WorldWideScience

Sample records for s1 nuclease mapping

  1. Characterization of a periplasmic S1-like nuclease coded by the Mesorhizobium loti symbiosis island

    International Nuclear Information System (INIS)

    Pimkin, Maxim; Miller, C. Glenn; Blakesley, Lauryn; Oleykowski, Catherine A.; Kodali, Nagendra S.; Yeung, Anthony T.

    2006-01-01

    DNA sequences encoding hypothetical proteins homologous to S1 nuclease from Aspergillus oryzae are found in many organisms including fungi, plants, pathogenic bacteria, and eukaryotic parasites. One of these is the M1 nuclease of Mesorhizobium loti which we demonstrate herein to be an enzymatically active, soluble, and stable S1 homolog that lacks the extensive mannosyl-glycosylation found in eukaryotic S1 nuclease homologs. We have expressed the cloned M1 protein in M. loti and purified recombinant native M1 to near homogeneity and have also isolated a homogeneous M1 carboxy-terminal hexahistidine tag fusion protein. Mass spectrometry and N-terminal Edman degradation sequencing confirmed the protein identity. The enzymatic properties of the purified M1 nuclease are similar to those of S1. At acidic pH M1 is 25 times more active on single-stranded DNA than on double-stranded DNA and 3 times more active on single-stranded DNA than on single-stranded RNA. At neutral pH the RNase activity of M1 exceeds the DNase activity. M1 nicks supercoiled RF-I plasmid DNA and rapidly cuts the phosphodiester bond across from the nick in the resultant relaxed RF-II plasmid DNA. Therefore, M1 represents an active bacterial S1 homolog in spite of great sequence divergence. The biochemical characterization of M1 nuclease supports our sequence alignment that reveals the minimal 21 amino acid residues that are necessarily conserved for the structure and functions of this enzyme family. The ability of M1 to degrade RNA at neutral pH implies previously unappreciated roles of these nucleases in biological systems

  2. Multispot array combined with S1 nuclease-mediated elimination of unpaired nucleotides

    DEFF Research Database (Denmark)

    Yoo, Seung Min; Kim, Dong Min; Lee, Sang Yup

    2015-01-01

    The accurate detection of mismatched base pairs is critical to many DNA hybridization-based applications in basic research and diagnostics. We herein demonstrate that mismatched DNAs on a multispot array can be accurately detected in a multiplexed way by employing the S1 nuclease-based mismatched...... base pair-specific cleavage system. After the optimization of the reaction condition, mismatched DNAs present in various pathogenic bacteria and genetic disorders could be successfully detected with stable hybridization signals regardless of the position of the fluorescent label relative to the probe......-target duplex. This technique of performing S1 nuclease-mediated cleavage on a multispot array offers high specificity and high-throughput detection of mismatched DNAs. It is expected that this assay system will prove useful for single-assay genotyping and/or the diagnosis of various diseases and pathogens....

  3. Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.

    Directory of Open Access Journals (Sweden)

    Tomáš Kovaľ

    Full Text Available The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.

  4. Mung Bean nuclease mapping of RNAs 3' end

    Directory of Open Access Journals (Sweden)

    Barbieri Rainer

    2009-05-01

    Full Text Available Abstract A method is described that allows an accurate mapping of 3' ends of RNAs. In this method a labeled DNA probe, containing the presumed 3' end of the RNA under analysis is allowed to anneals to the RNA itself. Mung-bean nuclease is then used to digest single strands of both RNA and DNA. Electrophoretic fractionation of "protected" undigested, labeled DNA is than performed using a sequence reaction of a known DNA as length marker. This procedure was applied to the analysis of both a polyA RNA (Interleukin 10 mRNA and non polyA RNAs (sea urchin 18S and 26S rRNAs. This method might be potentially relevant for the evaluation of the role of posttrascriptional control of IL-10 in the pathogenesis of the immune and inflammatory mediated diseases associated to ageing. This might allow to develop new strategies to approach to the diagnosis and therapy of age related diseases.

  5. Potential relationships between morphological differentiation and mutants with high nuclease P1 production of Penicillium citrinum

    Energy Technology Data Exchange (ETDEWEB)

    Xinle, Liang; Qian, Shou; Hong, Zhang; Min, Chen [Department of Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang (China); Xuan, Liu [Beihai Institute of Environmental Science, Beihai, Guangxi (China)

    2009-08-15

    Diversification of colony characteristics of mutants derived from Penicillium citrinum CICC 4011 treated with {sup 60}Co {gamma}-irradiation and protoplast fusion were analyzed. There were distinct differences among mutants with different nuclease P1 activity, especially in pigment productivity. Color of colony was changed from the original green to white, grey-green, or yellow-green etc., while the nuclease P1 activity would be fluctuated with the color change. The hypothesis was suggested that there would be a relationship between pigments and nuclease P1 production. Mutants with grey-green colony would give out high nuclease P1 outputs in a high probability such as mutant J1Y6 (nuclease P1 activity, 167.3U/ml) and fusant F-13 (nuclease P1 activity, 568.7U/ml), while others with deep-green colony observed low nuclease outputs. Four variation strains didn't show any significant difference in growth rate. Broom branches of conidiophore stem in J1Y6 and F-13 were obviously reduced, conidiophores productivity reduced, but hyphae growth haled. These suggested that nuclease P1 production was associated with growth phase, but pigment synthesis course wasn't. RAPD from 6 randomly selected primers was used to analyze the polymorphic rich of the four strains, the results showed that there were 70 percent polymorphism detection rate among those. UPGMA cluster analysis and genetic map constructed by NTSYS-PC software, which showed that J1Y6 and F-14 were clustered as one group at similar coefficient 0.9, where there was an appear distance from the group of 4011 and F-R-33 strains (similar coefficient 0.8). (authors)

  6. Potential relationships between morphological differentiation and mutants with high nuclease P1 production of Penicillium citrinum

