs and also informs the understanding of the action of AMPs in natural immune systems. Here, we selected six different AMPs from different organisms to test their individual and combined effects in vitro. We analyzed their pharmacodynamics based on the Hill function and evaluated the interaction of combinations of two and three AMPs. Interactions of AMPs in our study were mostly synergistic, and three-AMP combinations displayed stronger synergism than two-AMP combinations. This suggests synergism to be a common phenomenon in AMP interaction. Additionally, AMPs displayed a sharp increase in killing within a narrow dose range, contrasting with those of antibiotics. We suggest that our results could lead a way toward better evaluation of AMP application in practice and shed some light on the evolutionary consequences of antimicrobial peptide interactions within the immune system of organisms. PMID:26729502

  12. Assessing "Combining Forms" in Science.

    ERIC Educational Resources Information Center

    Floriani, Bernard P.; Cairns, Jack C.

    1982-01-01

    Since there appears to be a direct relationship between reading comprehension and vocabulary, an inventory is offered which assesses students' knowledge of the meaning of "combining forms" (automobile, aero-dynamics, etc.) and not words themselves. The inventory can serve as a model to develop additional inventories for Latin/Greek roots.…

  13. Property Attribution in Combined Concepts

    ERIC Educational Resources Information Center

    Spalding, Thomas L.; Gagné, Christina L.

    2015-01-01

    Recent research shows that the judged likelihood of properties of modified nouns ("baby ducks have webbed feet") is reduced relative to judgments for unmodified nouns ("ducks have webbed feet"). This modification effect has been taken as evidence both for and against the idea that combined concepts automatically inherit…

  14. [A study of serum protein fraction binding to indocyanine green (ICG) by combined method of immunoelectrophoresis and ICG fundus videosystem].

    PubMed

    Saito, T; Komatsu, Y; Mori, S; Deguchi, T; Koyama, I; Yoneya, S

    1996-08-01

    Binding characteristics of indocyanine green (ICG) to human serum were investigated, with a combination of immunoelectrophoresis and an ICG fundus video system. Serum samples were obtained from three healthy volunteers, 1 minute after intravenous administration of 50 mg/2 ml ICG, and then fractionated immunoelectrophoretically on agarose plates. Electrophoretic patterns on these plates could be observed with an ICG fundus video system as well as an immunoviewer. Using anti-human sera, only one infrared fluorescent line showing the ICG binding immunoprecipitate was recognized near the area of beta fraction, which was also identified by the use of anti-beta-lipoprotein (Lp) antibody. We also studied the affinity of ICG for apolipoproteins (Apo) AI, B, and CIII, which were the main protein components of serum Lps. Electrophoresis showed that ICG bound only to Apo-B, but not to the others. These results indicated that ICG mainly bound to beta-Lp in the blood, and that ICG angiographic patterns were directly reflecting the dynamics of serum Lps, especially for LDL. The high affinity of ICG for only Apo-B could explain the reason why ICG mainly bound to beta-Lp among several serum Lps, because large amounts of Apo-B are included in beta-Lp but a little in other serum Lps.

  15. [Familial combined hyperlipidemia: consensus document].

    PubMed

    Mata, Pedro; Alonso, Rodrigo; Ruíz-Garcia, Antonio; Díaz-Díaz, Jose L; González, Noemí; Gijón-Conde, Teresa; Martínez-Faedo, Ceferino; Morón, Ignacio; Arranz, Ezequiel; Aguado, Rocío; Argueso, Rosa; Perez de Isla, Leopoldo

    2014-10-01

    Familial combined hyperlipidemia (FCH) is a frequent disorder associated with premature coronary artery disease. It is transmitted in an autosomal dominant manner, although there is not a unique gene involved. The diagnosis is performed using clinical criteria, and variability in lipid phenotype and family history of hyperlipidemia are necessaries. Frequently, the disorder is associated with type2 diabetes mellitus, arterial hypertension and central obesity. Patients with FCH are considered as high cardiovascular risk and the lipid target is an LDL-cholesterol <100mg/dL, and <70mg/dL if cardiovascular disease or type 2 diabetes are present. Patients with FCH require lipid lowering treatment using potent statins and sometimes, combined lipid-lowering treatment. Identification and management of other cardiovascular risk factors as type 2 diabetes and hypertension are fundamental to reduce cardiovascular disease burden. This document gives recommendations for the diagnosis and global treatment of patients with FCH directed to specialists and general practitioners.

  16. Optimizing the new combination treatments.

    PubMed

    Hogan, C

    1996-08-01

    The National Institute of Health's (NIH) Community Programs for Clinical Research on AIDS (CPCRA) working group met in June to explore new treatment options and revisions to health care standards. Protease inhibitors have led to unprecedented effects in clinical trials and show great promise as AIDS treatments. However, little is known about the effect of their long term use, given complicating issues like toxicity and resistance. The group explored the questions of when to start protease inhibitor therapy, with which drug or combination, and when to modify the combination regimen. A consortium of researchers, clinicians, drug company officials, and government representatives, spearheaded by the White House, is working toward a similar standard of treatment. Both groups are exploring ways to design studies for the maximum benefit.

  17. Airbreathing combined cycle engine systems

    NASA Technical Reports Server (NTRS)

    Rohde, John

    1992-01-01

    The Air Force and NASA share a common interest in developing advanced propulsion systems for commercial and military aerospace vehicles which require efficient acceleration and cruise operation in the Mach 4 to 6 flight regime. The principle engine of interest is the turboramjet; however, other combined cycles such as the turboscramjet, air turborocket, supercharged ejector ramjet, ejector ramjet, and air liquefaction based propulsion are also of interest. Over the past months careful planning and program implementation have resulted in a number of development efforts that will lead to a broad technology base for those combined cycle propulsion systems. Individual development programs are underway in thermal management, controls materials, endothermic hydrocarbon fuels, air intake systems, nozzle exhaust systems, gas turbines and ramjet ramburners.

  18. [Familial combined hyperlipidemia: consensus document].

    PubMed

    Mata, Pedro; Alonso, Rodrigo; Ruíz-Garcia, Antonio; Díaz-Díaz, Jose L; González, Noemí; Gijón-Conde, Teresa; Martínez-Faedo, Ceferino; Morón, Ignacio; Arranz, Ezequiel; Aguado, Rocío; Argueso, Rosa; Perez de Isla, Leopoldo

    2014-10-01

    Familial combined hyperlipidemia (FCH) is a frequent disorder associated with premature coronary artery disease. It is transmitted in an autosomal dominant manner, although there is not a unique gene involved. The diagnosis is performed using clinical criteria, and variability in lipid phenotype and family history of hyperlipidemia are necessaries. Frequently, the disorder is associated with type2 diabetes mellitus, arterial hypertension and central obesity. Patients with FCH are considered as high cardiovascular risk and the lipid target is an LDL-cholesterol <100mg/dL, and <70mg/dL if cardiovascular disease or type 2 diabetes are present. Patients with FCH require lipid lowering treatment using potent statins and sometimes, combined lipid-lowering treatment. Identification and management of other cardiovascular risk factors as type 2 diabetes and hypertension are fundamental to reduce cardiovascular disease burden. This document gives recommendations for the diagnosis and global treatment of patients with FCH directed to specialists and general practitioners. PMID:25131181

  19. [Familial combined hyperlipidemia: consensus document].

    PubMed

    Mata, Pedro; Alonso, Rodrigo; Ruíz-Garcia, Antonio; Díaz-Díaz, Jose L; González, Noemí; Gijón-Conde, Teresa; Martínez-Faedo, Ceferino; Morón, Ignacio; Arranz, Ezequiel; Aguado, Rocío; Argueso, Rosa; Perez de Isla, Leopoldo

    2014-10-01

    Familial combined hyperlipidemia (FCH) is a frequent disorder associated with premature coronary artery disease. It is transmitted in an autosomal dominant manner, although there is not a unique gene involved. The diagnosis is performed using clinical criteria, and variability in lipid phenotype and family history of hyperlipidemia are necessaries. Frequently, the disorder is associated with type2 diabetes mellitus, arterial hypertension and central obesity. Patients with FCH are considered as high cardiovascular risk and the lipid target is an LDL-cholesterol <100mg/dL, and <70mg/dL if cardiovascular disease or type 2 diabetes are present. Patients with FCH require lipid lowering treatment using potent statins and sometimes, combined lipid-lowering treatment. Identification and management of other cardiovascular risk factors as type 2 diabetes and hypertension are fundamental to reduce cardiovascular disease burden. This document gives recommendations for the diagnosis and global treatment of patients with FCH directed to specialists and general practitioners. PMID:25034722

  20. NOVEL METHODS FOR TARGET PROTEIN IDENTIFICATION USING IMMUNOPRECIPITATION - LC/MS/MS

    EPA Science Inventory

    Proteomics provides a powerful approach to screen and analyze responses to environmental exposures which induce alterations in protein expression, phosphorylation. ubiquitinylation, oxidation. and modulation of general proteome function. Post-translational modifications (PTM) of ...

  1. Assays to Measure PTEN Lipid Phosphatase Activity In Vitro from Purified Enzyme or Immunoprecipitates.

    PubMed

    Spinelli, Laura; Leslie, Nicholas R

    2016-01-01

    PTEN is a one of the most frequently mutated tumor suppressors in human cancers. It is essential for regulating diverse biological processes and through its lipid phosphatase activity regulates the PI 3-Kinase signaling pathway. Sensitive phosphatase assays are employed to study the catalytic activity of PTEN against phospholipid substrates. Here we describe protocols to assay PTEN lipid phosphatase activity using either purified enzyme (purified PTEN lipid phosphatase assay) or PTEN immunopurified from tissues or cultured cells (cellular IP PTEN lipid phosphatase assay) against vesicles containing radiolabeled PIP3 substrate. PMID:27514802

  2. Insights into the polerovirus-plant interactome revealed by co-immunoprecipitation and mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The identification of host proteins that interact with virus proteins is a major challenge for the field of virology. Phloem-limited viruses pose extraordinary challenges for in vivo protein interaction experiments because these viruses are localized in very few and highly specialized host cells. ...

  3. AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation

    PubMed Central

    2013-01-01

    ChIP-seq is an established manually-performed method for identifying DNA-protein interactions genome-wide. Here, we describe a protocol for automated high-throughput (AHT) ChIP-seq. To demonstrate the quality of data obtained using AHT-ChIP-seq, we applied it to five proteins in mouse livers using a single 96-well plate, demonstrating an extremely high degree of qualitative and quantitative reproducibility among biological and technical replicates. We estimated the optimum and minimum recommended cell numbers required to perform AHT-ChIP-seq by running an additional plate using HepG2 and MCF7 cells. With this protocol, commercially available robotics can perform four hundred experiments in five days. PMID:24200198

  4. Imagining a Stata / Python Combination

    NASA Technical Reports Server (NTRS)

    Fiedler, James

    2012-01-01

    There are occasions when a task is difficult in Stata, but fairly easy in a more general programming language. Python is a popular language for a range of uses. It is easy to use, has many high ]quality packages, and programs can be written relatively quickly. Is there any advantage in combining Stata and Python within a single interface? Stata already offers support for user-written programs, which allow extensive control over calculations, but somewhat less control over graphics. Also, except for specifying output, the user has minimal programmatic control over the user interface. Python can be used in a way that allows more control over the interface and graphics, and in so doing provide a roundabout method for satisfying some user requests (e.g., transparency levels in graphics and the ability to clear the results window). My talk will explore these ideas, present a possible method for combining Stata and Python, and give examples to demonstrate how this combination might be useful.

  5. Combining Psychodynamic Psychotherapy and Pharmacotherapy.

    PubMed

    Gorman, Jack M

    2016-01-01

    Many patients with depression, anxiety disorders, and other psychiatric disorders are treated with combinations of psychodynamic psychotherapy and medication. Whether this is better than monotherapy is an empirical question that requires much more extensive research than is currently available. When medications were first introduced to treat psychiatric illnesses, some psychopharmacologists insisted that it heralded a new area of "biological psychiatry" that would ultimately render psychotherapy obsolete. Psychodynamic theorists and practitioners, on the other hand, argued that psychopharmacology offered only a superficial approach to treatment. Fortunately, these battles are now largely supplanted by the belief that whatever treatment offers the patient the best outcome should be employed, regardless of the therapist's theoretical outlook. This should motivate more extensive study of the value of combination treatment. So far, the few studies that have been done suggest that the combination of psychodynamic psychotherapy and medication may be superior for the treatment of mood and anxiety disorders, but most of these studies have small sample sizes and involve only short-term psychotherapy. An examination of the neuroscience of mood and anxiety disorders and of the mechanism of action of psychodynamic psychotherapy and of antidepressant medication suggests several routes by which the two treatment modalities could be synergistic: stimulation of hippocampal neurogenesis; epigenetic regulation of gene expression; dendritic remodeling; enhanced prefrontal cortical control of limbic system activity; and action at specific neurohormonal and neurotransmitter targets. The evidence for each of these mechanisms is reviewed with an eye toward potential experiments that might be relevant to them.

  6. Combined acoustic and optical trapping

    PubMed Central

    Thalhammer, G.; Steiger, R.; Meinschad, M.; Hill, M.; Bernet, S.; Ritsch-Marte, M.

    2011-01-01

    Combining several methods for contact free micro-manipulation of small particles such as cells or micro-organisms provides the advantages of each method in a single setup. Optical tweezers, which employ focused laser beams, offer very precise and selective handling of single particles. On the other hand, acoustic trapping with wavelengths of about 1 mm allows the simultaneous trapping of many, comparatively large particles. With conventional approaches it is difficult to fully employ the strengths of each method due to the different experimental requirements. Here we present the combined optical and acoustic trapping of motile micro-organisms in a microfluidic environment, utilizing optical macro-tweezers, which offer a large field of view and working distance of several millimeters and therefore match the typical range of acoustic trapping. We characterize the acoustic trapping forces with the help of optically trapped particles and present several applications of the combined optical and acoustic trapping, such as manipulation of large (75 μm) particles and active particle sorting. PMID:22025990

  7. Combining Speed Information Across Space

    NASA Technical Reports Server (NTRS)

    Verghese, Preeti; Stone, Leland S.

    1995-01-01

    We used speed discrimination tasks to measure the ability of observers to combine speed information from multiple stimuli distributed across space. We compared speed discrimination thresholds in a classical discrimination paradigm to those in an uncertainty/search paradigm. Thresholds were measured using a temporal two-interval forced-choice design. In the discrimination paradigm, the n gratings in each interval all moved at the same speed and observers were asked to choose the interval with the faster gratings. Discrimination thresholds for this paradigm decreased as the number of gratings increased. This decrease was not due to increasing the effective stimulus area as a control experiment that increased the area of a single grating did not show a similar improvement in thresholds. Adding independent speed noise to each of the n gratings caused thresholds to decrease at a rate similar to the original no-noise case, consistent with observers combining an independent sample of speed from each grating in both the added- and no-noise cases. In the search paradigm, observers were asked to choose the interval in which one of the n gratings moved faster. Thresholds in this case increased with the number of gratings, behavior traditionally attributed to an input bottleneck. However, results from the discrimination paradigm showed that the increase was not due to observers' inability to process these gratings. We have also shown that the opposite trends of the data in the two paradigms can be predicted by a decision theory model that combines independent samples of speed information across space. This demonstrates that models typically used in classical detection and discrimination paradigms are also applicable to search paradigms. As our model does not distinguish between samples in space and time, it predicts that discrimination performance should be the same regardless of whether the gratings are presented in two spatial intervals or two temporal intervals. Our last

  8. Combined immunodeficiency in a calf.

    PubMed

    Bartram, P A; Smith, B P; Holmberg, C; Mandell, C P

    1989-08-01

    Combined immunodeficiency was documented in a 6-week-old Angus calf. The calf had lymphopenia, undetectable serum IgM or IgA, and low concentrations of serum IgG (420 mg/dl). The calf was treated for diarrhea, pneumonia, and shock, and was given antimicrobial drugs, fluids, and plasma. The calf died of systemic candidiasis and Escherichia coli bacteremia. Aggregated lymphatic folliculi (Peyer patches), lymph nodes, and thymic and splenic lymphoid tissue could not be identified at necropsy. PMID:2768060

  9. Gap and stripline combined monitor

    DOEpatents

    Yin, Y.

    1986-08-19

    A combined gap and stripline monitor device for measuring the intensity and position of a charged particle beam bunch in a beam pipe of a synchrotron radiation facility is disclosed. The monitor has first and second beam pipe portions with an axial gap therebetween. An outer pipe cooperates with the first beam pipe portion to form a gap enclosure, while inner strips cooperate with the first beam pipe portion to form a stripline monitor, with the stripline length being the same as the gap enclosure length. 4 figs.

  10. Gap and stripline combined monitor

    DOEpatents

    Yin, Y.

    1984-02-16

    A combined gap and stripline monitor device for measuring the intensity and position of a charged particle beam bunch in a beam pipe of a synchrotron radiation facility. The monitor has first and second beam pipe portions with an axial gap therebetween. An outer pipe cooperates with the first beam pipe portion to form a gap enclosure, while inner strips cooperate with the first beam pipe portion to form a stripline monitor, with the stripline length being the same as the gap enclosure length.

  11. Gap and stripline combined monitor

    DOEpatents

    Yin, Yan

    1986-01-01

    A combined gap and stripline monitor device (10) for measuring the intensity and position of a charged particle beam bunch in a beam pipe of a synchotron radiation facility. The monitor has first and second beam pipe portions (11a, 11b) with an axial gap (12) therebetween. An outer pipe (14) cooperates with the first beam pipe portion (11a) to form a gap enclosure, while inner strips (23a-d) cooperate with the first beam pipe portion (11a) to form a stripline monitor, with the stripline length being the same as the gap enclosure length.

  12. TLR9 and MyD88 are crucial for the maturation and activation of dendritic cells by paromomycin–miltefosine combination therapy in visceral leishmaniasis

    PubMed Central

    Das, Sushmita; Rani, Mukta; Rabidas, Vidyanand; Pandey, Krishna; Sahoo, Ganesh Chandra; Das, Pradeep

    2014-01-01

    BACKGROUND AND PURPOSE The combination of paromomycin–miltefosine is a successful anti-leishmanial therapy in visceral leishmaniasis (VL). This encouraged us to study its effect on Toll-like receptor (TLR)-mediated immunomodulation of dendritic cells (DC), as DC maturation and activation is crucial for anti-leishmanial activity. EXPERIMENTAL APPROACH In silico protein–ligand interaction and biophysical characterization of TLR9–drug interaction was performed. Interaction assays of HEK293 cells with different concentrations of miltefosine and/or paromomycin were performed, and NF-κB promoter activity measured. The role of TLR9 and MyD88 in paromomycin/miltefosine-induced maturation and activation of DCs was evaluated through RNA interference techniques. The effect of drugs on DCs was measured in terms of counter-regulatory production of IL-12 over IL-10, and characterized by chromatin immunoprecipitation assay at the molecular level. KEY RESULTS Computational and biophysical studies revealed that paromomycin/miltefosine interact with TLR9. Both drugs, as a monotherapy/combination, induced TLR9-dependent NF-κB promoter activity through MyD88. Moreover, the drug combination induced TLR9/MyD88-dependent functional maturation of DCs, evident as an up-regulation of co-stimulatory markers, enhanced antigen presentation by increasing MHC II expression, and increased stimulation of naive T-cells to produce IFN-γ. Both drugs, by modifying histone H3 at the promoter level, increased the release of IL-12, but down-regulated IL-10 in a TLR9-dependent manner. CONCLUSIONS AND IMPLICATIONS These results provide the first evidence that the combination of paromomycin–miltefosine critically modifies the maturation, activation and development of host DCs through a mechanism dependent on TLR9 and MyD88. This has implications for evaluating the success of other combination anti-leishmanial therapies that act by targeting host DCs. PMID:24670148

  13. VACUUM TRAP AND VALVE COMBINATION

    DOEpatents

    Milleron, N.; Levenson, L.

    1963-02-19

    This patent relates to a vacuum trap and valve combination suitable for use in large ultra-high vacuum systems. The vacuum trap is a chamber having an inlet and outlet opening which may be made to communicate with a chamber to be evacuated and a diffusion pump, respectively. A valve is designed to hermeticaliy seal with inlet opening and, when opened, block the line-of- sight'' between the inlet and outlet openings, while allowing a large flow path between the opened vaive and the side walls of the trap. The interior of the trap and the side of the valve facing the inlet opening are covered with an impurity absorbent, such as Zeolite or activated aluminum. Besides the advantage of combining two components of a vacuum system into one, the present invention removes the need for a baffle between the pump and the chamber to be evacuated. In one use of a specific embodiment of this invention, the transmission probability was 45 and the partial pressure of the pump fluid vapor in the vacuum chamber was at least 100 times lower than its vapor pressure. (AEC)

  14. Radiation tolerant combinational logic cell

    NASA Technical Reports Server (NTRS)

    Maki, Gary R. (Inventor); Gambles, Jody W. (Inventor); Whitaker, Sterling (Inventor)

    2009-01-01

    A system has a reduced sensitivity to Single Event Upset and/or Single Event Transient(s) compared to traditional logic devices. In a particular embodiment, the system includes an input, a logic block, a bias stage, a state machine, and an output. The logic block is coupled to the input. The logic block is for implementing a logic function, receiving a data set via the input, and generating a result f by applying the data set to the logic function. The bias stage is coupled to the logic block. The bias stage is for receiving the result from the logic block and presenting it to the state machine. The state machine is coupled to the bias stage. The state machine is for receiving, via the bias stage, the result generated by the logic block. The state machine is configured to retain a state value for the system. The state value is typically based on the result generated by the logic block. The output is coupled to the state machine. The output is for providing the value stored by the state machine. Some embodiments of the invention produce dual rail outputs Q and Q'. The logic block typically contains combinational logic and is similar, in size and transistor configuration, to a conventional CMOS combinational logic design. However, only a very small portion of the circuits of these embodiments, is sensitive to Single Event Upset and/or Single Event Transients.

  15. Combined Corex/DRI technology

    SciTech Connect

    Flickenschild, A.J.; Reufer, F.; Eberle, A.; Siuka, D.

    1996-08-01

    A feasible steelmaking alternative, the Corex/direct reduction/electric arc furnace combination, provides an economic route for the production of high quality steel products. This combination is a major step into a new generation of iron and steel mills. These mills are based on the production of liquid steel using noncoking coal and comply with the increasing demands of environmental protection. The favorable production costs are based on: Utilization of Corex and DRI/HBI plants; Production of hot metal equal to blast furnace quality; Use of low cost raw materials such as noncoking coal and lump ore; Use of process gas as reducing agent for DRI/HBI production; and Use of electric arc furnace with high hot metal input as the steelmaking process. The high flexibility of the process permits the adjustment of production in accordance with the strategy of the steel mills. New but proven technologies and applications of the latest state of art steelmaking process, e.g., Corex, in conjunction with DRI production as basic raw material for an electric arc furnace, will insure high quality, high availability, optimized energy generation at high efficiency rates, and high product quality for steelmaking.

  16. [Tramadol/acetaminophen combination tablets].

    PubMed

    Yokotsuka, Shoko; Kato, Jitsu

    2013-07-01

    Tramadol/acetaminophen fixed-dose combination tablets (Tramse) combine tramadol, a centrally acting week opioid analgesic, with low-dose acetaminophen. The action of tramadol may be described as a weak agonist at the mu-opioid receptor, inhibition of serotonin reuptake, and inhibition of noradrenaline reuptake. The second component in these tablets, acetaminophen mainly appears to act through central mechanism. Chronic pain may be broadly classified into nociceptive, neuropathic and mixed. Tramset may exert additive or synergic benefits in treating the multiple mechanism of pain. Clinical studies have revealed its efficacy and safety for a variety of pain condition such as chronic low back pain, rheumatoid arthritis, fibromyalgia and painful diabetic peripheral neuropathy. It is expected that Tramset is going to induce pain relief and to improve disturbance of daily life in patients with intractable chronic pain. However overuse of Tramset may induce severe adverse effects such as addiction, abuse and hepatotoxicity. Therefore clinician should continuously assess pain intensity, activity of daily life, mode of its consumption, and adverse effects after prescription. PMID:23905401

  17. Curcumin in combined cancer therapy.

    PubMed

    Troselj, Koraljka Gall; Kujundzic, Renata Novak

    2014-01-01

    The mechanisms of beneficial preventive and therapeutic effects achieved by traditional and complementary medicine are currently being deciphered in molecular medicine. Curcumin, a yellow-colored polyphenol derived from the rhizome of turmeric (Curcuma longa), influences a wide variety of cellular processes through the reshaping of many molecular targets. One of them, nuclear factor kappa B (NF-κB), represents a strong mediator of inflammation and, in a majority of systems, supports the pro-proliferative features of cancer cells. The application of various anticancer drugs, cytostatics, triggers signals which lead to an increase in cellular NF-κB activity. As a consequence, cancer cells often reshape their survival signaling pathways and, over time, become resistant to applied therapy. Curcumin was shown to be a strong inhibitor of NF-κB activity and its inhibitory effect on NF-κB related pathways often leads to cellular apoptotic response. All these facts, tested and confirmed in many different biological systems, have paved the way for research aimed to elucidate the potential beneficial effects of combining curcumin and various anti-cancer drugs in order to establish more efficient and less toxic cancer treatment modalities. This review addresses certain aspects of NF-κB-related inflammatory response, its role in carcinogenesis and therapy benefits that may be gained through silencing NF-κB by selectively combining curcumin and various anticancer drugs.

  18. Phonological and Phonetic Asymmetries of Cw Combinations

    ERIC Educational Resources Information Center

    Suh, Yunju

    2009-01-01

    This thesis investigates the relationship between the phonological distribution of Cw combinations, and the acoustic/perceptual distinctiveness between syllables with plain C onsets and with Cw combination onsets. Distributional asymmetries of Cw combinations discussed in this thesis include the avoidance of Cw combinations in the labial consonant…

  19. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Standards for Grades of Apples Grades § 51.304 Combination grades. (a) Combinations of the above grades may... permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the higher grade in the combination....

  20. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Standards for Grades of Apples Grades § 51.304 Combination grades. (a) Combinations of the above grades may... permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the higher grade in the combination....

  1. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Standards for Grades of Apples Grades § 51.304 Combination grades. (a) Combinations of the above grades may... permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the higher grade in the combination....

  2. Ciprofloxacin Therapy Results in Mitigation of ATP Loss after Irradiation Combined with Wound Trauma: Preservation of Pyruvate Dehydrogenase and Inhibition of Pyruvate Dehydrogenase Kinase 1.

    PubMed

    Swift, Joshua M; Smith, Joan T; Kiang, Juliann G

    2015-06-01

    Ionizing radiation exposure combined with wound injury increases animal mortalities than ionizing radiation exposure alone. Ciprofloxacin (CIP) is in the fluroquinolone family of synthetic antibiotic that are available from the strategic national stockpile for emergency use and is known to inhibit bacterial sepsis. The purpose of this study was to evaluate the efficacy of ciprofloxacin as a countermeasure to combined injury mortality and determine the signaling proteins involved in energy machinery. B6D2F1/J female mice were randomly assigned to receive either 9.75 Gy irradiation with Co-60 gamma rays followed by skin wounding (combined injury; CI) or sham procedure (sham). Either ciprofloxacin (90 mg/kg/day) or vehicle (VEH) (water) was administered orally to these mice 2 h after wounding and thereafter daily for 10 days. Determination of tissue adenosine triphosphate (ATP) was conducted, and immunoblotting for signaling proteins involved in ATP machinery was performed. Combined injury resulted in 60% survival after 10 days compared to 100% survival in the sham group. Furthermore, combined injury caused significant reductions of ATP concentrations in ileum, pancreas, brain, spleen, kidney and lung (-25% to -95%) compared to the sham group. Ciprofloxacin administration after combined injury resulted in 100% survival and inhibited reductions in ileum and kidney ATP production. Ileum protein levels of heat-shock protein 70 kDa (HSP-70, a chaperone protein involved in ATP synthesis) and pyruvate dehydrogenase (PDH, an enzyme complex crucial to conversion of pyruvate to acetyl CoA for entrance into TCA cycle) were significantly lower in the CI group (vs. sham group). Using immunoprecipitation and immunoblotting, HSP-70-PDH complex was found to be present in the ileum tissue of CI mice treated with ciprofloxacin. Furthermore, phosphorylation of serine residues of PDH resulting in inactivating PDH enzymatic activity, which occurred after combined injury, was inhibited

  3. Digital Signal Combining for Conference Calling

    NASA Technical Reports Server (NTRS)

    Byrne, F.

    1986-01-01

    Signals combined with minimal noise by use of sums in read-only memories. Signals from subscribers A and B digitized, transmitted, and combined by addressing ROM. Combining operation electronic equivalent of looking up value of function of two variables in mathematical table. Combined digitized signal transmitted, converted to analog form, and delivered to subscriber C. System intended especially for combining number of separate audio signals into one signal for retransmission, as in telephone conference calling.

  4. Combined processing of lead concentrates

    NASA Astrophysics Data System (ADS)

    Kubasov, V. L.; Paretskii, V. M.; Sidorin, G. N.; Travkin, V. F.

    2013-06-01

    A combined scheme of processing of lead concentrates with the production of pure metallic lead and the important components containing in these concentrates is considered. This scheme includes sulfating roasting of the lead concentrates and two-stage leaching of the formed cinder with the formation of a sulfate solution and lead sulfate. When transformed into a carbonate form, lead sulfate is used for the production of pure metallic lead. Silver, indium, copper, cadmium, nickel, cobalt, and other important components are separately extracted from a solution. At the last stage, zinc is extracted by either extraction followed by electrolytic extraction of a metal or the return of the forming solution of sulfuric acid to cinder leaching.

  5. Combination drilling and skiving tool

    DOEpatents

    Stone, William J.

    1989-01-01

    A combination drilling and skiving tool including a longitudinally extending hollow skiving sleeve slidably and concentrically mounted on a right-handed twist drill. Dogs or pawls provided on the internal periphery of the skiving sleeve engage with the helical grooves of the drill. During a clockwise rotation of the tool, the drill moves downwardly and the sleeve translates upwardly, so that the drill performs a drilling operation on a workpiece. On the other hand, the drill moves upwardly and the sleeve translates downwardly, when the tool is rotated in a counter-clockwise direction, and the sleeve performs a skiving operation. The drilling and skiving operations are separate, independent and exclusive of each other.

