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Sample records for ago2 immunoprecipitation identifies

  1. Ago2 Immunoprecipitation Identifies Predicted MicroRNAs in Human Embryonic Stem Cells and Neural Precursors

    PubMed Central

    Swerdel, Mavis R.; Moore, Jennifer C.; Cohen, Rick I.; Wu, Hao; Sun, Yi E.; Hart, Ronald P.

    2009-01-01

    Background MicroRNAs are required for maintenance of pluripotency as well as differentiation, but since more microRNAs have been computationally predicted in genome than have been found, there are likely to be undiscovered microRNAs expressed early in stem cell differentiation. Methodology/Principal Findings SOLiD ultra-deep sequencing identified >107 unique small RNAs from human embryonic stem cells (hESC) and neural-restricted precursors that were fit to a model of microRNA biogenesis to computationally predict 818 new microRNA genes. These predicted genomic loci are associated with chromatin patterns of modified histones that are predictive of regulated gene expression. 146 of the predicted microRNAs were enriched in Ago2-containing complexes along with 609 known microRNAs, demonstrating association with a functional RISC complex. This Ago2 IP-selected subset was consistently expressed in four independent hESC lines and exhibited complex patterns of regulation over development similar to previously-known microRNAs, including pluripotency-specific expression in both hESC and iPS cells. More than 30% of the Ago2 IP-enriched predicted microRNAs are new members of existing families since they share seed sequences with known microRNAs. Conclusions/Significance Extending the classic definition of microRNAs, this large number of new microRNA genes, the majority of which are less conserved than their canonical counterparts, likely represent evolutionarily recent regulators of early differentiation. The enrichment in Ago2 containing complexes, the presence of chromatin marks indicative of regulated gene expression, and differential expression over development all support the identification of 146 new microRNAs active during early hESC differentiation. PMID:19784364

  2. Direct targets of the tomato-ripening regulator RIN identified by transcriptome and chromatin immunoprecipitation analyses.

    PubMed

    Fujisawa, Masaki; Shima, Yoko; Higuchi, Naoki; Nakano, Toshitsugu; Koyama, Yoshiyuki; Kasumi, Takafumi; Ito, Yasuhiro

    2012-06-01

    The physiological and biochemical changes in fruit ripening produce key attributes of fruit quality including color, taste, aroma and texture. These changes are driven by the highly regulated and synchronized activation of a huge number of ripening-associated genes. In tomato (Solanum lycopersicum), a typical climacteric fruit, the MADS-box transcription factor RIN is one of the earliest-acting ripening regulators, required for both ethylene-dependent and ethylene-independent pathways. Although we previously identified several direct RIN targets, many additional targets remain unidentified, likely including key ripening-associated genes. Here, we report the identification of novel RIN targets by transcriptome and chromatin immunoprecipitation (ChIP) analyses. Transcriptome comparisons by microarray of wild-type and rin mutant tomatoes identified 342 positively regulated genes and 473 negatively regulated genes by RIN during ripening. Most of the positively regulated genes contained possible RIN-binding (CArG-box) sequences in their promoters. Subsequently, we selected six genes from the positively regulated genes and a ripening regulator gene, CNR, and assayed their promoters by quantitative ChIP-PCR to examine RIN binding. All of the seven genes, which are involved in cell wall modification, aroma and flavor development, pathogen defense and transcriptional regulation during ripening, are targets of RIN, suggesting that RIN may control multiple diverse ripening processes. In particular, RIN directly regulates the expression of the ripening-associated transcription factors, CNR, TDR4 and a GRAS family gene, providing an important clue to elucidate the complicated transcriptional cascade for fruit ripening.

  3. Chromatin Immunoprecipitation Assay to Identify Genomic Binding Sites of Regulatory Factors.

    PubMed

    Wagner, Meike; Jung, Johannes; Koslowski, Michael; Türeci, Özlem; Tiwari, Vijay K; Sahin, Ugur

    2016-01-01

    DNA-protein interactions are vital to fundamental cellular events including transcription, replication, DNA repair, and recombination. Thus, their study holds the key to our understanding of mechanisms underlying normal development and homeostasis as well as disease. Transcriptional regulation is a highly complex process that involves recruitment of numerous factors resulting in formation of multi-protein complexes at gene promoters to regulate gene expression. The studied proteins can be, for example, transcription factors, epigenetic regulators, co-activators, co-repressors, or ligand-activated nuclear receptors as estrogen receptor-α (ERα) bound either directly to the DNA or indirectly by interaction with other DNA-bound factors. Chromatin immunoprecipitation (ChIP) assay is a powerful method to study interactions of proteins and a specific genomic DNA region. Recruitment of ERα to promoters of estrogen-dependent genes is a common mechanism to activate or enhance gene transcription in breast cancer thus promoting tumor progression. In this chapter, we demonstrate a stepwise protocol for ChIP assay using binding of ERα to its genomic targets after stimulation with 17β-estradiol (E2) in breast cancer cells as an example.

  4. RNA-Seq and RNA Immunoprecipitation Analyses of the Transcriptome of Streptomyces coelicolor Identify Substrates for RNase III

    PubMed Central

    Gatewood, Marcha L.; Bralley, Patricia; Weil, M. Ryan

    2012-01-01

    RNase III is a key enzyme in the pathways of RNA degradation and processing in bacteria and has been suggested as a global regulator of antibiotic production in Streptomyces coelicolor. Using RNA-Seq, we have examined the transcriptomes of S. coelicolor M145 and an RNase III (rnc)-null mutant of that strain. RNA preparations with reduced levels of structural RNAs were prepared by subtractive hybridization prior to RNA-Seq analysis. We initially identified 7,800 transcripts of known and putative protein-coding genes in M145 and the null mutant, JSE1880, along with transcripts of 21 rRNA genes and 65 tRNA genes. Approximately 3,100 of the protein-coding transcripts were categorized as low-abundance transcripts. For further analysis, we selected those transcripts of known and putative protein-coding genes whose levels changed by ≥2-fold between the two S. coelicolor strains and organized those transcripts into 16 functional categories. We refined our analysis by performing RNA immunoprecipitation of the mRNA preparation from JSE1880 using a mutant RNase III protein that binds to transcripts but does not cleave them. This analysis identified ca. 800 transcripts that were enriched in the RNA immunoprecipitates, including 28 transcripts whose levels also changed by ≥2-fold in the RNA-Seq analysis. We compare our results with those obtained by microarray analysis of the S. coelicolor transcriptome and with studies describing the characterization of small noncoding RNAs. We have also used the RNA immunoprecipitation results to identify new substrates for RNase III cleavage. PMID:22389483

  5. Target gene analysis by microarrays and chromatin immunoprecipitation identifies HEY proteins as highly redundant bHLH repressors.

    PubMed

    Heisig, Julia; Weber, David; Englberger, Eva; Winkler, Anja; Kneitz, Susanne; Sung, Wing-Kin; Wolf, Elmar; Eilers, Martin; Wei, Chia-Lin; Gessler, Manfred

    2012-01-01

    HEY bHLH transcription factors have been shown to regulate multiple key steps in cardiovascular development. They can be induced by activated NOTCH receptors, but other upstream stimuli mediated by TGFß and BMP receptors may elicit a similar response. While the basic and helix-loop-helix domains exhibit strong similarity, large parts of the proteins are still unique and may serve divergent functions. The striking overlap of cardiac defects in HEY2 and combined HEY1/HEYL knockout mice suggested that all three HEY genes fulfill overlapping function in target cells. We therefore sought to identify target genes for HEY proteins by microarray expression and ChIPseq analyses in HEK293 cells, cardiomyocytes, and murine hearts. HEY proteins were found to modulate expression of their target gene to a rather limited extent, but with striking functional interchangeability between HEY factors. Chromatin immunoprecipitation revealed a much greater number of potential binding sites that again largely overlap between HEY factors. Binding sites are clustered in the proximal promoter region especially of transcriptional regulators or developmental control genes. Multiple lines of evidence suggest that HEY proteins primarily act as direct transcriptional repressors, while gene activation seems to be due to secondary or indirect effects. Mutagenesis of putative DNA binding residues supports the notion of direct DNA binding. While class B E-box sequences (CACGYG) clearly represent preferred target sequences, there must be additional and more loosely defined modes of DNA binding since many of the target promoters that are efficiently bound by HEY proteins do not contain an E-box motif. These data clearly establish the three HEY bHLH factors as highly redundant transcriptional repressors in vitro and in vivo, which explains the combinatorial action observed in different tissues with overlapping expression.

  6. Chromatin immunoprecipitation scanning identifies glucocorticoid receptor binding regions in the proximal promoter of a ubiquitously expressed glucocorticoid target gene in brain.

    PubMed

    van der Laan, Siem; Sarabdjitsingh, R Angela; Van Batenburg, Marcel F; Lachize, Servane B; Li, Hualing; Dijkmans, Thomas F; Vreugdenhil, Erno; de Kloet, E Ron; Meijer, Onno C

    2008-09-01

    While the actions of glucocorticoids on brain functions have been comprehensively studied, the underlying genomic mechanisms are poorly understood. In this study, we show that glucocorticoid-induced leucine zipper (GILZ) mRNA is strongly and ubiquitously induced in rat brain. To decipher the molecular mechanisms underlying these genomic effects, it is of interest to identify the regulatory sites in the promoter region. Alignment of the rat GILZ promoter with the well-characterized human promoter resulted in poor sequence homology. Consequently, we analyzed the rat 5' flanking sequence by Matrix REDUCE and identified two high-affinity glucocorticoid response elements (GRE) located 2 kb upstream of the transcription start site. These findings were corroborated using the glucocorticoid receptor (GR) expressing Ns-1 PC12 rat cell-line. In these cells, dexamethasone treatment leads to a progressive increase of GILZ mRNA expression levels via a GR-dependent mechanism. Subsequently, using chromatin immunoprecipitation assays we show that the two high-affinity GREs are located within the GR-binding regions. Lastly, we demonstrate using multiple tissue in situ hybridization a marked increase in mRNA expression levels in spleen, thymus, heart, lung, liver, muscle, testis, kidney, colon, ileum, as well as in brain and conclude that the GILZ gene can be used to study glucocorticoid effects in many additional rodent tissues.

  7. Strong reduction of AGO2 expression in melanoma and cellular consequences

    PubMed Central

    Völler, D; Reinders, J; Meister, G; Bosserhoff, A-K

    2013-01-01

    Background: Processing of microRNAs (miRNAs) is a highly controlled process. Deregulation of miRNA expression was observed in several types of cancer but changes in the miRNA-processing enzymes have not been analysed until today. In this study, we analysed Argonaute2 (AGO2, EIF2C2), as one main factor of the miRNA processing ensemble, in the context of cancer development, especially in melanoma. Methods: We determined the AGO2 expression level in melanoma, as well as in other cancers, with biochemical approaches (qRT–PCR, western blot and immunofluorescence studies) and analysed the cell behaviour in migration assays. Results: Specifically in melanoma, we revealed a strong reduction of AGO2 expression compared with primary melanocytes. The reduction of AGO2 expression was only found on protein level, whereas the mRNA level stayed unchanged hinting to post-transcriptional regulation. We could show that re-expression of AGO2 in melanoma leads to a strong improvement of regulatory effects due to increased functionality of small-interfering RNAs and short hairpin RNAs. Conclusion: We identified melanoma-specific downregulation of AGO2 and corresponding reduced RNAi efficiency. These findings will help to understand the molecular basis of malignant melanoma and can potentially lead to an improvement of therapeutic strategies. PMID:24169347

  8. An Antiviral Defense Role of AGO2 in Plants

    PubMed Central

    Harvey, Jagger J. W.; Lewsey, Mathew G.; Patel, Kanu; Westwood, Jack; Heimstädt, Susanne; Carr, John P.; Baulcombe, David C.

    2011-01-01

    Background Argonaute (AGO) proteins bind to small-interfering (si)RNAs and micro (mi)RNAs to target RNA silencing against viruses, transgenes and in regulation of mRNAs. Plants encode multiple AGO proteins but, in Arabidopsis, only AGO1 is known to have an antiviral role. Methodology/Principal Findings To uncover the roles of specific AGOs in limiting virus accumulation we inoculated turnip crinkle virus (TCV) to Arabidopsis plants that were mutant for each of the ten AGO genes. The viral symptoms on most of the plants were the same as on wild type plants although the ago2 mutants were markedly hyper-susceptible to this virus. ago2 plants were also hyper-susceptible to cucumber mosaic virus (CMV), confirming that the antiviral role of AGO2 is not specific to a single virus. For both viruses, this phenotype was associated with transient increase in virus accumulation. In wild type plants the AGO2 protein was induced by TCV and CMV infection. Conclusions/Significance Based on these results we propose that there are multiple layers to RNA-mediated defense and counter-defense in the interactions between plants and their viruses. AGO1 represents a first layer. With some viruses, including TCV and CMV, this layer is overcome by viral suppressors of silencing that can target AGO1 and a second layer involving AGO2 limits virus accumulation. The second layer is activated when the first layer is suppressed because AGO2 is repressed by AGO1 via miR403. The activation of the second layer is therefore a direct consequence of the loss of the first layer of defense. PMID:21305057

  9. Distinct AGO1 and AGO2 associated miRNA profiles in human cells and blood plasma

    PubMed Central

    Turchinovich, Andrey; Burwinkel, Barbara

    2012-01-01

    Studies of miRNA association with Argonaute (AGO) proteins in mammalian cells have indicated lack of bias toward particular AGO. However, to our knowledge, the use of quantitative methods for studying miRNA association with different AGOs has not been reported so far. In this work we compared the total miRNA content in AGO1 and AGO2 immunoprecipitates obtained from MCF7 adenocarcinoma cells using TaqMan Low Density miRNA Arrays and successfully verified selected miRNAs with qPCR. For most of the miRNA species AGO1 and AGO2 profiles were well correlated, however, some miRNAs demonstrated consistent biases toward one of the Argonautes. Furthermore, miRNAs which were predominantly AGO2-associated derived mostly from sense strands of the corresponding pre-miRNAs while the majority of AGO1 biased miRNAs originated from antisense strands of the pre-miRNAs. Additionally, we show that circulating miRNA in human blood plasma can be immunoprecipitated with both AGO1 and AGO2 antibody. However, unlike in cell lysates, AGO1 and AGO2 associated miRNA profiles in plasma did not correlate, indicating that many cell types contribute to circulating miRNA (given that expression of AGO proteins is tissue specific). Furthermore, AGO-specific miRNA profiles in blood cells differed significantly from miRNAs profiles in plasma indicating that most circulating miRNAs are likely to derive from non-blood cells. Since circulating miRNAs hold great promise as biomarkers for numerous cancers and other diseases, we hypothesize that AGO-specific miRNA profiles might add an additional dimension to circulating miRNA-based diagnostics. PMID:22858679

  10. 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

    Penicillium chrysogenum is the sole industrial producer of the β-lactam antibiotic penicillin, which is the most commonly used drug for treating bacterial infections. In P. chrysogenum and other filamentous fungi, secondary metabolism and morphogenesis are controlled by the highly conserved multisubunit velvet complex. Here we present the first chromatin immunoprecipitation next-generation sequencing (ChIP-seq) analysis of a fungal velvet protein, providing experimental evidence that a velvet homologue in P. chrysogenum (PcVelA) acts as a direct transcriptional regulator at the DNA level in addition to functioning as a regulator at the protein level in P. chrysogenum, which was previously described. We identified many target genes that are related to processes known to be dependent on PcVelA, e.g., secondary metabolism as well as asexual and sexual development. We also identified seven PcVelA target genes that encode putative methyltransferases. Yeast two-hybrid and bimolecular fluorescence complementation analyses showed that one of the putative methyltransferases, PcLlmA, directly interacts with PcVelA. Furthermore, functional characterization of PcLlmA demonstrated that this protein is involved in the regulation of conidiosporogenesis, pellet formation, and hyphal morphology, all traits with major biotechnological relevance. IMPORTANCE Filamentous fungi are of major interest for biotechnological and pharmaceutical applications. This is due mainly to their ability to produce a wide variety of secondary metabolites, many of which are relevant as antibiotics. One of the most prominent examples is penicillin, a β-lactam antibiotic that is produced on the industrial scale by fermentation of P. chrysogenum. In recent years, the multisubunit protein complex velvet has been identified as one of the key regulators of fungal secondary metabolism and development. However, until recently, only a little has been known about how velvet mediates regulation at the

  11. 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

    ABSTRACT Penicillium chrysogenum is the sole industrial producer of the β-lactam antibiotic penicillin, which is the most commonly used drug for treating bacterial infections. In P. chrysogenum and other filamentous fungi, secondary metabolism and morphogenesis are controlled by the highly conserved multisubunit velvet complex. Here we present the first chromatin immunoprecipitation next-generation sequencing (ChIP-seq) analysis of a fungal velvet protein, providing experimental evidence that a velvet homologue in P. chrysogenum (PcVelA) acts as a direct transcriptional regulator at the DNA level in addition to functioning as a regulator at the protein level in P. chrysogenum, which was previously described. We identified many target genes that are related to processes known to be dependent on PcVelA, e.g., secondary metabolism as well as asexual and sexual development. We also identified seven PcVelA target genes that encode putative methyltransferases. Yeast two-hybrid and bimolecular fluorescence complementation analyses showed that one of the putative methyltransferases, PcLlmA, directly interacts with PcVelA. Furthermore, functional characterization of PcLlmA demonstrated that this protein is involved in the regulation of conidiosporogenesis, pellet formation, and hyphal morphology, all traits with major biotechnological relevance. IMPORTANCE Filamentous fungi are of major interest for biotechnological and pharmaceutical applications. This is due mainly to their ability to produce a wide variety of secondary metabolites, many of which are relevant as antibiotics. One of the most prominent examples is penicillin, a β-lactam antibiotic that is produced on the industrial scale by fermentation of P. chrysogenum. In recent years, the multisubunit protein complex velvet has been identified as one of the key regulators of fungal secondary metabolism and development. However, until recently, only a little has been known about how velvet mediates regulation at

  12. Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2.

    PubMed

    Frank, Filipp; Sonenberg, Nahum; Nagar, Bhushan

    2010-06-10

    MicroRNAs (miRNAs) mediate post-transcriptional gene regulation through association with Argonaute proteins (AGOs). Crystal structures of archaeal and bacterial homologues of AGOs have shown that the MID (middle) domain mediates the interaction with the phosphorylated 5' end of the miRNA guide strand and this interaction is thought to be independent of the identity of the 5' nucleotide in these systems. However, analysis of the known sequences of eukaryotic miRNAs and co-immunoprecipitation experiments indicate that there is a clear bias for U or A at the 5' position. Here we report the crystal structure of a MID domain from a eukaryotic AGO protein, human AGO2. The structure, in complex with nucleoside monophosphates (AMP, CMP, GMP, and UMP) mimicking the 5' end of miRNAs, shows that there are specific contacts made between the base of UMP or AMP and a rigid loop in the MID domain. Notably, the structure of the loop discriminates against CMP and GMP and dissociation constants calculated from NMR titration experiments confirm these results, showing that AMP (0.26 mM) and UMP (0.12 mM) bind with up to 30-fold higher affinity than either CMP (3.6 mM) or GMP (3.3 mM). This study provides structural evidence for nucleotide-specific interactions in the MID domain of eukaryotic AGO proteins and explains the observed preference for U or A at the 5' end of miRNAs.

  13. Argonaute 2 immunoprecipitation revealed large tumor suppressor kinase 1 as a novel proapoptotic target of miR-21 in T cells.

    PubMed

    Teteloshvili, Nato; Smigielska-Czepiel, Katarzyna; Yuan, Ye; Seitz, Annika; de Jong, Debora; Rutgers, Bea; Jellema, Pytrick; van der Lei, Roelof Jan; Slezak-Prochazka, Izabella; Brouwer, Elisabeth; Boots, Annemieke M H; Kroesen, Bart-Jan; van den Berg, Anke; Kluiver, Joost

    2017-02-01

    MicroRNA (miR)-21 is an important suppressor of T-cell apoptosis that is also overexpressed in many types of cancers. The exact mechanisms underlying the antiapoptotic effects of miR-21 are not well understood. In this study, we used the Jurkat T-cell line as a model to identify apoptosis-associated miR-21 target genes. We showed that expression of miR-21 rapidly increases upon αCD3/αCD28 activation of Jurkat cells. Inhibition of miR-21 reduced cell growth which could be explained by an increase in apoptosis. MicroRNA target gene identification by AGO2 RNA-immunoprecipitation followed by gene expression microarray (RIP-Chip) resulted in the identification of 72 predicted miR-21 target genes that were at least twofold enriched in the AGO2-IP fraction of miR-21 overexpressing cells. Of these, 71 were at least twofold more enriched in the AGO2-IP fraction of miR-21 overexpressing cells as compared to AGO2-IP fraction of control cells. The target gene for which the AGO2-IP enrichment was most prominently increased upon miR-21 overexpression was the proapoptotic protein LATS1. Luciferase reporter assays and western blot analysis confirmed targeting of LATS1 by miR-21. qRT-PCR analysis in primary T cells showed an inverse expression pattern between LATS1 transcript levels and miR-21 upon T-cell stimulation. Finally, LATS1 knockdown partially rescued the miR-21 inhibition-induced impaired cell growth. Collectively, these data identify LATS1 as a miR-21 target important for the antiapoptotic function of miR-21 in T cells and likely also in many types of cancer.

  14. Stilbene derivatives promote Ago2-dependent tumour-suppressive microRNA activity

    PubMed Central

    Hagiwara, Keitaro; Kosaka, Nobuyoshi; Yoshioka, Yusuke; Takahashi, Ryou-u; Takeshita, Fumitaka; Ochiya, Takahiro

    2012-01-01

    It is well known that natural products are a rich source of compounds for applications in medicine, pharmacy, and biology. However, the exact molecular mechanisms of natural agents in human health have not been clearly defined. Here, we demonstrate for the first time that the polyphenolic phytoalexin resveratrol promotes expression and activity of Argonaute2 (Ago2), a central RNA interference (RNAi) component, which thereby inhibits breast cancer stem-like cell characteristics by increasing the expression of a number of tumour-suppressive miRNAs, including miR-16, -141, -143, and -200c. Most importantly, resveratrol-induced Ago2 resulted in a long-term gene silencing response. We also found that pterostilbene, which is a natural dimethylated resveratrol analogue, is capable of mediating Ago2-dependent anti-cancer activity in a manner mechanistically similar to that of resveratrol. These findings suggest that the dietary intake of natural products contributes to the prevention and treatment of diseases by regulating the RNAi pathway. PMID:22423322

  15. eIF1A augments Ago2-mediated Dicer-independent miRNA biogenesis and RNA interference

    NASA Astrophysics Data System (ADS)

    Yi, Tingfang; Arthanari, Haribabu; Akabayov, Barak; Song, Huaidong; Papadopoulos, Evangelos; Qi, Hank H.; Jedrychowski, Mark; Güttler, Thomas; Guo, Cuicui; Luna, Rafael E.; Gygi, Steven P.; Huang, Stephen A.; Wagner, Gerhard

    2015-05-01

    MicroRNA (miRNA) biogenesis and miRNA-guided RNA interference (RNAi) are essential for gene expression in eukaryotes. Here we report that translation initiation factor eIF1A directly interacts with Ago2 and promotes Ago2 activities in RNAi and miR-451 biogenesis. Biochemical and NMR analyses demonstrate that eIF1A binds to the MID domain of Ago2 and this interaction does not impair translation initiation. Alanine mutation of the Ago2-facing Lys56 in eIF1A impairs RNAi activities in human cells and zebrafish. The eIF1A-Ago2 assembly facilitates Dicer-independent biogenesis of miR-451, which mediates erythrocyte maturation. Human eIF1A (heIF1A), but not heIF1A(K56A), rescues the erythrocyte maturation delay in eif1axb knockdown zebrafish. Consistently, miR-451 partly compensates erythrocyte maturation defects in zebrafish with eif1axb knockdown and eIF1A(K56A) expression, supporting a role of eIF1A in miRNA-451 biogenesis in this model. Our results suggest that eIF1A is a novel component of the Ago2-centred RNA-induced silencing complexes (RISCs) and augments Ago2-dependent RNAi and miRNA biogenesis.

  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. Chromatin Immunoprecipitation for Human Monocyte Derived Macrophages

    PubMed Central

    Wooden, Jessica; Ciborowski, Pawel

    2014-01-01

    The importance of Chromatin Immunoprecipitation (ChIP) technology has grown exponentially along with an increased interest in epigenetic regulation. The correlation of transcription factors with histone marks is now well established as the center of epigenetic studies; therefore, precise knowledge about histone marks is critical to unravel their molecular function and to understand their role in biological systems. This knowledge constantly accumulates and is provided openly in the expanding hubs of information such as the USCS Genome Browser. Nevertheless, as we gain more knowledge, we realize that the DNA-protein interactions are not driven by a “one size fits all” rule. Also, the diversity of interactions between DNA, histones, and transcriptional regulators is much bigger than previously considered. Besides a detailed protocol of sample preparation for the ChIP assay from primary human monocyte-derived macrophages (MDM)a, we show that differences between various types of cells exist. Furthermore, we can postulate that such variations exist between transformed macrophage-like cell lines and primary macrophages obtained from healthy volunteers. We found that the most efficient fixation time for MDM is 10 minutes. Finally, to perform multiple analytical assays, we showed that even with thorough methodology, the yield of material obtained from primary cells is the major challenge. PMID:25220915

  18. Bioenergetics and gene silencing approaches for unraveling nucleotide recognition by the human EIF2C2/Ago2 PAZ domain.

    PubMed

    Kandeel, Mahmoud; Al-Taher, Abdullah; Nakashima, Remi; Sakaguchi, Tomoya; Kandeel, Ali; Nagaya, Yuki; Kitamura, Yoshiaki; Kitade, Yukio

    2014-01-01

    Gene silencing and RNA interference are major cellular processes that control gene expression via the cleavage of target mRNA. Eukaryotic translation initiation factor 2C2 (EIF2C2, Argonaute protein 2, Ago2) is considered to be the major player of RNAi as it is the core component of RISC complexes. While a considerable amount of research has focused on RNA interference and its associated mechanisms, the nature and mechanisms of nucleotide recognition by the PAZ domain of EIF2C2/Ago2 have not yet been characterized. Here, we demonstrate that the EIF2C2/Ago2 PAZ domain has an inherent lack of binding to adenine nucleotides, a feature that highlights the poor binding of 3'-adenylated RNAs with the PAZ domain as well as the selective high trimming of the 3'-ends of miRNA containing adenine nucleotides. We further show that the PAZ domain selectively binds all ribonucleotides (except adenosine), whereas it poorly recognizes deoxyribonucleotides. In this context, the modification of dTMP to its ribonucleotide analogue gave a drastic improvement of binding enthalpy and, hence, binding affinity. Additionally, higher in vivo gene silencing efficacy was correlated with the stronger PAZ domain binders. These findings provide new insights into the nature of the interactions of the EIF2C2/Ago2 PAZ domain.

  19. Sequential Immunoprecipitation of Secretory Vesicle Proteins from Biosynthetically Labelled Cells.

    PubMed

    Guest, Paul C

    2017-01-01

    Pulse radiolabelling of cells with radioactive amino acids is a common method for studying the biosynthesis of proteins. The labelled proteins can then be immunoprecipitated and analysed by electrophoresis and imaging techniques. This chapter presents a protocol for the biosynthetic labelling and immunoprecipitation of pancreatic islet proteins which are known to be affected in psychiatric disorders such as schizophrenia.

  20. 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…

  1. 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.

  2. Taenia taeniaeformis: immunoprecipitation analysis of the protein antigens of oncospheres and larvae.

    PubMed

    Bowtell, D D; Mitchell, G F; Anders, R F; Lightowlers, M W; Rickard, M D

    1983-12-01

    Biosynthetically or exogenously labeled proteins and immunoprecipitated protein antigens of established 28-day-old larvae of Taenia taeniaeformis were compared with proteins and antigens of infective oncospheres using single and two-dimensional gel electrophoresis. Immunoprecipitation was carried out using sera from infected mice and mouse antisera raised to larvae or oncospheres, and emphasis was placed on identifying antigens common to both oncospheres and larvae. Two major larval antigens of Mr 40,000 and 200,000, designated Tt40 and Tt200, are common to somatic larval preparations and oncospheres. Additionally, two major oncosphere antigens of Mr 55,000 and 60,000, designated Tt55 and Tt60, are also present in larval excretory and secretory (i.e., ES or exoantigen) products. Information obtained from these immunoprecipitation analyses will facilitate isolation and production of common as well as stage-specific protein antigens in the development of defined-antigen vaccines in this model system of cysticercosis.

  3. RNA immunoprecipitation for determining RNA-protein associations in vivo.

    PubMed

    Gilbert, Chris; Svejstrup, Jesper Q

    2006-08-01

    Similar to chromatin immunoprecipitation (ChIP), RNA immunoprecipitation (RIP) can be used to detect the association of individual proteins with specific nucleic acid regions, in this case on RNA. Live cells are treated with formaldehyde to generate protein-RNA cross-links between molecules that are in close proximity in vivo. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the formaldehyde cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR. The basics of RIP are very similar to those of ChIP, but with some important caveats. This unit describes the RIP procedure for Saccharomyces cerevisiae. Although the corresponding steps for metazoan cells have not yet been worked out, it is likely that the yeast procedure can easily be adapted for use in other organisms.

  4. Whole genome methylation profiling by immunoprecipitation of methylated DNA.

    PubMed

    Sharp, Andrew J

    2012-01-01

    I provide a protocol for DNA methylation profiling based on immunoprecipitation of methylated DNA using commercially available monoclonal antibodies that specifically recognize 5-methylcytosine. Quantification of the level of enrichment of the resulting DNA enables DNA methylation to be assayed for any genomic locus, including entire chromosomes or genomes if appropriate microarray or high-throughput sequencing platforms are used. In previous studies (1, 2), I have used hybridization to oligonucleotide arrays from Roche Nimblegen Inc, which allow any genomic region of interest to be interrogated, dependent on the array design. For example, using modern tiling arrays comprising millions of oligonucleotide probes, several complete human chromosomes can be assayed at densities of one probe per 100 bp or greater, sufficient to yield high-quality data. However, other methods such as quantitative real-time PCR or high-throughput sequencing can be used, giving either measurement of methylation at a single locus or across the entire genome, respectively. While the data produced by single locus assays is relatively simple to analyze and interpret, global assays such as microarrays or high-throughput sequencing require more complex statistical approaches in order to effectively identify regions of differential methylation, and a brief outline of some approaches is given.

  5. Activated platelets can deliver mRNA regulatory Ago2•microRNA complexes to endothelial cells via microparticles.

    PubMed

    Laffont, Benoit; Corduan, Aurélie; Plé, Hélène; Duchez, Anne-Claire; Cloutier, Nathalie; Boilard, Eric; Provost, Patrick

    2013-07-11

    Platelets play a crucial role in the maintenance of hemostasis, as well as in thrombosis. Upon activation, platelets release small membrane-bound microparticles (MPs) containing bioactive proteins and genetic materials from their parental cells that may be transferred to, and exert potent biological effects in, recipient cells of the circulatory system. Platelets have been shown to contain an abundant and diverse array of microRNAs, and platelet-derived MPs are the most abundant microvesicles in the circulation. Here we demonstrate that human platelets activated with thrombin preferentially release their miR-223 content in MPs. These MPs can be internalized by human umbilical vein endothelial cells (HUVEC), leading to the accumulation of platelet-derived miR-223. Platelet MPs contain functional Argonaute 2 (Ago2)•miR-223 complexes that are capable of regulating expression of a reporter gene in recipient HUVEC. Moreover, we demonstrate a role for platelet MP-derived miR-223 in the regulation of 2 endogenous endothelial genes, both at the messenger RNA and protein levels. Our results support a scenario by which platelet MPs may act as intercellular carriers of functional Ago2•microRNA complexes that may exert heterotypic regulation of gene expression in endothelial cells, and possibly other recipient cells of the circulatory system.

  6. Identification of protein interaction partners in mammalian cells using SILAC-immunoprecipitation quantitative proteomics.

    PubMed

    Emmott, Edward; Goodfellow, Ian

    2014-07-06

    Quantitative proteomics combined with immuno-affinity purification, SILAC immunoprecipitation, represent a powerful means for the discovery of novel protein:protein interactions. By allowing the accurate relative quantification of protein abundance in both control and test samples, true interactions may be easily distinguished from experimental contaminants. Low affinity interactions can be preserved through the use of less-stringent buffer conditions and remain readily identifiable. This protocol discusses the labeling of tissue culture cells with stable isotope labeled amino acids, transfection and immunoprecipitation of an affinity tagged protein of interest, followed by the preparation for submission to a mass spectrometry facility. This protocol then discusses how to analyze and interpret the data returned from the mass spectrometer in order to identify cellular partners interacting with a protein of interest. As an example this technique is applied to identify proteins binding to the eukaryotic translation initiation factors: eIF4AI and eIF4AII.

  7. Perinatal protein malnutrition alters expression of miRNA biogenesis genes Xpo5 and Ago2 in mice brain.

    PubMed

    Berardino, Bruno G; Fesser, Estefanía A; Cánepa, Eduardo T

    2017-03-11

    Due to its widespread incidence, maternal malnutrition remains one of the major non-genetic factors affecting the development of newborn's brain. While all nutrients have certain influence on brain maturation, proteins appear to be the most critical for the development of neurological functions. An increasing number of studies point out that the effects of early-life nutritional inadequacy has long lasting effects on the brain and lead to permanent deficits in learning and behavior. Epigenetic mechanisms provide a potential link between the nutrition status during critical periods and changes in gene expression that may lead to disease phenotypes. Among those epigenetic mechanisms microRNAs (miRNAs) emerge as promising molecules for the link between nutrition and gene expression due to their relevance in many central nervous system functions. The objective of the current study was to evaluate the impact of perinatal protein malnutrition on the development of male and female mice offspring and to analyze the expression of the genes involved in the miRNA biogenesis pathway in different mouse brain structures. We demonstrated that early nutritional stress such as exposition to a protein-deficient diet during gestation and lactation reduced the hippocampal weight, delayed offspring's development and deregulated the expression of Xpo5 and Ago2 genes in hippocampus and hypothalamus of weanling mice. Moreover, an overall increase in mature miRNAs was consistent with the induction of Xpo5 mRNA. Altered miRNA biogenesis could modify the availability and functionality of miRNA becoming a causal factor of the adverse effects of protein malnutrition.

  8. The RIPper case: identification of RNA-binding protein targets by RNA immunoprecipitation.

    PubMed

    Köster, Tino; Haas, Meike; Staiger, Dorothee

    2014-01-01

    Control at the posttranscriptional level emerges as an important layer of regulation in the circadian timing system. RNA-binding proteins that specifically interact with cis-regulatory motifs within pre-mRNAs are key elements of this regulation. While the ability to interact with RNA in vitro has been demonstrated for numerous Arabidopsis RNA-binding proteins, a full understanding of posttranscriptional networks controlled by an RNA-binding protein requires the identification of its immediate in vivo targets. Here we describe differential RNA immunoprecipitation in transgenic Arabidopsis thaliana plants expressing RNA-binding protein variants epitope-tagged with green fluorescent protein. To control for RNAs that nonspecifically co-purify with the RNA-binding protein, transgenic plants are generated with a mutated version of the RNA-binding protein that is not capable of binding to its target RNAs. The RNA-binding protein variants are expressed under the control of their authentic promoter and cis-regulatory motifs. Incubation of the plants with formaldehyde in vivo cross-links the proteins to their RNA targets. A whole-cell extract is then prepared and subjected to immunoprecipitation with an antibody against the GFP tag and to mock precipitation with an antibody against the unrelated red fluorescent protein. The RNAs coprecipitating with the proteins are eluted from the immunoprecipitate and identified via reverse transcription-PCR.

  9. Chromatin immunoprecipitation in microfluidic droplets: towards fast and cheap analyses.

    PubMed

    Teste, Bruno; Champ, Jerome; Londono-Vallejo, Arturo; Descroix, Stéphanie; Malaquin, Laurent; Viovy, Jean-Louis; Draskovic, Irena; Mottet, Guillaume

    2017-01-31

    Genetic organization is governed by the interaction of DNA with histone proteins, and differential modifications of these proteins is a fundamental mechanism of gene regulation. Histone modifications are primarily studied through chromatin immunoprecipitation (ChIP) assays, however conventional ChIP procedures are time consuming, laborious and require a large number of cells. Here we report for the first time the development of ChIP in droplets based on a microfluidic platform combining nanoliter droplets, magnetic beads (MB) and magnetic tweezers (MT). The droplet approach enabled compartmentalization and improved mixing, while reducing the consumption of samples and reagents in an integrated workflow. Anti-histone antibodies grafted to MB were used as a solid support to capture and transfer the target chromatin from droplets to droplets in order to perform chromatin immunoprecipitation, washing, elution and purification of DNA. We designed a new ChIP protocol to investigate four different types of modified histones with known roles in gene activation or repression. We evaluated the performances of this new ChIP in droplet assay in comparison with conventional methods. The proposed technology dramatically reduces analytical time from a few days to 7 hours, simplifies the ChIP protocol and decreases the number of cells required by 100 fold while maintaining a high degree of sensitivity and specificity. Therefore this droplet-based ChIP assay represents a new, highly advantageous and convenient approach to epigenetic analyses.

  10. Phosphorylation of Ago2 and Subsequent Inactivation of let-7a RNP-Specific MicroRNAs Control Differentiation of Mammalian Sympathetic Neurons

    PubMed Central

    Patranabis, Somi

    2016-01-01

    MicroRNAs (miRNAs) are small regulatory RNAs that regulate gene expression posttranscriptionally by base pairing to the target mRNAs in animal cells. KRas, an oncogene known to be repressed by let-7a miRNAs, is expressed and needed for the differentiation of mammalian sympathetic neurons and PC12 cells. We documented a loss of let-7a activity during this differentiation process without any significant change in the cellular level of let-7a miRNA. However, the level of Ago2, an essential component that is associated with miRNAs to form RNP-specific miRNA (miRNP) complexes, shows an increase with neuronal differentiation. In this study, differentiation-induced phosphorylation and the subsequent loss of miRNA from Ago2 were noted, and these accounted for the loss of miRNA activity in differentiating neurons. Neuronal differentiation induces the phosphorylation of mitogen-activated protein kinase p38 and the downstream kinase mitogen- and stress-activated protein kinase 1 (MSK1). This in turn upregulates the phosphorylation of Ago2 and ensures the dissociation of miRNA from Ago2 in neuronal cells. MSK1-mediated miRNP inactivation is a prerequisite for the differentiation of neuronal cells, where let-7a miRNA gets unloaded from Ago2 to ensure the upregulation of KRas, a target of let-7a. We noted that the inactivation of let-7a is both necessary and sufficient for the differentiation of sympathetic neurons. PMID:26858302

  11. Methylation profiling using methylated DNA immunoprecipitation and tiling array hybridization.

    PubMed

    Cheung, Hoi-Hung; Lee, Tin-Lap; Rennert, Owen M; Chan, Wai-Yee

    2012-01-01

    DNA methylation is an important epigenetic modification that regulates development and plays a role in the pathophysiology of many diseases. It is dynamically changed during germline development. Methylated DNA immunoprecipitation (MeDIP) is an efficient, cost-effective method for locus-specific and genome-wide analysis. Methylated DNA fragments are enriched by a 5-methylcytidine-recognizing antibody, therefore allowing the analysis of both CpG and non-CpG methylation. The enriched DNA fragments can be amplified and hybridized to tiling arrays covering CpG islands, promoters, or the entire genome. Comparison of different methylomes permits the discovery of differentially methylated regions that might be important in disease- or tissue-specific expression. Here, we describe an established MeDIP protocol and tiling array hybridization method for profiling methylation of testicular germ cells.

  12. Parent-of-origin effects of A1CF and AGO2 on testicular germ-cell tumors, testicular abnormalities, and fertilization bias

    PubMed Central

    Carouge, Delphine; Blanc, Valerie; Knoblaugh, Sue E.; Hunter, Robert J.; Davidson, Nicholas O.; Nadeau, Joseph H.

    2016-01-01

    Testicular tumors, the most common cancer in young men, arise from abnormalities in germ cells during fetal development. Unconventional inheritance for testicular germ cell tumor (TGCT) risk both in humans and mice implicates epigenetic mechanisms. Apolipoprotein B mRNA-editing enzyme complex 1 (APOBEC1) cytidine deaminase and Deadend-1, which are involved in C-to-U RNA editing and microRNA-dependent mRNA silencing, respectively, are potent epigenetic modifiers of TGCT susceptibility in the genetically predisposed 129/Sv inbred mouse strain. Here, we show that partial loss of either APOBEC1 complementation factor (A1CF), the RNA-binding cofactor of APOBEC1 in RNA editing, or Argonaute 2 (AGO2), a key factor in the biogenesis of certain noncoding RNAs, modulates risk for TGCTs and testicular abnormalities in both parent-of-origin and conventional genetic manners. In addition, non-Mendelian inheritance was found among progeny of A1cf and Ago2 mutant intercrosses but not in backcrosses and without fetal loss. Together these findings suggest nonrandom union of gametes rather than meiotic drive or preferential lethality. Finally, this survey also suggested that A1CF contributes to long-term reproductive performance. These results directly implicate the RNA-binding proteins A1CF and AGO2 in the epigenetic control of germ-cell fate, urogenital development, and gamete functions. PMID:27582469

  13. Ribozyme-enhanced single-stranded Ago2-processed interfering RNA triggers efficient gene silencing with fewer off-target effects

    PubMed Central

    Shang, Renfu; Zhang, Fengjuan; Xu, Beiying; Xi, Hairui; Zhang, Xue; Wang, Weihua; Wu, Ligang

    2015-01-01

    Short-hairpin RNAs (shRNAs) are widely used to produce small-interfering RNAs (siRNAs) for gene silencing. Here we design an alternative siRNA precursor, named single-stranded, Argonaute 2 (Ago2)-processed interfering RNA (saiRNA), containing a 16–18 bp stem and a loop complementary to the target transcript. The introduction of a self-cleaving ribozyme derived from hepatitis delta virus to the 3′ end of the transcribed saiRNA dramatically improves its silencing activity by generating a short 3′ overhang that facilitates the efficient binding of saiRNA to Ago2. The same ribozyme also enhances the activity of Dicer-dependent shRNAs. Unlike a classical shRNA, the strand-specific cleavage of saiRNA by Ago2 during processing eliminates the passenger strand and prevents the association of siRNA with non-nucleolytic Ago proteins. As a result, off-target effects are reduced. In addition, saiRNA exhibits less competition with the biogenesis of endogenous miRNAs. Therefore, ribozyme-enhanced saiRNA provides a reliable tool for RNA interference applications. PMID:26455506

  14. Microfluidics Technologies for Low Cell Number Chromatin Immunoprecipitation.

    PubMed

    Wu, Angela R; Quake, Stephen R

    2016-04-01

    Protein-DNA interactions are responsible for numerous critical cellular events: For example, gene expression and silencing are mediated by transcription factor protein binding and histone protein modifications, and DNA replication and repair rely on site-specific protein binding. Chromatin immunoprecipitation (ChIP) is the only molecular assay that directly determines, in a living cell, the binding association between a protein of interest and specific genomic loci. It is an indispensible tool in the biologist's toolbox, but the many limitations of this technique prevent broad adoption of ChIP in biological studies. The typical ChIP assay can take up to 1 wk to complete, and the process is technically tricky, yet tedious. The ChIP assay yields are also low, thus requiring on the order of millions to billions of cells as starting material, which makes the assay unfeasible for studies using rare or precious samples. For example, fluorescence-activated cell sorting (FACS) of cancer stem cells (CSCs) obtained from primary tumors, rarely yields more than ~100,000 CSCs per tumor. This protocol describes a microfluidics-based strategy for performing ChIP, which uses automation and scalability to reduce both total and hands-on assay time, and improve throughput. It allows whole fixed cells as input, and enables automated ChIP from as few as 2000 cells.

  15. 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

  16. Characterization of a Protein Interactome by Co-Immunoprecipitation and Shotgun Mass Spectrometry.

    PubMed

    Maccarrone, Giuseppina; Bonfiglio, Juan Jose; Silberstein, Susana; Turck, Christoph W; Martins-de-Souza, Daniel

    2017-01-01

    Identifying the partners of a given protein (the interactome) may provide leads about the protein's function and the molecular mechanisms in which it is involved. One of the alternative strategies used to characterize protein interactomes consists of co-immunoprecipitation (co-IP) followed by shotgun mass spectrometry. This enables the isolation and identification of a protein target in its native state and its interactome from cells or tissue lysates under physiological conditions. In this chapter, we describe a co-IP protocol for interactome studies that uses an antibody against a protein of interest bound to protein A/G plus agarose beads to isolate a protein complex. The interacting proteins may be further fractionated by SDS-PAGE, followed by in-gel tryptic digestion and nano liquid chromatography high-resolution tandem mass spectrometry (nLC ESI-MS/MS) for identification purposes. The computational tools, strategy for protein identification, and use of interactome databases also will be described.

  17. Identification of Methylated Deoxyadenosines in Genomic DNA by dA6m DNA Immunoprecipitation

    PubMed Central

    Koziol, Magdalena J.; Bradshaw, Charles R.; Allen, George E.; Costa, Ana S.H.; Frezza, Christian

    2017-01-01

    dA6m DNA immunoprecipitation followed by deep sequencing (DIP-Seq) is a key tool in identifying and studying the genome-wide distribution of N6-methyldeoxyadenosine (dA6m). The precise function of this novel DNA modification remains to be fully elucidated, but it is known to be absent from transcriptional start sites and excluded from exons, suggesting a role in transcriptional regulation (Koziol et al., 2015). Importantly, its existence suggests that DNA might be more diverse than previously believed, as further DNA modifications might exist in eukaryotic DNA (Koziol et al., 2015). This protocol describes the method to perform dA6m DNA immunoprecipitation (DIP), as was applied to characterize the first dA6m methylome analysis in higher eukaryotes (Koziol et al., 2015). In this protocol, we describe how genomic DNA is isolated, fragmented and then DNA containing dA6m is pulled down with an antibody that recognizes dA6m in genomic DNA. After subsequent washes, DNA fragments that do not contain dA6m are eliminated, and the dA6m containing fragments are eluted from the antibody in order to be processed further for subsequent analyses. Background This protocol was developed in order to identify regions in the genome that contain dA6m. It can be used to detect dA6m in different genomes. As a guideline, this protocol was established from existing approaches used to detect adenosine methylation in RNA (Dominissini et al., 2013). We developed this protocol and adapted it for the detection of dA6m in DNA, rather than detecting adenosine methylation RNA. This was required, as no protocol was available at that time to allow the genome-wide identification of dA6m in eukaryotic DNA. PMID:28180135

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

    PubMed Central

    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

  19. Eubacterial components similar to small nuclear ribonucleoproteins: identification of immunoprecipitable proteins and capped RNAs in a cyanobacterium and a gram-positive eubacterium.

    PubMed Central

    Kovacs, S A; O'Neil, J; Watcharapijarn, J; Moe-Kirvan, C; Vijay, S; Silva, V

    1993-01-01

    Small nuclear ribonucleoprotein (snRNP) particles play an important role in the processing of pre-mRNA. snRNPs have been identified immunologically in a variety of cells, but none have ever been observed in prokaryotic systems. This report provides the first evidence for the presence of snRNP-like components in two types of prokaryotic cells: those of the cyanobacterium Synechococcus leopoliensis and those of the gram-positive eubacterium Bacillus subtilis. These components consist of snRNP-immunoreactive proteins and RNAs, including some with the snRNP-unique 5' m2,2,7G (m3G) cap. Immunoreactivity was determined by immunoprecipitation procedures, with either antinuclear-antibody-positive (RNP- and Sm-monospecific) patient sera or a m3G monoclonal antibody, with radiolabelled cell extracts that were preadsorbed with antinuclear-antibody-negative sera. S. leopoliensis immunoprecipitates showed the presence of high-molecular-mass proteins (14 to 70 kDa) and RNAs (138 to 243 nucleotides) that are analogous in size to proteins and RNAs found in human (HEp-2) cell immunoprecipitates but absent in Escherichia coli immunoprecipitates. Thin-layer chromatography of S. leopoliensis immunoprecipitates confirmed the presence of a capped nucleotide similar to a capped nucleotide in HEp-2 immunoprecipitates; no such nucleotide was observed in E. coli immunoprecipitates. Immunoreactive RNAs (117-170 nucleotides) were identified in a second eubacterium, B. subtilis, as well. This work suggests that snRNPs or their evolutionary predecessors predate the emergence of eukaryotic cells. Images PMID:8458830

  20. miR-346 and miR-138 competitively regulate hTERT in GRSF1- and AGO2-dependent manners, respectively

    PubMed Central

    Song, Ge; Wang, Renjie; Guo, Junfei; Liu, Xuyuan; Wang, Fang; Qi, Ying; Wan, Haiying; Liu, Min; Li, Xin; Tang, Hua

    2015-01-01

    miRNAs typically downregulate the expression of target genes by binding to their 3′UTR, and dysregulation of miRNAs may contribute to tumorigenesis. Here, we found that miR-346 and miR-138 competitively bind to a common region in the 3′UTR of hTERT mRNA and have opposite effects on the expression and function of hTERT in human cervical cancer cells. Furthermore, G-rich RNA sequence binding factor 1 (GRSF1) mediates the miR-346-dependent upregulation of hTERT by binding to the miR-346 middle sequence motif (CCGCAU) which forms a “bulge loop” when miR-346 is bound to the hTERT 3′UTR, facilitating the recruitment of hTERT mRNA to ribosomes to promote translation in an AGO2-independent manner. Conversely, miR-138 suppresses hTERT expression in an AGO2-dependent manner. Interestingly, replacement of the miR-138 middle sequence with that of miR-346 results in an upregulation of hTERT expression in a GRSF1-dependent manner. Moreover, miR-346 depends on GRSF1 to upregulate another target gene, activin A receptor, type IIB (ACVR2B), in which miR-346 “CCGCAU” motif is essential. These findings reveal novel mechanisms of miRNA-mediated upregulation of target gene expression and describe the coordinated action of multiple miRNAs to control the fate of a single target mRNA through binding to its 3′UTR. PMID:26507454

  1. 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

  2. A comparative analysis of shotgun-cloning and tagged-random amplification-cloning of chromatin immunoprecipitation-isolated genome fragments.

    PubMed

    White, Robert B; Ziman, Melanie R

    2006-07-28

    The cloning of transcription factor antibody-immunoprecipitated genomic fragments from chromatin immunoprecipitation (ChIP) experiments is a technically challenging procedure, especially when the input genomic DNA is isolated from whole tissues (in vivo) rather than cultured cells. Here we adapt a technique known as Tagged-Random PCR (T-PCR) to amplify ChIP-immunoprecipitated DNA from mouse embryonic tissue prior to cloning. Importantly, we then compare this technique with tandem shotgun-cloning experiments in terms of its capacity to identify target genes. We find that T-PCR dramatically increases the efficiency of cloning ChIP fragments without distortion of the relative location of cloned fragments to putative target genes. Thus, T-PCR is a simple procedure which greatly enhances the efficiency of cloning tissue-derived ChIP fragments.

  3. Multiplex Sequential Immunoprecipitation of Insulin Secretory Granule Proteins from Radiolabeled Pancreatic Islets.

    PubMed

    Guest, Paul C

    2017-01-01

    Pulse radiolabeling of cells with radioactive amino acids is a common method for tracking the biosynthesis of proteins. Specific proteins can then be immunoprecipitated and analyzed by electrophoresis and imaging techniques. This chapter presents a protocol for the biosynthetic labeling of pancreatic islets with (35)S-methionine, followed by multiplex sequential immunoprecipitation of insulin and three other secretory granule accessory proteins. This provided a means of distinguishing those pancreatic islet proteins with different biosynthetic rates in response to the media glucose concentrations.

  4. Features of Mammalian microRNA Promoters Emerge from Polymerase II Chromatin Immunoprecipitation Data

    PubMed Central

    Gordon, Ben; Bhattacharjee, Arindam; Kaminski, Naftali; Benos, Panayiotis V.

    2009-01-01

    Background MicroRNAs (miRNAs) are short, non-coding RNA regulators of protein coding genes. miRNAs play a very important role in diverse biological processes and various diseases. Many algorithms are able to predict miRNA genes and their targets, but their transcription regulation is still under investigation. It is generally believed that intragenic miRNAs (located in introns or exons of protein coding genes) are co-transcribed with their host genes and most intergenic miRNAs transcribed from their own RNA polymerase II (Pol II) promoter. However, the length of the primary transcripts and promoter organization is currently unknown. Methodology We performed Pol II chromatin immunoprecipitation (ChIP)-chip using a custom array surrounding regions of known miRNA genes. To identify the true core transcription start sites of the miRNA genes we developed a new tool (CPPP). We showed that miRNA genes can be transcribed from promoters located several kilobases away and that their promoters share the same general features as those of protein coding genes. Finally, we found evidence that as many as 26% of the intragenic miRNAs may be transcribed from their own unique promoters. Conclusion miRNA promoters have similar features to those of protein coding genes, but miRNA transcript organization is more complex. PMID:19390574

  5. Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation.

    PubMed

    Kondo, Yutaka; Shen, Lanlan; Yan, Pearlly S; Huang, Tim Hui-Ming; Issa, Jean-Pierre J

    2004-05-11

    Switching from acetylation to methylation at histone H3 lysine 9 (K9) has recently been shown to contribute to euchromatin gene silencing. To identify genes silenced by K9 modifications, we probed a human CpG island microarray with DNA obtained by chromatin immunoprecipitation (ChIP) in a cancer cell line using an anti-H3-K9 methylated antibody or an anti-H3-K9 acetylated antibody. Of the 27 clones with the highest signal ratio of K9 methylation over acetylation (Me/Ac), 13 contained repetitive sequences. Among 14 nonrepetitive clones, we identified 11 genes (seven known and four previously undescribed), one EST, and two unknown fragments. Using ChIP-PCR, all 18 examined clones showed higher ratios of H3-K9 Me/Ac than the active gene control, P21, thus confirming the microarray data. In addition, we found a strong correlation between the K9 Me/Ac ratio and CpG island DNA methylation (R = 0.92, P < 0.01), and five of seven genes examined (megalin, thrombospondin-4, KR18, latrophilin-3, and phosphatidylinositol-3-OH kinase P101 subunit) showed lack of expression by RT-PCR and reactivation by DNA methylation and/or histone deacetylase inhibition, suggesting that these genes are true targets of silencing through histone modifications. All five genes also showed significant DNA methylation in a cell line panel and in primary colon cancers. Our data suggest that CpG island microarray coupled with ChIP can identify novel targets of gene silencing in cancer. This unbiased approach confirms the tight coupling between DNA methylation and histone modifications in cancer and could be used to probe gene silencing in nonneoplastic conditions as well.

  6. 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

  7. A rapid immunoprecipitation assay for neomycin phosphotransferase II expression in transformed bacteria and plant tissues.

    PubMed

    Baszczynski, C L

    1990-06-01

    Anti-kanamycin antibodies produced in rabbits, following coupling of the antibiotic to bovine serum albumin, were used to immunoprecipitate radioactively labelled phosphorylated kanamycin from transformed bacterial or plant extracts in a novel assay system, for the detection of neomycin phosphotransferase II (NPTII) activity. Radioactive counts in the immunoprecipitated pellet give a semiquantitative measure of the kanamycin phosphorylation and hence the amount of NPTII activity. This assay is sensitive, uses very small amounts of radioactivity, and is very rapid, allowing many samples to be processed within a few hours. Immunoprecipitated counts from reactions with bacteria carrying a kanamycin resistance gene or from tobacco and Brassica napus plants transformed with NPTII gene-containing vectors were consistently higher than counts from nontransformed controls. Results obtained with this assay correlate well with those from the previously described gel overlay and dot-blot assays, but can be obtained in an appreciably shorter time frame.

  8. Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes.

    PubMed

    Mohammed, Hisham; Taylor, Christopher; Brown, Gordon D; Papachristou, Evaggelia K; Carroll, Jason S; D'Santos, Clive S

    2016-02-01

    Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) is a method that allows the study of protein complexes, in particular chromatin and transcription factor complexes, in a rapid and robust manner by mass spectrometry (MS). The method can be used in parallel with chromatin immunoprecipitation-sequencing (ChIP-seq) experiments to provide information on both the cistrome and interactome for a given protein. The method uses formaldehyde fixation to stabilize protein complexes. By using antibodies against the endogenous target, the cross-linked complex is immunoprecipitated, rigorously washed, and then digested into peptides while avoiding antibody contamination (on-bead digestion). By using this method, MS identification of the target protein and several dozen interacting proteins is possible using a 100-min LC-MS/MS run. The protocol does not require substantial proteomics expertise, and it typically takes 2-3 d from the collection of material to results.

  9. 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.

  10. Polysome immunoprecipitation of phenylalanine hydroxylase mRNA from rat liver and cloning of its cDNA.

    PubMed Central

    Robson, K J; Chandra, T; MacGillivray, R T; Woo, S L

    1982-01-01

    The mRNA for phenylalanine hydroxylase (phenylalanine 4-monooxygenase, EC 1.14.16.1) has been purified from total rat liver mRNAs, of which it constitutes less than 0.25%, to greater than 10% purity in a single step by specific polysome immunoprecipitation. The purified mRNA was used for synthesis and cloning of its cDNA. Recombinant colonies containing phenylalanine hydroxylase DNA sequences were identified by differential hybridization, hybrid-selected translation, and blot hybridization analysis. The rat cDNA clone was capable of hybridizing with human phenylalanine hydroxylase mRNA, which will permit the isolation of the corresponding human gene for analysis of phenylketonuria, a hereditary disorder in phenylalanine metabolism that causes permanent mental retardation in humans. Images PMID:6750607

  11. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.