    International Nuclear Information System (INIS)

    Liang Xinle; Shou Qian; Zhang Hong; Chen Min; Liu Xuan

    2009-01-01

    Diversification of colony characteristics of mutants derived from Penicillium citrinum CICC 4011 treated with 60 Co γ-irradiation and protoplast fusion were analyzed. There were distinct differences among mutants with different nuclease P1 activity, especially in pigment productivity. Color of colony was changed from the original green to white, grey-green, or yellow-green etc., while the nuclease P1 activity would be fluctuated with the color change. The hypothesis was suggested that there would be a relationship between pigments and nuclease P1 production. Mutants with grey-green colony would give out high nuclease P1 outputs in a high probability such as mutant J1Y6( nuclease P1 activity, 167.3U/ml) and fusant F-13 (nuclease P1 activity, 568.7U/ml), while others with deep-green colony observed low nuclease outputs. Four variation strains didn't show any significant difference in growth rate. Broom branches of conidiophore stem in J1Y6 and F-13 were obviously reduced, conidiophores productivity reduced, but hyphae growth haled. These suggested that nuclease P1 production was associated with growth phase, but pigment synthesis course wasn't. RAPD from 6 randomly selected primers was used to analyze the polymorphic rich of the four strains, the results showed that there were 70 percent polymorphism detection rate among those. UPGMA cluster analysis and genetic map constructed by NTSYS-PC software, which showed that J1Y6 and F-14 were clustered as one group at similar coefficient 0.9, where there was an appear distance from the group of 4011 and F-R-33 strains (similar coefficient 0.8). (authors)

  7. Mapping of gene transcripts by nuclease protection assays and cDNA primer extension

    International Nuclear Information System (INIS)

    Calzone, F.J.; Britten, R.J.; Davidson, E.J.

    1987-01-01

    An important problem often faced in the molecular characterization of genes is the precise mapping of those genomic sequences transcribed into RNA. This requires identification of the genomic site initiating gene transcription, the location of genomic sequences removed from the primary gene transcript during RNA processing, and knowledge of sequences terminating the processed gene transcript. The objective of the protocols described here is the generation of transcription maps utilizing relatively uncharacterized gene fragments. The basic approach is hybridization of a single-stranded DNA probe with cellular RNA, followed by treatment with a single-strand-specific nuclease that does not attack DNA-RNA hybrids, in order to destroy any unreacted probe sequences. Thus the probe sequences included in the hybrid duplexes are protected from nuclease digestion. The sizes of the protected probe fragments determined by gel electrophoresis correspond to the lengths of the hybridized sequence elements

  8. Antitumor activity od apoptotic nuclease TBN1 from L. esculentum

    Czech Academy of Sciences Publication Activity Database

    Matoušek, Jaroslav; Podzimek, Tomáš; Poučková, P.; Stehlík, Jan; Škvor, J.; Lipovová, P.; Matoušek, Josef

    2010-01-01

    Roč. 57, č. 4 (2010), s. 339-348 ISSN 0028-2685 R&D Projects: GA ČR GA521/06/1149; GA ČR GA521/09/1214 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50450515 Keywords : anticancerogenic and antiproliferative nuclease * dsRNase * human solid malignant tumors Subject RIV: FD - Oncology ; Hematology Impact factor: 1.449, year: 2010

  9. Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme

    Czech Academy of Sciences Publication Activity Database

    Stránský, J.; Koval, Tomáš; Podzimek, T.; Týcová, A.; Lipovová, P.; Matoušek, J.; Kolenko, Petr; Fejfarová, Karla; Dušková, J.; Skálová, T.; Hašek, J.; Dohnálek, Jan

    2015-01-01

    Roč. 71, č. 11 (2015), s. 1408-1415 ISSN 2053-230X R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109; GA MŠk(CZ) EE2.3.30.0029 Institutional support: RVO:61389013 Keywords : tomato multifunctional nuclease * TBN1 * type I nuclease Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.647, year: 2015

  10. Investigation of centers sensitive to S1-nuclease in the genoma of the yeast S. cerevisiae after in-vivo exposure to gamma radiation

    International Nuclear Information System (INIS)

    Geigl, E.M.

    1987-09-01

    The structure, distribution and repair of basal damage in DNS after exposure to 60 Co gamma radiation were investigated in S. cerevisiae cells. Small DNS regions with mispaired or unpaired bases of rather high stability were found whose rate of incidence and linear dose dependence appear to be similar to those of double strand breaks. In contrast to double strand breaks, they showed no statistical' distribution pattern across the genoma. Liquid holding experiments showed that centers sensitive to S1-nuclease will be repaired in S. cerevisiae by a combined process of recombination and postreplication repair; the gene products of the genes RAD50 and RAD18 are involved. (orig./AJ) [de

  11. Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme

    Czech Academy of Sciences Publication Activity Database

    Stránský, Jan; Koval, Tomáš; Podzimek, T.; Týcová, Anna; Lipovová, P.; Matoušek, Jaroslav; Kolenko, Petr; Fejfarová, Karla; Dušková, Jarmila; Skálová, Tereza; Hašek, Jindřich; Dohnálek, Jan

    2015-01-01

    Roč. 71, č. 11 (2015), s. 1408-1415 ISSN 2053-230X R&D Projects: GA MŠk LG14009; GA MŠk(CZ) EE2.3.30.0029; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:86652036 ; RVO:60077344 Keywords : tomato multifunctional nuclease * TBN1 * type I nuclease * superhelix Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.647, year: 2015

  12. A sensitive assay for Staphylococcus aureus nucleases

    Energy Technology Data Exchange (ETDEWEB)

    Kohli, J K; Vakil, B V; Patil, M S; Pandey, V N; Pradhan, D S [Bhabha Atomic Reserach Centre, Bombay (India). Biochemistry Div.