  6. How rats combine temporal cues.

    PubMed

    Guilhardi, Paulo; Keen, Richard; MacInnis, Mika L M; Church, Russell M

    2005-05-31

    The procedures for classical and operant conditioning, and for many timing procedures, involve the delivery of reinforcers that may be related to the time of previous reinforcers and responses, and to the time of onsets and terminations of stimuli. The behavior resulting from such procedures can be described as bouts of responding that occur in some pattern at some rate. A packet theory of timing and conditioning is described that accounts for such behavior under a wide range of procedures. Applications include the food searching by rats in Skinner boxes under conditions of fixed and random reinforcement, brief and sustained stimuli, and several response-food contingencies. The approach is used to describe how multiple cues from reinforcers and stimuli combine to determine the rate and pattern of response bouts.

  7. Combined PET/MRI scanner

    DOEpatents

    Schlyer, David; Woody, Craig L.; Rooney, William; Vaska, Paul; Stoll, Sean; Pratte, Jean-Francois; O'Connor, Paul

    2007-10-23

    A combined PET/MRI scanner generally includes a magnet for producing a magnetic field suitable for magnetic resonance imaging, a radiofrequency (RF) coil disposed within the magnetic field produced by the magnet and a ring tomograph disposed within the magnetic field produced by the magnet. The ring tomograph includes a scintillator layer for outputting at least one photon in response to an annihilation event, a detection array coupled to the scintillator layer for detecting the at least one photon outputted by the scintillator layer and for outputting a detection signal in response to the detected photon and a front-end electronic array coupled to the detection array for receiving the detection signal, wherein the front-end array has a preamplifier and a shaper network for conditioning the detection signal.

  8. [Combined orthodontic and restorative treatment].

    PubMed

    Kuijpers, M A R; Loomans, B

    2015-11-01

    In patients with agenesis or enamel anomalies in anterior teeth combined orthodontic and restorative treatment is often necessary to achieve an optimal aesthetic result. How both can best be achieved, but also how to maintain the result, requires communication between the dentist and the orthodontist. The orthodontic treatment plan needs to be established in cooperation with the dentist who will carry out the restorative treatment while the patient is at a young age. Since with these young patients, who are still growing craniofacially and whose teeth are still developing, possible future restorative and/or orthodontic treatment, as well as the means of orthodontic retention, need to be included in the treatment plan. In cleft palate patients, it is also important that methods of orthodontic retention of maxillary arch width are given timely attention in the restorative treatment plan because it is especially vulnerable to relapse. PMID:26568998

  9. Food combinations for cholesterol lowering.

    PubMed

    Harland, Janice I

    2012-12-01

    Reducing elevated LDL-cholesterol is a key public health challenge. There is substantial evidence from randomised controlled trials (RCT) that a number of foods and food components can significantly reduce LDL-cholesterol. Data from RCT have been reviewed to determine whether effects are additive when two or more of these components are consumed together. Typically components, such as plant stanols and sterols, soya protein, β-glucans and tree nuts, when consumed individually at their target rate, reduce LDL-cholesterol by 3-9 %. Improved dietary fat quality, achieved by replacing SFA with unsaturated fat, reduces LDL-cholesterol and can increase HDL-cholesterol, further improving blood lipid profile. It appears that the effect of combining these interventions is largely additive; however, compliance with multiple changes may reduce over time. Food combinations used in ten 'portfolio diet' studies have been reviewed. In clinical efficacy studies of about 1 month where all foods were provided, LDL-cholesterol is reduced by 22-30 %, whereas in community-based studies of >6 months' duration, where dietary advice is the basis of the intervention, reduction in LDL-cholesterol is about 15 %. Inclusion of MUFA into 'portfolio diets' increases HDL-cholesterol, in addition to LDL-cholesterol effects. Compliance with some of these dietary changes can be achieved more easily compared with others. By careful food component selection, appropriate to the individual, the effect of including only two components in the diet with good compliance could be a sustainable 10 % reduction in LDL-cholesterol; this is sufficient to make a substantial impact on cholesterol management and reduce the need for pharmaceutical intervention.

  10. Combining ESP and baghouse technology

    SciTech Connect

    Rowland, B.; Ganatra, C.P.; Woolston, J.

    1994-12-31

    The authors present a progressive application in the field of air pollution control technology. The content of this paper should appeal to operators who must operate out-of-compliance electrostatic precipitators (ESPs), or to those who strive for optimal emission control. St. Lawrence Cement Company, a plant in Beauport Canada, has been in operation since 1955. Their two wet process kilns have utilized electrostatic precipitator (ESP) filters since inception. Since 1965, this company has strived to reduce energy consumption by using alternative waste fuel. This, combined with the increased demand of low alkali cement, took its toll on the ESPs, causing the equipment and its performance to deteriorate. Pressure from environmental agencies to lower outlet emissions forced the company to consider ESP modifications. After investigating several alternatives, the optimal modification was to combine the ESP with bag filters. In addition to being the best choice from a performance standpoint, it was also the least expensive. This modification also allowed a reduced alkali dust from the ESP hoppers to be recirculated to the kilns. The latter two-thirds of the ESP were converted to a baghouse, and optimal system performance was achieved by using high efficiency expanded polytetrafluoroethylene (ePTFE) membrane filter bags. Despite the high moisture, submicron particle size, and cohesive nature of the alkaline dust, very low pressure differentials and extremely low emissions were achieved. Most notably, this complex project was completed within nine months, from concept to commissioning. The plant was shut down for only six weeks during the entire retrofit process. This economically attractive idea was readily accepted by St. Lawrence Cement personnel and the permitting agencies. After the first successful kiln/ESP retrofit, the second kiln/ESP conversion was completed the following year.

  11. Molecular diagnosis of Prader-Willi syndrome: Comparison of cytogenetic and molecular genetic data including parent of origin dependent methylation DNA patterns

    SciTech Connect

    Butler, M.G.

    1996-01-11

    This letter to the editor discusses a recent study concerning the parent-of-origin methylation site at D15S63 and its application in molecular diagnostics confirming Prader-Willi syndrome (PWS). It concludes that more research is needed to clear up questions which remain regarding the causation of PWS. 20 refs., 1 tab.

  12. The methylated-DNA binding protein MBD2 enhances NGFI-A (egr-1)-mediated transcriptional activation of the glucocorticoid receptor.

    PubMed

    Weaver, Ian C G; Hellstrom, Ian C; Brown, Shelley E; Andrews, Stephen D; Dymov, Sergiy; Diorio, Josie; Zhang, Tie-Yuan; Szyf, Moshe; Meaney, Michael J

    2014-09-26

    Variations in maternal care in the rat influence the epigenetic state and transcriptional activity of glucocorticoid receptor (GR) gene in the hippocampus. The mechanisms underlying this maternal effect remained to be defined, including the nature of the relevant maternally regulated intracellular signalling pathways. We show here that increased maternal licking/grooming (LG), which stably enhances hippocampal GR expression, paradoxically increases hippocampal expression of the methyl-CpG binding domain protein-2 (MBD2) and MBD2 binding to the exon 17 GR promoter. Knockdown experiments of MBD2 in hippocampal primary cell culture show that MBD2 is required for activation of exon 17 GR promoter. Ectopic co-expression of nerve growth factor-inducible protein A (NGFI-A) with MBD2 in HEK 293 cells with site-directed mutagenesis of the NGFI-A response element within the methylated exon 17 GR promoter supports the hypothesis that MBD2 collaborates with NGFI-A in binding and activation of this promoter. These data suggest a possible mechanism linking signalling pathways, which are activated by behavioural stimuli and activation of target genes.

  13. MeCP2 binds to non-CG methylated DNA as neurons mature, influencing transcription and the timing of onset for Rett syndrome.

    PubMed

    Chen, Lin; Chen, Kaifu; Lavery, Laura A; Baker, Steven Andrew; Shaw, Chad A; Li, Wei; Zoghbi, Huda Y

    2015-04-28

    Epigenetic mechanisms, such as DNA methylation, regulate transcriptional programs to afford the genome flexibility in responding to developmental and environmental cues in health and disease. A prime example involving epigenetic dysfunction is the postnatal neurodevelopmental disorder Rett syndrome (RTT), which is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MeCP2). Despite decades of research, it remains unclear how MeCP2 regulates transcription or why RTT features appear 6-18 months after birth. Here we report integrated analyses of genomic binding of MeCP2, gene-expression data, and patterns of DNA methylation. In addition to the expected high-affinity binding to methylated cytosine in the CG context (mCG), we find a distinct epigenetic pattern of substantial MeCP2 binding to methylated cytosine in the non-CG context (mCH, where H = A, C, or T) in the adult brain. Unexpectedly, we discovered that genes that acquire elevated mCH after birth become preferentially misregulated in mouse models of MeCP2 disorders, suggesting that MeCP2 binding at mCH loci is key for regulating neuronal gene expression in vivo. This pattern is unique to the maturing and adult nervous system, as it requires the increase in mCH after birth to guide differential MeCP2 binding among mCG, mCH, and nonmethylated DNA elements. Notably, MeCP2 binds mCH with higher affinity than nonmethylated identical DNA sequences to influence the level of Bdnf, a gene implicated in the pathophysiology of RTT. This study thus provides insight into the molecular mechanism governing MeCP2 targeting and sheds light on the delayed onset of RTT symptoms.

  14. Activating Transcription Factor 3 regulates in part the enhanced tumour cell cytotoxicity of the histone deacetylase inhibitor M344 and cisplatin in combination

    PubMed Central

    2010-01-01

    Background Activating Transcription Factor (ATF) 3 is a key regulator of the cellular integrated stress response whose expression has also been correlated with pro-apoptotic activities in tumour cell models. Combination treatments with chemotherapeutic drugs, such as cisplatin, and histone deacetylase (HDAC) inhibitors have been demonstrated to enhance tumour cell cytotoxicity. We recently demonstrated a role for ATF3 in regulating cisplatin-induced apoptosis and others have shown that HDAC inhibition can also induce cellular stress. In this study, we evaluated the role of ATF3 in regulating the co-operative cytotoxicity of cisplatin in combination with an HDAC inhibitor. Results The HDAC inhibitor M344 induced ATF3 expression at the protein and mRNA level in a panel of human derived cancer cell lines as determined by Western blot and quantitative RT-PCR analyses. Combination treatment with M344 and cisplatin lead to increased induction of ATF3 compared with cisplatin alone. Utilizing the MTT cell viability assay, M344 treatments also enhanced the cytotoxic effects of cisplatin in these cancer cell lines. The mechanism of ATF3 induction by M344 was found to be independent of MAPKinase pathways and dependent on ATF4, a known regulator of ATF3 expression. ATF4 heterozygote (+/-) and knock out (-/-) mouse embryonic fibroblast (MEF) as well as chromatin immunoprecipitation (ChIP) assays were utilized in determining the mechanistic induction of ATF3 by M344. We also demonstrated that ATF3 regulates the enhanced cytotoxicity of M344 in combination with cisplatin as evidenced by attenuation of cytotoxicity in shRNAs targeting ATF3 expressing cells. Conclusion This study identifies the pro-apoptotic factor, ATF3 as a novel target of M344, as well as a mediator of the co-operative effects of cisplatin and M344 induced tumour cell cytotoxicity. PMID:20828393

  15. [Keratoplasty combined with cataract surgery].

    PubMed

    Muraine, M; Gueudry, J; Retout, A; Genevois, O

    2012-09-01

    Corneal pathologies leading to keratoplasty are often associated with cataract and combined surgery is therefore mandatory. Triple procedure with penetrating keratoplasty and concurrent cataract extraction followed by intra ocular lens (IOL) implantation is usually the preferential choice because visual rehabilitation is theoretically more rapid. Surgeons have to be aware of surgical conditions during open-sky surgery because vitreous pressure is not counterbalanced by anterior chamber pressure. Today, many surgeons prefer non-simultaneous procedures with cataract surgery performed months after grafting because of the improvement in spherical refractive error. More recently, new triple procedures, Descemet's stripping automated keratoplasty and concurrent cataract surgery have gained popularity, especially in patients with Fuchs dystrophy associated with cataract. Surgery starts with phacoemulsification, followed by endothelium exchange through a 3 to 5 mm incision. Advantages against classic triple procedure are quick visual rehabilitation, fewer induced refractive errors, minimal postoperative discomfort and corneal integrity. Surgeons have to consider an eventual postoperative hyperopic shift secondary to corneal lenticule shape when choosing adequate intraocular lens. PMID:22921023

  16. [Keratoplasty combined with cataract surgery].

    PubMed

    Muraine, M; Gueudry, J; Retout, A; Genevois, O

    2012-09-01

    Corneal pathologies leading to keratoplasty are often associated with cataract and combined surgery is therefore mandatory. Triple procedure with penetrating keratoplasty and concurrent cataract extraction followed by intra ocular lens (IOL) implantation is usually the preferential choice because visual rehabilitation is theoretically more rapid. Surgeons have to be aware of surgical conditions during open-sky surgery because vitreous pressure is not counterbalanced by anterior chamber pressure. Today, many surgeons prefer non-simultaneous procedures with cataract surgery performed months after grafting because of the improvement in spherical refractive error. More recently, new triple procedures, Descemet's stripping automated keratoplasty and concurrent cataract surgery have gained popularity, especially in patients with Fuchs dystrophy associated with cataract. Surgery starts with phacoemulsification, followed by endothelium exchange through a 3 to 5 mm incision. Advantages against classic triple procedure are quick visual rehabilitation, fewer induced refractive errors, minimal postoperative discomfort and corneal integrity. Surgeons have to consider an eventual postoperative hyperopic shift secondary to corneal lenticule shape when choosing adequate intraocular lens.

  17. Pulling Seton: Combination of mechanisms

    PubMed Central

    Izadpanah, Ahmad; Rezazadehkermani, Mohammad; Hosseiniasl, Seyed Mohammad; Farghadin, Afrouz; Ghahramani, Leila; Bananzadeh, Alimohammad; Roshanravan, Reza; Izadpanah, Ahad

    2016-01-01

    Background: Seton-based techniques are among popular methods for treating high type anal fistula. These techniques are categorized to cutting and noncutting regarding their mechanism of action. In this report we are about to describe a new technique, which is a combination of both mechanisms; we call it Pulling Seton. Materials and Methods: In this technique after determining internal and external orifice of fistula, fistulectomy is done from both ends to the level of external sphincteric muscle. Finally, a remnant of fistula, which remains beneath external sphincteric muscle is excised, and Seton is passed instead of it and tied externally. After the wound heals, patient is asked to pull down the Seton for 3–4 min, 4 times a day. We prospectively enrolled 201 patients with high type anal fistula in this study. Results: Seton gradually passes through external sphincteric muscle till it is displaced outwards or removed by a surgeon via a small incision. 94% of patients treated by this method accomplished their treatment completely without recurrence. None of the patients developed permanent fecal or gas incontinence. Only 5% of patients developed with recurrence of fistula. Since Seton traction is not permanent in this technique, Seton cuts external sphincter slowly, and minimal rate of incontinence is reported. Conclusion: Pulling Seton seems to be an efficient way in treating high type anal fistula with minimal rate of recurrence and complications such as incontinence and authors suggest further randomized studies to compare its efficacy with other Seton-based techniques. PMID:27169099

  18. Combination coal and wood stove

    SciTech Connect

    Gillis, G.A.; Lucier, R.

    1983-05-17

    The combination stove has a fire chamber that is partially cylindrical including a side loading door for loading wood or other combustible material such as coke or coal into the fire chamber. The front of the stove may be opened to enable viewing of the wood or coal burning in the stove by means of an arcuate sliding door that is operable to substantially totally close the chamber or open a section of the front thereof for viewing purposes. The sliding door is covered by a window construction including a tempered glass face. The stove is provided with an open base for supporting the chamber in a shroud covering the top and back of the chamber, preferably including blower means associated therewith. Particularly for wood combustion, the chamber is provided with a top draft extending longitudinally of the chamber and has supported therein a grate. For coal combustion, air input draft is coupled under the grate, preferably also including the capability of forced air draft using a portion of the forced air from the blower.

  19. Externally fired combined cycle demonstration

    SciTech Connect

    Orozco, N.J.; Young, S.; LaHaye, P.G.; Strom-Olsen, J.; Seger, J.L.; Pickup, H.

    1995-11-01

    Externally Fired Combined Cycles (EFCCs) can increase the amount of electricity produced from ash bearing fuels up to 40%, with overall powerplant efficiencies in excess of 45%. Achieving such high efficiencies requires high temperature-high pressure air heaters capable of driving modern gas turbines from gas streams containing the products of coal combustion. A pilot plant has been constructed in Kennebunk, Maine to provide proof of concept and evaluation of system components. Tests using pulverized Western Pennsylvania bituminous coal have been carried out since April, 1995. The ceramic air heater extracts energy from the products of coal combustion to power a gas turbine. This air heater has operated at gas inlet temperatures over 1,095 C and pressures over 7.0 atm without damage to the ceramic tube string components. Stable gas turbine operation has been achieved with energy input from the air heater and a supplementary gas fired combustor. Efforts are underway to fire the cycle on coal only, and to increase the duration of the test runs. Air heater improvements are being implemented and evaluated. These improvements include installation of a second pass of ceramic tubes and evaluation of corrosion resistant coatings on the ceramic tubes.

  20. Combined control-structure optimization

    NASA Technical Reports Server (NTRS)

    Salama, M.; Milman, M.; Bruno, R.; Scheid, R.; Gibson, S.

    1989-01-01

    An approach for combined control-structure optimization keyed to enhancing early design trade-offs is outlined and illustrated by numerical examples. The approach employs a homotopic strategy and appears to be effective for generating families of designs that can be used in these early trade studies. Analytical results were obtained for classes of structure/control objectives with linear quadratic Gaussian (LQG) and linear quadratic regulator (LQR) costs. For these, researchers demonstrated that global optima can be computed for small values of the homotopy parameter. Conditions for local optima along the homotopy path were also given. Details of two numerical examples employing the LQR control cost were given showing variations of the optimal design variables along the homotopy path. The results of the second example suggest that introducing a second homotopy parameter relating the two parts of the control index in the LQG/LQR formulation might serve to enlarge the family of Pareto optima, but its effect on modifying the optimal structural shapes may be analogous to the original parameter lambda.

  1. Efficient Web Services Policy Combination

    NASA Technical Reports Server (NTRS)

    Vatan, Farrokh; Harman, Joseph G.

    2010-01-01

    Large-scale Web security systems usually involve cooperation between domains with non-identical policies. The network management and Web communication software used by the different organizations presents a stumbling block. Many of the tools used by the various divisions do not have the ability to communicate network management data with each other. At best, this means that manual human intervention into the communication protocols used at various network routers and endpoints is required. Developing practical, sound, and automated ways to compose policies to bridge these differences is a long-standing problem. One of the key subtleties is the need to deal with inconsistencies and defaults where one organization proposes a rule on a particular feature, and another has a different rule or expresses no rule. A general approach is to assign priorities to rules and observe the rules with the highest priorities when there are conflicts. The present methods have inherent inefficiency, which heavily restrict their practical applications. A new, efficient algorithm combines policies utilized for Web services. The method is based on an algorithm that allows an automatic and scalable composition of security policies between multiple organizations. It is based on defeasible policy composition, a promising approach for finding conflicts and resolving priorities between rules. In the general case, policy negotiation is an intractable problem. A promising method, suggested in the literature, is when policies are represented in defeasible logic, and composition is based on rules for non-monotonic inference. In this system, policy writers construct metapolicies describing both the policy that they wish to enforce and annotations describing their composition preferences. These annotations can indicate whether certain policy assertions are required by the policy writer or, if not, under what circumstances the policy writer is willing to compromise and allow other assertions to take

  2. Combining Individual Psychodynamics with Structural Family Therapy.

    ERIC Educational Resources Information Center

    Melito, Richard

    1988-01-01

    Presents integrative framework for combining central aspects of individual psychodynamics with structural family therapy in meaningful way. Explains how framework derives from developmental perspective. Presents case example to illustrate combined approach and demonstrate its utility. (Author/NB)

  3. Improving Writing with Sentence Combining Exercises.

    ERIC Educational Resources Information Center

    Nutter, Norma; Safran, Joan

    1984-01-01

    Sentence-combining exercises, which require students to combine simple sentences in any way they wish, have helped learning disabled elementary children improve skills in writing, reading, and spelling. The exercises are flexible, motivating, and simple to design. (CL)

  4. Combining fluorescence and bioluminescence microscopy.

    PubMed

    Goda, Kazuhito; Hatta-Ohashi, Yoko; Akiyoshi, Ryutaro; Sugiyama, Takashi; Sakai, Ikuko; Takahashi, Takeo; Suzuki, Hirobumi

    2015-08-01

    Bioluminescence microscopy has revealed that gene expression in individual cells can respond differently to the same stimulus. To understand this phenomenon, it is important to sequentially observe the series of events from cellular signal transduction to gene expression regulated by specific transcription factors derived from signaling cascades in individual cells. However, these processes have been separately analyzed with fluorescence and bioluminescence microscopy. Furthermore, in culture medium, the background fluorescence of luciferin-a substrate of luciferase in promoter assays of gene expression in cultured cells-confounds the simultaneous observation of fluorescence and bioluminescence. Therefore, we optimized conditions for optical filter sets based on spectral properties and the luciferin concentration based on cell permeability for fluorescence observation combined with bioluminescence microscopy. An excitation and emission filter set (492-506 nm and 524-578 nm) was suitable for green fluorescent protein and yellow fluorescent protein imaging of cells, and >100 μM luciferin was acceptable in culture medium based on kinetic constants and the estimated intracellular concentration. Using these parameters, we present an example of sequential fluorescence and bioluminescence microscopic observation of signal transduction (translocation of protein kinase C alpha from the cytoplasm to the plasma membrane) coupled with activation of gene expression by nuclear factor of kappa light polypeptide B in individual cells and show that the gene expression response is not completely concordant with upstream signaling following stimulation with phorbol-12-myristate-13-acetate. Our technique is a powerful imaging tool for analysis of heterogeneous gene expression together with upstream signaling in live single cells.

  5. Combining fluorescence and bioluminescence microscopy.

    PubMed

    Goda, Kazuhito; Hatta-Ohashi, Yoko; Akiyoshi, Ryutaro; Sugiyama, Takashi; Sakai, Ikuko; Takahashi, Takeo; Suzuki, Hirobumi

    2015-08-01

    Bioluminescence microscopy has revealed that gene expression in individual cells can respond differently to the same stimulus. To understand this phenomenon, it is important to sequentially observe the series of events from cellular signal transduction to gene expression regulated by specific transcription factors derived from signaling cascades in individual cells. However, these processes have been separately analyzed with fluorescence and bioluminescence microscopy. Furthermore, in culture medium, the background fluorescence of luciferin-a substrate of luciferase in promoter assays of gene expression in cultured cells-confounds the simultaneous observation of fluorescence and bioluminescence. Therefore, we optimized conditions for optical filter sets based on spectral properties and the luciferin concentration based on cell permeability for fluorescence observation combined with bioluminescence microscopy. An excitation and emission filter set (492-506 nm and 524-578 nm) was suitable for green fluorescent protein and yellow fluorescent protein imaging of cells, and >100 μM luciferin was acceptable in culture medium based on kinetic constants and the estimated intracellular concentration. Using these parameters, we present an example of sequential fluorescence and bioluminescence microscopic observation of signal transduction (translocation of protein kinase C alpha from the cytoplasm to the plasma membrane) coupled with activation of gene expression by nuclear factor of kappa light polypeptide B in individual cells and show that the gene expression response is not completely concordant with upstream signaling following stimulation with phorbol-12-myristate-13-acetate. Our technique is a powerful imaging tool for analysis of heterogeneous gene expression together with upstream signaling in live single cells. PMID:26096873

  6. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ..., DEPARTMENT OF THE TREASURY LIQUORS âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and distributing distilled spirits, wine, or malt beverages in combination... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Combination packaging....

  7. 49 CFR 387.305 - Combination vehicles.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 5 2011-10-01 2011-10-01 false Combination vehicles. 387.305 Section 387.305 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY... § 387.305 Combination vehicles. The following combinations will be regarded as one motor vehicle...

  8. 49 CFR 387.305 - Combination vehicles.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 5 2010-10-01 2010-10-01 false Combination vehicles. 387.305 Section 387.305 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL MOTOR CARRIER SAFETY... § 387.305 Combination vehicles. The following combinations will be regarded as one motor vehicle...

  9. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Apples Grades § 51.304 Combination grades...) Combinations other than these are not permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the...

  10. 7 CFR 51.304 - Combination grades.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Standards for Grades of Apples Grades § 51.304 Combination grades...) Combinations other than these are not permitted in connection with the U.S. apple grades. When Combination grades are packed, at least 50 percent of the apples in any lot shall meet the requirements of the...

  11. Power combining of semiconductor lasers: A review

    NASA Technical Reports Server (NTRS)

    Katz, J.

    1982-01-01

    Several methods of coherent power combining are described and compared. A comparison is also made between coherent and incoherent power combining, and important operational characteristics are considered. It is found that in communication links with demanding requirements coherent power combining is necessary.

  12. 7 CFR 4280.193 - Combined funding.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 15 2011-01-01 2011-01-01 false Combined funding. 4280.193 Section 4280.193... Efficiency Improvements Program Section D. Combined Funding § 4280.193 Combined funding. The requirements for... if the project meets the requirements specified in § 4280.109. (b) Funding. Funding provided...

  13. 7 CFR 4280.193 - Combined funding.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 15 2010-01-01 2010-01-01 false Combined funding. 4280.193 Section 4280.193... Efficiency Improvements Program Section D. Combined Funding § 4280.193 Combined funding. The requirements for... if the project meets the requirements specified in § 4280.109. (b) Funding. Funding provided...

  14. Early Combinations of Words and Actions.

    ERIC Educational Resources Information Center

    Shore, Cecilia

    Previous research has shown a similar starting time for early combinations of words and play actions in children and has suggested that similar cognitive processes underlie the transition to combining activities in language, symbolic play, and manipulative play. A study was undertaken to investigate combining activities in these three domains and…

  15. Comparative analysis of human mitochondrial methylomes shows distinct patterns of epigenetic regulation in mitochondria.

    PubMed

    Ghosh, Sourav; Sengupta, Shantanu; Scaria, Vinod

    2014-09-01

    DNA methylation and histone modifications across the nuclear genome have been extensively analyzed, but the epigenetic modifications associated with the mitochondrial genome have not yet been analyzed at high resolutions. In the present work, we analyzed methyl-cytosine profiles from methylated DNA immunoprecipitation datasets from 39 different human cell and tissue types from the NIH Roadmap Epigenomics project and validated the data using an orthologous bisulfite sequencing dataset. We observe a distinct distribution of zmethyl-cytosine in mitochondrial genomes which are conserved across all cell and tissue types. This study thus describes the first comprehensive map of methyl cytosines across the human mitochondrial genome.

  16. [FIXED COMBINATION ATORVASTATIN-EZETIMIBE (ATOZET®)].

    PubMed

    Scheen, A J

    2016-01-01

    Cardiovascular prevention in subjects at high or very high risk requires a drastic reduction in LDL cholesterol according to the concept "the lower, the better". The combination of an inhibitor of cholesterol synthesis and a selective inhibitor of intestinal absorption results in a complementary and synergistic LDL-lowering activity. Besides a first fixed combination ezetimibe-simvastatin (Inegy®), a new fixed combination is presented, Atozet® that combines atorvastatin and ezetimibe. Because atorvastatin is more potent than simvastatin, this novel fixed combination should facilitate reaching therapeutic goals in terms of LDL cholesterol amongst patients with severe hypercholesterolaemia and/or at high or very high cardiovascular risk.

  17. Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus

    PubMed Central

    Kim, Soonok; Hu, Jinnan; Oh, Yeonyee; Park, Jongsun; Choi, Jinhee; Lee, Yong-Hwan; Dean, Ralph A.; Mitchell, Thomas K.

    2010-01-01

    Significant progress has been made in defining the central signaling networks in many organisms, but collectively we know little about the downstream targets of these networks and the genes they regulate. To reconstruct the regulatory circuit of calcineurin signal transduction via MoCRZ1, a Magnaporthe oryzae C2H2 transcription factor activated by calcineurin dephosphorylation, we used a combined approach of chromatin immunoprecipitation - chip (ChIP-chip), coupled with microarray expression studies. One hundred forty genes were identified as being both a direct target of MoCRZ1 and having expression concurrently differentially regulated in a calcium/calcineurin/MoCRZ1 dependent manner. Highly represented were genes involved in calcium signaling, small molecule transport, ion homeostasis, cell wall synthesis/maintenance, and fungal virulence. Of particular note, genes involved in vesicle mediated secretion necessary for establishing host associations, were also found. MoCRZ1 itself was a target, suggesting a previously unreported autoregulation control point. The data also implicated a previously unreported feedback regulation mechanism of calcineurin activity. We propose that calcium/calcineurin regulated signal transduction circuits controlling development and pathogenicity manifest through multiple layers of regulation. We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen. PMID:20502632

  18. Design of photonic crystal splitters/combiners

    NASA Astrophysics Data System (ADS)

    Kim, Sangin; Park, Ikmo; Lim, Hanjo

    2004-10-01

    Photonic band gap (PBG) structures or photonic crystals have attracted a lot of interest since one of their promising applications is to build compact photonic integrated circuits (PIC). One of key components in PICs is a 1 x 2 optical power splitter or a 2 x 1 combiner. Design of 1 x 2 optical power splitters based on photonic crystal has been investigated by several research groups, but no attention has been paid to the design of 2 x 1 optical combiners. In conventional dielectric waveguide based circuits, optical combiners are obtained just by operating the splitters in the opposite direction and the isolation between two input ports in the combiners is naturally achieved. In photonic crystal based circuits, however, we have found that reciprocal operation of the splitters as combiners will not provide proper isolation between the input ports of the combiners. In this work, microwave-circuit concept has been adopted to obtain isolation between two input ports of the combiner and compact optical power splitters/combiners of good performance have been designed using 2-D photonic crystal. Numerical analysis of the designed splitters/combiners has been performed with the finite-difference time-domain method. The designed splitters/combiners show good isolation between input ports in combiner operation with small return losses.

  19. Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing.