    PubMed

    Marcon, Edyta; Jain, Harshika; Bhattacharya, Anandi; Guo, Hongbo; Phanse, Sadhna; Pu, Shuye; Byram, Gregory; Collins, Ben C; Dowdell, Evan; Fenner, Maria; Guo, Xinghua; Hutchinson, Ashley; Kennedy, Jacob J; Krastins, Bryan; Larsen, Brett; Lin, Zhen-Yuan; Lopez, Mary F; Loppnau, Peter; Miersch, Shane; Nguyen, Tin; Olsen, Jonathan B; Paduch, Marcin; Ravichandran, Mani; Seitova, Alma; Vadali, Gouri; Vogelsang, Maryann S; Whiteaker, Jeffrey R; Zhong, Guoqing; Zhong, Nan; Zhao, Lei; Aebersold, Ruedi; Arrowsmith, Cheryl H; Emili, Andrew; Frappier, Lori; Gingras, Anne-Claude; Gstaiger, Matthias; Paulovich, Amanda G; Koide, Shohei; Kossiakoff, Anthony A; Sidhu, Sachdev S; Wodak, Shoshana J; Gräslund, Susanne; Greenblatt, Jack F; Edwards, Aled M

    2015-08-01

    Antibodies are used in multiple cell biology applications, but there are no standardized methods to assess antibody quality-an absence that risks data integrity and reproducibility. We describe a mass spectrometry-based standard operating procedure for scoring immunoprecipitation antibody quality. We quantified the abundance of all the proteins in immunoprecipitates of 1,124 new recombinant antibodies for 152 chromatin-related human proteins by comparing normalized spectral abundance factors from the target antigen with those of all other proteins. We validated the performance of the standard operating procedure in blinded studies in five independent laboratories. Antibodies for which the target antigen or a member of its known protein complex was the most abundant protein were classified as 'IP gold standard'. This method generates quantitative outputs that can be stored and archived in public databases, and it represents a step toward a platform for community benchmarking of antibody quality.

  12. DNA-Binding Factor Target Identification by Chromatin Immunoprecipitation (ChIP) in Plants.

    PubMed

    Posé, David; Yant, Levi

    2016-01-01

    Chromatin immunoprecipitation (ChIP) allows the precise identification of genomic loci that physically interact with a protein of interest, whether that protein is a transcription factor, a core polymerase, a histone, or other chromatin-associated protein. In short, tissue is first cross-linked to freeze a population of DNA-protein interactions at a stage of interest. Chromatin is then extracted, fragmented, and incubated with a specific antibody against the protein of interest. Next, the resultant DNA-protein complexes are immunoprecipitated and captured using beads that bind to the antibody constant region. Samples are finally reverse cross-linked to separate the bound fragments and the DNA is purified. This DNA is analyzed by quantitative PCR for enrichment of genomic regions expected to be bound by the protein under study. The protocol detailed in this chapter has been successfully applied in the identification of target genes for seven transcriptional regulators of diverse classes involved in Arabidopsis thaliana floral transition.

  13. Yo antibodies in ovarian and breast cancer patients detected by a sensitive immunoprecipitation technique.

    PubMed

    Monstad, S E; Storstein, A; Dørum, A; Knudsen, A; Lønning, P E; Salvesen, H B; Aarseth, J H; Vedeler, C A

    2006-04-01

    Onconeural antibodies are found in patients with cancer and are associated with paraneoplastic neurological syndromes (PNS). The objective of the present study was to assess the frequency of Yo antibodies in ovarian and breast cancer using a sensitive immunoprecipitation technique, and to look for any association of Yo antibodies with neurological symptoms and prognostic factors. A multiwell adapted fluid-phase immunoassay using radiolabelled recombinant cerebellar degeneration related protein (cdr2), produced by coupled in vitro transcription/translation was used for the detection of Yo antibodies. This technique combines high specificity and sensitivity with high sample analysing capacity for the antibody in question. Sera or EDTA-blood from 810 ovarian (n = 557) and breast cancer (n = 253) patients were analysed for Yo antibodies by immunoprecipitation, as well as immunofluorescence and immune blots. Two hundred healthy blood donors and sera from 17 patients with paraneoplastic cerebellar degeneration and Yo antibodies served as controls. Immunoprecipitation was more sensitive in detecting Yo antibodies than immunofluorescence and immune blots. The prevalence of Yo antibodies was 13/557 (2.3%) in ovarian cancer and 4/253 (1.6%) in breast cancer using immunoprecipitation. Yo antibodies were not correlated with specific histological subgroups. The Yo index of ovarian cancer patients in FIGO stage IV was higher compared to FIGO stage I-III. The prevalence of Yo antibodies was 3 times higher in patients with stage III breast cancer than in stage I and II. Only 2/17 (11.8%) patients with Yo antibodies detected during the screen of 810 cancer patients had PNS. The results show that the prevalence of Yo antibodies is low in ovarian and breast cancer. Yo antibodies may be associated with advanced cancer, but less often with PNS.

  14. Probing activation/deactivation of the BRASSINOSTEROID INSENSITIVE1 receptor kinase by immunoprecipitation

    PubMed Central

    Martins, Sara; Vert, Grégory; Jaillais, Yvon

    2017-01-01

    Summary Brassinosteroids are plant sterol-derived hormones that control plant growth and development. The BR receptor complex is encoded by the BRASSINOSTEROID INSENSITIVE1 (BRI1) and members of the SOMATIC EMBRYOGENESIS RECEPTOR KINASE family. BR receptor complex activation and deactivation uses different post-translational modifications and recruitment of partner proteins. In this chapter, we describe optimized immunoprecipitation protocols and variants for biochemical analyses of BRI1 post-translational modification and protein-protein interaction. PMID:28124254

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

    PubMed Central

    2016-01-01

    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 106–107 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. PMID:26745449

  16. 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.

  17. Neuropilin-1 is a receptor for extracellular miRNA and AGO2/miRNA complexes and mediates the internalization of miRNAs that modulate cell function

    PubMed Central

    Prud'homme, Gerald J.; Glinka, Yelena; Lichner, Zsuzsanna; Yousef, George M.

    2016-01-01

    Extracellular miRNAs are increasingly studied as markers for specific diseases. They are released in biological fluids in a remarkably stable form, and may play a role in intercellular communication. They are thought to be protected against degradation by either encapsulation within microparticles, or by binding to proteins (mostly AGO2). The particulate forms may be internalized by endocytosis or membrane fusion, but the protein-bound forms require a receptor mechanism for their uptake. A major question is whether there are natural cell-membrane receptors that capture and internalize protein-bound functional miRNAs. We examined neuropilin-1 (NRP1), in view of its properties as a receptor for many ligands, including growth factors such as vascular endothelial growth factor (VEGF), and efficiency at mediating ligand internalization. It is expressed by endothelial cells, many other normal cell types, and cancer cells. Here, we report that NRP1 binds miRNAs with high affinity, and promotes their entry into the cell. Furthermore, the internalized miRNAs remain functional, as they specifically regulate proliferation and migration of cancer cells, as well as tube formation by human endothelial cells. Anti-NRP1 antibodies or NRP1 siRNA knockdown block miRNA effects, further confirming NRP1-mediated uptake. VEGF does not compete with miRNAs for binding to NRP1. In addition, NRP1 binds extracellular AGO2 (carrying miRNA or not), and internalizes AGO2/miRNA complexes. Because miRNA bound to AGO2 appears to the most abundant form in body fluids, this may have important physiological and pathological effects. PMID:27486976

  18. Sequential Co-immunoprecipitation and Immunoblot Approach to Determine Oligomerisation of G-Protein-Coupled Receptors.

    PubMed

    Guest, Paul C

    2017-01-01

    G-protein-coupled receptors (GPCRs) play a major role in psychiatric disorders and are the targets of several current therapeutic approaches in this field. A number of studies have now shown that GPCRs can assemble as high molecular weight homo- and hetero-oligomers, which could affect ligand binding, intracellular signalling or trafficking. This information could be critical in design of new drugs to treat neurological and psychiatric disorders. This chapter describes a sequential co-immunoprecipitation and immunoblot protocol for determining oligomerisation of the 5-hydroxytryptamine (HT)1A receptor with other GPCRs in co-transfected HEK-293 cells.

  19. Bioorthogonal click chemistry to assay mu-opioid receptor palmitoylation using 15-hexadecynoic acid and immunoprecipitation

    PubMed Central

    Ebersole, Brittany; Petko, Jessica; Levenson, Robert

    2014-01-01

    We have developed a modification of bioorthogonal click chemistry to assay the palmitoylation of cellular proteins. This assay utilizes 15-hexadecynoic acid (15-HDYA) as a chemical probe in combination with protein immunoprecipitation using magnetic beads in order to detect S-palmitoylation of proteins of interest. Here we demonstrate the utility of this approach for the mu-opioid receptor (MOR), a GPCR responsible for mediating the analgesic and addictive properties of most clinically relevant opioid agonist drugs. This technique provides a rapid, non-isotopic, and efficient method to assay the palmitoylation status of a variety of cellular proteins including most GPCRs. PMID:24463015

  20. Membrane-associated precursor to poliovirus VPg identified by immunoprecipitation with antibodies directed against a synthetic heptapeptide

    SciTech Connect

    Semelr, B.L.; Anderson, C.W.; Hanecak, R.; Dorner, L.F.; Wimmer, E.

    1982-02-01

    A synthetic heptapeptide corresponding to the C-terminal sequence of the poliovirus genome protein (VPg) has been linked to bovine serum albumin and used to raise antibodies in rabbits. These antibodies precipitate not only VPg but also at least two more virus-specific polypeptides. The smaller polypeptide, denoted P3-9 (12,000 daltons), has been mapped by Edman degradation and by fragmentation with cyanogen bromide and determined to be the N-terminal cleavage product of polypeptide P3-1b, a precursor to the RNA polymerase. P3-9 contains the sequence of the basic protein VPg (22 amino acids) at its C terminus. As predicted by the known RNA sequence of poliovirus, P3-9 also contains a hydrophobic region of 22 amino acids preceding VPg, an observation suggesting that P3-9 may be membrane-associated. This was confirmed by fractionation of infected cells in the presence or absence of detergent. We speculate that P3-9 may be the donor of VPg to RNA chains in the membrane-bound RNA replication complex.

  1. Fragment complementation and co-immunoprecipitation assays for understanding R protein structure and function.

    PubMed

    Moffett, Peter

    2011-01-01

    Plant disease resistance (R) proteins confer protection against specific pathogens or pathogen isolates. R proteins function by recognizing pathogen-encoded avirulence (Avr) proteins and translating this recognition event into an initiation of downstream signaling pathways. Key to understanding this process is the study of the protein-protein interactions involving R proteins. Recognition and signaling mechanisms are mediated by both intramolecular interactions that take place between different domains of R proteins as well as intermolecular interactions between R proteins and additional plant proteins. These processes have been studied in part by using Agrobacterium-mediated transient expression of R protein fragments in Nicotiana benthamiana which allows for the rapid assessment of functionality. Furthermore, pairs of proteins or protein fragments can be transiently expressed as fusions with different epitope tags. One putative protein partner is subjected to immunoprecipitation. Subsequent immunoblotting is performed to determine whether the second protein has remained associated (or co-immunoprecipitated) with the first, indicating a protein-protein interaction. This technique has contributed substantially to structure-function analyses of R proteins and to the characterization of interactions between R proteins and other plant proteins.

  2. Immunoprecipitation of Serum Albumin with Protein A-Sepharose: A Biochemistry Laboratory Experiment

    NASA Astrophysics Data System (ADS)

    Bohinski, Robert C.

    2000-11-01

    An exercise has been designed and optimized to acquaint students with the simple yet powerful technique of immunoprecipitation. Protein A-Sepharose (PA-S) is used as a solid-phase precipitant to recover bovine serum albumin (BSA, the antigen) recognized by anti-BSA antibody (Ab). The high degree of binding specificity between antigen and antibody is illustrated by recovery of BSA from a complex mixture of proteins obtained from wheat germ and chicken breast. Various controls are included for a thorough data analysis. The solid phase of Ag/Ab/PA-S is recovered by centrifugation, thoroughly washed, and treated to dissociate the BSA antigen. Samples are examined by discontinuous denaturing gel electrophoresis (SDS-PAGE) with Coomassie blue staining. The supernatants, containing proteins that are not precipitated, are also analyzed. Antigenic cross-reactivity, ranging from strong to none, is demonstrated in a second part by using serum albumins from seven different sources. Systems can be set up, shaken, and prepared for electrophoresis in a single lab period with time for laboratory lecture and discussion about antibody structure and function, antibody-based methods in general, and immunoprecipitation in particular.

  3. Trout red blood cell arrestin (TRCarr), a novel member of the arrestin family: cloning, immunoprecipitation and expression of recombinant TRCarr.

    PubMed

    Jahns, R; Borgese, F; Lindenthal, S; Straub, A; Motais, R; Fiévet, B

    1996-06-01

    Arrestins are cytosolic proteins involved in the desensitization of G-protein-coupled receptors. We report the cloning of trout red blood cell arrestin which shows 76, 82 and 52% identity with bovine beta-arrestin1, beta-arrestin2 and retinal arrestin respectively. Antibodies were generated against the C-terminus of trout red blood cell arrestin. These antibodies detected arrestin in erythrocyte cytosol and were able to precipitate the native protein. The Na+/H+ antiporter of trout red blood cell is activated by beta-adrenergic stimulation and is then desensitized whereas the transmembrane signalling pathway is not. To investigate the subcellular distribution of arrestin on beta-adrenergic activation and desensitization of the antiporter, precipitation experiments were carried out on trout erythrocytes. A desensitization-dependent shift in cytosolic arrestin to the membranes could not be detected using the immunoprecipitation technique but we cannot exclude the possibility that a small number of cytosolic arrestins might be involved in the regulation of membrane proteins in trout erythrocyte. Recombinant trout arrestin was produced in a protease-deficient Escherichia coli strain and its functionality was tested in a reconstituted rhodopsin assay. The recombinant protein provides a suitable tool for investigating the target for arrestin in trout red blood cell, which still remains to be identified.

  4. Mapping genomic targets of DNA helicases by chromatin immunoprecipitation in Saccharomyces cerevisiae.

    PubMed

    Cobb, Jennifer; van Attikum, Haico

    2010-01-01

    DNA helicases utilize the energy of nucleotide hydrolysis to unwind the two annealed strands of the DNA helix and are involved in many aspects of DNA metabolism such as replication, recombination, and repair. Chromatin immunoprecipitation (ChIP) has been instrumental in determining the genomic targets of many DNA helicases and DNA helicase-containing complexes including the minichromosome maintenance (Mcm) proteins 2-7, the RecQ helicase Sgs1 as well as the Rvb1 and Rvb2 helicase-containing INO80 and SWR1 chromatin remodeling complexes. Here we describe a ChIP method that has been successfully used to map these proteins at chromosomal double-strand breaks and replication forks in the model organism Saccharomyces cerevisiae.

  5. Immunoprecipitation of SV40 replicating minichromosomes complexed with bacteriophage T4 gene 32 protein.

    PubMed Central

    Miranda, E I; Garrido-Guerrero, E; Garcia-Carranca, A; Gariglio, P

    1992-01-01

    Simian Virus 40 (SV40) DNA replication is a useful model to study eukaryotic cell DNA replication because it encodes only one replication protein and its genome has a nucleoprotein structure ('minichromosome') indistinguishable from cellular chromatin. Late after infection SV40 replicating DNA molecules represent about 5% of total viral minichromosomes. Since gene 32 protein (P32) from bacteriophage T4 interacts with single-stranded DNA and SV40 replication complexes are expected to contain single-stranded regions at the replication forks, we asked whether P32 might be used to isolate replicating SV40 minichromosomes. When nuclear extracts from SV40 infected cells were treated sequentially with P32 and anti-P32 antibodies, pulse-labeled minichromosomes were selectively immunoprecipitated. Agarose gel electrophoresis analysis confirmed that immunoprecipitated material corresponded to SV40 replicative intermediates. Protein analysis of the pelleted material revealed several proteins of viral and cellular origin. Among them, T antigen and histones were found to be complexed with at least other three proteins from cellular origin, to the replicative complexes. Additionally, anti-P32 antibodies were able to detect three cellular proteins of approximately 70, 32 and 13 kDa in western blots. These proteins could correspond to those found as part of an eukaryotic multisubunit single-stranded DNA binding protein. The use of P32 and anti-P32 antibodies thus allows the separation of replicating from mature SV40 minichromosomes and can constitute a novel method to enrich and to study replicative active chromatin. Images PMID:1311833

  6. Measuring NLR Oligomerization I: Size Exclusion Chromatography, Co-immunoprecipitation, and Cross-Linking.

    PubMed

    Khare, Sonal; Radian, Alexander D; Dorfleutner, Andrea; Stehlik, Christian

    2016-01-01

    Oligomerization of nod-like receptors (NLRs) can be detected by several biochemical techniques dependent on the stringency of protein-protein interactions. Some of these biochemical methods can be combined with functional assays, such as caspase-1 activity assay. Size exclusion chromatography (SEC) allows separation of native protein lysates into different sized complexes by fast protein liquid chromatography (FPLC) for follow-up analysis. Using co-immunoprecipitation (co-IP), combined with SEC or on its own, enables subsequent antibody-based purification of NLR complexes and associated proteins, which can then be analyzed by immunoblot and/or subjected to functional caspase-1 activity assay. Chemical cross-linking covalently joins two or more molecules, thus capturing the oligomeric state with high sensitivity and stability. Apoptosis-associated speck-like protein containing a caspase activation domain (ASC) oligomerization has been successfully used as readout for NLR or AIM2-like receptor (ALR) inflammasome activation in response to various pathogen- or damage-associated molecular patterns (PAMPs or DAMPs) in human and mouse macrophages and THP-1 cells. Here, we provide a detailed description of the methods used for NLRP7 oligomerization in response to infection with Staphylococcus aureus (S. aureus) in primary human macrophages, co-immunoprecipitation and immunoblot analysis of NLRP7 and NLRP3 inflammasome complexes, as well as caspase-1 activity assays. Also, ASC oligomerization is shown in response to dsDNA, LPS/ATP, and LPS/nigericin in mouse bone marrow-derived macrophages (BMDMs) and/or THP-1 cells or human primary macrophages.

  7. 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

  8. Searching for Biomarkers: Humoral Response Profiling with Luciferase Immunoprecipitation Systems (LIPS)

    PubMed Central

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

    2013-01-01

    B-cell mediated humoral responses are triggered in many human diseases including autoimmune, cancer, 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 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 provide a framework for incorporating LIPS antibody profiling into global health initiatives and disease monitoring. PMID:21679112

  9. Protocol: Chromatin immunoprecipitation (ChIP) methodology to investigate histone modifications in two model diatom species

    PubMed Central

    2012-01-01

    In this report we describe a chromatin immunoprecipitation (ChIP) protocol for two fully sequenced model diatom species Phaeodactylum tricornutum and Thalassiosira pseudonana. This protocol allows the extraction of satisfactory amounts of chromatin and gives reproducible results. We coupled the ChIP assay with real time quantitative PCR. Our results reveal that the two major histone marks H3K4me2 and H3K9me2 exist in P. tricornutum and T. pseudonana. As in other eukaryotes, H3K4me2 marks active genes whereas H3K9me2 marks transcriptionally inactive transposable elements. Unexpectedly however, T. pseudonana housekeeping genes also show a relative enrichment of H3K9me2. We also discuss optimization of the procedure, including growth conditions, cross linking and sonication. Validation of the protocol provides a set of genes and transposable elements that can be used as controls for studies using ChIP in each diatom species. This protocol can be easily adapted to other diatoms and eukaryotic phytoplankton species for genetic and biochemical studies. PMID:23217141

  10. Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome.

    PubMed

    Kadota, Mitsutaka; Yang, Howard H; Hu, Nan; Wang, Chaoyu; Hu, Ying; Taylor, Philip R; Buetow, Kenneth H; Lee, Maxwell P

    2007-05-18

    Several recent studies have shown a genetic influence on gene expression variation, including variation between the two chromosomes within an individual and variation between individuals at the population level. We hypothesized that genetic inheritance may also affect variation in chromatin states. To test this hypothesis, we analyzed chromatin states in 12 lymphoblastoid cells derived from two Centre d'Etude du Polymorphisme Humain families using an allele-specific chromatin immunoprecipitation (ChIP-on-chip) assay with Affymetrix 10K SNP chip. We performed the allele-specific ChIP-on-chip assays for the 12 lymphoblastoid cells using antibodies targeting at RNA polymerase II and five post-translation modified forms of the histone H3 protein. The use of multiple cell lines from the Centre d'Etude du Polymorphisme Humain families allowed us to evaluate variation of chromatin states across pedigrees. These studies demonstrated that chromatin state clustered by family. Our results support the idea that genetic inheritance can determine the epigenetic state of the chromatin as shown previously in model organisms. To our knowledge, this is the first demonstration in humans that genetics may be an important factor that influences global chromatin state mediated by histone modification, the hallmark of the epigenetic phenomena.

  11. Keratin proteins in human lung carcinomas. Combined use of morphology, keratin immunocytochemistry, and keratin immunoprecipitation.

    PubMed Central

    Banks-Schlegel, S. P.; McDowell, E. M.; Wilson, T. S.; Trump, B. F.; Harris, C. C.

    1984-01-01

    Light-microscopic immunocytochemistry and electron microscopy demonstrated that adenocarcinomas (AC) and squamous cell (epidermoid) carcinomas (SCCs) of human lung contained keratin proteins in the form of tonofilament bundles. However, moderately differentiated (md) SCCs contained abundant keratin, whereas poorly differentiated (pd) SCCs and all ACs contained lesser amounts. Lung tumors with the diagnosis of AC or SCC, as defined by WHO criteria, were also analyzed by immunoprecipitation techniques for the presence of keratin proteins. Regardless of the degree of tumor differentiation, SCCs contained a 44 kd keratin which was lacking in ACs. Interestingly, normal bronchial epithelium also contained the same 44 kd keratin. In addition, as SCCs became more differentiated, they exhibited even greater differences in the profile of synthesized keratins. Specifically, the relative abundance of the intermediate-sized keratins (57 and 59 kd) was increased in the md SCCs. Although keratin protein patterns appear to be a valuable adjunct in distinguishing AC from SCC, their usefulness as a diagnostic tool will require survey of a larger number of poorly differentiated tumors. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 PMID:6198920

  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. RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases.

    PubMed

    Halász, László; Karányi, Zsolt; Boros-Oláh, Beáta; Rózsa, Tímea; Sipos, Éva; Nagy, Éva; Mosolygó-L, Ágnes; Mázló, Anett; Rajnavölgyi, Éva; Halmos, Gábor; Székvölgyi, Lóránt

    2017-03-24

    The impact of R-loops on the physiology and pathology of chromosomes has been demonstrated extensively by chromatin biology research. The progress in this field has been driven by technological advancement of R-loop mapping methods that largely relied on a single approach, DNA-RNA immunoprecipitation (DRIP). Most of the DRIP protocols use the experimental design that was developed by a few laboratories, without paying attention to the potential caveats that might affect the outcome of RNA-DNA hybrid mapping. To assess the accuracy and utility of this technology, we pursued an analytical approach to estimate inherent biases and errors in the DRIP protocol. By performing DRIP-sequencing, qPCR and receiver operator characteristic (ROC) analysis, we tested the effect of formaldehyde fixation, cell lysis temperature, mode of genome fragmentation, and removal of free RNA on the efficacy of RNA-DNA hybrid detection, and implemented workflows that were able to distinguish complex and weak DRIP signals in a noisy background with high confidence. We also show that some of the workflows perform poorly and generate random answers. Furthermore, we found that the most commonly used genome fragmentation method (restriction enzyme digestion) led to the overrepresentation of lengthy DRIP fragments over coding ORFs, and this bias was enhanced at the first exons. Biased genome sampling severely compromised the mapping resolution and prevented the assignment of precise biological function to a significant fraction of R-loops. The revised workflow presented herein is established and optimized using objective ROC analyses and provides reproducible and highly specific RNA-DNA hybrid detection.

  14. Immunoprecipitation of native botulinum neurotoxin complexes from Clostridium botulinum subtype A strains.

    PubMed

    Lin, Guangyun; Tepp, William H; Bradshaw, Marite; Fredrick, Chase M; Johnson, Eric A

    2015-01-01

    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.

  15. Racial Differences in Expression Levels of miRNA Machinery-Related Genes, Dicer, Drosha, DGCR8, and AGO2, in Asian Korean Papillary Thyroid Carcinoma and Comparative Validation Using the Cancer Genome Atlas

    PubMed Central

    Kim, Jaegil; Park, Woo-Jae; Jeong, Kwang-Joon; Kang, Sun Hee; Kwon, Sun Young

    2017-01-01

    Aberrant regulation of microRNA (miRNA) machinery components is associated with various human cancers, including papillary thyroid carcinoma (PTC), which is the most common type of thyroid cancer, and a higher prevalent female malignancy. The purpose of this study is to investigate racial differences in mRNA expression levels of four miRNA machinery components, Dicer, Drosha, DGCR8, and AGO2, and their correlations with clinicopathological characteristics. Forty PTC samples from female Asian Korean PTC patients were enrolled. Using qPCR, we examined mRNA expression levels of the components and next validated our results by comparison with results of female white American in the TCGA PTC project. Interestingly, mRNA expression levels of the selected factors were altered in the TCGA PTC samples. However, only Drosha showed a significantly lower expression level in Asian Korean PTC samples. Furthermore, the mRNA expression levels of the four components showed no association with clinicopathological characteristics in both groups. On the other hand, positive correlations were observed between altered mRNA expression levels of Dicer and Drosha and DGCR8 and Drosha in TCGA PTC samples. These findings collectively revealed that altered mRNA expression levels of miRNA machinery components might be responsible for racial differences in the carcinogenesis of PTC. PMID:28352639

  16. Improvements in immunoprecipitation of specific messenger RNA. Isolation of highly purified conalbumin mRNA in high yield.

    PubMed

    Payvar, F; Schimke, R T

    1979-11-01

    We have described previously procedures for the isolation of specific mRNA employing immunoprecipitation of polysomes. In spite of our success with ovalbumin mRNA in the chicken oviduct, we have had considerable difficulties in applying these same published techniques to the immunopurification of conalbumin mRNA, despite the fact that the chicken oviduct synthesizes up to 10% of protein as conalbumin. Here we describe a number of modifications and refinements which have proved essential in obtaining intact conalbumin mRNA in high purity and high yields. These refinements include: (a) improved purification of conalbumin in order to remove contaminating proteins that result in impure antibodies; (b) improved isolation of specific conalbumin antibody in high yields; (c) improved methods for reducing contamination by non-specific polysomes; (d) improved techniques for isolation of RNA from immunoprecipitates resulting in less degradation and higher recovery of conalbumin mRNA; (E) improved techniques for efficient translation of conalbumin mRNA involving treatment of the RNA with methylmercury prior to translation. We conclude that problems involved in the immunoprecipitation of different mRNAs may differ, and that various refinements in techniques may be required for obtaining highly purified preparations of intact mRNA in high yields.

  17. D-Isonucleotide (isoNA) incorporation around cleavage site of passenger strand promotes the vibration of Ago2-PAZ domain and enhances in vitro potency of siRNA.

    PubMed

    Huang, Ye; Tian, Miao; Zhang, Yichao; Sheng, Gang; Chen, Zhuo; Ma, Yuan; Chen, Yue; Peng, Yihong; Zhao, Yi-Lei; Wang, Yanli; Zhang, Lihe; Yang, Zhenjun

    2015-11-28

    It has been demonstrated that passenger strand cleavage is important for the activation of RNA-induced silencing complex (RISC), which is a crucial step for siRNA-mediated gene silencing. Herein, we report that isonucleotide (isoNA) modification around the cleavage site of the passenger strand would affect the in vitro potency of modified siRNAs by altering the motion pattern of the Ago2-PAZ domain. According to western blotting, q-PCR and antiviral test results, we proved that D-isonucleotide (isoNA) modification at the position 8 of the passenger strand (siMek1-S08D), which is adjacent to the cleavage site, markedly improved the in vitro potency of the modified siRNA, whereas siRNAs with D-isoNA incorporation at position 9 (siMek1-S09D) or L-isoNA incorporation at positions 8 and 9 (siMek1-S08L, siMek1-S09L) displayed lower activity compared to native siRNA. Kinetics evaluation of passenger strand cleavage induced by T. thermophilus Ago (Tt-Ago) showed that D-isoNA modification at position 8 of the passenger strand had no significant influence on the cleavage rate, but L-isoNA modification at position 8 slowed the cleavage rate markedly. Moreover, the results of molecular dynamics simulations showed that D-isoNA modification at position 8 affected the open-close motion of the PAZ domain in the Ago/siRNA complex, which may promote the loading of RISC and release of a passenger strand cleavage product, and consequently accelerate the activation of RISC and enhance silencing activity. However, D-isoNA modification at position 9 or L-isoNA modification at position 8 or 9 exerted opposite influences on the motion of the Ago-PAZ domain.

  18. 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.

  19. Urb-RIP – An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins

    PubMed Central

    Cottrell, Kyle A.; Djuranovic, Sergej

    2016-01-01

    Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application. Here we present a novel method for the immunoprecipitation of mRNAs and ncRNAs, Urb—RNA immunoprecipitation (Urb-RIP). This method employs the RRM1 domain of the “resurrected” snRNA-binding protein Urb to enrich messages containing a stem-loop tag. Unlike techniques which employ the MS2 protein, which require large repeats of the MS2 binding element, Urb-RIP requires only one stem-loop. This method routinely provides over ~100-fold enrichment of tagged messages. Using this technique we have shown enrichment of tagged mRNAs and lncRNAs as well as miRNAs and RNA-binding proteins bound to those messages. We have confirmed, using Urb-RIP, interaction between RNA PolIII transcribed lncRNA BC200 and polyA binding protein. PMID:27930710

  20. Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure.

    PubMed

    Harmeyer, Kayla M; South, Paul F; Bishop, Brett; Ogas, Joe; Briggs, Scott D

    2015-03-31

    Genome-wide chromatin immunoprecipitation (ChIP) studies have brought significant insight into the genomic localization of chromatin-associated proteins and histone modifications. The large amount of data generated by these analyses, however, require approaches that enable rapid validation and analysis of biological relevance. Furthermore, there are still protein and modification targets that are difficult to detect using standard ChIP methods. To address these issues, we developed an immediate chromatin immunoprecipitation procedure which we call ZipChip. ZipChip significantly reduces the time and increases sensitivity allowing for rapid screening of multiple loci. Here we describe how ZipChIP enables detection of histone modifications (H3K4 mono- and trimethylation) and two yeast histone demethylases, Jhd2 and Rph1, which were previously difficult to detect using standard methods. Furthermore, we demonstrate the versatility of ZipChIP by analyzing the enrichment of the histone deacetylase Sir2 at heterochromatin in yeast and enrichment of the chromatin remodeler, PICKLE, at euchromatin in Arabidopsis thaliana.

  1. Identification of novel 14-3-3ζ interacting proteins by quantitative immunoprecipitation combined with knockdown (QUICK).

    PubMed

    Ge, Feng; Li, Wen-Liang; Bi, Li-Jun; Tao, Sheng-Ce; Zhang, Zhi-Ping; Zhang, Xian-En

    2010-11-05

    The family of 14-3-3 proteins has emerged as critical regulators of diverse cellular responses under both physiological and pathological conditions. To gain insight into the molecular action of 14-3-3ζ in multiple myeloma (MM), we performed a systematic proteomic analysis of 14-3-3ζ-associated proteins. This analysis, recently developed by Matthias Mann, termed quantitative immunoprecipitation combined with knockdown (QUICK), integrates RNAi, SILAC, immunoprecipitation, and quantitative MS technologies. Quantitative mass spectrometry analysis allowed us to distinguish 14-3-3ζ-interacting proteins from background proteins, resulting in the identification of 292 proteins in total with 95 novel interactions. Three 14-3-3ζ-interacting proteins-BAX, HSP70, and BAG3-were further confirmed by reciprocal coimmunoprecipitations and colocalization analysis. Our results therefore not only uncover a large number of novel 14-3-3ζ-associated proteins that possess a variety of cellular functions, but also provide new research directions for the study of the functions of 14-3-3ζ. This study also demonstrated that QUICK is a useful approach to detect specific protein-protein interactions with very high confidence and may have a wide range of applications in the investigation of protein complex interaction networks.

  2. 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

  3. The relative infrequency and low levels of neutralising and immunoprecipitating antibody to herpes simplex viruses types 1 and 2 in patients with a history of recurrent herpes genitalis.

    PubMed

    Woodman, C B; Stocker, D; Sugrue, D; Desberbasques, M; Hartley, C E; Fuller, A; Buchan, A; Skinner, G R

    1983-01-01

    Twenty-seven per cent of 70 patients with a history of recurrent herpes genitalis but no concomitant history of recurrent oral or peri-genital disease, had no detectable neutralising antibody against type 1 or type 2 herpes simplex virus; the prevalence and levels of neutralising antibody were similar to 53 patients with no history of herpetic disease and significantly lower than 67 patients with a history of recurrent herpes genitalis in association with oral or peri-genital disease all of whom had neutralising antibody against both virus types. There were similar differences between groups for immunoprecipitating antibody where 80% of patients were herpes genitalis alone had no detectable immunoprecipitating antibody. The results indicate that the failure to detect immunising and immunoprecipitating antibody in an individual's serum is compatible with a long and even severe history of recurrent herpes genitalis and consequently that the development of neutralising antibody does not necessarily indicate an episode of primary herpetic disease.

  4. Multifunctionalization of cetuximab with bioorthogonal chemistries and parallel EGFR profiling of cell-lines using imaging, FACS and immunoprecipitation approaches.

    PubMed

    Reschke, Melanie L; Uprety, Rajendra; Bodhinayake, Imithri; Banu, Matei; Boockvar, John A; Sauve, Anthony A

    2014-12-01

    The ability to derivatize antibodies is currently limited by the chemical structure of antibodies as polypeptides. Modern methods of bioorthogonal and biocompatible chemical modifications could make antibody functionalization more predictable and easier, without compromising the functions of the antibody. To explore this concept, we modified the well-known anti-epidermal growth factor receptor (EGFR) drug, cetuximab (Erbitux®), with 5-azido-2-nitro-benzoyl (ANB) modifications by optimization of an acylation protocol. We then show that the resulting ANB-cetuximab can be reliably modified with dyes (TAMRA and carboxyrhodamine) or a novel synthesized cyclooctyne modified biotin. The resulting dye- and biotin-modified cetuximabs were then tested across several assay platforms with several cell lines including U87, LN229, F98EGFR, F98WT and HEK293 cells. The assay platforms included fluorescence microscopy, FACS and biotin-avidin based immunoprecipitation methods. The modified antibody performs consistently in all of these assay platforms, reliably determining relative abundances of EGFR expression on EGFR expressing cells (LN229 and F98EGFR) and failing to cross react with weak to negative EGFR expressing cells (U87, F98WT and HEK293). The ease of achieving diverse and assay relevant functionalizations as well as the consequent rapid construction of highly correlated antigen expression data sets highlights the power of bioorthogonal and biocompatible methods to conjugate macromolecules. These data provide a proof of concept for a multifunctionalization strategy that leverages the biochemical versatility and antigen specificity of antibodies.

  5. Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

    PubMed Central

    Statham, Aaron L.; Robinson, Mark D.; Song, Jenny Z.; Coolen, Marcel W.; Stirzaker, Clare; Clark, Susan J.

    2012-01-01

    The complex relationship between DNA methylation, chromatin modification, and underlying DNA sequence is often difficult to unravel with existing technologies. Here, we describe a novel technique based on high-throughput sequencing of bisulfite-treated chromatin immunoprecipitated DNA (BisChIP-seq), which can directly interrogate genetic and epigenetic processes that occur in normal and diseased cells. Unlike most previous reports based on correlative techniques, we found using direct bisulfite sequencing of Polycomb H3K27me3-enriched DNA from normal and prostate cancer cells that DNA methylation and H3K27me3-marked histones are not always mutually exclusive, but can co-occur in a genomic region-dependent manner. Notably, in cancer, the co-dependency of marks is largely redistributed with an increase of the dual repressive marks at CpG islands and transcription start sites of silent genes. In contrast, there is a loss of DNA methylation in intergenic H3K27me3-marked regions. Allele-specific methylation status derived from the BisChIP-seq data clearly showed that both methylated and unmethylated alleles can simultaneously be associated with H3K27me3 histones, highlighting that DNA methylation status in these regions is not dependent on Polycomb chromatin status. BisChIP-seq is a novel approach that can be widely applied to directly interrogate the genomic relationship between allele-specific DNA methylation, histone modification, or other important epigenetic regulators. PMID:22466171

  6. Development of microLIPS (Luciferase Immunoprecipitation Systems): a novel microfluidic assay for rapid serum antibody detection

    NASA Astrophysics Data System (ADS)

    Chandrangsu, Matt; Burbelo, Peter D.; Iadarola, Michael J.; Smith, Paul D.; Morgan, Nicole Y.

    2012-06-01

    There is considerable interest in the development of rapid, point-of-care antibody detection for the diagnosis of infectious and auto-immune diseases. In this paper, we present work on the development of a self-contained microfluidic format for the Luciferase Immunoprecipitation Systems (LIPS) assay. Whereas the majority of immunoassays for antigen-specific antibodies employ either bacteria- or yeast-expressed proteins and require the use of secondary antibodies, the LIPS technique uses a fusion protein comprised of a Renilla luciferase reporter and the antigen of interest produced via mammalian cell culture, ensuring the addition of mammalian post-translational modifications. Patient serum is mixed with the fusion protein and passed over immobilized Protein A/G; after washing, the only remaining luciferase-tagged antigens are those retained by specific antibodies. These can be quantitatively measured using chemiluminescence upon the introduction of coelenterazine. The assay has been successfully employed for a wide variety of diseases in a microwell format. We report on a recent demonstration of rapid HSV-2 diagnosis with the LIPS assay in a microfluidic format, using one microliter of serum and obtaining results in under ten minutes. We will also discuss recent progress on two fronts, both aimed at the deployment of this technology in the field: first, simplifying assay operation through the automation of flow control using power-free means; and second, efforts to increase signal levels, primarily through strategies to increase antibody binding capacity, in order to move towards portable battery powered electronics.

  7. 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.

  8. 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

  9. Analysis of antibody responses to Hymenolepis nana infection in mice by the enzyme-linked immunosorbent assay and immunoprecipitation.

    PubMed

    Ito, A; Honey, R D; Scanlon, T; Lightowlers, M W; Rickard, M D

    1988-05-01

    Serum antibody responses in two strains of mice infected with embryonated eggs of Hymenolepis nana were analysed by the enzyme-linked immunosorbent assay (ELISA) and immunoprecipitation (IP) using sodium deoxycholate (DOC)-solubilized antigens prepared from embryonated eggs (eggs), mouse-derived cysticercoids (cysts) and adult tapeworms with immature segments only (adults). Highly susceptible dd mice, which harbour mature tapeworms for a long period (greater than 70 days), produced high levels of antibodies to all three different stages of H. nana. BALB/c mice, almost all of which expel adult tapeworms by 30 days after infection, produced high levels of antibody against egg antigens only. The high antibody titres to cyst and adult antigens in dd mice did not lead to expulsion of the worms. However, worms are rejected early in BALB/c mice when there is little or no detectable serum antibody. The antibody responses to eggs seen in BALB/c mice which had long since shed their adult worms were probably due to ingestion of eggs from faeces of other infected mice. Antibodies to eggs were not detected in BALB/c mice which were initially inoculated with eggs (day 0) and then treated with praziquantel on day 6 after the tissue phase of infection only. The different antibody responses to egg antigens and the other two antigens (cyst and adult) in BALB/c mice suggest a difference in antigen specificity between eggs and both cysts and adults. A major antigen component with Mr 32,000 appears to be specific to the egg (or oncosphere) stage of H. nana. Antibody to this major component of eggs was absorbed only with intact eggs, but not with intact cysts nor adults with immature segments only, so that the antigen appears to be on the surface of the oncosphere.

  10. 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.

  11. Functional analysis of neuronal microRNAs in Caenorhabditis elegans dauer formation by combinational genetics and Neuronal miRISC immunoprecipitation.

    PubMed

    Than, Minh T; Kudlow, Brian A; Han, Min

    2013-06-01

    Identifying the physiological functions of microRNAs (miRNAs) is often challenging because miRNAs commonly impact gene expression under specific physiological conditions through complex miRNA::mRNA interaction networks and in coordination with other means of gene regulation, such as transcriptional regulation and protein degradation. Such complexity creates difficulties in dissecting miRNA functions through traditional genetic methods using individual miRNA mutations. To investigate the physiological functions of miRNAs in neurons, we combined a genetic "enhancer" approach complemented by biochemical analysis of neuronal miRNA-induced silencing complexes (miRISCs) in C. elegans. Total miRNA function can be compromised by mutating one of the two GW182 proteins (AIN-1), an important component of miRISC. We found that combining an ain-1 mutation with a mutation in unc-3, a neuronal transcription factor, resulted in an inappropriate entrance into the stress-induced, alternative larval stage known as dauer, indicating a role of miRNAs in preventing aberrant dauer formation. Analysis of this genetic interaction suggests that neuronal miRNAs perform such a role partly by regulating endogenous cyclic guanosine monophosphate (cGMP) signaling, potentially influencing two other dauer-regulating pathways. Through tissue-specific immunoprecipitations of miRISC, we identified miRNAs and their likely target mRNAs within neuronal tissue. We verified the biological relevance of several of these miRNAs and found that many miRNAs likely regulate dauer formation through multiple dauer-related targets. Further analysis of target mRNAs suggests potential miRNA involvement in various neuronal processes, but the importance of these miRNA::mRNA interactions remains unclear. Finally, we found that neuronal genes may be more highly regulated by miRNAs than intestinal genes. Overall, our study identifies miRNAs and their targets, and a physiological function of these miRNAs in neurons. It

  12. Performance of Competitive and Indirect Enzyme-Linked Immunosorbent Assays, Gel Immunoprecipitation with Native Hapten Polysaccharide, and Standard Serological Tests in Diagnosis of Sheep Brucellosis

    PubMed Central

    Marín, C. M.; Moreno, E.; Moriyón, I.; Díaz, R.; Blasco, J. M.

    1999-01-01

    Competitive and standard enzyme-linked immunosorbent assays (ELISAs), rose bengal (RB), complement fixation, and agar gel immunoprecipitation with native hapten (AGID-NH) were compared by using sera from Brucella-free, Brucella melitensis-infected, and B. melitensis Rev1-vaccinated sheep. The most sensitive tests were indirect ELISA and RB, and the most specific tests were AGID-NH and competitive ELISA. We show that RB followed by AGID-NH is a simple and effective system for diagnosing sheep brucellosis. PMID:10066666

  13. 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

  14. Detection of anti-U3-RNP/fibrillarin IgG antibodies by line immunoblot assay has comparable clinical significance to immunoprecipitation testing in systemic sclerosis.

    PubMed

    Peterson, Lisa K; Jaskowski, Troy D; Mayes, Maureen D; Tebo, Anne E

    2016-04-01

    The aim of this study was to evaluate the performance and clinical relevance of a commercially available line immunoblot assay (LIA) for detecting anti-U3-RNP/fibrillarin (anti-U3-RNP), against immunoprecipitation (gold standard). This study involved a multi-ethnic cohort of 1000 American systemic sclerosis (SSc) patients and 50 healthy controls. Antinuclear antibodies and centromere antibodies were detected by indirect immunofluorescent antibody test, anti-topo I by immunodiffusion and anti-RNAP III by ELISA. The presence of anti-U3-RNP in select serum samples was detected by immunoprecipitation (IP) and LIA. By IP, U3-RNP antibody was detected in 75 (7.5 %) patients with SSc. Overall agreement between LIA and IP was very good (κ = 0.966). Analytic sensitivity and specificity of the U3-RNP LIA was 100 and 94.7 %, respectively. Clinical features associated with positivity for the anti-U3-RNP antibody include diffuse cutaneous SSc and increased prevalence of renal crisis, consistent with previous studies that used IP. Testing for U3-RNP antibodies is only performed by a small number of laboratories due to the complexity of both performance and interpretation of the IP. LIA is faster and less complex than IP. Excellent agreement between IP and LIA demonstrates that LIA is an acceptable and attractive alternative to IP for anti-U3-RNP detection.

  15. Binding of lac repressor-GFP fusion protein to lac operator sites inserted in the tobacco chloroplast genome examined by chromatin immunoprecipitation.

    PubMed

    Newell, Christine A; Gray, John C

    2010-08-01

    Chromatin immunoprecipitation (ChIP) has been used to detect binding of DNA-binding proteins to sites in nuclear and mitochondrial genomes. Here, we describe a method for detecting protein-binding sites on chloroplast DNA, using modifications to the nuclear ChIP procedures. The method was developed using the lac operator (lacO)/lac repressor (LacI) system from Escherichia coli. The lacO sequences were integrated into a single site between the rbcL and accD genes in tobacco plastid DNA and homoplasmic transplastomic plants were crossed with transgenic tobacco plants expressing a nuclear-encoded plastid-targeted GFP-LacI fusion protein. In the progeny, the GFP-LacI fusion protein could be visualized in living tissues using confocal microscopy, and was found to co-localize with plastid nucleoids. Isolated chloroplasts from the lacO/GFP-LacI plants were lysed, treated with micrococcal nuclease to digest the DNA to fragments of approximately 600 bp and incubated with antibodies to GFP and protein A-Sepharose. PCR analysis on DNA extracted from the immunoprecipitate demonstrated IPTG (isopropylthiogalactoside)-sensitive binding of GFP-LacI to lacO. Binding of GFP-LacI to endogenous sites in plastid DNA showing sequence similarity to lacO was also detected, but required reversible cross-linking with formaldehyde. This may provide a general method for the detection of binding sites on plastid DNA for specific proteins.

  16. Expression of Ia-like antigens by human vascular endothelial cells is inducible in vitro: demonstration by monoclonal antibody binding and immunoprecipitation.

    PubMed Central

    Pober, J S; Gimbrone, M A

    1982-01-01

    The expression of Ia-like antigens by cultured human endothelial cells has been investigated by means of monoclonal antibody binding to intact cells and by immunoprecipitation of radioiodinated membrane proteins. Primary growing and confluent cultures of human umbilical vein endothelium express little, if any, detectable Ia-like antigens under standard culture conditions. However, treatment of primary cultures with the lectin phytohemagglutinin induces the expression of Ia-like antigens. This action of the lectin uniformly affects all the endothelial cells in a culture, does not depend on cell division, and is associated with a cell shape change. The data presented in this report provide unequivocal serological and biochemical demonstration of Ia-like antigens on human vascular endothelial cells. The fact that the expression of Ia-like antigens by endothelium can be induced may have important implications for organ transplantation and for regulation of the immunological response. Images PMID:6815654

  17. Identifying Hazards

    EPA Pesticide Factsheets

    The federal government has established a system of labeling hazardous materials to help identify the type of material and threat posed. Summaries of information on over 300 chemicals are maintained in the Envirofacts Master Chemical Integrator.

  18. 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

  19. Transcriptome-wide Identification of RNA-binding Protein Binding Sites Using Photoactivatable-Ribonucleoside-Enhanced Crosslinking Immunoprecipitation (PAR-CLIP).

    PubMed

    Maatz, Henrike; Kolinski, Marcin; Hubner, Norbert; Landthaler, Markus

    2017-04-03

    RNA-binding proteins (RBPs) mediate important co- and post-transcriptional gene regulation by binding pre-mRNA in a sequence- and/or structure-specific manner. For a comprehensive understanding of RBP function, transcriptome-wide mapping of the RNA-binding sites is essential, and CLIP-seq methods have been developed to elucidate protein/RNA interactions at high resolution. CLIP-seq combines protein/RNA UV-crosslinking with immunoprecipitation (CLIP) followed by high-throughput sequencing of crosslinked RNA fragments. To overcome the limitations of low RNA-protein crosslinking efficiency in standard CLIP-seq, photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP) has been developed. Here, living cells or whole organisms are fed photo-activatable nucleoside analogs that are incorporated into nascent RNA transcripts before UV treatment. This allows greater crosslinking efficiency at comparable radiation doses for enhanced RNA recovery and separation of crosslinked target RNA fragments from background RNA degradation products. Moreover, it facilitates the generation of specific UV-induced mutations that mark the crosslinking nucleotide and allow transcriptome-wide identification of RBP binding sites at single-nucleotide resolution. © by 2017 John Wiley & Sons, Inc.

  20. 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

  1. Study of Protein Phosphatase 2A (PP2A) Activity in LPS-Induced Tolerance Using Fluorescence-Based and Immunoprecipitation-Aided Methodology.

    PubMed

    Sun, Lei; Ii, Adlai L Pappy; Pham, Tiffany T; Shanley, Thomas P

    2015-06-29

    Protein phosphatase 2A (PP2A) is one of the most abundant intracellular serine/threonine (Ser/Thr) phosphatases accounting for 1% of the total cellular protein content. PP2A is comprised of a heterodimeric core enzyme and a substrate-specific regulatory subunit. Potentially, at least seventy different compositions of PP2A exist because of variable regulatory subunit binding that accounts for various activity modulating numerous cell functions. Due to the constitutive phosphatase activity present inside cells, a sensitive assay is required to detect the changes of PP2A activity under various experimental conditions. We optimized a fluorescence assay (DIFMU assay) by combining it with prior anti-PP2A immunoprecipitation to quantify PP2A-specific phosphatase activity. It is also known that prior exposure to lipopolysaccharides (LPS) induces "immune tolerance" of the cells to subsequent stimulation. Herein we report that PP2A activity is upregulated in tolerized peritoneal macrophages, corresponding to decreased TNF-α secretion upon second LPS stimulation. We further examined the role of PP2A in the tolerance effect by using PP2ACαl°xl°x;lyM-Cre conditional knockout macrophages. We found that PP2A phosphatase activity cannot be further increased by tolerance. TNF-α secretion from tolerized PP2ACαl°xl°x;lyM-Cre macrophages is higher than tolerized control macrophages. Furthermore, we showed that the increased TNF-α secretion may be due to an epigenetic transcriptionally active signature on the promoter of TNF-α gene rather than regulation of the NFκB/IκB signaling pathway. These results suggest a role for increased PP2A activity in the regulation of immune tolerance.

  2. Occurrence and significance of antibody to liver-specific membrane lipoprotein by double-antibody immunoprecipitation method in sera of patients with acute and chronic liver diseases.

    PubMed

    Kakumu, S; Arakawa, Y; Goji, H; Kashio, T; Yata, K

    1979-04-01

    A double-antibody immunoprecipitation method was developed for detecting antibody to liver-specific membrane lipoprotein (anti-LSP) in sera of patients with various liver diseases and primary nonhepatic autoimmune diseases. Liver-specific membrane lipoprotein prepared from normal rat livers was labeled with 125I (chloramine-T) and monospecific antibody raised in rabbits. Cross-reactivity and absorption studies demonstrated that the assay used was highly specific. The frequency and titer of anti-LSP were similar for HBsAg-positive and -negative patients with both acute and chronic liver diseases. Patients with chronic active hepatitis had the highest frequenzy (25 of 44 cases, 57%) when compared with those with chronic persistent hepatitis (5 of 23 cases, 22%) and nonalcoholic cirrhosis (8 of 21 cases, 38%). Of the anti-LSP positive cases, the mean titer in patients with chronic active hepatitis tended to be the highest. In patients recovered from acute viral hepatitis, anti-LSP was transiently positive (7 of 20 cases, 35%) in the acute phase. In those who progressed to chronic hepatitis, a late rise as well as an early rise occurred in 6 of 10 patients before the diagnosis was made. Two of 6 patients with primary biliary cirrhosis had anti-LSP, but none of 41 patients with other nonviral liver diseases and none of 60 patients with primary nonhepatic autoimmune diseases. These data indicate that an autoimmune reaction directed against LSP can be initiated during the acute phase of viral hepatitis and it may persist in chronic hepatitis in both HBsAg-positive and -negative cases.

  3. Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.

    PubMed

    Peach, Sally E; Rudomin, Emily L; Udeshi, Namrata D; Carr, Steven A; Jaffe, Jacob D

    2012-05-01

    The defining step in most chromatin immunoprecipitation (ChIP) assays is the use of an antibody to enrich for a particular protein or histone modification state associated with segments of chromatin. The specificity of the antibody is critical to the interpretation of the experiment, yet this property is rarely reported. Here, we present a quantitative method using mass spectrometry to characterize the specificity of key histone H3 modification-targeting antibodies that have previously been used to characterize the "histone code." We further extend the use of these antibody reagents to the observation of long range correlations among disparate histone modifications. Using purified human histones representing the mixture of chromatin states present in living cells, we were able to quantify the degree of target enrichment and the specificity of several commonly used, commercially available ChIP grade antibodies. We found significant differences in enrichment efficiency among various reagents directed against four frequently studied chromatin marks: H3K4me2, H3K4me3, H3K9me3, and H3K27me3. For some antibodies, we also detected significant off target enrichment of alternate modifications at the same site (i.e., enrichment of H3K4me2 by an antibody directed against H3K4me3). Through cluster analysis, we were able to recognize patterns of co-enrichment of marks at different sites on the same histone protein. Surprisingly, these co-enrichments corresponded well to "canonical" chromatin states that are exemplary of activated and repressed regions of chromatin. Altogether, our findings suggest that 1) the results of ChIP experiments need to be evaluated with caution given the potential for cross-reactivity of the commonly used histone modification recognizing antibodies, 2) multiple marks with consistent biological interpretation exist on the same histone protein molecule, and 3) some components of the histone code may be transduced on single proteins in living cells.

  4. 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).

  5. Transformation-Related Antigens Identified by Monoclonal Antibodies

    NASA Astrophysics Data System (ADS)

    Strand, Mette

    1980-06-01

    Tumor-cell proteins that were antigenic in a syngeneic animal were identified by immunoprecipitation with monoclonal antibodies. Spleen cells of BALB/c mice immunized with plasma membranes of Kirsten RNA sarcoma virus-transformed BALB/3T3 cells were fused with NS-l myeloma cells. Antibodies secreted into the culture fluid from these hybridomas were distinguished by their reactivity against proteins of different target cells. A total of 191 cultures were established; 143 produced antibodies that bound to BALB/3T3 cells transformed by the RNA sarcoma virus, of which antibodies from 82 bound to BALB/3T3 transformed with simian virus 40, and antibodies from 56 bound to BALB/3T3 cells. Thus, more than 50% of the cultures produced antibodies that possibly were specific to antigens of the transformed cell. Twenty different hybridomas have been cloned, and antibodies from eight of these were found to immunoprecipitate five different proteins. A protein of approximately 32,000 daltons was precipitated from BALB/3T3 cells transformed by the RNA sarcoma virus, simian virus 40, or methylcholanthrene but not from untransformed BALB/3T3 cells. A protein of about 300,000 daltons was precipitated from all four cell lines; precipitation was enhanced in the viral transformed cells. Proteins of approximately 57,000, 54,000, and 8500 daltons were immunoprecipitated from all four cell lines.

  6. Tyrosine phosphorylation of P-selectin in intact platelets and in a disulphide-linked complex with immunoprecipitated pp60c-src.

    PubMed Central

    Modderman, P W; von dem Borne, A E; Sonnenberg, A

    1994-01-01

    P-selectin is a 140 kDa membrane glycoprotein found in secretory granules of platelets and endothelial cells where it is rapidly translocated to the plasma membrane upon cell activation. It then functions as a receptor for various types of leucocytes. Metabolic labelling of resting platelets with 32Pi showed that P-selectin is primarily phosphorylated on serine residues, although some tyrosine phosphorylation was observed as well. However, tyrosine phosphorylation of P-selectin was greatly stimulated by treatment with the permeating phosphatase inhibitor, pervanadate. When P-selectin immunoprecipitates were incubated with [gamma-32P]ATP (in vitro kinase assay), a fraction of P-selectin was phosphorylated on its tyrosine residues by a co-precipitated kinase. P-selectin phosphorylated in vitro co-migrated with 140 kDa surface-labelled 125I-P-selectin during SDS/PAGE under reducing conditions. Under non-reducing conditions, however, phosphorylated P-selectin was disulphide-linked to unknown protein(s) in a 205 kDa complex. In vitro kinase assays of the most abundant platelet tyrosine kinase, pp60c-src, demonstrated the presence of similar 140 and 205 kDa phosphorylated proteins in SDS/PAGE under reducing and non-reducing conditions respectively. Extraction and reprecipitation studies with proteins phosphorylated in vitro indicated that P-selectin and pp60c-src form a 205 kDa 1:1 disulphide-linked complex. In the complex, pp60c-src autophosphorylation is inhibited and P-selectin is phosphorylated on tyrosine residues. As protein disulphides in the cytoplasm of intact cells are extremely rare, our results suggest that P-selectin and pp60c-src, which co-localize in platelet dense granules, may be non-covalently associated and spontaneously form disulphide bridges during lysis. In addition, the observed tyrosine phosphorylation of P-selectin in intact platelets suggests that its function might be regulated by phosphorylation by pp60c-src. Images Figure 1 Figure 2 Figure 3

  7. Quantitative Assessment of Chromatin Immunoprecipitation Grade Antibodies Directed against Histone Modifications Reveals Patterns of Co-occurring Marks on Histone Protein Molecules*

    PubMed Central

    Peach, Sally E.; Rudomin, Emily L.; Udeshi, Namrata D.; Carr, Steven A.; Jaffe, Jacob D.