    1989-10-01

    A sensitive assay for staphylococcal nuclease involving incubation of the enzyme sample with heat-denatured ({sup 3}H) thymidine labelled DNA from E.coli, precipitation with trichloroacetic acid and measurement of the radioactivity of acid-soluble nucleotides released has been developed. The assay is sensitive enough to be used for comparing the levels of nucleases elaborated by different strains of S. aureus as well as for determining the extent of contamination of S. aureus in food and water samples even at levels at which the conventional spectrophotometric and toluidine blue-DNA methods are totally inadequate. (author). 26 refs., 3 figs ., 3 tabs.

  13. Plant plasma membrane-bound staphylococcal-like DNases as a novel class of eukaryotic nucleases

    Directory of Open Access Journals (Sweden)

    Leśniewicz Krzysztof

    2012-10-01

    Full Text Available Abstract Background The activity of degradative nucleases responsible for genomic DNA digestion has been observed in all kingdoms of life. It is believed that the main function of DNA degradation occurring during plant programmed cell death is redistribution of nucleic acid derived products such as nitrogen, phosphorus and nucleotide bases. Plant degradative nucleases that have been studied so far belong mainly to the S1-type family and were identified in cellular compartments containing nucleic acids or in the organelles where they are stored before final application. However, the explanation of how degraded DNA components are exported from the dying cells for further reutilization remains open. Results Bioinformatic and experimental data presented in this paper indicate that two Arabidopsis staphylococcal-like nucleases, named CAN1 and CAN2, are anchored to the cell membrane via N-terminal myristoylation and palmitoylation modifications. Both proteins possess a unique hybrid structure in their catalytic domain consisting of staphylococcal nuclease-like and tRNA synthetase anticodon binding-like motifs. They are neutral, Ca2+-dependent nucleaces showing a different specificity toward the ssDNA, dsDNA and RNA substrates. A study of microarray experiments and endogenous nuclease activity revealed that expression of CAN1 gene correlates with different forms of programmed cell death, while the CAN2 gene is constitutively expressed. Conclusions In this paper we present evidence showing that two plant staphylococcal-like nucleases belong to a new, as yet unidentified class of eukaryotic nucleases, characterized by unique plasma membrane localization. The identification of this class of nucleases indicates that plant cells possess additional, so far uncharacterized, mechanisms responsible for DNA and RNA degradation. The potential functions of these nucleases in relation to their unique intracellular location are discussed.

  14. Crystallization and preliminary X-ray analysis of a RecB-family nuclease from the archaeon Pyrococcus abyssi

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Bin, E-mail: ren@csb.ki.se [Center for Structural Biochemistry, Karolinska Institute, NOVUM, S-141 57 Huddinge (Sweden); Kuhn, Joëlle; Meslet-Cladiere, Laurence; Myllykallio, Hannu [Université Paris-Sud, Institut de Génétique et Microbiologie, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8621, F-91405 Orsay CEDEX (France); Ladenstein, Rudolf [Center for Structural Biochemistry, Karolinska Institute, NOVUM, S-141 57 Huddinge (Sweden)

    2007-05-01

    A RecB-like nuclease from the archaeon Pyrococcus abyssi was expressed, purified and crystallized. The crystals belong to the orthorhombic space group C222{sub 1} with a = 81.5, b = 159.8, c = 100.8 Å, and a native data set was collected to 2.65 Å resolution. Nucleases are required to process and repair DNA damage in living cells. One of the best studied nucleases is the RecB protein, which functions in Escherichia coli as a component of the RecBCD enzyme complex that amends double-strand breaks in DNA. Although archaea do not contain the RecBCD complex, a RecB-like nuclease from Pyrococcus abyssi has been cloned, expressed and purified. The protein was crystallized by the sitting-drop vapour-diffusion method using polyethylene glycol 8000 as the precipitant. The crystals belong to the orthorhombic space group C222{sub 1}, with unit-cell parameters a = 81.5, b = 159.8, c = 100.8 Å. Self-rotation function and native Patterson map calculations revealed that there is a dimer in the asymmetric unit with its local twofold axis running parallel to the crystallographic twofold screw axis. The crystals diffracted to about 2 Å and a complete native data set was collected to 2.65 Å resolution.

  15. Antitumor Effects and Cytotoxicity of Recombinant Plant Nucleases

    Czech Academy of Sciences Publication Activity Database

    Matoušek, Jaroslav; Podzimek, Tomáš; Pouckova, P.; Stehlík, Jan; Škvor, J.; Souček, J.; Matoušek, Josef

    2009-01-01

    Roč. 18, č. 4 (2009), s. 163-171 ISSN 0965-0407 R&D Projects: GA ČR GA521/09/1214 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50450515 Keywords : Anticarcinogenic and antiproliferative nucleases * Human melanoma * Tumor xenografts * Nicotiana benthamina Subject RIV: FD - Oncology ; Hematology Impact factor: 1.478, year: 2009

  16. Medium optimization for nuclease P1 production by Penicillium citrinum in solid-state fermentation using polyurethane foam as inert carrier

    NARCIS (Netherlands)

    Zhu, Y.; Knol, W.; Smits, J.P.; Bol, J.

    1996-01-01

    A solid-state fermentation system, using polyurethane foam as an inert carrier, was used for the production of nuclease P1 by Penicillium citrinum. Optimization of nuclease P1 production was carried out using a synthetic liquid medium. After a two-step medium optimization using a fractional

  17. Mapping of Complete Set of Ribose and Base Modifications of Yeast rRNA by RP-HPLC and Mung Bean Nuclease Assay.

    Directory of Open Access Journals (Sweden)

    Jun Yang

    Full Text Available Ribosomes are large ribonucleoprotein complexes that are fundamental for protein synthesis. Ribosomes are ribozymes because their catalytic functions such as peptidyl transferase and peptidyl-tRNA hydrolysis depend on the rRNA. rRNA is a heterogeneous biopolymer comprising of at least 112 chemically modified residues that are believed to expand its topological potential. In the present study, we established a comprehensive modification profile of Saccharomyces cerevisiae's 18S and 25S rRNA using a high resolution Reversed-Phase High Performance Liquid Chromatography (RP-HPLC. A combination of mung bean nuclease assay, rDNA point mutants and snoRNA deletions allowed us to systematically map all ribose and base modifications on both rRNAs to a single nucleotide resolution. We also calculated approximate molar levels for each modification using their UV (254nm molar response factors, showing sub-stoichiometric amount of modifications at certain residues. The chemical nature, their precise location and identification of partial modification will facilitate understanding the precise role of these chemical modifications, and provide further evidence for ribosome heterogeneity in eukaryotes.