    PubMed

    Fujita, Toshitsugu; Yuno, Miyuki; Okuzaki, Daisuke; Ohki, Rieko; Fujii, Hodaka

    2015-01-01

    Accumulating evidence suggests that RNAs interacting with genomic regions play important roles in the regulation of genome functions, including X chromosome inactivation and gene expression. However, to our knowledge, no non-biased methods of identifying RNAs that interact with a specific genomic region have been reported. Here, we used enChIP-RNA-Seq, a combination of engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and RNA sequencing (RNA-Seq), to perform a non-biased search for RNAs interacting with telomeres. In enChIP-RNA-Seq, the target genomic regions are captured using an engineered DNA-binding molecule such as a transcription activator-like protein. Subsequently, RNAs that interact with the target genomic regions are purified and sequenced. The RNAs detected by enChIP-RNA-Seq contained known telomere-binding RNAs, including the telomerase RNA component (Terc), the RNA component of mitochondrial RNA processing endoribonuclease (Rmrp), and Cajal body-specific RNAs. In addition, a number of novel telomere-binding non-coding RNAs were also identified. Binding of two candidate non-coding RNAs to telomeres was confirmed by immunofluorescence microscopy and RNA fluorescence in situ hybridization (RNA-FISH) analyses. The novel telomere-binding non-coding RNAs identified here may play important roles in telomere functions. To our knowledge, this study is the first non-biased identification of RNAs associated with specific genomic regions. The results presented here suggest that enChIP-RNA-Seq analyses are useful for the identification of RNAs interacting with specific genomic regions, and may help to contribute to current understanding of the regulation of genome functions.

  20. IF-combined smRNA FISH reveals interaction of MCPIP1 protein with IER3 mRNA

    PubMed Central

    Kochan, Jakub; Wawro, Mateusz

    2016-01-01

    ABSTRACT MCPIP1 and IER3 are recently described proteins essential for maintenance of immune homeostasis. IER3 is involved in the regulation of apoptosis and differentiation and has been shown lately to protect activated T cells and macrophages from apoptosis. MCPIP1 is an RNase critical for controlling inflammation-related mRNAs. MCPIP1 interacts with and degrades a set of stem-loop-containing mRNAs (including IL-6). Our results demonstrate the involvement of MCPIP1 in the regulation of IER3 mRNA levels. A dual luciferase assay revealed that over-expression of MCPIP1 resulted in a decrease of luciferase activity in the samples co-transfected with constructs containing luciferase CDS attached to IER3 3′UTR. We identified a stem-loop structure similar to that described to be important for destabilization of the IL-6 mRNA by MCPIP1. Examination of IER3 3′UTR sequence, structure and evolutionary conservation revealed that the identified stem-loop is buried within a bigger element. Deletion of this fragment abolished the regulation of IER3 3′UTR-containing transcript by MCPIP1. Finally, using immunofluorescence-combined single-molecule RNA FISH we have shown that the MCPIP1 protein co-localizes with IER3 mRNA. By this method we also proved that the presence of the wild-type NYN/PIN-like domain of MCPIP1 correlated with the decreased level of IER3 mRNA. RNA immunoprecipitation further confirmed the interaction of MCPIP1 with IER3 transcripts in vivo. PMID:27256408

  1. Strategy application, observability, and the choice combinator.

    SciTech Connect

    Winter, Victor Lono

    2004-03-01

    In many strategic systems, the choice combinator provides a powerful mechanism for controlling the application of rules and strategies to terms. The ability of the choice combinator to exercise control over rewriting is based on the premise that the success and failure of strategy application can be observed. In this paper we present a higher-order strategic framework with the ability to dynamically construct strategies containing the choice combinator. To this framework, a combinator called hide is introduced that prevents the successful application of a strategy from being observed by the choice combinator. We then explore the impact of this new combinator on a real-world problem involving a restricted implementation of the Java Virtual Machine.

  2. Combined DSEK and Transconjunctival Pars Plana Vitrectomy

    PubMed Central

    Sane, Mona; Shaikh, Naazli

    2016-01-01

    We report here three patients who underwent combined Descemet's stripping with endothelial keratoplasty and transconjunctival pars plana vitrectomy for bullous keratopathy and posterior segment pathology. A surgical technique and case histories are described. Anatomic and visual outcomes of combined Descemet's stripping with endothelial keratoplasty and vitrectomy were excellent. Our experience provides technical guidelines and limitations. The combined minimally invasive techniques allow for rapid anatomical recovery and return of function and visual acuity in a single sitting. PMID:27413563

  3. Combined eye-atmosphere visibility model

    NASA Technical Reports Server (NTRS)

    Kaufman, Y. J.

    1981-01-01

    Existing models of the optical characteristics of the eye are combined with a recent model of optical characteristics of the atmosphere given by its modulation transfer function. This combination results in the combined eye-atmosphere performance given by the product of their modulation transfer functions. An application for the calculation of visibility thresholds in the case of a two-halves field is given.

  4. Combined Posterior and Anterior Ankle Arthroscopy

    PubMed Central

    Scholten, Peter E.; van Dijk, C. Niek

    2012-01-01

    Treatment of combined anterior and posterior ankle pathology usually consists of either combined anterior and posterior arthrotomies or anterior ankle arthroscopy with an additional posterolateral portal. The first technique bears the risk of complications associated with the extensive exposure, the latter technique provides limited access to the posterior ankle joint. A case is described of combined anterior and posterior arthroscopy, with the patient lying prone and then turned supine, addressing both anterior and posterior ankle pathologies in one tempo. This minimally invasive combined approach allows quick recovery and early return to work and sports activities. PMID:23227391

  5. MANAGEMENT AND CONTROL OF COMBINED SEWER OVERFLOWS

    EPA Science Inventory

    The paper gives a basic overview of the U.S. government's involvements in developing countermeasures for the abatement of combined sewer overflow pollution. batement or prevention of pollution stormwater runoff and combined sewer overflows is one of the most challenging areas in ...

  6. Convergence analysis of combinations of different methods

    SciTech Connect

    Kang, Y.

    1994-12-31

    This paper provides a convergence analysis for combinations of different numerical methods for solving systems of differential equations. The author proves that combinations of two convergent linear multistep methods or Runge-Kutta methods produce a new convergent method of which the order is equal to the smaller order of the two original methods.

  7. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Combination packaging. 6..., DEPARTMENT OF THE TREASURY LIQUORS âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and distributing distilled spirits, wine, or malt beverages in...

  8. Effects of Novel Conceptual Combination on Creativity.

    ERIC Educational Resources Information Center

    Wan, Wendy W. N.; Chiu, Chi-Yue

    2002-01-01

    Two experiments involving 44 Hong Kong undergraduates revealed that solving novel conceptual combination problems could enhance performance in a subsequent test of creativity. The evidence also showed that the beneficial effects of solving novel conceptual combination problems were mediated in part by the use of novel conceptual combination…

  9. Context and Structure in Conceptual Combination.

    ERIC Educational Resources Information Center

    Medin, Douglas L.; Shoben, Edward J.

    1988-01-01

    Three experiments evaluated modifications of conceptual knowledge associated with judgments of adjective-noun conceptual combinations. The subjects included 109 students at the University of Illinois (Champaign). Results indicate that models that attempt to explain combined categories by adding or changing a single feature are not successful. (TJH)

  10. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Combination packaging. 6.93 Section 6.93 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and...

  11. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Combination packaging. 6.93 Section 6.93 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and...

  12. 27 CFR 6.93 - Combination packaging.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Combination packaging. 6.93 Section 6.93 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL âTIED-HOUSEâ Exceptions § 6.93 Combination packaging. The act by an industry member of packaging and...

  13. OPTIMIZATION OF COMBINED SEWER OVERFLOW CONTROL SYSTEMS

    EPA Science Inventory

    The highly variable and intermittent pollutant concentrations and flowrates associated with wet-weather events in combined sewersheds necessitates the use of storage-treatment systems to control pollution.An optimized combined-sewer-overflow (CSO) control system requires a manage...

  14. Using sentence combining in technical writing classes

    NASA Technical Reports Server (NTRS)

    Rosner, M.; Paul, T.

    1981-01-01

    Sentence combining exercises are advanced as a way to teach technical writing style without reliance upon abstractions, from which students do not learn. Such exercises: (1) give students regular writing practice; (2) teach the logic of sentence structure, sentence editing, and punctuation; (3) paragraph development and organization; and (4) rhetorical stance. Typical sentence, paragraph, and discourse level sentence combining exercises are described.

  15. COMBINED-SEWER OVERFLOW CONTROL AND TREATMENT

    EPA Science Inventory

    Combined-sewer overflow (CSO), along with sanitary-sewer overflow and stormwater are significant contributors of contamination to surface waters. During a rain event, the flow in a combined sewer system may exceed the capacity of the intercepting sewer leading to the wastewater t...

  16. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 1 2013-01-01 2013-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  17. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 1 2011-01-01 2011-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  18. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 1 2014-01-01 2014-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  19. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 1 2012-01-01 2012-01-01 false Business combinations. 5.33 Section 5.33 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY RULES, POLICIES, AND PROCEDURES FOR CORPORATE ACTIVITIES Expansion of Activities § 5.33 Business combinations. (a) Authority. 12...

  20. OPIMIZATION OF COMBINED SEWER OVERFLOW CONTROL SYSTEMS

    EPA Science Inventory

    The highly variable and intermittent pollutant concentrations and flowrates associated with wet-weather events in combined sewersheds necessitates the use of storage-treatment systems to control pollution. A strategy should be adopted to develop an optimized combined sewer overfl...

  1. 12 CFR 32.5 - Combination rules.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 1 2011-01-01 2011-01-01 false Combination rules. 32.5 Section 32.5 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY LENDING LIMITS § 32.5 Combination rules. (a) General rule. Loans or extensions of credit to one borrower will be attributed to another...

  2. 38 CFR 21.124 - Combination course.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... vocational rehabilitation, a course will be considered to be a combination course, if the student spends full... pursue the components of a combination course in the following manner: (1) Concurrent school and on-job... objective which the student attains primarily through school instruction with the on-job portion...

  3. The GRAVITY integrated optics beam combination

    NASA Astrophysics Data System (ADS)

    Jocou, L.; Perraut, K.; Nolot, A.; Berger, J. P.; Moulin, T.; Labeye, P.; Lacour, S.; Perrin, G.; Lebouquin, J. B.; Bartko, H.; Thiel, M.; Eisenhauer, F.

    2010-07-01

    Gravity is a 2nd generation interferometric instrument for VLTI. It will combine 4 telescopes in dual feed in the K band to study general relativity effects around the Galactic Center black hole. The concept of Gravity is based on two equivalent beam combiner instruments: the scientific one fed by the science target (Sgr A*) and the fringe tracker fed by a bright reference star (See Gillessen et al.1). Both beam combination instruments are based on silica on silicon integrated optics (IO) component glued to fluoride glass fiber array. The beam combiners are implemented in a cryogenic vessel cooled at 200°K and back-illuminated by a high power laser used for metrology (Bartko et al.2). This paper is dedicated to the description of the development of the integrated beam combiner assembly.

  4. [Combination treatment of hypertension in 2015].

    PubMed

    Špinar, Jindřich; Vítovec, Jiří; Špinarová, Lenka; Bendová, Miroslava

    2015-05-01

    We present an overview of the present views on combination treatment and on fixed combinations in the treatment of hypertension according to guidelines of ESH/ESC and ČSH from 2013. The most frequently recommended dual combinations include a blocker of the renin-angiotensin system (ACEI or sartan) and a calcium channel blocker, and further a blocker of the renin-angiotensin system and a diuretic and a calcium channel blocker and a diuretic. In 2014 a fixed-dose combination of an ACE inhibitor (perindopril), a calcium channel blocker (amlodipine) and an diuretic (indapamide) appeared on the Czech market. Within the PIANIST study including 4 731 insufficiently controlled hypertensives, a fixed-dose triple combination of perindopril, amlodipine and indapamide led to a decrease in blood pressure by 28.3/13.8 mm Hg and to a sufficient control of hypertension in 92 % of patients. The advantage of fixed combinations primarily consists in greater compliance of patients and thereby in a better control of hypertension. About 1/3 of hypertensives need a triple combination for a satisfactory blood pressure control. PMID:26075856

  5. ASDCD: antifungal synergistic drug combination database.

    PubMed

    Chen, Xing; Ren, Biao; Chen, Ming; Liu, Ming-Xi; Ren, Wei; Wang, Quan-Xin; Zhang, Li-Xin; Yan, Gui-Ying

    2014-01-01

    Finding effective drugs to treat fungal infections has important clinical significance based on high mortality rates, especially in an immunodeficient population. Traditional antifungal drugs with single targets have been reported to cause serious side effects and drug resistance. Nowadays, however, drug combinations, particularly with respect to synergistic interaction, have attracted the attention of researchers. In fact, synergistic drug combinations could simultaneously affect multiple subpopulations, targets, and diseases. Therefore, a strategy that employs synergistic antifungal drug combinations could eliminate the limitations noted above and offer the opportunity to explore this emerging bioactive chemical space. However, it is first necessary to build a powerful database in order to facilitate the analysis of drug combinations. To address this gap in our knowledge, we have built the first Antifungal Synergistic Drug Combination Database (ASDCD), including previously published synergistic antifungal drug combinations, chemical structures, targets, target-related signaling pathways, indications, and other pertinent data. Its current version includes 210 antifungal synergistic drug combinations and 1225 drug-target interactions, involving 105 individual drugs from more than 12,000 references. ASDCD is freely available at http://ASDCD.amss.ac.cn.

  6. Combination solar photovoltaic heat engine energy converter

    NASA Technical Reports Server (NTRS)

    Chubb, Donald L.

    1987-01-01

    A combination solar photovoltaic heat engine converter is proposed. Such a system is suitable for either terrestrial or space power applications. The combination system has a higher efficiency than either the photovoltaic array or the heat engine alone can attain. Advantages in concentrator and radiator area and receiver mass of the photovoltaic heat engine system over a heat-engine-only system are estimated. A mass and area comparison between the proposed space station organic Rankine power system and a combination PV-heat engine system is made. The critical problem for the proposed converter is the necessity for high temperature photovoltaic array operation. Estimates of the required photovoltaic temperature are presented.

  7. Crankshaft position sensing with combined starter alternator

    SciTech Connect

    Brandenburg, L.R.; Miller, J.M.

    2000-06-13

    A crankshaft position sensing apparatus is described for use with an engine having a combined starter/alternator assembly. The crankshaft position sensing apparatus includes a tone ring with a sensor and bandpass filter, having a cylinder identification input from a camshaft sensor, and a gain limiter. The sensing apparatus mounts near the rotor of the combined starter/alternator assembly. The filtered crankshaft position signal can then be input into a vehicle system controller and an inner loop controller. The starter/alternator assembly in combination with an internal combustion engine is particularly useful for a hybrid electric vehicle system.

  8. Crankshaft position sensing with combined starter alternator

    DOEpatents

    Brandenburg, Larry Raymond; Miller, John Michael

    2000-06-13

    A crankshaft position sensing apparatus for use with an engine (16) having a combined starter/alternator assembly (18). The crankshaft position sensing apparatus includes a tone ring (38) with a sensor (36) and bandpass filter (46), having a cylinder identification input from a camshaft sensor (48), and a gain limiter (54). The sensing apparatus mounts near the rotor (30) of the combined starter/alternator assembly (18). The filtered crankshaft position signal can then be input into a vehicle system controller (58) and an inner loop controller (60). The starter/alternator assembly (18) in combination with an internal combustion engine is particularly useful for a hybrid electric vehicle system.

  9. Cost Comparison of Conventional Gray Combined Sewer Overflow Control Infrastructure versus a Green/Gray Combination

    EPA Science Inventory

    This paper outlines a life-cycle cost analysis comparing a green (rain gardens) and gray (tunnels) infrastructure combination to a gray-only option to control combined sewer overflow in the Turkey Creek Combined Sewer Overflow Basin, in Kansas City, MO. The plan area of this Bas...

  10. Intelligent design: combination therapy with oncolytic viruses.

    PubMed

    Ottolino-Perry, Kathryn; Diallo, Jean-Simon; Lichty, Brian D; Bell, John C; McCart, J Andrea

    2010-02-01

    Metastatic cancer remains an incurable disease in the majority of cases and thus novel treatment strategies such as oncolytic virotherapy are rapidly advancing toward clinical use. In order to be successful, it is likely that some type of combination therapy will be necessary to have a meaningful impact on this disease. Although it may be tempting to simply combine an oncolytic virus with the existing standard radiation or chemotherapeutics, the long-term goal of such treatments must be to have a rational, potentially synergistic combination strategy that can be safely and easily used in the clinical setting. The combination of oncolytic virotherapy with existing radiotherapy and chemotherapy modalities is reviewed along with novel biologic therapies including immunotherapies, in order to help investigators make intelligent decisions during the clinical development of these products.

  11. Synergistic combination of document security techniques

    NASA Astrophysics Data System (ADS)

    van Renesse, Rudolf L.

    2000-04-01

    The value of security features tends to decrease gradually, partly because of the continuously increasing ability of counterfeiters to counterfeit or imitate these features and partly because of the increasing capability and availability of equipment. As a countermeasure, numerous non-iridescent and iridescent optically variable devices (OVDs) are continuously being developed. The former comprise novel laser engraving techniques, the latter DOVIDs and ISISs. Although these novel techniques appear highly effective, there are indications that they are beginning to fail, not in the least because organized crime appears to have acquired some of those newer techniques. The response is the synergistic combination of those techniques, which combination expectedly remains beyond the capability of criminal organizations. This ongoing development is currently providing new and exciting security potential. Examples are combinations of diffractive and interference phenomena and of laser perforation techniques with OVDs. The latter combination provide strong protection against counterfeiting as well as forgery.

  12. Combined photoultrasonic treatment of infected wounds

    NASA Astrophysics Data System (ADS)

    Zharov, Vladimir P.; Menyaev, Yulian A.; Kalinin, Konstantin L.; Zmievskoy, Gregory N.; Velsher, Leonid Z.; Podkolzin, Alexander A.; Stakhanov, Mikhail L.; Gorchak, Yury Y.; Sarantsev, V. P.

    2001-05-01

    A new combined photoultrasonic (CPUS) technology for the treatment of infected wounds is suggested. The CPUS principal operation is based on the topical application of a photosensitizer followed by light irradiation in combination with low frequency ultrasonic (US) treatment of wounds. In CPUS, two methods - photodynamic (PDT) and ultrasonic therapies supplement each other beneficially and in conjunction provide a significant effect of deep suppurative inflammatory wounds treatment. The main advantages of the new technology are the combined application of an antibiotic solution and photodynamic therapy to destroy antibiotic- resistant microorganisms, an effective mixing of a photosensitizer in the wound, the US enhancement of photosensitizer impregnation into the membranes of bacteria, the US clearing of wound surface from necrotic products, an increased effective light dose exposure in the whole volume of the deep wound when the light does not penetrate totally inside the wound, an additional bactericidal effect under the US impact, and the combined effect of CPUS activation of the immune system.

  13. Unrewarded Object Combinations in Captive Parrots

    PubMed Central

    Auersperg, Alice Marie Isabel; Oswald, Natalie; Domanegg, Markus; Gajdon, Gyula Koppany; Bugnyar, Thomas

    2015-01-01

    In primates, complex object combinations during play are often regarded as precursors of functional behavior. Here we investigate combinatory behaviors during unrewarded object manipulation in seven parrot species, including kea, African grey parrots and Goffin cockatoos, three species previously used as model species for technical problem solving. We further examine a habitually tool using species, the black palm cockatoo. Moreover, we incorporate three neotropical species, the yellow- and the black-billed Amazon and the burrowing parakeet. Paralleling previous studies on primates and corvids, free object-object combinations and complex object-substrate combinations such as inserting objects into tubes/holes or stacking rings onto poles prevailed in the species previously linked to advanced physical cognition and tool use. In addition, free object-object combinations were intrinsically structured in Goffin cockatoos and in kea. PMID:25984564

  14. Genetics Home Reference: combined pituitary hormone deficiency

    MedlinePlus

    ... People with combined pituitary hormone deficiency may have hypothyroidism, which is underactivity of the butterfly-shaped thyroid gland in the lower neck. Hypothyroidism can cause many symptoms, including weight gain and ...

  15. Novel Combination Chemotherapy for Localized Ewing Sarcoma

    Cancer.gov

    In this clinical trial, researchers will test whether the addition of the drug combination vincristine, topotecan, and cyclophosphamide to a standard chemotherapy regimen improves overall survival in patients with extracranial Ewing

  16. Combination Classes and "Hora de comunicacion."

    ERIC Educational Resources Information Center

    Eldredge, Dee L.

    1989-01-01

    Ways to combine small classes of higher education students studying Spanish at various levels are described, including judicious use of language laboratories, staggering of the different level groups, and rotation of activities geared toward students' individual proficiency levels. (CB)

  17. Power combining considerations for Prometheus TWTAs

    NASA Technical Reports Server (NTRS)

    Komm, David S.; Smith, S. K.; Menninger, W. L.

    2005-01-01

    This slide presentation reviws the planning for a nuclear-electric spacecraft. It includes information concerning one considered mission, communications requirements, power combining, four-beam cluster antenna, and amplitude and phase variations.

  18. Ameliorative Effects of Herbal Combinations in Hyperlipidemia

    PubMed Central

    Visavadiya, Nishant P.; Narasimhacharya, A. V. R. L.

    2011-01-01

    The roots of Glycyrrhiza glabra, Withania somnifera, Asparagus racemosus, and Chlorophytum borivilianum and seeds of Sesamum indicum are ayurvedic medicinal plants used in India to treat several ailments. Our previous studies indicated that these plants possess hypolipidemic and antioxidant potential. The present study was aimed at investigating the composite effects of these plants on hypercholesterolemic rats. Three different combinations (5 gm%, given for four weeks) used in this study effectively reduced plasma and hepatic lipid profiles and increased fecal excretion of cholesterol, neutral sterol, and bile acid along with increasing the hepatic HMG-CoA reductase activity and bile acid content in hypercholesterolemic rats. Further, all three combinations also improved the hepatic antioxidant status (catalase, SOD, and ascorbic acid levels) and plasma total antioxidant capacity with reduced hepatic lipid peroxidation. Overall, combination I had the maximum effect on hypercholesterolemic rats followed by combinations II and III due to varying concentrations of the different classes of phytocomponents. PMID:21941605

  19. VLBI-SLR Combination Solution Using GEODYN

    NASA Technical Reports Server (NTRS)

    MacMillan, Dan; Pavlis, Despina; Lemoine, Frank; Chinn, Douglas; Rowlands, David

    2010-01-01

    We would like to generate a multi-technique solution combining all of the geodetic techniques (VLBI, SLR, GPS, and DORIS) using the same software and using the same a priori models. Here we use GEODYN software and consider only the VLBI-SLR combination. Here we report initial results of our work on the combination. We first performed solutions with GEODYN using only VLBI data and found that VLBI EOP solution results produced with GEODYN agree with results using CALC/SOLVE at the 1-sigma level. We then combined the VLBI normal equations in GEODYN with weekly SLR normal equations for the period 2007-2008. Agreement of estimated Earth orientation parameters with IERS C04 were not significantly different for the VLBI-only, SLR-only, and VLBI+SLR solutions

  20. Self-Calibrating Respiratory-Flowmeter Combination

    NASA Technical Reports Server (NTRS)

    Westenskow, Dwayne R.; Orr, Joseph A.

    1990-01-01

    Dual flowmeters ensure accuracy over full range of human respiratory flow rates. System for measurement of respiratory flow employs two flowmeters; one compensates for deficiencies of other. Combination yields easily calibrated system accurate over wide range of gas flow.

  1. Novel Combination Treatments in Multiple Myeloma.

    PubMed

    Nooka, Ajay K; Lonial, Sagar

    2016-05-01

    The last decade has witnessed the identification of several novel druggable targets in multiple myeloma, leading to identification of novel therapies with clinically proven efficacy, both in the newly diagnosed and relapsed setting. More importantly, a common theme of good outcomes was observed among prospective randomized studies that have utilized combinations of agents with different mechanisms of action. The correlation between achieving a deeper response and the improvement in progression-free survival and overall survival has never been so clear. In this article, we elucidate the rationale for use of novel drug combinations in patients with myeloma, and review current evidence-based data supporting the use of specific combinations in various settings. We also attempt to craft a framework to guide clinicians in optimizing the use of combination therapies, to enable patients to derive maximal benefit. PMID:27188677

  2. Simulation of a combined-cycle engine

    NASA Technical Reports Server (NTRS)

    Vangerpen, Jon

    1991-01-01

    A FORTRAN computer program was developed to simulate the performance of combined-cycle engines. These engines combine features of both gas turbines and reciprocating engines. The computer program can simulate both design point and off-design operation. Widely varying engine configurations can be evaluated for their power, performance, and efficiency as well as the influence of altitude and air speed. Although the program was developed to simulate aircraft engines, it can be used with equal success for stationary and automative applications.

  3. A study of RSI under combined stresses

    NASA Technical Reports Server (NTRS)

    Kibler, J. J.; Rosen, B. W.

    1974-01-01

    The behavior of typical rigidized surface insulation material (RSI) under combined loading states was investigated. In particular, the thermal stress states induced during reentry of the space shuttle were of prime concern. A typical RSI tile was analyzed for reentry thermal stresses under computed thermal gradients for a model of the RSI material. The results of the thermal stress analyses were then used to aid in defining typical combined stress states for the failure analysis of RSI.

  4. [Using combined magnetotherapy in patients with acne].

    PubMed

    Kul'chitskaia, D B; Orekhova, E M; Vasil'eva, E S

    2004-01-01

    Laser Doppler flowmetry discovered microcirculatory disorders in acne patients. Affected are arterioles as well as capillaries and venules. Combination of magnetotherapy with medication improves microcirculation in acne patients. More marked positive changes occurred in the microcirculatory system due to combined treatment compared to medication therapy only. Thus, laser Doppler flowmetry is a new, noninvasive method of assessing microcirculation in acne patients and can serve an objective criterion of treatment efficacy. PMID:15449670

  5. Recent Advances in Combined Modality Therapy

    PubMed Central

    Nyati, Mukesh K.; Morgan, Meredith A.; Lawrence, Theodore S.

    2010-01-01

    Combined modality therapy emerged from preclinical data showing that carefully chosen drugs could enhance the sensitivity of tumor cells to radiation while having nonoverlapping toxicities. Recent advances in molecular biology involving the identification of cellular receptors, enzymes, and pathways involved in tumor growth and immortality have resulted in the development of biologically targeted drugs. This review highlights the recent clinical data in support of newer generation cytotoxic chemotherapies and systemic targeted agents in combination with radiation therapy. PMID:20413642

  6. SPS solid state antenna power combiner

    NASA Technical Reports Server (NTRS)

    Fitzsimmons, G. W.

    1980-01-01

    A concept for a solar power satellite antenna power combiner which utilizes solid state dc-rf converters is described. To avoid the power combining losses associated with circuit hybrids it is proposed that the power from multiple solid state amplifiers be combined by direct coupling of each amplifier's output to the radiating antenna structure. The selected power-combining antenna consists of a printed (metalized) microstrip circuit on a ceramic type dielectric substrate which is backed by a shallow lightweight aluminum cavity which sums the power of four microwave sources. The antenna behaves like two one-half wavelength slot-line antennas coupled together via their common cavity structure. A significant feature of the antenna configuration selected is that the radiated energy is summed to yield a single radiated output phase which represents the average insertion phase of the four power amplifiers. This energy may be sampled and, by comparison with the input signal, one can phase error correct to maintain the insertion phase of all solid state power combining modules at exactly the same value. This insures that the insertion phase of each SPS power combining antenna module is identical. An experiment verification program is described.

  7. VLBI-SLR Combination Solution Using GEODYN

    NASA Astrophysics Data System (ADS)

    MacMillan, D. S.; Lemoine, F. G.; Chinn, D. S.; Pavlis, E. C.; Rowlands, D. D.

    2009-12-01

    The traditional procedure followed by the IERS for generating an ITRF is to perform a combination at the technique level. Each geodetic technique provides a solution that itself is a combination of the solutions produced by the technique analysis centers. Alternatively, we would like to generate a multi-technique solution using the same software and using the same a priori models. We seek to produce such a solution combining all of the geodetic techniques at the normal equation level using GEODYN but here, as a first step, consider only the SLR-VLBI combination. The data from each 24-hour VLBI session is initially processed to generate VLBI observation and solution parametrization files for input to GEODYN. Extensive tests have been performed to ensure that the VLBI theoretical delay as calculated by the VLBI Calc/Solve software is the same (to 1 ps) as that calculated by GEODYN. Initially, we ran test solutions with GEODYN using only VLBI data to verify that VLBI solution results produced with GEODYN agree with results using Calc/Solve. Then we combine the VLBI normal equations in GEODYN with weekly SLR normal equations for the period 2004-2008 Lageos1/2 to estimate station positions and Earth orientation parameters. To connect the techniques, we apply the ground ties used by the IERS. Here we report on the results of the combination.

  8. Assessment of global and gene-specific DNA methylation in rat liver and kidney in response to non-genotoxic carcinogen exposure.

    PubMed

    Ozden, Sibel; Turgut Kara, Neslihan; Sezerman, Osman Ugur; Durasi, İlknur Melis; Chen, Tao; Demirel, Goksun; Alpertunga, Buket; Chipman, J Kevin; Mally, Angela

    2015-12-01

    Altered expression of tumor suppressor genes and oncogenes, which is regulated in part at the level of DNA methylation, is an important event involved in non-genotoxic carcinogenesis. This may serve as a marker for early detection of non-genotoxic carcinogens. Therefore, we evaluated the effects of non-genotoxic hepatocarcinogens, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), hexachlorobenzene (HCB), methapyrilene (MPY) and male rat kidney carcinogens, d-limonene, p-dichlorobenzene (DCB), chloroform and ochratoxin A (OTA) on global and CpG island promoter methylation in their respective target tissues in rats. No significant dose-related effects on global DNA hypomethylation were observed in tissues of rats compared to vehicle controls using LC-MS/MS in response to short-term non-genotoxic carcinogen exposure. Initial experiments investigating gene-specific methylation using methylation-specific PCR and bisulfite sequencing, revealed partial methylation of p16 in the liver of rats treated with HCB and TCDD. However, no treatment related effects on the methylation status of Cx32, e-cadherin, VHL, c-myc, Igfbp2, and p15 were observed. We therefore applied genome-wide DNA methylation analysis using methylated DNA immunoprecipitation combined with microarrays to identify alterations in gene-specific methylation. Under the conditions of our study, some genes were differentially methylated in response to MPY and TCDD, whereas d-limonene, DCB and chloroform did not induce any methylation changes. 90-day OTA treatment revealed enrichment of several categories of genes important in protein kinase activity and mTOR cell signaling process which are related to OTA nephrocarcinogenicity.