    2012-01-01

    The defining step in most chromatin immunoprecipitation (ChIP) assays is the use of an antibody to enrich for a particular protein or histone modification state associated with segments of chromatin. The specificity of the antibody is critical to the interpretation of the experiment, yet this property is rarely reported. Here, we present a quantitative method using mass spectrometry to characterize the specificity of key histone H3 modification-targeting antibodies that have previously been used to characterize the “histone code.” We further extend the use of these antibody reagents to the observation of long range correlations among disparate histone modifications. Using purified human histones representing the mixture of chromatin states present in living cells, we were able to quantify the degree of target enrichment and the specificity of several commonly used, commercially available ChIP grade antibodies. We found significant differences in enrichment efficiency among various reagents directed against four frequently studied chromatin marks: H3K4me2, H3K4me3, H3K9me3, and H3K27me3. For some antibodies, we also detected significant off target enrichment of alternate modifications at the same site (i.e., enrichment of H3K4me2 by an antibody directed against H3K4me3). Through cluster analysis, we were able to recognize patterns of co-enrichment of marks at different sites on the same histone protein. Surprisingly, these co-enrichments corresponded well to “canonical” chromatin states that are exemplary of activated and repressed regions of chromatin. Altogether, our findings suggest that 1) the results of ChIP experiments need to be evaluated with caution given the potential for cross-reactivity of the commonly used histone modification recognizing antibodies, 2) multiple marks with consistent biological interpretation exist on the same histone protein molecule, and 3) some components of the histone code may be transduced on single proteins in living

  8. Dataset of integrin-linked kinase protein: Protein interactions in cardiomyocytes identified by mass spectrometry.

    PubMed

    Traister, Alexandra; Lu, Mingliang; Coles, John G; Maynes, Jason T

    2016-06-01

    Using hearts from mice overexpressing integrin linked kinase (ILK) behind the cardiac specific promoter αMHC, we have performed immunoprecipitation and mass spectrometry to identify novel ILK protein:protein interactions that regulate cardiomyocyte activity and calcium flux. Integrin linked kinase complexes were captured from mouse heart lysates using a commercial antibody, with subsequent liquid chromatography tandem mass spectral analysis. Interacting partners were identified using the MASCOT server, and important interactions verified using reverse immunoprecipitation and mass spectrometry. All ILK interacting proteins were identified in a non-biased manner, and are stored in the ProteomeXchange Consortium via the PRIDE partner repository (reference ID PRIDE: PXD001053). The functional role of identified ILK interactions in cardiomyocyte function and arrhythmia were subsequently confirmed in human iPSC-cardiomyocytes.

  9. 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

  10. Constitutive oligomerization of human D2 dopamine receptors expressed in Spodoptera frugiperda 9 (Sf9) and in HEK293 cells. Analysis using co-immunoprecipitation and time-resolved fluorescence resonance energy transfer.

    PubMed

    Gazi, Lucien; López-Giménez, Juan F; Rüdiger, Martin P; Strange, Philip G

    2003-10-01

    Human D2Long (D2L) and D2Short (D2S) dopamine receptor isoforms were modified at their N-terminus by the addition of a human immunodeficiency virus (HIV) or a FLAG epitope tag. The receptors were then expressed in Spodoptera frugiperda 9 (Sf9) cells using the baculovirus system, and their oligomerization was investigated by means of co-immunoprecipitation and time-resolved fluorescence resonance energy transfer (FRET). [3H]Spiperone labelled D2 receptors in membranes prepared from Sf9 cells expressing epitope-tagged D2L or D2S receptors, with a pKd value of approximately 10. Co-immunoprecipitation using antibodies specific for the tags showed constitutive homo-oligomerization of D2L and D2S receptors in Sf9 cells. When the FLAG-tagged D2S and HIV-tagged D2L receptors were co-expressed, co-immunoprecipitation showed that the two isoforms can also form hetero-oligomers in Sf9 cells. Time-resolved FRET with europium and XL665-labelled antibodies was applied to whole Sf9 cells and to membranes from Sf9 cells expressing epitope-tagged D2 receptors. In both cases, constitutive homo-oligomers were revealed for D2L and D2S isoforms. Time-resolved FRET also revealed constitutive homo-oligomers in HEK293 cells expressing FLAG-tagged D2S receptors. The D2 receptor ligands dopamine, R-(-)propylnorapomorphine, and raclopride did not affect oligomerization of D2L and D2S in Sf9 and HEK293 cells. Human D2 dopamine receptors can therefore form constitutive oligomers in Sf9 cells and in HEK293 cells that can be detected by different approaches, and D2 oligomerization in these cells is not regulated by ligands.

  11. Using Quantitative Seroproteomics to Identify Antibody Biomarkers in Pancreatic Cancer

    PubMed Central

    Jhaveri, Darshil T.; Kim, Min-Sik; Thompson, Elizabeth D.; Huang, Lanqing; Sharma, Rajni; Klein, Alison P.; Zheng, Lei; Le, Dung T.; Laheru, Daniel A.; Pandey, Akhilesh; Jaffee, Elizabeth M.; Anders, Robert A.

    2016-01-01

    Pancreatic cancer is the fourth leading cause of cancer deaths in the US. Less than 6% of patients survive beyond the fifth year due to inadequate early diagnostics and ineffective treatment options. Our lab has developed an allogeneic, granulocyte-macrophage colony-stimulating factor (GM-CSF) secreting pancreatic cancer vaccine (GVAX) that has been tested in phase II clinical trials. Here, we employed a novel Serum Antibodies based SILAC-Immunoprecipitation (SASI) approach to identify proteins that elicit an antibody response after vaccination. The SASI approach utilizes immunoprecipitation with patient derived antibodies that is coupled to quantitative stable isotope–labeled amino acids in cell culture (SILAC). Using mass spectrometric analysis, we identified more than 150 different proteins that induce an antibody response after vaccination. The regulatory subunit 12A of protein phosphatase 1 (MYPT1 or PPP1R12A), regulatory subunit 8 of the 26S proteasome (PSMC5), and the transferrin receptor (TFRC) were shown to be pancreatic cancer associated antigens recognized by post-vaccination antibodies in the sera of patients with favorable disease-free survival after GVAX therapy. We further interrogated these proteins in over 80 GVAX-treated patients’ pancreases and uniformly found a significant increase in the expression of MYPT1, PSMC5, and TFRC in neoplastic compared to non-neoplastic pancreatic ductal epithelium. We show that the novel SASI approach can identify antibody targets specifically expressed in patients with improved disease-free survival after cancer vaccine therapy. These targets need further validation to be considered as possible pancreatic cancer biomarkers. PMID:26842750

  12. Gang Identifiers and Terminology.

    ERIC Educational Resources Information Center

    Cantrell, Mary Lynn

    1992-01-01

    Provides lists of gang identifiers and terminology. Suggests that, to find out names and associated identifiers of local gangs, readers should talk to their local police. Included in listing are descriptions of gang-related symbols, physical signals, graffiti, slogans, right-left rules, colors, clothing, jewelry, hair styles, and fingernails. Also…

  13. 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

  14. Human Argonaute 2 Is Tethered to Ribosomal RNA through MicroRNA Interactions.

    PubMed

    Atwood, Blake L; Woolnough, Jessica L; Lefevre, Gaelle M; Saint Just Ribeiro, Mariana; Felsenfeld, Gary; Giles, Keith E

    2016-08-19

    The primary role of the RNAi machinery is to promote mRNA degradation within the cytoplasm in a microRNA-dependent manner. However, both Dicer and the Argonaute protein family have expanded roles in gene regulation within the nucleus. To further our understanding of this role, we have identified chromatin binding sites for AGO2 throughout the 45S region of the human rRNA gene. The location of these sites was mirrored by the positions of AGO2 cross-linking sites identified via PAR-CLIP-seq. AGO2 binding to the rRNA within the nucleus was confirmed by RNA immunoprecipitation and quantitative-PCR. To explore a possible mechanism by which AGO2 could be recruited to the rRNA, we identified 1174 regions within the 45S rRNA transcript that have the ability to form a perfect duplex with position 2-6 (seed sequence) of each microRNA expressed in HEK293T cells. Of these potential AGO2 binding sites, 479 occurred within experimentally verified AGO2-rRNA cross-linking sites. The ability of AGO2 to cross-link to rRNA was almost completely lost in a DICER knock-out cell line. The transfection of miR-92a-2-3p into the noDICE cell line facilitated AGO2 cross-linking at a region of the rRNA that has a perfect seed match at positions 3-8, including a single G-U base pair. Knockdown of AGO2 within HEK293T cells causes a slight, but statistically significant increase in the overall rRNA synthesis rate but did not impact the ratio of processing intermediates or the recruitment of the Pol I transcription factor UBTF.

  15. CLIP Identifies Nova-Regulated RNA Networks in the Brain

    NASA Astrophysics Data System (ADS)

    Ule, Jernej; Jensen, Kirk B.; Ruggiu, Matteo; Mele, Aldo; Ule, Aljaž; Darnell, Robert B.

    2003-11-01

    Nova proteins are neuron-specific antigens targeted in paraneoplastic opsoclonus myoclonus ataxia (POMA), an autoimmune neurologic disease characterized by abnormal motor inhibition. Nova proteins regulate neuronal pre-messenger RNA splicing by directly binding to RNA. To identify Nova RNA targets, we developed a method to purify protein-RNA complexes from mouse brain with the use of ultraviolet cross-linking and immunoprecipitation (CLIP). Thirty-four transcripts were identified multiple times by Nova CLIP. Three-quarters of these encode proteins that function at the neuronal synapse, and one-third are involved in neuronal inhibition. Splicing targets confirmed in Nova-/- mice include c-Jun N-terminal kinase 2, neogenin, and gephyrin; the latter encodes a protein that clusters inhibitory γ-aminobutyric acid and glycine receptors, two previously identified Nova splicing targets. Thus, CLIP reveals that Nova coordinately regulates a biologically coherent set of RNAs encoding multiple components of the inhibitory synapse, an observation that may relate to the cause of abnormal motor inhibition in POMA.

  16. A large-scale functional screen identifies Nova1 and Ncoa3 as regulators of neuronal miRNA function.

    PubMed

    Störchel, Peter H; Thümmler, Juliane; Siegel, Gabriele; Aksoy-Aksel, Ayla; Zampa, Federico; Sumer, Simon; Schratt, Gerhard

    2015-09-02

    MicroRNAs (miRNAs) are important regulators of neuronal development, network connectivity, and synaptic plasticity. While many neuronal miRNAs were previously shown to modulate neuronal morphogenesis, little is known regarding the regulation of miRNA function. In a large-scale functional screen, we identified two novel regulators of neuronal miRNA function, Nova1 and Ncoa3. Both proteins are expressed in the nucleus and the cytoplasm of developing hippocampal neurons. We found that Nova1 and Ncoa3 stimulate miRNA function by different mechanisms that converge on Argonaute (Ago) proteins, core components of the miRNA-induced silencing complex (miRISC). While Nova1 physically interacts with Ago proteins, Ncoa3 selectively promotes the expression of Ago2 at the transcriptional level. We further show that Ncoa3 regulates dendritic complexity and dendritic spine maturation of hippocampal neurons in a miRNA-dependent fashion. Importantly, both the loss of miRNA activity and increased dendrite complexity upon Ncoa3 knockdown were rescued by Ago2 overexpression. Together, we uncovered two novel factors that control neuronal miRISC function at the level of Ago proteins, with possible implications for the regulation of synapse development and plasticity.

  17. Identifying learning styles.

    PubMed

    Hughes, Grace

    2016-12-14

    What was the nature of the CPD activity, practice-related feedback and/or event and/or experience in your practice? The article explored different learning styles and outlined some of the models that can be used to identify them. It discussed the limitations of these models, indicating that although they can be helpful in identifying a student's preferred learning style, this is not 'fixed' and might change over time. Learning is also influenced by other factors, such as culture and age.

  18. Metal alloy identifier

    DOEpatents

    Riley, William D.; Brown, Jr., Robert D.

    1987-01-01

    To identify the composition of a metal alloy, sparks generated from the alloy are optically observed and spectrographically analyzed. The spectrographic data, in the form of a full-spectrum plot of intensity versus wavelength, provide the "signature" of the metal alloy. This signature can be compared with similar plots for alloys of known composition to establish the unknown composition by a positive match with a known alloy. An alternative method is to form intensity ratios for pairs of predetermined wavelengths within the observed spectrum and to then compare the values of such ratios with similar values for known alloy compositions, thereby to positively identify the unknown alloy composition.

  19. Luminescent Immunoprecipitation System (LIPS) for Detection of Autoantibodies Against ATP4A and ATP4B Subunits of Gastric Proton Pump H+,K+-ATPase in Atrophic Body Gastritis Patients

    PubMed Central

    Lahner, Edith; Brigatti, Cristina; Marzinotto, Ilaria; Carabotti, Marilia; Scalese, Giulia; Davidson, Howard W; Wenzlau, Janet M; Bosi, Emanuele; Piemonti, Lorenzo; Annibale, Bruno; Lampasona, Vito

    2017-01-01

    Objectives: Circulating autoantibodies targeting the H+/K+-ATPase proton pump of gastric parietal cells are considered markers of autoimmune gastritis, whose diagnostic accuracy in atrophic body gastritis, the pathological lesion of autoimmune gastritis, remains unknown. This study aimed to assess autoantibodies against ATP4A and ATP4B subunits of parietal cells H+, K+-ATPase in atrophic body gastritis patients and controls. Methods: One-hundred and four cases with atrophic body gastritis and 205 controls were assessed for serological autoantibodies specific for ATP4A or ATP4B subunits using luminescent immunoprecipitation system (LIPS). Recombinant luciferase-reporter-fused-antigens were expressed by in vitro transcription-translation (ATP4A) or after transfection in Expi293F cells (ATP4B), incubated with test sera, and immune complexes recovered using protein-A-sepharose. LIPS assays were compared with a commercial enzyme immunoassay (EIA) for parietal cell autoantibodies. Results: ATP4A and ATP4B autoantibody titers were higher in cases compared to controls (P<0.0001). The area under the receiver-operating characteristic curve was 0.98 (95% CI 0.965–0.996) for ATP4A, and 0.99 (95% CI 0.979–1.000) for ATP4B, both higher as compared with that of EIA: 0.86 (95% CI 0.809–0.896), P<0.0001. Sensitivity-specificity were 100–89% for ATP4A and 100–90% for ATP4B assay. Compared with LIPS, EIA for parietal cell autoantibodies showed a lower sensitivity (72%, P<0.0001) at a similar specificity (92%, P=0.558). Conclusions: Positivity to both, ATP4A and ATP4B autoantibodies is closely associated with atrophic body gastritis. Both assays had the highest sensitivity, at the cost of diagnostic accuracy (89 and 90% specificity), outperforming traditional EIA. Once validated, these LIPS assays should be valuable screening tools for detecting biomarkers of damaged atrophic oxyntic mucosa. PMID:28102858

  20. Identifying Early School Leaving

    ERIC Educational Resources Information Center

    Poole, Millicent E.

    1978-01-01

    Using a matched sample of students who stay in school and those who drop out, or leave early, an attempt was made, via multiple discriminant analysis, to identify the significant characteristics which distinguish "drop outs" from their peers who remain at school. Results indicated that both types of students have similar value orientations and…

  1. Identifying Nursing's Future Leaders.

    ERIC Educational Resources Information Center

    Gunning, Carolyn S.; Hawken, Patty L.

    1990-01-01

    A study determined that encouraging and supporting students in professional activities while they were still in school would lead those students to participate in professional nursing organizations after they graduated. Organized nursing needs to identify the factors that influence nurses to join organizations and concentrate on these factors to…

  2. Identifying Marine Phytoplankton

    NASA Astrophysics Data System (ADS)

    Hargraves, Paul E.

    Until recently, anyone who needed to accurately identify marine phytoplankton had one of four choices: use the outdated Englishlanguage volumes by E. E. Cupp and N. I. Hendey plus the more recent book by J. Dodge, acquire a working knowledge of German and use the old volumes by Schiller and Hustedt, spend huge amounts of time in an exceedingly well-equipped marine science library trying in vain to keep up with the rapidly evolving field of phytoplankton systematics and taxonomy, or track down one of the rarest of endangered species—a phytoplankton taxonomist—and beg for help.To these unfortunate choices is added one considerably more hopeful: Identifying Marine Phytoplankton. This volume, which has seven contributing authors, contains most of the taxonomic groups that make up the planktonic autotrophs and some heterotrophs of the seas, coasts, and estuaries of the world (missing are cyanobacteria and some of the picoplankton groups).

  3. On identified predictive control

    NASA Technical Reports Server (NTRS)

    Bialasiewicz, Jan T.

    1993-01-01

    Self-tuning control algorithms are potential successors to manually tuned PID controllers traditionally used in process control applications. A very attractive design method for self-tuning controllers, which has been developed over recent years, is the long-range predictive control (LRPC). The success of LRPC is due to its effectiveness with plants of unknown order and dead-time which may be simultaneously nonminimum phase and unstable or have multiple lightly damped poles (as in the case of flexible structures or flexible robot arms). LRPC is a receding horizon strategy and can be, in general terms, summarized as follows. Using assumed long-range (or multi-step) cost function the optimal control law is found in terms of unknown parameters of the predictor model of the process, current input-output sequence, and future reference signal sequence. The common approach is to assume that the input-output process model is known or separately identified and then to find the parameters of the predictor model. Once these are known, the optimal control law determines control signal at the current time t which is applied at the process input and the whole procedure is repeated at the next time instant. Most of the recent research in this field is apparently centered around the LRPC formulation developed by Clarke et al., known as generalized predictive control (GPC). GPC uses ARIMAX/CARIMA model of the process in its input-output formulation. In this paper, the GPC formulation is used but the process predictor model is derived from the state space formulation of the ARIMAX model and is directly identified over the receding horizon, i.e., using current input-output sequence. The underlying technique in the design of identified predictive control (IPC) algorithm is the identification algorithm of observer/Kalman filter Markov parameters developed by Juang et al. at NASA Langley Research Center and successfully applied to identification of flexible structures.

  4. Identifying Distant AGNs

    NASA Astrophysics Data System (ADS)

    Trouille, Laura; Barger, Amy; Tremonti, Christy

    2014-07-01

    The Baldwin, Phillips, and Terlevich emission-line ratio diagnostic ([OIII]/Hβ versus [NII]/Hα, hereafter BPT diagram) efficiently separates galaxies whose signal is dominated by star formation (BPT-SF) from those dominated by AGN activity (BPT-AGN). Yet the BPT diagram is limited to z<0.5, the redshift at which [NII]λ6584 leaves the optical spectral window. Using the Sloan Digital Sky Survey (SDSS), we construct a new diagnostic, or TBT diagram, that is based on rest-frame g-z color, [NeIII]λ3869, and [OII]λλ3726+3729 and can be used for galaxies out to z<1.4. The TBT diagram identifies 98.7% of the SDSS BPT-AGN as TBT-AGN and 97% of the SDSS BPT-SF as TBT-SF. Furthermore, it identifies 97% of the OPTX Chandra X-ray selected AGNs as TBT-AGN. This is in contrast to the BPT diagram, which misidentifies 20% of X-ray selected AGNs as BPT-SF.

  5. List identifies threatened ecosystems

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-09-01

    The International Union for Conservation of Nature (IUCN) announced on 9 September that it will develop a new Red List of Ecosystems that will identify which ecosystems are vulnerable or endangered. The list, which is modeled on the group's Red List of Threatened Species™, could help to guide conservation activities and influence policy processes such as the Convention on Biological Diversity, according to the group. “We will assess the status of marine, terrestrial, freshwater, and subterranean ecosystems at local, regional, and global levels,” stated Jon Paul Rodriguez, leader of IUCN's Ecosystems Red List Thematic Group. “The assessment can then form the basis for concerted implementation action so that we can manage them sustainably if their risk of collapse is low or restore them if they are threatened and then monitor their recovery.”

  6. Identifying potential academic leaders

    PubMed Central

    White, David; Krueger, Paul; Meaney, Christopher; Antao, Viola; Kim, Florence; Kwong, Jeffrey C.

    2016-01-01

    Objective To identify variables associated with willingness to undertake leadership roles among academic family medicine faculty. Design Web-based survey. Bivariate and multivariable analyses (logistic regression) were used to identify variables associated with willingness to undertake leadership roles. Setting Department of Family and Community Medicine at the University of Toronto in Ontario. Participants A total of 687 faculty members. Main outcome measures Variables related to respondents’ willingness to take on various academic leadership roles. Results Of all 1029 faculty members invited to participate in the survey, 687 (66.8%) members responded. Of the respondents, 596 (86.8%) indicated their level of willingness to take on various academic leadership roles. Multivariable analysis revealed that the predictors associated with willingness to take on leadership roles were as follows: pursuit of professional development opportunities (odds ratio [OR] 3.79, 95% CI 2.29 to 6.27); currently holding at least 1 leadership role (OR 5.37, 95% CI 3.38 to 8.53); a history of leadership training (OR 1.86, 95% CI 1.25 to 2.78); the perception that mentorship is important for one’s current role (OR 2.25, 95% CI 1.40 to 3.60); and younger age (OR 0.97, 95% CI 0.95 to 0.99). Conclusion Willingness to undertake new or additional leadership roles was associated with 2 variables related to leadership experiences, 2 variables related to perceptions of mentorship and professional development, and 1 demographic variable (younger age). Interventions that support opportunities in these areas might expand the pool and strengthen the academic leadership potential of faculty members. PMID:27331226

  7. Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.

    PubMed

    Sugimoto, Yoichiro; Chakrabarti, Anob M; Luscombe, Nicholas M; Ule, Jernej

    2017-03-01

    The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing. Mapping of the sequenced arms to a reference transcriptome identifies the exact locations of duplexes. hiCLIP data can directly identify all types of RNA duplexes bound by RBPs, including those that are challenging to predict computationally, such as intermolecular and long-range intramolecular duplexes. Moreover, the use of an adaptor that links the two arms of the RNA duplex permits hiCLIP to unambiguously identify the duplexes. Here we describe in detail the procedure for a hiCLIP experiment and the subsequent streamlined data analysis with an R package, 'hiclipr' (https://github.com/luslab/hiclipr/). Preparation of the library for high-throughput DNA sequencing takes ∼7 d and the basic bioinformatic pipeline takes 1 d.

  8. Monoclonal antibody OKB7, which identifies the 14OKd complement receptor type 2 (CR/sub 2/), also identifies a 72Kd secreted fragment of CR/sub 2/ that contains the C3d-binding site

    SciTech Connect

    Myones, B.L.; Ross, G.D.

    1986-03-05

    CR/sub 2/ is a 140-145Kd glycoprotein expressed on B lymphocytes which binds both C3d and Epstein-Barr virus (EBV). OKB7, an IgG/sub 2a/ monoclonal antibody to CR/sub 2/, blocks C3d and EBV binding, while HB-5, another monoclonal IgG/sub 2a/ anti-CR/sub 2/, does not. A 72Kd C3d-binding glycoprotein (gp72), isolated from Raji cell media, was previously thought to be CR/sub 2/ because a polyclonal rabbit anti-gp72 inhibited EC3d rosettes. ELISA assay demonstrated that OKB7, but not HB-5, bound to purified gp72 fixed to microtiter wells. Insoluble and soluble gp72 blocked Raji cell uptake of /sup 125/I-labeled OKB7, but not labeled anti-B2 or HB-5. Rabbit anti-gp72 immunoprecipitated bands at 140Kd and 72Kd from /sup 125/I-labelled and solubilized B cell membranes. Culture media from Raji cells grown in the presence /sup 3/H-labeled amino acids was sequentially immunoprecipitated by irrelevant antibody, OKB7, and HB-5. A single 72Kd radiolabeled band was demonstrated only with OKB7, and this was identical to that produced by the immunoprecipitation of /sup 125/I-labeled gp72 with rabbit anti-gp72. Thus, OKB7, which identifies the 140Kd CR/sub 2/ molecule, also identifies a 72Kd shed fragment of CR/sub 2/ isolated from Raji cell media, which contains the C3d-binding site.

  9. Blood pressure loci identified with a gene-centric array.

    PubMed

    Johnson, Toby; Gaunt, Tom R; Newhouse, Stephen J; Padmanabhan, Sandosh; Tomaszewski, Maciej; Kumari, Meena; Morris, Richard W; Tzoulaki, Ioanna; O'Brien, Eoin T; Poulter, Neil R; Sever, Peter; Shields, Denis C; Thom, Simon; Wannamethee, Sasiwarang G; Whincup, Peter H; Brown, Morris J; Connell, John M; Dobson, Richard J; Howard, Philip J; Mein, Charles A; Onipinla, Abiodun; Shaw-Hawkins, Sue; Zhang, Yun; Davey Smith, George; Day, Ian N M; Lawlor, Debbie A; Goodall, Alison H; Fowkes, F Gerald; Abecasis, Gonçalo R; Elliott, Paul; Gateva, Vesela; Braund, Peter S; Burton, Paul R; Nelson, Christopher P; Tobin, Martin D; van der Harst, Pim; Glorioso, Nicola; Neuvrith, Hani; Salvi, Erika; Staessen, Jan A; Stucchi, Andrea; Devos, Nabila; Jeunemaitre, Xavier; Plouin, Pierre-François; Tichet, Jean; Juhanson, Peeter; Org, Elin; Putku, Margus; Sõber, Siim; Veldre, Gudrun; Viigimaa, Margus; Levinsson, Anna; Rosengren, Annika; Thelle, Dag S; Hastie, Claire E; Hedner, Thomas; Lee, Wai K; Melander, Olle; Wahlstrand, Björn; Hardy, Rebecca; Wong, Andrew; Cooper, Jackie A; Palmen, Jutta; Chen, Li; Stewart, Alexandre F R; Wells, George A; Westra, Harm-Jan; Wolfs, Marcel G M; Clarke, Robert; Franzosi, Maria Grazia; Goel, Anuj; Hamsten, Anders; Lathrop, Mark; Peden, John F; Seedorf, Udo; Watkins, Hugh; Ouwehand, Willem H; Sambrook, Jennifer; Stephens, Jonathan; Casas, Juan-Pablo; Drenos, Fotios; Holmes, Michael V; Kivimaki, Mika; Shah, Sonia; Shah, Tina; Talmud, Philippa J; Whittaker, John; Wallace, Chris; Delles, Christian; Laan, Maris; Kuh, Diana; Humphries, Steve E; Nyberg, Fredrik; Cusi, Daniele; Roberts, Robert; Newton-Cheh, Christopher; Franke, Lude; Stanton, Alice V; Dominiczak, Anna F; Farrall, Martin; Hingorani, Aroon D; Samani, Nilesh J; Caulfield, Mark J; Munroe, Patricia B

    2011-12-09

    Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies.

  10. An Improved Method for Identifying Specific DNA-Protein-Binding Sites In Vitro.

    PubMed

    Wang, Liangyan; Lu, Huizhi; Wang, Yunguang; Yang, Su; Xu, Hong; Cheng, Kaiying; Zhao, Ye; Tian, Bing; Hua, Yuejin

    2017-03-01

    Binding of proteins to specific DNA sequences is essential for a variety of cellular processes such as DNA replication, transcription and responses to external stimuli. Chromatin immunoprecipitation is widely used for determining intracellular DNA fragments bound by a specific protein. However, the subsequent specific or accurate DNA-protein-binding sequence is usually determined by DNA footprinting. Here, we report an alternative method for identifying specific sites of DNA-protein-binding (designated SSDP) in vitro. This technique is mainly dependent on antibody-antigen immunity, simple and convenient, while radioactive isotope labeling and optimization of partial degradation by deoxyribonuclease (DNase) are avoided. As an example, the specific binding sequence of a target promoter by DdrO (a DNA damage response protein from Deinococcus radiodurans) in vitro was determined by the developed method. The central sequence of the binding site could be easily located using this technique.

  11. Machine Learning Helps Identify CHRONO as a Circadian Clock Component

    PubMed Central

    Venkataraman, Anand; Ramanathan, Chidambaram; Kavakli, Ibrahim H.; Hughes, Michael E.; Baggs, Julie E.; Growe, Jacqueline; Liu, Andrew C.; Kim, Junhyong; Hogenesch, John B.

    2014-01-01

    Over the last decades, researchers have characterized a set of “clock genes” that drive daily rhythms in physiology and behavior. This arduous work has yielded results with far-reaching consequences in metabolic, psychiatric, and neoplastic disorders. Recent attempts to expand our understanding of circadian regulation have moved beyond the mutagenesis screens that identified the first clock components, employing higher throughput genomic and proteomic techniques. In order to further accelerate clock gene discovery, we utilized a computer-assisted approach to identify and prioritize candidate clock components. We used a simple form of probabilistic machine learning to integrate biologically relevant, genome-scale data and ranked genes on their similarity to known clock components. We then used a secondary experimental screen to characterize the top candidates. We found that several physically interact with known clock components in a mammalian two-hybrid screen and modulate in vitro cellular rhythms in an immortalized mouse fibroblast line (NIH 3T3). One candidate, Gene Model 129, interacts with BMAL1 and functionally represses the key driver of molecular rhythms, the BMAL1/CLOCK transcriptional complex. Given these results, we have renamed the gene CHRONO (computationally highlighted repressor of the network oscillator). Bi-molecular fluorescence complementation and co-immunoprecipitation demonstrate that CHRONO represses by abrogating the binding of BMAL1 to its transcriptional co-activator CBP. Most importantly, CHRONO knockout mice display a prolonged free-running circadian period similar to, or more drastic than, six other clock components. We conclude that CHRONO is a functional clock component providing a new layer of control on circadian molecular dynamics. PMID:24737000

  12. Infected erythrocyte-derived extracellular vesicles alter vascular function via regulatory Ago2-miRNA complexes in malaria

    PubMed Central

    Mantel, Pierre-Yves; Hjelmqvist, Daisy; Walch, Michael; Kharoubi-Hess, Solange; Nilsson, Sandra; Ravel, Deepali; Ribeiro, Marina; Grüring, Christof; Ma, Siyuan; Padmanabhan, Prasad; Trachtenberg, Alexander; Ankarklev, Johan; Brancucci, Nicolas M.; Huttenhower, Curtis; Duraisingh, Manoj T.; Ghiran, Ionita; Kuo, Winston P.; Filgueira, Luis; Martinelli, Roberta; Marti, Matthias

    2016-01-01

    Malaria remains one of the greatest public health challenges worldwide, particularly in sub-Saharan Africa. The clinical outcome of individuals infected with Plasmodium falciparum parasites depends on many factors including host systemic inflammatory responses, parasite sequestration in tissues and vascular dysfunction. Production of pro-inflammatory cytokines and chemokines promotes endothelial activation as well as recruitment and infiltration of inflammatory cells, which in turn triggers further endothelial cell activation and parasite sequestration. Inflammatory responses are triggered in part by bioactive parasite products such as hemozoin and infected red blood cell-derived extracellular vesicles (iRBC-derived EVs). Here we demonstrate that such EVs contain functional miRNA-Argonaute 2 complexes that are derived from the host RBC. Moreover, we show that EVs are efficiently internalized by endothelial cells, where the miRNA-Argonaute 2 complexes modulate target gene expression and barrier properties. Altogether, these findings provide a mechanistic link between EVs and vascular dysfunction during malaria infection. PMID:27721445

  13. Identifying combinatorial regulation of transcription factors and binding motifs

    PubMed Central

    Kato, Mamoru; Hata, Naoya; Banerjee, Nilanjana; Futcher, Bruce; Zhang, Michael Q

    2004-01-01

    Background Combinatorial interaction of transcription factors (TFs) is important for gene regulation. Although various genomic datasets are relevant to this issue, each dataset provides relatively weak evidence on its own. Developing methods that can integrate different sequence, expression and localization data have become important. Results Here we use a novel method that integrates chromatin immunoprecipitation (ChIP) data with microarray expression data and with combinatorial TF-motif analysis. We systematically identify combinations of transcription factors and of motifs. The various combinations of TFs involved multiple binding mechanisms. We reconstruct a new combinatorial regulatory map of the yeast cell cycle in which cell-cycle regulation can be drawn as a chain of extended TF modules. We find that the pairwise combination of a TF for an early cell-cycle phase and a TF for a later phase is often used to control gene expression at intermediate times. Thus the number of distinct times of gene expression is greater than the number of transcription factors. We also see that some TF modules control branch points (cell-cycle entry and exit), and in the presence of appropriate signals they can allow progress along alternative pathways. Conclusions Combining different data sources can increase statistical power as demonstrated by detecting TF interactions and composite TF-binding motifs. The original picture of a chain of simple cell-cycle regulators can be extended to a chain of composite regulatory modules: different modules may share a common TF component in the same pathway or a TF component cross-talking to other pathways. PMID:15287978

  14. Stochastic control system parameter identifiability

    NASA Technical Reports Server (NTRS)

    Lee, C. H.; Herget, C. J.

    1975-01-01

    The parameter identification problem of general discrete time, nonlinear, multiple input/multiple output dynamic systems with Gaussian white distributed measurement errors is considered. The knowledge of the system parameterization was assumed to be known. Concepts of local parameter identifiability and local constrained maximum likelihood parameter identifiability were established. A set of sufficient conditions for the existence of a region of parameter identifiability was derived. A computation procedure employing interval arithmetic was provided for finding the regions of parameter identifiability. If the vector of the true parameters is locally constrained maximum likelihood (CML) identifiable, then with probability one, the vector of true parameters is a unique maximal point of the maximum likelihood function in the region of parameter identifiability and the constrained maximum likelihood estimation sequence will converge to the vector of true parameters.

  15. Interaction of Proteus mirabilis Urease Apoenzyme and Accessory Proteins Identified with Yeast Two-Hybrid Technology

    PubMed Central

    Heimer, Susan R.; Mobley, Harry L. T.

    2001-01-01

    Proteus mirabilis, a gram-negative bacterium associated with complicated urinary tract infections, produces a metalloenzyme urease which hydrolyzes urea to ammonia and carbon dioxide. The apourease is comprised of three structural subunits, UreA, UreB, and UreC, assembled as a homotrimer of individual UreABC heterotrimers (UreABC)3. To become catalytically active, apourease acquires divalent nickel ions through a poorly understood process involving four accessory proteins, UreD, UreE, UreF, and UreG. While homologues of UreD, UreF, and UreG have been copurified with apourease, it remains unclear specifically how these polypeptides associate with the apourease or each other. To identify interactions among P. mirabilis accessory proteins, in vitro immunoprecipitation and in vivo yeast two-hybrid assays were employed. A complex containing accessory protein UreD and structural protein UreC was isolated by immunoprecipitation and characterized with immunoblots. This association occurs independently of coaccessory proteins UreE, UreF, and UreG and structural protein UreA. In a yeast two-hybrid screen, UreD was found to directly interact in vivo with coaccessory protein UreF. Unique homomultimeric interactions of UreD and UreF were also detected in vivo. To substantiate the study of urease proteins with a yeast two-hybrid assay, previously described UreE dimers and homomultimeric UreA interactions among apourease trimers were confirmed in vivo. Similarly, a known structural interaction involving UreA and UreC was also verified. This report suggests that in vivo, P. mirabilis UreD may be important for recruitment of UreF to the apourease and that crucial homomultimeric associations occur among these accessory proteins. PMID:11157956

  16. Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase.

    PubMed

    Peace, Jared M; Villwock, Sandra K; Zeytounian, John L; Gan, Yan; Aparicio, Oscar M

    2016-03-01

    The Saccharomyces cerevisiae Forkhead Box (FOX) proteins, Fkh1 and Fkh2, regulate diverse cellular processes including transcription, long-range DNA interactions during homologous recombination, and replication origin timing and long-range origin clustering. We hypothesized that, as stimulators of early origin activation, Fkh1 and Fkh2 abundance limits the rate of origin activation genome-wide. Existing methods, however, are not well-suited to quantitative, genome-wide measurements of origin firing between strains and conditions. To overcome this limitation, we developed qBrdU-seq, a quantitative method for BrdU incorporation analysis of replication dynamics, and applied it to show that overexpression of Fkh1 and Fkh2 advances the initiation timing of many origins throughout the genome resulting in a higher total level of origin initiations in early S phase. The higher initiation rate is accompanied by slower replication fork progression, thereby maintaining a normal length of S phase without causing detectable Rad53 checkpoint kinase activation. The advancement of origin firing time, including that of origins in heterochromatic domains, was established in late G1 phase, indicating that origin timing can be reset subsequently to origin licensing. These results provide novel insights into the mechanisms of origin timing regulation by identifying Fkh1 and Fkh2 as rate-limiting factors for origin firing that determine the ability of replication origins to accrue limiting factors and have the potential to reprogram replication timing late in G1 phase.

  17. Identifying Insect Bites and Stings

    MedlinePlus

    ... or Animals > Identifying Insect Bites and Stings Health Issues Listen Español Text Size Email Print Share Identifying Insect Bites and Stings Page Content Article Body Mosquitoes Mosquitoes are generally found near water (pools, lakes, birdbaths) and are attracted by bright ...

  18. Identifying the Emergency Management Profession.

    ERIC Educational Resources Information Center

    Chiesa, Adele M.

    1987-01-01

    In building an emergency management library collection within a training institution, technical data become secondary to identifying common goals, methods, and systems found at the federal, state, and local levels for responding to and planning for disasters and crises. These goals help identify emergency management skills public officials should…

  19. Identifying Occupationally Specific Affective Behaviors.

    ERIC Educational Resources Information Center

    Pucel, David J.

    1993-01-01

    Data from two groups of cosmetology instructors (n=15) and two groups of machinist instructors (n=17) validated the Occupational Affective Behavior Analysis instrument as capable of identifying affective behaviors viewed as important to success in a given occupation. (SK)

  20. Methods for identifying translational researchers.

    PubMed

    Feeney, Mary K; Johnson, Timothy; Welch, Eric W

    2014-03-01

    There is currently no generally accepted method for identifying the community of translational researchers when evaluating Clinical and Translational Science Centers. We use data from the multiyear evaluation of the University of Illinois at Chicago Center for Clinical and Translational Science (CCTS) to investigate the complexities of reliably identifying translational researchers. We use three methods to identify translational researchers: (1) participating in CCTS services and programs; (2) self-identifying as a translational researcher; and (3) engaging in activities that are characteristic of translational science. We find little overlap of these differently defined research groups. We conclude with a discussion of how the findings suggest challenges for evaluating translational science programs and the need for better definition, communication, and demonstration of translational science for scientists and evaluators.

  1. Identifying Context Variables in Research.

    ERIC Educational Resources Information Center

    Piazza, Carolyn L.

    1987-01-01

    Identifies context variables in written composition from theoretical perspectives in cognitive psychology, sociology, and anthropology. Considers how multiple views of context from across the disciplines can build toward a broader definition of writing. (JD)

  2. Identifying discharge practice training needs.

    PubMed

    Lees, L; Emmerson, K

    A training needs analysis tool was developed to identify nurses' discharge training needs and to improve discharge practice. The tool includes 49 elements of discharge practice subdivided into four areas: corporate, operational, clinical and nurse-led discharge. The tool was disseminated to 15 wards on two hospital sites with assistance from the practice development team. Analysis of discharge training is important to assess discharge training needs and to identify staff who may assist with training.

  3. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers.

    PubMed

    Algee-Hewitt, Bridget F B; Edge, Michael D; Kim, Jaehee; Li, Jun Z; Rosenberg, Noah A

    2016-04-04

    Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

  4. Identifying tier one key suppliers.

    PubMed

    Wicks, Steve

    2013-01-01

    In today's global marketplace, businesses are becoming increasingly reliant on suppliers for the provision of key processes, activities, products and services in support of their strategic business goals. The result is that now, more than ever, the failure of a key supplier has potential to damage reputation, productivity, compliance and financial performance seriously. Yet despite this, there is no recognised standard or guidance for identifying a tier one key supplier base and, up to now, there has been little or no research on how to do so effectively. This paper outlines the key findings of a BCI-sponsored research project to investigate good practice in identifying tier one key suppliers, and suggests a scalable framework process model and risk matrix tool to help businesses effectively identify their tier one key supplier base.

  5. Persistent Identifiers Implementation in EOSDIS

    NASA Technical Reports Server (NTRS)

    Ramapriyan, H. K. " Rama"

    2016-01-01

    This presentation provides the motivation for and status of implementation of persistent identifiers in NASA's Earth Observation System Data and Information System (EOSDIS). The motivation is provided from the point of view of long-term preservation of datasets such that a number of questions raised by current and future users can be answered easily and precisely. A number of artifacts need to be preserved along with datasets to make this possible, especially when the authors of datasets are no longer available to address users questions. The artifacts and datasets need to be uniquely and persistently identified and linked with each other for full traceability, understandability and scientific reproducibility. Current work in the Earth Science Data and Information System (ESDIS) Project and the Distributed Active Archive Centers (DAACs) in assigning Digital Object Identifiers (DOI) is discussed as well as challenges that remain to be addressed in the future.

  6. [Advances in recently identified coronaviruses].

    PubMed

    Geng, He-Yuan; Tan, Wen-Jie

    2013-01-01

    Coronaviruses are a large family of viruses which include viruses that cause the common cold and severe acute respiratory syndrome (SARS) in humans and other diseases in animals. There are considerable genetic diversities within coronaviruses due to their wide rang hosts and their special gene replication and transcription mechanisms. During this process, gene recombinations often occur, resulting in novel subtype or coronavirus emerge constantly. Of note are SARS-like-CoVs and novel HCoV-EMC identified in 2012. This minireview summarized major advances of recently identified coronaviruses, focusing on the genome structures and interspecies jumping mechanism of coronavirus.

  7. Regulatory O-GlcNAcylation sites on FoxO1 are yet to be identified

    SciTech Connect

    Fardini, Yann; Perez-Cervera, Yobana; Camoin, Luc; Pagesy, Patrick; Lefebvre, Tony; Issad, Tarik

    2015-06-26

    O-GlcNAcylation is a reversible post-translational modification that regulates cytosolic and nuclear proteins. We and others previously demonstrated that FoxO1 is O-GlcNAcylated in different cell types, resulting in an increase in its transcriptional activity. Four O-GlcNAcylation sites were identified in human FOXO1 but directed mutagenesis of each site individually had modest (T317) or no effect (S550, T648, S654) on its O-GlcNAcylation status and transcriptional activity. Moreover, the consequences of mutating all four sites had not been investigated. In the present work, we mutated these sites in the mouse Foxo1 and found that mutation of all four sites did not decrease Foxo1 O-GlcNAcylation status and transcriptional activity, and would even tend to increase them. In an attempt to identify other O-GlcNAcylation sites, we immunoprecipitated wild-type O-GlcNAcylated Foxo1 and analysed the tryptic digest peptides by mass spectrometry using High-energy Collisional Dissociation. We identified T646 as a new O-GlcNAcylation site on Foxo1. However, site directed mutagenesis of this site individually or together with all four previously identified residues did not impair Foxo1 O-GlcNAcylation and transcriptional activity. These results suggest that residues important for the control of Foxo1 activity by O-GlcNAcylation still remain to be identified. - Highlights: • We mutate four previously identified O-GlcNAcylation sites on Foxo1. • Unexpectedly, these mutations do not reduce Foxo1 O-GlcNAcylation. • These mutation do not reduce Foxo1 transcriptional activity. • We identify a new O-GlcNAcylation site on Foxo1 by mass spectrometry. • Mutation of this site increases Foxo1 transcriptional activity.

  8. Identifying Deceptive Speech Across Cultures

    DTIC Science & Technology

    2016-06-25

    AFRL-AFOSR-VA-TR-2016-0267 IDENTIFYING DECEPTIVE SPEECH ACROSS CULTURES Julia Hirschberg THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK...PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK SPONSORED PROJECTS ADMINISTRATION 8

  9. Identifying Innovative Agricultural Education Programs

    ERIC Educational Resources Information Center

    Rayfield, John; Murphy, Tim; Briers, Gary; Lewis, Lauren

    2012-01-01

    Researchers identified innovative agricultural education programs across the United States. A Delphi study was conducted with the teachers in innovative programs. According to the teachers, innovative programs in 2020 will use hands-on activities and will be run by highly motivated teachers. The purpose of innovative programs in the future will be…

  10. Identifiability, exchangeability and confounding revisited

    PubMed Central

    Greenland, Sander; Robins, James M

    2009-01-01

    In 1986 the International Journal of Epidemiology published "Identifiability, Exchangeability and Epidemiological Confounding". We review the article from the perspective of a quarter century after it was first drafted and relate it to subsequent developments on confounding, ignorability, and collapsibility. PMID:19732410

  11. Identifying the Gifted Child Humorist.

    ERIC Educational Resources Information Center

    Fern, Tami L.

    1991-01-01

    This study attempted to identify gifted child humorists among 1,204 children in grades 3-6. Final identification of 13 gifted child humorists was determined through application of such criteria as funniness, originality, and exemplary performance or product. The influence of intelligence, development, social factors, sex differences, family…

  12. "Geriatricizing" Hospitalists: Identifying Educational Opportunities

    ERIC Educational Resources Information Center

    Friedman, Susan M.; Gillespie, Suzanne M.; Medina-Walpole, Annette M.; Caprio, Thomas V.; Karuza, Jurgis; McCann, Robert M.

    2013-01-01

    The objective of this study was to identify differences between geriatricians and hospitalists in caring for hospitalized older adults, so as to inform faculty development programs that have the goal of improving older patient care. Eleven hospitalists and 13 geriatricians were surveyed regarding knowledge, confidence, and practice patterns in…

  13. Identified Sins in Teaching Reading.

    ERIC Educational Resources Information Center

    Ediger, Marlow

    This paper cites as selected taboos in teaching reading (identified by educators very frequently) the following: (1) homogeneous grouping; (2) round robin reading; (3) use of textbooks and workbooks in the curriculum; (4) individual endeavors in school work; (5) memorization of content; and (6) the controlled vocabulary in reading. The paper…

  14. Methods of Identifying Marketing Competencies

    ERIC Educational Resources Information Center

    Crawford, Lucy C.; Ertel, Kenneth A.

    1970-01-01

    The competency pattern and the task analysis are two approaches used to identify content that affects the distributive education curriculum. These and other research tools provide essential information about capabilities required for entrance into and persistence in careers at prescribed levels of distributive jobs. (Author)

  15. Identifying predictors of treatment response.

    PubMed

    Yoder, Paul; Compton, Don

    2004-01-01

    This article provides a rationale for considering predictors of growth in a treatment group as inadequate to identifying predictors of treatment response. When we interpret predictors of growth in a treatment group as synonymous with predictors of treatment response, we implicitly attribute all of the treated children's growth to the treatment, an untenable assumption under most conditions. We also contend that the use of standard scores in predictors of growth studies does not allow us to differentiate growth from treatment, from growth from other factors. We present two research methodologies that are appropriate methods of identifying predictors of treatment response: (a) single-subject experimental logic utilized to identify the specific participants in which treatment responses (not just growth) were found, combined with follow-up group comparison logic to identify the characteristics on which responders and nonresponders differ, and (b) statistical interactions among child/family/context characteristics and randomly assigned group membership. Principles for selecting potential predictors of treatment response are provided.

  16. Towards an immuno-precipitated neurodevelopmental animal model of schizophrenia.

    PubMed

    Meyer, Urs; Feldon, Joram; Schedlowski, Manfred; Yee, Benjamin K

    2005-01-01

    Epidemiological studies have indicated an association between maternal bacterial and viral infections during pregnancy and the higher incidence of schizophrenia in the resultant offspring post-puberty. One hypothesis asserts that the reported epidemiological link is mediated by prenatal activation of the foetal immune system in response to the elevation of maternal cytokine level due to infection. Here, we report that pregnant mouse dams receiving a single exposure to the cytokine-releasing agent, polyriboinosinic-polyribocytidilic acid (PolyI:C; at 2.5, 5.0, or 10.0 mg/kg) on gestation day 9 produced offspring that subsequently exhibited multiple schizophrenia-related behavioural deficits in adulthood, in comparison to offspring from vehicle injected or non-injected control dams. The efficacy of the PolyI:C challenge to induce cytokine responses in naïve non-pregnant adult female mice and in foetal brain tissue when injected to pregnant mice were further ascertained in separate subjects: (i) a dose-dependent elevation of interleukin-10 was detected in the adult female mice at 1 and 6h post-injection, (ii) 12 h following prenatal PolyI:C challenge, the foetal levels of interleukin-1beta were elevated. The spectrum of abnormalities included impairments in exploratory behaviour, prepulse inhibition, latent inhibition, the US-pre-exposure effect, spatial working memory; and enhancement in the locomotor response to systemic amphetamine (2.5 mg/kg, i.p.) as well as in discrimination reversal learning. The neuropsychological parallels between prenatal PolyI:C treatment in mice and psychosis in humans, demonstrated here, leads us to conclude that prenatal PolyI:C treatment represents one of the most powerful environmental-developmental models of schizophrenia to date. The uniqueness of this model lies in its epidemiological and immunological relevance. It is, sui generis, ideally suited for the investigation of the neuropsychoimmunological mechanisms implicated in the developmental aetiology and disease processes of schizophrenia.

  17. Identifying the potential rural optometrist.

    PubMed

    Kegel-Flom, P

    1976-09-01

    Rural optometrists were found to differ from urban optometrists in background, environmental attitude, and interest patterns. Attitude toward the urban environment and place of origin were the best predictors of an optometrist's practice location. When "urbanism" and "origin" were scaled and placed in a multiple regression equation to predict practice location, identification of an optometrist's location as rural or urban was highly accurate. Most importantly, scores on the equation were predictive of optometry students' future practice locations. A single cut-off point on the equation correctly identified 79% of students who entered rural or isolated small city practice and 81% of those who entered urban practice. The findings suggest that optometry students most likely to enter rural (or indeed urban) practice can be objectively identified early in, or even prior to, training. Such identification may assist educators in selecting and training optometrists who will deliver vision care to people in areas of greatest need.

  18. Identifying Targets from Filtering Effects

    DTIC Science & Technology

    2012-10-24

    Introduction Considering a radar (or sonar) target as more than a simple point scatterer brings up the possibility of identifying the target based on the...2000. [8] M. Vespe, C. J. Baker, and H. D. Griffiths , "Automatic target regognition using multi-diversity radar," Radar, Sonar \\& Navigation, IET, vol...A. Taflove and S. C. Hagness, Computational Electrodynamics : The Finite Difference Time Domain Method. Norwood, MA: Artech House, 2005.

  19. Identifying and managing problem drinkers.

    PubMed Central

    Kahan, M.

    1996-01-01

    Problem drinking is far more common than severe alcohol dependence and is associated with considerable morbidity and health care costs. Whereas patients with alcohol dependence respond best to intensive treatment, one or more brief sessions of physician advice and counseling reduces alcohol consumption among problem drinkers. The two most useful tools to identify problem drinkers are the CAGE and the drinking problem question. PMID:8653034

  20. The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies.

    PubMed

    Machyna, Martin; Kehr, Stephanie; Straube, Korinna; Kappei, Dennis; Buchholz, Frank; Butter, Falk; Ule, Jernej; Hertel, Jana; Stadler, Peter F; Neugebauer, Karla M

    2014-11-06

    Coilin protein scaffolds Cajal bodies (CBs)-subnuclear compartments enriched in small nuclear RNAs (snRNAs)-and promotes efficient spliceosomal snRNP assembly. The molecular function of coilin, which is intrinsically disordered with no defined motifs, is poorly understood. We use UV crosslinking and immunoprecipitation (iCLIP) to determine whether mammalian coilin binds RNA in vivo and to identify targets. Robust detection of snRNA transcripts correlated with coilin ChIP-seq peaks on snRNA genes, indicating that coilin binding to nascent snRNAs is a site-specific CB nucleator. Surprisingly, several hundred small nucleolar RNAs (snoRNAs) were identified as coilin interactors, including numerous unannotated mouse and human snoRNAs. We show that all classes of snoRNAs concentrate in CBs. Moreover, snoRNAs lacking specific CB retention signals traffic through CBs en route to nucleoli, consistent with the role of CBs in small RNP assembly. Thus, coilin couples snRNA and snoRNA biogenesis, making CBs the cellular hub of small ncRNA metabolism.

  1. Molecular profiling of activated olfactory neurons identifies odorant receptors for odors in vivo

    PubMed Central

    Jiang, Yue; Gong, Naihua Natalie; Hu, Xiaoyang Serene; Ni, Mengjue Jessica; Pasi, Radhika

    2015-01-01

    The mammalian olfactory system uses a large family of odorant receptors to detect and discriminate amongst a myriad of volatile odor molecules. Understanding odor coding requires comprehensive mapping between odorant receptors and corresponding odors. Here we present high–throughput in vivo identification of odorant receptor repertoires responding to odorants, using phosphorylated ribosome immunoprecipitation of mRNA from olfactory epithelium of odor–stimulated mice followed by RNA–Seq. This approach screens the endogenously expressed odorant receptors against an odor in one set of experiments, using awake and freely behaving mice. In combination with validations in a heterologous system, we identify sets of odorant receptors for two odorants, acetophenone and 2,5–dihydro–2,4,5–trimethylthiazoline (TMT), encompassing 69 odorant receptor–odorant pairs. We also identified shared amino acid residues specific to the acetophenone or TMT receptors, and developed models to predict receptor activation by acetophenone. This study provides a means to understand the combinatorial coding of odors in vivo. PMID:26322927

  2. A Genome-Wide Regulatory Framework Identifies Maize Pericarp Color1 Controlled Genes[C][W

    PubMed Central

    Morohashi, Kengo; Casas, María Isabel; Ferreyra, Lorena Falcone; Mejía-Guerra, María Katherine; Pourcel, Lucille; Yilmaz, Alper; Feller, Antje; Carvalho, Bruna; Emiliani, Julia; Rodriguez, Eduardo; Pellegrinet, Silvina; McMullen, Michael; Casati, Paula; Grotewold, Erich

    2012-01-01

    Pericarp Color1 (P1) encodes an R2R3-MYB transcription factor responsible for the accumulation of insecticidal flavones in maize (Zea mays) silks and red phlobaphene pigments in pericarps and other floral tissues, which makes P1 an important visual marker. Using genome-wide expression analyses (RNA sequencing) in pericarps and silks of plants with contrasting P1 alleles combined with chromatin immunoprecipitation coupled with high-throughput sequencing, we show here that the regulatory functions of P1 are much broader than the activation of genes corresponding to enzymes in a branch of flavonoid biosynthesis. P1 modulates the expression of several thousand genes, and ∼1500 of them were identified as putative direct targets of P1. Among them, we identified F2H1, corresponding to a P450 enzyme that converts naringenin into 2-hydroxynaringenin, a key branch point in the P1-controlled pathway and the first step in the formation of insecticidal C-glycosyl flavones. Unexpectedly, the binding of P1 to gene regulatory regions can result in both gene activation and repression. Our results indicate that P1 is the major regulator for a set of genes involved in flavonoid biosynthesis and a minor modulator of the expression of a much larger gene set that includes genes involved in primary metabolism and production of other specialized compounds. PMID:22822204

  3. Identifying Network Perturbation in Cancer

    PubMed Central

    Logsdon, Benjamin A.; Gentles, Andrew J.; Lee, Su-In

    2016-01-01

    We present a computational framework, called DISCERN (DIfferential SparsE Regulatory Network), to identify informative topological changes in gene-regulator dependence networks inferred on the basis of mRNA expression datasets within distinct biological states. DISCERN takes two expression datasets as input: an expression dataset of diseased tissues from patients with a disease of interest and another expression dataset from matching normal tissues. DISCERN estimates the extent to which each gene is perturbed—having distinct regulator connectivity in the inferred gene-regulator dependencies between the disease and normal conditions. This approach has distinct advantages over existing methods. First, DISCERN infers conditional dependencies between candidate regulators and genes, where conditional dependence relationships discriminate the evidence for direct interactions from indirect interactions more precisely than pairwise correlation. Second, DISCERN uses a new likelihood-based scoring function to alleviate concerns about accuracy of the specific edges inferred in a particular network. DISCERN identifies perturbed genes more accurately in synthetic data than existing methods to identify perturbed genes between distinct states. In expression datasets from patients with acute myeloid leukemia (AML), breast cancer and lung cancer, genes with high DISCERN scores in each cancer are enriched for known tumor drivers, genes associated with the biological processes known to be important in the disease, and genes associated with patient prognosis, in the respective cancer. Finally, we show that DISCERN can uncover potential mechanisms underlying network perturbation by explaining observed epigenomic activity patterns in cancer and normal tissue types more accurately than alternative methods, based on the available epigenomic data from the ENCODE project. PMID:27145341

  4. Identifying the health conscious consumer.

    PubMed

    Kraft, F B; Goodell, P W

    1993-01-01

    Individuals who lead a "wellness-oriented" lifestyle are concerned with nutrition, fitness, stress, and their environment. They accept responsibility for their health and are excellent customers for health-related products and services. Those who lack a wellness orientation are identified as higher health risks and become candidates for health promotion program intervention. The authors report a new scale by which to measure the wellness-oriented lifestyle. Scale development procedures are detailed, followed by information from five studies that support its validity. The authors suggest ways health care marketers may use the Wellness Scale to segment and target potential customers and position their products and services.

  5. Identifying teaching in wild animals.

    PubMed

    Thornton, Alex; Raihani, Nichola J

    2010-08-01

    After a long period of neglect, the study of teaching in nonhuman animals is beginning to take a more prominent role in research on social learning. Unlike other forms of social learning, teaching requires knowledgeable individuals to play an active role in facilitating learning by the naive. Casting aside anthropocentric requirements for cognitive mechanisms assumed to underpin teaching in our own species, researchers are now beginning to discover evidence for teaching across a wide range of taxa. Nevertheless, unequivocal evidence for teaching remains scarce, with convincing experimental data limited to meerkats, pied babblers, and tandem-running ants. In this review, our aim is to stimulate further research in different species and contexts by providing conceptual and methodological guidelines for identifying teaching, with a focus on natural populations. We begin by highlighting the fact that teaching is a form of cooperative behavior that functions to promote learning in others and show that consideration of these key characteristics is critical in helping to identify suitable targets for future research. We then go on to discuss potential observational, experimental, and statistical techniques that may assist researchers in providing evidence that the criteria that make up the accepted operational definition of teaching have been met. Supplemental materials for this article may be downloaded from http://lb.psychonomic-journals.org/content/supplemental.