  18. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials.

    Science.gov (United States)

    Bikard, David; Euler, Chad W; Jiang, Wenyan; Nussenzweig, Philip M; Goldberg, Gregory W; Duportet, Xavier; Fischetti, Vincent A; Marraffini, Luciano A

    2014-11-01

    Antibiotics target conserved bacterial cellular pathways or growth functions and therefore cannot selectively kill specific members of a complex microbial population. Here, we develop programmable, sequence-specific antimicrobials using the RNA-guided nuclease Cas9 (refs.1,2) delivered by a bacteriophage. We show that Cas9, reprogrammed to target virulence genes, kills virulent, but not avirulent, Staphylococcus aureus. Reprogramming the nuclease to target antibiotic resistance genes destroys staphylococcal plasmids that harbor antibiotic resistance genes and immunizes avirulent staphylococci to prevent the spread of plasmid-borne resistance genes. We also show that CRISPR-Cas9 antimicrobials function in vivo to kill S. aureus in a mouse skin colonization model. This technology creates opportunities to manipulate complex bacterial populations in a sequence-specific manner.

  19. Antitumor and biological effects of black pine (Pinus nigra) pollen nuclease

    Czech Academy of Sciences Publication Activity Database

    Lipovová, P.; Podzimek, T.; Orctová, Lidmila; Matoušek, Jaroslav; Poučková, P.; Souček, J.; Matoušek, Josef

    2008-01-01

    Roč. 55, - (2008), s. 158-164 ISSN 0028-2685 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50450515 Keywords : pollen nuclease * Antitumor effect Subject RIV: FD - Oncology ; Hematology Impact factor: 1.179, year: 2008

  20. Minimizing off-Target Mutagenesis Risks Caused by Programmable Nucleases.

    Science.gov (United States)

    Ishida, Kentaro; Gee, Peter; Hotta, Akitsu

    2015-10-16

    Programmable nucleases, such as zinc finger nucleases (ZFNs), transcription activator like effector nucleases (TALENs), and clustered regularly interspersed short palindromic repeats associated protein-9 (CRISPR-Cas9), hold tremendous potential for applications in the clinical setting to treat genetic diseases or prevent infectious diseases. However, because the accuracy of DNA recognition by these nucleases is not always perfect, off-target mutagenesis may result in undesirable adverse events in treated patients such as cellular toxicity or tumorigenesis. Therefore, designing nucleases and analyzing their activity must be carefully evaluated to minimize off-target mutagenesis. Furthermore, rigorous genomic testing will be important to ensure the integrity of nuclease modified cells. In this review, we provide an overview of available nuclease designing platforms, nuclease engineering approaches to minimize off-target activity, and methods to evaluate both on- and off-target cleavage of CRISPR-Cas9.

  1. Potentiometric sensing of nuclease activities and oxidative damage of single-stranded DNA using a polycation-sensitive membrane electrode.

    Science.gov (United States)

    Ding, Jiawang; Qin, Wei

    2013-09-15

    A simple, general and label-free potentiometric method to measure nuclease activities and oxidative DNA damage in a homogeneous solution using a polycation-sensitive membrane electrode is reported. Protamine, a linear polyionic species, is used as an indicator to report the cleavage of DNA by nucleases such as restriction and nonspecific nucleases, and the damage of DNA induced by hydroxyl radicals. Measurements can be done with a titration mode or a direct detection mode. For the potentiometric titration mode, the enzymatic cleavage dramatically affects the electrostatical interaction between DNA and protamine and thus shifts the response curve for the potentiometric titration of the DNA with protamine. Under the optimized conditions, the enzyme activities can be sensed potentiometrically with detection limits of 2.7×10(-4)U/µL for S1 nuclease, and of 3.9×10(-4)U/µL for DNase I. For the direct detection mode, a biocomplex between protamine and DNA is used as a substrate. The nuclease of interest cleaves the DNA from the protamine/DNA complex into smaller fragments, so that free protamine is generated and can be detected potentiometrically via the polycation-sensitive membrane electrode. Using a direct measurement, the nuclease activities could be rapidly detected with detection limits of 3.2×10(-4)U/µL for S1 nuclease, and of 4.5×10(-4)U/µL for DNase I. Moreover, the proposed potentiometric assays demonstrate the potential applications in the detection of hydroxyl radicals. It is anticipated that the present potentiometric strategy will provide a promising platform for high-throughput screening of nucleases, reactive oxygen species and the drugs with potential inhibition abilities. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Crystal structures of two eukaryotic nucleases involved in RNA metabolism

    DEFF Research Database (Denmark)

    Jonstrup, Anette Thyssen; Midtgaard, Søren Fuglsang; Van, Lan Bich

    RNA serves a number of functions in the cell: mRNAs are the carriers of information between gene and protein, tRNAs and rRNAs are involved in the synthesis of proteins, whereas a number of additional RNA species are responsible for other functions in the cell. The quality of the different RNAs...... RNAs. We have solved the structures of two nucleases involved in 3'-5' degradation of RNA; the S. pombe Pop2p and the S. cerevisiae Rrp6p. Pop2p is part of the main cytoplasmatic deadenylation complex in yeast, which also contains the nuclease Ccr4p. Deadenylation, where the poly(A)-tail is removed...... specific transcripts. Here, we present the crystal structure of the S. pombe Pop2p protein to 1.4 Å resolution. The high resolution structure provides a clear picture of the active site architecture. Structural alignment of single nucleotides and poly(A)-oligonucleotides from earlier co-crystal structures...