  9. An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line

    PubMed Central

    Kim, Myung-Chul; Kim, Na-Yon; Seo, Yu-Ri; Kim, Yongbaek

    2016-01-01

    Intratumoral heterogeneity is a hallmark of all cancers and functions as the major barrier against effective cancer therapy. In contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous cancer cells remains largely undetermined. This study was performed to evaluate the epigenetic mechanisms involved in the tumor cell heterogeneity using side population (SP) and non-SP cells isolated from a human malignant mesothelioma (HMM) cell line. The subpopulations of cancer cells were analyzed by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) and RNA-seq methodology. The RNA-seq data were analyzed with the MeDIP-seq data in an integrated way to identify the epigenetically modified genes that defined the SP. Concomitant changes in mRNA expression and DNA methylation were found in 122 genes, including 118 down-regulated genes with hypermethylation and 4 up-regulated genes with hypomethylation. Gene ontology revealed that a large portion of the genes belonged to the groups of biological processes such as stem cell maintenance, stem cell development, stem cell differentiation, and the negative regulation of the developmental process. Among these genes, BNC1, RPS6KA3, TWSG1 and DUSP15 contained aberrant methylation in the CpG islands of the promoter region, indicating that the genes regulated by DNA methylation characterized a distinct subpopulation of HMM cells. The present study provided valuable information to shed light on the epigenetic contributions to the generation and maintenance of tumor cell heterogeneity. PMID:27698904

  10. Targeted DNA methylation analysis by next-generation sequencing.

    PubMed

    Masser, Dustin R; Stanford, David R; Freeman, Willard M

    2015-02-24

    The role of epigenetic processes in the control of gene expression has been known for a number of years. DNA methylation at cytosine residues is of particular interest for epigenetic studies as it has been demonstrated to be both a long lasting and a dynamic regulator of gene expression. Efforts to examine epigenetic changes in health and disease have been hindered by the lack of high-throughput, quantitatively accurate methods. With the advent and popularization of next-generation sequencing (NGS) technologies, these tools are now being applied to epigenomics in addition to existing genomic and transcriptomic methodologies. For epigenetic investigations of cytosine methylation where regions of interest, such as specific gene promoters or CpG islands, have been identified and there is a need to examine significant numbers of samples with high quantitative accuracy, we have developed a method called Bisulfite Amplicon Sequencing (BSAS). This method combines bisulfite conversion with targeted amplification of regions of interest, transposome-mediated library construction and benchtop NGS. BSAS offers a rapid and efficient method for analysis of up to 10 kb of targeted regions in up to 96 samples at a time that can be performed by most research groups with basic molecular biology skills. The results provide absolute quantitation of cytosine methylation with base specificity. BSAS can be applied to any genomic region from any DNA source. This method is useful for hypothesis testing studies of target regions of interest as well as confirmation of regions identified in genome-wide methylation analyses such as whole genome bisulfite sequencing, reduced representation bisulfite sequencing, and methylated DNA immunoprecipitation sequencing.

  11. An Integrated Analysis of the Genome-Wide Profiles of DNA Methylation and mRNA Expression Defining the Side Population of a Human Malignant Mesothelioma Cell Line

    PubMed Central

    Kim, Myung-Chul; Kim, Na-Yon; Seo, Yu-Ri; Kim, Yongbaek

    2016-01-01

    Intratumoral heterogeneity is a hallmark of all cancers and functions as the major barrier against effective cancer therapy. In contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous cancer cells remains largely undetermined. This study was performed to evaluate the epigenetic mechanisms involved in the tumor cell heterogeneity using side population (SP) and non-SP cells isolated from a human malignant mesothelioma (HMM) cell line. The subpopulations of cancer cells were analyzed by methylated DNA immunoprecipitation combined with high-throughput sequencing (MeDIP-seq) and RNA-seq methodology. The RNA-seq data were analyzed with the MeDIP-seq data in an integrated way to identify the epigenetically modified genes that defined the SP. Concomitant changes in mRNA expression and DNA methylation were found in 122 genes, including 118 down-regulated genes with hypermethylation and 4 up-regulated genes with hypomethylation. Gene ontology revealed that a large portion of the genes belonged to the groups of biological processes such as stem cell maintenance, stem cell development, stem cell differentiation, and the negative regulation of the developmental process. Among these genes, BNC1, RPS6KA3, TWSG1 and DUSP15 contained aberrant methylation in the CpG islands of the promoter region, indicating that the genes regulated by DNA methylation characterized a distinct subpopulation of HMM cells. The present study provided valuable information to shed light on the epigenetic contributions to the generation and maintenance of tumor cell heterogeneity.

  12. Combination genetic therapy to inhibit HIV-1.

    PubMed

    Strayer, David S; Branco, Francisco; Landré, Julien; BouHamdan, Mohamad; Shaheen, Farida; Pomerantz, Roger J

    2002-01-01

    Compared with single agents, combination antilentiviral pharmacotherapy targets multiple HIV-1 functions simultaneously, maximizing efficacy and decreasing chances of escape mutations. Combination genetic therapy could theoretically enhance efficacy similarly, but delivery of even single genes to high percentages of hematopoietic cells or their derivatives has proven problematic. Because of their high efficiency of gene delivery, we tested recombinant SV40-derived vectors (rSV40s) for this purpose. We made six rSV40s, each carrying a different transgene that targeted a different lentiviral function. We tested the ability of these constructs, individually and in double and triple combinations, to protect SupT1 human T lymphoma cells from HIV-1 challenge. Single chain antibodies (SFv) against CXCR4 and against HIV-1 reverse transcriptase (RT) and integrase (IN) were used, as were polymeric TAR decoys (PolyTAR) and a dominant-negative mutant of HIV-1 Rev (RevM10). Immunostaining showed that virtually all doubly treated cells expressed both transgenes. All transgenes individually protected from HIV-1 but, except for anti-CXCR4 SFv, their effectiveness diminished as challenge doses increased from 40 through 2500 tissue culture infectious dose(50) (TCID(50))/10(6) cells. However, all combinations of transgenes protected target cells better than individual transgenes, even from the highest challenge doses. Thus, combination gene therapies may inhibit HIV-1 better than single agents, and rSV40s may facilitate delivery of multigene therapeutics.

  13. A combined cycle engine test facility

    SciTech Connect

    Engers, R.; Cresci, D.; Tsai, C.

    1995-09-01

    Rocket-Based Combined-Cycle (RBCC) engines intended for missiles and/or space launch applications incorporate features of rocket propulsion systems operating in concert with airbreathing engine cycles. Performance evaluation of these types of engines, which are intended to operate from static sea level take-off to supersonic cruise or accerlerate to orbit, requires ground test capabilities which integrate rocket component testing with airbreathing engine testing. A combined cycle engine test facility has been constructed in the General Applied Science Laboratories, Inc. (GASL) Aeropropulsion Test Laboratory to meet this requirement. The facility was designed to support the development of an innovative combined cycle engine concept which features a rocket based ramjet combustor. The test requirements included the ability to conduct tests in which the propulsive force was generated by rocket only, the ramjet only and simultaneous rocket and ramjet power (combined cycle) to evaluate combustor operation over the entire engine cycle. The test facility provides simulation over the flight Mach number range of 0 to 8 and at various trajectories. The capabilities of the combined cycle engine test facility are presented.

  14. A combination approach to treating fungal infections

    PubMed Central

    Shrestha, Sanjib K.; Fosso, Marina Y.; Garneau-Tsodikova, Sylvie

    2015-01-01

    Azoles are antifungal drugs used to treat fungal infections such as candidiasis in humans. Their extensive use has led to the emergence of drug resistance, complicating antifungal therapy for yeast infections in critically ill patients. Combination therapy has become popular in clinical practice as a potential strategy to fight resistant fungal isolates. Recently, amphiphilic tobramycin analogues, C12 and C14, were shown to display antifungal activities. Herein, the antifungal synergy of C12 and C14 with four azoles, fluconazole (FLC), itraconazole (ITC), posaconazole (POS), and voriconazole (VOR), was examined against seven Candida albicans strains. All tested strains were synergistically inhibited by C12 when combined with azoles, with the exception of C. albicans 64124 and MYA-2876 by FLC and VOR. Likewise, when combined with POS and ITC, C14 exhibited synergistic growth inhibition of all C. albicans strains, except C. albicans MYA-2876 by ITC. The combinations of FLC-C14 and VOR-C14 showed synergistic antifungal effect against three C. albicans and four C. albicans strains, respectively. Finally, synergism between C12/C14 and POS were confirmed by time-kill and disk diffusion assays. These results suggest the possibility of combining C12 or C14 with azoles to treat invasive fungal infections at lower administration doses or with a higher efficiency. PMID:26594050

  15. A combination approach to treating fungal infections.

    PubMed

    Shrestha, Sanjib K; Fosso, Marina Y; Garneau-Tsodikova, Sylvie

    2015-01-01

    Azoles are antifungal drugs used to treat fungal infections such as candidiasis in humans. Their extensive use has led to the emergence of drug resistance, complicating antifungal therapy for yeast infections in critically ill patients. Combination therapy has become popular in clinical practice as a potential strategy to fight resistant fungal isolates. Recently, amphiphilic tobramycin analogues, C12 and C14, were shown to display antifungal activities. Herein, the antifungal synergy of C12 and C14 with four azoles, fluconazole (FLC), itraconazole (ITC), posaconazole (POS), and voriconazole (VOR), was examined against seven Candida albicans strains. All tested strains were synergistically inhibited by C12 when combined with azoles, with the exception of C. albicans 64124 and MYA-2876 by FLC and VOR. Likewise, when combined with POS and ITC, C14 exhibited synergistic growth inhibition of all C. albicans strains, except C. albicans MYA-2876 by ITC. The combinations of FLC-C14 and VOR-C14 showed synergistic antifungal effect against three C. albicans and four C. albicans strains, respectively. Finally, synergism between C12/C14 and POS were confirmed by time-kill and disk diffusion assays. These results suggest the possibility of combining C12 or C14 with azoles to treat invasive fungal infections at lower administration doses or with a higher efficiency. PMID:26594050

  16. Kalina combined cycle performance and operability

    SciTech Connect

    Smith, R.W.; Ranasinghe, J.; Stats, D.; Dykas, S.

    1996-12-31

    Gas turbine combined cycles using Rankine bottoming cycles have gained broad market acceptance. The favorable plant economics derive from their high efficiency, short construction cycles and excellent environmental performance. The responsive operating characteristics of combined cycles is another key advantage for customers. Duty cycles cover the spectrum from daily start stop (DSS) to base load. Performance and economics of combined cycles have progressed with advances in gas turbine technology as well as the introduction of increasingly efficient multi-pressure Rankine bottoming cycles. Further advances in gas turbine technology and Rankine bottoming cycle performance are becoming incrementally more difficult and costly to achieve. The availability of the Kalina cycle presents a clear path toward improved combined-cycle system performance and reduced cost of electricity. This paper presents detailed performance and operating characteristics of a STAG 207FA combined cycle employing the Kalina bottoming cycle. These characteristics are compared to a conventional three-pressure reheat Rankine bottoming cycle. The Kalina cycle is shown to have performance and operability advantages throughout the range of site conditions and operating regimes, such as base load, load following, DSS duty, wet and dry cooling tower applications and unattended operation. These advantages derive from a single-pressure once-through heat recovery system, above atmospheric working fluid pressure throughout the system, above atmospheric working fluid pressure throughout the system, very high thermal efficiency ({approximately}2.0 to 2.5 percentage points better than the best Rankine), and compatibility with sub-freezing ambient conditions.

  17. Combined acetabulum and pelvic ring injuries.

    PubMed

    Halvorson, Jason J; Lamothe, Jeremy; Martin, C Ryan; Grose, Andrew; Asprinio, David E; Wellman, David; Helfet, David L

    2014-05-01

    Combined fractures of the acetabulum and pelvic ring are more common than previously believed, with an incidence as high as 15.7%. Recent series that include combined injuries indicate that the incidence of lateral compression and anteroposterior compression pelvic ring injuries is similar and that transverse and both-column acetabular fractures are the most common acetabular fracture patterns. Combined injuries most often are the result of high-energy mechanisms, and, compared with patients who present with isolated pelvic or acetabular injury, patients with combined injury typically have higher injury severity scores, higher transfusion requirements, and lower systolic blood pressure, with reported mortality rates of 1.5% to 13%. Treatment requires a multidisciplinary approach. The first priority is resuscitation following the Advanced Trauma Life Support protocols. Once the patient is stable, acetabular fractures and pelvic ring injuries should be assessed individually, and the most appropriate treatment for each should be outlined. These treatments should then be integrated to develop the most appropriate overall treatment strategy. Although outcomes data are available for isolated acetabulum and pelvic ring disruptions, no such data currently exist for combined injuries.

  18. Fumigant combinations for Cyperus esculentum L control.

    PubMed

    Hutchinson, Chad M; McGiffen, Milton E; Sims, James J; Becker, J Ole

    2004-04-01

    The phase-out of methyl bromide as a soil fumigant has stimulated research into the use of other soil fumigants for weed control. Methyl bromide, methyl iodide, propargyl bromide, 1,3-dichloropropene (1,3-D) and metam-sodium were tested alone and in combination with chloropicrin in laboratory experiments to determine their efficacy against Cyperus esculentus L (yellow nutsedge) tubers. Propargyl bromide and metam-sodium were the most efficacious fumigants tested, with EC50 values of 3.7 and 6.5 microM, respectively. The relative potencies of methyl iodide and chloropicrin were not significantly different but were 2.6 and 2.9 times more potent than methyl bromide, respectively. The EC50 values for all fumigants other than 1,3-D were significantly lower than that of methyl bromide. Combining each fumigant with 17% chloropicrin resulted in a synergistic interaction. The greatest increase in potency between the expected result and the actual result was a relative potency of 3.8 with the methyl bromide/chloropicrin combination. The smallest increase in efficacy was with propargyl bromide and chloropicrin, with a relative potency of 1.5. There was no significant difference between the EC50 values of methyl bromide/chloropicrin and methyl iodide/chloropicrin combinations. Combining 1,3-D with 17% chloropicrin resulted in an EC50 value for C. esculentus control similar to that of methyl iodide applied alone. PMID:15119599

  19. Amodiaquine and Ciprofloxacin Combination in Plasmodiasis Therapy

    PubMed Central

    Ubulom, Peace Mayen Edwin; Udobi, Chinweizu Ejikeme; Madu, Mark Iheukwumere

    2015-01-01

    Objective. The study was designed to determine the efficacy of combined Amodiaquine and Ciprofloxacin in plasmodiasis therapy. Method. The in vivo antiplasmodial effect of different dosage levels of Amodiaquine, Ciprofloxacin, and their combinations against Plasmodium berghei berghei was evaluated using Swiss albino mice. Results. Amodiaquine (a known antiplasmodial agent) had a fairly significant antiplasmodial effect reducing the parasites for every 100 red blood cells (RBC) from 66 to 16 (75.75%) at the tolerable dosage level of 7.5 mg/kg body weight while Ciprofloxacin (an antibiotic known to have antimalarial effect) showed an insignificant antiplasmodial effect reducing the parasites for every 100 RBC from 65 to 64 (1.53%) at the tolerable dosage level of 10.7 mg/kg body weight. Conversely, the combination therapy of Amodiaquine and Ciprofloxacin had a significant antiplasmodial effect at all the doses administered. The combination of 7.5 mg/kg of Amodiaquine and 12.8 mg/kg of Ciprofloxacin, however, showed the most significant antiplasmodial effect of the doses used reducing the number of parasites per 100 RBC from 60 to 10 (83.33%). Conclusions. Appropriate Amodiaquine and Ciprofloxacin combination will be effective for the treatment of malaria and better than either Amodiaquine or Ciprofloxacin singly at their recommended dosage levels. PMID:26491456

  20. Amodiaquine and Ciprofloxacin Combination in Plasmodiasis Therapy.

    PubMed

    Ubulom, Peace Mayen Edwin; Udobi, Chinweizu Ejikeme; Madu, Mark Iheukwumere

    2015-01-01

    Objective. The study was designed to determine the efficacy of combined Amodiaquine and Ciprofloxacin in plasmodiasis therapy. Method. The in vivo antiplasmodial effect of different dosage levels of Amodiaquine, Ciprofloxacin, and their combinations against Plasmodium berghei berghei was evaluated using Swiss albino mice. Results. Amodiaquine (a known antiplasmodial agent) had a fairly significant antiplasmodial effect reducing the parasites for every 100 red blood cells (RBC) from 66 to 16 (75.75%) at the tolerable dosage level of 7.5 mg/kg body weight while Ciprofloxacin (an antibiotic known to have antimalarial effect) showed an insignificant antiplasmodial effect reducing the parasites for every 100 RBC from 65 to 64 (1.53%) at the tolerable dosage level of 10.7 mg/kg body weight. Conversely, the combination therapy of Amodiaquine and Ciprofloxacin had a significant antiplasmodial effect at all the doses administered. The combination of 7.5 mg/kg of Amodiaquine and 12.8 mg/kg of Ciprofloxacin, however, showed the most significant antiplasmodial effect of the doses used reducing the number of parasites per 100 RBC from 60 to 10 (83.33%). Conclusions. Appropriate Amodiaquine and Ciprofloxacin combination will be effective for the treatment of malaria and better than either Amodiaquine or Ciprofloxacin singly at their recommended dosage levels.

  1. Combined mechanical loading of composite tubes

    NASA Technical Reports Server (NTRS)

    Derstine, Mark S.; Pindera, Marek-Jerzy; Bowles, David E.

    1988-01-01

    An analytical/experimental investigation was performed to study the effect of material nonlinearities on the response of composite tubes subjected to combined axial and torsional loading. The effect of residual stresses on subsequent mechanical response was included in the investigation. Experiments were performed on P75/934 graphite-epoxy tubes with a stacking sequence of (15/0/ + or - 10/0/ -15), using pure torsion and combined axial/torsional loading. In the presence of residual stresses, the analytical model predicted a reduction in the initial shear modulus. Experimentally, coupling between axial loading and shear strain was observed in laminated tubes under combined loading. The phenomenon was predicted by the nonlinear analytical model. The experimentally observed linear limit of the global shear response was found to correspond to the analytically predicted first ply failure. Further, the failure of the tubes was found to be path dependent above a critical load level.

  2. Eigenvalue Detonation of Combined Effects Aluminized Explosives

    NASA Astrophysics Data System (ADS)

    Capellos, Christos; Baker, Ernest; Balas, Wendy; Nicolich, Steven; Stiel, Leonard

    2007-06-01

    This paper reports on the development of theory and performance for recently developed combined effects aluminized explosives. Traditional high energy explosives used for metal pushing incorporate high loading percentages of HMX or RDX, whereas blast explosives incorporate some percentage of aluminum. However, the high blast explosives produce increased blast energies, with reduced metal pushing capability due to late time aluminum reaction. Metal pushing capability refers to the early volume expansion work produced during the first few volume expansions associated with cylinder wall velocities and Gurney energies. Our Recently developed combined effects aluminized explosives (PAX-29C, PAX-30, PAX-42) are capable of achieving excellent metal pushing and high blast energies. Traditional Chapman-Jouguet detonation theory does not explain the observed detonation states achieved by these combined effects explosives. This work demonstrates, with the use of cylinder expansion data and thermochemical code calculations (JAGUAR and CHEETAH), that eigenvalue detonation theory explains the observed behavior.

  3. Combined Confocal and Magnetic Resonance Microscopy

    SciTech Connect

    Wind, Robert A.; Majors, Paul D.; Minard, Kevin R.; Ackerman, Eric J.; Daly, Don S.; Holtom, Gary R.; Thrall, Brian D.; Weber, Thomas J.

    2002-05-12

    Confocal and magnetic resonance microscopy are both used to study live cells in a minimally invasive way. Both techniques provide complementary information. Therefore, by examining cells simultaneously with both methodologies, more detailed information is obtained than is possible with each of the microscopes individually. In this paper two configurations of a combined confocal and magnetic resonance microscope described. In both cases the sample compartment is part of a temperature regulated perfusion system. The first configuration is capable of studying large single cells or three-dimensional cell agglomerates, whereas with the second configuration monolayers of mammalian cells can be investigated . Combined images are shown of Xenopus laevis frog oocytes, model JB6 tumor spheroids, and a single layer of Chinese hamster ovary cells. Finally, potential applications of the combined microscope are discussed.

  4. Combination therapy for metastatic renal cell carcinoma

    PubMed Central

    Buonerba, Carlo; Di Lorenzo, Giuseppe

    2016-01-01

    Current therapy for metastatic clear cell renal cell carcinoma (RCC) consists of the serial administration of single agents. Combinations of VEGF and mTOR inhibitors have been disappointing in previous randomized trials. However, the combination of lenvatinib, a multitargeted agent that inhibits VEGF as well as FGF receptors, and everolimus demonstrated promising results in a randomized phase II trial. Moreover, the emergence of programmed cell death 1 (PD-1) and programmed cell death ligand 1 (PD-L1) inhibitors has spawned the investigation of combinations of these agents with VEGF inhibitors and cytotoxic T-lymphocyte antigen 4 (CTLA-4) inhibitors. These ongoing phase III trials in conjunction with the development of predictive biomarkers and agents inhibiting novel therapeutic targets may provide much needed advances in this still largely incurable disease. PMID:27047959

  5. [Combination of appendicitis with gynecologic diseases].

    PubMed

    Makhovskií, V Z; Aksenenko, V A; Mazikina, L M; Madagov, L A

    1997-01-01

    782 patients with combined diseases of abdominal and retroperitoneal organs were operated on from 1970 to 1996. In 321 patients (41.0%) at the age from 15 to 80 years appendectomy in combination with gynaecologic operations were performed. The catarral appendicitis was detected in 202 patients, phlegmonous--in 113, gangrenous--in 6 patients. The rate of inflammatory genital disorders was variable: ovarian cyst rupture (183 patients), suppuration (7 patients), over-winding (15 patients), purulent salpingitis (76 patients), ulchanges cyst (6 patients). The extirpation and supravaginal amputation of the uterus were performed in 34 patients. The abdominal exudate was detected in 284 patients. The oblique incision in the ilias region was used in 177 patients. In was extended in 80 patients. The median laparotomy was performed in 64 patients. The combination of appendicitis and gynaecologic diseases are commonly seen in clinical practice.

  6. Efficient power combiner for THz radiation

    NASA Astrophysics Data System (ADS)

    Seidfaraji, Hamide; Fuks, Mikhail I.; Christodoulou, Christos; Schamiloglu, Edl

    2016-08-01

    Most dangerous explosive materials, both toxic and radioactive, contain nitrogen salts with resonant absorption lines in the frequency range 0.3-10 THz. Therefore, there has been growing interest in remotely detecting such materials by observing the spectrum of reflected signals when the suspicious material is interrogated by THz radiation. Practical portable THz sources available today generate only 20-40 mW output power. This power level is too low to interrogate suspicious material from a safe distance, especially if the material is concealed. Hence, there is a need for sources that can provide greater power in the THz spectrum. Generating and extracting high output power from THz sources is complicated and inefficient. The efficiency of vacuum electronic microwave sources is very low when scaled to the THz range and THz sources based on scaling down semiconductor laser sources have low efficiency as well, resulting in the well known "THz gap." The reason for such low efficiencies for both source types is material losses in the THz band. In this article an efficient power combiner is described that is based on scaling to higher frequencies a microwave combiner that increases the output power in the THz range of interest in simulation studies. The proposed power combiner not only combines the THz power output from several sources, but can also form a Gaussian wavebeam output. A minimum conversion efficiency of 89% with cophased inputs in a lossy copper power combiner and maximum efficiency of 100% in a Perfect Electric Conductor (PEC)-made power combiner were achieved in simulations. Also, it is shown that the TE01 output mode is a reasonable option for THz applications due to the fact that conductive loss decreases for this mode as frequency increases.

  7. Potential Outcome Factors in Subacute Combined Degeneration

    PubMed Central

    Vasconcelos, Olavo M; Poehm, Erika H; McCarter, Robert J; Campbell, William W; Quezado, Zenaide M N

    2006-01-01

    BACKGROUND Subacute combined degeneration is an acquired myelopathy caused by vitamin B12 deficiency. Therapy with B12 leads to improvement in most but to complete recovery in only a few patients. Prognostic indicators in subacute combined degeneration are unknown; therefore, predicting complete recovery of neurologic deficits is challenging. PURPOSE To identify potential correlates of outcome and to generate hypotheses concerning predictors of complete resolution of neurologic deficits in subacute combined degeneration. DATA SOURCE We searched EMBASE (1974 to October 2005), MEDLINE (1968 to October 2005), and references from identified reports. REPORTS SELECTION Reports of patients with subacute combined degeneration containing results of magnetic resonance imaging (MRI) and description of outcome and 1 patient treated by the authors. DATA EXTRACTION, SYNTHESIS We extracted data from 45 reports and 57 patients (36 males, 21 females; age range: 10 to 81) with a diagnosis of subacute combined degeneration, and estimated the strength of association between clinical, laboratory, and radiological factors and complete resolution of signs and symptoms. RESULTS Eight patients (14%) achieved clinical resolution and 49 (86%) improved with B12 therapy. The absence of sensory dermatomal deficit, Romberg, and Babinski signs were associated with a higher complete resolution rate. Patients with MRI lesions in ≤7 segments and age less than 50 also appear to have higher rates of complete resolution. CONCLUSIONS B12 therapy is reported to stop progression and improve neurologic deficits in most patients with subacute combined degeneration. However, complete resolution only occurs in a small percentage of patients and appears to be associated with factors suggestive of less severe disease at the time of diagnosis. PMID:16970556

  8. Optimizing neurotrophic factor combinations for neurite outgrowth

    NASA Astrophysics Data System (ADS)

    Deister, C.; Schmidt, C. E.

    2006-06-01

    Most neurotrophic factors are members of one of three families: the neurotrophins, the glial cell-line derived neurotrophic factor family ligands (GFLs) and the neuropoietic cytokines. Each family activates distinct but overlapping cellular pathways. Several studies have shown additive or synergistic interactions between neurotrophic factors from different families, though generally only a single combination has been studied. Because of possible interactions between the neurotrophic factors, the optimum concentration of a factor in a mixture may differ from the optimum when applied individually. Additionally, the effect of combinations of neurotrophic factors from each of the three families on neurite extension is unclear. This study examines the effects of several combinations of the neurotrophin nerve growth factor (NGF), the GFL glial cell-line derived neurotrophic factor (GDNF) and the neuropoietic cytokine ciliary neurotrophic factor (CNTF) on neurite outgrowth from young rat dorsal root ganglion (DRG) explants. The combination of 50 ng ml-1 NGF and 10 ng ml-1 of each GDNF and CNTF induced the highest level of neurite outgrowth at a 752 ± 53% increase over untreated DRGs and increased the longest neurite length to 2031 ± 97 µm compared to 916 ± 64 µm for untreated DRGs. The optimum concentrations of the three factors applied in combination corresponded to the optimum concentration of each factor when applied individually. These results indicate that the efficacy of future therapies for nerve repair would be enhanced by the controlled release of a combination of neurotrophins, GFLs and neuropoietic cytokines at higher concentrations than used in previous conduit designs.

  9. Combined GMSK Communications and PN Ranging

    NASA Technical Reports Server (NTRS)

    Orr, Richard; Divsalar, Dariush

    2008-01-01

    A document discusses a method by which GMSK (Gaussian minimum shift keying) modulation and a pseudonoise (PN) ranging signal may be combined. By isolating the in-phase and quadrature components after carrier lock, and extracting their low-pass and band-pass filtered components, there is enough information available to both demodulate data and track the PN signal. The proposed combined GMSK communications and PN ranging is one potential approach to address emerging requirements for simultaneous high data rate communications from and tracking of vehicles in deep space or at the Moon.

  10. Combined cycle comes to the Philippines

    SciTech Connect

    1995-03-01

    The first combined cycle power station in the Philippines has gone into operation at National Power Corporation`s (NPC) Limay Bataan site, some 40 km west of Manila. The plant comprises two 300 MW blocks in 3+3+1 configuration, based on ABB Type GT11N gas turbines. It was built by a consortium of ABB, with their Japanese licensee Kawasaki Heavy Industries, and Marubeni Corporation. This paper discusses Philippine power production, design and operation of the Limay Bataan plant, and conversion of an existing turbine of the nuclear plant project that was abandoned earlier, into a combined cycle operation. 6 figs.

  11. Combination neutron-gamma ray detector

    DOEpatents

    Stuart, Travis P.; Tipton, Wilbur J.

    1976-10-26

    A radiation detection system capable of detecting neutron and gamma events and distinguishing therebetween. The system includes a detector for a photomultiplier which utilizes a combination of two phosphor materials, the first of which is in the form of small glass beads which scintillate primarily in response to neutrons and the second of which is a plastic matrix which scintillates in response to gammas. A combination of pulse shape and pulse height discrimination techniques is utilized to provide an essentially complete separation of the neutron and gamma events.

  12. Eigenvalue Detonation of Combined Effects Aluminized Explosives

    NASA Astrophysics Data System (ADS)

    Capellos, C.; Baker, E. L.; Nicolich, S.; Balas, W.; Pincay, J.; Stiel, L. I.

    2007-12-01

    Theory and performance for recently developed combined—effects aluminized explosives are presented. Our recently developed combined-effects aluminized explosives (PAX-29C, PAX-30, PAX-42) are capable of achieving excellent metal pushing, as well as high blast energies. Metal pushing capability refers to the early volume expansion work produced during the first few volume expansions associated with cylinder and wall velocities and Gurney energies. Eigenvalue detonation explains the observed detonation states achieved by these combined effects explosives. Cylinder expansion data and thermochemical calculations (JAGUAR and CHEETAH) verify the eigenvalue detonation behavior.

  13. EARS, MARS combined radio observations - 2014

    NASA Astrophysics Data System (ADS)

    Tomezzoli, Giancarlo

    2014-02-01

    The Lyrid meteor shower was generated on 21-22 April 2014 by the passage of the Earth through the path of the debris of the comet C/1861 G1 (Thatcher). The Camelopardalids meteor shower was generated on 23-24 May 2014 by the passage of the Earth through the path of the debris of the comet 209P/Linear. The EurAstro Radio Station (EARS) and the Malta Astro Radio Station (MARS) were operated in parallel for two combined radio observation campaigns. The campaigns revealed that further combined radio observation campaigns are necessary to solve the problem of estimating the number of lost radio meteor echoes.