  6. Selecting SNPs to Identify Ancestry

    PubMed Central

    Sampson, Joshua; Kidd, Kenneth K; Kidd, Judith R; Zhao, Hongyu

    2011-01-01

    Background/Aims An individual’s genotypes at a group of Single Nucleotide Polymorphisms (SNPs) can be used to predict that individual’s ethnicity, or ancestry. In medical studies, knowledge of a subject’s ancestry can minimize possible confounding, and in forensic applications, such knowledge can help direct investigations. Our goal is to select a small subset of SNPs, from the millions already identified in the human genome, that can predict ancestry with a minimal error rate. Methods The general form for this variable selection procedure is to estimate the expected error rates for sets of SNPs using a training dataset and consider those sets with the lowest error rates given their size. The quality of the estimate for the error rate determines the quality of the resulting SNPs. As the apparent error rate performs poorly when either the number of SNPs or the number of populations is large, we propose a new estimate, the Improved Bayesian Estimate. Conclusions We demonstrate that selection procedures based on this estimate produce small sets of SNPs that can accurately predict ancestry. We also provide a list of the 100 optimal SNPs for identifying ancestry. R functions are available at http://bioinformatics.med.yale.edu/group/josh/index.html. PMID:21668909

  7. Identifying infection hotspots early on.

    PubMed

    Shabha, Ghasson

    2012-04-01

    According to many published studies, 'ducting in ventilation and air-conditioning are largely overlooked and ignored, as they are out of sight and out of mind', despite mounting evidence indicating a higher risk in spreading airborne infections'. So says Ghasson Shabha BSc (Arch) MSc, PhD (Arch), MBIFM, Associate CIBSE, PG Cert Ed, of the Faculty of Technology, Engineering and the Environment (TEE), at the Birmingham School of the Built Environment (BSBE) at Birmingham City University, who adds that CIBSE estimates that fewer than 5% of buildings with air-conditioning systems above 12 kW have been inspected so far. Here he argues that incorporating 3D building information modelling software into existing computer-aided facilities management software systems will enable hospitals' 'infection hotspots' to be far more quickly identified, and subsequently monitored, to prevent future problems.

  8. Identifying methamphetamine exposure in children

    PubMed Central

    Castaneto, Marisol S.; Barnes, Allan J.; Scheidweiler, Karl B.; Schaffer, Michael; Rogers, Kristen K.; Stewart, Deborah; Huestis, Marilyn A.

    2013-01-01

    Introduction Methamphetamine (MAMP) use, distribution and manufacture remain a serious public health and safety problem in the United States, and children environmentally exposed to MAMP face a myriad of developmental, social and health risks, including severe abuse and neglect necessitating child protection involvement. It is recommended that drug-endangered children receive medical evaluation and care with documentation of overall physical and mental conditions and have urine drug testing.1 The primary aim of this study was to determine the best biological matrix to detect MAMP, amphetamine (AMP), methylenedioxymethamphetamine (MDMA), methylenedioxyamphetamine (MDA) and methylenedioxyethylamphetamine (MDEA) in environmentally exposed children. Method 91 children, environmentally exposed to household MAMP intake, were medically evaluated at the Child and Adolescent Abuse Resource and Evaluation (CAARE) Diagnostic and Treatment Center at the University of California, Davis (UCD) Children's Hospital. MAMP, AMP, MDMA, MDA and MDEA were quantified in urine and oral fluid (OF) by gas chromatography mass spectrometry (GCMS) and in hair by liquid chromatography tandem mass spectrometry (LCMSMS). Results Overall drug detection rates in OF, urine and hair were 6.9%, 22.1% and 77.8%, respectively. Seventy children (79%) tested positive for 1 or more drugs in 1 or more matrices. MAMP was the primary analyte detected in all 3 biological matrices. All positive OF (n=5) and 18 of 19 positive urine specimens also had a positive hair test. Conclusion Hair analysis offered a more sensitive tool for identifying MAMP, AMP and MDMA environmental exposure in children than urine or OF testing. A negative urine, or hair test does not exclude the possibility of drug exposure, but hair testing provided the greatest sensitivity for identifying drug-exposed children. PMID:24263642

  9. Identifying and Inactivating Bacterial Spores

    NASA Technical Reports Server (NTRS)

    Newcombe, David; Dekas, Anne; Venkateswaran, Kasthuri

    2009-01-01

    Problems associated with, and new strategies for, inactivating resistant organisms like Bacillus canaveralius (found at Kennedy Space Center during a survey of three NASA cleanrooms) have been defined. Identifying the particular component of the spore that allows its heightened resistance can guide the development of sterilization procedures that are targeted to the specific molecules responsible for resistance, while avoiding using unduly harsh methods that jeopardize equipment. The key element of spore resistance is a multilayered protein shell that encases the spore called the spore coat. The coat of the best-studied spore-forming microbe, B. subtilis, consists of at least 45 proteins, most of which are poorly characterized. Several protective roles for the coat are well characterized including resistance to desiccation, large toxic molecules, ortho-phthalaldehyde, and ultraviolet (UV) radiation. One important long-term specific goal is an improved sterilization procedure that will enable NASA to meet planetary protection requirements without a terminal heat sterilization step. This would support the implementation of planetary protection policies for life-detection missions. Typically, hospitals and government agencies use biological indicators to ensure the quality control of sterilization processes. The spores of B. canaveralius that are more resistant to osmotic stress would serve as a better biological indicator for potential survival than those in use currently.

  10. Identifying Chemical Groups for Biomonitoring

    PubMed Central

    Krowech, Gail; Hoover, Sara; Plummer, Laurel; Sandy, Martha; Zeise, Lauren; Solomon, Gina

    2016-01-01

    Summary: Regulatory agencies face daunting challenges identifying emerging chemical hazards because of the large number of chemicals in commerce and limited data on exposure and toxicology. Evaluating one chemical at a time is inefficient and can lead to replacement with uncharacterized chemicals or chemicals with structural features already linked to toxicity. The Office of Environmental Health Hazard Assessment (OEHHA) has developed a process for constructing and assessing chemical groups for potential biomonitoring in California. We screen for chemicals with significant exposure potential and propose possible chemical groups, based on structure and function. To support formal consideration of these groups by Biomonitoring California’s Scientific Guidance Panel, we conduct a detailed review of exposure and toxicity data and examine the likelihood of detection in biological samples. To date, 12 chemical groups have been constructed and added to the pool of chemicals that can be selected for Biomonitoring California studies, including p,p´-bisphenols, brominated and chlorinated organic compounds used as flame retardants, non-halogenated aromatic phosphates, and synthetic polycyclic musks. Evaluating chemical groups, rather than individual chemicals, is an efficient way to respond to shifts in chemical use and the emergence of new chemicals. This strategy can enable earlier identification of important chemicals for monitoring and intervention. PMID:27905275

  11. Strategies to identify disease genes.

    PubMed

    Ashton, Gabrielle H S; McGrath, John A; South, Andrew P

    2002-04-01

    The correlation between genes and disease began in earnest in the early 1900s with the identification of Mendelian-like inheritance of "inborn errors of metabolism." Since then, the ever-broadening field of genetics has been established as one of the most important and groundbreaking branches of science and medicine to date. With the announcement of a "working draft" sequence of the human genome in 2001, the vast array of both genomic and expressed sequence information available in the public databases alone has meant that the concept of hunting for genes is evolving. Nowadays, researchers can substitute many labor-intensive hours in the lab for less time searching on the World Wide Web. Specialization within genetics has been continuously providing subsets of the genre such as genomics, pharmacogenetics, chemogenomics, gene therapy, proteomics and functional genomics, all of which are based on the fundamental starting block, the gene. This review aims to summarize both traditional and current strategies for identifying susceptibility and monogenetic disease genes and describes how these strategies have evolved in tune with the ever-expanding wealth of information now available at our fingertips.

  12. Identifying problem and compulsive gamblers.

    PubMed Central

    van Es, R.

    2000-01-01

    OBJECTIVE: To present a meta-analysis of current research on the prevalence, identification, and treatment of problem and compulsive gamblers. QUALITY OF EVIDENCE: Problem and compulsive gambling was not a socio-scientific concern until the last two decades. Hence research on this topic is limited. The summary and analysis for this paper relied on computer searches of journal and news abstracts in addition to direct contact with organizations addressing the identification and treatment of compulsive gamblers. MAIN MESSAGE: An estimated 5% of those who gamble run into problems. About 1% of those who gamble are predicted to experience serious problems. Successful treatment of problem and compulsive gambling continues to be a challenge. Although cognitive therapy has been the favoured approach, a combination of several therapeutic approaches is advocated. CONCLUSIONS: Problem and compulsive gambling can present a real health threat. As with other addictions, treatment strategies continue to be a baffling social problem. Aware and informed physicians can have a pivotal role in the difficult process of identifying, acknowledging, and remediating problem and compulsive gambling. PMID:10907572

  13. RECOVIR Software for Identifying Viruses

    NASA Technical Reports Server (NTRS)

    Chakravarty, Sugoto; Fox, George E.; Zhu, Dianhui

    2013-01-01

    Most single-stranded RNA (ssRNA) viruses mutate rapidly to generate a large number of strains with highly divergent capsid sequences. Determining the capsid residues or nucleotides that uniquely characterize these strains is critical in understanding the strain diversity of these viruses. RECOVIR (an acronym for "recognize viruses") software predicts the strains of some ssRNA viruses from their limited sequence data. Novel phylogenetic-tree-based databases of protein or nucleic acid residues that uniquely characterize these virus strains are created. Strains of input virus sequences (partial or complete) are predicted through residue-wise comparisons with the databases. RECOVIR uses unique characterizing residues to identify automatically strains of partial or complete capsid sequences of picorna and caliciviruses, two of the most highly diverse ssRNA virus families. Partition-wise comparisons of the database residues with the corresponding residues of more than 300 complete and partial sequences of these viruses resulted in correct strain identification for all of these sequences. This study shows the feasibility of creating databases of hitherto unknown residues uniquely characterizing the capsid sequences of two of the most highly divergent ssRNA virus families. These databases enable automated strain identification from partial or complete capsid sequences of these human and animal pathogens.

  14. Identifying acid salts of magnesium

    SciTech Connect

    Plumb, R.; Thivierge, R.F. Jr.; Xu, W.W.

    1987-11-05

    In preliminary work they found that significant quantities of certain nitrogen oxides and of sulfuric acid were absorbed by lower hydrates of magnesium sulfate. It appeared that acid salts were being formed but the known chemistry of group IIA (group 2) sulfates and acid sulfates which was worked out many years ago did not provide an explanation of their observations. They developed a new technique for delineating the solidus boundary of ternary mixtures using friability tests and applied it to the systems of interest. Magnesium acid salt hydrates with compositions on the solidus boundary could be readily identified. X-ray powder patterns confirmed the existence of two previously unknown ternary compounds, Mg/sub 2/(HSO/sub 4/)/sub 2/SO/sub 4/ x 4H/sub 2/O and Mg(HSO/sub 4/)/sub 2/ x H/sub 2/SO/sub 4/ x 3H/sub 2/O. Mixed acid sulfate-nitrate-hydrates could be detected but fuming at room temperatures interfered with quantitative determinations of the solidus boundary and X-ray measurements.

  15. Identifying ELIXIR Core Data Resources

    PubMed Central

    Durinx, Christine; McEntyre, Jo; Appel, Ron; Apweiler, Rolf; Barlow, Mary; Blomberg, Niklas; Cook, Chuck; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Valencia, Alfonso

    2017-01-01

    The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR’s sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure. PMID:27803796

  16. Identifying ELIXIR Core Data Resources.

    PubMed

    Durinx, Christine; McEntyre, Jo; Appel, Ron; Apweiler, Rolf; Barlow, Mary; Blomberg, Niklas; Cook, Chuck; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Valencia, Alfonso

    2016-01-01

    The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR's sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.

  17. A novel single cell method to identify the genetic composition at a single nuclear body

    PubMed Central

    Anchel, David; Ching, Reagan W.; Cotton, Rachel; Li, Ren; Bazett-Jones, David P.

    2016-01-01

    Gene loci make specific associations with compartments of the nucleus (e.g. the nuclear envelope, nucleolus, and transcription factories) and this association may determine or reflect a mechanism of genetic control. With current methods, it is not possible to identify sets of genes that converge to form a “gene hub” as there is a reliance on loci-specific probes, or immunoprecipitation of a particular protein from bulk cells. We introduce a method that will allow for the identification of loci contained within the vicinity of a single nuclear body in a single cell. For the first time, we demonstrate that the DNA sequences originating from a single sub-nuclear structure in a single cell targeted by two-photon irradiation can be determined, and mapped to a particular locus. Its application to single PML nuclear bodies reveals ontologically related loci that frequently associate with each other and with PML bodies in a population of cells, and a possible nuclear body targeting role for specific transcription factor binding sites. PMID:27389808

  18. A genome-wide survey of CD4+ lymphocyte regulatory genetic variants identifies novel asthma genes

    PubMed Central

    Sharma, Sunita; Zhou, Xiaobo; Thibault, Derek M.; Himes, Blanca E.; Liu, Andy; Szefler, Stanley J.; Strunk, Robert; Castro, Mario; Hansel, Nadia N.; Diette, Gregory B.; Vonakis, Becky M.; Adkinson, N. Franklin; Avila, Lydiana; Soto-Quiros, Manuel; Barraza-Villareal, Albino; Lemanske, Robert F.; Solway, Julian; Krishnan, Jerry; White, Steven R.; Cheadle, Chris; Berger, Alan E.; Fan, Jinshui; Boorgula, Meher Preethi; Nicolae, Dan; Gilliland, Frank; Barnes, Kathleen; London, Stephanie J.; Martinez, Fernando; Ober, Carole; Celedón, Juan C.; Carey, Vincent J.; Weiss, Scott T.; Raby, Benjamin A.

    2014-01-01

    Background Genome-wide association studies have yet to identify the majority of genetic variants involved in asthma. We hypothesized that expression quantitative trait locus (eQTL) mapping can identify novel asthma genes by enabling prioritization of putative functional variants for association testing. Objective We evaluated 6,706 cis-acting expression-associated variants (eSNP) identified through a genome-wide eQTL survey of CD4+ lymphocytes for association with asthma. Methods eSNP were tested for association with asthma in 359 asthma cases and 846 controls from the Childhood Asthma Management Program, with verification using family-based testing. Significant associations were tested for replication in 579 parent-child trios with asthma from Costa Rica. Further functional validation was performed by Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE)-qPCR and Chromatin-Immunoprecipitation (ChIP)-PCR in lung derived epithelial cell lines (Beas-2B and A549) and Jurkat cells, a leukemia cell line derived from T lymphocytes. Results Cis-acting eSNP demonstrated associations with asthma in both cohorts. We confirmed the previously-reported association of ORMDL3/GSDMB variants with asthma (combined p=2.9 × 108). Reproducible associations were also observed for eSNP in three additional genes: FADS2 (p=0.002), NAGA (p=0.0002), and F13A1 (p=0.0001). We subsequently demonstrated that FADS2 mRNA is increased in CD4+ lymphocytes in asthmatics, and that the associated eSNPs reside within DNA segments with histone modifications that denote open chromatin status and confer enhancer activity. Conclusions Our results demonstrate the utility of eQTL mapping in the identification of novel asthma genes, and provide evidence for the importance of FADS2, NAGA, and F13A1 in the pathogenesis of asthma. PMID:24934276

  19. An in vivo hypoxia metagene identifies the novel hypoxia inducible factor target gene SLCO1B3.

    PubMed

    Ramachandran, Anassuya; Betts, Guy; Bhana, Sara; Helme, Gemma; Blick, Christopher; Moller-Levet, Carla; Saunders, Emma; Valentine, Helen; Pepper, Stuart; Miller, Crispin J; Buffa, Francesca; Harris, Adrian L; West, Catharine M L

    2013-05-01

    A hypoxia-associated gene signature (metagene) was previously derived via in vivo data-mining. In this study, we aimed to investigate whether this approach could identify novel hypoxia regulated genes. From an initial list of nine genes, three were selected for further study (BCAR1, IGF2BP2 and SLCO1B3). Ten cell lines were exposed to hypoxia and interrogated for the expression of the three genes. All three genes were hypoxia inducible in at least one of the 10 cell lines with SLCO1B3 induced in seven. SLCO1B3 was studied further using chromatin immunoprecipitation and luciferase assays to investigate hypoxia inducible factor (HIF) dependent transcription. Two functional HIF response elements were identified within intron 1 of the gene. The functional importance of SLCO1B3 was studied by gene knockdown experiments followed by cell growth assays, flow cytometry and Western blotting. SLCO1B3 knockdown reduced cell size and 3-dimensional spheroid volume, which was associated with decreased activation of the mammalian target of rapamycin (mTOR) pathway. Finally, Oncomine analysis revealed that head and neck and colorectal tumours had higher levels of SLCO1B3 compared to normal tissue. Thus, the knowledge based approach for deriving gene signatures can identify novel biologically relevant genes.

  20. Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation.

    PubMed

    Alajem, Adi; Biran, Alva; Harikumar, Arigela; Sailaja, Badi Sri; Aaronson, Yair; Livyatan, Ilana; Nissim-Rafinia, Malka; Sommer, Andreia Gianotti; Mostoslavsky, Gustavo; Gerbasi, Vincent R; Golden, Daniel E; Datta, Arnab; Sze, Siu Kwan; Meshorer, Eran

    2015-03-31

    Embryonic stem cells (ESCs) possess a distinct chromatin conformation maintained by specialized chromatin proteins. To identify chromatin regulators in ESCs, we developed a simple biochemical assay named D-CAP (differential chromatin-associated proteins), using brief micrococcal nuclease digestion of chromatin, followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Using D-CAP, we identified several differentially chromatin-associated proteins between undifferentiated and differentiated ESCs, including the chromatin remodeling protein SMARCD1. SMARCD1 depletion in ESCs led to altered chromatin and enhanced endodermal differentiation. Gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggested that SMARCD1 is both an activator and a repressor and is enriched at developmental regulators and that its chromatin binding coincides with H3K27me3. SMARCD1 knockdown caused H3K27me3 redistribution and increased H3K4me3 around the transcription start site (TSS). One of the identified SMARCD1 targets was Klf4. In SMARCD1-knockdown clones, KLF4, as well as H3K4me3 at the Klf4 locus, remained high and H3K27me3 was abolished. These results propose a role for SMARCD1 in restricting pluripotency and activating lineage pathways by regulating H3K27 methylation.

  1. Characterization of Human Macrophage Antigens Identified by Monoclonal Antibodies

    DTIC Science & Technology

    1984-01-01

    Total extracts of iodinated glycoproteins or iodinated surface proteins were dis- solved in 50 pLl O’Farrell Buffer A [9,5 M urea. 2% (w,’v) nonidet -P...the c:ll surface labeled by vectorial iodination. p40 skas not immunoprecipitable from an iodinated concanavalin A-glycoprotein fraction of U937...of U937 cells. T cell clone. B cell clone, and peripheral blood granulocytes and monocytes. but not lymphocytes (Table 3). p40 was also detected in

  2. Mass spectroscopy identifies the splicing-associated proteins, PSF, hnRNP H3, hnRNP A2/B1, and TLS/FUS as interacting partners of the ZNF198 protein associated with rearrangement in myeloproliferative disease

    SciTech Connect

    Kasyapa, Chitta S.; Kunapuli, Padmaja; Cowell, John K. . E-mail: John.Cowell@RoswellPark.org

    2005-09-10

    ZNF198 is fused with FGFR1 in an atypical myeloproliferative disease that results in constitutive activation of the kinase domain and mislocalization to the cytoplasm. We have used immunoprecipitation of a GFP-tagged ZNF198 combined with MALDI-TOF mass spectroscopy to identify interacting proteins. P splicing factor (PSF) was identified as one of the proteins and this interaction was confirmed by Western blotting. Other proteins identified were the spliceosomal components hnRNP A2/B1, hnRNP H3, and TLS/FUS. PSF is also known to interact with PTB, another member of the hnRNP family of proteins, and we further demonstrated that PTB interacts with ZNF198. The interaction between TLS/FUS and ZNF198 was confirmed using Western blot analysis. In 293 cells expressing the ZNF198/FGFR1 fusion protein, neither PSF nor PTB binds to the fusion protein, possibly because of their differential localization in the cell.

  3. Novel Human Embryonic Stem Cell Regulators Identified by Conserved and Distinct CpG Island Methylation State

    PubMed Central

    Pells, Steve; Koutsouraki, Eirini; Morfopoulou, Sofia; Valencia-Cadavid, Sara; Tomlinson, Simon R.; Kalathur, Ravi; Futschik, Matthias E.; De Sousa, Paul A.

    2015-01-01

    Human embryonic stem cells (hESCs) undergo epigenetic changes in vitro which may compromise function, so an epigenetic pluripotency “signature” would be invaluable for line validation. We assessed Cytosine-phosphate-Guanine Island (CGI) methylation in hESCs by genomic DNA hybridisation to a CGI array, and saw substantial variation in CGI methylation between lines. Comparison of hESC CGI methylation profiles to corresponding somatic tissue data and hESC mRNA expression profiles identified a conserved hESC-specific methylation pattern associated with expressed genes. Transcriptional repressors and activators were over-represented amongst genes whose associated CGIs were methylated or unmethylated specifically in hESCs, respectively. Knockdown of candidate transcriptional regulators (HMGA1, GLIS2, PFDN5) induced differentiation in hESCs, whereas ectopic expression in fibroblasts modulated iPSC colony formation. Chromatin immunoprecipitation confirmed interaction between the candidates and the core pluripotency transcription factor network. We thus identify novel pluripotency genes on the basis of a conserved and distinct epigenetic configuration in human stem cells. PMID:26151932

  4. Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control.

    PubMed

    Grant, Gavin D; Gamsby, Joshua; Martyanov, Viktor; Brooks, Lionel; George, Lacy K; Mahoney, J Matthew; Loros, Jennifer J; Dunlap, Jay C; Whitfield, Michael L

    2012-08-01

    We developed a system to monitor periodic luciferase activity from cell cycle-regulated promoters in synchronous cells. Reporters were driven by a minimal human E2F1 promoter with peak expression in G1/S or a basal promoter with six Forkhead DNA-binding sites with peak expression at G2/M. After cell cycle synchronization, luciferase activity was measured in live cells at 10-min intervals across three to four synchronous cell cycles, allowing unprecedented resolution of cell cycle-regulated gene expression. We used this assay to screen Forkhead transcription factors for control of periodic gene expression. We confirmed a role for FOXM1 and identified two novel cell cycle regulators, FOXJ3 and FOXK1. Knockdown of FOXJ3 and FOXK1 eliminated cell cycle-dependent oscillations and resulted in decreased cell proliferation rates. Analysis of genes regulated by FOXJ3 and FOXK1 showed that FOXJ3 may regulate a network of zinc finger proteins and that FOXK1 binds to the promoter and regulates DHFR, TYMS, GSDMD, and the E2F binding partner TFDP1. Chromatin immunoprecipitation followed by high-throughput sequencing analysis identified 4329 genomic loci bound by FOXK1, 83% of which contained a FOXK1-binding motif. We verified that a subset of these loci are activated by wild-type FOXK1 but not by a FOXK1 (H355A) DNA-binding mutant.

  5. Meta-analysis of IDH-mutant cancers identifies EBF1 as an interaction partner for TET2.

    PubMed

    Guilhamon, Paul; Eskandarpour, Malihe; Halai, Dina; Wilson, Gareth A; Feber, Andrew; Teschendorff, Andrew E; Gomez, Valenti; Hergovich, Alexander; Tirabosco, Roberto; Fernanda Amary, M; Baumhoer, Daniel; Jundt, Gernot; Ross, Mark T; Flanagan, Adrienne M; Beck, Stephan

    2013-01-01

    Isocitrate dehydrogenase (IDH) genes 1 and 2 are frequently mutated in acute myeloid leukaemia (AML), low-grade glioma, cholangiocarcinoma (CC) and chondrosarcoma (CS). For AML, low-grade glioma and CC, mutant IDH status is associated with a DNA hypermethylation phenotype, implicating altered epigenome dynamics in the aetiology of these cancers. Here we show that the IDH variants in CS are also associated with a hypermethylation phenotype and display increased production of the oncometabolite 2-hydroxyglutarate, supporting the role of mutant IDH-produced 2-hydroxyglutarate as an inhibitor of TET-mediated DNA demethylation. Meta-analysis of the acute myeloid leukaemia, low-grade glioma, cholangiocarcinoma and CS methylation data identifies cancer-specific effectors within the retinoic acid receptor activation pathway among the hypermethylated targets. By analysing sequence motifs surrounding hypermethylated sites across the four cancer types, and using chromatin immunoprecipitation and western blotting, we identify the transcription factor EBF1 (early B-cell factor 1) as an interaction partner for TET2, suggesting a sequence-specific mechanism for regulating DNA methylation.

  6. 10 Ways to Identify Hearing Loss

    MedlinePlus

    Skip Navigation Bar Home Current Issue Past Issues 10 Ways to Identify Hearing Loss Past Issues / Spring ... due to excessive noise exposure and other causes. 10 Ways to Identify Hearing Loss Take the following ...

  7. 10 Ways to Identify Hearing Loss

    MedlinePlus

    ... page please turn JavaScript on. Feature: Hearing Loss 10 Ways to Identify Hearing Loss Past Issues / Spring ... Research / Screening Newborns / How Loud Is Too Loud? / 10 Ways to Identify Hearing Loss Spring 2015 Issue: ...

  8. Structural Identifiability of Viscoelastic Mechanical Systems

    PubMed Central

    2014-01-01

    We solve the local and global structural identifiability problems for viscoelastic mechanical models represented by networks of springs and dashpots. We propose a very simple characterization of both local and global structural identifiability based on identifiability tables, with the purpose of providing a guideline for constructing arbitrarily complex, identifiable spring-dashpot networks. We illustrate how to use our results in a number of examples and point to some applications in cardiovascular modeling. PMID:24523860

  9. Ability of Slovakian Pupils to Identify Birds

    ERIC Educational Resources Information Center

    Prokop, Pavol; Rodak, Rastislav

    2009-01-01

    A pupil's ability to identify common organisms is necessary for acquiring further knowledge of biology. We investigated how pupils were able to identify 25 bird species following their song, growth habits, or both features presented simultaneously. Just about 19% of birds were successfully identified by song, about 39% by growth habit, and 45% of…

  10. Method of identifying plant pathogen tolerance

    DOEpatents

    Ecker, J.R.; Staskawicz, B.J.; Bent, A.F.; Innes, R.W.

    1997-10-07

    A process for identifying a plant having disease tolerance comprising administering to a plant an inhibitory amount of ethylene and screening for ethylene insensitivity, thereby identifying a disease tolerant plant, is described. Plants identified by the foregoing process are also described. 7 figs.

  11. Method of identifying plant pathogen tolerance

    DOEpatents

    Ecker, Joseph R.; Staskawicz, Brian J.; Bent, Andrew F.; Innes, Roger W.

    1997-10-07

    A process for identifying a plant having disease tolerance comprising administering to a plant an inhibitory amount of ethylene and screening for ethylene insensitivity, thereby identifying a disease tolerant plant, is described. Plants identified by the foregoing process are also described.

  12. Identifying Codes on Directed De Bruijn Graphs

    DTIC Science & Technology

    2015-08-27

    JOURNAL ARTICLE (POST PRINT) 3. DATES COVERED (From - To) JUN 2013 – AUG 2015 4. TITLE AND SUBTITLE IDENTIFYING CODES ON DIRECTED DE BRUIJN GRAPHS 5a...owner. 14. ABSTRACT For a directed graph G, a t-identifying code is a subset S ⊆ V (G) with the property that for each vertex v ∈ V (G) the set of...t-identifying code . This paper shows that the directed de Bruijn graph B(d, n) is t- identifiable for n ≥ 2t−1, and is not t-identifiable for n ≤ 2t

  13. Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci.

    PubMed

    Sazonova, Olga; Zhao, Yuqi; Nürnberg, Sylvia; Miller, Clint; Pjanic, Milos; Castano, Victor G; Kim, Juyong B; Salfati, Elias L; Kundaje, Anshul B; Bejerano, Gill; Assimes, Themistocles; Yang, Xia; Quertermous, Thomas

    2015-05-01

    To functionally link coronary artery disease (CAD) causal genes identified by genome wide association studies (GWAS), and to investigate the cellular and molecular mechanisms of atherosclerosis, we have used chromatin immunoprecipitation sequencing (ChIP-Seq) with the CAD associated transcription factor TCF21 in human coronary artery smooth muscle cells (HCASMC). Analysis of identified TCF21 target genes for enrichment of molecular and cellular annotation terms identified processes relevant to CAD pathophysiology, including "growth factor binding," "matrix interaction," and "smooth muscle contraction." We characterized the canonical binding sequence for TCF21 as CAGCTG, identified AP-1 binding sites in TCF21 peaks, and by conducting ChIP-Seq for JUN and JUND in HCASMC confirmed that there is significant overlap between TCF21 and AP-1 binding loci in this cell type. Expression quantitative trait variation mapped to target genes of TCF21 was significantly enriched among variants with low P-values in the GWAS analyses, suggesting a possible functional interaction between TCF21 binding and causal variants in other CAD disease loci. Separate enrichment analyses found over-representation of TCF21 target genes among CAD associated genes, and linkage disequilibrium between TCF21 peak variation and that found in GWAS loci, consistent with the hypothesis that TCF21 may affect disease risk through interaction with other disease associated loci. Interestingly, enrichment for TCF21 target genes was also found among other genome wide association phenotypes, including height and inflammatory bowel disease, suggesting a functional profile important for basic cellular processes in non-vascular tissues. Thus, data and analyses presented here suggest that study of GWAS transcription factors may be a highly useful approach to identifying disease gene interactions and thus pathways that may be relevant to complex disease etiology.

  14. Computational analysis of siRNA recognition by the Ago2 PAZ domain and identification of the determinants of RNA-induced gene silencing.

    PubMed

    Kandeel, Mahmoud; Kitade, Yukio

    2013-01-01

    RNA interference (RNAi) is a highly specialized process of protein-siRNA interaction that results in the regulation of gene expression and cleavage of target mRNA. The PAZ domain of the Argonaute proteins binds to the 3' end of siRNA, and during RNAi the attaching end of the siRNA switches between binding and release from its binding pocket. This biphasic interaction of the 3' end of siRNA with the PAZ domain is essential for RNAi activity; however, it remains unclear whether stronger or weaker binding with PAZ domain will facilitate or hinder the overall RNAi process. Here we report the correlation between the binding of modified siRNA 3' overhang analogues and their in vivo RNAi efficacy. We found that higher RNAi efficacy was associated with the parameters of lower Ki value, lower total intermolecular energy, lower free energy, higher hydrogen bonding, smaller total surface of interaction and fewer van der Waals interactions. Electrostatic interaction was a minor contributor to compounds recognition, underscoring the presence of phosphate groups in the modified analogues. Thus, compounds with lower binding affinity are associated with better gene silencing. Lower binding strength along with the smaller interaction surface, higher hydrogen bonding and fewer van der Waals interactions were among the markers for favorable RNAi activity. Within the measured parameters, the interaction surface, van der Waals interactions and inhibition constant showed a statistically significant correlation with measured RNAi efficacy. The considerations provided in this report will be helpful in the design of new compounds with better gene silencing ability.

  15. On the identifiability of metabolic network models.

    PubMed

    Berthoumieux, Sara; Brilli, Matteo; Kahn, Daniel; de Jong, Hidde; Cinquemani, Eugenio

    2013-12-01

    A major problem for the identification of metabolic network models is parameter identifiability, that is, the possibility to unambiguously infer the parameter values from the data. Identifiability problems may be due to the structure of the model, in particular implicit dependencies between the parameters, or to limitations in the quantity and quality of the available data. We address the detection and resolution of identifiability problems for a class of pseudo-linear models of metabolism, so-called linlog models. Linlog models have the advantage that parameter estimation reduces to linear or orthogonal regression, which facilitates the analysis of identifiability. We develop precise definitions of structural and practical identifiability, and clarify the fundamental relations between these concepts. In addition, we use singular value decomposition to detect identifiability problems and reduce the model to an identifiable approximation by a principal component analysis approach. The criterion is adapted to real data, which are frequently scarce, incomplete, and noisy. The test of the criterion on a model with simulated data shows that it is capable of correctly identifying the principal components of the data vector. The application to a state-of-the-art dataset on central carbon metabolism in Escherichia coli yields the surprising result that only 4 out of 31 reactions, and 37 out of 100 parameters, are identifiable. This underlines the practical importance of identifiability analysis and model reduction in the modeling of large-scale metabolic networks. Although our approach has been developed in the context of linlog models, it carries over to other pseudo-linear models, such as generalized mass-action (power-law) models. Moreover, it provides useful hints for the identifiability analysis of more general classes of nonlinear models of metabolism.

  16. Self-Identifying Emergency Radio Beacons

    NASA Technical Reports Server (NTRS)

    Friedman, Morton L.

    1987-01-01

    Rescue teams aided by knowledge of vehicle in distress. Similar to conventional emergency transmitters except contains additional timing and modulating circuits. Additions to standard emergency transmitter enable transmitter to send rescuers identifying signal in addition to conventional distress signal created by sweep generator. Data generator contains identifying code.

  17. Identifying Bilingual Semantic Neural Representations across Languages

    ERIC Educational Resources Information Center

    Buchweitz, Augusto; Shinkareva, Svetlana V.; Mason, Robert A.; Mitchell, Tom M.; Just, Marcel Adam

    2012-01-01

    The goal of the study was to identify the neural representation of a noun's meaning in one language based on the neural representation of that same noun in another language. Machine learning methods were used to train classifiers to identify which individual noun bilingual participants were thinking about in one language based solely on their…

  18. Healthcare Identifiers legislation: a whiff of fourberie.

    PubMed

    Mendelson, Danuta

    2010-05-01

    The Healthcare Identifiers Bill 2010 (Cth), which will establish "the national e-health Healthcare Identifiers Service to provide that patients, healthcare providers and provider organisations can be consistently identified", is in the process of being enacted by the Australian Federal Parliament. The legislation will enable the government to assign to each "healthcare recipient" a 26-digit electronic "Healthcare Identifier", which will be accessible, with or without the recipient's consent, to a broad range of health care service providers as well as other entities. The individual Healthcare Identifier file will initially contain such identifying information as, where applicable, the Medicare number and/or the Veterans' Affairs number; name; address; gender; date of birth; and "the date of birth accuracy indicator" presumably birth certificate. However, since each "service" provided by a health care provider to a health care recipient will be automatically recorded on each individual's Healthcare Identifier file, in time these electronic files should contain a full record of such services or contacts. Moreover, the Healthcare Identifiers are considered a "key" to, or a "foundation stone" for, the implementation of the shared electronic health records scheme, because they will enable linkage with and retrieval of each patient's clinical records throughout the health care service system. However, there has been virtually no discussion about the legal, ethical and social implications of this legislation.

  19. Identifying Information Focuses in Listening Comprehension

    ERIC Educational Resources Information Center

    Zhang, Hong-yan

    2011-01-01

    The study explains the process of learners' listening comprehension within Halliday's information theory in functional grammar, including the skills of identifying focuses while listening in college English teaching. Identifying information focuses in listening is proved to improve the students' communicative listening ability by the means of a…

  20. Identifying Opinion Leaders to Promote Behavior Change

    ERIC Educational Resources Information Center

    Valente, Thomas W.; Pumpuang, Patchareeya

    2007-01-01

    This article reviews 10 techniques used to identify opinion leaders to promote behavior change. Opinion leaders can act as gatekeepers for interventions, help change social norms, and accelerate behavior change. Few studies document the manner in which opinion leaders are identified, recruited, and trained to promote health. The authors categorize…

  1. Portable Radiometer Identifies Minerals in the Field

    NASA Technical Reports Server (NTRS)

    Goetz, A. F. H.; Machida, R. A.

    1982-01-01

    Hand-held optical instrument aids in identifying minerals in field. Can be used in exploration for minerals on foot or by aircraft. The radiometer is especially suitable for identifying clay and carbonate minerals. Radiometer measures reflectances of mineral at two wavelengths, computes ratio of reflectances, and displays ratio to user.

  2. Parameter Identifiability of Fundamental Pharmacodynamic Models

    PubMed Central

    Janzén, David L. I.; Bergenholm, Linnéa; Jirstrand, Mats; Parkinson, Joanna; Yates, James; Evans, Neil D.; Chappell, Michael J.

    2016-01-01

    Issues of parameter identifiability of routinely used pharmacodynamics models are considered in this paper. The structural identifiability of 16 commonly applied pharmacodynamic model structures was analyzed analytically, using the input-output approach. Both fixed-effects versions (non-population, no between-subject variability) and mixed-effects versions (population, including between-subject variability) of each model structure were analyzed. All models were found to be structurally globally identifiable under conditions of fixing either one of two particular parameters. Furthermore, an example was constructed to illustrate the importance of sufficient data quality and show that structural identifiability is a prerequisite, but not a guarantee, for successful parameter estimation and practical parameter identifiability. This analysis was performed by generating artificial data of varying quality to a structurally identifiable model with known true parameter values, followed by re-estimation of the parameter values. In addition, to show the benefit of including structural identifiability as part of model development, a case study was performed applying an unidentifiable model to real experimental data. This case study shows how performing such an analysis prior to parameter estimation can improve the parameter estimation process and model performance. Finally, an unidentifiable model was fitted to simulated data using multiple initial parameter values, resulting in highly different estimated uncertainties. This example shows that although the standard errors of the parameter estimates often indicate a structural identifiability issue, reasonably “good” standard errors may sometimes mask unidentifiability issues. PMID:27994553

  3. Marking Identifiable Scripts: Following up Student Concerns

    ERIC Educational Resources Information Center

    Owen, Cathy; Stefaniak, John; Corrigan, Gerry

    2010-01-01

    Introduction: Medical student concern that the submission of named examination scripts to examiners could cause bias initiated a study on the effect of identified and de-identified scripts on assessment outcome. Methods: Data were collected from a convenience examination sample of Year 1 (n = 88 students; n = 29 questions) and Year 2 scripts (n =…

  4. EZID: Long term identifiers made easy (Invited)

    NASA Astrophysics Data System (ADS)

    Starr, J.

    2013-12-01

    Scholarly research is producing ever increasing amounts of digital research data, and this data should be managed throughout the research life cycle both as part of good scientific practice, but also to comply with funder mandates, such as the 2013 OSTP Public Access Memo (http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf). By assigning unique and persistent identifiers to data objects, data managers can gain control and flexibility over what can be a daunting task. This is due to the fact that the objects can be moved to new locations without disruption to links, as long as the identifier target is maintained. EZID is a tool that makes assigning and maintaining unique, persistent identifiers easy. It was designed and built by California Digital Library (CDL) and has both a user interface and a RESTful API. EZID currently offers services for two globally unique, persistent identifier schemes: Digital Object Identifiers (DOIs) and Archival Resource Keys (ARKs). DOIs are identifiers originating from the publishing world and are in widespread use for journal articles. CDL is able to offer DOIs because of being a founding member of DataCite (http://www.datacite.org/), an international consortium established to provide easier access to scientific research data on the Internet. ARKs are identifiers originating from the library, archive and museum community. Like DOIs, they become persistent when the objects and identifier forwarding information is maintained. DOIs and ARKs have a key role in data management and, therefore, in data management plans. DOIs are the recommended identifier for use in data citation, and ARKs provide the maximum flexibility needed for data documentation and management throughout the early phases of a project. The two identifier schemes are able to be used together, and EZID is made to work with both. EZID clients, coming from education, research, government, and the private sector, are utilizing the

  5. RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

    PubMed Central

    2014-01-01

    Background Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects of gene regulation. Comprehensive knowledge of the RNA components of Sm RNPs is critical for understanding their functions. Results We developed a multi-targeting RNA-immunoprecipitation sequencing (RIP-seq) strategy to reliably identify Sm-associated RNAs from Drosophila ovaries and cultured human cells. Using this method, we discovered three major categories of Sm-associated transcripts: small nuclear (sn)RNAs, small Cajal body (sca)RNAs and mRNAs. Additional RIP-PCR analysis showed both ubiquitous and tissue-specific interactions. We provide evidence that the mRNA-Sm interactions are mediated by snRNPs, and that one of the mechanisms of interaction is via base pairing. Moreover, the Sm-associated mRNAs are mature, indicating a splicing-independent function for Sm RNPs. Conclusions This study represents the first comprehensive analysis of eukaryotic Sm-containing RNPs, and provides a basis for additional functional analyses of Sm proteins and their associated snRNPs outside of the context of pre-mRNA splicing. Our findings expand the repertoire of eukaryotic Sm-containing RNPs and suggest new functions for snRNPs in mRNA metabolism. PMID:24393626

  6. Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb.

    PubMed

    Zhao, Liang; Glazov, Evgeny A; Pattabiraman, Diwakar R; Al-Owaidi, Faisal; Zhang, Ping; Brown, Matthew A; Leo, Paul J; Gonda, Thomas J

    2011-06-01

    To gain insight into the mechanisms by which the Myb transcription factor controls normal hematopoiesis and particularly, how it contributes to leukemogenesis, we mapped the genome-wide occupancy of Myb by chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) in ERMYB myeloid progenitor cells. By integrating the genome occupancy data with whole genome expression profiling data, we identified a Myb-regulated transcriptional program. Gene signatures for leukemia stem cells, normal hematopoietic stem/progenitor cells and myeloid development were overrepresented in 2368 Myb regulated genes. Of these, Myb bound directly near or within 793 genes. Myb directly activates some genes known critical in maintaining hematopoietic stem cells, such as Gfi1 and Cited2. Importantly, we also show that, despite being usually considered as a transactivator, Myb also functions to repress approximately half of its direct targets, including several key regulators of myeloid differentiation, such as Sfpi1 (also known as Pu.1), Runx1, Junb and Cebpb. Furthermore, our results demonstrate that interaction with p300, an established coactivator for Myb, is unexpectedly required for Myb-mediated transcriptional repression. We propose that the repression of the above mentioned key pro-differentiation factors may contribute essentially to Myb's ability to suppress differentiation and promote self-renewal, thus maintaining progenitor cells in an undifferentiated state and promoting leukemic transformation.

  7. Structural Identifiability of Dynamic Systems Biology Models

    PubMed Central

    Villaverde, Alejandro F.

    2016-01-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas. PMID:27792726

  8. Identifying Codes on Directed De Bruijn Graphs

    DTIC Science & Technology

    2014-12-19

    ar X iv :1 41 2. 58 42 v1 [ m at h. C O ] 1 8 D ec 2 01 4 Identifying Codes on Directed De Bruijn Graphs Debra Boutin ∗ Department of...Mathematics Hamilton College Victoria Horan † Air Force Research Laboratory Information Directorate December 19, 2014 Abstract For a directed graph G, a t...length at most t is both non-empty and unique. A graph is called t-identifiable if there exists a t-identifying code. This paper shows that the de

  9. Asteroid Redirect Mission: Identify, Redirect, Explore

    NASA Video Gallery

    NASA is developing a first-ever mission to identify, capture and redirect a near-Earth asteroid to a stable orbit around the moon, where astronauts will explore it in the 2020s, returning with samp...

  10. Study Identifies New Lymphoma Treatment Target

    Cancer.gov

    NCI researchers have identified new therapeutic targets for diffuse large B-cell lymphoma. Drugs that hit these targets are under clinical development and the researchers hope to begin testing them in clinical trials of patients with DLBCL.

  11. Identifying associations between genomic alterations in tumors.

    PubMed

    George, Joshy; Gorringe, Kylie L; Smyth, Gordon K; Bowtell, David D L

    2013-01-01

    Single-nucleotide polymorphism (SNP) mapping arrays are a reliable method for identifying somatic copy number alterations in cancer samples. Though this is immensely useful to identify potential driver genes, it is not sufficient to identify genes acting in a concerted manner. In cancer cells, co-amplified genes have been shown to provide synergistic effects, and genomic alterations targeting a pathway have been shown to occur in a mutually exclusive manner. We therefore developed a bioinformatic method for detecting such gene pairs using an integrated analysis of genomic copy number and gene expression data. This approach allowed us to identify a gene pair that is co-amplified and co-expressed in high-grade serous ovarian cancer. This finding provided information about the interaction of specific genetic events that contribute to the development and progression of this disease.

  12. Determining the identifiability of DNA database entries.

    PubMed Central

    Malin, B.; Sweeney, L.

    2000-01-01

    CleanGene is a software program that helps determine the identifiability of sequenced DNA, independent of any explicit demographics or identifiers maintained with the DNA. The program computes the likelihood that the release of DNA database entries could be related to specific individuals that are the subjects of the data. The engine within CleanGene relies on publicly available health care data and on knowledge of particular diseases to help relate identified individuals to DNA entries. Over 20 diseases, ranging over ataxias, blood diseases, and sex-linked mutations are accounted for, with 98-100% of individuals found identifiable. We assume the genetic material is released in a linear sequencing format from an individual's genome. CleanGene and its related experiments are useful tools for any institution seeking to provide anonymous genetic material for research purposes. PMID:11079941

  13. IDENTIFYING KEY CONTRIBUTIONS TO INFORMATION SCIENCE,

    DTIC Science & Technology

    Several alternative approaches were examined to determine how one might identify some of the key (written) contributions to ’ information science ’. The...references. The unclear selective patterns in current bibliographies in the information science field also present problems. It is suggested that in...identifying key contributions we are far from common agreement on the conceptual, methodological or practical contributions to the information science field

  14. Identifying ECM Mediators of Tumor Cell Dormancy

    DTIC Science & Technology

    2008-05-01

    proliferating cells. f) At time of euthanasia, stage of estrous will be determined by vaginal smear so that inter- animal variation due to estrous...ratio of the number of distinct peptides identified for each protein divided by the total number of peptides identified in the two hour run are...displayed as the peptide count ratio. Using this peptide counting label-free quantification approach, surprisingly, suggested that the three fibrillar

  15. Identifying ECM Mediators of Tumor Cell Dormancy

    DTIC Science & Technology

    2009-05-01

    determined by vaginal smear so that inter- animal variation due to estrous can be controlled for across groups. Further, cervical samples will be... peptides identified for each protein divided by the total number of peptides identified in the two hour run are displayed as the peptide count ratio...Using this peptide counting label-free quantification approach, surprisingly, suggested that the three fibrillar collagen chains were at lower levels in

  16. Newly identified YSO candidates towards LDN 1188

    NASA Astrophysics Data System (ADS)

    Marton , G.; Verebélyi, E.; Kiss, Cs.; Smidla, J.

    2013-11-01

    We present an analysis of young stellar object (YSO) candidates towards the LDN 1188 molecular cloud. The YSO candidates were selected from the WISE all-sky catalogue, based on a statistical method. We found 601 candidates in the region, and classified them as Class I, Flat, and Class II YSOs. Groups were identified and described with the Minimal Spanning Tree (MST) method. Previously identified molecular cores show evidence of ongoing star formation at different stages throughout the cloud complex.

  17. ORCID Author Identifiers: A Primer for Librarians.

    PubMed

    Akers, Katherine G; Sarkozy, Alexandra; Wu, Wendy; Slyman, Alison

    2016-01-01

    The ORCID (Open Researcher and Contributor ID) registry helps disambiguate authors and streamline research workflows by assigning unique 16-digit author identifiers that enable automatic linkages between researchers and their scholarly activities. This article describes how ORCID works, the benefits of using ORCID, and how librarians can promote ORCID at their institutions by raising awareness of ORCID, helping researchers create and populate ORCID profiles, and integrating ORCID identifiers into institutional repositories and other university research information systems.

  18. Exploiting intrinsic fluctuations to identify model parameters.

    PubMed

    Zimmer, Christoph; Sahle, Sven; Pahle, Jürgen

    2015-04-01

    Parameterisation of kinetic models plays a central role in computational systems biology. Besides the lack of experimental data of high enough quality, some of the biggest challenges here are identification issues. Model parameters can be structurally non-identifiable because of functional relationships. Noise in measured data is usually considered to be a nuisance for parameter estimation. However, it turns out that intrinsic fluctuations in particle numbers can make parameters identifiable that were previously non-identifiable. The authors present a method to identify model parameters that are structurally non-identifiable in a deterministic framework. The method takes time course recordings of biochemical systems in steady state or transient state as input. Often a functional relationship between parameters presents itself by a one-dimensional manifold in parameter space containing parameter sets of optimal goodness. Although the system's behaviour cannot be distinguished on this manifold in a deterministic framework it might be distinguishable in a stochastic modelling framework. Their method exploits this by using an objective function that includes a measure for fluctuations in particle numbers. They show on three example models, immigration-death, gene expression and Epo-EpoReceptor interaction, that this resolves the non-identifiability even in the case of measurement noise with known amplitude. The method is applied to partially observed recordings of biochemical systems with measurement noise. It is simple to implement and it is usually very fast to compute. This optimisation can be realised in a classical or Bayesian fashion.

  19. IDENTIFYING COLLISIONAL FAMILIES IN THE KUIPER BELT

    SciTech Connect

    Marcus, Robert A.; Ragozzine, Darin; Murray-Clay, Ruth A.; Holman, Matthew J.

    2011-05-20

    The identification and characterization of numerous collisional families-clusters of bodies with a common collisional origin-in the asteroid belt has added greatly to the understanding of asteroid belt formation and evolution. More recent study has also led to an appreciation of physical processes that had previously been neglected (e.g., the Yarkovsky effect). Collisions have certainly played an important role in the evolution of the Kuiper Belt as well, though only one collisional family has been identified in that region to date, around the dwarf planet Haumea. In this paper, we combine insights into collisional families from numerical simulations with the current observational constraints on the dynamical structure of the Kuiper Belt to investigate the ideal sizes and locations for identifying collisional families. We find that larger progenitors (r {approx} 500 km) result in more easily identifiable families, given the difficulty in identifying fragments of smaller progenitors in magnitude-limited surveys, despite their larger spread and less frequent occurrence. However, even these families do not stand out well from the background. Identifying families as statistical overdensities is much easier than characterizing families by distinguishing individual members from interlopers. Such identification seems promising, provided the background population is well known. In either case, families will also be much easier to study where the background population is small, i.e., at high inclinations. Overall, our results indicate that entirely different techniques for identifying families will be needed for the Kuiper Belt, and we provide some suggestions.

  20. Identifying nineteenth century genealogical links from genotypes.

    PubMed

    Stankovich, Jim; Bahlo, Melanie; Rubio, Justin P; Wilkinson, Christopher R; Thomson, Russell; Banks, Annette; Ring, Maree; Foote, Simon J; Speed, Terence P

    2005-07-01

    We have developed a likelihood method to identify moderately distant genealogical relationships from genomewide scan data. The aim is to compare the genotypes of many pairs of people and identify those pairs most likely to be related to one another. We have tested the algorithm using the genotypes of 170 Tasmanians with multiple sclerosis recruited into a haplotype association study. It is estimated from genealogical records that approximately 65% of Tasmania's current population of 470,000 are direct descendants of the 13,000 female founders living in this island state of Australia in the mid-nineteenth century. All cases and four to five relatives of each case have been genotyped with microsatellite markers at a genomewide average density of 4 cM. Previous genealogical research has identified 51 pairwise relationships linking 56 of the 170 cases. Testing the likelihood calculation on these known relative pairs, we have good power to identify relationships up to degree eight (e.g. third cousins once removed). Applying the algorithm to all other pairs of cases, we have identified a further 61 putative relative pairs, with an estimated false discovery rate of 10%. The power to identify genealogical links should increase when the new, denser sets of SNP markers are used. Except in populations where there is a searchable electronic database containing virtually all genealogical links in the past six generations, the algorithm should be a useful aid for genealogists working on gene-mapping projects, both linkage studies and association studies.

  1. Combined Antibody/Lectin Enrichment Identifies Extensive Changes in the O-GlcNAc Sub-proteome upon Oxidative Stress.

    PubMed

    Lee, Albert; Miller, Devin; Henry, Roger; Paruchuri, Venkata D P; O'Meally, Robert N; Boronina, Tatiana; Cole, Robert N; Zachara, Natasha E

    2016-12-02

    O-Linked N-acetyl-β-d-glucosamine (O-GlcNAc) is a dynamic post-translational modification that modifies and regulates over 3000 nuclear, cytoplasmic, and mitochondrial proteins. Upon exposure to stress and injury, cells and tissues increase the O-GlcNAc modification, or O-GlcNAcylation, of numerous proteins promoting the cellular stress response and thus survival. The aim of this study was to identify proteins that are differentially O-GlcNAcylated upon acute oxidative stress (H2O2) to provide insight into the mechanisms by which O-GlcNAc promotes survival. We achieved this goal by employing Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC) and a novel "G5-lectibody" immunoprecipitation strategy that combines four O-GlcNAc-specific antibodies (CTD110.6, RL2, HGAC39, and HGAC85) and the lectin WGA. Using the G5-lectibody column in combination with basic reversed phase chromatography and C18 RPLC-MS/MS, 990 proteins were identified and quantified. Hundreds of proteins that were identified demonstrated increased (>250) or decreased (>110) association with the G5-lectibody column upon oxidative stress, of which we validated the O-GlcNAcylation status of 24 proteins. Analysis of proteins with altered glycosylation suggests that stress-induced changes in O-GlcNAcylation cluster into pathways known to regulate the cell's response to injury and include protein folding, transcriptional regulation, epigenetics, and proteins involved in RNA biogenesis. Together, these data suggest that stress-induced O-GlcNAcylation regulates numerous and diverse cellular pathways to promote cell and tissue survival.

  2. Genome-wide analysis of glucocorticoid receptor-binding sites in myotubes identifies gene networks modulating insulin signaling.

    PubMed

    Kuo, Taiyi; Lew, Michelle J; Mayba, Oleg; Harris, Charles A; Speed, Terence P; Wang, Jen-Chywan

    2012-07-10

    Glucocorticoids elicit a variety of biological responses in skeletal muscle, including inhibiting protein synthesis and insulin-stimulated glucose uptake and promoting proteolysis. Thus, excess or chronic glucocorticoid exposure leads to muscle atrophy and insulin resistance. Glucocorticoids propagate their signal mainly through glucocorticoid receptors (GR), which, upon binding to ligands, translocate to the nucleus and bind to genomic glucocorticoid response elements to regulate the transcription of nearby genes. Using a combination of chromatin immunoprecipitation sequencing and microarray analysis, we identified 173 genes in mouse C2C12 myotubes. The mouse genome contains GR-binding regions in or near these genes, and gene expression is regulated by glucocorticoids. Eight of these genes encode proteins known to regulate distinct signaling events in insulin/insulin-like growth factor 1 pathways. We found that overexpression of p85α, one of these eight genes, caused a decrease in C2C12 myotube diameters, mimicking the effect of glucocorticoids. Moreover, reducing p85α expression by RNA interference in C2C12 myotubes significantly compromised the ability of glucocorticoids to inhibit Akt and p70 S6 kinase activity and reduced glucocorticoid induction of insulin receptor substrate 1 phosphorylation at serine 307. This phosphorylation is associated with insulin resistance. Furthermore, decreasing p85α expression abolished glucocorticoid inhibition of protein synthesis and compromised glucocorticoid-induced reduction of cell diameters in C2C12 myotubes. Finally, a glucocorticoid response element was identified in the p85α GR-binding regions. In summary, our studies identified GR-regulated transcriptional networks in myotubes and showed that p85α plays a critical role in glucocorticoid-induced insulin resistance and muscle atrophy in C2C12 myotubes.

  3. Identifying glass compositions in fly ash

    NASA Astrophysics Data System (ADS)

    Aughenbaugh, Katherine; Stutzman, Paul; Juenger, Maria

    2016-01-01

    In this study, four Class F fly ashes were studied with a scanning electron microscope; the glassy phases were identified and their compositions quantified using point compositional analysis with k-means clustering and multispectral image analysis. The results showed that while the bulk oxide contents of the fly ashes were different, the four fly ashes had somewhat similar glassy phase compositions. Aluminosilicate glasses (AS), calcium aluminosilicate glasses (CAS), a mixed glass, and, in one case, a high iron glass were identified in the fly ashes. Quartz and iron crystalline phases were identified in each fly ash as well. The compositions of the three main glasses identified, AS, CAS, and mixed glass, were relatively similar in each ash. The amounts of each glass were varied by fly ash, with the highest calcium fly ash containing the most of calcium-containing glass. Some of the glasses were identified as intermixed in individual particles, particularly the calcium-containing glasses. Finally, the smallest particles in the fly ashes, with the most surface area available to react in alkaline solution, such as when mixed with portland cement or in alkali-activated fly ash, were not different in composition than the large particles, with each of the glasses represented. The method used in the study may be applied to a fly ash of interest for use as a cementing material in order to understand its potential for reactivity.

  4. Argonaute proteins regulate HIV-1 multiply spliced RNA and viral production in a Dicer independent manner.

    PubMed

    Eckenfelder, Agathe; Ségéral, Emmanuel; Pinzón, Natalia; Ulveling, Damien; Amadori, Céline; Charpentier, Marine; Nidelet, Sabine; Concordet, Jean-Paul; Zagury, Jean-François; Paillart, Jean-Christophe; Berlioz-Torrent, Clarisse; Seitz, Hervé; Emiliani, Stéphane; Gallois-Montbrun, Sarah

    2016-12-20

    Argonaute (Ago) proteins associate with microRNAs (miRNAs) to form the core of the RNA-induced silencing complex (RISC) that mediates post-transcriptional gene silencing of target mRNAs. As key players in anti-viral defense, Ago proteins are thought to have the ability to interact with human immunodeficiency virus type 1 (HIV-1) RNA. However, the role of this interaction in regulating HIV-1 replication has been debated. Here, we used high throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) to explore the interaction between Ago2 and HIV-1 RNA in infected cells. By only considering reads of 50 nucleotides length in our analysis, we identified more than 30 distinct binding sites for Ago2 along the viral RNA genome. Using reporter assays, we found four binding sites, located near splice donor sites, capable of repressing Luciferase gene expression in an Ago-dependent manner. Furthermore, inhibition of Ago1 and Ago2 levels in cells expressing HIV-1 led to an increase of viral multiply spliced transcripts and to a strong reduction in the extracellular CAp24 level. Depletion of Dicer did not affect these activities. Our results highlight a new role of Ago proteins in the control of multiply spliced HIV-1 transcript levels and viral production, independently of the miRNA pathway.

  5. Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data–Application to Monocyte Gene Regulation

    PubMed Central

    Choudhury, Mudra; Ramsey, Stephen A.

    2016-01-01

    We describe a novel computational approach to identify transcription factors (TFs) that are candidate regulators in a human cell type of interest. Our approach involves integrating cell type-specific expression quantitative trait locus (eQTL) data and TF data from chromatin immunoprecipitation-to-tag-sequencing (ChIP-seq) experiments in cell lines. To test the method, we used eQTL data from human monocytes in order to screen for TFs. Using a list of known monocyte-regulating TFs, we tested the hypothesis that the binding sites of cell type-specific TF regulators would be concentrated in the vicinity of monocyte eQTLs. For each of 397 ChIP-seq data sets, we obtained an enrichment ratio for the number of ChIP-seq peaks that are located within monocyte eQTLs. We ranked ChIP-seq data sets according to their statistical significances for eQTL overlap, and from this ranking, we observed that monocyte-regulating TFs are more highly ranked than would be expected by chance. We identified 27 TFs that had significant monocyte enrichment scores and mapped them into a protein interaction network. Our analysis uncovered two novel candidate monocyte-regulating TFs, BCLAF1 and SIN3A. Our approach is an efficient method to identify candidate TFs that can be used for any cell/tissue type for which eQTL data are available. PMID:28008225

  6. Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data-Application to Monocyte Gene Regulation.