  3. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.

    Science.gov (United States)

    Zhu, Lihua Julie; Lawrence, Michael; Gupta, Ankit; Pagès, Hervé; Kucukural, Alper; Garber, Manuel; Wolfe, Scot A

    2017-05-15

    Genome editing technologies developed around the CRISPR-Cas9 nuclease system have facilitated the investigation of a broad range of biological questions. These nucleases also hold tremendous promise for treating a variety of genetic disorders. In the context of their therapeutic application, it is important to identify the spectrum of genomic sequences that are cleaved by a candidate nuclease when programmed with a particular guide RNA, as well as the cleavage efficiency of these sites. Powerful new experimental approaches, such as GUIDE-seq, facilitate the sensitive, unbiased genome-wide detection of nuclease cleavage sites within the genome. Flexible bioinformatics analysis tools for processing GUIDE-seq data are needed. Here, we describe an open source, open development software suite, GUIDEseq, for GUIDE-seq data analysis and annotation as a Bioconductor package in R. The GUIDEseq package provides a flexible platform with more than 60 adjustable parameters for the analysis of datasets associated with custom nuclease applications. These parameters allow data analysis to be tailored to different nuclease platforms with different length and complexity in their guide and PAM recognition sequences or their DNA cleavage position. They also enable users to customize sequence aggregation criteria, and vary peak calling thresholds that can influence the number of potential off-target sites recovered. GUIDEseq also annotates potential off-target sites that overlap with genes based on genome annotation information, as these may be the most important off-target sites for further characterization. In addition, GUIDEseq enables the comparison and visualization of off-target site overlap between different datasets for a rapid comparison of different nuclease configurations or experimental conditions. For each identified off-target, the GUIDEseq package outputs mapped GUIDE-Seq read count as well as cleavage score from a user specified off-target cleavage score prediction

  4. Mung bean sprout (Phaseolus aureus) nuclease and its biological and antitumor effects

    Czech Academy of Sciences Publication Activity Database

    Souček, J.; Škvor, J.; Poučková, P.; Matoušek, Jaroslav; Slavík, Tomáš; Matoušek, Josef

    2006-01-01

    Roč. 53, - (2006), s. 402-409 ISSN 0028-2685 R&D Projects: GA ČR GA521/06/1149; GA ČR GA523/04/0755 Keywords : mung bean * nuclease Subject RIV: FD - Oncology ; Hematology Impact factor: 1.247, year: 2006

  5. Defects in MAP1S-mediated autophagy turnover of fibronectin cause renal fibrosis.

    Science.gov (United States)

    Xu, Guibin; Yue, Fei; Huang, Hai; He, Yongzhong; Li, Xun; Zhao, Haibo; Su, Zhengming; Jiang, Xianhan; Li, Wenjiao; Zou, Jing; Chen, Qi; Liu, Leyuan

    2016-05-01

    Excessive deposition of extracellular matrix proteins in renal tissues causes renal fibrosis and renal function failure. Mammalian cells primarily use the autophagy-lysosome system to degrade misfolded/aggregated proteins and dysfunctional organelles. MAP1S is an autophagy activator and promotes the biogenesis and degradation of autophagosomes. Previously, we reported that MAP1S suppresses hepatocellular carcinogenesis in a mouse model and predicts a better prognosis in patients suffering from clear cell renal cell carcinomas. Furthermore, we have characterized that MAP1S enhances the turnover of fibronectin, and mice overexpressing LC3 but with MAP1S deleted accumulate fibronectin and develop liver fibrosis because of the synergistic impact of LC3-induced over-synthesis of fibronectin and MAP1S depletion-caused impairment of fibronectin degradation. Here we show that a suppression of MAP1S in renal cells caused an impairment of autophagy clearance of fibronectin and an activation of pyroptosis. Depletion of MAP1S in mice leads to an accumulation of fibrosis-related proteins and the development of renal fibrosis in aged mice. The levels of MAP1S were dramatically reduced and levels of fibronectin were greatly elevated in renal fibrotic tissues from patients diagnosed as renal atrophy and renal failure. Therefore, MAP1S deficiency may cause the accumulation of fibronectin and the development of renal fibrosis.

  6. S1-sensitive sites in DNA after γ-irradiation

    International Nuclear Information System (INIS)

    Martin-Bertram, H.

    1981-01-01

    DNA from γ-irradiated T 1 bacteriophages was analyzed for 'single-stranded' sites by cleavage with S1 nuclease from Aspergillus oryzae as lesion probe. The ratio of 'S1-sensitive sites' to the amount of radiation-induced single-strand breaks was about one. Presumably these 'denatured' sites were associated with single-strand breaks. The subsequent check for the persistence of 'single-stranded' sites within the DNA molecule by thermokinetics demonstrated a strong affinity of the nuclease to its substrate, the single-stranded lesion, and a perfect excision. It is assumed that the direct absorption of radiation energy in the DNA gives rise to the formation of such bulky lesions. (Auth.)

  7. Recombinant Cyclophilins Lack Nuclease Activity

    OpenAIRE

    Manteca, Angel; Sanchez, Jesus

    2004-01-01

    Several single-domain prokaryotic and eukaryotic cyclophilins have been identified as also being unspecific nucleases with a role in DNA degradation during the lytic processes that accompany bacterial cell death and eukaryotic apoptosis. Evidence is provided here that the supposed nuclease activity of human and bacterial recombinant cyclophilins is due to contamination of the proteins by the host Escherichia coli endonuclease and is not an intrinsic property of these proteins.