  14. Combined air and water pollution control system

    NASA Technical Reports Server (NTRS)

    Wolverton, Billy C. (Inventor); Jarrell, Lamont (Inventor)

    1990-01-01

    A bioaquatic air pollution control system for controlling both water and atmospheric pollution is disclosed. The pollution control system includes an exhaust for directing polluted gases out of a furnace and a fluid circulating system which circulates fluid, such as waste water, from a source, past the furnace where the fluid flow entrains the pollutants from the furnace. The combined fluid and pollutants are then directed through a rock/plant/microbial filtering system. A suction pump pumps the treated waste water from the filter system past the exhaust to again entrain more pollutants from the furnace where they are combined with the fluid (waste water) and directed to the filter system.

  15. [When to propose a combined surgery].

    PubMed

    Lachkar, Y

    2009-03-01

    Combined cataract and glaucoma surgery is underused, generallly due to a fear of per- et postsurgical complications. It is a more difficult surgery than simple phacoemulsification, but its benefit on intraocular pressure is established and is maintained over the time (at the difference of phacoemulsification), and permit to preserve the visual field. Optimal surgical technique and adequate follow-up are able to limit postoperative complications. Guidelines published by the European Glaucoma Society (EGS) clearly defined the combined surgery indications: cataract, in a patient with glaucoma uncontrolled by medical treatment or treated with a burdensome multitherapy. PMID:19515339

  16. Raman beam combining for laser brightness enhancement

    DOEpatents

    Dawson, Jay W.; Allen, Graham S.; Pax, Paul H.; Heebner, John E.; Sridharan, Arun K.; Rubenchik, Alexander M.; Barty, Chrisopher B. J.

    2015-10-27

    An optical source capable of enhanced scaling of pulse energy and brightness utilizes an ensemble of single-aperture fiber lasers as pump sources, with each such fiber laser operating at acceptable pulse energy levels. Beam combining involves stimulated Raman scattering using a Stokes' shifted seed beam, the latter of which is optimized in terms of its temporal and spectral properties. Beams from fiber lasers can thus be combined to attain pulses with peak energies in excess of the fiber laser self-focusing limit of 4 MW while retaining the advantages of a fiber laser system of high average power with good beam quality.

  17. Tendon Transfers for Combined Peripheral Nerve Injuries.

    PubMed

    Makarewich, Christopher A; Hutchinson, Douglas T

    2016-08-01

    Combined peripheral nerve injuries present a unique set of challenges to the hand surgeon when considering tendon transfers. They are often associated with severe soft tissue trauma, including lacerations to remaining innervated muscles and tendons, significant scar formation, and substantial sensory loss. In the case of combined nerve injuries, there are typically fewer options for tendon transfers due to fewer tendons of shared function that are expendable as well as associated injuries to tendon or muscle bellies. As such, careful preoperative planning must be performed to make the most of remaining muscle tendon units. PMID:27387081

  18. Rationale for combining immunotherapy with chemotherapy.

    PubMed

    Dalgleish, Angus G

    2015-01-01

    Immunotherapy has usually been considered as an alternative to more traditional modalities. Moreover, it has previously been felt that chemotherapy is inherently immunosuppressive and not suitable for combining with immunotherapy. In this review, the concept of combining different modalities that result in cell death, such as radiotherapy and chemotherapy, with immunotherapy is explored. Tumors actively cause immune suppression which can be reversed by their removal but when this is not possible, enhancing the immune response with nonspecific immune stimulation can enhance the response to other modalities, such as radiotherapy and chemotherapy. Additionally, several chemotherapy agents at low doses selectively inhibit regulatory and suppressor cells.

  19. Combination hepatitis a-hepatitis B vaccine.

    PubMed

    Wagstaff, A J; Balfour, J A

    1997-09-01

    The adult formulation of this combination hepatitis A-hepatitis B vaccine contains 720 enzyme-linked immunosorbent assay units (EU) of formalin-inactivated hepatitis A virus strain HM175 and 20mug of recombinant DNA yeast-derived hepatitis B surface antigen adsorbed onto aluminium salts in 1ml for injection. The paediatric formulation contains half this dosage in 0.5ml for injection. The combination vaccine has been shown to be highly immunogenic in healthy young adults after the full dosage schedule of 3 doses at 0, 1 and 6 months. Trials in older adults and children indicate that immunogenicity is adequate in these groups also. The immunogenicity of the combination vaccine appears to be similar to that of hepatitis A vaccine and hepatitis B vaccine administered separately. Possible advantages for the combination vaccine recipient include fewer injections and lower costs. Local adverse reactions such as soreness at the injection site, redness and swelling occur often with the first dose of the series, but the incidence falls with subsequent doses. Local reactions are usually mild and transient, and reported systemic reactions (fatigue, headache) are thought not to have a causal link with the vaccine. PMID:18020513

  20. A combination therapy for cystic fibrosis.

    PubMed

    Brodsky, Jeffrey L; Frizzell, Raymond A

    2015-09-24

    The most prevalent form of cystic fibrosis arises from an amino acid deletion in the cystic fibrosis transmembrane conductance regulator, CFTR. A recently approved treatment for individuals homozygous for this mutation combines a chemical corrector, which helps CFTR fold, and a potentiator that increases CFTR channel activity. PMID:26406363

  1. Combined solar collector and energy storage system

    NASA Technical Reports Server (NTRS)

    Jensen, R. N. (Inventor)

    1980-01-01

    A combined solar energy collector, fluid chiller and energy storage system is disclosed. A movable interior insulated panel in a storage tank is positionable flush against the storage tank wall to insulate the tank for energy storage. The movable interior insulated panel is alternately positionable to form a solar collector or fluid chiller through which the fluid flows by natural circulation.

  2. Evaluation of antifungal combination against Cryptococcus spp.

    PubMed

    Reichert-Lima, Franqueline; Busso-Lopes, Ariane F; Lyra, Luzia; Peron, Isabela Haddad; Taguchi, Hideaki; Mikami, Yuzuru; Kamei, Katsuiko; Moretti, Maria Luiza; Schreiber, Angelica Z

    2016-09-01

    The second cause of death among systemic mycoses, cryptococcosis treatment represents a challenge since that 5-flucytosine is not currently available in Brazil. Looking for alternatives, this study evaluated antifungal agents, alone and combined, correlating susceptibility to genotypes. Eighty Cryptococcus clinical isolates were genotyped by URA5 gene restriction fragment length polymorphism. Antifungal susceptibility was assessed following CLSI-M27A3 for amphotericin (AMB), 5-flucytosine (5FC), fluconazole (FCZ), voriconazole (VRZ), itraconazole (ITZ) and terbinafine (TRB). Drug interaction chequerboard assay evaluated: AMB + 5FC, AMB + FCZ, AMB + TRB and FCZ + TRB. Molecular typing divided isolates into 14 C. deuterogattii (VGII) and C. neoformans isolates were found to belong to genotype VNI (n = 62) and VNII (n = 4). C. neoformans VNII was significantly less susceptible than VNI (P = 0.0407) to AMB; C. deuterogattii was significantly less susceptible than VNI and VNII to VRZ (P < 0.0001). C. deuterogattii was less susceptible than C. neoformans VNI for FCZ (P = 0.0170), ITZ (P < 0.0001) and TRB (P = 0.0090). The combination FCZ + TRB showed 95.16% of synergistic effect against C. neoformans genotype VNI isolates and all combinations showed 100% of synergism against genotype VNII isolates, suggesting the relevance of cryptococcal genotyping as it is widely known that the various genotypes (now species) have significant impact in antifungal susceptibilities and clinical outcome. In difficult-to-treat cryptococcosis, terbinafine and different antifungal combinations might be alternatives to 5FC. PMID:27135278

  3. Combination solar hothouse and silkworm breeding house

    SciTech Connect

    Vardiashvili, A.B.; Muradov, M.; Kim, V.D.

    1980-01-01

    The basic arrangement is shown for a combination silkworm breeding house and solar hothouse with subsoil irrigation and accumulation of heat; it employs a semicylindrical film covering. The process of accumulation of solar heat in the subsoil pebble stores, in water-heater banks, and in the soil is described.

  4. MANUAL: REAL TIME CONTROL OF COMBINED SEWERS

    EPA Science Inventory

    Managers, engineers, and operators of combined urban sewer systems are faced with difficult problems related to the operation and maintenance of their facilities. In addition to the issues related to the operation and upkeep of the system, many sewerage agencies are facing increa...

  5. Combined treatment in punctate inner choroidopathy

    PubMed Central

    Terelak-Borys, Barbara; Zagajewska, Katarzyna; Jankowska-Lech, Irmina; Tesla, Piotr; Grabska-Liberek, Iwona

    2016-01-01

    Purpose The purpose of this study was to describe a combination treatment for choroidal neovascular (CNV) membrane, secondary to punctate inner choroidopathy (PIC). Patient and methods A 44-year-old female patient was diagnosed with PIC complicated by the development of recurrent juxtafoveal neovascular membrane. The treatment included a sequence of monotherapy regimens: systemic steroid therapy, photodynamic therapy, and intravitreal injections of vascular endothelial growth factor (VEGF) inhibitor (anti-VEGF). Owing to the CNV membrane resistance to various types of monotherapy, a combination treatment consisting of local injections of steroid underneath the Tenon’s capsule and intravitreal anti-VEGF injections was used. Results Systemic steroid therapy resulted in rapid local improvement with a very short remission period. No positive effects of photodynamic therapy were observed. Sequential anti-VEGF injections led to remission periods of several months. Permanent regression of CNV membrane was achieved following combined local application of steroid and intravitreal anti-VEGF injections. Conclusion A combination treatment including steroid and anti-VEGF medication characterized by anti-inflammatory and antiangiogenic effects may be a very beneficial option for the treatment of recurrent CNV membrane as a complication of PIC. PMID:27729795

  6. 77 FR 1064 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-09

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP12-261-000....

  7. A combination therapy for cystic fibrosis.

    PubMed

    Brodsky, Jeffrey L; Frizzell, Raymond A

    2015-09-24

    The most prevalent form of cystic fibrosis arises from an amino acid deletion in the cystic fibrosis transmembrane conductance regulator, CFTR. A recently approved treatment for individuals homozygous for this mutation combines a chemical corrector, which helps CFTR fold, and a potentiator that increases CFTR channel activity.

  8. 78 FR 79432 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP14-293-000....

  9. Urban Runoff and Combined Sewer Overflow.

    ERIC Educational Resources Information Center

    Field, Richard; Gardner, Bradford B.

    1978-01-01

    Presents a literature review of wastewater treatment, covering publications of 1976-77. This review includes areas such as: (1) urban runoff quality and quantity; (2) urban hydrology; (3) management practices; and (4) combined sewer overflows. A list of 140 references is also presented. (HM)

  10. Learning Geography by Combining Fieldwork with GIS

    ERIC Educational Resources Information Center

    Favier, Tim; van der Schee, Joop

    2009-01-01

    Geographic information systems (GIS) offer many possibilities for supporting student research projects. This paper deals with the results of the first phase of a design study on student research projects that combine (quantitative) data collection in the field with data visualisation, manipulation and analysis in GIS. In this study, we try to…

  11. Idea Combining: Synthesizing Syntax and Meaning.

    ERIC Educational Resources Information Center

    Barabas, Christine

    Concerns that sentence combining has become the sole means of instruction in some college composition courses, that students are inadvertently getting the view that writing is essentially a mechanical manipulation of parts strung together, and that writing research has reduced writing to architectural structuralism made up of prewriting, writing,…

  12. 75 FR 32935 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-10

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings June 1, 2010. Take notice that the...: Kinder Morgan Interstate Gas Transmission LLC submits Twenty-seventh Revised Sheet No 4G.01 to its...

  13. 75 FR 17138 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings March 26, 2010. Take notice that the Commission... Gas Transmission, LLC submits Eleventh Revised Sheet 4G.02 to its FERC Gas Tariff, Fourth...

  14. 75 FR 47296 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings July 29, 2010. Take notice that the Commission... Interstate Gas Transmission LLC submits Thirteenth Revised Sheet 4G.02 to FERC Gas Tariff, Fourth...

  15. 12 CFR 5.33 - Business combinations.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... approval for any merger between the national bank and one or more of its nonbank affiliates. (d... combination means any merger or consolidation between a national bank and one or more depository institutions in which the resulting institution is a national bank, the acquisition by a national bank of all,...

  16. 7 CFR 29.1008 - Combination symbols.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... REGULATIONS TOBACCO INSPECTION Standards Official Standard Grades for Flue-Cured Tobacco (u.s. Types 11, 12, 13, 14 and Foreign Type 92) § 29.1008 Combination symbols. A color or group symbol used with another..., XO—oxidized lugs or cutters, BO—oxidized leaf or smoking leaf, GL—thin-bodied nondescript,...

  17. 7 CFR 29.1008 - Combination symbols.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... REGULATIONS TOBACCO INSPECTION Standards Official Standard Grades for Flue-Cured Tobacco (u.s. Types 11, 12, 13, 14 and Foreign Type 92) § 29.1008 Combination symbols. A color or group symbol used with another..., XO—oxidized lugs or cutters, BO—oxidized leaf or smoking leaf, GL—thin-bodied nondescript,...

  18. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  19. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  20. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  1. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  2. 21 CFR 610.17 - Permissible combinations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Permissible combinations. 610.17 Section 610.17 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS GENERAL BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.17 Permissible...

  3. 78 FR 76142 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-16

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: RP14-254-000....

  4. 78 FR 8507 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: CP13-57-000 Applicants:...

  5. Experiment of rocket-ram combined combustor

    NASA Astrophysics Data System (ADS)

    Sato, Kazuo; Sakamoto, Hiroshi; Sasaki, Masaki; Ono, Fumiei; Yatsuyanagi, Nobuyuki

    1994-10-01

    There are limitations to achieve high specific impulse with rocket engine operations alone. However, in the flight at low altitude, combined engines with an airbreathing ramjet engine and a rocket engine can be expected to increase the specific impulse significantly in parallel operation. In this paper, the superiority in the specific impulse of the double-nozzle type of rocket-ram combined engine over the single-nozzle type combined engine was shown by performance calculations. Then, a double-nozzle type of rocket-ram combined combustor with a total thrust of 5kN was designed and experimentally tested with varying ratios of thrust produced by rocket and ramjet. The propellants are LOX/kerosene+ hydrogen for rocket combustion and air-hydrogen for ram combustion. With the thrust chamber having different diverging half-angles, namely 10 deg 18 min, and 6 deg 40 min, thrust and pressure distribution along the common expansion nozzle were measured to investigate the effect of interaction of the expanding gases of rocket and ram on thrust. Enhancement of the specific impulse was experimentally verified. That is, the specific impulse which was gained in rocket-ram parallel operations, when the thrust ratio of rocket to ram was 50 to 50, was found to increase 90 percent over those in pure rocket operations.

  6. 24 CFR 3285.313 - Combination systems.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 24 Housing and Urban Development 5 2014-04-01 2014-04-01 false Combination systems. 3285.313 Section 3285.313 Housing and Urban Development Regulations Relating to Housing and Urban Development... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Foundations § 3285.313...

  7. 24 CFR 3285.313 - Combination systems.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 5 2010-04-01 2010-04-01 false Combination systems. 3285.313 Section 3285.313 Housing and Urban Development Regulations Relating to Housing and Urban Development... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Foundations § 3285.313...

  8. 24 CFR 3285.313 - Combination systems.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 24 Housing and Urban Development 5 2013-04-01 2013-04-01 false Combination systems. 3285.313 Section 3285.313 Housing and Urban Development Regulations Relating to Housing and Urban Development... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Foundations § 3285.313...

  9. 24 CFR 3285.313 - Combination systems.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 24 Housing and Urban Development 5 2012-04-01 2012-04-01 false Combination systems. 3285.313 Section 3285.313 Housing and Urban Development Regulations Relating to Housing and Urban Development... URBAN DEVELOPMENT MODEL MANUFACTURED HOME INSTALLATION STANDARDS Foundations § 3285.313...

  10. 77 FR 58984 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-25

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... Numbers: RP12-1041-000. Applicants: Hess Corporation, Delta Energy, LLC, DE of Ohio, LLC....

  11. Fixed-combination and emerging glaucoma therapies.

    PubMed

    Woodward, David F; Chen, June

    2007-05-01

    Ocular hypotensive agents are the only approved pharmacotherapy for glaucoma. Despite significant advances during the past two decades, a large proportion of glaucoma patients require more than one drug. The most recent additions to the armamentarium of antiglaucoma drugs are fixed-combination products for the glaucoma patient who is insufficiently responsive to monotherapy. Fixed-combination products have the combined efficacy of two ocular hypotensive drugs, and the convenience of a two-drug treatment regimen in a single container, which may aid patient adherence to treatment. Available fixed-combination products consist of timolol 0.5% as an invariant with brimonidine 0.2%, dorzolamide 2%, travoprost 0.004%, latanoprost 0.005% or bimatoprost 0.03%. Research on more advanced antiglaucoma medications continues. Promising new directions appear to be the Rho-kinase inhibitors, microtubule-disrupting agents, serotonergics and cannabimimetics. Efforts continue to improve existing antiglaucoma drugs in an attempt to design second-generation cholinomimetics, adrenergics, prostaglandins and prostamides. PMID:17604504

  12. Combination Administrative Positions in North Dakota Schools.

    ERIC Educational Resources Information Center

    Klein, Robert E.

    Decreasing enrollments and financial problems have led to considerable restructuring in North Dakota schools. One form of restructuring was the creation of dual-role administrative positions combining two or all of the roles of superintendent, elementary principal, and secondary principal. In 1987, 47 of 51 administrators holding such positions…

  13. Combining Qualitative and Quantitative Data: An Example.

    ERIC Educational Resources Information Center

    Sikka, Anjoo; And Others

    Methodology from an ongoing research study to validate teaching techniques for deaf and blind students provides an example of the ways that several types of quantitative and qualitative data can be combined in analysis. Four teacher and student pairs were selected. The students were between 14 and 21 years old, had both auditory and visual…

  14. Prevalence of Combined Reading and Arithmetic Disabilities

    ERIC Educational Resources Information Center

    Dirks, Evelien; Spyer, Ginny; van Lieshout, Ernest C. D. M.; de Sonneville, Leo

    2008-01-01

    This study assesses the prevalence of combined reading and arithmetic disabilities in 799 Dutch schoolchildren using standardized school achievement tests. Scores of arithmetic, word recognition, reading comprehension, and spelling of children in fourth and fifth grade were used. The main interest involved the co-occurrence of word recognition and…

  15. 78 FR 26635 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-07

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the...-000. Applicants: Alliance Pipeline L.P. Description: May 1--31 2013 Auction to be effective...

  16. 38 CFR 21.5231 - Combination.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2013-07-01 2013-07-01 false Combination. 21.5231 Section 21.5231 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-Vietnam Era Veterans' Educational Assistance Under 38...

  17. 38 CFR 21.5231 - Combination.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2010-07-01 2010-07-01 false Combination. 21.5231 Section 21.5231 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-Vietnam Era Veterans' Educational Assistance Under 38...

  18. 38 CFR 21.5231 - Combination.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Combination. 21.5231 Section 21.5231 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-Vietnam Era Veterans' Educational Assistance Under 38...

  19. 38 CFR 21.5231 - Combination.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2012-07-01 2012-07-01 false Combination. 21.5231 Section 21.5231 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-Vietnam Era Veterans' Educational Assistance Under 38...

  20. 38 CFR 21.5231 - Combination.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2011-07-01 2011-07-01 false Combination. 21.5231 Section 21.5231 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS (CONTINUED) VOCATIONAL REHABILITATION AND EDUCATION Post-Vietnam Era Veterans' Educational Assistance Under 38...

  1. 77 FR 2967 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-20

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Docket Numbers: RP12-302-000. Applicants: Transcontinental Gas Pipe Line...

  2. [Combined physiotherapy of chronic infectious prostatitis].

    PubMed

    Churakov, A A; Popkov, V M; Zemskov, S P; Glybochko, P V; Bliumberg, B I

    2007-01-01

    Our experience with therapy of 259 outpatients with chronic infectious prostatitis (CIP) aged 16-55 years has demonstrated that combined treatment of CIP with rectal digital massage of the prostate, electrophoresis of chimotripsin solution with dimexide and local magnetotherapy (Intramag unit) significantly raises treatment efficacy, shortens treatment, prevents complications. PMID:17472003

  3. A Framework for Remediating Number Combination Deficits

    ERIC Educational Resources Information Center

    Fuchs, Lynn S.; Powell, Sarah R.; Seethaler, Pamela M.; Fuchs, Douglas; Hamlett, Carol L.; Cirino, Paul T.; Fletcher, Jack M.

    2010-01-01

    This article introduces a framework for the remediation of number combination (NC) deficits. Research on the remediation of NC deficits is summarized, and research program studies are used to illustrate the 3 approaches to remediation. The Framework comprises a 2-stage system of remediation. The less intensive stage implementing 1 of 3…

  4. 77 FR 71408 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-30

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... Numbers: RP13-298-000. Applicants: National Fuel Gas Supply Corporation. ] Description: Market Pooling...

  5. 75 FR 61730 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-06

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings September 21, 2010. Take notice that the...: RP10-1313-000. Applicants: National Grid LNG, LP. Description: National Grid LNG, LP submits...

  6. 75 FR 17136 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-05

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings March 24, 2010. Take notice that the Commission...-503-000. Applicants: CenterPoint Energy Gas Transmission Company. Description: CenterPoint Energy...

  7. 75 FR 1764 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-01-13

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings January 4, 2010. Take notice that the Commission..., January 11, 2010. Docket Numbers: RP10-273-000. Applicants: EnergyMark, LLC. Description:...

  8. 77 FR 70426 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-26

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... Energy Merchants, LLC (RTS) 6040-39 & -40 to be effective 12/1/2012. Filed Date: 11/15/12....

  9. Hybrid Laser Would Combine Power With Efficiency

    NASA Technical Reports Server (NTRS)

    Sipes, Donald L., Jr

    1986-01-01

    Efficient laser system constructed by using two semiconductor lasers to pump neodymium yttrium aluminum garnet (Nd:YAG) device. Hybrid concept allows digital transmission at data rates of several megabits per second with reasonably sized optical aperture of 20 cm. Beams from two GaAs lasers efficiently coupled for pumping Nd:YAG crystal. Combination of lasers exploits best features of each.

  10. 75 FR 42734 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-22

    ... Energy Regulatory Commission Combined Notice of Filings July 6, 2010. Take notice that the Commission has.... Accession Number: 20100702-0202. Comment Date: 5 p.m. Eastern Time on Tuesday, July 13, 2010. Docket Numbers... on Tuesday, July 13, 2010. Docket Numbers: RP10-940-000. Applicants: ANR Pipeline...

  11. Bulimia, anorexia nervosa, and diabetes. Deadly combinations.

    PubMed

    Hillard, J R; Hillard, P J

    1984-06-01

    Bulimia, anorexia nervosa, and diabetes often coexist, and eating disorders among diabetics frequently go unrecognized. This combination of conditions can have life-threatening effects. Consequently, diagnosis and the medical and psychological management of these patients is of critical importance. The authors outline the complex interactions among the biologic, psychological, and social factors involved in these disorders.

  12. 78 FR 39722 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-02

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the... Numbers: RP13-212-000. Applicants: Boardwalk Storage Company, LLC. Description: Operational Purchases...

  13. Articulated Multimedia Physics, Lesson 7, Combining Forces.

    ERIC Educational Resources Information Center

    New York Inst. of Tech., Old Westbury.

    As the seventh lesson of the Articulated Multimedia Physics Course, instructional materials are presented in this study guide with relation to the force combination. The topics are concerned with the definition and units of forces, sliding forces on inclined planes, and the equilibrant of two or more forces. The content is arranged in scrambled…

  14. American Holidays: Culture and Language Learning Combined.

    ERIC Educational Resources Information Center

    Wylie, Grace Scott

    Suggestions for combining cultural exposure and language instruction through class activities geared to American holidays are outlined. General information about gathering holiday-related realia and instructional materials from local newspapers and magazines is provided, and four specific holidays are highlighted. For each holiday, sources of…

  15. Combined cycle power plant incorporating coal gasification

    DOEpatents

    Liljedahl, Gregory N.; Moffat, Bruce K.

    1981-01-01

    A combined cycle power plant incorporating a coal gasifier as the energy source. The gases leaving the coal gasifier pass through a liquid couplant heat exchanger before being used to drive a gas turbine. The exhaust gases of the gas turbine are used to generate both high pressure and low pressure steam for driving a steam turbine, before being exhausted to the atmosphere.

  16. 78 FR 71597 - Combined Notice of Filings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-29

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Combined Notice of Filings Take notice that the Commission has received the following Natural Gas Pipeline Rate and Refund Report filings: Filings Instituting Proceedings Docket Numbers: PR14-7-000. Applicants: Lee...

  17. Combined Direct and Indirect CT Venography (Combined CTV) in Detecting Lower Extremity Deep Vein Thrombosis

    PubMed Central

    Shi, Wan-Yin; Wang, Li-Wei; Wang, Shao-Juan; Yin, Xin-Dao; Gu, Jian-Ping

    2016-01-01

    Abstract This study aimed to evaluate the diagnostic accuracy of combined direct and indirect CT venography (combined CTV) in the detection of lower extremity deep vein thrombosis (LEDVT). The institutional review board approved the study protocol, and patients or qualifying family members provided informed consent. A total of 96 consecutive patients undergoing combined CTV were prospectively enrolled. A combined examination with digital subtraction angiography (DSA) plus duplex ultrasonography (US) was used as the criterion standard. Three observers were blinded to clinical, DSA, and US results, and they independently analyzed all combined CTV datasets. Interobserver agreement was expressed in terms of the Cohen k value for categorical variables. Accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of combined CTV in the detection of LEDVT were determined by using patient- and location-based evaluations. Of the 96 patients, DSA plus US revealed LEDVT in 125 segmental veins in 63 patients. Patient-based evaluation with combined CTV yielded an accuracy of 96.9% to 97.9%, a sensitivity of 95.2% to 96.8%, a specificity of 100% to 100%, a PPV of 100% to 100%, and an NPV of 91.7% to 94.3% in the detection of LEDVT. Location-based evaluation yielded similar results. Through combined direct and indirect CTV, patients obtained a combined CT angiogram on the diseased limb and an indirect CT angiogram on the opposite side. The image quality of combined CTV was superior to an indirect venogram. Combined CTV shows promising diagnostic accuracy in the detection of LEDVT with 3-dimensional modeling of the lower limb venous system. PMID:26986113

  18. Combined Direct and Indirect CT Venography (Combined CTV) in Detecting Lower Extremity Deep Vein Thrombosis.

    PubMed

    Shi, Wan-Yin; Wang, Li-Wei; Wang, Shao-Juan; Yin, Xin-Dao; Gu, Jian-Ping

    2016-03-01

    This study aimed to evaluate the diagnostic accuracy of combined direct and indirect CT venography (combined CTV) in the detection of lower extremity deep vein thrombosis (LEDVT). The institutional review board approved the study protocol, and patients or qualifying family members provided informed consent. A total of 96 consecutive patients undergoing combined CTV were prospectively enrolled. A combined examination with digital subtraction angiography (DSA) plus duplex ultrasonography (US) was used as the criterion standard. Three observers were blinded to clinical, DSA, and US results, and they independently analyzed all combined CTV datasets. Interobserver agreement was expressed in terms of the Cohen k value for categorical variables. Accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of combined CTV in the detection of LEDVT were determined by using patient- and location-based evaluations. Of the 96 patients, DSA plus US revealed LEDVT in 125 segmental veins in 63 patients. Patient-based evaluation with combined CTV yielded an accuracy of 96.9% to 97.9%, a sensitivity of 95.2% to 96.8%, a specificity of 100% to 100%, a PPV of 100% to 100%, and an NPV of 91.7% to 94.3% in the detection of LEDVT. Location-based evaluation yielded similar results. Through combined direct and indirect CTV, patients obtained a combined CT angiogram on the diseased limb and an indirect CT angiogram on the opposite side. The image quality of combined CTV was superior to an indirect venogram. Combined CTV shows promising diagnostic accuracy in the detection of LEDVT with 3-dimensional modeling of the lower limb venous system.