    PubMed

    Choudhury, Mudra; Ramsey, Stephen A

    2016-01-01

    We describe a novel computational approach to identify transcription factors (TFs) that are candidate regulators in a human cell type of interest. Our approach involves integrating cell type-specific expression quantitative trait locus (eQTL) data and TF data from chromatin immunoprecipitation-to-tag-sequencing (ChIP-seq) experiments in cell lines. To test the method, we used eQTL data from human monocytes in order to screen for TFs. Using a list of known monocyte-regulating TFs, we tested the hypothesis that the binding sites of cell type-specific TF regulators would be concentrated in the vicinity of monocyte eQTLs. For each of 397 ChIP-seq data sets, we obtained an enrichment ratio for the number of ChIP-seq peaks that are located within monocyte eQTLs. We ranked ChIP-seq data sets according to their statistical significances for eQTL overlap, and from this ranking, we observed that monocyte-regulating TFs are more highly ranked than would be expected by chance. We identified 27 TFs that had significant monocyte enrichment scores and mapped them into a protein interaction network. Our analysis uncovered two novel candidate monocyte-regulating TFs, BCLAF1 and SIN3A. Our approach is an efficient method to identify candidate TFs that can be used for any cell/tissue type for which eQTL data are available.

  7. Identifying non-resonant Kepler planetary systems

    NASA Astrophysics Data System (ADS)

    Veras, Dimitri; Ford, Eric B.

    2012-02-01

    The Kepler mission has discovered a plethora of multiple transiting planet candidate exosystems, many of which feature putative pairs of planets near mean motion resonance commensurabilities. Identifying potentially resonant systems could help guide future observations and enhance our understanding of planetary formation scenarios. We develop and apply an algebraic method to determine which Kepler two-planet systems cannot be in a first-fourth order resonance, given the current, publicly available data. This method identifies when any potentially resonant angle of a system must circulate. We identify and list 70 near-resonant systems which cannot actually reside in resonance, assuming a widely used formulation for deriving planetary masses from their observed radii and that these systems do not contain unseen bodies that affect the interactions of the observed planets. This work strengthens the argument that a high fraction of exoplanetary systems may be near resonance but not actually in resonance.

  8. Identifying Turbulent Structures through Topological Segmentation

    SciTech Connect

    Bremer, Peer-Timo; Gruber, Andrea; Bennett, Janine C.; Gyulassy, Attila; Kolla, Hemanth; Chen, Jacqueline H.; Grout, Ray W.

    2016-01-01

    A new method of extracting vortical structures from a turbulent flow is proposed whereby topological segmentation of an indicator function scalar field is used to identify the regions of influence of the individual vortices. This addresses a long-standing challenge in vector field topological analysis: indicator functions commonly used produce a scalar field based on the local velocity vector field; reconstructing regions of influence for a particular structure requires selecting a threshold to define vortex extent. In practice, the same threshold is rarely meaningful throughout a given flow. By also considering the topology of the indicator field function, the characteristics of vortex strength and extent can be separated and the ambiguity in the choice of the threshold reduced. The proposed approach is able to identify several types of vortices observed in a jet in cross-flow configuration simultaneously where no single threshold value for a selection of common indicator functions appears able to identify all of these vortex types.

  9. Scientometric methods for identifying emerging technologies

    DOEpatents

    Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

    2015-11-03

    Provided is a method of generating a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain.

  10. Photoacoustic tomography to identify inflammatory arthritis

    NASA Astrophysics Data System (ADS)

    Rajian, Justin Rajesh; Girish, Gandikota; Wang, Xueding

    2012-09-01

    Identifying neovascularity (angiogenesis) as an early feature of inflammatory arthritis can help in early accurate diagnosis and treatment monitoring of this disease. Photoacoustic tomography (PAT) is a hybrid imaging modality which relies on intrinsic differences in the optical absorption among the tissues being imaged. Since blood has highly absorbing chromophores including both oxygenated and deoxygenated hemoglobin, PAT holds potential in identifying early angiogenesis associated with inflammatory joint diseases. PAT is used to identify changes in the development of inflammatory arthritis in a rat model. Imaging at two different wavelengths, 1064 nm and 532 nm, on rats revealed that there is a significant signal enhancement in the ankle joints of the arthritis affected rats when compared to the normal control group. Histology images obtained from both the normal and the arthritis affected rats correlated well with the PAT findings. Results support the fact that the emerging PAT could become a new tool for clinical management of inflammatory arthritis.

  11. Computational methods to identify new antibacterial targets.

    PubMed

    McPhillie, Martin J; Cain, Ricky M; Narramore, Sarah; Fishwick, Colin W G; Simmons, Katie J

    2015-01-01

    The development of resistance to all current antibiotics in the clinic means there is an urgent unmet need for novel antibacterial agents with new modes of action. One of the best ways of finding these is to identify new essential bacterial enzymes to target. The advent of a number of in silico tools has aided classical methods of discovering new antibacterial targets, and these programs are the subject of this review. Many of these tools apply a cheminformatic approach, utilizing the structural information of either ligand or protein, chemogenomic databases, and docking algorithms to identify putative antibacterial targets. Considering the wealth of potential drug targets identified from genomic research, these approaches are perfectly placed to mine this rich resource and complement drug discovery programs.

  12. On identifiability of flexible structure parameters

    NASA Technical Reports Server (NTRS)

    Joshi, S. M.; Goglia, G. L.

    1983-01-01

    This report investigates the identifiability of modal parameters of flexible structures. Expressions are derived for Cramer-Rao lower bounds for the modal parameters, that is, frequencies, damping ratios and mode shapes or slopes. The optimal initial state, which maximizes the trace of the Fisher information matrix in the absence of persistent input, is obtained. The concepts discussed are applied to a finite-element model of the 122 meter hoop/column antenna. The numerical results show that the identifiability of the structural frequencies is excellent, followed by that of the damping ratios and the mode-slopes.

  13. Minimal covariant observables identifying all pure states

    NASA Astrophysics Data System (ADS)

    Carmeli, Claudio; Heinosaari, Teiko; Toigo, Alessandro

    2013-09-01

    It has been recently shown by Heinosaari, Mazzarella and Wolf (2013) [1] that an observable that identifies all pure states of a d-dimensional quantum system has minimally 4d-4 outcomes or slightly less (the exact number depending on d). However, no simple construction of this type of minimal observable is known. We investigate covariant observables that identify all pure states and have minimal number of outcomes. It is shown that the existence of this kind of observables depends on the dimension of the Hilbert space.

  14. Identifying the substance abuser in clinical practice.

    PubMed

    Bell, K

    1992-01-01

    Illicit drugs are used regularly by 14.5 million Americans. By identifying patients who abuse substances, the nurse will be better able to provide for the treatment interventions needed and omit ineffective treatment interventions. The patient will benefit by receiving timely and appropriate care. To identify substance abusers, the nurse must know effects of commonly abused drugs, their routes of administration, withdrawal signs, and the physical assessments that should be performed. The most common drugs abused are narcotics, depressants, antidepressants, anti-anxiety drugs, stimulants, hallucinogens, and marijuana.

  15. Identifying gaps in international food safety regulation.

    PubMed

    McGrady, Benn; Ho, Christina S

    2011-01-01

    The rise in food importation in countries such as the United States, coupled with food safety incidents, has led to increased concern with the safety of imported food. This concern has prompted discussion of how international law and governance mechanisms might enhance food safety. This paper identifies the objectives underlying multilateral approaches to food safety such as raising food safety standards abroad, information sharing and ensuring market access. The paper then explores how these objectives are integrated into the international system and identifies how the current state of the law creates imbalances in the pursuit of these objectives.

  16. Identifying node importance in complex networks

    NASA Astrophysics Data System (ADS)

    Hu, Ping; Fan, Wenli; Mei, Shengwei

    2015-07-01

    In this paper, we propose a novel node importance evaluation method from the perspective of the existence of mutual dependence among nodes. The node importance comprises its initial importance and the importance contributions from both the adjacent and non-adjacent nodes according to the dependence strength between them. From the simulation analyses on an example network and the ARPA network, we observe that our method can well identify the node importance. Then, the cascading failures on the Netscience and E-mail networks demonstrate that the networks are more vulnerable when continuously removing the important nodes identified by our method, which further proves the accuracy of our method.

  17. Interchange. Program Improvement Products Identified through Networking.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. National Center for Research in Vocational Education.

    This catalog lists exemplary field-based program improvement products identified by the Dissemination and Utilization Products and Services Program (D&U) at the National Center for Research in Vocational Education. It is designed to increase awareness of these products among vocational educators and to provide information about them that…

  18. Diagnostics Tools Identify Faults Prior to Failure

    NASA Technical Reports Server (NTRS)

    2013-01-01

    Through the SBIR program, Rochester, New York-based Impact Technologies LLC collaborated with Ames Research Center to commercialize the Center s Hybrid Diagnostic Engine, or HyDE, software. The fault detecting program is now incorporated into a software suite that identifies potential faults early in the design phase of systems ranging from printers to vehicles and robots, saving time and money.

  19. 29 CFR 4010.7 - Identifying information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    .... (a) Filers. Each filer is required to provide, in accordance with the instructions on PBGC's Web site... controlled group as of the end of the filer's information year— (i) The name, address, and telephone number... instructions on PBGC's Web site, http://www.pbgc.gov, the following identifying information with respect...

  20. 29 CFR 4010.7 - Identifying information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    .... (a) Filers. Each filer is required to provide, in accordance with the instructions on PBGC's Web site... controlled group as of the end of the filer's information year— (i) The name, address, and telephone number... instructions on PBGC's Web site, http://www.pbgc.gov, the following identifying information with respect...

  1. 29 CFR 4010.7 - Identifying information.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    .... (a) Filers. Each filer is required to provide, in accordance with the instructions on PBGC's Web site... controlled group as of the end of the filer's information year— (i) The name, address, and telephone number... instructions on PBGC's Web site, http://www.pbgc.gov, the following identifying information with respect...

  2. Identifying personal microbiomes using metagenomic codes.

    PubMed

    Franzosa, Eric A; Huang, Katherine; Meadow, James F; Gevers, Dirk; Lemon, Katherine P; Bohannan, Brendan J M; Huttenhower, Curtis

    2015-06-02

    Community composition within the human microbiome varies across individuals, but it remains unknown if this variation is sufficient to uniquely identify individuals within large populations or stable enough to identify them over time. We investigated this by developing a hitting set-based coding algorithm and applying it to the Human Microbiome Project population. Our approach defined body site-specific metagenomic codes: sets of microbial taxa or genes prioritized to uniquely and stably identify individuals. Codes capturing strain variation in clade-specific marker genes were able to distinguish among 100s of individuals at an initial sampling time point. In comparisons with follow-up samples collected 30-300 d later, ∼30% of individuals could still be uniquely pinpointed using metagenomic codes from a typical body site; coincidental (false positive) matches were rare. Codes based on the gut microbiome were exceptionally stable and pinpointed >80% of individuals. The failure of a code to match its owner at a later time point was largely explained by the loss of specific microbial strains (at current limits of detection) and was only weakly associated with the length of the sampling interval. In addition to highlighting patterns of temporal variation in the ecology of the human microbiome, this work demonstrates the feasibility of microbiome-based identifiability-a result with important ethical implications for microbiome study design. The datasets and code used in this work are available for download from huttenhower.sph.harvard.edu/idability.

  3. Diffraction gratings used as identifying markers

    DOEpatents

    Deason, Vance A.; Ward, Michael B.

    1991-01-01

    A finely detailed defraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the defraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating.

  4. Identifying Benefit Segments among College Students.

    ERIC Educational Resources Information Center

    Brown, Joseph D.

    1991-01-01

    Using concept of market segmentation (dividing market into distinct groups requiring different product benefits), surveyed 398 college students to determine benefit segments among students selecting a college to attend and factors describing each benefit segment. Identified one major segment of students (classroomers) plus three minor segments…

  5. Identify Your Brand, Before You Market.

    ERIC Educational Resources Information Center

    Claggett, Laura

    2002-01-01

    Discusses marketing in special libraries and suggests that librarians need to identify library services that set them apart from others. Highlights include the competitive environment and alternatives for the consumer; value that the library offers; targeting consumers; return on investment; and determining why consumers choose your services. (LRW)

  6. Identifying Advanced Technologies for Education's Future.

    ERIC Educational Resources Information Center

    Moore, Gwendolyn B.; Yin, Robert K.

    A study to determine how three advanced technologies might be applied to the needs of special education students helped inspire the development of a new method for identifying such applications. This new method, named the "Hybrid Approach," combines features of the two traditional methods: technology-push and demand-pull. Technology-push involves…

  7. Neoplasms identified in free-flying birds

    USGS Publications Warehouse

    Siegfried, L.M.

    1983-01-01

    Nine neoplasms were identified in carcasses of free-flying wild birds received at the National Wildlife Health Laboratory; gross and microscopic descriptions are reported herein. The prevalence of neoplasia in captive and free-flying birds is discussed, and lesions in the present cases are compared with those previously described in mammals and birds.

  8. Identifying Ethical Hypernorms for Accounting Educators

    ERIC Educational Resources Information Center

    Siegel, Philip H.; Mintz, Steven; Naser-Tavakolian, Mohsen; O'Shaughnessy, John

    2012-01-01

    Accounting educators have a unique role in academe because students learn about codes of ethics that will guide their actions as professionals. We identify hypernorms related to internal auditing educators that reflect unethical behaviors believed to be universally unacceptable by that community. We then compare the results to a prior survey of…

  9. Identifying Effectiveness Criteria for Internet Payment Systems.

    ERIC Educational Resources Information Center

    Shon, Tae-Hwan; Swatman, Paula M. C.

    1998-01-01

    Examines Internet payment systems (IPS): third-party, card, secure Web server, electronic token, financial electronic data interchange (EDI), and micropayment based. Reports the results of a Delphi survey of experts identifying and classifying IPS effectiveness criteria and classifying types of IPS providers. Includes the survey invitation letter…

  10. Identifying marker typing incompatibilities in linkage analysis

    SciTech Connect

    Stringham, H.M.; Boehnke, M.

    1996-10-01

    A common problem encountered in linkage analyses is that execution of the computer program is halted because of genotypes in the data that are inconsistent with Mendelian inheritance. Such inconsistencies may arise because of pedigree errors or errors in typing. In some cases, the source of the inconsistencies is easily identified by examining the pedigree. In others, the error is not obvious, and substantial time and effort are required to identify the responsible genotypes. We have developed two methods for automatically identifying those individuals whose genotypes are most likely the cause of the inconsistencies. First, we calculate the posterior probability of genotyping error for each member of the pedigree, given the marker data on all pedigree members and allowing anyone in the pedigree to have an error. Second, we identify those individuals whose genotypes could be solely responsible for the inconsistency in the pedigree. We illustrate these methods with two examples: one a pedigree error, the second a genotyping error. These methods have been implemented as a module of the pedigree analysis program package MENDEL. 9 refs., 2 figs., 2 tabs.

  11. Methods for identifying cardiovascular agents: a review.

    PubMed

    Tulis, David Anthony

    2006-01-01

    Basic and clinical investigation into many of the diverse aspects of cardiovascular drug discovery employs varied approaches aimed at determining physiologic and pathophysiologic efficacy of candidate agents for therapeutic utility with the ultimate hope of identifying those agents capable of exerting salutary influence upon cardiac and vascular tissues. Promising compounds may then be used for prophylactic cardiovascular protection and for the treatment of various disorders including hypertension, cardiomyopathy, occlusive vascular disease, and heart failure. The invention disclosed in Methods for identifying cardiovascular agents [1] provides screening methods which can be used to identify certain suspected cardiovascular agents that inhibit vascular smooth muscle cell (VSMC) activation and/or proliferation, functional adaptations inherent in the responses to disease or injury, or those that enhance vascular endothelial cell (VEC) activation and/or proliferation, processes thought to provide protection to jeopardized blood vessels. Additionally, these screening assays include agents that activate estrogen responsive genes in vascular cells, considering that estrogen signaling is generally suggested to serve pivotal functions in preventing many of the pathologic mechanisms contributing to occlusive vascular complications. The findings of this primary patent are directly relevant for discoveries in related inventions that disclose various provisions for cardiovascular drug discovery. This review will provide detailed synopses of these function-based screening methods capable of identifying cardiovascular protective agents for use in basic science research and clinical drug discovery.

  12. Zebrafish phenotypic screen identifies novel Notch antagonists.

    PubMed

    Velaithan, Vithya; Okuda, Kazuhide Shaun; Ng, Mei Fong; Samat, Norazwana; Leong, Sze Wei; Faudzi, Siti Munirah Mohd; Abas, Faridah; Shaari, Khozirah; Cheong, Sok Ching; Tan, Pei Jean; Patel, Vyomesh

    2017-04-01

    Zebrafish represents a powerful in vivo model for phenotype-based drug discovery to identify clinically relevant small molecules. By utilizing this model, we evaluated natural product derived compounds that could potentially modulate Notch signaling that is important in both zebrafish embryogenesis and pathogenic in human cancers. A total of 234 compounds were screened using zebrafish embryos and 3 were identified to be conferring phenotypic alterations similar to embryos treated with known Notch inhibitors. Subsequent secondary screens using HEK293T cells overexpressing truncated Notch1 (HEK293TΔE) identified 2 compounds, EDD3 and 3H4MB, to be potential Notch antagonists. Both compounds reduced protein expression of NOTCH1, Notch intracellular domain (NICD) and hairy and enhancer of split-1 (HES1) in HEK293TΔE and downregulated Notch target genes. Importantly, EDD3 treatment of human oral cancer cell lines demonstrated reduction of Notch target proteins and genes. EDD3 also inhibited proliferation and induced G0/G1 cell cycle arrest of ORL-150 cells through inducing p27(KIP1). Our data demonstrates the utility of the zebrafish phenotypic screen and identifying EDD3 as a promising Notch antagonist for further development as a novel therapeutic agent.

  13. Identifying Protein-Calorie Malnutrition Workshop.

    ERIC Educational Resources Information Center

    Walker, Susan S.; Barker, Ellen M.

    Instructional materials are provided for a workshop to enable participants to assist in identifying patients at risk with protein-calorie malnutrition and in corrrecting this nutritional deficiency. Representative topics are nutrients; protein, mineral, and vitamin sources, functions, and deficiency symptoms; malnutrition; nutritional deficiency…

  14. Identifying the Multiple Intelligences of Your Students

    ERIC Educational Resources Information Center

    McClellan, Joyce A.; Conti, Gary J.

    2008-01-01

    One way of addressing individual differences among adult learners is to identify the Multiple Intelligences of the learner. Multiple Intelligences refers to the concept developed by Howard Gardner that challenges the traditional view of intelligence and explains the presence of nine different Multiple Intelligences. The purpose of this study was…

  15. Identifying Fallacies of Reference in Argumentation

    ERIC Educational Resources Information Center

    Gough, Jim

    2009-01-01

    The experience of teaching informal logic (sometimes called practical logic) at the introductory level over the last fifteen years has allowed the author the opportunity to identify some interesting problems. These problems have been encountered by students attempting to understand some of the ideas presented in the informal logic course and by…

  16. Identifying the Rhetoric of Uncertainty Reduction.

    ERIC Educational Resources Information Center

    Williams, David E.

    Offering a rhetorical perspective of uncertainty reduction, this paper (1) discusses uncertainty reduction theory and dramatism; (2) identifies rhetorical strategies inherent in C. W. Berger and R. J. Calabrese's theory; (3) extends predicted outcome value to influenced outcome value; and (4) argues that the goal of uncertainty reduction and…

  17. Identifying Specific Comprehension Deficits in Children

    ERIC Educational Resources Information Center

    Gifford, Diane Baty

    2013-01-01

    Research has shown that educators may be missing an under-identified population of approximately 10 percent of typically developing children, who have fluent, age-appropriate decoding and word recognition skills, yet have specific difficulties with other higher-level text processing factors. These children are said to have specific comprehension…

  18. Avoiding medication mixups. Identifiable imprint codes.

    PubMed Central

    Vasudevan, P; Del Gianni, T; Robertson, W O

    1996-01-01

    This study was done to determine if current imprinting of solid medication forms permits health care professionals to identify the manufacturers involved so as to be able to activate the hierarchic identification system mandated by the Food and Drug Administration. We tested 15 representatives of 6 groups of health professionals for their ability to identify the manufacturer after having examined 30 solid-dosage forms drawn from a pseudo-random sample of stock hospital formulary products. The correct identification of the manufacturer was the sole criterion. Of the 2,700 opportunities, the manufacturer was able to be identified for only 43%. Nurses and medical students had a 35% success rate, pharmacists and poison center specialists a 55% success rate, and residents and attending physicians a 40% rate. None approached 95% accuracy. Currently employed imprints fail in their objective to permit health care professionals--or the general public--to rapidly identify prescription drugs. The manufacturers' logotypes need to be modified if this identification system is to be implemented. We propose a simple voluntary collaborative effort by the pharmaceutical industry to solve the problem. PMID:9000855

  19. Identifiability and Equivalence of GLLIRM Models

    ERIC Educational Resources Information Center

    Revuelta, Javier

    2009-01-01

    The generalized logit-linear item response model (GLLIRM) is a linearly constrained nominal categories model (NCM) that computes the scale and intercept parameters for categories as a weighted sum of basic parameters. This paper addresses the problems of the identifiability of the basic parameters and the equivalence between different GLLIRM…

  20. Identifying Teaching Methods that Engage Entrepreneurship Students

    ERIC Educational Resources Information Center

    Balan, Peter; Metcalfe, Mike

    2012-01-01

    Purpose: Entrepreneurship education particularly requires student engagement because of the complexity of the entrepreneurship process. The purpose of this paper is to describe how an established measure of engagement can be used to identify relevant teaching methods that could be used to engage any group of entrepreneurship students.…

  1. Identifying Depression in Students with Mental Retardation.

    ERIC Educational Resources Information Center

    Stough, Laura M.; Baker, Lynn

    1999-01-01

    Offers guidelines to teachers for identifying depression in students with mental retardation. Discusses prevalence and symptoms of depression, causes of depression, difficulty of diagnosis in students with mental retardation, detecting symptoms in the classroom, treatment of depression, and psychological services. Inserts list ideas for helping…

  2. International Team Identifies Biomarker for Scleroderma

    MedlinePlus

    ... that are under development for this disease," said study author Robert Lafyatis, M.D., of the Boston University School of Medicine. "This would enable us to more rapidly identify new therapies in early clinical trials." With this goal in mind, Dr. Lafyatis helped form an international network of ...

  3. Professional Development: Identifying Effective Instructional Coaching Activities

    ERIC Educational Resources Information Center

    Mannino, Gina

    2014-01-01

    The purpose of this study was to identify the instructional coaching activities most used by instructional coaches in southeast Texas school districts and to test if there was a relationship between the use of instructional coaching and perceived improvement in the instructional practices of teachers and student achievement. The participants for…

  4. Identifying the Context of Postsecondary Instructional Programs.

    ERIC Educational Resources Information Center

    Levinson-Rose, Judith; Menges, Robert J.

    A framework for articulating postsecondary instructional programs is described. The framework identifies two important sources of influence on programs: the type of institution within which the program operates and the program objectives. These factors influence both program components and how these components are linked and processes that are…

  5. Identifying Mentors for Student Employees on Campus

    ERIC Educational Resources Information Center

    Frock, David

    2015-01-01

    Purpose: This exploratory research project aims to seek an effective process for identifying supervisors of part-time student employees who also serve in a mentoring capacity. Design/methodology/approach: This paper is based on a review of literature and an evaluation process focused on established traits and functions of mentoring as applied to…

  6. 34 CFR 300.32 - Personally identifiable.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 2 2013-07-01 2013-07-01 false Personally identifiable. 300.32 Section 300.32 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION...

  7. 34 CFR 300.32 - Personally identifiable.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 2 2014-07-01 2013-07-01 true Personally identifiable. 300.32 Section 300.32 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION OF CHILDREN...

  8. Problems identified with home infusion pumps.

    PubMed

    Koeppen, M A; Caspers, S M

    1994-01-01

    A variety of infusion pumps and devices are available on the market today. In this article, the authors examine these products based on questionnaires sent out to typical consumers, including hospitals and caregivers. Using the results of this questionnaire, the authors identify whether or not users of home infusion pumps and devices find them difficult to operate.

  9. Techniques for identifying predators of goose nests

    USGS Publications Warehouse

    Anthony, R. Michael; Grand, J.B.; Fondell, T.F.; Miller, David A.

    2006-01-01

    We used cameras and artificial eggs to identify nest predators of dusky Canada goose Branta canadensis occidentalis nests during 1997-2000. Cameras were set up at 195 occupied goose nests and 60 artificial nests. We placed wooden eggs and domestic goose eggs that were emptied and then filled with wax or foam in an additional 263 natural goose nests to identify predators from marks in the artificial eggs. All techniques had limitations, but each correctly identified predators and estimated their relative importance. Nests with cameras had higher rates of abandonment than natural nests, especially during laying. Abandonment rates were reduced by deploying artificial eggs late in laying and reducing time at nests. Predation rates for nests with cameras were slightly lower than for nests without cameras. Wax-filled artificial eggs caused mortality of embryos in natural nests, but were better for identifying predator marks at artificial nests. Use of foam-filled artificial eggs in natural nests was the most cost effective means of monitoring nest predation. ?? Wildlife Biology (2006).

  10. [Identifying Gifted American Indian Students.] What Works.

    ERIC Educational Resources Information Center

    Davidson, Karen

    1997-01-01

    In Hardin (Montana) schools, where 55% of students are American Indians, the same identification methods are used to identify gifted students among all cultural groups. These methods include nonverbal standardized tests and subjective recommendations based on the Frasier Talent Assessment Profile. Other equitable practices include equal…

  11. 34 CFR 300.32 - Personally identifiable.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false Personally identifiable. 300.32 Section 300.32 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION...

  12. A screening cascade to identify ERβ ligands

    PubMed Central

    Filgueira, Carly S.; Benod, Cindy; Lou, Xiaohua; Gunamalai, Prem S.; Villagomez, Rosa A.; Strom, Anders; Gustafsson, Jan-Åke; Berkenstam, Anders L.; Webb, Paul

    2014-01-01

    The establishment of effective high throughput screening cascades to identify nuclear receptor (NR) ligands that will trigger defined, therapeutically useful sets of NR activities is of considerable importance. Repositioning of existing approved drugs with known side effect profiles can provide advantages because de novo drug design suffers from high developmental failure rates and undesirable side effects which have dramatically increased costs. Ligands that target estrogen receptor β (ERβ) could be useful in a variety of diseases ranging from cancer to neurological to cardiovascular disorders. In this context, it is important to minimize cross-reactivity with ERα, which has been shown to trigger increased rates of several types of cancer. Because of high sequence similarities between the ligand binding domains of ERα and ERβ, preferentially targeting one subtype can prove challenging. Here, we describe a sequential ligand screening approach comprised of complementary in-house assays to identify small molecules that are selective for ERβ. Methods include differential scanning fluorimetry, fluorescence polarization and a GAL4 transactivation assay. We used this strategy to screen several commercially-available chemical libraries, identifying thirty ERβ binders that were examined for their selectivity for ERβ versus ERα, and tested the effects of selected ligands in a prostate cancer cell proliferation assay. We suggest that this approach could be used to rapidly identify candidates for drug repurposing. PMID:25422593

  13. Identify, Organize, and Retrieve Items Using Zotero

    ERIC Educational Resources Information Center

    Clark, Brian; Stierman, John

    2009-01-01

    Librarians build collections. To do this they use tools that help them identify, organize, and retrieve items for the collection. Zotero (zoh-TAIR-oh) is such a tool that helps the user build a library of useful books, articles, web sites, blogs, etc., discovered while surfing online. A visit to Zotero's homepage, www.zotero.org, shows a number of…

  14. Problems Identifying Independent and Dependent Variables

    ERIC Educational Resources Information Center

    Leatham, Keith R.

    2012-01-01

    This paper discusses one step from the scientific method--that of identifying independent and dependent variables--from both scientific and mathematical perspectives. It begins by analyzing an episode from a middle school mathematics classroom that illustrates the need for students and teachers alike to develop a robust understanding of…

  15. Methods for Identifying Versioned and Plagiarized Documents.

    ERIC Educational Resources Information Center

    Hoad, Timothy C.; Zobel, Justin

    2003-01-01

    Describes research that was conducted to develop and evaluate techniques for identifying plagiarism, revisions, and different versions of online documents. Highlights include ranking; parsing; similarity measures; identity measures; fingerprinting documents; measuring effectiveness via recall and precision; and experiments on two document…

  16. Ideas Identified and Distributed through Project IDEA.

    ERIC Educational Resources Information Center

    American Alliance for Health, Physical Education, and Recreation, Washington, DC.

    This document contains ideas on a variety of subjects directed at the physical educator. The work was compiled by Project IDEA (Identify, Distribute, Exchange for Action). Topics include the following: (a) scheduling, (b) curriculum, (c) games, (d) specific courses, (e) life sports, (f) fitness, (g) adaptive Physical education, (h) course methods,…

  17. Embedded sensor having an identifiable orientation

    DOEpatents

    Bennett, Thomas E.; Nelson, Drew V.

    2002-01-01

    An apparatus and method is described wherein a sensor, such as a mechanical strain sensor, embedded in a fiber core, is "flagged" to identify a preferred orientation of the sensor. The identifying "flag" is a composite material, comprising a plurality of non-woven filaments distributed in a resin matrix, forming a small planar tab. The fiber is first subjected to a stimulus to identify the orientation providing the desired signal response, and then sandwiched between first and second layers of the composite material. The fiber, and therefore, the sensor orientation is thereby captured and fixed in place. The process for achieving the oriented fiber includes, after identifying the fiber orientation, carefully laying the oriented fiber onto the first layer of composite, moderately heating the assembled layer for a short period in order to bring the composite resin to a "tacky" state, heating the second composite layer as the first, and assembling the two layers together such that they merge to form a single consolidated block. The consolidated block achieving a roughly uniform distribution of composite filaments near the embedded fiber such that excess resin is prevented from "pooling" around the periphery of the fiber.

  18. Identifying Concrete and Formal Operational Children.

    ERIC Educational Resources Information Center

    Docherty, Edward M.

    This paper presents a study designed to determine if groups of concrete and formal operational children can be identified through the technique of cluster analysis, using a battery of Piagetian tasks. A Total of 64 subjects, 8 boys and 8 girls from each of the second, fourth, sixth, and eighth grade levels, were selected from a public elementary…

  19. How to Identify High-Growth Schools

    ERIC Educational Resources Information Center

    Pfeiffer, Linda E.

    2015-01-01

    When researching school options, parents may want to look for schools with high-growth scores which, according to research, may be indicators of other characteristics such as programming, leadership, culture, and size. This quick guide offers parents tips on how to identify high-growth schools and what to ask when evaluating school options. An…

  20. Using lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Osenton, P.C.; Price, R.W.

    1995-01-01

    Avian lice may link fledgling Brown-headed Cowbirds to the host species that raised them. Lice, if host-specific and transferred to nestling cowbirds, could serve to identify the principal host species raising cowbirds in a local area. This approach of trapping cowbird fledglings in a feeding flock, then collecting and identifying the lice they carry is economical. The alternative requires a team of people to locate large numbers of parasitized host nests. We trapped 250 cowbird fledglings during June-August 1994 on Patuxent Research Center, and from them we collected 426 lice identified as representing 6 genera and 12 species. We. also collected and identified 347 lice from 30 known host species that were mist-netted on our Center. The lice found on cowbird fledglings in this population can be linked to Wood Thrush, Red-eyed Vireo, Common Yellowthroat, Rufous-sided Towhee, Red-winged Blackbird, Common Grackle, Song Sparrow, Field Sparrow, and Tree sparrow, based on this study and also on published reports.

  1. National Board Certification Identifies Strong Teachers

    ERIC Educational Resources Information Center

    Education Digest: Essential Readings Condensed for Quick Review, 2009

    2009-01-01

    Advanced certification through the National Board for Professional Teaching Standards (NBPTS) is an effective way to identify highly skilled teachers, according to a congressionally mandated report from the National Research Council. Students taught by NBPTS-certified teachers make greater gains on achievement tests than students taught by…

  2. Systematic Determination of Human Cyclin Dependent Kinase (CDK)-9 Interactome Identifies Novel Functions in RNA Splicing Mediated by the DEAD Box (DDX)-5/17 RNA Helicases.

    PubMed

    Yang, Jun; Zhao, Yingxin; Kalita, Mridul; Li, Xueling; Jamaluddin, Mohammad; Tian, Bing; Edeh, Chukwudi B; Wiktorowicz, John E; Kudlicki, Andrzej; Brasier, Allan R

    2015-10-01

    Inducible transcriptional elongation is a rapid, stereotypic mechanism for activating immediate early immune defense genes by the epithelium in response to viral pathogens. Here, the recruitment of a multifunctional complex containing the cyclin dependent kinase 9 (CDK9) triggers the process of transcriptional elongation activating resting RNA polymerase engaged with innate immune response (IIR) genes. To identify additional functional activity of the CDK9 complex, we conducted immunoprecipitation (IP) enrichment-stable isotope labeling LC-MS/MS of the CDK9 complex in unstimulated cells and from cells activated by a synthetic dsRNA, polyinosinic/polycytidylic acid [poly (I:C)]. 245 CDK9 interacting proteins were identified with high confidence in the basal state and 20 proteins in four functional classes were validated by IP-SRM-MS. These data identified that CDK9 interacts with DDX 5/17, a family of ATP-dependent RNA helicases, important in alternative RNA splicing of NFAT5, and mH2A1 mRNA two proteins controlling redox signaling. A direct comparison of the basal versus activated state was performed using stable isotope labeling and validated by IP-SRM-MS. Recruited into the CDK9 interactome in response to poly(I:C) stimulation are HSPB1, DNA dependent kinases, and cytoskeletal myosin proteins that exchange with 60S ribosomal structural proteins. An integrated human CDK9 interactome map was developed containing all known human CDK9- interacting proteins. These data were used to develop a probabilistic global map of CDK9-dependent target genes that predicted two functional states controlling distinct cellular functions, one important in immune and stress responses. The CDK9-DDX5/17 complex was shown to be functionally important by shRNA-mediated knockdown, where differential accumulation of alternatively spliced NFAT5 and mH2A1 transcripts and alterations in downstream redox signaling were seen. The requirement of CDK9 for DDX5 recruitment to NFAT5 and mH2A1

  3. Data Identifiers and Citations Enable Reproducible Science

    NASA Astrophysics Data System (ADS)

    Tilmes, C.

    2011-12-01

    Modern science often involves data processing with tremendous volumes of data. Keeping track of that data has been a growing challenge for data center. Researchers who access and use that data don't always reference and cite their data sources adequately for consumers of their research to follow their methodology or reproduce their analyses or experiments. Recent research has led to recommendations for good identifiers and citations that can help address this problem. This paper will describe some of the best practices in data identifiers, reference and citation. Using a simplified example scenario based on a long term remote sensing satellite mission, it will explore issues in identifying dynamic data sets and the importance of good data citations for reproducibility. It will describe the difference between granule and collection level identifiers, using UUIDs and DOIs to illustrate some recommendations for developing identifiers and assigning them during data processing. As data processors create data products, the provenance of the input products and precise steps that led to their creation are recorded and published for users of the data to see. As researchers access the data from an archive, they can use the provenance to help understand the genesis of the data, which could have effects on their usage of the data. By citing the data on publishing their research, others can retrieve the precise data used in their research and reproduce the analyses and experiments to confirm the results. Describing the experiment to a sufficient extent to reproduce the research enforces a formal approach that lends credibility to the results, and ultimately, to the policies of decision makers depending on that research.

  4. Trustworthy persistent identifier systems of the future

    NASA Astrophysics Data System (ADS)

    Golodoniuc, Pavel; Klump, Jens; Car, Nicholas

    2016-04-01

    Over the last two decades, persistent identifier (PID) systems have seen some significant changes in their governance policies, system capabilities, and technology. The development of most systems was driven by two main application areas, namely archives and libraries. Guidelines and criteria for trustworthy PID systems have been clearly devised (Bütikofer, 2009) and many PID system implementations for the identification of static digital objects have been built (e.g., PURL). However systems delivering persistent identifiers for dynamic datasets are not yet mature. There has been a rapid proliferation of different PID systems caused by the specific technical or organisational requirements of various communities that could not be met by existing systems such as DOI, ISBN, and EAN. Many of these different systems were limited by their inability to provide native means of persistent identifier resolution. This has prompted a decoupling of PID-associated data from the resolution service and this is where the Handle system has played a significant role. The Handle allowed to build a distributed system of independently managed resolver services. A trustworthy PID system must be designed to outlive the objects it provides persistent identifiers for, which may cease to exist or otherwise be deprecated, and the technology used to implement it, which will certainly need to change with time. We propose that such a system should rest on four pillars of agreements - (i) definitions, (ii) policies, (iii) services, and (iv) data services, to ensure longevity. While we believe all four pillars are equally important, we intentionally leave regulating aspects of issuing of identifiers and their registration out of the scope of this paper and focus on the agreements that have to be established between PID resolver services and the data sources indicated by the persistent identifiers. We propose an approach to development of PID systems that combines the use of (a) the Handle system

  5. Persistent Identifiers for Dutch cultural heritage institutions

    NASA Astrophysics Data System (ADS)

    Ras, Marcel; Kruithof, Gijsbert

    2016-04-01

    Over the past years, more and more collections belonging to archives, libraries, media, museums, and knowledge institutes are being digitised and made available online. These are exciting times for ALM institutions. They are realising that, in the information society, their collections are goldmines. Unfortunately most heritage institutions in the Netherlands do not yet meet the basic preconditions for long-term availability of their collections. The digital objects often have no long lasting fixed reference yet. URL's and web addresses change. Some digital objects that were referenced in Europeana and other portals can no longer be found. References in scientific articles have a very short life span, which is damaging for scholarly research. In 2015, the Dutch Digital Heritage Network (NDE) has started a two-year work program to co-ordinate existing initiatives in order to improve the (long-term) accessibility of the Dutch digital heritage for a wide range of users, anytime, anyplace. The Digital Heritage Network is a partnership established on the initiative of the Ministry of Education, Culture and Science. The members of the NDE are large, national institutions that strive to professionally preserve and manage digital data, e.g. the National Library, The Netherlands Institute for Sound and Vision, the Netherlands Cultural Heritage Agency, the Royal Netherlands Academy of Arts and Sciences, the National Archive of the Netherlands and the DEN Foundation, and a growing number of associations and individuals both within and outside the heritage sector. By means of three work programmes the goals of the Network should be accomplished and improve the visibility, the usability and the sustainability of digital heritage. Each programme contains of a set of projects. Within the sustainability program a project on creating a model for persistent identifiers is taking place. The main goals of the project are (1) raise awareness among cultural heritage institutions on the

  6. Using filtering effects to identify objects

    NASA Astrophysics Data System (ADS)

    Carroll, T. L.; Rachford, Frederic J.

    2012-06-01

    Reflecting signals off of targets is a method widely used to locate objects, but the reflected signal also contains information that can be used to identify the object. In radar or sonar, the signal amplitudes used are small enough that only linear effects are present, so we can consider the effect of the target on the signal as a linear filter. Using the known effects of linear filters on chaotic signals, we can create a reference that allows us to match a particular target to a particular reflected signal. Furthermore, if some parts of this "filter" vary only slowly as the aspect angle of the object changes, we can produce a reference that averages out the parts that are highly angle dependent so that one reference can be used to identify the target over a range of angles.

  7. Chemical Proteomic Platform To Identify Citrullinated Proteins

    PubMed Central

    2015-01-01

    Anti-citrullinated protein antibodies (ACPAs) are a hallmark of rheumatoid arthritis (RA) and are routinely used for disease diagnosis. Protein citrullination is also increased in cancer and other autoimmune disorders, suggesting that citrullinated proteins may serve as biomarkers for diseases beyond RA. To identify these citrullinated proteins, we developed biotin-conjugated phenylglyoxal (biotin-PG). Using this probe and our platform technology, we identified >50 intracellular citrullinated proteins. More than 20 of these are involved in RNA splicing, suggesting, for the first time, that citrullination modulates RNA biology. Overall, this chemical proteomic platform will play a key role in furthering our understanding of protein citrullination in rheumatoid arthritis and potentially a wider spectrum of inflammatory diseases. PMID:26360112

  8. Identifying sex and age of akiapolaau

    USGS Publications Warehouse

    Pratt, T.K.; Fancy, S.G.; Harada, C.K.; Lindsey, G.D.; Jacobi, J.D.

    1994-01-01

    Methods for identifying the sex and age of the Akiapolaau (Hemignathus munroi), an endangered honeycreeper found only on the island of Hawaii, were developed by examination and measurement of 73 museum specimens and 24 live birds captured in mist nests. Akiapolaau probably undergo a single annual molt, with most birds molting between February and July. The mottled juvenal plumage is replaced by a first basic plumage characterized by yellowish-gray or yellowish-green underparts and often by retained wingbars. Male Akiapolaau may not attain adult plumage until their third molt. In adult females, only the throat and upper breast become yellow, whereas in adult males the superciliaries, cheeks, and entire underparts are yellow. Adult males have greater exposed culmen, gonys, wing chord, tail, and tarsus lengths than do females. Akiapolaau in first prebasic molt or older can be identified as to sex by culmen length, that of males being >23.4 mm.

  9. Framework for Identifying Cybersecurity Risks in Manufacturing

    DOE PAGES

    Hutchins, Margot J.; Bhinge, Raunak; Micali, Maxwell K.; ...

    2015-10-21

    Increasing connectivity, use of digital computation, and off-site data storage provide potential for dramatic improvements in manufacturing productivity, quality, and cost. However, there are also risks associated with the increased volume and pervasiveness of data that are generated and potentially accessible to competitors or adversaries. Enterprises have experienced cyber attacks that exfiltrate confidential and/or proprietary data, alter information to cause an unexpected or unwanted effect, and destroy capital assets. Manufacturers need tools to incorporate these risks into their existing risk management processes. This article establishes a framework that considers the data flows within a manufacturing enterprise and throughout its supplymore » chain. The framework provides several mechanisms for identifying generic and manufacturing-specific vulnerabilities and is illustrated with details pertinent to an automotive manufacturer. Finally, in addition to providing manufacturers with insights into their potential data risks, this framework addresses an outcome identified by the NIST Cybersecurity Framework.« less

  10. Identifying bilingual semantic neural representations across languages

    PubMed Central

    Buchweitz, Augusto; Shinkareva, Svetlana V.; Mason, Robert A.; Mitchell, Tom M.; Just, Marcel Adam

    2015-01-01

    The goal of the study was to identify the neural representation of a noun's meaning in one language based on the neural representation of that same noun in another language. Machine learning methods were used to train classifiers to identify which individual noun bilingual participants were thinking about in one language based solely on their brain activation in the other language. The study shows reliable (p < .05) pattern-based classification accuracies for the classification of brain activity for nouns across languages. It also shows that the stable voxels used to classify the brain activation were located in areas associated with encoding information about semantic dimensions of the words in the study. The identification of the semantic trace of individual nouns from the pattern of cortical activity demonstrates the existence of a multi-voxel pattern of activation across the cortex for a single noun common to both languages in bilinguals. PMID:21978845

  11. Wham: Identifying Structural Variants of Biological Consequence.

    PubMed

    Kronenberg, Zev N; Osborne, Edward J; Cone, Kelsey R; Kennedy, Brett J; Domyan, Eric T; Shapiro, Michael D; Elde, Nels C; Yandell, Mark

    2015-12-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools-Lumpy, Delly and SoftSearch-and demonstrate Wham's ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.

  12. Framework for Identifying Cybersecurity Risks in Manufacturing

    SciTech Connect

    Hutchins, Margot J.; Bhinge, Raunak; Micali, Maxwell K.; Robinson, Stefanie L.; Sutherland, John W.; Dornfeld, David

    2015-10-21

    Increasing connectivity, use of digital computation, and off-site data storage provide potential for dramatic improvements in manufacturing productivity, quality, and cost. However, there are also risks associated with the increased volume and pervasiveness of data that are generated and potentially accessible to competitors or adversaries. Enterprises have experienced cyber attacks that exfiltrate confidential and/or proprietary data, alter information to cause an unexpected or unwanted effect, and destroy capital assets. Manufacturers need tools to incorporate these risks into their existing risk management processes. This article establishes a framework that considers the data flows within a manufacturing enterprise and throughout its supply chain. The framework provides several mechanisms for identifying generic and manufacturing-specific vulnerabilities and is illustrated with details pertinent to an automotive manufacturer. Finally, in addition to providing manufacturers with insights into their potential data risks, this framework addresses an outcome identified by the NIST Cybersecurity Framework.

  13. Wham: Identifying Structural Variants of Biological Consequence

    PubMed Central

    Kronenberg, Zev N.; Osborne, Edward J.; Cone, Kelsey R.; Kennedy, Brett J.; Domyan, Eric T.; Shapiro, Michael D.; Elde, Nels C.; Yandell, Mark

    2015-01-01

    Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/. PMID:26625158

  14. Identifying Groundwater Recharge in Arid Regions

    NASA Astrophysics Data System (ADS)

    Thomas, B. F.; Famiglietti, J. S.

    2015-12-01

    Recharge epodicity in arid regions provides a method to estimate annual groundwater recharge given a relationship expressed as the recharge to precipitation ratio. Traditionally, in-situ observations are required to identify aquifer recharge events, while more advanced approaches such as the water-table fluctuation method or the episodic master recession method are necessary to delineate the recharge event. Our study uses the Gravity Recovery and Climate Experiment (GRACE) observations to estimate monthly changes in groundwater storage which are attributed to the combination of groundwater abstraction and episodic recharge in the arid southwestern United States. Our results illustrate the ability of remote sensing technologies to identify episodic groundwater recharge in arid regions which can be used within sustainable groundwater management frameworks to effectively manage groundwater resources.

  15. Identifying essential genes in Arabidopsis thaliana.

    PubMed

    Meinke, David; Muralla, Rosanna; Sweeney, Colleen; Dickerman, Allan

    2008-09-01

    Eight years after publication of the Arabidopsis genome sequence and two years before completing the first phase of an international effort to characterize the function of every Arabidopsis gene, plant biologists remain unable to provide a definitive answer to the following basic question: what is the minimal gene set required for normal growth and development? The purpose of this review is to summarize different strategies employed to identify essential genes in Arabidopsis, an important component of the minimal gene set in plants, to present an overview of the datasets and specific genes identified to date, and to discuss the prospects for future saturation of this important class of genes. The long-term goal of this collaborative effort is to facilitate basic research in plant biology and complement ongoing research with other model organisms.

  16. Guidelines for identifying suspect/counterfeit material

    SciTech Connect

    1995-09-01

    These guidelines are intended to assist users of products in identifying: substandard, misrepresented, or fraudulently marked items. The guidelines provide information about such topics as: precautions, inspection and testing, dispositioning identified items, installed inspection and reporting suspect/counterfeit materials. These guidelines apply to users who are developing procurement documents, product acceptance/verification methods, company procedures, work instructions, etc. The intent of these SM guidelines in relation to the Quality Assurance Program Description (QAPD) and implementing company Management Control Procedures is not to substitute or replace existing requirements, as defined in either the QAPD or company implementing instructions (Management Control Procedures). Instead, the guidelines are intended to provide a consolidated source of information addressing the issue of Suspect/Counterfeit materials. These guidelines provide an extensive suspect component listing and suspect indications listing. Users can quickly check their suspect items against the list of manufacturers products (i.e., type, LD. number, and nameplate information) by consulting either of these listings.

  17. Identifying a novel locus for psoriatic arthritis

    PubMed Central

    Budu-Aggrey, Ashley; Bowes, John

    2016-01-01

    A number of studies have identified genetic risk loci for PsA, the majority of which also confer risk for psoriasis. The stronger heritability of PsA in comparison with psoriasis suggests that there should be risk loci that are specific for PsA. Identifying such loci could potentially inform therapy development to provide more effective treatments for PsA patients, especially with a considerable proportion being non-responsive to current therapies. Evidence of a PsA-specific locus has been previously found at HLA-B27 within the MHC region. A recent study has provided evidence of non-HLA risk loci that are specific for PsA at IL23R, PTPN22 and on chromosome 5q31. Functional characterization of these loci will provide further understanding of the pathways underlying PsA, and enable us to apply genetic findings for patient benefit. PMID:26255310

  18. Identifying Topics in Microblogs Using Wikipedia.

    PubMed

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail.

  19. Identifying spatial priorities for protecting ecosystem services

    PubMed Central

    Luck, Gary W

    2012-01-01

    Priorities for protecting ecosystem services must be identified to ensure future human well-being. Approaches to broad-scale spatial prioritization of ecosystem services are becoming increasingly popular and are a vital precursor to identifying locations where further detailed analyses of the management of ecosystem services is required (e.g., examining trade-offs among management actions). Prioritization approaches often examine the spatial congruence between priorities for protecting ecosystem services and priorities for protecting biodiversity; therefore, the spatial prioritization method used is crucial because it will influence the alignment of service protection and conservation goals. While spatial prioritization of ecosystem services and prioritization for conservation share similarities, such as the need to document threats and costs, the former differs substantially from the latter owing to the requirement to measure the following components: supply of services; availability of human-derived alternatives to service provision; capacity to meet beneficiary demand; and site dependency in and scale of service delivery. We review studies that identify broad-scale spatial priorities for managing ecosystem services and demonstrate that researchers have used different approaches and included various measures for identifying priorities, and most studies do not consider all of the components listed above. We describe a conceptual framework for integrating each of these components into spatial prioritization of ecosystem services and illustrate our approach using a worked example for water provision. A fuller characterization of the biophysical and social context for ecosystem services that we call for should improve future prioritization and the identification of locations where ecosystem-service management is especially important or cost effective. PMID:24555017

  20. Diffraction gratings used as identifying markers

    SciTech Connect

    Deason, V.A.; Ward, M.B.

    1989-08-03

    A finely detailed defraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the defraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating. 7 figs.

  1. Data Identifiers, Versioning, and Micro-citation

    NASA Astrophysics Data System (ADS)

    Parsons, M. A.; Duerr, R. E.

    2012-12-01

    Data citation, especially using Digital Object Identifiers (DOIs), is an increasingly accepted scientific practice. For example, the AGU Council asserts that data "publications" should "be credited and cited like the products of any other scientific activity," and Thomson Reuters has recently announced a data citation index built from DOIs assigned to data sets. Correspondingly, formal guidelines for how to cite a data set (using DOIs or similar identifiers/locators) have recently emerged, notably those from the international DataCite consortium, the UK Digital Curation Centre, and the US Federation of Earth Science Information Partners. These different data citation guidelines are largely congruent. They agree on the basic practice and elements of data citation, especially for relatively static, whole data collections. There is less agreement on some of the more subtle nuances of data citation. They define different methods for handling different data set versions, especially for the very dynamic, growing data sets that are common in Earth Sciences. They also differ in how people should cite specific, arbitrarily large elements, "passages," or subsets of a larger data collection, i.e., the precise data records actually used in a study. This detailed "micro-citation", and careful reference to exact versions of data are essential to ensure scientific reproducibility. Identifiers such as DOIs are necessary but not sufficient for the precise, detailed, references necessary. Careful practice must be coupled with the use of curated identifiers. In this paper we review the pros and cons of different approaches to versioning and micro-citation. We suggest a workable solution for most existing Earth science data and suggest a more rigorous path forward for the future.

  2. Identifying Topics in Microblogs Using Wikipedia

    PubMed Central

    Yıldırım, Ahmet; Üsküdarlı, Suzan; Özgür, Arzucan

    2016-01-01

    Twitter is an extremely high volume platform for user generated contributions regarding any topic. The wealth of content created at real-time in massive quantities calls for automated approaches to identify the topics of the contributions. Such topics can be utilized in numerous ways, such as public opinion mining, marketing, entertainment, and disaster management. Towards this end, approaches to relate single or partial posts to knowledge base items have been proposed. However, in microblogging systems like Twitter, topics emerge from the culmination of a large number of contributions. Therefore, identifying topics based on collections of posts, where individual posts contribute to some aspect of the greater topic is necessary. Models, such as Latent Dirichlet Allocation (LDA), propose algorithms for relating collections of posts to sets of keywords that represent underlying topics. In these approaches, figuring out what the specific topic(s) the keyword sets represent remains as a separate task. Another issue in topic detection is the scope, which is often limited to specific domain, such as health. This work proposes an approach for identifying domain-independent specific topics related to sets of posts. In this approach, individual posts are processed and then aggregated to identify key tokens, which are then mapped to specific topics. Wikipedia article titles are selected to represent topics, since they are up to date, user-generated, sophisticated articles that span topics of human interest. This paper describes the proposed approach, a prototype implementation, and a case study based on data gathered during the heavily contributed periods corresponding to the four US election debates in 2012. The manually evaluated results (0.96 precision) and other observations from the study are discussed in detail. PMID:26991442

  3. Identifying Fossil Bacteria in Martian Materials

    NASA Technical Reports Server (NTRS)

    Westall, F.; McKay, D. S.; Gibson, E. K., Jr.

    1999-01-01

    Within the next decade, robotic missions are going to Mars with the search for evidence for extant and extinct life as at least one of the mission objectives. Moreover, the first Martian samples will be returned to Earth in 2008. It is therefore imperative that we can be certain that we can identify life in Martian rocks. In this paper we will not be discussing extant life but will concentrate on fossil life.

  4. Diffraction gratings used as identifying markers

    DOEpatents

    Deason, V.A.; Ward, M.B.

    1991-03-26

    A finely detailed diffraction grating is applied to an object as an identifier or tag which is unambiguous, difficult to duplicate, or remove and transfer to another item, and can be read and compared with prior readings with relative ease. The exact pattern of the diffraction grating is mapped by diffraction moire techniques and recorded for comparison with future readings of the same grating. 7 figures.

  5. Identifying Proper Names in Parallel Medical Terminologies

    PubMed Central

    Bodenreider, Olivier; Zweigenbaum, Pierre

    2006-01-01

    We propose several criteria to identify proper names in biomedical terminologies. Traditional, pattern-based methods that rely on the immediate context of a proper name are not applicable. However, the availability of translations of some terminologies supports methods based on invariant words instead. A combination of five criteria achieved 86% precision and 88% recall on the 16,401 word forms of the International Classification of Diseases. PMID:11187591

  6. Identifying familiar strangers in human encounter networks

    NASA Astrophysics Data System (ADS)

    Liang, Di; Li, Xiang; Zhang, Yi-Qing

    2016-10-01

    Familiar strangers, pairs of individuals who encounter repeatedly but never know each other, have been discovered for four decades yet lack an effective method to identify. Here we propose a novel method called familiar stranger classifier (FSC) to identify familiar strangers from three empirical datasets, and classify human relationships into four types, i.e., familiar stranger (FS), in-role (IR), friend (F) and stranger (S). The analyses of the human encounter networks show that the average number of FS one may encounter is finite but larger than the Dunbar Number, and their encounters are structurally more stable and denser than those of S, indicating the encounters of FS are not limited by the social capacity, and more robust than the random scenario. Moreover, the temporal statistics of encounters between FS over the whole time span show strong periodicity, which are diverse from the bursts of encounters within one day, suggesting the significance of longitudinal patterns of human encounters. The proposed method to identify FS in this paper provides a valid framework to understand human encounter patterns and analyse complex human social behaviors.

  7. Dynamic Method for Identifying Collected Sample Mass

    NASA Technical Reports Server (NTRS)

    Carson, John

    2008-01-01

    G-Sample is designed for sample collection missions to identify the presence and quantity of sample material gathered by spacecraft equipped with end effectors. The software method uses a maximum-likelihood estimator to identify the collected sample's mass based on onboard force-sensor measurements, thruster firings, and a dynamics model of the spacecraft. This makes sample mass identification a computation rather than a process requiring additional hardware. Simulation examples of G-Sample are provided for spacecraft model configurations with a sample collection device mounted on the end of an extended boom. In the absence of thrust knowledge errors, the results indicate that G-Sample can identify the amount of collected sample mass to within 10 grams (with 95-percent confidence) by using a force sensor with a noise and quantization floor of 50 micrometers. These results hold even in the presence of realistic parametric uncertainty in actual spacecraft inertia, center-of-mass offset, and first flexibility modes. Thrust profile knowledge is shown to be a dominant sensitivity for G-Sample, entering in a nearly one-to-one relationship with the final mass estimation error. This means thrust profiles should be well characterized with onboard accelerometers prior to sample collection. An overall sample-mass estimation error budget has been developed to approximate the effect of model uncertainty, sensor noise, data rate, and thrust profile error on the expected estimate of collected sample mass.

  8. Identifying chemicals that are planetary boundary threats.

    PubMed

    MacLeod, Matthew; Breitholtz, Magnus; Cousins, Ian T; de Wit, Cynthia A; Persson, Linn M; Rudén, Christina; McLachlan, Michael S

    2014-10-07

    Rockström et al. proposed a set of planetary boundaries that delimit a "safe operating space for humanity". Many of the planetary boundaries that have so far been identified are determined by chemical agents. Other chemical pollution-related planetary boundaries likely exist, but are currently unknown. A chemical poses an unknown planetary boundary threat if it simultaneously fulfills three conditions: (1) it has an unknown disruptive effect on a vital Earth system process; (2) the disruptive effect is not discovered until it is a problem at the global scale, and (3) the effect is not readily reversible. In this paper, we outline scenarios in which chemicals could fulfill each of the three conditions, then use the scenarios as the basis to define chemical profiles that fit each scenario. The chemical profiles are defined in terms of the nature of the effect of the chemical and the nature of exposure of the environment to the chemical. Prioritization of chemicals in commerce against some of the profiles appears feasible, but there are considerable uncertainties and scientific challenges that must be addressed. Most challenging is prioritizing chemicals for their potential to have a currently unknown effect on a vital Earth system process. We conclude that the most effective strategy currently available to identify chemicals that are planetary boundary threats is prioritization against profiles defined in terms of environmental exposure combined with monitoring and study of the biogeochemical processes that underlie vital Earth system processes to identify currently unknown disruptive effects.