  8. Halophilic Nuclease from a Moderately Halophilic Micrococcus varians

    Science.gov (United States)

    Kamekura, Masahiro; Onishi, Hiroshi

    1974-01-01

    The moderately halophilic bacterium Micrococcus varians, isolated from soy sauce mash, produced extracellular nuclease when cultivated aerobically in media containing 1 to 4 M NaCl or KCl. The enzyme, purified to an electrophoretically homogeneous state, had both ribonuclease and deoxyribonuclease activities. The nuclease had maximal activity in the presence of 2.9 M NaCl or 2.1 M KCl at 40 C. The enzymatic activity was lost by dialysis against low-salt buffer, whereas when the inactivated enzyme was dialyzed against 3.4 M NaCl buffer as much as 77% of the initial activity could be restored. Images PMID:4852218

  9. SModelS v1.1 user manual: Improving simplified model constraints with efficiency maps

    Science.gov (United States)

    Ambrogi, Federico; Kraml, Sabine; Kulkarni, Suchita; Laa, Ursula; Lessa, Andre; Magerl, Veronika; Sonneveld, Jory; Traub, Michael; Waltenberger, Wolfgang

    2018-06-01

    SModelS is an automatized tool for the interpretation of simplified model results from the LHC. It allows to decompose models of new physics obeying a Z2 symmetry into simplified model components, and to compare these against a large database of experimental results. The first release of SModelS, v1.0, used only cross section upper limit maps provided by the experimental collaborations. In this new release, v1.1, we extend the functionality of SModelS to efficiency maps. This increases the constraining power of the software, as efficiency maps allow to combine contributions to the same signal region from different simplified models. Other new features of version 1.1 include likelihood and χ2 calculations, extended information on the topology coverage, an extended database of experimental results as well as major speed upgrades for both the code and the database. We describe in detail the concepts and procedures used in SModelS v1.1, explaining in particular how upper limits and efficiency map results are dealt with in parallel. Detailed instructions for code usage are also provided.

  10. Response surface optimization of carbon and nitrogen sources for nuclease P1 production by Penicillium citrinum F-5-5

    International Nuclear Information System (INIS)

    Liang Xinle; Huang Yingying; Zhang Hong; Chen Min; Liu Xuan

    2011-01-01

    Penicillium citrinum F-5-5, a nuclease P1 high-producing strain with 978.6 U/ml in potato glucose medium, was derived from the original Penicillium citrinum CICC 4011 with 60 Co γ-rays irradiation mutation and then protoplasts fusion treatment. Culture components were optimized for the nuclease P1 production, and response surface methodology was applied for the critical medium components(carbon and nitrogen sources) which were preselected by Plackett-Burman design approach. Glucose, soluble starch and corn steep powder showed significant effects on production of nuclease. Central composite design was used for the optimization levels by software Minitab 15, and it showed that, the optimal values for the concentration of glucose, soluble starch and corn steep powder were 30.89, 42.46 and 11.60 g/L, respectively. With this medium,an enzyme activity of 1687.16 U/ml could be obtained theoretically. Using this optimized medium, an experimental enzyme activity of 1672.6 U/ml was reached. (authors)

  11. Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

    Science.gov (United States)

    Canver, Matthew C; Lessard, Samuel; Pinello, Luca; Wu, Yuxuan; Ilboudo, Yann; Stern, Emily N; Needleman, Austen J; Galactéros, Frédéric; Brugnara, Carlo; Kutlar, Abdullah; McKenzie, Colin; Reid, Marvin; Chen, Diane D; Das, Partha Pratim; A Cole, Mitchel; Zeng, Jing; Kurita, Ryo; Nakamura, Yukio; Yuan, Guo-Cheng; Lettre, Guillaume; Bauer, Daniel E; Orkin, Stuart H

    2017-04-01

    Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, which is associated with red-blood-cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false-positive regions, thus emphasizing the importance of off-target analysis in the design of saturating-mutagenesis experiments. Together, these data establish a widely applicable high-throughput and high-resolution methodology to identify minimal functional sequences within large disease- and trait-associated regions.

  12. The hypersurfaces with conformal normal Gauss map in Hn+1 and S1n+1

    Directory of Open Access Journals (Sweden)

    Shuguo Shi

    2008-03-01

    Full Text Available In this paper, we introduce the fourth fundamental forms for hypersurfaces in Hn+1 and space-like hypersurfaces in S1n+1, and discuss the conformality of the normal Gauss map of the hypersurfaces in Hn+1 and S1n+1. Particularly, we discuss the surfaces with conformal normal Gauss map in H³ and S³1, and prove a duality property. We give a Weierstrass representation formula for space-like surfaces in S³1 with conformal normal Gauss map. We also state the similar results for time-like surfaces in S³1. Some examples of surfaces in S³1 with conformal normal Gauss map are given and a fully nonlinear equation of Monge-Ampère type for the graphs in S³1 with conformal normal Gauss map is derived.Neste artigo, introduzimos a quarta forma fundamental de uma hipersuperfície em Hn+1 de uma hipersuperfície tipo-espaço em S1n+1, e discutimos a conformalidade da aplicação normal de Gauss de tais hipersuperfícies. Em particular, investigamos o caso de superfícies com aplicação normal de Gauss conforme em H³ e S³1, e provamos um teorema de dualidade. Apresentamos uma representação de Weierstrass para superfícies tipo-espaço em S³1 com aplicação de Gauss conforme. Enunciamos também resultados semelhantes para superfícies tipo-tempo em S³1. São dados alguns exemplos de superfícies em S³1 com aplicações de Gauss conformes, e é deduzida uma equação totalmente não-linear do tipo Monge-Ampère para gráficos em S³1 com aplicações de Gauss conformes.