  19. Combined Direct and Indirect CT Venography (Combined CTV) in Detecting Lower Extremity Deep Vein Thrombosis.

    PubMed

    Shi, Wan-Yin; Wang, Li-Wei; Wang, Shao-Juan; Yin, Xin-Dao; Gu, Jian-Ping

    2016-03-01

    This study aimed to evaluate the diagnostic accuracy of combined direct and indirect CT venography (combined CTV) in the detection of lower extremity deep vein thrombosis (LEDVT). The institutional review board approved the study protocol, and patients or qualifying family members provided informed consent. A total of 96 consecutive patients undergoing combined CTV were prospectively enrolled. A combined examination with digital subtraction angiography (DSA) plus duplex ultrasonography (US) was used as the criterion standard. Three observers were blinded to clinical, DSA, and US results, and they independently analyzed all combined CTV datasets. Interobserver agreement was expressed in terms of the Cohen k value for categorical variables. Accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of combined CTV in the detection of LEDVT were determined by using patient- and location-based evaluations. Of the 96 patients, DSA plus US revealed LEDVT in 125 segmental veins in 63 patients. Patient-based evaluation with combined CTV yielded an accuracy of 96.9% to 97.9%, a sensitivity of 95.2% to 96.8%, a specificity of 100% to 100%, a PPV of 100% to 100%, and an NPV of 91.7% to 94.3% in the detection of LEDVT. Location-based evaluation yielded similar results. Through combined direct and indirect CTV, patients obtained a combined CT angiogram on the diseased limb and an indirect CT angiogram on the opposite side. The image quality of combined CTV was superior to an indirect venogram. Combined CTV shows promising diagnostic accuracy in the detection of LEDVT with 3-dimensional modeling of the lower limb venous system. PMID:26986113

  20. Combining joint models for biomedical event extraction

    PubMed Central

    2012-01-01

    Background We explore techniques for performing model combination between the UMass and Stanford biomedical event extraction systems. Both sub-components address event extraction as a structured prediction problem, and use dual decomposition (UMass) and parsing algorithms (Stanford) to find the best scoring event structure. Our primary focus is on stacking where the predictions from the Stanford system are used as features in the UMass system. For comparison, we look at simpler model combination techniques such as intersection and union which require only the outputs from each system and combine them directly. Results First, we find that stacking substantially improves performance while intersection and union provide no significant benefits. Second, we investigate the graph properties of event structures and their impact on the combination of our systems. Finally, we trace the origins of events proposed by the stacked model to determine the role each system plays in different components of the output. We learn that, while stacking can propose novel event structures not seen in either base model, these events have extremely low precision. Removing these novel events improves our already state-of-the-art F1 to 56.6% on the test set of Genia (Task 1). Overall, the combined system formed via stacking ("FAUST") performed well in the BioNLP 2011 shared task. The FAUST system obtained 1st place in three out of four tasks: 1st place in Genia Task 1 (56.0% F1) and Task 2 (53.9%), 2nd place in the Epigenetics and Post-translational Modifications track (35.0%), and 1st place in the Infectious Diseases track (55.6%). Conclusion We present a state-of-the-art event extraction system that relies on the strengths of structured prediction and model combination through stacking. Akin to results on other tasks, stacking outperforms intersection and union and leads to very strong results. The utility of model combination hinges on complementary views of the data, and we show that our

  1. Pegvisomant and cabergoline combination therapy in acromegaly.

    PubMed

    Bernabeu, I; Alvarez-Escolá, C; Paniagua, A E; Lucas, T; Pavón, I; Cabezas-Agrícola, J M; Casanueva, F F; Marazuela, M

    2013-03-01

    Combination with cabergoline may offer additional benefits to acromegalic patients on pegvisomant monotherapy. We evaluated the safety and efficacy profile of this combination and investigated the determinants of response. An observational, retrospective, cross-sectional study. Fourteen acromegalic patients (9 females), who were partially resistant to somatostatin analogs and on pegvisomant monotherapy. Cabergoline was added because of the presence of persistent mildly increased IGF-I. The mean follow-up time was 18.3 ± 10.4 months. The efficacy and safety profile was assessed. The influence of clinical and biochemical characteristics on treatment efficacy was studied. IGF-I levels returned to normal in 4 patients (28%) at the end of the study. In addition, some decline in IGF-I levels was observed in a further 5 patients. The % IGF-I decreased from 158 ± 64% to 124 ± 44% (p = 0.001). The average change in IGF-I was -18 ± 27% (range -67 to +24%). Lower baseline IGF-I (p = 0.007), female gender (p = 0.013), lower body weight (p = 0.031), and higher prolactin (PRL) levels (p = 0.007) were associated with a better response to combination therapy. There were no significant severe adverse events. Significant tumour shrinkage was observed in 1 patient. Combination therapy with pegvisomant and cabergoline could provide better control of IGF-I in some patients with acromegaly. Baseline IGF-I levels, female gender, body weight, and PRL levels affect the response to this combination therapy.

  2. Towards combined global monthly gravity field solutions

    NASA Astrophysics Data System (ADS)

    Jaeggi, Adrian; Meyer, Ulrich; Beutler, Gerhard; Weigelt, Matthias; van Dam, Tonie; Mayer-Gürr, Torsten; Flury, Jakob; Flechtner, Frank; Dahle, Christoph; Lemoine, Jean-Michel; Bruinsma, Sean

    2014-05-01

    Currently, official GRACE Science Data System (SDS) monthly gravity field solutions are generated independently by the Centre for Space Research (CSR) and the German Research Centre for Geosciences (GFZ). Additional GRACE SDS monthly fields are provided by the Jet Propulsion Laboratory (JPL) for validation and outside the SDS by a number of other institutions worldwide. Although the adopted background models and processing standards have been harmonized more and more by the various processing centers during the past years, notable differences still exist and the users are more or less left alone with a decision which model to choose for their individual applications. This procedure seriously limits the accessibility of these valuable data. Combinations are well established in the area of other space geodetic techniques, such as the Global Navigation Satellite Systems (GNSS), Satellite Laser Ranging (SLR), and Very Long Baseline Interferometry (VLBI). Regularly comparing and combining space-geodetic products has tremendously increased the usefulness of the products in a wide range of disciplines and scientific applications. Therefore, we propose in a first step to mutually compare the large variety of available monthly GRACE gravity field solutions, e.g., by assessing the signal content over selected regions, by estimating the noise over the oceans, and by performing significance tests. We make the attempt to assign different solution characteristics to different processing strategies in order to identify subsets of solutions, which are based on similar processing strategies. Using these subsets we will in a second step explore ways to generate combined solutions, e.g., based on a weighted average of the individual solutions using empirical weights derived from pair-wise comparisons. We will also assess the quality of such a combined solution and discuss the potential benefits for the GRACE and GRACE-FO user community, but also address minimum processing

  3. Identification of miR-215 mediated targets/pathways via translational immunoprecipitation expression analysis (TrIP-chip)

    PubMed Central

    Fesler, Andrew; Xu, Xiao; Zheng, Xiao; Li, Xiaodong; Jiang, Jingting; Russo, James J.; Ju, Jingfang

    2015-01-01

    Steady state mRNA expression profiling can identify the majority of miRNA targets. However, some translationally repressed miRNA targets are missed and thus not considered for functional validation. Therefore, analysis of mRNA translation can enhance miRNA target identification for functional studies. We have applied a unique approach to identify miRNA targets in a small number of cells. Actively translating mRNAs are associated with polyribosomes and newly synthesized peptide chains are associated with molecular chaperones such as HSP70s. Affinity capture beads were used to capture HSP70 chaperones associated with polyribosome complexes. The isolated actively translating mRNAs were used for high throughput expression profiling analysis. miR-215 is an important miRNA in colorectal cancer and loss of miR-215 is significantly associated with prognosis of this disease. miR-215 suppresses the expression of several key targets. We utilized the affinity capture approach to isolate miR-215 mediated mRNA target transcripts. This approach provides a unique way to identify targets regulated by non-coding RNAs and RNA binding proteins from a small number of cells. PMID:26287603

  4. Quantitative evaluation of his-tag purification and immunoprecipitation of tristetraprolin and its mutant proteins from transfected human cells

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Histidine (His)-tag is widely used for affinity purification of recombinant proteins, but the yield and purity of expressed proteins are quite different. Little information is available about quantitative evaluation of this procedure. The objective of the current study was to evaluate the His-tag pr...

  5. PARP1 genomics: chromatin immunoprecipitation approach using anti-PARP1 antibody (ChIP and ChIP-seq)

    PubMed Central

    Lodhi, Niraj; Tulin, Alexei V.

    2011-01-01

    Poly(ADP-ribose) polymerase1 (PARP1) is a global regulator of different cellular mechanisms, ranging from DNA damage repair to control of gene expression. Since PARP1 protein and pADPr have been shown to persist in chromatin through cell cycle, they may both act as epigenetic markers. However, it is not known how many loci are occupied by PARP1 protein during mitosis genome-wide. To reveal the genome-wide PARP1 binding sites, we used the ChIP-seq approach, an emerging technique to study genome-wide PARP1 protein interaction with chromatin. Here, we describe how to perform ChIP-seq in the context of PARP1 binding sites identification in chromatin, using human embryonic kidney cell lines. PMID:21870262

  6. The Strutjet Rocket Based Combined Cycle Engine

    NASA Technical Reports Server (NTRS)

    Siebenhaar, A.; Bulman, M. J.; Bonnar, D. K.

    1998-01-01

    The multi stage chemical rocket has been established over many years as the propulsion System for space transportation vehicles, while, at the same time, there is increasing concern about its continued affordability and rather involved reusability. Two broad approaches to addressing this overall launch cost problem consist in one, the further development of the rocket motor, and two, the use of airbreathing propulsion to the maximum extent possible as a complement to the limited use of a conventional rocket. In both cases, a single-stage-to-orbit (SSTO) vehicle is considered a desirable goal. However, neither the "all-rocket" nor the "all-airbreathing" approach seems realizable and workable in practice without appreciable advances in materials and manufacturing. An affordable system must be reusable with minimal refurbishing on-ground, and large mean time between overhauls, and thus with high margins in design. It has been suggested that one may use different engine cycles, some rocket and others airbreathing, in a combination over a flight trajectory, but this approach does not lead to a converged solution with thrust-to-mass, specific impulse, and other performance and operational characteristics that can be obtained in the different engines. The reason is this type of engine is simply a combination of different engines with no commonality of gas flowpath or components, and therefore tends to have the deficiencies of each of the combined engines. A further development in this approach is a truly combined cycle that incorporates a series of cycles for different modes of propulsion along a flight path with multiple use of a set of components and an essentially single gas flowpath through the engine. This integrated approach is based on realizing the benefits of both a rocket engine and airbreathing engine in various combinations by a systematic functional integration of components in an engine class usually referred to as a rocket-based combined cycle (RBCC) engine

  7. Wideband unbalanced waveguide power dividers and combiners

    DOEpatents

    Halligan, Matthew; McDonald, Jacob Jeremiah; Strassner, II, Bernd H.

    2016-05-17

    The various technologies presented herein relate to waveguide dividers and waveguide combiners for application in radar systems, wireless communications, etc. Waveguide dividers-combiners can be manufactured in accordance with custom dimensions, as well as in accordance with waveguide standards such that the input and output ports are of a defined dimension and have a common impedance. Various embodiments are presented which can incorporate one or more septum(s), one or more pairs of septums, an iris, an input matching region, a notch located on the input waveguide arm, waveguide arms having stepped transformer regions, etc. The various divider configurations presented herein can be utilized in high fractional bandwidth applications, e.g., a fractional bandwidth of about 30%, and RF applications in the Ka frequency band (e.g., 26.5-40 GHz).

  8. Combined additive manufacturing approaches in tissue engineering.

    PubMed

    Giannitelli, S M; Mozetic, P; Trombetta, M; Rainer, A

    2015-09-01

    Advances introduced by additive manufacturing (AM) have significantly improved the control over the microarchitecture of scaffolds for tissue engineering. This has led to the flourishing of research works addressing the optimization of AM scaffolds microarchitecture to optimally trade-off between conflicting requirements (e.g. mechanical stiffness and porosity level). A fascinating trend concerns the integration of AM with other scaffold fabrication methods (i.e. "combined" AM), leading to hybrid architectures with complementary structural features. Although this innovative approach is still at its beginning, significant results have been achieved in terms of improved biological response to the scaffold, especially targeting the regeneration of complex tissues. This review paper reports the state of the art in the field of combined AM, posing the accent on recent trends, challenges, and future perspectives.

  9. Object attributes combine additively in visual search.

    PubMed

    Pramod, R T; Arun, S P

    2016-01-01

    We perceive objects as containing a variety of attributes: local features, relations between features, internal details, and global properties. But we know little about how they combine. Here, we report a remarkably simple additive rule that governs how these diverse object attributes combine in vision. The perceived dissimilarity between two objects was accurately explained as a sum of (a) spatially tuned local contour-matching processes modulated by part decomposition; (b) differences in internal details, such as texture; (c) differences in emergent attributes, such as symmetry; and (d) differences in global properties, such as orientation or overall configuration of parts. Our results elucidate an enduring question in object vision by showing that the whole object is not a sum of its parts but a sum of its many attributes. PMID:26967014

  10. Object attributes combine additively in visual search

    PubMed Central

    Pramod, R. T.; Arun, S. P.

    2016-01-01

    We perceive objects as containing a variety of attributes: local features, relations between features, internal details, and global properties. But we know little about how they combine. Here, we report a remarkably simple additive rule that governs how these diverse object attributes combine in vision. The perceived dissimilarity between two objects was accurately explained as a sum of (a) spatially tuned local contour-matching processes modulated by part decomposition; (b) differences in internal details, such as texture; (c) differences in emergent attributes, such as symmetry; and (d) differences in global properties, such as orientation or overall configuration of parts. Our results elucidate an enduring question in object vision by showing that the whole object is not a sum of its parts but a sum of its many attributes. PMID:26967014

  11. Analysis of fractals with combined partition

    NASA Astrophysics Data System (ADS)

    Dedovich, T. G.; Tokarev, M. V.

    2016-03-01

    The space—time properties in the general theory of relativity, as well as the discreteness and non-Archimedean property of space in the quantum theory of gravitation, are discussed. It is emphasized that the properties of bodies in non-Archimedean spaces coincide with the properties of the field of P-adic numbers and fractals. It is suggested that parton showers, used for describing interactions between particles and nuclei at high energies, have a fractal structure. A mechanism of fractal formation with combined partition is considered. The modified SePaC method is offered for the analysis of such fractals. The BC, PaC, and SePaC methods for determining a fractal dimension and other fractal characteristics (numbers of levels and values of a base of forming a fractal) are considered. It is found that the SePaC method has advantages for the analysis of fractals with combined partition.

  12. Combined loading criterial influence on structural performance

    NASA Technical Reports Server (NTRS)

    Kuchta, B. J.; Sealey, D. M.; Howell, L. J.

    1972-01-01

    An investigation was conducted to determine the influence of combined loading criteria on the space shuttle structural performance. The study consisted of four primary phases: Phase (1) The determination of the sensitivity of structural weight to various loading parameters associated with the space shuttle. Phase (2) The determination of the sensitivity of structural weight to various levels of loading parameter variability and probability. Phase (3) The determination of shuttle mission loading parameters variability and probability as a function of design evolution and the identification of those loading parameters where inadequate data exists. Phase (4) The determination of rational methods of combining both deterministic time varying and probabilistic loading parameters to provide realistic design criteria. The study results are presented.

  13. [Switching and combining strategies of antidepressant medications].

    PubMed

    Charpeaud, Thomas; Moliere, Fanny; Bubrovszky, Maxime; Haesebaert, Frédéric; Allaïli, Najib; Bation, Rémy; Nieto, Isabel; Richieri, Raphaëlle; Saba, Ghassen; Bellivier, Frank; Bennabi, Djamila; Holtzmann, Jérôme; Camus, Vincent; Courtet, Philippe; Courvoisier, Pierre; d'Amato, Thierry; Doumy, Olivier; Garnier, Marion; Bougerol, Thierry; Lançon, Christophe; Haffen, Emmanuel; Leboyer, Marion; Llorca, Pierre-Michel; Vaiva, Guillaume; El-Hage, Wissam; Aouizerate, Bruno

    2016-03-01

    Switching antidepressant medication may be helpful in depressed patients having no benefit from the initial antidepressant treatment. Before considering switching strategy, the initial antidepressant treatment should produce no therapeutic effect after at least 4 weeks of administration at adequate dosage. Choosing an antidepressant of pharmacologically distinct profile fails to consistently demonstrate a significant superiority in terms of effectiveness over the switching to another antidepressant within the same pharmacological class. Augmenting SSRI/SNRIs with mirtazapine/mianserin has become the most recommended strategy of antidepressant combinations. Augmenting SSRI with tricyclic drugs is now a less recommended strategy of antidepressant combinations given the increased risk for the occurrence of pharmacokinetic drug-drug interactions and adverse effects.

  14. Rationale for combining surgery and radiation therapy

    SciTech Connect

    Suit, H.D.; Todoroki, T.

    1985-05-01

    The combination of radiation and surgery is being employed increasingly in preference to radical surgery alone or high radiation dose alone in the treatment of malignant epithelial and mesenchymal neoplasms. The basis for this interest is that the scope of the surgery and/or the radiation dose level are less than if either were employed alone. A reduction in treatment related morbidity, improved cosmetic and functional status, and in some instances a lower local failure rate may be achieved by this approach. The rationale for combining radiation and surgery is that radiation at moderate dose levels is effective in the eradication of microscopic extensions of tumor beyond the clearly obvious mass while the surgery (usually more conservative) removes the principal mass.

  15. Fulminant Myocarditis with Combination Immune Checkpoint Blockade.

    PubMed

    Johnson, Douglas B; Balko, Justin M; Compton, Margaret L; Chalkias, Spyridon; Gorham, Joshua; Xu, Yaomin; Hicks, Mellissa; Puzanov, Igor; Alexander, Matthew R; Bloomer, Tyler L; Becker, Jason R; Slosky, David A; Phillips, Elizabeth J; Pilkinton, Mark A; Craig-Owens, Laura; Kola, Nina; Plautz, Gregory; Reshef, Daniel S; Deutsch, Jonathan S; Deering, Raquel P; Olenchock, Benjamin A; Lichtman, Andrew H; Roden, Dan M; Seidman, Christine E; Koralnik, Igor J; Seidman, Jonathan G; Hoffman, Robert D; Taube, Janis M; Diaz, Luis A; Anders, Robert A; Sosman, Jeffrey A; Moslehi, Javid J

    2016-11-01

    Immune checkpoint inhibitors have improved clinical outcomes associated with numerous cancers, but high-grade, immune-related adverse events can occur, particularly with combination immunotherapy. We report the cases of two patients with melanoma in whom fatal myocarditis developed after treatment with ipilimumab and nivolumab. In both patients, there was development of myositis with rhabdomyolysis, early progressive and refractory cardiac electrical instability, and myocarditis with a robust presence of T-cell and macrophage infiltrates. Selective clonal T-cell populations infiltrating the myocardium were identical to those present in tumors and skeletal muscle. Pharmacovigilance studies show that myocarditis occurred in 0.27% of patients treated with a combination of ipilimumab and nivolumab, which suggests that our patients were having a rare, potentially fatal, T-cell-driven drug reaction. (Funded by Vanderbilt-Ingram Cancer Center Ambassadors and others.).

  16. Fatal combination of moclobemide overdose and whisky.

    PubMed

    Bleumink, G S; van Vliet, A C M; van der Tholen, A; Stricker, B H Ch

    2003-03-01

    The antidepressant moclobemide (Aurorix) is a reversible inhibitor of monoamine oxidase-A. Pure moclobemide overdose is considered to be relatively safe. Mixed drug overdoses including moclobemide are potentially lethal, especially when serotonergical drugs are involved. So far, only one fatality due to moclobemide mono-overdose has been reported. We report here on a fatality following the ingestion of a moclobemide overdose in combination with half a bottle of whisky. Although dietary restrictions during moclobemide therapy are not considered necessary, the combination of large quantities of moclobemide and tyramine-containing products seems to be lethal, probably because monoamine oxidase-A selectivity is overwhelmed after massive overdoses. Since there is no specific antidote and treatment is only symptomatic, the severity of an overdose with moclobemide must not be underestimated.

  17. Ovarian cystectomy in endometriomas: Combined approach

    PubMed Central

    Ünlü, Cihat; Yıldırım, Gazi

    2014-01-01

    Endometrioma is one of the most frequent adnexal masses in the premenopausal population, but the recommended treatment is still a subject of debate. Medical therapy is inefficient and can not be recommended in the management of ovarian endometriomas. The general consensus is that ovarian endometriomas larger than 4 cm should be removed, both to reduce pain and to improve spontaneous conception rates. The removal of ovarian endometriomas can be difficult, as the capsule is often densely adherent. While the surgical treatment of choice is surgical laparoscopy, for conservative treatment, the preferred method is modified combined cystectomy. Cystectomy can be destructive for the ovary, whereas ablation may be incomplete, with a greater risk of recurrence. To the best of our knowledge, the modified combined technique seems to be more efficient in the treatment of endometriomas. PMID:25317047

  18. Probabilistic Cue Combination: Less is More

    PubMed Central

    Yurovsky, Daniel; Boyer, Ty W.; Smith, Linda B.; Yu, Chen

    2012-01-01

    Learning about the structure of the world requires learning probabilistic relationships: rules in which cues do not predict outcomes with certainty. However, in some cases, the ability to track probabilistic relationships is a handicap, leading adults to perform non-normatively in prediction tasks. For example, in the dilution effect, predictions made from the combination of two cues of different strengths are less accurate than those made from the stronger cue alone. Here we show that dilution is an adult problem; 11-month-old infants combine strong and weak predictors normatively. These results extend and add support for the less is more hypothesis: limited cognitive resources can lead children to represent probabilistic information differently from adults, and this difference in representation can have important downstream consequences for prediction. PMID:23432826

  19. Inpainting with sparse linear combinations of exemplars

    SciTech Connect

    Wohlberg, Brendt

    2008-01-01

    We introduce a new exemplar-based inpainting algorithm based on representing the region to be inpainted as a sparse linear combination of blocks extracted from similar parts of the image being inpainted. This method is conceptually simple, being computed by functional minimization, and avoids the complexity of correctly ordering the filling in of missing regions of other exemplar-based methods. Initial performance comparisons on small inpainting regions indicate that this method provides similar or better performance than other recent methods.

  20. Hybrid compounds: from simple combinations to nanomachines.

    PubMed

    Müller-Schiffmann, Andreas; Sticht, Heinrich; Korth, Carsten

    2012-02-01

    The combination of two different and independently acting compounds into one covalently linked hybrid compound can convey synergy from the effects of both independently acting moieties to the new composite compound, leading to a pharmacological potency greater than the sum of each individual moiety's potencies. Here, we review a variety of such hybrid compounds, which can consist of various functional parts, molecular recognition or subcellular targeting moieties, or combinations thereof, acting either simultaneously or sequentially. Such moieties within a hybrid compound can consist of a variety of substance classes, including small organic molecules, polypeptides or nucleic acids identified either via rational molecular design or selection from libraries. Precedent for hybrid compounds comes from naturally occurring proteins and small molecules, such as botulinum toxin and bleomycin, which are secreted by micro-organisms. We review the high degree of suitability of hybrid compounds for the treatment of multifactorial diseases by simultaneously hitting several targets along an identified disease pathway. Examples are hybrid compounds against Alzheimer's disease, against the cancer-relevant phosphoinisitide-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) and epidermal growth factor signaling cascade, or in antimalarial therapy via simultaneous hitting of different mechanisms of hemozoin formation. Molecular recognition by peptides or aptamers (recognition-specific RNA or peptide sequences) can be combined with the transport of small molecule β-sheet breakers or toxins, or targeting to ubiquitin-dependent proteolysis. The vision of molecular nanomachines is currently realized in sequentially acting modular nanotransporters, consisting of four modules including a target, a membrane and nuclear translocation sequence, as well as a drug attachment domain. Through the rational combination of existing drugs and the synergy of their effects, a rapid

  1. Combined Cancer Immunotherapy Against Aurora Kinase A.

    PubMed

    Kaštánková, Iva; Poláková, Ingrid; Dušková, Martina; Šmahel, Michal

    2016-05-01

    Aurora kinase A (AURKA) is a centrosomal protein that is overexpressed in a number of human malignancies and can contribute to tumor progression. As we used this protein as a target of DNA immunization, we increased its immunogenicity by the addition of the PADRE helper epitope and decreased its potential oncogenicity by mutagenesis of the kinase domain. For in vitro analysis of induced immune responses in mice, we identified the Aurka(220-228) nonapeptide representing an H-2Kb epitope. As DNA vaccination against the Aurka self-antigen by a gene gun did not show any antitumor effect, we combined DNA immunization with anti-CD25 treatment that depletes mainly regulatory T cells. Whereas 1 anti-CD25 dose injected before DNA vaccination did not enhance the activation of Aurka-specific splenocytes, 3 doses administered on days of immunizations augmented about 10-fold immunity against Aurka. However, an opposite effect was found for antitumor immunity-only 1 anti-CD25 dose combined with DNA vaccination reduced tumor growth. Moreover, the administration of 3 doses of anti-CD25 antibody alone accelerated tumor growth. Analysis of tumor-infiltrating cells showed that 3 anti-CD25 doses not only efficiently depleted regulatory T cells but also activated helper T cells and CD3(-)CD25(+) cells. Next, we found that blockade of the PD-1 receptor initiated 1 week after the first immunization was necessary for significant inhibition of tumor growth with therapeutic DNA vaccination against Aurka combined with depletion of CD25 cells. Our results suggest that combined cancer immunotherapy should be carefully evaluated to achieve the optimal antitumor effect. PMID:27070447

  2. Three allele combinations associated with Multiple Sclerosis

    PubMed Central

    Favorova, Olga O; Favorov, Alexander V; Boiko, Alexey N; Andreewski, Timofey V; Sudomoina, Marina A; Alekseenkov, Alexey D; Kulakova, Olga G; Gusev, Eugenyi I; Parmigiani, Giovanni; Ochs, Michael F

    2006-01-01

    Background Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As genotyping methods improve throughput, approaches that can explore multigene interactions appropriately should lead to improved understanding of MS. Methods 286 unrelated patients with definite MS and 362 unrelated healthy controls of Russian descent were genotyped at polymorphic loci (including SNPs, repeat polymorphisms, and an insertion/deletion) of the DRB1, TNF, LT, TGFβ1, CCR5 and CTLA4 genes and TNFa and TNFb microsatellites. Each allele carriership in patients and controls was compared by Fisher's exact test, and disease-associated combinations of alleles in the data set were sought using a Bayesian Markov chain Monte Carlo-based method recently developed by our group. Results We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*04 were also reidentified as MS-associated. Conclusion These results represent an independent validation of MS association with DRB1*15(2) and TNFa9 in Russians and are the first to find the interplay of three loci in conferring susceptibility to MS. They demonstrate the efficacy of our approach for the identification of complex-disease-associated combinations of alleles. PMID:16872485

  3. Features in visual search combine linearly

    PubMed Central

    Pramod, R. T.; Arun, S. P.

    2014-01-01

    Single features such as line orientation and length are known to guide visual search, but relatively little is known about how multiple features combine in search. To address this question, we investigated how search for targets differing in multiple features (intensity, length, orientation) from the distracters is related to searches for targets differing in each of the individual features. We tested race models (based on reaction times) and co-activation models (based on reciprocal of reaction times) for their ability to predict multiple feature searches. Multiple feature searches were best accounted for by a co-activation model in which feature information combined linearly (r = 0.95). This result agrees with the classic finding that these features are separable i.e., subjective dissimilarity ratings sum linearly. We then replicated the classical finding that the length and width of a rectangle are integral features—in other words, they combine nonlinearly in visual search. However, to our surprise, upon including aspect ratio as an additional feature, length and width combined linearly and this model outperformed all other models. Thus, length and width of a rectangle became separable when considered together with aspect ratio. This finding predicts that searches involving shapes with identical aspect ratio should be more difficult than searches where shapes differ in aspect ratio. We confirmed this prediction on a variety of shapes. We conclude that features in visual search co-activate linearly and demonstrate for the first time that aspect ratio is a novel feature that guides visual search. PMID:24715328

  4. Combinational concentration gradient confinement through stagnation flow.

    PubMed

    Alicia, Toh G G; Yang, Chun; Wang, Zhiping; Nguyen, Nam-Trung

    2016-01-21

    Concentration gradient generation in microfluidics is typically constrained by two conflicting mass transport requirements: short characteristic times (τ) for precise temporal control of concentration gradients but at the expense of high flow rates and hence, high flow shear stresses (σ). To decouple the limitations from these parameters, here we propose the use of stagnation flows to confine concentration gradients within large velocity gradients that surround the stagnation point. We developed a modified cross-slot (MCS) device capable of feeding binary and combinational concentration sources in stagnation flows. We show that across the velocity well, source-sink pairs can form permanent concentration gradients. As source-sink concentration pairs are continuously supplied to the MCS, a permanently stable concentration gradient can be generated. Tuning the flow rates directly controls the velocity gradients, and hence the stagnation point location, allowing the confined concentration gradient to be focused. In addition, the flow rate ratio within the MCS rapidly controls (τ ∼ 50 ms) the location of the stagnation point and the confined combinational concentration gradients at low flow shear (0.2 Pa < σ < 2.9 Pa). The MCS device described in this study establishes the method for using stagnation flows to rapidly generate and position low shear combinational concentration gradients for shear sensitive biological assays. PMID:26671507

  5. Antimalarial drug resistance and combination chemotherapy.

    PubMed Central

    White, N

    1999-01-01

    Antimarial drug resistance develops when spontaneously occurring parasite mutants with reduced susceptibility are selected, and are then transmitted. Drugs for which a single point mutation confers a marked reduction in susceptibility are particularly vulnerable. Low clearance and a shallow concentration-effect relationship increase the chance of selection. Use of combinations of antimalarials that do not share the same resistance mechanisms will reduce the chance of selection because the chance of a resistant mutant surviving is the product of the per parasite mutation rates for the individual drugs, multiplied by the number of parasites in an infection that are exposed to the drugs. Artemisinin derivatives are particularly effective combination partners because (i) they are very active antimalarials, producing up to 10,000-fold reductions in parasite biomass per asexual cycle; (ii) they reduce malaria transmissibility; and (iii) no resistance to these drugs has been reported yet. There are good arguments for no longer using antimalarial drugs alone in treatment, and instead always using a combination with artemisinin or one of its derivatives. PMID:10365399

  6. Unsupervised Retinal Vessel Segmentation Using Combined Filters

    PubMed Central

    Oliveira, Wendeson S.; Teixeira, Joyce Vitor; Ren, Tsang Ing; Cavalcanti, George D. C.; Sijbers, Jan

    2016-01-01

    Image segmentation of retinal blood vessels is a process that can help to predict and diagnose cardiovascular related diseases, such as hypertension and diabetes, which are known to affect the retinal blood vessels’ appearance. This work proposes an unsupervised method for the segmentation of retinal vessels images using a combined matched filter, Frangi’s filter and Gabor Wavelet filter to enhance the images. The combination of these three filters in order to improve the segmentation is the main motivation of this work. We investigate two approaches to perform the filter combination: weighted mean and median ranking. Segmentation methods are tested after the vessel enhancement. Enhanced images with median ranking are segmented using a simple threshold criterion. Two segmentation procedures are applied when considering enhanced retinal images using the weighted mean approach. The first method is based on deformable models and the second uses fuzzy C-means for the image segmentation. The procedure is evaluated using two public image databases, Drive and Stare. The experimental results demonstrate that the proposed methods perform well for vessel segmentation in comparison with state-of-the-art methods. PMID:26919587

  7. Unsupervised Retinal Vessel Segmentation Using Combined Filters.

    PubMed

    Oliveira, Wendeson S; Teixeira, Joyce Vitor; Ren, Tsang Ing; Cavalcanti, George D C; Sijbers, Jan

    2016-01-01

    Image segmentation of retinal blood vessels is a process that can help to predict and diagnose cardiovascular related diseases, such as hypertension and diabetes, which are known to affect the retinal blood vessels' appearance. This work proposes an unsupervised method for the segmentation of retinal vessels images using a combined matched filter, Frangi's filter and Gabor Wavelet filter to enhance the images. The combination of these three filters in order to improve the segmentation is the main motivation of this work. We investigate two approaches to perform the filter combination: weighted mean and median ranking. Segmentation methods are tested after the vessel enhancement. Enhanced images with median ranking are segmented using a simple threshold criterion. Two segmentation procedures are applied when considering enhanced retinal images using the weighted mean approach. The first method is based on deformable models and the second uses fuzzy C-means for the image segmentation. The procedure is evaluated using two public image databases, Drive and Stare. The experimental results demonstrate that the proposed methods perform well for vessel segmentation in comparison with state-of-the-art methods.