  9. Interrogator system for identifying electrical circuits

    DOEpatents

    Jatko, William B.; McNeilly, David R.

    1988-01-01

    A system for interrogating electrical leads to correctly ascertain the identity of equipment attached to remote ends of the leads. The system includes a source of a carrier signal generated in a controller/receiver to be sent over the leads and an identifier unit at the equipment. The identifier is activated by command of the carrier and uses a portion of the carrier to produce a supply voltage. Each identifier is uniquely programmed for a specific piece of equipment, and causes the impedance of the circuit to be modified whereby the carrier signal is modulated according to that program. The modulation can be amplitude, frequency or phase modulation. A demodulator in the controller/receiver analyzes the modulated carrier signal, and if a verified signal is recognized displays and/or records the information. This information can be utilized in a computer system to prepare a wiring diagram of the electrical equipment attached to specific leads. Specific circuit values are given for amplitude modulation, and the system is particularly described for use with thermocouples.

  10. Interrogator system for identifying electrical circuits

    DOEpatents

    Jatko, W.B.; McNeilly, D.R.

    1988-04-12

    A system for interrogating electrical leads to correctly ascertain the identity of equipment attached to remote ends of the leads is disclosed. The system includes a source of a carrier signal generated in a controller/receiver to be sent over the leads and an identifier unit at the equipment. The identifier is activated by command of the carrier and uses a portion of the carrier to produce a supply voltage. Each identifier is uniquely programmed for a specific piece of equipment, and causes the impedance of the circuit to be modified whereby the carrier signal is modulated according to that program. The modulation can be amplitude, frequency or phase modulation. A demodulator in the controller/receiver analyzes the modulated carrier signal, and if a verified signal is recognized displays and/or records the information. This information can be utilized in a computer system to prepare a wiring diagram of the electrical equipment attached to specific leads. Specific circuit values are given for amplitude modulation, and the system is particularly described for use with thermocouples. 6 figs.

  11. Identifying differentially regulated subnetworks from phosphoproteomic data

    PubMed Central

    2010-01-01

    Background Various high throughput methods are available for detecting regulations at the level of transcription, translation or posttranslation (e.g. phosphorylation). Integrating these data with protein networks should make it possible to identify subnetworks that are significantly regulated. Furthermore, such integration can support identification of regulated entities from often noisy high throughput data. In particular, processing mass spectrometry-based phosphoproteomic data in this manner may expose signal transduction pathways and, in the case of experiments with drug-treated cells, reveal the drug's mode of action. Results Here, we introduce SubExtractor, an algorithm that combines phosphoproteomic data with protein network information from STRING to identify differentially regulated subnetworks and individual proteins. The method is based on a Bayesian probabilistic model combined with a genetic algorithm and rigorous significance testing. The Bayesian model accounts for information about both differential regulation and network topology. The method was tested with artificial data and subsequently applied to a comprehensive phosphoproteomics study investigating the mode of action of sorafenib, a small molecule kinase inhibitor. Conclusions SubExtractor reliably identifies differentially regulated subnetworks from phosphoproteomic data by integrating protein networks. The method can also be applied to gene or protein expression data. PMID:20584295

  12. DEVELOPMENT OF A MOLECULAR METHOD TO IDENTIFY ...

    EPA Pesticide Factsheets

    Hepatitis E virus (HEV) is an emerging pathogen that causes significant illness in the developing world. Like the hepatitis A virus, it is transmitted via the fecal-oral route and can cause short-term, acute hepatitis. In addition, hepatitis E has been found to cause a significant rate of mortality in pregnant women. Thus far, a hepatitis E outbreak has not been reported in the U. S. although a swine variant of the virus is common in Midwestern hogs. Since it will be important to identify the presence of this virus in the water supply, we have developed and are testing a reverse transcription-polymerase chain reaction (RT-PCR) method that should be able to identify all of the known HEV strains. Develop sensitive techniques to detect and identify emerging human waterborne pathogenic viruses and viruses on the CCL.Determine effectiveness of viral indicators to measure microbial quality in water matrices.Support activities: (a) culture and distribution of mammalian cells for Agency and scientific community research needs, (b) provide operator expertise for research requiring confocal and electron microscopy, (c) glassware cleaning, sterilization and biological waste disposal for the Cincinnati EPA facility, (d) operation of infectious pathogenic suite, (e) maintenance of walk-in constant temperature rooms and (f) provide Giardia cysts.

  13. Identifying web usage behavior of bank customers

    NASA Astrophysics Data System (ADS)

    Araya, Sandro; Silva, Mariano; Weber, Richard

    2002-03-01

    The bank Banco Credito e Inversiones (BCI) started its virtual bank in 1996 and its registered customers perform currently more than 10,000 Internet transactions daily, which typically cause les than 10% of traditional transaction costs. Since most of the customers are still not registered for online banking, one of the goals of the virtual bank is to increase then umber of registered customers. Objective of the presented work was to identify customers who are likely to perform online banking but still do not use this medium for their transactions. This objective has been reached by determining profiles of registered customers who perform many transactions online. Based on these profiles the bank's Data Warehouse is explored for twins of these heavy users that are still not registered for online banking. We applied clustering in order to group the registered customers into five classes. One of these classes contained almost 30% of all registered customers and could clearly be identified as class of heavy users. Next a neural network assigned online customers to the previously found five classes. Applying the network trained on online customers to all the bank customers identified twins of heavy users that, however had not performed online transactions so far. A mailing to these candidates informing about the advantages of online banking doubled the number of registrations compared to previous campaigns.

  14. Persistent Identifiers, Discoverability and Open Science (Communication)

    NASA Astrophysics Data System (ADS)

    Murphy, Fiona; Lehnert, Kerstin; Hanson, Brooks

    2016-04-01

    Early in 2016, the American Geophysical Union announced it was incorporating ORCIDs into its submission workflows. This was accompanied by a strong statement supporting the use of other persistent identifiers - such as IGSNs, and the CrossRef open registry 'funding data'. This was partly in response to funders' desire to track and manage their outputs. However the more compelling argument, and the reason why the AGU has also signed up to the Center for Open Science's Transparency and Openness Promotion (TOP) Guidelines (http://cos.io/top), is that ultimately science and scientists will be the richer for these initiatives due to increased opportunities for interoperability, reproduceability and accreditation. The AGU has appealed to the wider community to engage with these initiatives, recognising that - unlike the introduction of Digital Object Identifiers (DOIs) for articles by CrossRef - full, enriched use of persistent identifiers throughout the scientific process requires buy-in from a range of scholarly communications stakeholders. At the same time, across the general research landscape, initiatives such as Project CRediT (contributor roles taxonomy), Publons (reviewer acknowledgements) and the forthcoming CrossRef DOI Event Tracker are contributing to our understanding and accreditation of contributions and impact. More specifically for earth science and scientists, the cross-functional Coalition for Publishing Data in the Earth and Space Sciences (COPDESS) was formed in October 2014 and is working to 'provide an organizational framework for Earth and space science publishers and data facilities to jointly implement and promote common policies and procedures for the publication and citation of data across Earth Science journals'. Clearly, the judicious integration of standards, registries and persistent identifiers such as ORCIDs and International Geo Sample Numbers (IGSNs) to the research and research output processes is key to the success of this venture

  15. S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation

    PubMed Central

    Wahba, Lamia; Costantino, Lorenzo; Tan, Frederick J.; Zimmer, Anjali; Koshland, Douglas

    2016-01-01

    R loops form when transcripts hybridize to homologous DNA on chromosomes, yielding a DNA:RNA hybrid and a displaced DNA single strand. R loops impact the genome of many organisms, regulating chromosome stability, gene expression, and DNA repair. Understanding the parameters dictating R-loop formation in vivo has been hampered by the limited quantitative and spatial resolution of current genomic strategies for mapping R loops. We report a novel whole-genome method, S1-DRIP-seq (S1 nuclease DNA:RNA immunoprecipitation with deep sequencing), for mapping hybrid-prone regions in budding yeast Saccharomyces cerevisiae. Using this methodology, we identified ∼800 hybrid-prone regions covering 8% of the genome. Given the pervasive transcription of the yeast genome, this result suggests that R-loop formation is dictated by characteristics of the DNA, RNA, and/or chromatin. We successfully identified two features highly predictive of hybrid formation: high transcription and long homopolymeric dA:dT tracts. These accounted for >60% of the hybrid regions found in the genome. We demonstrated that these two factors play a causal role in hybrid formation by genetic manipulation. Thus, the hybrid map generated by S1-DRIP-seq led to the identification of the first global genomic features causal for R-loop formation in yeast. PMID:27298336

  16. CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

    PubMed Central

    Hestand, Matthew S; van Galen, Michiel; Villerius, Michel P; van Ommen, Gert-Jan B; den Dunnen, Johan T; 't Hoen, Peter AC

    2008-01-01

    Background The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for over-representation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments. Results We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices from the TRANSFACR database that are over-represented in an experimental set compared to a random set of promoters and identifies cross-species conservation of the predicted transcription factor binding sites. The algorithm has been evaluated with expression and chromatin-immunoprecipitation on microarray data. We also implement and demonstrate the importance of matching the random set of promoters to the experimental promoters by GC content, which is a unique feature of our tool. Conclusion The program CORE_TF is accessible in a user friendly web interface at . It provides a table of over-represented transcription factor binding sites in the users input genes' promoters and a graphical view of evolutionary conserved transcription factor binding sites. In our test data sets it successfully predicts target transcription factors and their binding sites. PMID:19036135

  17. Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses.

    PubMed

    Sokol, Martin; Jessen, Karen Margrethe; Pedersen, Finn Skou

    2016-01-01

    Several studies have shown that human endogenous retroviruses and endogenous retrovirus-like repeats (here collectively HERVs) impose direct regulation on human genes through enhancer and promoter motifs present in their long terminal repeats (LTRs). Although chimeric transcription in which novel gene isoforms containing retroviral and human sequence are transcribed from viral promoters are commonly associated with disease, regulation by HERVs is beneficial in other settings; for example, in human testis chimeric isoforms of TP63 induced by an ERV9 LTR protect the male germ line upon DNA damage by inducing apoptosis, whereas in the human globin locus the γ- and β-globin switch during normal hematopoiesis is mediated by complex interactions of an ERV9 LTR and surrounding human sequence. The advent of deep sequencing or next-generation sequencing (NGS) has revolutionized the way researchers solve important scientific questions and develop novel hypotheses in relation to human genome regulation. We recently applied next-generation paired-end RNA-sequencing (RNA-seq) together with chromatin immunoprecipitation with sequencing (ChIP-seq) to examine ERV9 chimeric transcription in human reference cell lines from Encyclopedia of DNA Elements (ENCODE). This led to the discovery of advanced regulation mechanisms by ERV9s and other HERVs across numerous human loci including transcription of large gene-unannotated genomic regions, as well as cooperative regulation by multiple HERVs and non-LTR repeats such as Alu elements. In this article, well-established examples of human gene regulation by HERVs are reviewed followed by a description of paired-end RNA-seq, and its application in identifying chimeric transcription genome-widely. Based on integrative analyses of RNA-seq and ChIP-seq, data we then present novel examples of regulation by ERV9s of tumor suppressor genes CADM2 and SEMA3A, as well as transcription of an unannotated region. Taken together, this article highlights

  18. Identifying suitable sites for Florida panther reintroduction

    USGS Publications Warehouse

    Thatcher, Cindy; van Manen, Frank T.; Clark, Joseph D.

    2006-01-01

    A major objective of the 1995 Florida Panther (Puma concolor cory) Recovery Plan is the establishment of 2 additional panther populations within the historic range. Our goal was to identify prospective sites for Florida panther reintroduction within the historic range based on quantitative landscape assessments. First, we delineated 86 panther home ranges using telemetry data collected from 1981 to 2001 in south Florida to develop a Mahalanobis distance (D2) habitat model, using 4 anthropogenic variables and 3 landscape variables mapped at a 500-m resolution. From that analysis, we identified 9 potential reintroduction sites of sufficient size to support a panther population. We then developed a similar D2 model at a higher spatial resolution to quantify the area of favorable panther habitat at each site. To address potential for the population to expand, we calculated the amount of favorable habitat adjacent to each prospective reintroduction site within a range of dispersal distances of female panthers. We then added those totals to the contiguous patches to estimate the total amount of effective panther habitat at each site. Finally, we developed an expert-assisted model to rank and incorporate potentially important habitat variables that were not appropriate for our empirical analysis (e.g., area of public lands, livestock density). Anthropogenic factors heavily influenced both the landscape and the expert-assisted models. Of the 9 areas we identified, the Okefenokee National Wildlife Refuge, Ozark National Forest, and Felsenthal National Wildlife Refuge regions had the highest combination of effective habitat area and expert opinion scores. Sensitivity analyses indicated that variability among key model parameters did not affect the high ranking of those sites. Those sites should be considered as starting points for the field evaluation of potential reintroduction sites.

  19. Identifying Airborne Pathogens in Time to Respond

    SciTech Connect

    Hazi, A

    2006-01-25

    Among the possible terrorist activities that might threaten national security is the release of an airborne pathogen such as anthrax. Because the potential damage to human health could be severe, experts consider 1 minute to be an operationally useful time limit for identifying the pathogen and taking action. Many commercial systems can identify airborne pathogenic microbes, but they take days or, at best, hours to produce results. The Department of Homeland Security (DHS) and other U.S. government agencies are interested in finding a faster approach. To answer this national need, a Livermore team, led by scientist Eric Gard, has developed the bioaerosol mass spectrometry (BAMS) system--the only instrument that can detect and identify spores at low concentrations in less than 1 minute. BAMS can successfully distinguish between two related but different spore species. It can also sort out a single spore from thousands of other particles--biological and nonbiological--with no false positives. The BAMS team won a 2005 R&D 100 Award for developing the system. Livermore's Laboratory Directed Research and Development (LDRD) Program funded the biomedical aspects of the BAMS project, and the Department of Defense's Technical Support Working Group and Defense Advanced Research Project Agency funded the biodefense efforts. Developing a detection system that can analyze small samples so quickly has been challenging. Livermore engineer Vincent Riot, who worked on the BAMS project, explains, ''A typical spore weighs approximately one-trillionth of a gram and is dispersed in the atmosphere, which contains naturally occurring particles that could be present at concentrations thousands of times higher. Previous systems also had difficulty separating benign organisms from those that are pathogenic but very similar, which has resulted in false alarms''.

  20. Identifying bacterial predictors of honey bee health.

    PubMed

    Budge, Giles E; Adams, Ian; Thwaites, Richard; Pietravalle, Stéphane; Drew, Georgia C; Hurst, Gregory D D; Tomkies, Victoria; Boonham, Neil; Brown, Mike

    2016-11-01

    Non-targeted approaches are useful tools to identify new or emerging issues in bee health. Here, we utilise next generation sequencing to highlight bacteria associated with healthy and unhealthy honey bee colonies, and then use targeted methods to screen a wider pool of colonies with known health status. Our results provide the first evidence that bacteria from the genus Arsenophonus are associated with poor health in honey bee colonies. We also discovered Lactobacillus and Leuconostoc spp. were associated with healthier honey bee colonies. Our results highlight the importance of understanding how the wider microbial population relates to honey bee colony health.

  1. Method of identifying defective particle coatings

    DOEpatents

    Cohen, Mark E.; Whiting, Carlton D.

    1986-01-01

    A method for identifying coated particles having defective coatings desig to retain therewithin a build-up of gaseous materials including: (a) Pulling a vacuum on the particles; (b) Backfilling the particles at atmospheric pressure with a liquid capable of wetting the exterior surface of the coated particles, said liquid being a compound which includes an element having an atomic number higher than the highest atomic number of any element in the composition which forms the exterior surface of the particle coating; (c) Drying the particles; and (d) Radiographing the particles. By television monitoring, examination of the radiographs is substantially enhanced.

  2. IDENTIFYING PERFORMANCE ASSURANCE CHALLENGES FOR SMART MANUFACTURING

    PubMed Central

    Helu, Moneer; Morris, Katherine; Jung, Kiwook; Lyons, Kevin; Leong, Swee

    2015-01-01

    Smart manufacturing has the potential to address many of the challenges faced by industry. However, the manufacturing community often needs assistance to leverage available technologies to improve their systems. To assure the performance of these technologies, this paper proposes a shared knowledge base that collects problem areas, solutions, and best practices for manufacturing technology. An Implementation Risk Assessment Framework (IRAF) is also described to identify the primary weaknesses of technologies in specific manufacturing contexts. Such approaches have the potential to stimulate new ideas and drive standardization activities critical to scale up and deploy smart manufacturing technologies successfully and quickly. PMID:26783512

  3. Identifying inference attacks against healthcare data repositories

    PubMed Central

    Vaidya, Jaideep; Shafiq, Basit; Jiang, Xiaoqian; Ohno-Machado, Lucila

    Health care data repositories play an important role in driving progress in medical research. Finding new pathways to discovery requires having adequate data and relevant analysis. However, it is critical to ensure the privacy and security of the stored data. In this paper, we identify a dangerous inference attack against naive suppression based approaches that are used to protect sensitive information. We base our attack on the querying system provided by the Healthcare Cost and Utilization Project, though it applies in general to any medical database providing a query capability. We also discuss potential solutions to this problem. PMID:24303279

  4. IDENTIFYING PERFORMANCE ASSURANCE CHALLENGES FOR SMART MANUFACTURING.

    PubMed

    Helu, Moneer; Morris, Katherine; Jung, Kiwook; Lyons, Kevin; Leong, Swee

    2015-10-01

    Smart manufacturing has the potential to address many of the challenges faced by industry. However, the manufacturing community often needs assistance to leverage available technologies to improve their systems. To assure the performance of these technologies, this paper proposes a shared knowledge base that collects problem areas, solutions, and best practices for manufacturing technology. An Implementation Risk Assessment Framework (IRAF) is also described to identify the primary weaknesses of technologies in specific manufacturing contexts. Such approaches have the potential to stimulate new ideas and drive standardization activities critical to scale up and deploy smart manufacturing technologies successfully and quickly.

  5. Nocturnal Sleep Dynamics Identify Narcolepsy Type 1

    PubMed Central

    Pizza, Fabio; Vandi, Stefano; Iloti, Martina; Franceschini, Christian; Liguori, Rocco; Mignot, Emmanuel; Plazzi, Giuseppe

    2015-01-01

    Study Objectives: To evaluate the reliability of nocturnal sleep dynamics in the differential diagnosis of central disorders of hypersomnolence. Design: Cross-sectional. Setting: Sleep laboratory. Patients: One hundred seventy-five patients with hypocretin-deficient narcolepsy type 1 (NT1, n = 79), narcolepsy type 2 (NT2, n = 22), idiopathic hypersomnia (IH, n = 22), and “subjective” hypersomnolence (sHS, n = 52). Interventions: None. Methods: Polysomnographic (PSG) work-up included 48 h of continuous PSG recording. From nocturnal PSG conventional sleep macrostructure, occurrence of sleep onset rapid eye movement period (SOREMP), sleep stages distribution, and sleep stage transitions were calculated. Patient groups were compared, and receiver operating characteristic (ROC) curve analysis was used to test the diagnostic utility of nocturnal PSG data to identify NT1. Results: Sleep macrostructure was substantially stable in the 2 nights of each diagnostic group. NT1 and NT2 patients had lower latency to rapid eye movement (REM) sleep, and NT1 patients showed the highest number of awakenings, sleep stage transitions, and more time spent in N1 sleep, as well as most SOREMPs at daytime PSG and at multiple sleep latency test (MSLT) than all other groups. ROC curve analysis showed that nocturnal SOREMP (area under the curve of 0.724 ± 0.041, P < 0.0001), percent of total sleep time spent in N1 (0.896 ± 0.023, P < 0.0001), and the wakefulness-sleep transition index (0.796 ± 0.034, P < 0.0001) had a good sensitivity and specificity profile to identify NT1 sleep, especially when used in combination (0.903 ± 0.023, P < 0.0001), similarly to SOREMP number at continuous daytime PSG (0.899 ± 0.026, P < 0.0001) and at MSLT (0.956 ± 0.015, P < 0.0001). Conclusions: Sleep macrostructure (i.e. SOREMP, N1 timing) including stage transitions reliably identifies hypocretin-deficient narcolepsy type 1 among central disorders of hypersomnolence. Citation: Pizza F, Vandi S

  6. [Identifying children at risk for cardiorespiratory arrest].

    PubMed

    Carrillo Alvarez, A; Martínez Gutiérrez, A; Salvat Germán, F

    2004-08-01

    Cardiorespiratory arrest in children with severe disease does not usually present suddenly or unexpectedly but is often the result of a progressive deterioration of respiratory and/or circulatory function. Before failure of these functions occurs, there is a series of clinical signs that serve as a warning. Health professionals should not only evaluate clinical signs of respiratory and/or circulatory insufficiency but should also be able to identify these warning signs as early as possible, preferably in the compensation phase, given that the possibility that this process can be reversed by therapeutic measures decreases as the process progresses.

  7. Identifying related journals through log analysis

    PubMed Central

    Lu, Zhiyong; Xie, Natalie; Wilbur, W. John

    2009-01-01

    Motivation: With the explosion of biomedical literature and the evolution of online and open access, scientists are reading more articles from a wider variety of journals. Thus, the list of core journals relevant to their research may be less obvious and may often change over time. To help researchers quickly identify appropriate journals to read and publish in, we developed a web application for finding related journals based on the analysis of PubMed log data. Availability: http://www.ncbi.nlm.nih.gov/IRET/Journals Contact: luzh@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19734155

  8. DNA Barcoding Identifies Illegal Parrot Trade.

    PubMed

    Gonçalves, Priscila F M; Oliveira-Marques, Adriana R; Matsumoto, Tania E; Miyaki, Cristina Y

    2015-01-01

    Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool.

  9. ABCB5 identifies immunoregulatory dermal cells

    PubMed Central

    Schatton, Tobias; Yang, Jun; Kleffel, Sonja; Uehara, Mayuko; Barthel, Steven R.; Schlapbach, Christoph; Zhan, Qian; Dudeney, Stephen; Mueller, Hansgeorg; Lee, Nayoung; de Vries, Juliane C.; Meier, Barbara; Vander Beken, Seppe; Kluth, Mark A.; Ganss, Christoph; Sharpe, Arlene H.; Waaga-Gasser, Ana Maria; Sayegh, Mohamed H.; Abdi, Reza; Scharffetter-Kochanek, Karin; Murphy, George F.; Kupper, Thomas S.; Frank, Natasha Y.; Frank, Markus H.

    2015-01-01

    Summary Cell-based strategies represent a new frontier in the treatment of immune-mediated disorders. However, the paucity of markers for isolation of molecularly-defined immunomodulatory cell populations poses a barrier to this field. Here we show that ATP-binding cassette member B5 (ABCB5) identifies dermal immunoregulatory cells (DIRCs) capable of exerting therapeutic immunoregulatory functions through engagement of programmed cell death 1 (PD-1). Purified Abcb5+ DIRCs suppressed T-cell proliferation, evaded immune rejection, homed to recipient immune tissues and induced Tregs in vivo. In fully MHC-mismatched cardiac allotransplantation models, allogeneic DIRCs significantly prolonged allograft survival. Blockade of DIRC-expressed PD-1 reversed the inhibitory effects of DIRCs on T-cell activation, inhibited DIRC-dependent Treg induction, and attenuated DIRC-induced prolongation of cardiac allograft survival, indicating that DIRC immunoregulatory function is mediated, at least in part, through PD-1. Our results identify ABCB5+ DIRCs as a distinct immunoregulatory cell population and suggest promising roles of this expandable cell subset in cellular immunotherapy. PMID:26321644

  10. Identifying hearing loss by means of iridology.

    PubMed

    Stearn, Natalie; Swanepoel, De Wet

    2006-11-13

    Isolated reports of hearing loss presenting as markings on the iris exist, but to date the effectiveness of iridology to identify hearing loss has not been investigated. This study therefore aimed to determine the efficacy of iridological analysis in the identification of moderate to profound sensorineural hearing loss in adolescents. A controlled trial was conducted with an iridologist, blind to the actual hearing status of participants, analyzing the irises of participants with and without hearing loss. Fifty hearing impaired and fifty normal hearing subjects, between the ages of 15 and 19 years, controlled for gender, participated in the study. An experienced iridologist analyzed the randomised set of participants' irises. A 70% correct identification of hearing status was obtained by iridological analyses with a false negative rate of 41% compared to a 19% false positive rate. The respective sensitivity and specificity rates therefore came to 59% and 81%. Iridological analysis of hearing status indicated a statistically significant relationship to actual hearing status (P < 0.05). Although statistically significant sensitivity and specificity rates for identifying hearing loss by iridology were not comparable to those of traditional audiological screening procedures.

  11. Identifying Novel Transcriptional Regulators with Circadian Expression

    PubMed Central

    Schick, Sandra; Thakurela, Sudhir; Fournier, David; Hampel, Mareike Hildegard

    2015-01-01

    Organisms adapt their physiology and behavior to the 24-h day-night cycle to which they are exposed. On a cellular level, this is regulated by intrinsic transcriptional-translational feedback loops that are important for maintaining the circadian rhythm. These loops are organized by members of the core clock network, which further regulate transcription of downstream genes, resulting in their circadian expression. Despite progress in understanding circadian gene expression, only a few players involved in circadian transcriptional regulation, including transcription factors, epigenetic regulators, and long noncoding RNAs, are known. Aiming to discover such genes, we performed a high-coverage transcriptome analysis of a circadian time course in murine fibroblast cells. In combination with a newly developed algorithm, we identified many transcription factors, epigenetic regulators, and long intergenic noncoding RNAs that are cyclically expressed. In addition, a number of these genes also showed circadian expression in mouse tissues. Furthermore, the knockdown of one such factor, Zfp28, influenced the core clock network. Mathematical modeling was able to predict putative regulator-effector interactions between the identified circadian genes and may help for investigations into the gene regulatory networks underlying circadian rhythms. PMID:26644408

  12. Identifying nonlinear biomechanical models by multicriteria analysis

    NASA Astrophysics Data System (ADS)

    Srdjevic, Zorica; Cveticanin, Livija

    2012-02-01

    In this study, the methodology developed by Srdjevic and Cveticanin (International Journal of Industrial Ergonomics 34 (2004) 307-318) for the nonbiased (objective) parameter identification of the linear biomechanical model exposed to vertical vibrations is extended to the identification of n-degree of freedom (DOF) nonlinear biomechanical models. The dynamic performance of the n-DOF nonlinear model is described in terms of response functions in the frequency domain, such as the driving-point mechanical impedance and seat-to-head transmissibility function. For randomly generated parameters of the model, nonlinear equations of motion are solved using the Runge-Kutta method. The appropriate data transformation from the time-to-frequency domain is performed by a discrete Fourier transformation. Squared deviations of the response functions from the target values are used as the model performance evaluation criteria, thus shifting the problem into the multicriteria framework. The objective weights of criteria are obtained by applying the Shannon entropy concept. The suggested methodology is programmed in Pascal and tested on a 4-DOF nonlinear lumped parameter biomechanical model. The identification process over the 2000 generated sets of parameters lasts less than 20 s. The model response obtained with the imbedded identified parameters correlates well with the target values, therefore, justifying the use of the underlying concept and the mathematical instruments and numerical tools applied. It should be noted that the identified nonlinear model has an improved accuracy of the biomechanical response compared to the accuracy of a linear model.

  13. Identifying barriers to Muslim integration in France

    PubMed Central

    Adida, Claire L.; Laitin, David D.; Valfort, Marie-Anne

    2010-01-01

    Is there a Muslim disadvantage in economic integration for second-generation immigrants to Europe? Previous research has failed to isolate the effect that religion may have on an immigrant family's labor market opportunities because other factors, such as country of origin or race, confound the result. This paper uses a correspondence test in the French labor market to identify and measure this religious effect. The results confirm that in the French labor market, anti-Muslim discrimination exists: a Muslim candidate is 2.5 times less likely to receive a job interview callback than is his or her Christian counterpart. A high-n survey reveals, consistent with expectations from the correspondence test, that second-generation Muslim households in France have lower income compared with matched Christian households. The paper thereby contributes to both substantive debates on the Muslim experience in Europe and methodological debates on how to measure discrimination. Following the National Academy of Sciences’ 2001 recommendations on combining a variety of methodologies and applying them to real-world situations, this research identifies, measures, and infers consequences of discrimination based on religious affiliation, controlling for potentially confounding factors, such as race and country of origin. PMID:21098283

  14. Identifying barriers to Muslim integration in France.

    PubMed

    Adida, Claire L; Laitin, David D; Valfort, Marie-Anne

    2010-12-28

    Is there a Muslim disadvantage in economic integration for second-generation immigrants to Europe? Previous research has failed to isolate the effect that religion may have on an immigrant family's labor market opportunities because other factors, such as country of origin or race, confound the result. This paper uses a correspondence test in the French labor market to identify and measure this religious effect. The results confirm that in the French labor market, anti-Muslim discrimination exists: a Muslim candidate is 2.5 times less likely to receive a job interview callback than is his or her Christian counterpart. A high-n survey reveals, consistent with expectations from the correspondence test, that second-generation Muslim households in France have lower income compared with matched Christian households. The paper thereby contributes to both substantive debates on the Muslim experience in Europe and methodological debates on how to measure discrimination. Following the National Academy of Sciences' 2001 recommendations on combining a variety of methodologies and applying them to real-world situations, this research identifies, measures, and infers consequences of discrimination based on religious affiliation, controlling for potentially confounding factors, such as race and country of origin.

  15. Identifying emotional intelligence in professional nursing practice.

    PubMed

    Kooker, Barbara Molina; Shoultz, Jan; Codier, Estelle E

    2007-01-01

    The National Center for Health Workforce Analysis projects that the shortage of registered nurses in the United States will double by 2010 and will nearly quadruple to 20% by 2015 (Bureau of Health Professionals Health Resources and Services Administration. [2002]. Projected supply, demand, and shortages of registered nurses, 2000-2020 [On-line]. Available: http:bhpr.hrsa.gov/healthworkforce/reports/rnprojects/report.htm). The purpose of this study was to use the conceptual framework of emotional intelligence to analyze nurses' stories about their practice to identify factors that could be related to improved nurse retention and patient/client outcomes. The stories reflected evidence of the competencies and domains of emotional intelligence and were related to nurse retention and improved outcomes. Nurses recognized their own strengths and limitations, displayed empathy and recognized client needs, nurtured relationships, used personal influence, and acted as change agents. Nurses were frustrated when organizational barriers conflicted with their knowledge/intuition about nursing practice, their communications were disregarded, or their attempts to create a shared vision and teamwork were ignored. Elements of professional nursing practice, such as autonomy, nurse satisfaction, respect, and the professional practice environment, were identified in the excerpts of the stories. The shortage of practicing nurses continues to be a national issue. The use of emotional intelligence concepts may provide fresh insights into ways to keep nurses engaged in practice and to improve nurse retention and patient/client outcomes.

  16. Identifying Synonymous Regulatory Elements in Vertebrate Genomes

    SciTech Connect

    Ovcharenko, I; Nobrega, M A

    2005-02-07

    Synonymous gene regulation, defined as driving shared temporal and/or spatial expression of groups of genes, is likely predicated on genomic elements that contain similar modules of certain transcription factor binding sites (TFBS). We have developed a method to scan vertebrate genomes for evolutionary conserved modules of TFBS in a predefined configuration, and created a tool, named SynoR that identify synonymous regulatory elements (SREs) in vertebrate genomes. SynoR performs de novo identification of SREs utilizing known patterns of TFBS in active regulatory elements (REs) as seeds for genome scans. Layers of multiple-species conservation allow the use of differential phylogenetic sequence conservation filters in the search of SREs and the results are displayed as to provide an extensive annotation of genes containing detected REs. Gene Ontology categories are utilized to further functionally classify the identified genes, and integrated GNF Expression Atlas 2 data allow the cataloging of tissue-specificities of the predicted SREs. We illustrate how this new tool can be used to establish a linkage between human diseases and noncoding genomic content. SynoR is publicly available at http://synor.dcode.org.

  17. White dwarfs identified in LAMOST DR 2

    NASA Astrophysics Data System (ADS)

    Guo, Jincheng; Zhao, Jingkun; Tziamtzis, Anestis; Liu, Jifeng; Li, Lifang; Zhang, Yong; Hou, Yonghui; Wang, Yuefei

    2015-12-01

    Here we present a catalogue of 1056 spectroscopically identified hydrogen-dominated white dwarfs (DAWDs), 34 helium-dominated white dwarfs (DBWDs) and 276 white dwarf main sequence (WDMS) binaries from the Large sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) survey data release 2 (DR2). 383 DAWDs, 4 DBWDs and 138 WDMSs are new identifications after cross-match with literature. There are ˜4100 k spectra in total from DR 2. The low ratio of white dwarfs found in LAMOST is attributed to biased selection of LAMOST input catalogue and much brighter targets relative to stars observed in Sloan Digital Sky Survey. In this paper, a new DAWD selection method is adopted as a new attempt and supplement to the traditional methods. The effective temperature, surface gravity, mass, cooling age and distance of high signal-to-noise DAWDs are estimated. The peak of the mass distribution is found to be ˜0.6 M⊙, which is consistent with previous work. The parameters of WDMS binaries are also provided in this paper. As the foundation of our future work, which is to identify more WDs with debris disc, WDs found in LAMOST showed a lot of potential. Interesting infrared-excess WDs will be reported in our forthcoming paper.

  18. Intraoperative molecular imaging to identify lung adenocarcinomas

    PubMed Central

    Newton, Andrew D.; Kennedy, Gregory T.; Predina, Jarrod D.; Low, Philip S.

    2016-01-01

    Intraoperative molecular imaging is a promising new technology with numerous applications in lung cancer surgery. Accurate identification of small nodules and assessment of tumor margins are two challenges in pulmonary resections for cancer, particularly with increasing use of video-assisted thoracoscopic surgery (VATS). One potential solution to these problems is intraoperative use of a fluorescent contrast agent to improve detection of cancer cells. This technology requires both a targeted fluorescent dye that will selectively accumulate in cancer cells and a specialized imaging system to detect the cells. In several studies, we have shown that intraoperative imaging with indocyanine green (ICG) can be used to accurately identify indeterminate pulmonary nodules. The use of a folate-tagged fluorescent molecule targeted to the folate receptor-α (FRα) further improves the sensitivity and specificity of detecting lung adenocarcinomas. We have demonstrated this technology can be used as an “optical biopsy” to differentiate adenocarcinoma versus other histological subtypes of pulmonary nodules. This strategy has potential applications in assessing bronchial stump margins, identifying synchronous or metachronous lesions, and rapidly assessing lymph nodes for lung adenocarcinoma. PMID:28066672

  19. Identifying Bitcoin users by transaction behavior

    NASA Astrophysics Data System (ADS)

    Monaco, John V.

    2015-05-01

    Digital currencies, such as Bitcoin, offer convenience and security to criminals operating in the black marketplace. Some Bitcoin marketplaces, such as Silk Road, even claim anonymity. This claim contradicts the findings in this work, where long term transactional behavior is used to identify and verify account holders. Transaction timestamps and network properties observed over time contribute to this finding. The timestamp of each transaction is the result of many factors: the desire purchase an item, daily schedule and activities, as well as hardware and network latency. Dynamic network properties of the transaction, such as coin flow and the number of edge outputs and inputs, contribute further to reveal account identity. In this paper, we propose a novel methodology for identifying and verifying Bitcoin users based on the observation of Bitcoin transactions over time. The behavior we attempt to quantify roughly occurs in the social band of Newell's time scale. A subset of the Blockchain 230686 is taken, selecting users that initiated between 100 and 1000 unique transactions per month for at least 6 different months. This dataset shows evidence of being nonrandom and nonlinear, thus a dynamical systems approach is taken. Classification and authentication accuracies are obtained under various representations of the monthly Bitcoin samples: outgoing transactions, as well as both outgoing and incoming transactions are considered, along with the timing and dynamic network properties of transaction sequences. The most appropriate representations of monthly Bitcoin samples are proposed. Results show an inherent lack of anonymity by exploiting patterns in long-term transactional behavior.

  20. Using Dissimilarity Metrics to Identify Interesting Designs

    NASA Technical Reports Server (NTRS)

    Feather, Martin; Kiper, James

    2006-01-01

    A computer program helps to blend the power of automated-search software, which is able to generate large numbers of design solutions, with the insight of expert designers, who are able to identify preferred designs but do not have time to examine all the solutions. From among the many automated solutions to a given design problem, the program selects a smaller number of solutions that are worthy of scrutiny by the experts in the sense that they are sufficiently dissimilar from each other. The program makes the selection in an interactive process that involves a sequence of data-mining steps interspersed with visual displays of results of these steps to the experts. At crucial points between steps, the experts provide directives to guide the process. The program uses heuristic search techniques to identify nearly optimal design solutions and uses dissimilarity metrics defined by the experts to characterize the degree to which solutions are interestingly different. The search, data-mining, and visualization features of the program were derived from previously developed risk-management software used to support a risk-centric design methodology

  1. Identifying MMORPG Bots: A Traffic Analysis Approach

    NASA Astrophysics Data System (ADS)

    Chen, Kuan-Ta; Jiang, Jhih-Wei; Huang, Polly; Chu, Hao-Hua; Lei, Chin-Laung; Chen, Wen-Chin

    2008-12-01

    Massively multiplayer online role playing games (MMORPGs) have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1) the regularity in the release time of client commands, 2) the trend and magnitude of traffic burstiness in multiple time scales, and 3) the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  2. Regional Seismic Methods of Identifying Explosions

    NASA Astrophysics Data System (ADS)

    Walter, W. R.; Ford, S. R.; Pasyanos, M.; Pyle, M. L.; Hauk, T. F.

    2013-12-01

    A lesson from the 2006, 2009 and 2013 DPRK declared nuclear explosion Ms:mb observations is that our historic collection of data may not be representative of future nuclear test signatures (e.g. Selby et al., 2012). To have confidence in identifying future explosions amongst the background of other seismic signals, we need to put our empirical methods on a firmer physical footing. Here we review the two of the main identification methods: 1) P/S ratios and 2) Moment Tensor techniques, which can be applied at the regional distance (200-1600 km) to very small events, improving nuclear explosion monitoring and confidence in verifying compliance with the Comprehensive Nuclear-Test-Ban Treaty (CTBT). Amplitude ratios of seismic P-to-S waves at sufficiently high frequencies (~>2 Hz) can identify explosions among a background of natural earthquakes (e.g. Walter et al., 1995). However the physical basis for the generation of explosion S-waves, and therefore the predictability of this P/S technique as a function of event properties such as size, depth, geology and path, remains incompletely understood. Calculated intermediate period (10-100s) waveforms from regional 1-D models can match data and provide moment tensor results that separate explosions from earthquakes and cavity collapses (e.g. Ford et al. 2009). However it has long been observed that some nuclear tests produce large Love waves and reversed Rayleigh waves that complicate moment tensor modeling. Again the physical basis for the generation of these effects from explosions remains incompletely understood. We are re-examining regional seismic data from a variety of nuclear test sites including the DPRK and the former Nevada Test Site (now the Nevada National Security Site (NNSS)). Newer relative amplitude techniques can be employed to better quantify differences between explosions and used to understand those differences in term of depth, media and other properties. We are also making use of the Source Physics

  3. Military unique curriculum: identifying and prioritizing content.

    PubMed

    Cloonan, Clifford; Fauver, Howard E; Holloway, Harry C; Hospenthal, Duane R; Hutton, John; Lewis, Evelyn; Madrigal, Vinicio E; Maliner, Beverly; Nelson, Michael; Reynolds, Paul C; Staunton, Michael; Wayne, Barry A; Roy, Michael J

    2003-09-01

    We have identified and prioritized a series of objectives that warrant inclusion in the continuum of military medical education. Although participants in the 16th Conference on Military Medicine also discussed whether each objective should be taught at the medical student, resident, or staff physician level, to a large extent this distinction is not helpful, since many, if not most, of these topic areas would likely require incorporation at each of these three levels to achieve the desired level of competence in staff physicians. Incorporation of new curricular elements poses a significant challenge, since it is already difficult to fit the existing curriculum into the available time. It is not reasonable to consider increasing the number of lecture hours. Therefore, it is probable that some elements of the existing curriculum will need to be pared down or eliminated to incorporate new material. In the past, when new material has been added to the existing curriculum, such as when the pathogenesis of human immunodeficiency virus was added, it has generally been done at the individual teacher or at most departmental level. Although this approach has the advantage of having a subject matter expert decide how best to insert new material within the fabric of the existing curriculum, there are a couple of problems with widespread use of this approach. First, some of these new objectives may not fit clearly within an existing course curriculum or department's educational mission. Second, such an approach may not provide the degree of coordination that is necessary to ensure that a new curricular item is adequately covered in all respects, and it may result in unnecessary overlap in instruction when different professors incorporate similar elements. Therefore, the prioritization of newer curricular items, as has been done during this conference, may serve as a useful guide in this process. However, a corresponding effort is needed to identify and prioritize existing

  4. Process Architecture for Managing Digital Object Identifiers

    NASA Astrophysics Data System (ADS)

    Wanchoo, L.; James, N.; Stolte, E.

    2014-12-01

    In 2010, NASA's Earth Science Data and Information System (ESDIS) Project implemented a process for registering Digital Object Identifiers (DOIs) for data products distributed by Earth Observing System Data and Information System (EOSDIS). For the first 3 years, ESDIS evolved the process involving the data provider community in the development of processes for creating and assigning DOIs, and guidelines for the landing page. To accomplish this, ESDIS established two DOI User Working Groups: one for reviewing the DOI process whose recommendations were submitted to ESDIS in February 2014; and the other recently tasked to review and further develop DOI landing page guidelines for ESDIS approval by end of 2014. ESDIS has recently upgraded the DOI system from a manually-driven system to one that largely automates the DOI process. The new automated feature include: a) reviewing the DOI metadata, b) assigning of opaque DOI name if data provider chooses, and c) reserving, registering, and updating the DOIs. The flexibility of reserving the DOI allows data providers to embed and test the DOI in the data product metadata before formally registering with EZID. The DOI update process allows the changing of any DOI metadata except the DOI name unless the name has not been registered. Currently, ESDIS has processed a total of 557 DOIs of which 379 DOIs are registered with EZID and 178 are reserved with ESDIS. The DOI incorporates several metadata elements that effectively identify the data product and the source of availability. Of these elements, the Uniform Resource Locator (URL) attribute has the very important function of identifying the landing page which describes the data product. ESDIS in consultation with data providers in the Earth Science community is currently developing landing page guidelines that specify the key data product descriptive elements to be included on each data product's landing page. This poster will describe in detail the unique automated process and

  5. Identifying DNA methylation in a nanochannel

    PubMed Central

    Sun, Xiaoyin; Yasui, Takao; Yanagida, Takeshi; Kaji, Noritada; Rahong, Sakon; Kanai, Masaki; Nagashima, Kazuki; Kawai, Tomoji; Baba, Yoshinobu

    2016-01-01

    Abstract DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24–96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h. PMID:27877910

  6. Identifying the immunomodulatory components of helminths.

    PubMed

    Shepherd, C; Navarro, S; Wangchuk, P; Wilson, D; Daly, N L; Loukas, A

    2015-06-01

    Immunomodulatory components of helminths offer great promise as an entirely new class of biologics for the treatment of inflammatory diseases. Here, we discuss the emerging themes in helminth-driven immunomodulation in the context of therapeutic drug discovery. We broadly define the approaches that are currently applied by researchers to identify these helminth molecules, highlighting key areas of potential exploitation that have been mostly neglected thus far, notably small molecules. Finally, we propose that the investigation of immunomodulatory compounds will enable the translation of current and future research efforts into potential treatments for autoimmune and allergic diseases, while at the same time yielding new insights into the molecular interface of host-parasite biology.

  7. Method of identifying features in indexed data

    DOEpatents

    Jarman, Kristin H [Richland, WA; Daly, Don Simone [Richland, WA; Anderson, Kevin K [Richland, WA; Wahl, Karen L [Richland, WA

    2001-06-26

    The present invention is a method of identifying features in indexed data, especially useful for distinguishing signal from noise in data provided as a plurality of ordered pairs. Each of the plurality of ordered pairs has an index and a response. The method has the steps of: (a) providing an index window having a first window end located on a first index and extending across a plurality of indices to a second window end; (b) selecting responses corresponding to the plurality of indices within the index window and computing a measure of dispersion of the responses; and (c) comparing the measure of dispersion to a dispersion critical value. Advantages of the present invention include minimizing signal to noise ratio, signal drift, varying baseline signal and combinations thereof.

  8. Identifying financial crises in real time

    NASA Astrophysics Data System (ADS)

    da Fonseca, Eder Lucio; Ferreira, Fernando F.; Muruganandam, Paulsamy; Cerdeira, Hilda A.

    2013-03-01

    Following the thermodynamic formulation of a multifractal measure that was shown to enable the detection of large fluctuations at an early stage, here we propose a new index which permits us to distinguish events like financial crises in real time. We calculate the partition function from which we can obtain thermodynamic quantities analogous to the free energy and specific heat. The index is defined as the normalized energy variation and it can be used to study the behavior of stochastic time series, such as financial market daily data. Famous financial market crashes-Black Thursday (1929), Black Monday (1987) and the subprime crisis (2008)-are identified with clear and robust results. The method is also applied to the market fluctuations of 2011. From these results it appears as if the apparent crisis of 2011 is of a different nature to the other three. We also show that the analysis has forecasting capabilities.

  9. Identifying and Analyzing Web Server Attacks

    SciTech Connect

    Seifert, Christian; Endicott-Popovsky, Barbara E.; Frincke, Deborah A.; Komisarczuk, Peter; Muschevici, Radu; Welch, Ian D.

    2008-08-29

    Abstract: Client honeypots can be used to identify malicious web servers that attack web browsers and push malware to client machines. Merely recording network traffic is insufficient to perform comprehensive forensic analyses of such attacks. Custom tools are required to access and analyze network protocol data. Moreover, specialized methods are required to perform a behavioral analysis of an attack, which helps determine exactly what transpired on the attacked system. This paper proposes a record/replay mechanism that enables forensic investigators to extract application data from recorded network streams and allows applications to interact with this data in order to conduct behavioral analyses. Implementations for the HTTP and DNS protocols are presented and their utility in network forensic investigations is demonstrated.

  10. Advances in identifying beryllium sensitization and disease.

    PubMed

    Middleton, Dan; Kowalski, Peter

    2010-01-01

    Beryllium is a lightweight metal with unique qualities related to stiffness, corrosion resistance, and conductivity. While there are many useful applications, researchers in the 1930s and 1940s linked beryllium exposure to a progressive occupational lung disease. Acute beryllium disease is a pulmonary irritant response to high exposure levels, whereas chronic beryllium disease (CBD) typically results from a hypersensitivity response to lower exposure levels. A blood test, the beryllium lymphocyte proliferation test (BeLPT), was an important advance in identifying individuals who are sensitized to beryllium (BeS) and thus at risk for developing CBD. While there is no true "gold standard" for BeS, basic epidemiologic concepts have been used to advance our understanding of the different screening algorithms.

  11. Identifying states of a financial market.

    PubMed

    Münnix, Michael C; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H; Guhr, Thomas; Stanley, H Eugene

    2012-01-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical "market states". Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

  12. Identifying Health-Related Topics on Twitter

    NASA Astrophysics Data System (ADS)

    Prier, Kyle W.; Smith, Matthew S.; Giraud-Carrier, Christophe; Hanson, Carl L.

    Public health-related topics are difficult to identify in large conversational datasets like Twitter. This study examines how to model and discover public health topics and themes in tweets. Tobacco use is chosen as a test case to demonstrate the effectiveness of topic modeling via LDA across a large, representational dataset from the United States, as well as across a smaller subset that was seeded by tobacco-related queries. Topic modeling across the large dataset uncovers several public health-related topics, although tobacco is not detected by this method. However, topic modeling across the tobacco subset provides valuable insight about tobacco use in the United States. The methods used in this paper provide a possible toolset for public health researchers and practitioners to better understand public health problems through large datasets of conversational data.

  13. Identifying States of a Financial Market

    NASA Astrophysics Data System (ADS)

    Münnix, Michael C.; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H.; Guhr, Thomas; Stanley, H. Eugene

    2012-09-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical ``market states''. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

  14. Identifying States of a Financial Market

    PubMed Central

    Münnix, Michael C.; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H.; Guhr, Thomas; Stanley, H. Eugene

    2012-01-01

    The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992–2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical “market states”. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen. PMID:22966419

  15. Identifying decohering paths in closed quantum systems

    NASA Technical Reports Server (NTRS)

    Albrecht, Andreas

    1990-01-01

    A specific proposal is discussed for how to identify decohering paths in a wavefunction of the universe. The emphasis is on determining the correlations among subsystems and then considering how these correlations evolve. The proposal is similar to earlier ideas of Schroedinger and of Zeh, but in other ways it is closer to the decoherence functional of Griffiths, Omnes, and Gell-Mann and Hartle. There are interesting differences with each of these which are discussed. Once a given coarse-graining is chosen, the candidate paths are fixed in this scheme, and a single well defined number measures the degree of decoherence for each path. The normal probability sum rules are exactly obeyed (instantaneously) by these paths regardless of the level of decoherence. Also briefly discussed is how one might quantify some other aspects of classicality. The important role that concrete calculations play in testing this and other proposals is stressed.

  16. Automatic Prosodic Analysis to Identify Mild Dementia

    PubMed Central

    Gonzalez-Moreira, Eduardo; Torres-Boza, Diana; Kairuz, Héctor Arturo; Ferrer, Carlos; Garcia-Zamora, Marlene; Espinoza-Cuadros, Fernando; Hernandez-Gómez, Luis Alfonso

    2015-01-01

    This paper describes an exploratory technique to identify mild dementia by assessing the degree of speech deficits. A total of twenty participants were used for this experiment, ten patients with a diagnosis of mild dementia and ten participants like healthy control. The audio session for each subject was recorded following a methodology developed for the present study. Prosodic features in patients with mild dementia and healthy elderly controls were measured using automatic prosodic analysis on a reading task. A novel method was carried out to gather twelve prosodic features over speech samples. The best classification rate achieved was of 85% accuracy using four prosodic features. The results attained show that the proposed computational speech analysis offers a viable alternative for automatic identification of dementia features in elderly adults. PMID:26558287

  17. Identifying cryptic diversity with predictive phylogeography.

    PubMed

    Espíndola, Anahí; Ruffley, Megan; Smith, Megan L; Carstens, Bryan C; Tank, David C; Sullivan, Jack

    2016-10-26

    Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.

  18. Identifying hidden voice and video streams

    NASA Astrophysics Data System (ADS)

    Fan, Jieyan; Wu, Dapeng; Nucci, Antonio; Keralapura, Ram; Gao, Lixin

    2009-04-01

    Given the rising popularity of voice and video services over the Internet, accurately identifying voice and video traffic that traverse their networks has become a critical task for Internet service providers (ISPs). As the number of proprietary applications that deliver voice and video services to end users increases over time, the search for the one methodology that can accurately detect such services while being application independent still remains open. This problem becomes even more complicated when voice and video service providers like Skype, Microsoft, and Google bundle their voice and video services with other services like file transfer and chat. For example, a bundled Skype session can contain both voice stream and file transfer stream in the same layer-3/layer-4 flow. In this context, traditional techniques to identify voice and video streams do not work. In this paper, we propose a novel self-learning classifier, called VVS-I , that detects the presence of voice and video streams in flows with minimum manual intervention. Our classifier works in two phases: training phase and detection phase. In the training phase, VVS-I first extracts the relevant features, and subsequently constructs a fingerprint of a flow using the power spectral density (PSD) analysis. In the detection phase, it compares the fingerprint of a flow to the existing fingerprints learned during the training phase, and subsequently classifies the flow. Our classifier is not only capable of detecting voice and video streams that are hidden in different flows, but is also capable of detecting different applications (like Skype, MSN, etc.) that generate these voice/video streams. We show that our classifier can achieve close to 100% detection rate while keeping the false positive rate to less that 1%.

  19. Newly Identified Pathogens Associated with Periodontitis

    PubMed Central

    Pérez-Chaparro, P.J.; Gonçalves, C.; Figueiredo, L.C.; Faveri, M.; Lobão, E.; Tamashiro, N.; Duarte, P.; Feres, M.

    2014-01-01

    There is substantial evidence supporting the role of certain oral bacteria species in the onset and progression of periodontitis. Nevertheless, results of independent-culture diagnostic methods introduced about a decade ago have pointed to the existence of new periodontal pathogens. However, the data of these studies have not been evaluated together, which may generate some misunderstanding on the actual role of these microorganisms in the etiology of periodontitis. The aim of this systematic review was to determine the current weight of evidence for newly identified periodontal pathogens based on the results of “association” studies. This review was conducted and reported in accordance with the PRISMA statement. The MEDLINE, EMBASE, and Cochrane databases were searched up to September 2013 for studies (1) comparing microbial data of subgingival plaque samples collected from subjects with periodontitis and periodontal health and (2) evaluating at least 1 microorganism other than the already-known periodontal pathogens. From 1,450 papers identified, 41 studies were eligible. The data were extracted and registered in predefined piloted forms. The results suggested that there is moderate evidence in the literature to support the association of 17 species or phylotypes from the phyla Bacteroidetes, Candidatus Saccharibacteria, Firmicutes, Proteobacteria, Spirochaetes, and Synergistetes. The phylum Candidatus Saccharibacteria and the Archaea domain also seem to have an association with disease. These data point out the importance of previously unidentified species in the etiology of periodontitis and might guide future investigations on the actual role of these suspected new pathogens in the onset and progression of this infection. PMID:25074492

  20. Melanoma biomolecules: independently identified but functionally intertwined.

    PubMed

    Dye, Danielle E; Medic, Sandra; Ziman, Mel; Coombe, Deirdre R

    2013-09-24

    The majority of patients diagnosed with melanoma present with thin lesions and generally these patients have a good prognosis. However, 5% of patients with early melanoma (<1 mm thick) will have recurrence and die within 10 years, despite no evidence of local or metastatic spread at the time of diagnosis. Thus, there is a need for additional prognostic markers to help identify those patients that may be at risk of recurrent disease. Many studies and several meta-analyses have compared gene and protein expression in melanocytes, naevi, primary, and metastatic melanoma in an attempt to find informative prognostic markers for these patients. However, although a large number of putative biomarkers have been described, few of these molecules are informative when used in isolation. The best approach is likely to involve a combination of molecules. We believe one approach could be to analyze the expression of a group of interacting proteins that regulate different aspects of the metastatic pathway. This is because a primary lesion expressing proteins involved in multiple stages of metastasis may be more likely to lead to secondary disease than one that does not. This review focuses on five putative biomarkers - melanoma cell adhesion molecule (MCAM), galectin-3 (gal-3), matrix metalloproteinase 2 (MMP-2), chondroitin sulfate proteoglycan 4 (CSPG4), and paired box 3 (PAX3). The goal is to provide context around what is known about the contribution of these biomarkers to melanoma biology and metastasis. Although each of these molecules have been independently identified as likely biomarkers, it is clear from our analyses that each are closely linked with each other, with intertwined roles in melanoma biology.

  1. Vulnerability of critical infrastructures : identifying critical nodes.

    SciTech Connect

    Cox, Roger Gary; Robinson, David Gerald

    2004-06-01

    The objective of this research was the development of tools and techniques for the identification of critical nodes within critical infrastructures. These are nodes that, if disrupted through natural events or terrorist action, would cause the most widespread, immediate damage. This research focuses on one particular element of the national infrastructure: the bulk power system. Through the identification of critical elements and the quantification of the consequences of their failure, site-specific vulnerability analyses can be focused at those locations where additional security measures could be effectively implemented. In particular, with appropriate sizing and placement within the grid, distributed generation in the form of regional power parks may reduce or even prevent the impact of widespread network power outages. Even without additional security measures, increased awareness of sensitive power grid locations can provide a basis for more effective national, state and local emergency planning. A number of methods for identifying critical nodes were investigated: small-world (or network theory), polyhedral dynamics, and an artificial intelligence-based search method - particle swarm optimization. PSO was found to be the only viable approach and was applied to a variety of industry accepted test networks to validate the ability of the approach to identify sets of critical nodes. The approach was coded in a software package called Buzzard and integrated with a traditional power flow code. A number of industry accepted test networks were employed to validate the approach. The techniques (and software) are not unique to power grid network, but could be applied to a variety of complex, interacting infrastructures.

  2. Identifying environmental correlates of intraspecific genetic variation.

    PubMed

    Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

    2016-09-01

    Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution).

  3. Ultrasonic Detectors Safely Identify Dangerous, Costly Leaks

    NASA Technical Reports Server (NTRS)

    2013-01-01

    In 1990, NASA grounded its space shuttle fleet. The reason: leaks detected in the hydrogen fuel systems of the Space Shuttles Atlantis and Columbia. Unless the sources of the leaks could be identified and fixed, the shuttles would not be safe to fly. To help locate the existing leaks and check for others, Kennedy Space Center engineers used portable ultrasonic detectors to scan the fuel systems. As a gas or liquid escapes from a leak, the resulting turbulence creates ultrasonic noise, explains Gary Mohr, president of Elmsford, New York-based UE Systems Inc., a long-time leader in ultrasonic detector technologies. "In lay terms, the leak is like a dog whistle, and the detector is like the dog ear." Because the ultrasound emissions from a leak are highly localized, they can be used not only to identify the presence of a leak but also to help pinpoint a leak s location. The NASA engineers employed UE s detectors to examine the shuttle fuel tanks and solid rocket boosters, but encountered difficulty with the devices limited range-certain areas of the shuttle proved difficult or unsafe to scan up close. To remedy the problem, the engineers created a long-range attachment for the detectors, similar to "a zoom lens on a camera," Mohr says. "If you are on the ground, and the leak is 50 feet away, the detector would now give you the same impression as if you were only 25 feet away." The enhancement also had the effect of reducing background noise, allowing for a clearer, more precise detection of a leak s location.