  13. Creating Directed Double-strand Breaks with the Ref Protein: A Novel Rec A-Dependent Nuclease from Bacteriophage P1

    Energy Technology Data Exchange (ETDEWEB)

    Gruenig, Marielle C.; Lu, Duo; Won, Sang Joon; Dulberger, Charles L.; Manlick, Angela J.; Keck, James L.; Cox, Michael M. (UW)

    2012-03-16

    The bacteriophage P1-encoded Ref protein enhances RecA-dependent recombination in vivo by an unknown mechanism. We demonstrate that Ref is a new type of enzyme; that is, a RecA-dependent nuclease. Ref binds to ss- and dsDNA but does not cleave any DNA substrate until RecA protein and ATP are added to form RecA nucleoprotein filaments. Ref cleaves only where RecA protein is bound. RecA functions as a co-nuclease in the Ref/RecA system. Ref nuclease activity can be limited to the targeted strands of short RecA-containing D-loops. The result is a uniquely programmable endonuclease activity, producing targeted double-strand breaks at any chosen DNA sequence in an oligonucleotide-directed fashion. We present evidence indicating that cleavage occurs in the RecA filament groove. The structure of the Ref protein has been determined to 1.4 {angstrom} resolution. The core structure, consisting of residues 77-186, consists of a central 2-stranded {beta}-hairpin that is sandwiched between several {alpha}-helical and extended loop elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity. The overall structure of Ref, including several putative active site histidine residues, defines a new subclass of HNH-family nucleases. We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks.

  14. Genome Editing in Rats Using TALE Nucleases.

    Science.gov (United States)

    Tesson, Laurent; Remy, Séverine; Ménoret, Séverine; Usal, Claire; Thinard, Reynald; Savignard, Chloé; De Cian, Anne; Giovannangeli, Carine; Concordet, Jean-Paul; Anegon, Ignacio

    2016-01-01

    The rat is an important animal model to understand gene function and model human diseases. Since recent years, the development of gene-specific nucleases has become important for generating new rat models of human diseases, to analyze the role of genes and to generate human antibodies. Transcription activator-like (TALE) nucleases efficiently create gene-specific knockout rats and lead to the possibility of gene targeting by homology-directed recombination (HDR) and generating knock-in rats. We describe a detailed protocol for generating knockout and knock-in rats via microinjection of TALE nucleases into fertilized eggs. This technology is an efficient, cost- and time-effective method for creating new rat models.

  15. Development of synthetic selfish elements based on modular nucleases in Drosophila melanogaster

    OpenAIRE

    Simoni, A; Siniscalchi, C; Chan, Y-S; Huen, DS; Russell, S; Windbichler, N; Crisanti, A

    2014-01-01

    Selfish genes are DNA elements that increase their rate of genetic transmission at the expense of other genes in the genome and can therefore quickly spread within a population. It has been suggested that selfish elements could be exploited to modify the genome of entire populations for medical and ecological applications. Here we report that transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) can be engineered into site-specific synthetic selfish elements (S...

  16. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity ...

    Indian Academy of Sciences (India)

    s12039-016-1125-x. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity of lanthanide(III) complexes of 2-benzoylpyridine acetylhydrazone. KARREDDULA RAJA, AKKILI SUSEELAMMA and KATREDDI HUSSAIN REDDY. ∗.

  17. A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases.

    Science.gov (United States)

    Periwal, Vinita

    2017-07-01

    Genome editing with engineered nucleases (zinc finger nucleases, TAL effector nucleases s and Clustered regularly inter-spaced short palindromic repeats/CRISPR-associated) has recently been shown to have great promise in a variety of therapeutic and biotechnological applications. However, their exploitation in genetic analysis and clinical settings largely depends on their specificity for the intended genomic target. Large and complex genomes often contain highly homologous/repetitive sequences, which limits the specificity of genome editing tools and could result in off-target activity. Over the past few years, various computational approaches have been developed to assist the design process and predict/reduce the off-target activity of these nucleases. These tools could be efficiently used to guide the design of constructs for engineered nucleases and evaluate results after genome editing. This review provides a comprehensive overview of various databases, tools, web servers and resources for genome editing and compares their features and functionalities. Additionally, it also describes tools that have been developed to analyse post-genome editing results. The article also discusses important design parameters that could be considered while designing these nucleases. This review is intended to be a quick reference guide for experimentalists as well as computational biologists working in the field of genome editing with engineered nucleases. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. Nucleases as a barrier to gene silencing in the cotton boll weevil, Anthonomus grandis.

    Science.gov (United States)

    Almeida Garcia, Rayssa; Lima Pepino Macedo, Leonardo; Cabral do Nascimento, Danila; Gillet, François-Xavier; Moreira-Pinto, Clidia Eduarda; Faheem, Muhammad; Moreschi Basso, Angelina Maria; Mattar Silva, Maria Cristina; Grossi-de-Sa, Maria Fatima

    2017-01-01

    RNA interference (RNAi) approaches have been applied as a biotechnological tool for controlling plant insect pests via selective gene down regulation. However, the inefficiency of RNAi mechanism in insects is associated with several barriers, including dsRNA delivery and uptake by the cell, dsRNA interaction with the cellular membrane receptor and dsRNA exposure to insect gut nucleases during feeding. The cotton boll weevil (Anthonomus grandis) is a coleopteran in which RNAi-mediated gene silencing does not function efficiently through dsRNA feeding, and the factors involved in the mechanism remain unknown. Herein, we identified three nucleases in the cotton boll weevil transcriptome denoted AgraNuc1, AgraNuc2, and AgraNuc3, and the influences of these nucleases on the gene silencing of A. grandis chitin synthase II (AgraChSII) were evaluated through oral dsRNA feeding trials. A phylogenetic analysis showed that all three nucleases share high similarity with the DNA/RNA non-specific endonuclease family of other insects. These nucleases were found to be mainly expressed in the posterior midgut region of the insect. Two days after nuclease RNAi-mediated gene silencing, dsRNA degradation by the gut juice was substantially reduced. Notably, after nucleases gene silencing, the orally delivered dsRNA against the AgraChSII gene resulted in improved gene silencing efficiency when compared to the control (non-silenced nucleases). The data presented here demonstrates that A. grandis midgut nucleases are effectively one of the main barriers to dsRNA delivery and emphasize the need to develop novel RNAi delivery strategies focusing on protecting the dsRNA from gut nucleases and enhancing its oral delivery and uptake to crop insect pests.