  8. The effect of prosody on conceptual combination.

    PubMed

    Lynott, Dermot; Connell, Louise

    2010-08-01

    Research into people's comprehension of novel noun-noun phrases has long neglected the possible influences of prosody during meaning construction. At the same time, work in conceptual combination has disagreed about whether different classes of interpretation emerge from single or multiple processes; for example, whether people use distinct mechanisms when they interpret octopus apartment as property-based (e.g., an apartment with eight rooms) or relation-based (e.g., an apartment where an octopus lives). In two studies, we manipulate the prosodic emphasis patterns of novel noun-noun combinations (placing stress on the modifier noun, the head noun, or dual stress on both nouns) and ask participants to generate an interpretation for the novel phrase. Results show that people are faster to generate property-based interpretations when dual emphasis stresses both nouns equally, with prosody having little effect on the speed of relation-based interpretations. These findings highlight a role for prosody during meaning construction and underline important differences between relation- and property-based interpretations that are difficult to reconcile with unitary process views of conceptual combination. PMID:21564245

  9. Combining Epidemiologic Information Across Space Agencies

    NASA Technical Reports Server (NTRS)

    Minard, Charles G.; Clark, April L.; Wear, Mary L.; Mason, Sara; Van Baalen, Mary

    2010-01-01

    Space flight is a very unique occupational exposure with potential hazards that are not fully understood. A limited number of individuals have experienced the exposures incurred during space flight, and epidemiologic research would benefit from shared information across space agencies. However, data sharing can be problematic due to agency protection policies for personally identifiable information as well as medical records. Compliance with these protocols in the astronaut population is particularly difficult given the small, high-profile population under study. Creativity in combining data is necessary in order to overcome these difficulties and improve statistical power in research. This study presents methods in meta-analysis that may be used to combine non-attributable data across space agencies so that meaningful conclusions may be drawn about study interests. Methods for combining epidemiologic data across space agencies are presented, and the processes are demonstrated using life-time mortality data in U.S. astronauts and Russian cosmonauts. This proof of concept was found to be an acceptable way of sharing data across agencies, and will be used in the future as more relevant research interests are identified.

  10. Combinational concentration gradient confinement through stagnation flow.

    PubMed

    Alicia, Toh G G; Yang, Chun; Wang, Zhiping; Nguyen, Nam-Trung

    2016-01-21

    Concentration gradient generation in microfluidics is typically constrained by two conflicting mass transport requirements: short characteristic times (τ) for precise temporal control of concentration gradients but at the expense of high flow rates and hence, high flow shear stresses (σ). To decouple the limitations from these parameters, here we propose the use of stagnation flows to confine concentration gradients within large velocity gradients that surround the stagnation point. We developed a modified cross-slot (MCS) device capable of feeding binary and combinational concentration sources in stagnation flows. We show that across the velocity well, source-sink pairs can form permanent concentration gradients. As source-sink concentration pairs are continuously supplied to the MCS, a permanently stable concentration gradient can be generated. Tuning the flow rates directly controls the velocity gradients, and hence the stagnation point location, allowing the confined concentration gradient to be focused. In addition, the flow rate ratio within the MCS rapidly controls (τ ∼ 50 ms) the location of the stagnation point and the confined combinational concentration gradients at low flow shear (0.2 Pa < σ < 2.9 Pa). The MCS device described in this study establishes the method for using stagnation flows to rapidly generate and position low shear combinational concentration gradients for shear sensitive biological assays.

  11. Correcting and combining time series forecasters.

    PubMed

    Firmino, Paulo Renato A; de Mattos Neto, Paulo S G; Ferreira, Tiago A E

    2014-02-01

    Combined forecasters have been in the vanguard of stochastic time series modeling. In this way it has been usual to suppose that each single model generates a residual or prediction error like a white noise. However, mostly because of disturbances not captured by each model, it is yet possible that such supposition is violated. The present paper introduces a two-step method for correcting and combining forecasting models. Firstly, the stochastic process underlying the bias of each predictive model is built according to a recursive ARIMA algorithm in order to achieve a white noise behavior. At each iteration of the algorithm the best ARIMA adjustment is determined according to a given information criterion (e.g. Akaike). Then, in the light of the corrected predictions, it is considered a maximum likelihood combined estimator. Applications involving single ARIMA and artificial neural networks models for Dow Jones Industrial Average Index, S&P500 Index, Google Stock Value, and Nasdaq Index series illustrate the usefulness of the proposed framework. PMID:24239986

  12. Combination immunotherapies for type 1 diabetes mellitus.

    PubMed

    Pozzilli, Paolo; Maddaloni, Ernesto; Buzzetti, Raffaella

    2015-05-01

    Immunotherapies for type 1 diabetes mellitus (T1DM) have been the focus of intense basic and clinical research over the past few decades. Restoring β-cell function is the ultimate goal of intervention trials that target the immune system in T1DM. In an attempt to achieve this aim, different combination therapies have been proposed over the past few years that are based on treatments tackling the various mechanisms involved in the destruction of β cells. The results of clinical trials have not matched expectations based on the positive results from preclinical studies. The heterogeneity of T1DM might explain the negative results obtained, but previous trials have not addressed this issue. However, novel promising combination therapies are being developed, including those that couple immunomodulators with drugs that stimulate β-cell regeneration in order to restore normoglycaemia. This strategy is an encouraging one to pursue the goal of finding a cure for T1DM. This Review summarizes the available data about combination immunotherapies in T1DM, particularly addressing their clinical importance. The available data supporting the use of registered drugs, such as proton pump inhibitors and incretin-based agents, that have been shown to induce β-cell regeneration will also be discussed.

  13. On Coding Non-Contiguous Letter Combinations

    PubMed Central

    Dandurand, Frédéric; Grainger, Jonathan; Duñabeitia, Jon Andoni; Granier, Jean-Pierre

    2011-01-01

    Starting from the hypothesis that printed word identification initially involves the parallel mapping of visual features onto location-specific letter identities, we analyze the type of information that would be involved in optimally mapping this location-specific orthographic code onto a location-invariant lexical code. We assume that some intermediate level of coding exists between individual letters and whole words, and that this involves the representation of letter combinations. We then investigate the nature of this intermediate level of coding given the constraints of optimality. This intermediate level of coding is expected to compress data while retaining as much information as possible about word identity. Information conveyed by letters is a function of how much they constrain word identity and how visible they are. Optimization of this coding is a combination of minimizing resources (using the most compact representations) and maximizing information. We show that in a large proportion of cases, non-contiguous letter sequences contain more information than contiguous sequences, while at the same time requiring less precise coding. Moreover, we found that the best predictor of human performance in orthographic priming experiments was within-word ranking of conditional probabilities, rather than average conditional probabilities. We conclude that from an optimality perspective, readers learn to select certain contiguous and non-contiguous letter combinations as information that provides the best cue to word identity. PMID:21734901

  14. SPS solid state antenna power combiner

    NASA Technical Reports Server (NTRS)

    Fitzsimmons, G. W.

    1980-01-01

    Solid state dc-rf converters offer potential improvements in reliability, mass and low voltage operation, provided that anticipated efficiencies in excess of 80 percent can be realized. Field effect transistors offer the greatest potential in the SPS frequency band at 2.45 GHz. To implement this approach it is essential that means be found to sum the power of many relatively low power solid state sources in a low-loss manner, and that means be provided to properly control the phase of the outputs of the large number of solid state sources required. To avoid the power combining losses associated with circuit hybrids it was proposed that the power from multiple solid state amplifiers be combined by direct coupling of each amplifier's output to the radiating antenna structure. The selected power-combining antenna consists of a unique printed (metalized) microstrip circuit on a ceramic type dielectric substrate which is backed by a shallow lightweight aluminum cavity which sums the power of four microwave sources. The antenna behaves like two one-half wavelength slot-line antennas coupled together via their common cavity structure.

  15. Combined photovacuum therapy of copulative dysfunction

    NASA Astrophysics Data System (ADS)

    Menyaev, Yulian A.; Zharov, Vladimir P.; Mishanin, Evgeniy A.; Kuzmich, Aleksandr P.; Bessonov, Sergey E.

    2006-02-01

    One of the important problems of modern medicine is treatment of urogenital diseases. 1-2 There is a set of the treatment methods for such problems, but any of them does not obey the modern physicians completely. 3-4 Our aim is to present the new combined therapeutic apparatus called "Yarovit" (produced in Russia, in collaboration between Bauman Moscow State University of Technology and Scientific Production Association and Medical Center "Yarovit") which successfully applied in clinics for cure the patients with copulative dysfunction diseases. 5-6 At this apparatus "Yarovit" (description model have abbreviation AMVL-0 1) there is a combination of vacuum decompression (0.1-0.4 kgs/cm2) and light emitting diodes matrix system (660 nm, 1-3 mW/cm2). In treatment procedure apparatus can be applied together with expanded module "Intratherm" (39 °C on average), which has rectal heating elements. The latest clinical studies were made together with volunteer participation of more then one hundred patients, and received results showed the good dynamic of healing. That let to conclude these combinations of physical therapeutic methods supplement each other and in conjunction provides a significant clinical effect. The further developments of such apparatuses are discussed.

  16. Combined second and third toe transfer.

    PubMed

    Wei, F C; Colony, L H; Chen, H C; Chuang, C C; Noordhoff, M S

    1989-10-01

    Historically, restoration of hand function following multiple digital amputation has been unsatisfactory. The evolution of digital reconstruction with toe transfer has enabled surgeons to reestablish prehension in these severely injured hands. A 4-year experience with 26 consecutive combined second and third toe transfers to replace missing adjacent fingers was reviewed in order to delineate the indications and technical considerations and to emphasize prevention of donor-site complications. Combined second and third toe transfer is reserved for adjacent finger amputations proximal to the digital web space with remaining fingers no longer than the small finger. Radial amputations are replaced with contralateral combined toe units, while ipsilateral toes are more ideal for ulnar amputations. Limited dorsal and plantar skin flaps extending only to the midpoint of the first and third digital web spaces allow for direct donor-site closure and uncomplicated healing. Maintenance of the plantar metatarsal arch by avoiding metatarsal shaft osteotomies or bone grafting-shortened metatarsals eliminates potential gait disturbances. When properly applied in selected patients, this single-stage microsurgical procedure can restore prehensile function, improve the appearance of the hand with multiple digital amputations, and preserve near-normal donor-foot function.

  17. Combining disparate data for decision making

    NASA Astrophysics Data System (ADS)

    Gettings, M. E.

    2010-12-01

    Combining information of disparate types from multiple data or model sources is a fundamental task in decision making theory. Procedures for combining and utilizing quantitative data with uncertainties are well-developed in several approaches, but methods for including qualitative and semi-quantitative data are much less so. Possibility theory offers an approach to treating all three data types in an objective and repeatable way. In decision making, biases are frequently present in several forms, including those arising from data quality, data spatial and temporal distribution, and the analyst's knowledge and beliefs as to which data or models are most important. The latter bias is particularly evident in the case of qualitative data and there are numerous examples of analysts feeling that a qualitative dataset is more relevant than a quantified one. Possibility theory and fuzzy logic now provide fairly general rules for quantifying qualitative and semi-quantitative data in ways that are repeatable and minimally biased. Once a set of quantified data and/or model layers is obtained, there are several methods of combining them to obtain insight useful in decision making. These include: various combinations of layers using formal fuzzy logic (for example, layer A and (layer B or layer C) but not layer D); connecting the layers with varying influence links in a Fuzzy Cognitive Map; and using the set of layers for the universe of discourse for agent based model simulations. One example of logical combinations that have proven useful is the definition of possible habitat for valley fever fungus (Coccidioides sp.) using variables such as soil type, altitude, aspect, moisture and temperature. A second example is the delineation of the lithology and possible mineralization of several areas beneath basin fill in southern Arizona. A Fuzzy Cognitive Map example is the impacts of development and operation of a hypothetical mine in an area adjacent to a city. In this model

  18. New 1F1N Species Combinations in Ophiocordycipitaceae (Hypocreales).

    PubMed

    Spatafora, Joseph W; Quandt, C Alisha; Kepler, Ryan M; Sung, Gi-Ho; Shrestha, Bhushan; Hywel-Jones, Nigel L; Luangsa-Ard, J Jennifer

    2015-12-01

    Based on the taxonomic and nomenclatural recommendations of Quandt et al. (2014) new species combinations are made for Ophiocordycipitaceae. These new combinations are compliant with recent changes in the International Code of Nomenclature for algae, fungi, and plants (ICN) and the abolition of the dual system of nomenclature for fungi. These changes include 10 new combinations into Drechmeria, four new combinations into Harposporium, 23 new combinations and 15 synonymies in Ophiocordyceps, and one new combination into Purpureocillium. PMID:26734546

  19. 21 CFR 347.20 - Permitted combinations of active ingredients.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...) Combinations of skin protectant and sunscreen active ingredients. Any one (two when required to be in... single sunscreen active ingredient, or any permitted combination of these ingredients, provided...

  20. 21 CFR 347.20 - Permitted combinations of active ingredients.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ...) Combinations of skin protectant and sunscreen active ingredients. Any one (two when required to be in... single sunscreen active ingredient, or any permitted combination of these ingredients, provided...

  1. 21 CFR 347.20 - Permitted combinations of active ingredients.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...) Combinations of skin protectant and sunscreen active ingredients. Any one (two when required to be in... single sunscreen active ingredient, or any permitted combination of these ingredients, provided...

  2. 21 CFR 347.20 - Permitted combinations of active ingredients.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...) Combinations of skin protectant and sunscreen active ingredients. Any one (two when required to be in... single sunscreen active ingredient, or any permitted combination of these ingredients, provided...

  3. 21 CFR 347.20 - Permitted combinations of active ingredients.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...) Combinations of skin protectant and sunscreen active ingredients. Any one (two when required to be in... single sunscreen active ingredient, or any permitted combination of these ingredients, provided...

  4. Signal-to-noise Ratio and Combiner Weight Estimation for Symbol Stream Combining

    NASA Technical Reports Server (NTRS)

    Vo, Q. D.

    1984-01-01

    A method is presented for signal to noise ratio (SNR) and symbol stream combiner weight estimation. The SNR estimator employs absolute value moments as in an earlier method. The main contribution is that a new algorithm is derived for the combiner weight estimator to remove the large bias at low SNRs. The new algorithm is simulated to combine two independent symbol streams at various SNRs. As an example, the combining two symbol streams at SNRs of -1 dB and -7 dB, conbiner weight estimates using 1000 samples for the -1 dB stream and 10,000 samples for the -7 dB stream achieve an output SNR of -0.039 dB, which is just 0.012 dB below the theoretical limit achievable with perfect knowledge of the SNRs.

  5. Combination Antiretroviral Use and Preterm Birth

    PubMed Central

    Watts, D. Heather; Williams, Paige L.; Kacanek, Deborah; Griner, Raymond; Rich, Kenneth; Hazra, Rohan; Mofenson, Lynne M.; Mendez, Hermann A.

    2013-01-01

    Background. Use of antiretroviral drugs (ARVs) during pregnancy has been associated with higher risk of preterm birth. Methods. The Pediatric HIV/AIDS Cohort Study network's Surveillance Monitoring for ART Toxicities study is a US-based cohort of human immunodeficiency virus (HIV)–exposed uninfected children. We evaluated maternal ARV use during pregnancy and the risk of any type of preterm birth (ie, birth before 37 completed weeks of gestation), the risk of spontaneous preterm birth (ie, preterm birth that occurred after preterm labor or membrane rupture, without other complications), and the risk of small for gestational age (SGA; ie, a birth weight of <10th percentile for gestational age). Multivariable logistic regression models were used to evaluate the association of ARVs and timing of exposure, while adjusting for maternal characteristics. Results. Among 1869 singleton births, 18.6% were preterm, 10.2% were spontaneous preterm, and 7.3% were SGA. A total of 89% used 3-drug combination ARV regimens during pregnancy. In adjusted models, the odds of preterm birth and spontaneous preterm birth were significantly greater among mothers who used protease inhibitors during the first trimester (adjusted odds ratios, 1.55 and 1.59, respectively) but not among mothers who used nonnucleoside reverse-transcriptase inhibitor or triple-nucleoside regimens during the first trimester. Combination ARV exposure starting later in pregnancy was not associated with increased risk. No associations were observed between SGA and exposure to combination ARV regimens. Conclusions. Protease inhibitor use early in pregnancy may be associated with increased risk for prematurity. PMID:23204173

  6. Binocular combination in abnormal binocular vision.

    PubMed

    Ding, Jian; Klein, Stanley A; Levi, Dennis M

    2013-02-08

    We investigated suprathreshold binocular combination in humans with abnormal binocular visual experience early in life. In the first experiment we presented the two eyes with equal but opposite phase shifted sine waves and measured the perceived phase of the cyclopean sine wave. Normal observers have balanced vision between the two eyes when the two eyes' images have equal contrast (i.e., both eyes contribute equally to the perceived image and perceived phase = 0°). However, in observers with strabismus and/or amblyopia, balanced vision requires a higher contrast image in the nondominant eye (NDE) than the dominant eye (DE). This asymmetry between the two eyes is larger than predicted from the contrast sensitivities or monocular perceived contrast of the two eyes and is dependent on contrast and spatial frequency: more asymmetric with higher contrast and/or spatial frequency. Our results also revealed a surprising NDE-to-DE enhancement in some of our abnormal observers. This enhancement is not evident in normal vision because it is normally masked by interocular suppression. However, in these abnormal observers the NDE-to-DE suppression was weak or absent. In the second experiment, we used the identical stimuli to measure the perceived contrast of a cyclopean grating by matching the binocular combined contrast to a standard contrast presented to the DE. These measures provide strong constraints for model fitting. We found asymmetric interocular interactions in binocular contrast perception, which was dependent on both contrast and spatial frequency in the same way as in phase perception. By introducing asymmetric parameters to the modified Ding-Sperling model including interocular contrast gain enhancement, we succeeded in accounting for both binocular combined phase and contrast simultaneously. Adding binocular contrast gain control to the modified Ding-Sperling model enabled us to predict the results of dichoptic and binocular contrast discrimination experiments

  7. Combined load test apparatus for flat panels

    NASA Astrophysics Data System (ADS)

    McWithey, Robert R.; Martin, Carl J., Jr.; Cerro, Jeffrey A.

    1992-04-01

    Future hypersonic aircraft such as the National Aero-Space Plane and a high speed civil transport will require the design and use of efficient, highly-loaded, flat structural panels to achieve mission requirements. These panels will be subjected to severe combinations of in-plane mechanical distributed loads (i.e., normal loads in two perpendicular directions plus a shear load), in addition to pressure and thermal loads. A testing apparatus is provided for applying uniform combined in-plane stresses to a flat panel containing an interior test area. Actuators cause two sets of load rods to apply loads to the edge of the flat panel. The first set applies loads which are perpendicular to and independent of the loads applied by the second set. The loads are applied according to a cosine load distribution to obtain a uniform stress field within the test area. The flat panel may be rotated with respect to the applied loads to obtain a wide range of combined stresses in the test area. Movement outside the plane of the flat panel may be selectively prevented by connecting the flat panel to a restraining disk by support rods. The support rods then define the test area. A thermal load may be applied to one side of the flat panel and a pressure load may be applied to the other side. The novelty of this method is found in providing a testing apparatus which allows mechanical, thermal and pressure loads to be applied simultaneously to a flat panel for testing purposes.

  8. Combining cluster number counts and galaxy clustering

    NASA Astrophysics Data System (ADS)

    Lacasa, Fabien; Rosenfeld, Rogerio

    2016-08-01

    The abundance of clusters and the clustering of galaxies are two of the important cosmological probes for current and future large scale surveys of galaxies, such as the Dark Energy Survey. In order to combine them one has to account for the fact that they are not independent quantities, since they probe the same density field. It is important to develop a good understanding of their correlation in order to extract parameter constraints. We present a detailed modelling of the joint covariance matrix between cluster number counts and the galaxy angular power spectrum. We employ the framework of the halo model complemented by a Halo Occupation Distribution model (HOD). We demonstrate the importance of accounting for non-Gaussianity to produce accurate covariance predictions. Indeed, we show that the non-Gaussian covariance becomes dominant at small scales, low redshifts or high cluster masses. We discuss in particular the case of the super-sample covariance (SSC), including the effects of galaxy shot-noise, halo second order bias and non-local bias. We demonstrate that the SSC obeys mathematical inequalities and positivity. Using the joint covariance matrix and a Fisher matrix methodology, we examine the prospects of combining these two probes to constrain cosmological and HOD parameters. We find that the combination indeed results in noticeably better constraints, with improvements of order 20% on cosmological parameters compared to the best single probe, and even greater improvement on HOD parameters, with reduction of error bars by a factor 1.4-4.8. This happens in particular because the cross-covariance introduces a synergy between the probes on small scales. We conclude that accounting for non-Gaussian effects is required for the joint analysis of these observables in galaxy surveys.

  9. Combining Multiple Gyroscope Outputs for Increased Accuracy

    NASA Technical Reports Server (NTRS)

    Bayard, David S.

    2003-01-01

    A proposed method of processing the outputs of multiple gyroscopes to increase the accuracy of rate (that is, angular-velocity) readings has been developed theoretically and demonstrated by computer simulation. Although the method is applicable, in principle, to any gyroscopes, it is intended especially for application to gyroscopes that are parts of microelectromechanical systems (MEMS). The method is based on the concept that the collective performance of multiple, relatively inexpensive, nominally identical devices can be better than that of one of the devices considered by itself. The method would make it possible to synthesize the readings of a single, more accurate gyroscope (a virtual gyroscope) from the outputs of a large number of microscopic gyroscopes fabricated together on a single MEMS chip. The big advantage would be that the combination of the MEMS gyroscope array and the processing circuitry needed to implement the method would be smaller, lighter in weight, and less power-hungry, relative to a conventional gyroscope of equal accuracy. The method (see figure) is one of combining and filtering the digitized outputs of multiple gyroscopes to obtain minimum-variance estimates of rate. In the combining-and-filtering operations, measurement data from the gyroscopes would be weighted and smoothed with respect to each other according to the gain matrix of a minimum- variance filter. According to Kalman-filter theory, the gain matrix of the minimum-variance filter is uniquely specified by the filter covariance, which propagates according to a matrix Riccati equation. The present method incorporates an exact analytical solution of this equation.

  10. remote sensing data combinations - global AOD maps

    NASA Astrophysics Data System (ADS)

    Kinne, S.

    2009-04-01

    More accurate and more complete measurement-based data-sets are needed to constrain the freedom of global modeling and raise confidence in model predictions. In remote sensing, different methods and sensors frequently yield estimates for the same (or a strongly related) atmospheric property. For maximum benefit to data-users (e.g. input or evaluation data to modeling) - in the context of differences in sensor capabilities and retrieval limitations - there is a desire to combine the strengths of these individual data sources for superior products. In a demonstration, different multi-annual global monthly maps for aerosol optical depth (AOD) from satellite remote sensing been compared and scored against local quality reference data from ground remote sensing. The regionally best performing satellite data-sets have been combined into global monthly AOD maps. As expected, this satellite composite scores better than any individual satellite retrieval. Further improvements are achieved by merging statistics of ground remote sensing into the composite. The global average mid-visible AOD of this remote sensing composite is near 0.13 annually, with lower values during northern hemispheric fall and winter (0.12) and larger values during northern hemispheric spring and summer (0.14). This measurement based data composite also reveals characteristic deficiencies in global modeling: Modeling tends to overestimates AOD over the northern mid-latitudes and to underestimate AOD over tropical and sub-tropical land regions. Also noteworthy are AOD underestimates by modeling in remote oceanic regions, though only in relative sense as AOD values in that region as small. The AOD remote sensing data composite is far from perfect, but it demonstrates the extra value of data-combinations.

  11. Finding a Panacea Among Combination Cancer Therapies

    PubMed Central

    Yamaguchi, Ryuji; Perkins, Guy

    2012-01-01

    Since each cancer is a heterogeneous mix of cancer cells at different stages of development, we are faced with trying to treat many different diseased cells all at once. An authentic approach is to build a genomic and proteomic profile of a patient, identify the target oncogenes and prescribe the combination of targeted drugs tailored for that patient. However, there are many practical problems with this personalized medicine approach: (1) cancers often generate treatment-resistant phenotypes, (2) the treatment could be enormously expensive, and (3) most of the targeted drugs have not been developed yet. We propose a different approach: therapies that combine 2-deoxyglucose (2DG) with Bcl-2 antagonist such as ABT-263/737 (ABT). Pro-apoptotic protein Bak is normally sequestered by Mcl-1 and Bcl-xL. Only when Bak is released from both Mcl-1 and Bcl-xL, can it induce apoptosis. 2DG can prime highly glycolytic cells by dissociating Bak-Mcl-1 complex. Cells primed by 2DG are some brain cells and most cancer cells. ABT can bind to Bcl-xL, dissociating Bak-Bcl-xL complex, freeing Bak and inducing apoptosis. Since ABT cannot cross blood-brain barrier, only cells exposed to both agents are highly glycolytic cancer cells located outside the brain. Because ABT directly triggers apoptosis at the step very near the terminal point of apoptosis, 2DG-ABT combination therapies are applicable to many types of cancer at all stages of development, with little side effect. PMID:22052464

  12. Systemic therapy and synergies by combination.

    PubMed

    Wörns, Marcus-Alexander

    2013-01-01

    After years of therapeutic nihilism due to the inefficacy of conventional cytotoxic chemotherapy, the multikinase inhibitor sorafenib was the first agent to demonstrate a significant improvement in the survival of patients with advanced hepatocellular carcinoma (HCC). However, survival benefits on sorafenib treatment remain modest in clinical practice and developing more effective systemic therapies is challenging. No other targeted agent or regimen has proven efficacy to improve survival in a phase III trial in the first- or second-line setting, and no standard treatment option currently exists outside of clinical trials for patients with acquired resistance or intolerance to sorafenib. In contrast to other malignancies, no oncogene addiction has been identified in hepatocarcinogenesis thus far, which may explain why currently tested agents do not achieve sustained partial or complete response in the majority of patients. Several agents with mainly antiangiogenic properties are currently in phase II and III development, including brivanib, ramucirumab, everolimus, tivantinib and resminostat. In addition, the role of molecularly targeted therapy (MTT) in earlier stages of the disease in combination with transcatheter arterial chemoembolization or in the adjuvant setting after potentially curative approaches is under investigation. The identification of the key driver mutations and the assessment of relevant targets for specific subpopulations of patients according to their biomarker-based profile will hopefully lead to a more personalized medicine. This article attempts to provide a concise overview on recent developments of MTT in the phase II-III setting in advanced HCC with an additional focus on synergistic combinations and combined treatment approaches. PMID:23797131

  13. Homogenization in compiling ICRF combined catalogs

    NASA Astrophysics Data System (ADS)

    Marco, F. J.; Martínez, M. J.; López, J. A.

    2013-10-01

    Context. The International Astronomical Union (IAU) recommendations regarding the International Celestial Reference Frame (ICRF) realizations require the construction of radio sources catalogs obtained using very-long-baseline interferometry (VLBI) methods. The improvement of these catalogs is a necessary procedure for the further densification of the ICRF over the celestial sphere. Aims: The different positions obtained from several catalogs using common sources to the ICRF make it necessary to critically revise the different methods employed in improving the ICRF from several radio sources catalogs. In this sense, a revision of the analytical and the statistical methods is necessary in line with their advantages and disadvantages. We have a double goal: first, we propose an adequate treatment of the residual of several catalogs to obtain a homogeneous catalog; second, we attempt to discern whether a combined catalog is homogeneous. Methods: We define homogeneity as applied to our problem in a dual sense: the first deals with the spatial distribution of the data over the celestial sphere. The second has a statistical meaning, as we consider that homogeneity exists when the residual between a given catalog and the ICRF behaves as a unimodal pure Gaussian. We use a nonparametrical method, which enables us to homogeneously extend the statistical properties of the residual over the entire sphere. This intermediate adjustment allows for subsequent computation of the coefficients for any parametrical adjustment model that has a higher accuracy and greater stability, and it prevents problems related with direct adjustments using the models. On the other hand, the homogeneity of the residuals in a catalog is tested using different weights. Our procedure also serves to propose the most suitable weights to maintain homogeneity in the final results. We perform a test using the ICRF-Ext2, JPL, and USNO quasar catalogs. Results: We show that a combination of catalogs can only

  14. Anticancer Efficacy of Polyphenols and Their Combinations

    PubMed Central

    Niedzwiecki, Aleksandra; Roomi, Mohd Waheed; Kalinovsky, Tatiana; Rath, Matthias

    2016-01-01

    Polyphenols, found abundantly in plants, display many anticarcinogenic properties including their inhibitory effects on cancer cell proliferation, tumor growth, angiogenesis, metastasis, and inflammation as well as inducing apoptosis. In addition, they can modulate immune system response and protect normal cells against free radicals damage. Most investigations on anticancer mechanisms of polyphenols were conducted with individual compounds. However, several studies, including ours, have indicated that anti-cancer efficacy and scope of action can be further enhanced by combining them synergistically with chemically similar or different compounds. While most studies investigated the anti-cancer effects of combinations of two or three compounds, we used more comprehensive mixtures of specific polyphenols and mixtures of polyphenols with vitamins, amino acids and other micronutrients. The mixture containing quercetin, curcumin, green tea, cruciferex, and resveratrol (PB) demonstrated significant inhibition of the growth of Fanconi anemia head and neck squamous cell carcinoma and dose-dependent inhibition of cell proliferation, matrix metalloproteinase (MMP)-2 and -9 secretion, cell migration and invasion through Matrigel. PB was found effective in inhibition of fibrosarcoma HT-1080 and melanoma A2058 cell proliferation, MMP-2 and -9 expression, invasion through Matrigel and inducing apoptosis, important parameters for cancer prevention. A combination of polyphenols (quercetin and green tea extract) with vitamin C, amino acids and other micronutrients (EPQ) demonstrated significant suppression of ovarian cancer ES-2 xenograft tumor growth and suppression of ovarian tumor growth and lung metastasis from IP injection of ovarian cancer A-2780 cells. The EPQ mixture without quercetin (NM) also has shown potent anticancer activity in vivo and in vitro in a few dozen cancer cell lines by inhibiting tumor growth and metastasis, MMP-2 and -9 secretion, invasion, angiogenesis

  15. Anticancer Efficacy of Polyphenols and Their Combinations.

    PubMed

    Niedzwiecki, Aleksandra; Roomi, Mohd Waheed; Kalinovsky, Tatiana; Rath, Matthias

    2016-09-09

    Polyphenols, found abundantly in plants, display many anticarcinogenic properties including their inhibitory effects on cancer cell proliferation, tumor growth, angiogenesis, metastasis, and inflammation as well as inducing apoptosis. In addition, they can modulate immune system response and protect normal cells against free radicals damage. Most investigations on anticancer mechanisms of polyphenols were conducted with individual compounds. However, several studies, including ours, have indicated that anti-cancer efficacy and scope of action can be further enhanced by combining them synergistically with chemically similar or different compounds. While most studies investigated the anti-cancer effects of combinations of two or three compounds, we used more comprehensive mixtures of specific polyphenols and mixtures of polyphenols with vitamins, amino acids and other micronutrients. The mixture containing quercetin, curcumin, green tea, cruciferex, and resveratrol (PB) demonstrated significant inhibition of the growth of Fanconi anemia head and neck squamous cell carcinoma and dose-dependent inhibition of cell proliferation, matrix metalloproteinase (MMP)-2 and -9 secretion, cell migration and invasion through Matrigel. PB was found effective in inhibition of fibrosarcoma HT-1080 and melanoma A2058 cell proliferation, MMP-2 and -9 expression, invasion through Matrigel and inducing apoptosis, important parameters for cancer prevention. A combination of polyphenols (quercetin and green tea extract) with vitamin C, amino acids and other micronutrients (EPQ) demonstrated significant suppression of ovarian cancer ES-2 xenograft tumor growth and suppression of ovarian tumor growth and lung metastasis from IP injection of ovarian cancer A-2780 cells. The EPQ mixture without quercetin (NM) also has shown potent anticancer activity in vivo and in vitro in a few dozen cancer cell lines by inhibiting tumor growth and metastasis, MMP-2 and -9 secretion, invasion, angiogenesis

  16. Solid oxide fuel cell combined cycles

    SciTech Connect

    Bevc, F.P.; Lundberg, W.L.; Bachovchin, D.M.