  4. Electrophoretic mobility shift assay identifies vitamin D binding protein (Gc-globulin) in human, rat, and mouse sera.

    PubMed

    Tang, W X; Bazaraa, H M; Magiera, H; Cooke, N E; Haddad, J G

    1996-06-01

    Serum vitamin D binding protein (DBP, also known as Gc-globulin) is a multifunctional protein capable of binding both vitamin D metabolites and actin. DBP can be visualized when analyzed by polyacrylamide gel electrophoresis followed by staining. Confirmation of its identity had previously required immunoprecipitation with specific anti-DBP antisera or occupancy of the protein with radioactive vitamin D sterols. We present studies showing that preincubation of G-actin with mammalian sera produced a discernible DBP protein band shift on native gel electrophoresis. Addition of DNaseI, a 33-kDa intracellular protein with an avid actin-binding site, to the incubations resulted in a supershift of DBP-actin complexes to an even more cathodal region of the gels. Following incubations with human, rat, and murine sera the same actin shift occurred as did the actin plus DNaseI supershift. The migrations of each complex were correlated with purified DBP migrations under identical conditions. It was confirmed that the supershifted bands contained DBP by Western blotting and detection of DBP by binding of 25-OH[3H]D3. After intravenous G-actin injections into living mice, a serum DBP-actin complex could be detected on native gels as the uncomplexed DBP band decreased in intensity. This simple, direct-staining technique appears to be suitable for identifying DBP/Gc phenotypes in human populations as well as for semiquantitatively monitoring the plasma actin-scavenger system in vivo in animal models or in human diseases.

  5. Small RNA and RNA-IP Sequencing Identifies and Validates Novel MicroRNAs in Human Mesenchymal Stem Cells.

    PubMed

    Tsai, Chin-Han; Liao, Ko-Hsun; Shih, Chuan-Chi; Chan, Chia-Hao; Hsieh, Jui-Yu; Tsai, Cheng-Fong; Wang, Hsei-Wei; Chang, Shing-Jyh

    2016-03-01

    Organ regeneration therapies using multipotent mesenchymal stem cells (MSCs) are currently being investigated for a variety of common complex diseases. Understanding the molecular regulation of MSC biology will benefit regenerative medicine. MicroRNAs (miRNAs) act as regulators in MSC stemness. There are approximately 2500 currently known human miRNAs that have been recorded in the miRBase v21 database. In the present study, we identified novel microRNAs involved in MSC stemness and differentiation by obtaining the global microRNA expression profiles (miRNomes) of MSCs from two anatomical locations bone marrow (BM-MSCs) and umbilical cord Wharton's jelly (WJ-MSCs) and from osteogenically and adipogenically differentiated progenies of BM-MSCs. Small RNA sequencing (smRNA-seq) and bioinformatics analyses predicted that 49 uncharacterized miRNA candidates had high cellular expression values in MSCs. Another independent batch of Ago1/2-based RNA immunoprecipitation (RNA-IP) sequencing datasets validated the existence of 40 unreported miRNAs in cells and their associations with the RNA-induced silencing complex (RISC). Nine of these 40 new miRNAs were universally overexpressed in both MSC types; nine others were overexpressed in differentiated cells. A novel miRNA (UNI-118-3p) was specifically expressed in BM-MSCs, as verified using RT-qPCR. Taken together, this report offers comprehensive miRNome profiles for two MSC types, as well as cells differentiated from BM-MSCs. MSC transplantation has the potential to ameliorate degenerative disorders and repair damaged tissues. Interventions involving the above 40 new microRNA members in transplanted MSCs may potentially guide future clinical applications.

  6. Notch3 Interactome Analysis Identified WWP2 as a Negative Regulator of Notch3 Signaling in Ovarian Cancer

    PubMed Central

    Guan, Bin; Wu, Ren-Chin; Zhu, Heng; Blackshaw, Seth; Shih, Ie-Ming; Wang, Tian-Li

    2014-01-01

    The Notch3 signaling pathway is thought to play a critical role in cancer development, as evidenced by the Notch3 amplification and rearrangement observed in human cancers. However, the molecular mechanism by which Notch3 signaling contributes to tumorigenesis is largely unknown. In an effort to identify the molecular modulators of the Notch3 signaling pathway, we screened for Notch3-intracellular domain (N3-ICD) interacting proteins using a human proteome microarray. Pathway analysis of the Notch3 interactome demonstrated that ubiquitin C was the molecular hub of the top functional network, suggesting the involvement of ubiquitination in modulating Notch3 signaling. Thereby, we focused on functional characterization of an E3 ubiquitin-protein ligase, WWP2, a top candidate in the Notch3 interactome list. Co-immunoprecipitation experiments showed that WWP2 interacted with N3-ICD but not with intracellular domains from other Notch receptors. Wild-type WWP2 but not ligase-deficient mutant WWP2 increases mono-ubiquitination of the membrane-tethered Notch3 fragment, therefore attenuating Notch3 pathway activity in cancer cells and leading to cell cycle arrest. The mono-ubiquitination by WWP2 may target an endosomal/lysosomal degradation fate for Notch3 as suggested by the fact that the process could be suppressed by the endosomal/lysosomal inhibitor. Analysis of The Cancer Genome Atlas dataset showed that the majority of ovarian carcinomas harbored homozygous or heterozygous deletions in WWP2 locus, and there was an inverse correlation in the expression levels between WWP2 and Notch3 in ovarian carcinomas. Furthermore, ectopic expression of WWP2 decreased tumor development in a mouse xenograft model and suppressed the Notch3-induced phenotypes including increase in cancer stem cell-like cell population and platinum resistance. Taken together, our results provide evidence that WWP2 serves as a tumor suppressor by negatively regulating Notch3 signaling in ovarian cancer

  7. Phosphorylation Sites Identified in the NEIL1 DNA Glycosylase Are Potential Targets for the JNK1 Kinase

    PubMed Central

    Prakash, Aishwarya; Cao, Vy Bao; Doublié, Sylvie

    2016-01-01

    The NEIL1 DNA glycosylase is one of eleven mammalian DNA glycosylases that partake in the first step of the base excision repair (BER) pathway. NEIL1 recognizes and cleaves mainly oxidized pyrimidines from DNA. The past decade has witnessed the identification of an increasing number of post-translational modifications (PTMs) in BER enzymes including phosphorylation, acetylation, and sumoylation, which modulate enzyme function. In this work, we performed the first comprehensive analysis of phosphorylation sites in human NEIL1 expressed in human cells. Mass spectrometry (MS) analysis revealed phosphorylation at three serine residues: S207, S306, and a third novel site, S61. We expressed, purified, and characterized phosphomimetic (glutamate) and phosphoablating (alanine) mutants of the three phosphorylation sites in NEIL1 revealed by the MS analysis. All mutant enzymes were active and bound tightly to DNA, indicating that phosphorylation does not affect DNA binding and enzyme activity at these three serine sites. We also characterized phosphomimetic mutants of two other sites of phosphorylation, Y263 and S269, reported previously, and observed that mutation of Y263 to E yielded a completely inactive enzyme. Furthermore, based on sequence motifs and kinase prediction algorithms, we identified the c-Jun N-terminal kinase 1 (JNK1) as the kinase involved in the phosphorylation of NEIL1. JNK1, a member of the mitogen activated protein kinase (MAPK) family, was detected in NEIL1 immunoprecipitates, interacted with NEIL1 in vitro, and was able to phosphorylate the enzyme at residues S207, S306, and S61. PMID:27518429

  8. Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence

    PubMed Central

    Reid, Daniel C.; Chang, Brian L.; Gunderson, Samuel I.; Alpert, Lauren; Thompson, William A.; Fairbrother, William G.

    2009-01-01

    Many splicing factors interact with both mRNA and pre-mRNA. The identification of these interactions has been greatly improved by the development of in vivo cross-linking immunoprecipitation. However, the output carries a strong sampling bias in favor of RNPs that form on more abundant RNA species like mRNA. We have developed a novel in vitro approach for surveying binding on pre-mRNA, without cross-linking or sampling bias. Briefly, this approach entails specifically designed oligonucleotide pools that tile through a pre-mRNA sequence. The pool is then partitioned into bound and unbound fractions, which are quantified by a two-color microarray. We applied this approach to locating splicing factor binding sites in and around ∼4000 exons. We also quantified the effect of secondary structure on binding. The method is validated by the finding that U1snRNP binds at the 5′ splice site (5′ss) with a specificity that is nearly identical to the splice donor motif. In agreement with prior reports, we also show that U1snRNP appears to have some affinity for intronic G triplets that are proximal to the 5′ss. Both U1snRNP and the polypyrimidine tract binding protein (PTB) avoid exonic binding, and the PTB binding map shows increased enrichment at the polypyrimidine tract. For PTB, we confirm polypyrimidine specificity and are also able to identify structural determinants of PTB binding. We detect multiple binding motifs enriched in the PTB bound fraction of oligonucleotides. These motif combinations augment binding in vitro and are also enriched in the vicinity of exons that have been determined to be in vivo targets of PTB. PMID:19861426

  9. Identifying sites for elk restoration in Arkansas

    USGS Publications Warehouse

    Telesco, R.L.; Van Manen, F.T.; Clark, J.D.; Cartwright, Michael E.

    2007-01-01

    We used spatial data to identify potential areas for elk (Cervus elaphus) restoration in Arkansas. To assess habitat, we used locations of 239 elk groups collected from helicopter surveys in the Buffalo National River area of northwestern Arkansas, USA, from 1992 to 2002. We calculated the Mahalanobis distance (D2) statistic based on the relationship between those elk-group locations and a suite of 9 landscape variables to evaluate winter habitat in Arkansas. We tested model performance in the Buffalo National River area by comparing the D2 values of pixels representing areas with and without elk pellets along 19 fixed-width transects surveyed in March 2002. Pixels with elk scat had lower D2 values than pixels in which we found no pellets (logistic regression: Wald χ2 = 24.37, P < 0.001), indicating that habitat characteristics were similar to those selected by the aerially surveyed elk. Our D2 model indicated that the best elk habitat primarily occurred in northern and western Arkansas and was associated with areas of high landscape heterogeneity, heavy forest cover, gently sloping ridge tops and valleys, low human population density, and low road densities. To assess the potential for elk–human conflicts in Arkansas, we used the analytical hierarchy process to rank the importance of 8 criteria based on expert opinion from biologists involved in elk management. The biologists ranked availability of forage on public lands as having the strongest influence on the potential for elk–human conflict (33%), followed by human population growth rate (22%) and the amount of private land in row crops (18%). We then applied those rankings in a weighted linear summation to map the relative potential for elk–human conflict. Finally, we used white-tailed deer (Odocoileus virginianus) densities to identify areas where success of elk restoration may be hampered due to meningeal worm (Parelaphostrongylus tenuis) transmission. By combining results of the 3 spatial data layers

  10. Using Hyperspectral Imagery to Identify Turfgrass Stresses

    NASA Technical Reports Server (NTRS)

    Hutto, Kendall; Shaw, David

    2008-01-01

    The use of a form of remote sensing to aid in the management of large turfgrass fields (e.g. golf courses) has been proposed. A turfgrass field of interest would be surveyed in sunlight by use of an airborne hyperspectral imaging system, then the raw observational data would be preprocessed into hyperspectral reflectance image data. These data would be further processed to identify turfgrass stresses, to determine the spatial distributions of those stresses, and to generate maps showing the spatial distributions. Until now, chemicals and water have often been applied, variously, (1) indiscriminately to an entire turfgrass field without regard to localization of specific stresses or (2) to visible and possibly localized signs of stress for example, browning, damage from traffic, or conspicuous growth of weeds. Indiscriminate application is uneconomical and environmentally unsound; the amounts of water and chemicals consumed could be insufficient in some areas and excessive in most areas, and excess chemicals can leak into the environment. In cases in which developing stresses do not show visible signs at first, it could be more economical and effective to take corrective action before visible signs appear. By enabling early identification of specific stresses and their locations, the proposed method would provide guidance for planning more effective, more economical, and more environmentally sound turfgrass-management practices, including application of chemicals and water, aeration, and mowing. The underlying concept of using hyperspectral imagery to generate stress maps as guides to efficient management of vegetation in large fields is not new; it has been applied in the growth of crops to be harvested. What is new here is the effort to develop an algorithm that processes hyperspectral reflectance data into spectral indices specific to stresses in turfgrass. The development effort has included a study in which small turfgrass plots that were, variously, healthy or

  11. Use of lice to identify cowbird hosts

    USGS Publications Warehouse

    Hahn, D.C.; Price, R.D.; Osenton, P.C.

    2000-01-01

    The host specificity of avian lice (Phthiraptera) may be utilized by biologists to investigate the brood parasitism patterns of Brown-headed Cowbirds (Molothrus ater). As nestlings, brood parasites have a unique opportunity to encounter lice that are typically host specific. Lice are permanent hemimetabolic ectoparasites, a group found strictly on the body of the host, and they are transferred almost exclusively by bodily contact between hosts during care of young and at copulation. We investigated whether cowbird nestlings become infested with avian lice from their host parents and carry these lice away when they fledge, in effect bearing ectoparasite indicators of the species that raised them. The technique of examining the lice on cowbird fledglings to identify their foster parents would be much less costly than hiring a team of experts to determine parasitism patterns in the conventional way by finding hundreds of songbird nests. We examined 244 cowbird fledglings and found that they carried a rich fauna of lice representing 11 species and six genera, almost the entire spectrum of louse genera known to occur on passerines. We also examined 320 songbirds from 30 species, all known hosts of the Brown-headed Cowbird. As a group the host birds bore a diversity of louse species comparable to that on the fledgling cowbirds: 13 species of lice from seven genera. In contrast, most individual passerine host species yielded only 1 or 2 louse species, significantly fewer than the cowbird fledglings (p < 0.0001). Of 44 fledgling cowbirds carrying lice, 11 were linked to their probable avian foster parents via louse indicators, and these are the Wood Thrush and Red-winged Blackbird. Eighteen additional fledglings were linked to one of two possible foster parents. We concluded that cowbird fledglings do carry away host lice and this survey technique provides a partial assessment of local community parasitism patterns. The incomplete state of passerine louse taxonomy requires

  12. Utilizing Surface Sensors to Identify Wake Regimes

    NASA Astrophysics Data System (ADS)

    Wang, Mengying; Hemati, Maziar S.

    2016-11-01

    Marine swimmers often exploit external flow structures to reduce locomotive effort. To achieve this advantage, these swimmers utilize mechanosensory organs on the surface of their bodies to detect hydrodynamic signals from the surrounding fluid, which can then be used to inform the control task. Recently, there has been a growing interest in developing similar flow sensing systems to achieve enhanced propulsive efficiency and maneuverability in human-engineered underwater vehicles. In particular, much attention has been given to the problem of wake sensing; however, these investigations have concentrated on a restricted class of wakes-i.e., Kármán-type vortex streets-whereas more complicated wake structures can arise in practice. In this talk, we will explore the possibility of identifying wake regimes through the use of surface sensors. Potential flow theory is adopted to simulate the interactions of various wakes with a fish-like body. Wakes in different dynamical regimes impart distinct hydrodynamic signatures on the body, which permits these regimes to be distinguished from one another in an automated fashion. Our results can provide guidance for improving flow sensing capabilities in human-engineered systems and hint at how marine swimmers may sense their hydrodynamic surroundings.

  13. Identifying dark matter interactions in monojet searches

    DOE PAGES

    Agrawal, Prateek; Rentala, Vikram

    2014-05-22

    We study the discrimination of quark-initiated jets from gluon-initiated jets in monojet searches for dark matter using the technique of averaged jet energy profiles. We demonstrate our results in the context of effective field theories of dark matter interactions with quarks and gluons, but our methods apply more generally to a wide class of models. Different effective theories of dark matter and the standard model backgrounds each have a characteristic quark/gluon fraction for the leading jet. When used in conjunction with the traditional cut-and-count monojet search, the jet energy profile can be used to set stronger bounds on contact interactionsmore » of dark matter. In the event of a discovery of a monojet excess at the 14 TeV LHC, contact interactions between dark matter with quarks or with gluons can be differentiated at the 95% confidence level. For a given rate at the LHC, signal predictions at direct detection experiments for different dark matter interactions can span five orders of magnitude. Lastly, the ability to identify these interactions allows us to make a tighter connection between LHC searches and direct detection experiments.« less

  14. Identifying and quantifying urban recharge: a review

    NASA Astrophysics Data System (ADS)

    Lerner, David N.

    2002-02-01

    The sources of and pathways for groundwater recharge in urban areas are more numerous and complex than in rural environments. Buildings, roads, and other surface infrastructure combine with man-made drainage networks to change the pathways for precipitation. Some direct recharge is lost, but additional recharge can occur from storm drainage systems. Large amounts of water are imported into most cities for supply, distributed through underground pipes, and collected again in sewers or septic tanks. The leaks from these pipe networks often provide substantial recharge. Sources of recharge in urban areas are identified through piezometry, chemical signatures, and water balances. All three approaches have problems. Recharge is quantified either by individual components (direct recharge, water-mains leakage, septic tanks, etc.) or holistically. Working with individual components requires large amounts of data, much of which is uncertain and is likely to lead to large uncertainties in the final result. Recommended holistic approaches include the use of groundwater modelling and solute balances, where various types of data are integrated. Urban recharge remains an under-researched topic, with few high-quality case studies reported in the literature.

  15. Identifying Wind and Solar Ramping Events: Preprint

    SciTech Connect

    Florita, A.; Hodge, B. M.; Orwig, K.

    2013-01-01

    Wind and solar power are playing an increasing role in the electrical grid, but their inherent power variability can augment uncertainties in power system operations. One solution to help mitigate the impacts and provide more flexibility is enhanced wind and solar power forecasting; however, its relative utility is also uncertain. Within the variability of solar and wind power, repercussions from large ramping events are of primary concern. At the same time, there is no clear definition of what constitutes a ramping event, with various criteria used in different operational areas. Here the Swinging Door Algorithm, originally used for data compression in trend logging, is applied to identify variable generation ramping events from historic operational data. The identification of ramps in a simple and automated fashion is a critical task that feeds into a larger work of 1) defining novel metrics for wind and solar power forecasting that attempt to capture the true impact of forecast errors on system operations and economics, and 2) informing various power system models in a data-driven manner for superior exploratory simulation research. Both allow inference on sensitivities and meaningful correlations, as well as the ability to quantify the value of probabilistic approaches for future use in practice.

  16. Identifying the extent of a Superfund site

    SciTech Connect

    Gowland, P.A.; Chantry, W.; Wisniewski, R.

    1995-12-31

    There has been considerable misunderstanding regarding the extent of private and Federal facility sites listed under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) or Superfund program. This problem, which occurs primarily at the time of proposal or finalization of a site to the National Priorities List (NPL), seems to be due both to semantics and errors in perception. The term ``site`` has been used differently in performing CERCLA removal and remediation activities, in the installation restoration programs of various Federal agencies, and by the public when preparing comments on proposed NPL sites. It has been confused with the terms source, solid waste management unit, and facility. The most common interpretation by the public of the term ``site`` and its extent is that the site encompasses the property owned by the facility named in the NPL designation or at which a removal has occurred. However, based on the related definitions in CERCLA, a site is best defined as the location of a release (or releases) of hazardous substances and wherever the hazardous substances have come to be located. The extent of a site neither is limited by property boundaries, nor does it include clean areas within a facility`s boundaries. This paper will identify the basis for the Environmental Protection Agency`s (EPA`s) definition of site for Superfund purposes, including aggregated sites, relevant court decisions and statements of EPA policy, and provide case histories of how this definition has been applied at both private and Federal facilities.

  17. Indexing molecules with chemical graph identifiers.

    PubMed

    Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi

    2011-09-01

    Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used.

  18. The Ku-band polarization identifier

    NASA Astrophysics Data System (ADS)

    Gundersen, J. O.; Kupid Collaboration

    2003-12-01

    The Ku-band polarization identifier (KUPID) will integrate a very low noise 12-18 GHz, correlation polarimeter onto the Crawford Hill seven meter, millimeter-wave antenna. The primary components of the polarimeter will be built at the University of Miami and other key components, including the microwave horn and data acquisition system will be built at the University of Chicago and Princeton University. This project will measure the Q and U Stokes parameters in regions near the north celestial pole, in regions of low galactic contamination, and in regions near the galactic plane. The KUPID survey experiment makes use of many of the techniques employed in the Princeton IQU experiment (PIQUE) that was developed by the members of this collaboration to detect CMB polarization at shorter wavelengths. The KUPID experiment will be constructed in parallel and on the same timescale as the CAPMAP experiment (see Barkats, this volume) which is the follow-on experiment to PIQUE. KUPID will observe on the Crawford Hill antenna from late spring until early autumn, while CAPMAP will observe during the lower water vapor months of late autumn until early spring.

  19. Identifying recycled ash in basaltic eruptions

    NASA Astrophysics Data System (ADS)

    D'Oriano, Claudia; Bertagnini, Antonella; Cioni, Raffaello; Pompilio, Massimo

    2014-07-01

    Deposits of mid-intensity basaltic explosive eruptions are characterized by the coexistence of different types of juvenile clasts, which show a large variability of external properties and texture, reflecting alternatively the effects of primary processes related to magma storage or ascent, or of syn-eruptive modifications occurred during or immediately after their ejection. If fragments fall back within the crater area before being re-ejected during the ensuing activity, they are subject to thermally- and chemically-induced alterations. These `recycled' clasts can be considered as cognate lithic for the eruption/explosion they derive. Their exact identification has consequences for a correct interpretation of eruption dynamics, with important implications for hazard assessment. On ash erupted during selected basaltic eruptions (at Stromboli, Etna, Vesuvius, Gaua-Vanuatu), we have identified a set of characteristics that can be associated with the occurrence of intra-crater recycling processes, based also on the comparison with results of reheating experiments performed on primary juvenile material, at variable temperature and under different redox conditions.

  20. Identifying a new particle with jet substructures

    NASA Astrophysics Data System (ADS)

    Han, Chengcheng; Kim, Doojin; Kim, Minho; Kong, Kyoungchul; Lim, Sung Hak; Park, Myeonghun

    2017-01-01

    We investigate a potential of determining properties of a new heavy resonance of mass O(1) TeV which decays to collimated jets via heavy Standard Model intermediary states, exploiting jet substructure techniques. Employing the Z gauge boson as a concrete example for the intermediary state, we utilize a "merged jet" defined by a large jet size to capture the two quarks from its decay. The use of the merged jet benefits the identification of a Z-induced jet as a single, reconstructed object without any combinatorial ambiguity. We find that jet substructure procedures may enhance features in some kinematic observables formed with subjet four-momenta extracted from a merged jet. This observation motivates us to feed subjet momenta into the matrix elements associated with plausible hypotheses on the nature of the heavy resonance, which are further processed to construct a matrix element method (MEM)-based observable. For both moderately and highly boosted Z bosons, we demonstrate that the MEM in combination with jet substructure techniques can be a very powerful tool for identifying its physical properties. We also discuss effects from choosing different jet sizes for merged jets and jet-grooming parameters upon the MEM analyses.

  1. Strategies for identifying new prions in yeast.

    PubMed

    MacLea, Kyle S; Ross, Eric D

    2011-01-01

    The unexpected discovery of two prions, [URE3] and [PSI+], in Saccharomyces cerevisiae led to questions about how many other proteins could undergo similar prion-based structural conversions. However, [URE3] and [PSI+] were discovered by serendipity in genetic screens. Cataloging the full range of prions in yeast or in other organisms will therefore require more systematic search methods. Taking advantage of some of the unique features of prions, various researchers have developed bioinformatic and experimental methods for identifying novel prion proteins. These methods have generated long lists of prion candidates. The systematic testing of some of these prion candidates has led to notable successes; however, even in yeast, where rapid growth rate and ease of genetic manipulation aid in testing for prion activity, such candidate testing is laborious. Development of better methods to winnow the field of prion candidates will greatly aid in the discovery of new prions, both in yeast and in other organisms, and help us to better understand the role of prions in biology.

  2. Identifying image preferences based on demographic attributes

    NASA Astrophysics Data System (ADS)

    Fedorovskaya, Elena A.; Lawrence, Daniel R.

    2014-02-01

    The intent of this study is to determine what sorts of images are considered more interesting by which demographic groups. Specifically, we attempt to identify images whose interestingness ratings are influenced by the demographic attribute of the viewer's gender. To that end, we use the data from an experiment where 18 participants (9 women and 9 men) rated several hundred images based on "visual interest" or preferences in viewing images. The images were selected to represent the consumer "photo-space" - typical categories of subject matter found in consumer photo collections. They were annotated using perceptual and semantic descriptors. In analyzing the image interestingness ratings, we apply a multivariate procedure known as forced classification, a feature of dual scaling, a discrete analogue of principal components analysis (similar to correspondence analysis). This particular analysis of ratings (i.e., ordered-choice or Likert) data enables the investigator to emphasize the effect of a specific item or collection of items. We focus on the influence of the demographic item of gender on the analysis, so that the solutions are essentially confined to subspaces spanned by the emphasized item. Using this technique, we can know definitively which images' ratings have been influenced by the demographic item of choice. Subsequently, images can be evaluated and linked, on one hand, to their perceptual and semantic descriptors, and, on the other hand, to the preferences associated with viewers' demographic attributes.

  3. Canopy hot-spot as crop identifier

    SciTech Connect

    Gerstl, S.A.W.; Simmer, C.; Powers, B.J.

    1986-05-01

    Illuminating any reflective rough or structured surface by a directional light source results in an angular reflectance distribution that shows a narrow peak in the direction of retro-reflection. This is called the Heiligenschein or hot-spot of vegetation canopies and is caused by mutual shading of leaves. The angular intensity distribution of the hot-spot, its brightness and slope, are therefore indicators of the plant's geometry. We propose the use of hot-spot characteristics as crop identifiers in satellite remote sensing because the canopy hot-spot carries information about plant stand architecture that is more distinctive for different plant species than, for instance, their spectral reflectance characteristics. A simple three-dimensional Monte Carlo/ray tracing model and an analytic two-dimensional model are developed to estimate the angular distribution of the hot-spot as a function of the size of the plant leaves. The results show that the brightness-distribution and slope of the hot-spot change distinctively for different leaf sizes indicating a much more peaked maximum for the smaller leaves.

  4. Identifying murder victims with endodontic radiographs.

    PubMed

    Silva, Rhonan Ferreira; Franco, Ademir; Mendes, Solon Diego Santos Carvalho; Picoli, Fernando Fortes; Nunes, Fernando Gomes; Estrela, Carlos

    2016-01-01

    Endodontics is a special branch of dentistry constantly guided by imaging examinations. From a forensic scope, endodontics plays a valuable role providing solid antemortem (AM) radiographic evidence for comparison with postmortem findings in human identifications. This study illustrates the interface between endodontics and forensic odontology describing three cases of human identification based on radiographic endodontic records. From 2009 to 2012, three unknown male victims of murder were examined in a local Brazilian medico-legal institute to retrieve identity and potential cause of death. Specifically, when asked for AM data, a relative of the three victims provided periapical radiographs of endodontic treatments. Based on that, forensic dentists reproduced the same imaging acquisition techniques obtaining similar periapical radiographs, enabling a comparative dental identification. All the victims were positively identified based on patterns of dental morphology and treatment intervention. This study draws the attention of general and forensic dentists highlight the importance of properly recording dental treatments and searching for evidence in AM endodontic data, respectively.

  5. Monoclonal Antibodies Identify Novel Neural Antigens

    NASA Astrophysics Data System (ADS)

    Hawkes, Richard; Niday, Evelyn; Matus, Andrew

    1982-04-01

    Monoclonal antibodies (Mabs) were raised against synaptic plasma membranes from rat cerebellum. The hybridomas were screened with a solid-phase immunoassay, the positive lines were characterized by their immunoperoxidase staining pattern on cerebellum, and the specific polypeptide antigens were identified on protein blots. Among the Mabs described are some that stain only neurons or only glia and others that react with specific parts of cells, such as axons, dendrites, and synapses. Many Mabs reveal novel relationships between antigens and the cells in which they occur. For example, a Mab designated 7D5 reacts with a family of > 30 proteins but stains only glial cells. Several Mabs stain punctate sites of synaptic size and distribution in the cerebellar cortex but each reacts with a different subset of polypeptides. One of the most restricted cytological staining patterns is given by 12D5, which stains punctate sites in the granular layer of the cerebellar cortex and reacts with a single polypeptide band of apparent Mr 270,000. These results illustrate the feasibility of raising Mabs that can be used to follow the expression of specific gene products during brain development.

  6. RECOGNIZING AND IDENTIFYING PEOPLE: A neuropsychological review

    PubMed Central

    Barton, Jason J S; Corrow, Sherryse L

    2016-01-01

    Recognizing people is a classic example of a cognitive function that involves multiple processing stages and parallel routes of information. Neuropsychological data have provided important evidence for models of this process, particularly from case reports; however, the quality and extent of the data varies widely between studies. In this review we first discuss the requirements and logical basis of the types of neuropsychological evidence to support conclusions about the modules in this process. We then survey the adequacy of the current body of reports to address two key issues. First is the question of which cognitive operation generates a sense of familiarity: the current debate revolves around whether familiarity arises in modality-specific recognition units or later amodal processes. Key evidence on this point comes from the search for dissociations between familiarity for faces, voices and names. The second question is whether lesions can differentially affect the abilities to link diverse sources of person information (e.g. face, voice, name, biographic data). Dissociations of these linkages may favour a distributed-only model of the organization of semantic knowledge, whereas a ‘person-hub’ model would predict uniform impairments of all linkages. While we conclude that there is reasonable evidence for dissociations in name, voice and face familiarity in regards to the first question, the evidence for or against dissociated linkages between information stores in regards to the second is tenuous at best. We identify deficiencies in the current literature that should motivate and inform the design of future studies. PMID:26773237

  7. Identifying murder victims with endodontic radiographs

    PubMed Central

    Silva, Rhonan Ferreira; Franco, Ademir; Mendes, Solon Diego Santos Carvalho; Picoli, Fernando Fortes; Nunes, Fernando Gomes; Estrela, Carlos

    2016-01-01

    Endodontics is a special branch of dentistry constantly guided by imaging examinations. From a forensic scope, endodontics plays a valuable role providing solid antemortem (AM) radiographic evidence for comparison with postmortem findings in human identifications. This study illustrates the interface between endodontics and forensic odontology describing three cases of human identification based on radiographic endodontic records. From 2009 to 2012, three unknown male victims of murder were examined in a local Brazilian medico-legal institute to retrieve identity and potential cause of death. Specifically, when asked for AM data, a relative of the three victims provided periapical radiographs of endodontic treatments. Based on that, forensic dentists reproduced the same imaging acquisition techniques obtaining similar periapical radiographs, enabling a comparative dental identification. All the victims were positively identified based on patterns of dental morphology and treatment intervention. This study draws the attention of general and forensic dentists highlight the importance of properly recording dental treatments and searching for evidence in AM endodontic data, respectively. PMID:28123272

  8. Can we identify source lithology of basalt?

    PubMed Central

    Yang, Zong-Feng; Zhou, Jun-Hong

    2013-01-01

    The nature of source rocks of basaltic magmas plays a fundamental role in understanding the composition, structure and evolution of the solid earth. However, identification of source lithology of basalts remains uncertainty. Using a parameterization of multi-decadal melting experiments on a variety of peridotite and pyroxenite, we show here that a parameter called FC3MS value (FeO/CaO-3*MgO/SiO2, all in wt%) can identify most pyroxenite-derived basalts. The continental oceanic island basalt-like volcanic rocks (MgO>7.5%) (C-OIB) in eastern China and Mongolia are too high in the FC3MS value to be derived from peridotite source. The majority of the C-OIB in phase diagrams are equilibrium with garnet and clinopyroxene, indicating that garnet pyroxenite is the dominant source lithology. Our results demonstrate that many reputed evolved low magnesian C-OIBs in fact represent primary pyroxenite melts, suggesting that many previous geological and petrological interpretations of basalts based on the single peridotite model need to be reconsidered. PMID:23676779

  9. IDENTIFYING ANOMALIES IN GRAVITATIONAL LENS TIME DELAYS

    SciTech Connect

    Congdon, Arthur B.; Keeton, Charles R.; Nordgren, C. Erik E-mail: keeton@physics.rutgers.ed

    2010-02-01

    We examine the ability of gravitational lens time delays to reveal complex structure in lens potentials. In a previous paper, we predicted how the time delay between the bright pair of images in a 'fold' lens scales with the image separation, for smooth lens potentials. Here we show that the proportionality constant increases with the quadrupole moment of the lens potential, and depends only weakly on the position of the source along the caustic. We use Monte Carlo simulations to determine the range of time delays that can be produced by realistic smooth lens models consisting of isothermal ellipsoid galaxies with tidal shear. We can then identify outliers as 'time delay anomalies'. We find evidence for anomalies in close image pairs in the cusp lenses RX J1131 - 1231 and B1422+231. The anomalies in RX J1131 - 1231 provide strong evidence for substructure in the lens potential, while at this point the apparent anomalies in B1422+231 mainly indicate that the time delay measurements need to be improved. We also find evidence for time delay anomalies in larger-separation image pairs in the fold lenses, B1608+656 and WFI 2033 - 4723, and the cusp lens RX J0911+0551. We suggest that these anomalies are caused by some combination of substructure and a complex lens environment. Finally, to assist future monitoring campaigns we use our smooth models with shear to predict the time delays for all known four-image lenses.

  10. A Novel Method for Identifying Exoplanetary Rings

    NASA Astrophysics Data System (ADS)

    Zuluaga, Jorge I.; Kipping, David M.; Sucerquia, Mario; Alvarado, Jaime A.

    2015-04-01

    The discovery of rings around extrasolar planets (“exorings”) is one of the next breakthroughs in exoplanetary research. Previous studies have explored the feasibility of detecting exorings with present and future photometric sensitivities by seeking anomalous deviations in the residuals of a standard transit light curve fit, at the level of ≃ 100 ppm for Kronian rings. In this work, we explore two much larger observational consequences of exorings: (1) the significant increase in transit depth that may lead to the misclassification of ringed planetary candidates as false-positives and/or the underestimation of planetary density; and (2) the so-called “photo-ring” effect, a new asterodensity profiling effect, revealed by a comparison of the light curve derived stellar density to that measured with independent methods (e.g., asteroseismology). While these methods do not provide an unambiguous detection of exorings, we show that the large amplitude of these effects, combined with their relatively simple analytic description, makes them highly suited to large-scale surveys to identify candidate ringed planets worthy of more detailed investigation. Moreover, these methods lend themselves to ensemble analyses seeking to uncover evidence of a population of ringed planets. We describe the method in detail, develop the basic underlying formalism, and test it in the parameter space of rings and transit configuration. We discuss the prospects of using this method for the first systematic search of exoplanetary rings in the Kepler database and provide a basic computational code for implementing it.

  11. Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes

    PubMed Central

    Edmunds, Richard C.; Su, Baofeng; Balhoff, James P.; Eames, B. Frank; Dahdul, Wasila M.; Lapp, Hilmar; Lundberg, John G.; Vision, Todd J.; Dunham, Rex A.; Mabee, Paula M.; Westerfield, Monte

    2016-01-01

    Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology. PMID:26500251

  12. Identifying dark matter interactions in monojet searches

    SciTech Connect

    Agrawal, Prateek; Rentala, Vikram

    2014-05-22

    We study the discrimination of quark-initiated jets from gluon-initiated jets in monojet searches for dark matter using the technique of averaged jet energy profiles. We demonstrate our results in the context of effective field theories of dark matter interactions with quarks and gluons, but our methods apply more generally to a wide class of models. Different effective theories of dark matter and the standard model backgrounds each have a characteristic quark/gluon fraction for the leading jet. When used in conjunction with the traditional cut-and-count monojet search, the jet energy profile can be used to set stronger bounds on contact interactions of dark matter. In the event of a discovery of a monojet excess at the 14 TeV LHC, contact interactions between dark matter with quarks or with gluons can be differentiated at the 95% confidence level. For a given rate at the LHC, signal predictions at direct detection experiments for different dark matter interactions can span five orders of magnitude. Lastly, the ability to identify these interactions allows us to make a tighter connection between LHC searches and direct detection experiments.

  13. Identifying orthoimages in Web Map Services

    NASA Astrophysics Data System (ADS)

    Florczyk, A. J.; Nogueras-Iso, J.; Zarazaga-Soria, F. J.; Béjar, R.

    2012-10-01

    Orthoimages are essential in many Web applications to facilitate the background context that helps to understand other georeferenced information. Catalogues and service registries of Spatial Data Infrastructures do not necessarily register all the services providing access to imagery data on the Web, and it is not easy to automatically identify whether the data offered by a Web service are directly imagery data or not. This work presents a method for an automatic detection of the orthoimage layers offered by Web Map Services. The method combines two types of heuristics. The first one consists in analysing the text in the capabilities document. The second type is content-based heuristics, which analyse the content offered by the Web Map Service layers. These heuristics gather and analyse the colour features of a sample collection of image fragments that represent the offered content. An experiment has been performed over a set of Web Map Service layers, which have been fetched from a repository of capabilities documents gathered from the Web. This has proven the efficiency of the method (precision of 87% and recall of 60%). This functionality has been offered as a Web Processing Service, and it has been integrated within the Virtual Spain project to provide a catalogue of orthoimages and build realistic 3D views.

  14. Astrobiology: Identifying Bacteria from Extreme Environments

    NASA Astrophysics Data System (ADS)

    Quan, Tiffany K.; Dorighi, Kristel M.; Cooksey, Kathy L.

    2010-12-01

    COSMOS is a four-week summer residential academic and enrichment program for high school students interested in science and mathematics, sponsored by the University of California. Since 2001, participants in the Center for Adaptive Optics (CfAO) Professional Development Program (PDP) have developed and instructed a general astronomy and biology COSMOS course cluster. This cluster provides an optimal venue for piloting newly designed activities, as well as an opportunity for PDP participants to obtain practical teaching experience. In 2007, we designed an astrobiology-based project for five of the 17 students in our cluster. This project aimed to bridge the gap between the astronomy and biology sides of Cluster 7: Stars and Cells. We facilitated the process whereby the students designed and implemented their own experimental plan to identify unknown extremophilic bacteria. Their findings allowed them to extrapolate and discuss what it means to be alive and how these factors would impact life on other planets. Here we provide details of the entire project design and reflect on its success.

  15. Can we identify source lithology of basalt?

    PubMed

    Yang, Zong-Feng; Zhou, Jun-Hong

    2013-01-01

    The nature of source rocks of basaltic magmas plays a fundamental role in understanding the composition, structure and evolution of the solid earth. However, identification of source lithology of basalts remains uncertainty. Using a parameterization of multi-decadal melting experiments on a variety of peridotite and pyroxenite, we show here that a parameter called FC3MS value (FeO/CaO-3*MgO/SiO2, all in wt%) can identify most pyroxenite-derived basalts. The continental oceanic island basalt-like volcanic rocks (MgO>7.5%) (C-OIB) in eastern China and Mongolia are too high in the FC3MS value to be derived from peridotite source. The majority of the C-OIB in phase diagrams are equilibrium with garnet and clinopyroxene, indicating that garnet pyroxenite is the dominant source lithology. Our results demonstrate that many reputed evolved low magnesian C-OIBs in fact represent primary pyroxenite melts, suggesting that many previous geological and petrological interpretations of basalts based on the single peridotite model need to be reconsidered.

  16. Identifying recycled ash in basaltic eruptions.

    PubMed

    D'Oriano, Claudia; Bertagnini, Antonella; Cioni, Raffaello; Pompilio, Massimo

    2014-07-28

    Deposits of mid-intensity basaltic explosive eruptions are characterized by the coexistence of different types of juvenile clasts, which show a large variability of external properties and texture, reflecting alternatively the effects of primary processes related to magma storage or ascent, or of syn-eruptive modifications occurred during or immediately after their ejection. If fragments fall back within the crater area before being re-ejected during the ensuing activity, they are subject to thermally- and chemically-induced alterations. These 'recycled' clasts can be considered as cognate lithic for the eruption/explosion they derive. Their exact identification has consequences for a correct interpretation of eruption dynamics, with important implications for hazard assessment. On ash erupted during selected basaltic eruptions (at Stromboli, Etna, Vesuvius, Gaua-Vanuatu), we have identified a set of characteristics that can be associated with the occurrence of intra-crater recycling processes, based also on the comparison with results of reheating experiments performed on primary juvenile material, at variable temperature and under different redox conditions.

  17. Identifying recycled ash in basaltic eruptions

    PubMed Central

    D'Oriano, Claudia; Bertagnini, Antonella; Cioni, Raffaello; Pompilio, Massimo

    2014-01-01

    Deposits of mid-intensity basaltic explosive eruptions are characterized by the coexistence of different types of juvenile clasts, which show a large variability of external properties and texture, reflecting alternatively the effects of primary processes related to magma storage or ascent, or of syn-eruptive modifications occurred during or immediately after their ejection. If fragments fall back within the crater area before being re-ejected during the ensuing activity, they are subject to thermally- and chemically-induced alterations. These ‘recycled' clasts can be considered as cognate lithic for the eruption/explosion they derive. Their exact identification has consequences for a correct interpretation of eruption dynamics, with important implications for hazard assessment. On ash erupted during selected basaltic eruptions (at Stromboli, Etna, Vesuvius, Gaua-Vanuatu), we have identified a set of characteristics that can be associated with the occurrence of intra-crater recycling processes, based also on the comparison with results of reheating experiments performed on primary juvenile material, at variable temperature and under different redox conditions. PMID:25069064

  18. In vivo phage display screening for tumor vascular targets in glioblastoma identifies a llama nanobody against dynactin-1-p150Glued

    PubMed Central

    Verhoeff, Joost J.C.; Mäkinen, Petri I.; Lappalainen, Jari P.; Ylä-Herttuala, Seppo; Raats, Jos; van Wijk, Erwin; Roepman, Ronald; Letteboer, Stef J.; Verrijp, Kiek; Leenders, William P.J.

    2016-01-01

    Diffuse gliomas are primary brain cancers that are characterised by infiltrative growth. Whereas high-grade glioma characteristically presents with perinecrotic neovascularisation, large tumor areas thrive on pre-existent vasculature as well. Clinical studies have revealed that pharmacological inhibition of the angiogenic process does not improve survival of glioblastoma patients. Direct targeting of tumor vessels may however still be an interesting therapeutic approach as it allows pinching off the blood supply to tumor cells. Such tumor vessel targeting requires the identification of tumor-specific vascular targeting agents (TVTAs). Here we describe a novel TVTA, C-C7, which we identified via in vivo biopanning of a llama nanobody phage display library in an orthotopic mouse model of diffuse glioma. We show that C-C7 recognizes a subpopulation of tumor blood vessels in glioma xenografts and clinical glioma samples. Additionally, C-C7 recognizes macrophages and activated endothelial cells in atherosclerotic lesions. By using C-C7 as bait in yeast-2-hybrid (Y2H) screens we identified dynactin-1-p150Glued as its binding partner. The interaction was confirmed by co-immunostainings with C-C7 and a commercial anti-dynactin-1-p150Glued antibody, and via co-immunoprecipitation/western blot studies. Normal brain vessels do not express dynactin-1-p150Glued and its expression is reduced under anti-VEGF therapy, suggesting that dynactin-1-p150Glued is a marker for activated endothelial cells. In conclusion, we show that in vivo phage display combined with Y2H screenings provides a powerful approach to identify tumor-targeting nanobodies and their binding partners. Using this combination of methods we identify dynactin-1-p150Glued as a novel targetable protein on activated endothelial cells and macrophages. PMID:27689404

  19. Identifying Thresholds for Ecosystem-Based Management

    PubMed Central

    Samhouri, Jameal F.; Levin, Phillip S.; Ainsworth, Cameron H.

    2010-01-01

    Background One of the greatest obstacles to moving ecosystem-based management (EBM) from concept to practice is the lack of a systematic approach to defining ecosystem-level decision criteria, or reference points that trigger management action. Methodology/Principal Findings To assist resource managers and policymakers in developing EBM decision criteria, we introduce a quantitative, transferable method for identifying utility thresholds. A utility threshold is the level of human-induced pressure (e.g., pollution) at which small changes produce substantial improvements toward the EBM goal of protecting an ecosystem's structural (e.g., diversity) and functional (e.g., resilience) attributes. The analytical approach is based on the detection of nonlinearities in relationships between ecosystem attributes and pressures. We illustrate the method with a hypothetical case study of (1) fishing and (2) nearshore habitat pressure using an empirically-validated marine ecosystem model for British Columbia, Canada, and derive numerical threshold values in terms of the density of two empirically-tractable indicator groups, sablefish and jellyfish. We also describe how to incorporate uncertainty into the estimation of utility thresholds and highlight their value in the context of understanding EBM trade-offs. Conclusions/Significance For any policy scenario, an understanding of utility thresholds provides insight into the amount and type of management intervention required to make significant progress toward improved ecosystem structure and function. The approach outlined in this paper can be applied in the context of single or multiple human-induced pressures, to any marine, freshwater, or terrestrial ecosystem, and should facilitate more effective management. PMID:20126647

  20. Dopamine effects on identified rat vagal motoneurons

    PubMed Central

    Zheng, Zhongling; Travagli, R. Alberto

    2011-01-01

    Catecholaminergic neurons of the A2 area play a prominent role in brain stem vagal circuits. It is not clear, however, whether these neurons are noradrenergic or adrenergic, i.e., display tyrosine hydroxylase (TH) and dopamine-β-hydroxylase (DβH) immunoreactivity (-IR) or dopaminergic (i.e., TH- but not DβH-IR). Our aims were to investigate whether a subpopulation of neurons in the A2 area was dopaminergic and, if so, to investigate the effects of dopamine (DA) on the membrane of gastric-projecting vagal motoneurons. We observed that although the majority of A2 neurons were both TH- and DβH-IR, a small percentage of nucleus tractus solitarius neurons were TH-IR only, suggesting that DA itself may play role in these circuits. Whole cell recordings from thin brain stem slices showed that 71% of identified gastric-projecting motoneurons responded to DA (1–300 µM) with either an excitation (28%) or an inhibition (43%) of the membrane; the remaining 29% of the neurons were unresponsive. The DA-induced depolarization was mimicked by SK 38393 and prevented by pretreatment with SCH 23390. Conversely, the DA-induced inhibition was mimicked by bromoergocryptine and prevented by pretreatment with L741626. When tested on the same neuron, the effects of DA and NE were not always similar. In fact, in neurons in which DA induced a membrane depolarization, 77% were inhibited by NE, whereas 75% of neurons unresponsive to DA were inhibited by NE. Our data suggest that DA modulates the membrane properties of gastric-projecting motoneurons via D1- and D2-like receptors, and DA may play different roles than norepinephrine in brain stem vagal circuits. PMID:17170022

  1. Identifying potential PARIS homologs in D. melanogaster.

    PubMed

    Merzetti, E M; Staveley, B E

    2016-11-03

    Mitochondrial destruction leads to the formation of reactive oxygen species, increases cellular stress, causes apoptotic cell death, and involves a cascade of proteins including PARKIN, PINK1, and Mitofusin2. Mitochondrial biogenesis pathways depend upon the activity of the protein PGC-1α. These two processes are coordinated by the activity of a transcriptional repressor, Parkin interacting substrate (PARIS). The PARIS protein is degraded through the activity of the PARKIN protein, which in turn eliminates the transcriptional repression that PARIS imposes upon a downstream target, PGC-1α. Genes in this pathway have been implicated in Parkinson's disease, and there is a strong relationship between mitochondrial dysfunction and pre-mature neuron death. The identification of a PARIS homolog in Drosophila melanogaster would increase our understanding of the roles that PARIS and interacting genes play in higher organisms. We identified three potential PARIS homologs in D. melanogaster, one of which encodes a protein with similar domains to the Homo sapiens PARIS protein, CG15436. The Drosophila eye is formed from neuronal precursors, making it an ideal system to assay the effects of altered gene expression on neuronal tissue formation. The eye-specific expression of RNAi constructs for these genes revealed that both CG15269 and Crol caused neurodegenerative phenotypes, whereas CG15436 produced a phenotype similar to srl-EY. Crol-RNAi expression reduced mean lifespan when expressed in dopaminergic neurons, whereas CG15436-RNAi significantly increased lifespan. CG15436 was PARIS-like in both structure and function, and we characterized the effects of decreased gene expression in both the neuron-rich D. melanogaster eye and in dopaminergic neurons.

  2. Identifying Predictive Markers for Personalized Treatment Selection

    PubMed Central

    Shen, Yuanyuan

    2017-01-01

    Summary It is now well recognized that the effectiveness and potential risk of a treatment often vary by patient subgroups. Although trial-and-error and one-size-fits-all approaches to treatment selection remains a common practice, much recent focus has been placed on individualized treatment selection based on patient information (La Thangue and Kerr, 2011; Ong et al., 2012). Genetic and molecular markers are becoming increasingly available to guide treatment selection for various diseases including HIV and breast cancer (Mallal et al., 2008; Zujewski and Kamin, 2008). In recent years, many statistical procedures for developing individualized treatment rules (ITRs) have been proposed. However, less focus has been given to efficient selection of predictive biomarkers for treatment selection. The standard Wald test for interactions between treatment and the set of markers of interest may not work well when the marker effects are non-linear. Furthermore, interaction based test is scale dependent and may fail to capture markers useful for predicting individualized treatment differences. In this paper, we propose to overcome these difficulties by developing a kernel machine (KM) score test that can efficiently identify markers predictive of treatment difference. Simulation studies show that our proposed KM based score test is more powerful than the Wald test when there is non-linear effect among the predictors and when the outcome is binary with non-linear link functions. Furthermore, when there is high-correlation among predictors and when the number of predictors is not small, our method also over-performs Wald test. The proposed method is illustrated with two randomized clinical trials. PMID:26999054

  3. STK11 Mutation Identified in Thyroid Carcinoma.

    PubMed

    Wei, Shuanzeng; LiVolsi, Virginia A; Brose, Marcia S; Montone, Kathleen T; Morrissette, Jennifer J D; Baloch, Zubair W

    2016-03-01

    Peutz-Jeghers syndrome (PJS) is an autosomal-dominant disorder, in which germline mutation of serine threonine-protein kinase 11 (STK11) is identified in up to 90 % of the patients who meet clinical criteria for PJS. Hematoxylin and eosin (H&E) slides of the tumor were reviewed to confirm areas with at least 25 % of tumor cellularity. Then, the designated area was extracted for genomic DNA. Targeted next-generation sequencing analysis was performed using a 47-gene panel. Case 1 is a 71-year-old man with high grade follicular thyroid carcinoma with clear cell and oncocytic features. The carcinoma showed a missense mutation in TP53 (p.R342G, c.1024C > G) and a 16-nucleotide intronic deletion started next to the 3' of exon 6 (involving the canonical +1 and +2 bases of the splice donor site) in STK11 (p.?, c.862 + 1_862 + 16delGTGGGAGCCTCATCCC). Case 2 is a 76-year-old woman with tall cell variant papillary thyroid carcinoma. The carcinoma demonstrated a missense mutation in BRAF (p.V600E, c.1799T > A) and a missense mutation in STK11 (p.F354L, c.1062C > G). In summary, we present two elderly patients with thyroid carcinoma harboring STK11 mutation without clinical manifestation of PJS. The findings suggest that STK11 may play a role in thyroid carcinoma development.

  4. Identifying human influences on atmospheric temperature.

    PubMed

    Santer, Benjamin D; Painter, Jeffrey F; Mears, Carl A; Doutriaux, Charles; Caldwell, Peter; Arblaster, Julie M; Cameron-Smith, Philip J; Gillett, Nathan P; Gleckler, Peter J; Lanzante, John; Perlwitz, Judith; Solomon, Susan; Stott, Peter A; Taylor, Karl E; Terray, Laurent; Thorne, Peter W; Wehner, Michael F; Wentz, Frank J; Wigley, Tom M L; Wilcox, Laura J; Zou, Cheng-Zhi

    2013-01-02

    We perform a multimodel detection and attribution study with climate model simulation output and satellite-based measurements of tropospheric and stratospheric temperature change. We use simulation output from 20 climate models participating in phase 5 of the Coupled Model Intercomparison Project. This multimodel archive provides estimates of the signal pattern in response to combined anthropogenic and natural external forcing (the fingerprint) and the noise of internally generated variability. Using these estimates, we calculate signal-to-noise (S/N) ratios to quantify the strength of the fingerprint in the observations relative to fingerprint strength in natural climate noise. For changes in lower stratospheric temperature between 1979 and 2011, S/N ratios vary from 26 to 36, depending on the choice of observational dataset. In the lower troposphere, the fingerprint strength in observations is smaller, but S/N ratios are still significant at the 1% level or better, and range from three to eight. We find no evidence that these ratios are spuriously inflated by model variability errors. After removing all global mean signals, model fingerprints remain identifiable in 70% of the tests involving tropospheric temperature changes. Despite such agreement in the large-scale features of model and observed geographical patterns of atmospheric temperature change, most models do not replicate the size of the observed changes. On average, the models analyzed underestimate the observed cooling of the lower stratosphere and overestimate the warming of the troposphere. Although the precise causes of such differences are unclear, model biases in lower stratospheric temperature trends are likely to be reduced by more realistic treatment of stratospheric ozone depletion and volcanic aerosol forcing.

  5. Quality gaps identified through mortality review

    PubMed Central

    Kobewka, Daniel M; van Walraven, Carl; Turnbull, Jeffrey; Worthington, James; Calder, Lisa; Forster, Alan

    2017-01-01

    Background Hospital mortality rate is a common measure of healthcare quality. Morbidity and mortality meetings are common but there are few reports of hospital-wide mortality-review processes to provide understanding of quality-of-care problems associated with patient deaths. Objective To describe the implementation and results from an institution-wide mortality-review process. Design A nurse and a physician independently reviewed every death that occurred at our multisite teaching institution over a 3-month period. Deaths judged by either reviewer to be unanticipated or to have any opportunity for improvement were reviewed by a multidisciplinary committee. We report characteristics of patients with unanticipated death or opportunity for improved care and summarise the opportunities for improved care. Results Over a 3-month period, we reviewed all 427 deaths in our hospital in detail; 33 deaths (7.7%) were deemed unanticipated and 100 (23.4%) were deemed to be associated with an opportunity for improvement. We identified 97 opportunities to improve care. The most common gap in care was: ‘goals of care not discussed or the discussion was inadequate’ (n=25 (25.8%)) and ‘delay or failure to achieve a timely diagnosis’ (n=8 (8.3%)). Patients who had opportunities for improvement had longer length of stay and a lower baseline predicted risk of death in hospital. Nurse and physician reviewers spent approximately 142 h reviewing cases outside of committee meetings. Conclusions Our institution-wide mortality review found many quality gaps among decedents, in particular inadequate discussion of goals of care. PMID:26856617

  6. Identifying Fishes through DNA Barcodes and Microarrays

    PubMed Central

    Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N.; Weber, Hannes; Blohm, Dietmar

    2010-01-01

    Background International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of “DNA barcoding” and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the “position of label” effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Conclusions/Significance Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products. PMID

  7. Identifying human influences on atmospheric temperature

    PubMed Central

    Santer, Benjamin D.; Painter, Jeffrey F.; Mears, Carl A.; Doutriaux, Charles; Caldwell, Peter; Arblaster, Julie M.; Cameron-Smith, Philip J.; Gillett, Nathan P.; Gleckler, Peter J.; Lanzante, John; Perlwitz, Judith; Solomon, Susan; Stott, Peter A.; Taylor, Karl E.; Terray, Laurent; Thorne, Peter W.; Wehner, Michael F.; Wentz, Frank J.; Wigley, Tom M. L.; Wilcox, Laura J.; Zou, Cheng-Zhi

    2013-01-01

    We perform a multimodel detection and attribution study with climate model simulation output and satellite-based measurements of tropospheric and stratospheric temperature change. We use simulation output from 20 climate models participating in phase 5 of the Coupled Model Intercomparison Project. This multimodel archive provides estimates of the signal pattern in response to combined anthropogenic and natural external forcing (the fingerprint) and the noise of internally generated variability. Using these estimates, we calculate signal-to-noise (S/N) ratios to quantify the strength of the fingerprint in the observations relative to fingerprint strength in natural climate noise. For changes in lower stratospheric temperature between 1979 and 2011, S/N ratios vary from 26 to 36, depending on the choice of observational dataset. In the lower troposphere, the fingerprint strength in observations is smaller, but S/N ratios are still significant at the 1% level or better, and range from three to eight. We find no evidence that these ratios are spuriously inflated by model variability errors. After removing all global mean signals, model fingerprints remain identifiable in 70% of the tests involving tropospheric temperature changes. Despite such agreement in the large-scale features of model and observed geographical patterns of atmospheric temperature change, most models do not replicate the size of the observed changes. On average, the models analyzed underestimate the observed cooling of the lower stratosphere and overestimate the warming of the troposphere. Although the precise causes of such differences are unclear, model biases in lower stratospheric temperature trends are likely to be reduced by more realistic treatment of stratospheric ozone depletion and volcanic aerosol forcing. PMID:23197824

  8. Identifying natural flow regimes using fish communities

    NASA Astrophysics Data System (ADS)

    Chang, Fi-John; Tsai, Wen-Ping; Wu, Tzu-Ching; Chen, Hung-kwai; Herricks, Edwin E.

    2011-10-01

    SummaryModern water resources management has adopted natural flow regimes as reasonable targets for river restoration and conservation. The characterization of a natural flow regime begins with the development of hydrologic statistics from flow records. However, little guidance exists for defining the period of record needed for regime determination. In Taiwan, the Taiwan Eco-hydrological Indicator System (TEIS), a group of hydrologic statistics selected for fisheries relevance, is being used to evaluate ecological flows. The TEIS consists of a group of hydrologic statistics selected to characterize the relationships between flow and the life history of indigenous species. Using the TEIS and biosurvey data for Taiwan, this paper identifies the length of hydrologic record sufficient for natural flow regime characterization. To define the ecological hydrology of fish communities, this study connected hydrologic statistics to fish communities by using methods to define antecedent conditions that influence existing community composition. A moving average method was applied to TEIS statistics to reflect the effects of antecedent flow condition and a point-biserial correlation method was used to relate fisheries collections with TEIS statistics. The resulting fish species-TEIS (FISH-TEIS) hydrologic statistics matrix takes full advantage of historical flows and fisheries data. The analysis indicates that, in the watersheds analyzed, averaging TEIS statistics for the present year and 3 years prior to the sampling date, termed MA(4), is sufficient to develop a natural flow regime. This result suggests that flow regimes based on hydrologic statistics for the period of record can be replaced by regimes developed for sampled fish communities.

  9. Defining and identifying Sleeping Beauties in science

    PubMed Central

    Ke, Qing; Ferrara, Emilio; Radicchi, Filippo; Flammini, Alessandro

    2015-01-01

    A Sleeping Beauty (SB) in science refers to a paper whose importance is not recognized for several years after publication. Its citation history exhibits a long hibernation period followed by a sudden spike of popularity. Previous studies suggest a relative scarcity of SBs. The reliability of this conclusion is, however, heavily dependent on identification methods based on arbitrary threshold parameters for sleeping time and number of citations, applied to small or monodisciplinary bibliographic datasets. Here we present a systematic, large-scale, and multidisciplinary analysis of the SB phenomenon in science. We introduce a parameter-free measure that quantifies the extent to which a specific paper can be considered an SB. We apply our method to 22 million scientific papers published in all disciplines of natural and social sciences over a time span longer than a century. Our results reveal that the SB phenomenon is not exceptional. There is a continuous spectrum of delayed recognition where both the hibernation period and the awakening intensity are taken into account. Although many cases of SBs can be identified by looking at monodisciplinary bibliographic data, the SB phenomenon becomes much more apparent with the analysis of multidisciplinary datasets, where we can observe many examples of papers achieving delayed yet exceptional importance in disciplines different from those where they were originally published. Our analysis emphasizes a complex feature of citation dynamics that so far has received little attention, and also provides empirical evidence against the use of short-term citation metrics in the quantification of scientific impact. PMID:26015563

  10. Identifying Groundwater Droughts using standardized Water Levels

    NASA Astrophysics Data System (ADS)

    Haas, J. C.; Birk, S.

    2015-12-01

    Drought indices are frequently used to compare the occurrence and characteristics of droughts at different sites as well as to characterize different hydrometeorological aspects of drought. The existing indices have been mostly focused on precipitation, soil moisture, and surface waters though. To enable a comparison of groundwater drought with other hydrometeorological aspects of drought, the Standardized Groundwater level Index SGI was proposed by Bloomfield and Marchant (2013). So far, the SGI has been applied only to consolidated aquifers in the UK. The purpose of this work is to assess the applicability and performance of the SGI in unconsolidated, porous aquifers situated in valleys, which represent the main sources of drinking water in many regions. For this purpose, long-term time series of groundwater levels both in wet and dry regions of Austria are analyzed and compared with time series of precipitation, evapotranspiration and river stages. It is shown that large drought events, such as 2003 with only 79% of the long-term average precipitation, but also less severe events are reflected by negative SGI anomalies. To identify and classify time periods with a groundwater deficit, such benchmark years are used to propose a threshold value of the SGI defining the onset of a drought. Time periods where a clear drop in SGI does not correspond to a significant anomaly in precipitation are also visible in the data. More detailed investigations into small valley fill aquifers in the south-east of Austria reveal that the SGI may closely correlate with river stage fluctuations. Also, effects of the geographic setting (mountainous area vs. lowland) and the impacts of human activities (hydropower, drinking water extraction) are shown. Bloomfield, J. P., Marchant, B. P., Analysis of groundwater drought building on the standardised precipitation index approach, Hydrology and Earth System Sciences, 17, 4769-4787, 2013.

  11. Computerized feature systems for identifying suspects

    NASA Astrophysics Data System (ADS)

    Lee, Eric; Whalen, Thom; McCarthy, Andrew; Sakalauskas, John; Wotton, Cynthia

    1995-09-01

    In suspect identification, witnesses examine photos of known offenders in mugshot albums. The probability of correct identification deteriorates rapidly, however, as the number of mugshots examined increases. Feature approaches, where mugshots are displayed in order of similarity to witness descriptions of suspects, increase identification success by reducing this number. In our computerized feature system, both police raters and witnesses describe facial features of suspects on rating scales such as nose size: small 1 2 3 4 5 large. Feature users consistently identify more target suspects correctly than do album users. Previous experimental tests have failed, however, to examine the effects of feature system performance of the use of live targets as suspects rather than photos, the use of realistic crime scenarios, the number of police raters/mugshot, and differences among raters in their effect on system perfomance. In three experiments, we investigated those four issues. The first experiment used photos as target suspects but with multiple distractors, the second tested live suspects, while the third tested live suspects in a realistic crime scenario. The database contained the official mugshots of 1,000 offenders. Across the three experiments, a second and sometimes a third rater/mugshot significantly reduced the number of photos examined. More raters/mugshot did not affect performance further. Raters differed significantly in their effect on system perfomance. Significantly, our feature system performed well both with target suspects seen live and with live suspects in realistic crime scenarios (performance was comparable to that in previous experiments for photos of target suspects). These results strongly support our contention that feature systems are superior to album systems.

  12. Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis.

    PubMed

    Wang, Qi; Drouin, Elise E; Yao, Chunxiang; Zhang, Jiyang; Huang, Yu; Leon, Deborah R; Steere, Allen C; Costello, Catherine E

    2017-01-06

    Human leukocyte antigen-antigen D related (HLA-DR) molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory forms of arthritis. Here, we used LC-MS/MS to identify HLA-DR-presented self-peptides in cells taken directly from clinical samples: ST, synovial fluid mononuclear cells (SFMC), or peripheral blood mononuclear cells (PBMC) from five patients with rheumatoid arthritis (RA) and eight with Lyme arthritis (LA). We identified 1593 non-redundant HLA-DR-presented peptides, derived from 870 source proteins. A total of 67% of the peptides identified in SFMC and 55% of those found in PBMC were found in ST, but analysis of SFMC/PBMC also revealed new antigen-presented peptides. Peptides were synthesized and examined for reactivity with the patients' PBMC. To date, three autoantigens in RA and four novel autoantigens in LA, presented in ST and/or PBMC, were shown to be targets of T- and B-cell responses in these diseases; ongoing analyses may add to this list. Thus, immunoprecipitation and LC-MS/MS can now identify hundreds of HLA-DR-presented self-peptides from individual patients' tissues or fluids with mixed cell populations. Importantly, identification of HLA-DR-presented peptides from SFMC or PBMC allows testing of more patients, including those early in the disease. Direct analysis of clinical samples facilitates identification of novel immunogenic T-cell epitopes.

  13. Stathmin, a new target of PRL-3 identified by proteomic methods, plays a key role in progression and metastasis of colorectal cancer.

    PubMed

    Zheng, Ping; Liu, Yong-Xia; Chen, Lin; Liu, Xun-Hua; Xiao, Zheng-Quan; Zhao, Liang; Li, Guang-Qiu; Zhou, Jun; Ding, Yan-Qing; Li, Jian-Ming

    2010-10-01

    To better understand the role of PRL-3 in progression and metastasis of colorectal cancer (CRC), we searched for PRL-3 associated proteins using proteomic methods. We identified 39 PRL-3 associated proteins based on proteomic strategy. Stathmin, a key oncoprotein, was proved to be a new PRL-3 associated protein. Notably, co-immunoprecipitation assays in both endogenous CRC cell lines and CRC tissues indicated that PRL-3 could interact with stathmin. And, both stathmin and PRL-3 contributed to microtubule (MT) destabilization of CRC cells. Moreover, gain-of-function and loss-of-function analyses revealed that stathmin promoted proliferation, cell adhesion, and migration of human CRC cells. Immunohistochemical analysis of 149 colorectal tumor samples showed that overexpression of stathmin was strongly correlated with tumor differentiation (P = 0.035), tumor invasion (P = 0.024), lymph node status (P < 0.001), Dukes classification (P < 0.001), and TNM staging (P < 0.001) of CRC patients. Univariate and multivariate survival analyses further supported that overexpression of stathmin protein was a potential independent poor prognostic factor for CRC. Our results reveal many PRL-3 associated proteins for the first time. The oncoprotein stathmin plays a key role in CRC as a new target of PRL-3. Interaction between PRL-3 and stathmin leads to MT destabilization of CRC cells, which contributes to progression and metastasis of CRC.

  14. A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system.

    PubMed

    Mandin, Pierre; Gottesman, Susan

    2009-05-01

    In Escherichia coli, the largest class of small regulatory RNAs binds to the RNA chaperone Hfq and regulates the stability and/or translation of specific mRNAs. While recent studies have shown that some mRNAs could be subject to post-transcriptional regulation by sRNAs (e.g. mRNAs found by co-immunoprecipitation with Hfq), no method has yet been described to identify small RNAs that regulate them. We developed a method to easily make translational fusions of genes of interest to the lacZ reporter gene, under the control of a P(BAD)-inducible promoter. A multicopy plasmid library of the E. coli genome can then be used to screen for small RNAs that affect the activity of the fusion. This screening method was first applied to the dpiB gene from the dpiBA operon, which encodes a two-component signal transduction system involved in the SOS response to beta-lactams. One small RNA, RybC, was found to negatively regulate the expression of dpiB. Using mutants in the dpiB-lacZ fusion and compensatory mutations in the RybC sRNA, we demonstrate that RybC directly base pairs with the dpiBA mRNA.

  15. Identifying the Important HIV-1 Recombination Breakpoints

    PubMed Central

    Fan, Jun; Simon-Loriere, Etienne; Arts, Eric J.; Negroni, Matteo; Robertson, David L.

    2008-01-01

    Recombinant HIV-1 genomes contribute significantly to the diversity of variants within the HIV/AIDS pandemic. It is assumed that some of these mosaic genomes may have novel properties that have led to their prevalence, particularly in the case of the circulating recombinant forms (CRFs). In regions of the HIV-1 genome where recombination has a tendency to convey a selective advantage to the virus, we predict that the distribution of breakpoints—the identifiable boundaries that delimit the mosaic structure—will deviate from the underlying null distribution. To test this hypothesis, we generate a probabilistic model of HIV-1 copy-choice recombination and compare the predicted breakpoint distribution to the distribution from the HIV/AIDS pandemic. Across much of the HIV-1 genome, we find that the observed frequencies of inter-subtype recombination are predicted accurately by our model. This observation strongly indicates that in these regions a probabilistic model, dependent on local sequence identity, is sufficient to explain breakpoint locations. In regions where there is a significant over- (either side of the env gene) or under- (short regions within gag, pol, and most of env) representation of breakpoints, we infer natural selection to be influencing the recombination pattern. The paucity of recombination breakpoints within most of the envelope gene indicates that recombinants generated in this region are less likely to be successful. The breakpoints at a higher frequency than predicted by our model are approximately at either side of env, indicating increased selection for these recombinants as a consequence of this region, or at least part of it, having a tendency to be recombined as an entire unit. Our findings thus provide the first clear indication of the existence of a specific portion of the genome that deviates from a probabilistic null model for recombination. This suggests that, despite the wide diversity of recombinant forms seen in the viral

  16. Identifying Topological Order from the Entanglement Spectrum

    NASA Astrophysics Data System (ADS)

    Haldane, F. D. M.

    2011-03-01

    contribution to the O(L) part has a universal character not visible in the numerical value of the entropy itself. In general, (including also systems such as topological or Chern insulators), the signature of topological order is the occurrence of gapless mode in the entanglement spectrum, providing a fingerprint from which this order can be identified. Supported in part by NSF MRSEC DMR-0819860.

  17. Identifying hidden sexual bridging communities in Chicago.

    PubMed

    Youm, Yoosik; Mackesy-Amiti, Mary Ellen; Williams, Chyvette T; Ouellet, Lawrence J

    2009-07-01

    Bridge populations can play a central role in the spread of human immunodeficiency virus (HIV) by providing transmission links between higher and lower prevalence populations. While social network methods are well suited to the study of bridge populations, analyses tend to focus on dyads (i.e., risk between drug and/or sex partners) and ignore bridges between distinct subpopulations. This study takes initial steps toward moving the analysis of sexual network linkages beyond individual and risk group levels to a community level in which Chicago's 77 community areas are examined as subpopulations for the purpose of identifying potential bridging communities. Of particular interest are "hidden" bridging communities; that is, areas with above-average levels of sexual ties with other areas but whose below-average AIDS prevalence may hide their potential importance for HIV prevention. Data for this analysis came from the first wave of recruiting at the Chicago Sexual Acquisition and Transmission of HIV Cooperative Agreement Program site. Between August 2005 through October 2006, respondent-driven sampling was used to recruit users of heroin, cocaine, or methamphetamine, men who have sex with men regardless of drug use, the sex partners of these two groups, and sex partners of the sex partners. In this cross-sectional study of the sexual transmission of HIV, participants completed a network-focused computer-assisted self-administered interview, which included questions about the geographic locations of sexual contacts with up to six recent partners. Bridging scores for each area were determined using a matrix representing Chicago's 77 community areas and were assessed using two measures: non-redundant ties and flow betweenness. Bridging measures and acquired immunodeficiency syndrome (AIDS) case prevalence rates were plotted for each community area on charts representing four conditions: below-average bridging and AIDS prevalence, below-average bridging and above

  18. CONVENTIONAL VIDEOENDOSCOPY CAN IDENTIFY HELICOBACTER PYLORI GASTRITIS?

    PubMed Central

    GOMES, Alexandre; SKARE, Thelma Larocca; PRESTES, Manoel Alberto; COSTA, Maiza da Silva; Petisco, Roberta Dombroski; RAMOS, Gabriela Piovezani

    2016-01-01

    ABSTRACT Background: Studies with latest technologies such as endoscopy with magnification and chromoendoscopy showed that various endoscopic aspects are clearly related to infection by Helicobacter pylori (HP). The description of different patterns of erythema in gastric body under magnification of images revived interest in identifying these patterns by standard endoscopy. Aim: To validate the morphologic features of gastric mucosa related to H. pylori infection gastritis allowing predictability of their diagnosis as well as proper targeting biopsies. Methods: Prospective study of 339 consecutive patients with the standard videoendoscope image analysis were obtained, recorded and stored in a program database. These images were studied with respect to the presence or absence of H. pylori, diagnosed by rapid urease test and/or by histological analysis. Were studied: a) normal mucosa appearance; b) mucosal nodularity; c) diffuse nonspecific erythema or redness (with or without edema of folds and exudate) of antrum and body; d) mosaic pattern with focal area of hyperemia; e) erythema in streaks or bands (red streak); f) elevated (raised) erosion; g) flat erosions; h) fundic gland polyps. The main exclusion criteria were the use of drugs, HP pre-treatment and other entities that could affect results. Results: Applying the exclusion criteria, were included 170 of the 339 patients, of which 52 (30.58%) were positive for HP and 118 negative. On the positive findings, the most associated with infection were: nodularity in the antrum (26.92%); presence of raised erosion (15.38%) and mosaic mucosa in the body (21.15%). On the negative group the normal appearance of the mucosa was 66.94%; erythema in streaks or bands in 9.32%; flat erosions 11.86%; and fundic gland polyps 11.86%. Conclusion: Endoscopic findings are useful in the predictability of the result and in directing biopsies. The most representative form of HP related gastritis was the nodularity of the antral mucosa

  19. Identifying Canadian Freshwater Fishes through DNA Barcodes

    PubMed Central

    Hubert, Nicolas; Hanner, Robert; Holm, Erling; Mandrak, Nicholas E.; Taylor, Eric; Burridge, Mary; Watkinson, Douglas; Dumont, Pierre; Curry, Allen; Bentzen, Paul; Zhang, Junbin; April, Julien; Bernatchez, Louis

    2008-01-01

    efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics. PMID:22423312

  20. Identifying Riverine Erosional Hotspots Using Airborne Lidar

    NASA Astrophysics Data System (ADS)

    Wick, M. J.; Gran, K. B.

    2012-12-01

    New high-resolution airborne lidar data may make it possible to develop a predictive model for stream erosion using only remote data. These data could be invaluable to help identify sediment sources in turbidity-impaired streams, simplifying the development of management plans to reduce sediment loading. The recent release of lidar-derived 3m DEMs (digital elevation models) for Northeastern Minnesota, USA, offers a unique opportunity to test this possibility. Here, we develop a GIS-based predictive model for erosion potential along Amity Creek in Duluth, Minnesota, and compare the results to two field datasets: Bank Erosion Hazard Index (BEHI) assessments, and field data collected after a large flood in June 2012. Three major factors were used to predict erosion potential: a stream-power based erosion index, channel confinement, and soil erodibility. A stream-power based erosion index was calculated with slope and upstream area derived from Lidar data. Because erosion potential is elevated where the stream interacts with high valley walls cut into till, we also included a valley confinement factor that included proximity to high valley bluffs. Lastly, we use the Soil Survey Geographic (SSURGO) database to extract K values, the erodibility factor in the Revised Universal Soil Loss equation, along the channel corridor. Two separate field surveys were conducted for comparison to one another and to GIS-based predictions: BEHI assessments at 27 points along the river and river walk surveys to assess erosion that occurred during an estimated >100-year flood on June 19th - 20th, 2012. This historic flood event offered us the opportunity to collect post-storm data that can be used to assess the validity of our predictive model. We mapped all observable erosion features including undercutting, slumps, and scouring, as well as when the bank and bed geology changed from sediments to bedrock. Preliminary results show the GIS-based erosion predictions do have a positive

  1. Identifying and Tracing Persistent Identifiers of Research Resources : Automation, Metrics and Analytics

    NASA Astrophysics Data System (ADS)

    Maull, K. E.; Hart, D.; Mayernik, M. S.

    2015-12-01

    Formal and informal citations and acknowledgements for research infrastructures, such as data collections, software packages, and facilities, are an increasingly important function of attribution in scholarly literature. While such citations provide the appropriate links, even if informally, to their origins, they are often done so inconsistently, making such citations hard to analyze. While significant progress has been made in the past few years in the development of recommendations, policies, and procedures for creating and promoting citable identifiers, progress has been mixed in tracking how data sets and other digital infrastructures have actually been identified and cited in the literature. Understanding the full extent and value of research infrastructures through the lens of scholarly literature requires significant resources, and thus, we argue must rely on automated approaches that mine and track persistent identifiers to scientific resources. Such automated approaches, however, face a number of unique challenges, from the inconsistent and informal referencing practices of authors, to unavailable, embargoed or hard-to-obtain full-text resources for text analytics, to inconsistent and capricious impact metrics. This presentation will discuss work to develop and evaluate tools for automating the tracing of research resource identification and referencing in the research literature via persistent citable identifiers. Despite the impediments, automated processes are of considerable importance in enabling these traceability efforts to scale, as the numbers of identifiers being created for unique scientific resources continues to grow rapidly. Such efforts, if successful, should improve the ability to answer meaningful questions about research resources as they continue to grow as a target of advanced analyses in research metrics.

  2. Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†.

    PubMed

    Kirsten, Holger; Al-Hasani, Hoor; Holdt, Lesca; Gross, Arnd; Beutner, Frank; Krohn, Knut; Horn, Katrin; Ahnert, Peter; Burkhardt, Ralph; Reiche, Kristin; Hackermüller, Jörg; Löffler, Markus; Teupser, Daniel; Thiery, Joachim; Scholz, Markus

    2015-08-15

    Genetics of gene expression (eQTLs or expression QTLs) has proved an indispensable tool for understanding biological pathways and pathomechanisms of trait-associated SNPs. However, power of most genome-wide eQTL studies is still limited. We performed a large eQTL study in peripheral blood mononuclear cells of 2112 individuals increasing the power to detect trans-effects genome-wide. Going beyond univariate SNP-transcript associations, we analyse relations of eQTLs to biological pathways, polygenetic effects of expression regulation, trans-clusters and enrichment of co-localized functional elements. We found eQTLs for about 85% of analysed genes, and 18% of genes were trans-regulated. Local eSNPs were enriched up to a distance of 5 Mb to the transcript challenging typically implemented ranges of cis-regulations. Pathway enrichment within regulated genes of GWAS-related eSNPs supported functional relevance of identified eQTLs. We demonstrate that nearest genes of GWAS-SNPs might frequently be misleading functional candidates. We identified novel trans-clusters of potential functional relevance for GWAS-SNPs of several phenotypes including obesity-related traits, HDL-cholesterol levels and haematological phenotypes. We used chromatin immunoprecipitation data for demonstrating biological effects. Yet, we show for strongly heritable transcripts that still little trans-chromosomal heritability is explained by all identified trans-eSNPs; however, our data suggest that most cis-heritability of these transcripts seems explained. Dissection of co-localized functional elements indicated a prominent role of SNPs in loci of pseudogenes and non-coding RNAs for the regulation of coding genes. In summary, our study substantially increases the catalogue of human eQTLs and improves our understanding of the complex genetic regulation of gene expression, pathways and disease-related processes.

  3. Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†

    PubMed Central

    Kirsten, Holger; Al-Hasani, Hoor; Holdt, Lesca; Gross, Arnd; Beutner, Frank; Krohn, Knut; Horn, Katrin; Ahnert, Peter; Burkhardt, Ralph; Reiche, Kristin; Hackermüller, Jörg; Löffler, Markus; Teupser, Daniel; Thiery, Joachim; Scholz, Markus

    2015-01-01

    Genetics of gene expression (eQTLs or expression QTLs) has proved an indispensable tool for understanding biological pathways and pathomechanisms of trait-associated SNPs. However, power of most genome-wide eQTL studies is still limited. We performed a large eQTL study in peripheral blood mononuclear cells of 2112 individuals increasing the power to detect trans-effects genome-wide. Going beyond univariate SNP-transcript associations, we analyse relations of eQTLs to biological pathways, polygenetic effects of expression regulation, trans-clusters and enrichment of co-localized functional elements. We found eQTLs for about 85% of analysed genes, and 18% of genes were trans-regulated. Local eSNPs were enriched up to a distance of 5 Mb to the transcript challenging typically implemented ranges of cis-regulations. Pathway enrichment within regulated genes of GWAS-related eSNPs supported functional relevance of identified eQTLs. We demonstrate that nearest genes of GWAS-SNPs might frequently be misleading functional candidates. We identified novel trans-clusters of potential functional relevance for GWAS-SNPs of several phenotypes including obesity-related traits, HDL-cholesterol levels and haematological phenotypes. We used chromatin immunoprecipitation data for demonstrating biological effects. Yet, we show for strongly heritable transcripts that still little trans-chromosomal heritability is explained by all identified trans-eSNPs; however, our data suggest that most cis-heritability of these transcripts seems explained. Dissection of co-localized functional elements indicated a prominent role of SNPs in loci of pseudogenes and non-coding RNAs for the regulation of coding genes. In summary, our study substantially increases the catalogue of human eQTLs and improves our understanding of the complex genetic regulation of gene expression, pathways and disease-related processes. PMID:26019233

  4. Integration of Cistromic and Transcriptomic Analyses Identifies Nphs2, Mafb, and Magi2 as Wilms’ Tumor 1 Target Genes in Podocyte Differentiation and Maintenance

    PubMed Central

    Dong, Lihua; Pietsch, Stefan; Tan, Zenglai; Perner, Birgit; Sierig, Ralph; Kruspe, Dagmar; Groth, Marco; Witzgall, Ralph; Gröne, Hermann-Josef; Platzer, Matthias

    2015-01-01

    The Wilms’ tumor suppressor gene 1 (WT1) encodes a zinc finger transcription factor. Mutation of WT1 in humans leads to Wilms’ tumor, a pediatric kidney tumor, or other kidney diseases, such as Denys–Drash and Frasier syndromes. We showed previously that inactivation of WT1 in podocytes of adult mice results in proteinuria, foot process effacement, and glomerulosclerosis. However, the WT1-dependent transcriptional network regulating podocyte development and maintenance in vivo remains unknown. Here, we performed chromatin immunoprecipitation followed by high-throughput sequencing with glomeruli from wild-type mice. Additionally, we performed a cDNA microarray screen on an inducible podocyte–specific WT1 knockout mouse model. By integration of cistromic and transcriptomic analyses, we identified the WT1 targetome in mature podocytes. To further analyze the function and targets of WT1 in podocyte maturation, we used an Nphs2-Cre model, in which WT1 is deleted during podocyte differentiation. These mice display anuria and kidney hemorrhage and die within 24 hours after birth. To address the evolutionary conservation of WT1 targets, we performed functional assays using zebrafish as a model and identified Nphs2, Mafb, and Magi2 as novel WT1 target genes required for podocyte development. Our data also show that both Mafb and Magi2 are required for normal development of the embryonic zebrafish kidney. Collectively, our work provides insights into the transcriptional networks controlled by WT1 and identifies novel WT1 target genes that mediate the function of WT1 in podocyte differentiation and maintenance. PMID:25556170

  5. CFHT and VLT Identify Extremely Remote Galaxy

    NASA Astrophysics Data System (ADS)

    2003-05-01

    , the chances for detecting those distant objects are optimal. The astronomers talk about "maximizing the contrast" of objects showing emission lines at this wavelength. The CFHT Search Programme ESO PR Photo 13b/03 ESO PR Photo 13b/03 [Preview - JPEG: 494 x 400 pix - 83k [Normal - JPEG: 987 x 800 pix - 920k] Caption : PR Photo 13b/03 displays the image of a particular object (at the center), as seen at various wavelengths (colours) on CCD-frames obtained through different optical filters with the CFH12K camera at the CFHT. The object is only visible in the NB920 frame in which emission at the near-infrared wavelength 920 nm is registered (upper left). It is not seen in any of the others ( B lue [450 nm], V isual [550 nm], R ed [650 nm], I [800 nm]), nor in a combination of these (the "sum" of BVRI , the so-called "detection" image, here labeled as "Det"; it is used to detect closer objects from their optical colours for spectroscopic follow-up observations). The indicated object was later shown to be an extremely distant galaxy and has been designated z6VDF J022803-041618 . Each of the six photos covers 20 x 20 arcsec 2 ; North is up, East is right. Based on the above considerations, an international team of astronomers [2] installed a narrow-band optical filter centered at the near-infrared wavelength 920 nm on the CFH12K instrument at the Canada-France-Hawaii telescope on Mauna Kea (Hawaii, USA) to search for extremely distant galaxies. The CFH12K is a wide-field camera used at the prime focus of the CFHT, providing a field-of-view of approx. 30 x 40 arcmin 2 , somewhat larger than the full moon [5]. By comparing images of the same sky field taken through different filters, the astronomers were able to identify objects which appear comparatively "bright" in the NB920 image and "faint" (or are even not visible) in the corresponding images obtained through the other filters. A striking example is shown in PR Photo 13b/03 - the object at the center is well visible in

  6. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  7. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  8. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  9. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  10. 28 CFR 22.25 - Final disposition of identifiable materials.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... RESEARCH AND STATISTICAL INFORMATION § 22.25 Final disposition of identifiable materials. Upon completion of a research or statistical project the security of identifiable research or statistical...

  11. 10 CFR 784.5 - Waiver of identified inventions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Waiver of identified inventions. 784.5 Section 784.5 Energy DEPARTMENT OF ENERGY PATENT WAIVER REGULATION § 784.5 Waiver of identified inventions. This... particular identified subject invention. In determining whether such a waiver of an identified invention...

  12. 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. ...

  13. Genome-Wide Mapping of 5mC and 5hmC Identified Differentially Modified Genomic Regions in Late-Onset Severe Preeclampsia: A Pilot Study

    PubMed Central

    Zhu, Lisha; Lv, Ruitu; Kong, Lingchun; Cheng, Haidong; Lan, Fei; Li, Xiaotian

    2015-01-01

    Preeclampsia (PE) is a leading cause of perinatal morbidity and mortality. However, as a common form of PE, the etiology of late-onset PE is elusive. We analyzed 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels in the placentas of late-onset severe PE patients (n = 4) and normal controls (n = 4) using a (hydroxy)methylated DNA immunoprecipitation approach combined with deep sequencing ([h]MeDIP-seq), and the results were verified by (h)MeDIP-qPCR. The most significant differentially methylated regions (DMRs) were verified by MassARRAY EppiTYPER in an enlarged sample size (n = 20). Bioinformatics analysis identified 714 peaks of 5mC that were associated with 403 genes and 119 peaks of 5hmC that were associated with 61 genes, thus showing significant differences between the PE patients and the controls (>2-fold, p<0.05). Further, only one gene, PTPRN2, had both 5mC and 5hmC changes in patients. The ErbB signaling pathway was enriched in those 403 genes that had significantly different5mC level between the groups. This genome-wide mapping of 5mC and 5hmC in late-onset severe PE and normal controls demonstrates that both 5mC and 5hmC play epigenetic roles in the regulation of the disease, but work independently. We reveal the genome-wide mapping of DNA methylation and DNA hydroxymethylation in late-onset PE placentas for the first time, and the identified ErbB signaling pathway and the gene PTPRN2 may be relevant to the epigenetic pathogenesis of late-onset PE. PMID:26214307

  14. Systematic Mutational Analysis of Histidine Kinase Genes in the Nosocomial Pathogen Stenotrophomonas maltophilia Identifies BfmAK System Control of Biofilm Development

    PubMed Central

    Zheng, Liu; Wang, Fang-Fang; Ren, Bao-Zhen; Liu, Wei

    2016-01-01

    The Gram-negative bacterium Stenotrophomonas maltophilia lives in diverse ecological niches. As a result of its formidable capabilities of forming biofilm and its resistance to multiple antibiotic agents, the bacterium is also a nosocomial pathogen of serious threat to the health of patients whose immune systems are suppressed or compromised. Besides the histidine kinase RpfC, the two-component signal transduction system (TCS), which is the canonical regulatory machinery used by most bacterial pathogens, has never been experimentally investigated in S. maltophilia. Here, we annotated 62 putative histidine kinase genes in the S. maltophilia genome and successfully obtained 51 mutants by systematical insertional inactivation. Phenotypic characterization identified a series of mutants with deficiencies in bacterial growth, swimming motility, and biofilm development. A TCS, named here BfmA-BfmK (Smlt4209-Smlt4208), was genetically confirmed to regulate biofilm formation in S. maltophilia. Together with interacting partner prediction and chromatin immunoprecipitation screens, six candidate promoter regions bound by BfmA in vivo were identified. We demonstrated that, among them, BfmA acts as a transcription factor that binds directly to the promoter regions of bfmA-bfmK and Smlt0800 (acoT), a gene encoding an acyl coenzyme A thioesterase that is associated with biofilm development, and positively controls their transcription. Genome-scale mutational analyses of histidine kinase genes and functional dissection of BfmK-BfmA regulation in biofilm provide genetic information to support more in-depth studies on cellular signaling in S. maltophilia, in the context of developing novel approaches to fight this important bacterial pathogen. PMID:26873318

  15. A practical guideline for identifying research intent with projects that collect private, identifiable health information.

    PubMed

    Amdur, Robert J; Speers, Marjorie A

    2003-06-01

    Radiation oncologists frequently engage in activities that involve the collection and analysis of data from medical records. Access to health information is an ethical issue because, if not done according to appropriate guidelines, it constitutes an invasion of privacy or breach in confidentiality. To protect patients for the social harm that may result from medical record review, our society has established laws and regulations that apply to projects that require medical record review. A major branch point in the guidelines for such projects is whether private information will be collected for research or nonresearch purposes. However, a problem with discussing privacy protection in terms of a research versus nonresearch model is that it is difficult to make this distinction for many kinds of projects. The purpose of this paper is to establish a practical guideline that can be used to decide if a project that involves analysis of private, identifiable medical information should be considered research from the regulatory standpoint.

  16. EPA Plan for Reducing Personally Identifiable Information, January 2013

    EPA Pesticide Factsheets

    The EPA Privacy Policy, issued in 2007, establishes the framework and accountability for reducing Agency personally identifiable information (PII). Learn about the Agency's plan to reduce the collection of Personally Identifiable Information (PII).

  17. Using the Classroom to Identify Children from Alcoholic Homes.

    ERIC Educational Resources Information Center

    Newlon, Betty J.; Furrow, William V.

    1986-01-01

    Offers suggestions for identifying children of alcoholic parents and through school counseling, helping them to understand and cope with their familial problems. Points out the difficulties in identifying and offering assistance to these children. (Author/ABB)

  18. 45 CFR 162.514 - Other entity identifier.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... obtain an NPI. (4) Is not an individual. (b) An OEID must be obtained from the Enumeration System... Enumeration System to identify itself or have itself identified on all covered transactions in which it...

  19. 45 CFR 162.514 - Other entity identifier.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... obtain an NPI. (4) Is not an individual. (b) An OEID must be obtained from the Enumeration System... Enumeration System to identify itself or have itself identified on all covered transactions in which it...

  20. 45 CFR 162.514 - Other entity identifier.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... obtain an NPI. (4) Is not an individual. (b) An OEID must be obtained from the Enumeration System... Enumeration System to identify itself or have itself identified on all covered transactions in which it...

  1. Teacher Effectiveness in Identifying High-Risk Kindergarten Children.

    ERIC Educational Resources Information Center

    Colarusso, Ronald P.; And Others

    1979-01-01

    Teacher effectiveness in identifying children "at risk" for learning problems was studied with five Head Start teachers. Results showed that, after training in classroom observation techniques, paraprofessional teachers are capable of identifying developmental delays in children. (PHR)

  2. Whole genome sequencing identifies a deletion in protein phosphatase 2A that affects its stability and localization in Chlamydomonas reinhardtii.

    PubMed

    Lin, Huawen; Miller, Michelle L; Granas, David M; Dutcher, Susan K

    2013-01-01

    Whole genome sequencing is a powerful tool in the discovery of single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels) among mutant strains, which simplifies forward genetics approaches. However, identification of the causative mutation among a large number of non-causative SNPs in a mutant strain remains a big challenge. In the unicellular biflagellate green alga Chlamydomonas reinhardtii, we generated a SNP/indel library that contains over 2 million polymorphisms from four wild-type strains, one highly polymorphic strain that is frequently used in meiotic mapping, ten mutant strains that have flagellar assembly or motility defects, and one mutant strain, imp3, which has a mating defect. A comparison of polymorphisms in the imp3 strain and the other 15 strains allowed us to identify a deletion of the last three amino acids, Y313F314L315, in a protein phosphatase 2A catalytic subunit (PP2A3) in the imp3 strain. Introduction of a wild-type HA-tagged PP2A3 rescues the mutant phenotype, but mutant HA-PP2A3 at Y313 or L315 fail to rescue. Our immunoprecipitation results indicate that the Y313, L315, or YFLΔ mutations do not affect the binding of PP2A3 to the scaffold subunit, PP2A-2r. In contrast, the Y313, L315, or YFLΔ mutations affect both the stability and the localization of PP2A3. The PP2A3 protein is less abundant in these mutants and fails to accumulate in the basal body area as observed in transformants with either wild-type HA-PP2A3 or a HA-PP2A3 with a V310T change. The accumulation of HA-PP2A3 in the basal body region disappears in mated dikaryons, which suggests that the localization of PP2A3 may be essential to the mating process. Overall, our results demonstrate that the terminal YFL tail of PP2A3 is important in the regulation on Chlamydomonas mating.

  3. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 1 2014-04-01 2014-04-01 false Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  4. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 1 2012-04-01 2011-04-01 true Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  5. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  6. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  7. 25 CFR 23.82 - Assistance in identifying language interpreters.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false Assistance in identifying language interpreters. 23.82... WELFARE ACT Assistance to State Courts § 23.82 Assistance in identifying language interpreters. Upon the... shall assist in identifying language interpreters. Such requests for assistance should be sent to...

  8. Identifying microRNAs that Regulate Neuroblastoma Cell Differentiation

    DTIC Science & Technology

    2014-09-01

    AD_________________ Award Number: W81XWH-13-1-0241 TITLE: Identifying that Regulate Neuroblastoma ...Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT We identified 14 microRNA candidates that induce neuroblastoma cell differentiation based on a high...content screening of neurite outgrowth — the morphological differentiation marker of neuroblastoma cells. We further validated that the identified

  9. 17 CFR 45.5 - Unique swap identifiers.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... transmit a unique swap identifier as provided in paragraphs (a)(1) and (2) of this section. (1) Creation... prior to the reporting of required swap creation data. The unique swap identifier shall consist of a... execution facility or designated contract market with respect to unique swap identifier creation; and...

  10. 13 CFR 108.130 - Identified Low Income Geographic Areas.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Identified Low Income Geographic Areas. 108.130 Section 108.130 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION NEW MARKETS... Identified Low Income Geographic Areas. A NMVC Company must identify the specific LI Areas in which...

  11. Identifying Novice Student Programming Misconceptions and Errors from Summative Assessments

    ERIC Educational Resources Information Center

    Veerasamy, Ashok Kumar; D'Souza, Daryl; Laakso, Mikko-Jussi

    2016-01-01

    This article presents a study aimed at examining the novice student answers in an introductory programming final e-exam to identify misconceptions and types of errors. Our study used the Delphi concept inventory to identify student misconceptions and skill, rule, and knowledge-based errors approach to identify the types of errors made by novices…

  12. 76 FR 39234 - Federal Acquisition Regulation; Unique Procurement Instrument Identifier

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-05

    ... agreement number in conjunction with the contract number (see 4.1602). Supplementary procurement instrument... Procurement Instrument Identifiers Sec. 4.1600 Scope of subpart. 4.1601 Policy. 4.1602 Identifying the PIID... both the original and the newly assigned PIID. 4.1602 Identifying the PIID and supplementary PIID....

  13. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Bacillus thuringiensis modified Cry1Ab... Tolerance Exemptions § 174.529 Bacillus thuringiensis modified Cry1Ab protein as identified under OECD... Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN-IR67B-1...

  14. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  15. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  16. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  17. 40 CFR 174.529 - Bacillus thuringiensis modified Cry1Ab protein as identified under OECD Unique Identifier SYN...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... protein as identified under OECD Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement... Unique Identifier SYN-IR67B-1 in cotton; exemption from the requirement of a tolerance. Residues of... exempt from the requirement of a tolerance when used as a plant-incorporated protectant in cotton;...

  18. HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages

    PubMed Central

    Kishore, Shivendra; Jaskiewicz, Lukasz; Hall, Jonathan; Günthard, Huldrych F.; Beerenwinkel, Niko; Metzner, Karin J.

    2015-01-01

    Background MiRNAs and other small noncoding RNAs (sncRNAs) are key players in post-transcriptional gene regulation. HIV-1 derived small noncoding RNAs (sncRNAs) have been described in HIV-1 infected cells, but their biological functions still remain to be elucidated. Here, we approached the question whether viral sncRNAs may play a role in the RNA interference (RNAi) pathway or whether viral mRNAs are targeted by cellular miRNAs in human monocyte derived macrophages (MDM). Methods The incorporation of viral sncRNAs and/or their target RNAs into RNA-induced silencing complex was investigated using photoactivatable ribonucleoside-induced cross-linking and immunoprecipitation (PAR-CLIP) as well as high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP), which capture Argonaute2-bound miRNAs and their target RNAs. HIV-1 infected monocyte-derived macrophages (MDM) were chosen as target cells, as they have previously been shown to express HIV-1 sncRNAs. In addition, we applied small RNA deep sequencing to study differential cellular miRNA expression in HIV-1 infected versus non-infected MDMs. Results and Conclusion PAR-CLIP and HITS-CLIP data demonstrated the absence of HIV-1 RNAs in Ago2-RISC, although the presence of a multitude of HIV-1 sncRNAs in HIV-1 infected MDMs was confirmed by small RNA sequencing. Small RNA sequencing revealed that 1.4% of all sncRNAs were of HIV-1 origin. However, neither HIV-1 derived sncRNAs nor putative HIV-1 target sequences incorporated into Ago2-RISC were identified suggesting that HIV-1 sncRNAs are not involved in the canonical RNAi pathway nor is HIV-1 targeted by this pathway in HIV-1 infected macrophages. PMID:26226348

  19. [3H]Azidodantrolene photoaffinity labeling, synthetic domain peptides and monoclonal antibody reactivity identify the dantrolene binding sequence on RyR1

    SciTech Connect

    Paul-Pletzer, Kalanethee; Yamamoto, Takeshi; Bhat, Manju B.; Ma, Jianjie; Ikemoto, Noriaki; Jimenez, Leslie S.; Morimoto, Hiromi; Williams, Philip G.; Parness, Jerome

    2002-06-14

    Dantrolene is a drug that suppresses intracellular Ca2+ release from sarcoplasmic reticulum in normal skeletal muscle and is used as a therapeutic agent in individuals susceptible to malignant hyperthermia. Though its precise mechanism of action has not been elucidated, we have identified the N-terminal region (amino acids 1-1400) of the skeletal muscle isoform of the ryanodine receptor (RyR1), the primary Ca2+ release channel in sarcoplasmic reticulum, as a molecular target for dantrolene using the photoaffinity analog [3H]azidodantrolene(1). Here, we demonstrate that heterologously expressed RyR1 retains its capacity to be specifically labeled with [3H]azidodantrolene,indicating that muscle specific factors are not required for this ligand-receptor interaction. Synthetic domain peptides of RyR1, previously shown to affect RyR1 function in vitro and in vivo, were exploited as potential drug binding site mimics and used in photoaffinity labeling experiments. Only DP1 and DP1-2, peptide s containing the amino acid sequence corresponding to RyR1 residues 590-609, were specifically labeled by [3H]azidodantrolene. A monoclonal anti-RyR1 antibody which recognizes RyR1 and its 1400 amino acid N-terminal fragment, recognizes DP1 and DP1-2 in both Western blots and immunoprecipitation assays, and specifically inhibits [3H]azidodantrolene photolabeling of RyR1 and its N-terminal fragment in sarcoplasmic reticulum. Our results indicate that synthetic domain peptides can mimic a native, ligand binding conformation in vitro, and that the dantrolene binding site and the epitope for the monoclonal antibody on RyR1 are equivalent and composed of amino-acids 590-609.

  20. m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks

    PubMed Central

    Zhang, Song-Yao; Zhang, Shao-Wu; Liu, Lian; Huang, Yufei

    2016-01-01

    As the most prevalent mammalian mRNA epigenetic modification, N6-methyladenosine (m6A) has been shown to possess important post-transcriptional regulatory functions. However, the regulatory mechanisms and functional circuits of m6A are still largely elusive. To help unveil the regulatory circuitry mediated by mRNA m6A methylation, we develop here m6A-Driver, an algorithm for predicting m6A-driven genes and associated networks, whose functional interactions are likely to be actively modulated by m6A methylation under a specific condition. Specifically, m6A-Driver integrates the PPI network and the predicted differential m6A methylation sites from methylated RNA immunoprecipitation sequencing (MeRIP-Seq) data using a Random Walk with Restart (RWR) algorithm and then builds a consensus m6A-driven network of m6A-driven genes. To evaluate the performance, we applied m6A-Driver to build the context-specific m6A-driven networks for 4 known m6A (de)methylases, i.e., FTO, METTL3, METTL14 and WTAP. Our results suggest that m6A-Driver can robustly and efficiently identify m6A-driven genes that are functionally more enriched and associated with higher degree of differential expression than differential m6A methylated genes. Pathway analysis of the constructed context-specific m6A-driven gene networks further revealed the regulatory circuitry underlying the dynamic interplays between the methyltransferases and demethylase at the epitranscriptomic layer of gene regulation. PMID:28027310

  1. Integrating ChIP-sequencing and digital gene expression profiling to identify BRD7 downstream genes and construct their regulating network.

    PubMed

    Xu, Ke; Xiong, Wei; Zhou, Ming; Wang, Heran; Yang, Jing; Li, Xiayu; Chen, Pan; Liao, Qianjin; Deng, Hao; Li, Xiaoling; Li, Guiyuan; Zeng, Zhaoyang

    2016-01-01

    BRD7 is a single bromodomain-containing protein that functions as a subunit of the SWI/SNF chromatin-remodeling complex to regulate transcription. It also interacts with the well-known tumor suppressor protein p53 to trans-activate genes involved in cell cycle arrest. In this paper, we report an integrative analysis of genome-wide chromatin occupancy of BRD7 by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and digital gene expression (DGE) profiling by RNA-sequencing upon the overexpression of BRD7 in human cells. We localized 156 BRD7-binding peaks representing 184 genes by ChIP-sequencing, and most of these peaks were co-localized with histone modification sites. Four novel motifs were significantly represented in these BRD7-enriched regions. Ingenuity pathway analysis revealed that 22 of these BRD7 target genes were involved in a network regulating cell death and survival. DGE profiling identified 560 up-regulated genes and 1088 down-regulated genes regulated by BRD7. Using Gene Ontology and pathway analysis, we found significant enrichment of the cell cycle and apoptosis pathway genes. For the integrative analysis of the ChIP-seq and DEG data, we constructed a regulating network of BRD7 downstream genes, and this network suggests multiple feedback regulations of the pathways. Furthermore, we validated BIRC2, BIRC3, TXN2, and NOTCH1 genes as direct, functional BRD7 targets, which were involved in the cell cycle and apoptosis pathways. These results provide a genome-wide view of chromatin occupancy and the gene regulation network of the BRD7 signaling pathway.

  2. Use cases for identifiers and data citation - Separating concerns.

    NASA Astrophysics Data System (ADS)

    Fox, Peter; Parsons, Mark

    2016-04-01

    Over the past two decades, the data management community has worked to codify many aspects modern data management. Our interest in clarifying and promoting data citation policies and practices naturally involves associated technologies such as persistent identifiers and automated indices. While the use of dataset identifiers is on the rise; the datasets identified are rarely cited formally for myriad reasons. Data managers often expect too much from data citation, assuming false parallels to literature citation; i.e, the use cases for literature citation and data citation are often different, and thus identifier utilization differs. We call for a closer examination of the purpose and practice of data citation, and relation to identifiers. We will present several relevant use cases that convolve citation and identifiers and suggest possible approaches for addressing these use cases. We seek to engage the community in a more exploratory conversation on the topic that separates concerns appropriately.

  3. Parameter Identifiability in Statistical Machine Learning: A Review.

    PubMed

    Ran, Zhi-Yong; Hu, Bao-Gang

    2017-02-09

    This review examines the relevance of parameter identifiability for statistical models used in machine learning. In addition to defining main concepts, we address several issues of identifiability closely related to machine learning, showing the advantages and disadvantages of state-of-the-art research and demonstrating recent progress. First, we review criteria for determining the parameter structure of models from the literature. This has three related issues: parameter identifiability, parameter redundancy, and reparameterization. Second, we review the deep influence of identifiability on various aspects of machine learning from theoretical and application viewpoints. In addition to illustrating the utility and influence of identifiability, we emphasize the interplay among identifiability theory, machine learning, mathematical statistics, information theory, optimization theory, information geometry, Riemann geometry, symbolic computation, Bayesian inference, algebraic geometry, and others. Finally, we present a new perspective together with the associated challenges.

  4. BN+1 Bayesian network expansion for identifying molecular pathway elements

    PubMed Central

    Hodges, Andrew P; Woolf, Peter

    2010-01-01

    A Bayesian network expansion algorithm called BN+1 was developed to identify undocumented gene interactions in a known pathway using microarray gene expression data. In our recent paper, the BN+1 algorithm has been successfully used to identify key regulators including uspE in the E. coli ROS pathway and biofilm formation.18 In this report, a synthetic network was designed to further evaluate this algorithm. The BN+1 method was found to identify both linear and nonlinear relationships and correctly identify variables near the starting network. Using experimentally derived data, the BN+1 method identifies the gene fdhE as a potentially new ROS regulator. Finally, a range of possible score cutoff methods are explored to identify a set of criteria for selecting BN+1 calls. PMID:21331236

  5. Identifying single points of failure in your organisation.

    PubMed

    Bryant, Robby J

    2013-01-01

    Single points of failure may spell disaster for businesses that have not adequately identified and mitigated these critical risks. A single point of failure audit will identify the single points of failure in all functional areas that may negatively impact organisational processes and process flows. This paper provides a holistic approach to constructing a successful single point of failure audit and identifies the systems that are frequently the sources of single points of failure. It also examines the internal and external risks that may spawn single points of failure and provides various mitigation strategies for the systems identified.

  6. National variety trials identify clones with high potential

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quality potato varieties are the backbone of a strong potato industry. Variety trials have been used to identify promising new varieties for well over a century. Trials are repeated and information collected over many years in order to confidently identify lines that may be well suited for productio...

  7. Contact endoscopy for identifying the parathyroid glands during thyroidectomy.

    PubMed

    Guimarães, A V; Brandão, L G; Dedivitis, R A

    2010-02-01

    Aim of this study was to analyse contact endoscopy as an auxiliary method for identifying parathyroid glands during thyroid surgery and to identify other variables that may interfere with this correlation. Overall, 125 patients underwent thyroid surgery between January 2004 and February 2006. The variables analysed were: the total duration of surgery; time taken to locate and identify parathyroid glands; improvement in identifying these; numbers of parathyroid glands located by the surgeon and confirmed by contact endoscopy; histopathological diagnosis; presence of thyroiditis; thyroid weight; number of parathyroid glands left in thyroid specimens; and number of parathyroid gland autotransplantations. A total of 331 parathyroid glands were observed by the surgeon. However, 282 glands were identified by contact endoscopy. Nine parathyroid glands (7.2%) were observed together with thyroid specimens (Kappa = 0.534). The longer the total duration of surgery (p = 0.03) and time taken to locate and identify (p = 0.00) the parathyroid glands by contact endoscopy, the lower the observed agreement. The second year of performing contact endoscopy led to better agreement between the results (p = 0.02). In conclusion, contact endoscopy is an efficient auxiliary method for identifying parathyroid glands during thyroid surgery. During the period studied, association between total duration of surgery and time taken to locate and identify parathyroid glands was statistically significant.

  8. Overcoming Challenges and Identifying a Consensus about Autism Intervention Programming

    ERIC Educational Resources Information Center

    Stephens, Carolyn E.

    2005-01-01

    Identifying effective interventions to help children with autism reach their potential has been a source of disagreement among professionals and parents for decades. The complexities of the challenges that face children with autism, and uncertainty about best practices, have delayed progress. This article identifies seven critical program…

  9. 36 CFR 1223.16 - How are vital records identified?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... informational content of records series and electronic records systems determines which are vital records. Only... ADMINISTRATION RECORDS MANAGEMENT MANAGING VITAL RECORDS § 1223.16 How are vital records identified? Agencies identify vital records in the context of the emergency management function. Vital records are those...

  10. 36 CFR 1223.16 - How are vital records identified?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... informational content of records series and electronic records systems determines which are vital records. Only... ADMINISTRATION RECORDS MANAGEMENT MANAGING VITAL RECORDS § 1223.16 How are vital records identified? Agencies identify vital records in the context of the emergency management function. Vital records are those...

  11. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 6 2011-10-01 2011-10-01 false Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  12. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 6 2012-10-01 2012-10-01 false Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  13. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 6 2010-10-01 2010-10-01 true Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  14. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 6 2014-10-01 2014-10-01 false Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  15. 37 CFR 211.5 - Deposit of identifying material.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2011-07-01 2011-07-01 false Deposit of identifying material. 211.5 Section 211.5 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS COPYRIGHT OFFICE AND PROCEDURES MASK WORK PROTECTION § 211.5 Deposit of identifying material. (a)...

  16. 37 CFR 211.5 - Deposit of identifying material.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2014-07-01 2014-07-01 false Deposit of identifying material. 211.5 Section 211.5 Patents, Trademarks, and Copyrights U.S. COPYRIGHT OFFICE, LIBRARY OF CONGRESS COPYRIGHT OFFICE AND PROCEDURES MASK WORK PROTECTION § 211.5 Deposit of identifying material....

  17. 37 CFR 211.5 - Deposit of identifying material.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Deposit of identifying material. 211.5 Section 211.5 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS COPYRIGHT OFFICE AND PROCEDURES MASK WORK PROTECTION § 211.5 Deposit of identifying material. (a)...

  18. 37 CFR 211.5 - Deposit of identifying material.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2012-07-01 2012-07-01 false Deposit of identifying material. 211.5 Section 211.5 Patents, Trademarks, and Copyrights COPYRIGHT OFFICE, LIBRARY OF CONGRESS COPYRIGHT OFFICE AND PROCEDURES MASK WORK PROTECTION § 211.5 Deposit of identifying material. (a)...

  19. Identifying Internet Sites to Coordinate with National Science Education Standards

    ERIC Educational Resources Information Center

    Fehrenbach, Carolyn R.; Morris, Maxine G.

    2004-01-01

    Identifying Internet sites to coordinate with National Science Education Standards can be challenging for teachers and students. By identifying quality free Internet sites in science, teachers and students can use the extensive resources of the Internet to enhance learning and instruction while meeting National Science Education Content Standards…

  20. Identifiability Results for Several Classes of Linear Compartment Models.

    PubMed

    Meshkat, Nicolette; Sullivant, Seth; Eisenberg, Marisa

    2015-08-01

    Identifiability concerns finding which unknown parameters of a model can be estimated, uniquely or otherwise, from given input-output data. If some subset of the parameters of a model cannot be determined given input-output data, then we say the model is unidentifiable. In this work, we study linear compartment models, which are a class of biological models commonly used in pharmacokinetics, physiology, and ecology. In past work, we used commutative algebra and graph theory to identify a class of linear compartment models that we call identifiable cycle models, which are unidentifiable but have the simplest possible identifiable functions (so-called monomial cycles). Here we show how to modify identifiable cycle models by adding inputs, adding outputs, or removing leaks, in such a way that we obtain an identifiable model. We also prove a constructive result on how to combine identifiable models, each corresponding to strongly connected graphs, into a larger identifiable model. We apply these theoretical results to several real-world biological models from physiology, cell biology, and ecology.

  1. Identifying Roads and Trains Under Canopy Using Lidar

    DTIC Science & Technology

    2007-09-01

    NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release; distribution is unlimited IDENTIFYING ROADS AND...identifying roads and trails hidden under dense jungle and forest canopies. The four analyzed regions include the Elkhorn Slough in Central California ...canopies. The four analyzed regions include the Elkhorn Slough in Central California (2005), Kahuku Training Area on the North side of Oahu Island in Hawaii

  2. Mothers' Ability To Identify Infants' Communicative Acts Consistently.

    ERIC Educational Resources Information Center

    Meadows, Denis; Elias, Gordon; Bain, John

    2000-01-01

    Investigated the ability of 35 mothers to identify consistently what they perceived to be communicative acts by infants at three ages (6 months, 9 months, and 1 year). Comparisons of the mothers coded records indicated that they were able to identify infants' communicative acts consistently at each age. (Author/VWL)

  3. 26 CFR 301.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    .... (e) Banks, and brokers and dealers in securities. For additional requirements relating to deposits... social security number is generally identified in the records and database of the Internal Revenue... identification number. An employer identification number is generally identified in the records and database...

  4. 26 CFR 301.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... individual taxpayer identification number. (e) Banks, and brokers and dealers in securities. For additional...) Social security number. A social security number is generally identified in the records and database of... identified in the records and database of the Internal Revenue Service as a number belonging to a U.S....

  5. 26 CFR 301.6109-1 - Identifying numbers.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    .... (e) Banks, and brokers and dealers in securities. For additional requirements relating to deposits... social security number is generally identified in the records and database of the Internal Revenue... identification number. An employer identification number is generally identified in the records and database...

  6. Identifying causal effects of climate extremes on societies

    NASA Astrophysics Data System (ADS)

    Hsiang, S. M.

    2015-12-01

    We discuss recent advances in the application of quasi-experimental techniques to identify causal effects of climate extremes on human societies using historical data. Results identifying effects on economic productivity, violence, migration, and global trade will be discussed. We will discuss how these statistical findings can be applied to calibrate modeling exercises and areas for future research.

  7. 48 CFR 2009.570-7 - Conflicts identified after award.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 6 2013-10-01 2013-10-01 false Conflicts identified after... COMMISSION COMPETITION AND ACQUISITION PLANNING CONTRACTOR QUALIFICATIONS Organizational Conflicts of Interest 2009.570-7 Conflicts identified after award. If potential organizational conflicts of interest...

  8. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  9. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  10. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  11. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  12. 28 CFR 22.22 - Revelation of identifiable data.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... STATISTICAL INFORMATION § 22.22 Revelation of identifiable data. (a) Except as noted in paragraph (b) of this section, research and statistical information relating to a private person may be revealed in identifiable... Act. (3) Persons or organizations for research or statistical purposes. Information may only...

  13. Identifying Twice Exceptional Children: A Toolkit for Success

    ERIC Educational Resources Information Center

    Rizza, Mary G.; Morrison, William F.

    2007-01-01

    Students identified as gifted who also display one or more areas of disability remain under-identified both in special and gifted education programs. All too often school personnel do not have the resources necessary to make decisions about this unique group of students commonly called the twice-exceptional. The purpose of this article is to…

  14. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 1 2012-07-01 2012-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals. The operator must evaluate each chemical brought on mine property and each chemical produced on mine...

  15. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals. The operator must evaluate each chemical brought on mine property and each chemical produced on mine...

  16. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals. The operator must evaluate each chemical brought on mine property and each chemical produced on mine...

  17. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 1 2013-07-01 2013-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals. The operator must evaluate each chemical brought on mine property and each chemical produced on mine...

  18. 30 CFR 47.21 - Identifying hazardous chemicals.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 1 2014-07-01 2014-07-01 false Identifying hazardous chemicals. 47.21 Section... TRAINING HAZARD COMMUNICATION (HazCom) Hazard Determination § 47.21 Identifying hazardous chemicals. The operator must evaluate each chemical brought on mine property and each chemical produced on mine...

  19. 17 CFR 45.6 - Legal entity identifiers

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... entity or entities in the record. (c) Governance principles for the legal entity identifier. The legal... conform to the governance principles set forth in paragraphs (c)(1) through (4) of this section. (1) International governance. The issuance of the legal entity identifier used pursuant to this section, and...

  20. 17 CFR 45.6 - Legal entity identifiers

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... entity or entities in the record. (c) Governance principles for the legal entity identifier. The legal... conform to the governance principles set forth in paragraphs (c)(1) through (4) of this section. (1) International governance. The issuance of the legal entity identifier used pursuant to this section, and...