    1996-12-31

    The integration of the solid oxide fuel cell and combustion turbine technologies can result in combined-cycle power plants, fueled with natural gas, that have high efficiencies and clean gaseous emissions. Results of a study are presented in which conceptual designs were developed for 3 power plants based upon such an integration, and ranging in rating from 3 to 10 MW net ac. The plant cycles are described and characteristics of key components summarized. Also, plant design-point efficiency estimates are presented as well as values of other plant performance parameters.

  17. Combined fluidized bed retort and combustor

    DOEpatents

    Shang, Jer-Yu; Notestein, John E.; Mei, Joseph S.; Zeng, Li-Wen

    1984-01-01

    The present invention is directed to a combined fluidized bed retorting and combustion system particularly useful for extracting energy values from oil shale. The oil-shale retort and combustor are disposed side-by-side and in registry with one another through passageways in a partition therebetween. The passageways in the partition are submerged below the top of the respective fluid beds to preclude admixing or the product gases from the two chambers. The solid oil shale or bed material is transported through the chambers by inclining or slanting the fluidizing medium distributor so that the solid bed material, when fluidized, moves in the direction of the downward slope of the distributor.

  18. A Combined Preconditioning Strategy for Nonsymmetric Systems

    SciTech Connect

    de Dios, B. Ayuso; Barker, A. T.; Vassilevski, P. S.

    2014-11-04

    Here, we present and analyze a class of nonsymmetric preconditioners within a normal (weighted least-squares) matrix form for use in GMRES to solve nonsymmetric matrix problems that typically arise in finite element discretizations. An example of the additive Schwarz method applied to nonsymmetric but definite matrices is presented for which the abstract assumptions are verified. Variable preconditioner, which combines the original nonsymmetric one and a weighted least-squares version of it, and it is shown to be convergent and provides a viable strategy for using nonsymmetric preconditioners in practice. Numerical results are included to assess the theory and the performance of the proposed preconditioners.

  19. The combined epithelial odontogenic tumour in Malaysians.

    PubMed

    Siar, C H; Ng, K H

    1991-04-01

    The combined epithelial odontogenic tumour represents a hybrid lesion comprising primarily areas of adenomatoid odontogenic tumour intermixed with foci of calcifying epithelial odontogenic tumour. Five such cases retrieved from the files of the Division of Stomatology, Institute for Medical Research, Kuala Lumpur, and four others from the existing literature were analysed. A mean age of 18.8 years, a female preponderance (66.7%) with a male to female ratio of 1:2 and predilection for the mandible (55.6%) were observed. All cases were treated by conservative surgery and the lack of recurrence confirmed the innocuous nature of this lesion.

  20. Combination free-electron and gaseous laser

    SciTech Connect

    Brau, C.A.; Rockwood, S.D.; Stein, W.E.

    1981-06-08

    A multiple laser having one or more gaseous laser stages and one or more free electron stages is described. Each of the free electron laser stages is sequentially pumped by a microwave linear accelerator. Subsequently, the electron beam is directed through a gaseous laser, in the preferred embodiment, and in an alternative embodiment, through a microwave accelerator to lower the energy level of the electron beam to pump one or more gaseous lasers. The combination laser provides high pulse repetition frequencies, on the order of 1 kHz or greater, high power capability, high efficiency, and tunability in the synchronous production of multiple beams of coherent optical radiation.

  1. Combined constraints on holographic bosonic technicolor

    SciTech Connect

    Carone, Christopher D.; Primulando, Reinard

    2010-07-01

    We consider a model of strong electroweak symmetry breaking in which the expectation value of an additional, possibly composite, scalar field is responsible for the generation of fermion masses. The dynamics of the strongly coupled sector is defined and studied via its holographic dual, and does not correspond to a simple, scaled-up version of QCD. We consider the bounds from perturbative unitarity, the S parameter, and the mass of the Higgs-like scalar. We show that the combination of these constraints leaves a relatively limited region of parameter space viable, and suggests the qualitative features of the model that might be probed at the LHC.

  2. Anticancer Efficacy of Polyphenols and Their Combinations.

    PubMed

    Niedzwiecki, Aleksandra; Roomi, Mohd Waheed; Kalinovsky, Tatiana; Rath, Matthias

    2016-01-01

    Polyphenols, found abundantly in plants, display many anticarcinogenic properties including their inhibitory effects on cancer cell proliferation, tumor growth, angiogenesis, metastasis, and inflammation as well as inducing apoptosis. In addition, they can modulate immune system response and protect normal cells against free radicals damage. Most investigations on anticancer mechanisms of polyphenols were conducted with individual compounds. However, several studies, including ours, have indicated that anti-cancer efficacy and scope of action can be further enhanced by combining them synergistically with chemically similar or different compounds. While most studies investigated the anti-cancer effects of combinations of two or three compounds, we used more comprehensive mixtures of specific polyphenols and mixtures of polyphenols with vitamins, amino acids and other micronutrients. The mixture containing quercetin, curcumin, green tea, cruciferex, and resveratrol (PB) demonstrated significant inhibition of the growth of Fanconi anemia head and neck squamous cell carcinoma and dose-dependent inhibition of cell proliferation, matrix metalloproteinase (MMP)-2 and -9 secretion, cell migration and invasion through Matrigel. PB was found effective in inhibition of fibrosarcoma HT-1080 and melanoma A2058 cell proliferation, MMP-2 and -9 expression, invasion through Matrigel and inducing apoptosis, important parameters for cancer prevention. A combination of polyphenols (quercetin and green tea extract) with vitamin C, amino acids and other micronutrients (EPQ) demonstrated significant suppression of ovarian cancer ES-2 xenograft tumor growth and suppression of ovarian tumor growth and lung metastasis from IP injection of ovarian cancer A-2780 cells. The EPQ mixture without quercetin (NM) also has shown potent anticancer activity in vivo and in vitro in a few dozen cancer cell lines by inhibiting tumor growth and metastasis, MMP-2 and -9 secretion, invasion, angiogenesis

  3. Combined Therapy of Gastrointestinal Stromal Tumors.

    PubMed

    Rutkowski, Piotr; Hompes, Daphne

    2016-10-01

    Radical surgery is the mainstay of therapy for primary resectable, localized gastrointestinal stromal tumors (GIST). Nevertheless, approximately 40% to 50% of patients with potentially curative resections develop recurrent or metastatic disease. The introduction of imatinib mesylate has revolutionized the therapy of advanced (inoperable and/or metastatic) GIST and has become the standard of care in treatment of patients with advanced GIST. This article discusses the proper selection of candidates for adjuvant and neoadjuvant treatment in locally advanced GIST, exploring the available evidence behind the combination of preoperative imatinib and surgery. PMID:27591496

  4. Strongyloides Hyperinfection Syndrome Combined with Cytomegalovirus Infection

    PubMed Central

    Alsaeed, Mohammed; Ballool, Sulafa; Attia, Ashraf

    2016-01-01

    The mortality in Strongyloides hyperinfection syndrome (SHS) is alarmingly high. This is particularly common in bone marrow, renal, and other solid organ transplant (SOT) patients, where figures may reach up to 50–85%. Immunosuppressives, principally corticosteroids, are the primary triggering factor. In general, the clinical features of Strongyloides stercoralis hyperinfection are nonspecific; therefore, a high index of suspicion is required for early diagnosis and starting appropriate therapy. Although recurrent Gram-negative sepsis and meningitis have been previously reported, the combination of both cytomegalovirus (CMV) and strongyloidiasis had rarely been associated. We here describe a patient who survived SHS with recurrent Escherichia coli (E. coli) urosepsis and CMV infection. PMID:27703835

  5. Combination free electron and gaseous laser

    DOEpatents

    Brau, Charles A.; Rockwood, Stephen D.; Stein, William E.

    1980-01-01

    A multiple laser having one or more gaseous laser stages and one or more free electron stages. Each of the free electron laser stages is sequentially pumped by a microwave linear accelerator. Subsequently, the electron beam is directed through a gaseous laser, in the preferred embodiment, and in an alternative embodiment, through a microwave accelerator to lower the energy level of the electron beam to pump one or more gaseous lasers. The combination laser provides high pulse repetition frequencies, on the order of 1 kHz or greater, high power capability, high efficiency, and tunability in the synchronous production of multiple beams of coherent optical radiation.

  6. Combination strategies to enhance antitumor ADCC

    PubMed Central

    Kohrt, Holbrook E; Houot, Roch; Marabelle, Aurélien; Cho, Hearn Jay; Osman, Keren; Goldstein, Matthew; Levy, Ronald; Brody, Joshua

    2012-01-01

    The clinical efficacy of monoclonal antibodies as cancer therapeutics is largely dependent upon their ability to target the tumor and induce a functional antitumor immune response. This two-step process of ADCC utilizes the response of innate immune cells to provide antitumor cytotoxicity triggered by the interaction of the Fc portion of the antibody with the Fc receptor on the immune cell. Immunotherapeutics that target NK cells, γδ T cells, macrophages and dendritic cells can, by augmenting the function of the immune response, enhance the antitumor activity of the antibodies. Advantages of such combination strategies include: the application to multiple existing antibodies (even across multiple diseases), the feasibility (from a regulatory perspective) of combining with previously approved agents and the assurance (to physicians and trial participants) that one of the ingredients – the antitumor antibody – has proven efficacy on its own. Here we discuss current strategies, including biologic rationale and clinical results, which enhance ADCC in the following ways: strategies that increase total target–monoclonal antibody–effector binding, strategies that trigger effector cell ‘activating’ signals and strategies that block effector cell ‘inhibitory’ signals. PMID:22642334

  7. A combinational theory for maintenance of sex

    PubMed Central

    Hörandl, E

    2010-01-01

    Sexual reproduction implies high costs, but it is difficult to give evidence for evolutionary advantages that would explain the predominance of meiotic sex in eukaryotes. A combinational theory discussing evolution, maintenance and loss of sex may resolve the problem. The main function of sex is the restoration of DNA and consequently a higher quality of offspring. Recombination at meiosis evolved, perhaps, as a repair mechanism of DNA strand damages. This mechanism is most efficient for DNA restoration in multicellular eukaryotes, because the initial cell starts with a re-optimized genome, which is passed to all the daughter cells. Meiosis acts also as creator of variation in haploid stages, in which selection can purge most efficiently deleterious mutations. A prolonged diploid phase buffers the effects of deleterious recessive alleles as well as epigenetic defects and is thus optimal for prolonged growth periods. For complex multicellular organisms, the main advantage of sexuality is thus the alternation of diploid and haploid stages, combining advantages of both. A loss of sex is constrained by several, partly group-specific, developmental features. Hybridization may trigger shifts from sexual to asexual reproduction, but crossing barriers of the parental sexual species limit this process. For the concerted break-up of meiosis-outcrossing cycles plus silencing of secondary features, various group-specific changes in the regulatory system may be required. An establishment of asexuals requires special functional modifications and environmental opportunities. Costs for maintenance of meiotic sex are consequently lower than a shift to asexual reproduction. PMID:19623209

  8. Testing a combined vibration and acceleration environment.

    SciTech Connect

    Jepsen, Richard Alan; Romero, Edward F.

    2005-01-01

    Sandia National Laboratories has previously tested a capability to impose a 7.5 g-rms (30 g peak) radial vibration load up to 2 kHz on a 25 lb object with superimposed 50 g acceleration at its centrifuge facility. This was accomplished by attaching a 3,000 lb Unholtz-Dickie mechanical shaker at the end of the centrifuge arm to create a 'Vibrafuge'. However, the combination of non-radial vibration directions, and linear accelerations higher than 50g's are currently not possible because of the load capabilities of the shaker and the stresses on the internal shaker components due to the combined centrifuge acceleration. Therefore, a new technique using amplified piezo-electric actuators has been developed to surpass the limitations of the mechanical shaker system. They are lightweight, modular and would overcome several limitations presented by the current shaker. They are 'scalable', that is, adding more piezo-electric units in parallel or in series can support larger-weight test articles or displacement/frequency regimes. In addition, the units could be mounted on the centrifuge arm in various configurations to provide a variety of input directions. The design along with test results will be presented to demonstrate the capabilities and limitations of the new piezo-electric Vibrafuge.

  9. SHIELDING ANALYSIS FOR PORTABLE GAUGING COMBINATION SOURCES

    SciTech Connect

    J. TOMPKINS; L. LEONARD; ET AL

    2000-08-01

    Radioisotopic decay has been used as a source of photons and neutrons for industrial gauging operations since the late 1950s. Early portable moisture/density gauging equipment used Americium (Am)-241/Beryllium (Be)/Cesium (Cs)-137 combination sources to supply the required nuclear energy for gauging. Combination sources typically contained 0.040 Ci of Am-241 and 0.010 Ci of CS-137 in the same source capsule. Most of these sources were manufactured approximately 30 years ago. Collection, transportation, and storage of these sources once removed from their original device represent a shielding problem with distinct gamma and neutron components. The Off-Site Source Recovery (OSR) Project is planning to use a multi-function drum (MFD) for the collection, shipping, and storage of AmBe sources, as well as the eventual waste package for disposal. The MFD is an approved TRU waste container design for DOE TRU waste known as the 12 inch Pipe Component Overpack. As the name indicates, this drum is based on a 12 inch ID stainless steel weldment approximately 25 inch in internal length. The existing drum design allows for addition of shielding within the pipe component up to the 110 kg maximum pay load weight. The 12 inch pipe component is packaged inside a 55-gallon drum, with the balance of the interior space filled with fiberboard dunnage. This packaging geometry is similar to the design of a DOT 6M, Type B shipping container.

  10. Fixed-dose combination therapy for psoriasis.

    PubMed

    Guenther, Lyn C

    2004-01-01

    Fixed-dose combination therapy offers stable products containing two or more medications with different mechanisms of action and safety profiles. It is also convenient for patients since only one product rather than two or more needs to be applied. Topical corticosteroids are often the mainstay of therapy in psoriasis. Diprosalic and Nerisalic contain a topical corticosteroid (betamethasone dipropionate and diflucortolone, respectively) and salicylic acid. A left/right study showed that both products have comparable efficacy. It has also been shown that betamethasone dipropionate + salicylic acid ointment has similar efficacy to clobetasol and calcipotriene (calcipotriol) ointments. Betamethasone dipropionate + salicylic acid lotion has similar efficacy to clobetasol lotion. Faster improvement of scaling, itching, and redness was noted with betamethasone dipropionate + salicylic acid lotion compared with betamethasone dipropionate alone. Dovobet (Daivobet) ointment is a fixed-dose combination product containing betamethasone dipropionate and calcipotriene. Clinical studies have shown that it has greater efficacy and a faster speed of onset than the individual components or tacalcitol. Once daily and twice daily treatments have similar efficacy. Psoriasis Area and Severity Index reductions of approximately 40% after 1 week and 70% after 4 weeks of therapy were consistently noted in six large international studies involving >6000 patients. Betamethasone dipropionate + calcipotriene treatment is associated with approximately 75% less adverse cutaneous events as compared with tacalcitol, 50% less compared with calcipotriene, and a similar number as treatment with betamethasone dipropionate.

  11. Modeling antibody hypervariable loops: a combined algorithm.

    PubMed Central

    Martin, A C; Cheetham, J C; Rees, A R

    1989-01-01

    To be of any value, a predicted model of an antibody combining site should have an accuracy approaching that of antibody structures determined by x-ray crystallography (1.6-2.7 A). A number of modeling protocols have been proposed, which fall into two main categories--those that adopt a knowledge-based approach and those that attempt to construct the hypervariable loop regions of the antibody ab initio. Here we present a combined algorithm requiring no arbitrary decisions on the part of the user, which has been successfully applied to the modeling of the individual loops in two systems: the anti-lysozyme antibody HyHel-5, the crystal structure of which is as a complex with lysozyme [Sheriff, S., Silverton, E. W., Padlan, E. A., Cohen, G. H., Smith-Gill, S. J., Finzel, B. C. & Davies, D. R. (1987) Proc. Natl. Acad. Sci. USA 84, 8075-8079], and the free antigen binding fragment (Fab) of the anti-lysozyme peptide antibody, Gloop2. This protocol may be used with a high degree of confidence to model single-loop replacements, insertions, deletions, and side-chain replacements. In addition, it may be used in conjunction with other modeling protocols as a method by which to model particular loops whose conformations are predicted poorly by these methods. PMID:2594766

  12. Combined Solar and Wind Energy Systems

    NASA Astrophysics Data System (ADS)

    Tripanagnostopoulos, Y.; Souliotis, M.; Makris, Th.

    2010-01-01

    In this paper we present the new concept of combined solar and wind energy systems for buildings applications. Photovoltaics (PV) and small wind turbines (WTs) can be install on buildings, in case of sufficient wind potential, providing the building with electricity. PVs can be combined with thermal collectors to form the hybrid photovoltaic/thermal (PV/T) systems. The PVs (or the PV/Ts) and WT subsystems can supplement each other to cover building electrical load. In case of using PV/T collectors, the surplus of electricity, if not used or stored in batteries, can increase the temperature of the thermal storage tank of the solar thermal unit. The description of the experimental set-up of the suggested PV/T/WT system and experimental results are presented. In PV/T/WT systems the output from the solar part depends on the sunshine time and the output of the wind turbine part depends on the wind speed and is obtained any time of day or night. The use of the three subsystems can cover a great part of building energy load, contributing to conventional energy saving and environment protection. The PV/T/WT systems are considered suitable in rural and remote areas with electricity supply from stand-alone units or mini-grid connection. PV/T/WT systems can also be used in typical grid connected applications.

  13. Fixed-dose combination therapy for psoriasis.

    PubMed

    Guenther, Lyn C

    2004-01-01

    Fixed-dose combination therapy offers stable products containing two or more medications with different mechanisms of action and safety profiles. It is also convenient for patients since only one product rather than two or more needs to be applied. Topical corticosteroids are often the mainstay of therapy in psoriasis. Diprosalic and Nerisalic contain a topical corticosteroid (betamethasone dipropionate and diflucortolone, respectively) and salicylic acid. A left/right study showed that both products have comparable efficacy. It has also been shown that betamethasone dipropionate + salicylic acid ointment has similar efficacy to clobetasol and calcipotriene (calcipotriol) ointments. Betamethasone dipropionate + salicylic acid lotion has similar efficacy to clobetasol lotion. Faster improvement of scaling, itching, and redness was noted with betamethasone dipropionate + salicylic acid lotion compared with betamethasone dipropionate alone. Dovobet (Daivobet) ointment is a fixed-dose combination product containing betamethasone dipropionate and calcipotriene. Clinical studies have shown that it has greater efficacy and a faster speed of onset than the individual components or tacalcitol. Once daily and twice daily treatments have similar efficacy. Psoriasis Area and Severity Index reductions of approximately 40% after 1 week and 70% after 4 weeks of therapy were consistently noted in six large international studies involving >6000 patients. Betamethasone dipropionate + calcipotriene treatment is associated with approximately 75% less adverse cutaneous events as compared with tacalcitol, 50% less compared with calcipotriene, and a similar number as treatment with betamethasone dipropionate. PMID:15109271

  14. Efficacy of amikacin combinations for nocardiosis.

    PubMed

    Kanemitsu, Keiji; Kunishima, Hiroyuki; Saga, Tomoo; Harigae, Hideo; Ishikawa, Shiho; Takemura, Hiromu; Kaku, Mitsuo

    2003-11-01

    We isolated five bacterial strains from patients diagnosed as having nocardiosis. Bacterial species were identified based on the similarities in the nucleotide sequences of 16S ribosomal RNAs. Three of the five strains were identified as Nocardia asteroids, but unexpectedly other two were Streptomyces hygroscopicus and Rothia dentocariosa. The latter two species are not members of the family Nocardiaceae. We investigated the susceptibilities of these five strains to the following nine antimicrobial agents: trimethoprim/sulfamethoxazole (TMP/SMX), minocycline (MINO), erythromycin (EM), amikacin (AMK), cefotaxime (CTX), faropenem (FRPM), imipenem (IPM), ciprofloxacin (CPFX), and sparfloxacin (SPFX). The minimum inhibitory concentration (MIC) ranges (mg/ml) were as follows: TMP-SMX, 4- > 32; MINO, 0.125-8; EM, < or = 0.016- > 32; AMK, 1-2; CTX, 0.063- > 32; FRPM, 0.063-16; IPM, 0.125-2; CPFX, 4-32; and SPFX, 0.5-16. Moreover, the synergistic effects of AMK in combination with each of TMP-SMX, MINO, EM, CTX, IPM, and SPFX were investigated by checkerboard synergy testing. No antagonism was recognized for the three N. asteroides strains. Synergistic and additive effects were observed for the combinations of AMK with CTX, IPM, or SPFX. PMID:14649737

  15. Computational investigation of rocket based combined cycle

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-bo; Wang, Zhan-xue; Liu, Zeng-wen

    2013-03-01

    Based on Computational Fluid Dynamic technology, the mixing process of Rocket Based Combined Cycle (RBCC) propulsion system is researched. The idea of RBCC propulsion system means combining rocket engine with ramjet engine effectively, which can flight from sea level to high altitude in wide Mach ranges. In order to analyze how the length of the mixing part affects mixing process, different length of mixing part are researched. As it is indicated, with a constant Mach number, increasing the length of mixing part makes main flow and second flow mix more evenly. Moreover, the length of mixing part has a slight impact on the thrust. Obviously the main consequence of increasing the length of mixing part is promoting the mix of main flow and second flow. Therefore, in order to decrease the weight of aircraft, it is of importance to reduce the length. Through comparing distribution of different cases, when working in the situation of maximum power, the flow in the nozzle of rocket engine is under expansion, while that in the nozzle is fully expanded. Nevertheless, in the case of high altitude and high Mach number, there exists a vortex in the nozzle of rocket engine because of over expansion; meanwhile, the flow in the nozzle is under expansion. Therefore, it is necessary to adjust nozzle throat area in order to increase the thrust of RBCC at high altitude.

  16. Combined SM Higgs Limits at the Tevatron

    SciTech Connect

    Krumnack, N.

    2009-10-01

    We combine results from CDF and D{sup 0} on direct searches for a standard model (SM) Higgs boson (H) in p{bar p} collisions at the Fermilab Tevatron at {radical}s = 1.96 TeV. Compared to the previous Higgs Tevatron combination, more data and new channels WH {yields} {tau}{nu}b{bar b}, VH {yields} {tau}{tau}b{bar b}/jj{tau}{tau}, VH {yields} jjb{bar b}, t{bar t}H {yields} t{bar t}b{bar b} have been added. Most previously used channels have been reanalyzed to gain sensitivity. We use the latest parton distribution functions and gg {yields} H theoretical cross sections when comparing our limits to the SM predictions. With 2.0-3.6 fb{sup -1} of data analyzed at CDF, and 0.9-4.2 fb{sup -1} at D{sup 0}, the 95% C.L. upper limits on Higgs boson production are a factor of 2.5 (0.86) times the SM cross section for a Higgs boson mass of m{sub H} = 115 (165) GeV/c{sup 2}. Based on simulation, the corresponding median expected upper limits are 2.4 (1.1). The mass range excluded at 95% C.L. for a SM Higgs has been extended to 160 < m{sub H} < 170 GeV/c{sup 2}.

  17. Combined Immunodeficiency Associated with DOCK8 Mutations

    PubMed Central

    Zhang, Qian; Davis, Jeremiah C.; Lamborn, Ian T.; Freeman, Alexandra F.; Jing, Huie; Favreau, Amanda J.; Matthews, Helen F.; Davis, Joie; Turner, Maria L.; Uzel, Gulbu; Holland, Steven M.; Su, Helen C.

    2010-01-01

    BACKGROUND Recurrent sinopulmonary and cutaneous viral infections with elevated serum levels of IgE are features of some variants of combined immunodeficiency. The genetic causes of these variants are unknown. METHODS We collected longitudinal clinical data on 11 patients from eight families who had recurrent sinopulmonary and cutaneous viral infections. We performed comparative genomic hybridization arrays and targeted gene sequencing. Variants with predicted loss-of-expression mutations were confirmed by means of a quantitative reverse-transcriptase –polymerase-chain-reaction assay and immunoblotting. We evaluated the number and function of lymphocytes with the use of in vitro assays and flow cytometry. RESULTS Patients had recurrent otitis media, sinusitis, and pneumonias; recurrent Staphylococcus aureus skin infections with otitis externa; recurrent, severe herpes simplex virus or herpes zoster infections; extensive and persistent infections with molluscum contagiosum; and human papillomavirus infections. Most patients had severe atopy with anaphylaxis; several had squamous-cell carcinomas, and one had T-cell lymphoma –leukemia. Elevated serum IgE levels, hypereosinophilia, low numbers of T cells and B cells, low serum IgM levels, and variable IgG antibody responses were common. Expansion in vitro of activated CD8 T cells was impaired. Novel homozygous or compound heterozygous deletions and point mutations in the gene encoding the dedicator of cytokinesis 8 protein (DOCK8) led to the absence of DOCK8 protein in lymphocytes. CONCLUSIONS Autosomal recessive DOCK8 deficiency is associated with a novel variant of combined immunodeficiency. PMID:19776401

  18. Hybrid nanoparticles for combination therapy of cancer.

    PubMed

    He, Chunbai; Lu, Jianqin; Lin, Wenbin

    2015-12-10

    Nanoparticle anticancer drug delivery enhances therapeutic efficacies and reduces side effects by improving pharmacokinetics and biodistributions of the drug payloads in animal models. Despite promising preclinical efficacy results, monotherapy nanomedicines have failed to produce enhanced response rates over conventional chemotherapy in human clinical trials. The discrepancy between preclinical data and clinical outcomes is believed to result from the less pronounced enhanced permeability and retention (EPR) effect in and the heterogeneity of human tumors as well as the intrinsic/acquired drug resistance to monotherapy over the treatment course. To address these issues, recent efforts have been devoted to developing nanocarriers that can efficiently deliver multiple therapeutics with controlled release properties and increased tumor deposition. In ideal scenarios, the drug or therapeutic modality combinations have different mechanisms of action to afford synergistic effects. In this review, we summarize recent progress in designing hybrid nanoparticles for the co-delivery of combination therapies, including multiple chemotherapeutics, chemotherapeutics and biologics, chemotherapeutics and photodynamic therapy, and chemotherapeutics and radiotherapy. The in vitro and in vivo anticancer effects are also discussed.

  19. Cue combination for 3D location judgements.

    PubMed

    Svarverud, Ellen; Gilson, Stuart J; Glennerster, Andrew

    2010-01-01

    Cue combination rules have often been applied to the perception of surface shape but not to judgements of object location. Here, we used immersive virtual reality to explore the relationship between different cues to distance. Participants viewed a virtual scene and judged the change in distance of an object presented in two intervals, where the scene changed in size between intervals (by a factor of between 0.25 and 4). We measured thresholds for detecting a change in object distance when there were only 'physical' (stereo and motion parallax) or 'texture-based' cues (independent of the scale of the scene) and used these to predict biases in a distance matching task. Under a range of conditions, in which the viewing distance and position of the target relative to other objects was varied, the ratio of 'physical' to 'texture-based' thresholds was a good predictor of biases in the distance matching task. The cue combination approach, which successfully accounts for our data, relies on quite different principles from those underlying traditional models of 3D reconstruction. PMID:20143898

  20. Combined cannabinoid therapy via an oromucosal spray.

    PubMed

    Perez, Jordi

    2006-08-01

    Extensive basic science research has identified the potential therapeutic benefits of active compounds extracted from the Cannabis sativa L. plant (the cannabinoids). It is recognized that a significant proportion of patients suffering with the debilitating symptoms of pain and spasticity in multiple sclerosis or other conditions smoke cannabis despite the legal implications and stigma associated with this controlled substance. GW Pharmaceuticals have developed Sativex (GW- 1,000-02), a combined cannabinoid medicine that delivers and maintains therapeutic levels of two principal cannabinoids, delta-9-tetrahydrocannabinol (THC) and cannabidiol (CBD), via an oromucosal pump spray, that aims to minimize psychotropic side effects. Sativex has proved to be well tolerated and successfully self-administered and self-titrated in both healthy volunteers and patient cohorts. Clinical assessment of this combined cannabinoid medicine has demonstrated efficacy in patients with intractable pain (chronic neuropathic pain, pain due to brachial plexus nerve injury, allodynic peripheral neuropathic pain and advanced cancer pain), rheumatoid arthritis and multiple sclerosis (bladder problems, spasticity and central pain), with no significant intoxication-like symptoms, tolerance or withdrawal syndrome. PMID:16969427