  19. Plant Ribonucleases and Nucleases as Antiproliferative Agens Targeting Human Tumors Growing in Mice

    Czech Academy of Sciences Publication Activity Database

    Matoušek, Jaroslav; Matoušek, Josef

    2010-01-01

    Roč. 4, č. 1 (2010), s. 29-39 ISSN 1872-2156 R&D Projects: GA ČR GA521/06/1149; GA ČR GA521/09/1214 Institutional research plan: CEZ:AV0Z50510513; CEZ:AV0Z50450515 Keywords : antiproliferative cytotoxic * effect human * plant nuclease Subject RIV: EB - Genetics ; Molecular Biology

  20. Structure features of TBN1, a P1/S1-like nuclease

    Czech Academy of Sciences Publication Activity Database

    Koval, Tomáš; Stránský, Jan; Lipovová, P.; Podzimek, Tomáš; Matoušek, Jaroslav; Dušková, Jarmila; Skálová, Tereza; Hašek, Jindřich; Fejfarová, Karla; Kolenko, Petr; Dohnálek, Jan

    2014-01-01

    Roč. 281, Supplement s1 (2014), s. 601 ISSN 1742-464X. [FEBS EMBO 2014 Conference. 30.08.2014-04.09.2014, Paris] R&D Projects: GA MŠk(CZ) EE2.3.30.0029; GA MŠk LG14009; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 ; RVO:86652036 ; RVO:60077344 Keywords : chitin * chitinase * clostridium Subject RIV: CE - Biochemistry; EI - Biotechnology ; Bionics (BTO-N); EB - Genetics ; Molecular Biology (BC-A) http://onlinelibrary.wiley.com/doi/10.1111/febs.12919/abstract

  1. Applications of Alternative Nucleases in the Age of CRISPR/Cas9

    Directory of Open Access Journals (Sweden)

    Tuhin K. Guha

    2017-11-01

    Full Text Available Breakthroughs in the development of programmable site-specific nucleases, including zinc-finger nucleases (ZFNs, transcription activator-like effector nucleases (TALENs, meganucleases (MNs, and most recently, the clustered regularly interspaced short palindromic repeats (CRISPR associated proteins (including Cas9 have greatly enabled and accelerated genome editing. By targeting double-strand breaks to user-defined locations, the rates of DNA repair events are greatly enhanced relative to un-catalyzed events at the same sites. However, the underlying biology of each genome-editing nuclease influences the targeting potential, the spectrum of off-target cleavages, the ease-of-use, and the types of recombination events at targeted double-strand breaks. No single genome-editing nuclease is optimized for all possible applications. Here, we focus on the diversity of nuclease domains available for genome editing, highlighting biochemical properties and the potential applications that are best suited to each domain.

  2. Application of a 5 ' nuclease assay for detection of Lawsonia intracellularis in fecal samples from pigs

    DEFF Research Database (Denmark)

    Lindecrona, R. H.; Jensen, Tim Kåre; Andersen, P. H.

    2002-01-01

    A 5' nuclease assay was developed to detect Lawsonia intracellularis in porcine fecal samples. The specific probe and primers were chosen by using the 16S ribosomal DNA gene as a target. The 5' nuclease assay was used with a total of 204 clinical samples, and the results were compared to those of...

  3. S1 nuclease from Aspergillus oryzae for the detection of DNA damage and repair in the gamma-irradiated intracerebral rat gliosarcoma 9L

    International Nuclear Information System (INIS)

    Gutin, P.H.; Hilton, J.; Fein, V.J.; Allen, A.E.; Walker, M.D.

    1977-01-01

    DNA damage and repair in a rat brain tumor following irradiation in vivo were measured by analysis of the rate of strand separation of the tumor DNA in alkali. Tumors were removed after irradiation and mechanically dissociated to a cellular suspension. Tumor cells were injected into alkali (pH 12) for 20 min at 22 0 C. The fraction of tumor DNA remaining double-stranded after this exposure to alkali was determined by its resistance to S 1 nuclease from Aspergillus oryzae. Double-stranded DNA remains (after enzyme exposure) acid-precipitable for fluorescent assay. The double-stranded fraction after exposure to alkali decreases with increasing radiation dose following first-order kinetics. DNA from tumors excised at intervals after irradiation showed a greater double-stranded fraction in alkali than that from tumors excised immediately, indicating repair of single-strand breaks. Repair of damage produced by 600 rad proceeded with a half-time of approximately 15 min

  4. Transcription Activator-Like Effectors (TALEs) Hybrid Nucleases for Genome Engineering Application

    KAUST Repository

    Wibowo, Anjar

    2011-06-06

    Gene targeting is a powerful genome engineering tool that can be used for a variety of biotechnological applications. Genomic double-strand DNA breaks generated by engineered site-specific nucleases can stimulate gene targeting. Hybrid nucleases are composed of DNA binding module and DNA cleavage module. Zinc Finger Nucleases were used to generate double-strand DNA breaks but it suffers from failures and lack of reproducibility. The transcription activator–like effectors (TALEs) from plant pathogenic Xanthomonas contain a unique type of DNA-binding domain that bind specific DNA targets. The purpose of this study is to generate novel sequence specific nucleases by fusing a de novo engineered Hax3 TALE-based DNA binding domain to a FokI cleavage domain. Our data show that the de novo engineered TALE nuclease can bind to its target sequence and create double-strand DNA breaks in vitro. We also show that the de novo engineered TALE nuclease is capable of generating double-strand DNA breaks in its target sequence in vivo, when transiently expressed in Nicotiana benthamiana leaves. In conclusion, our data demonstrate that TALE-based hybrid nucleases can be tailored to bind a user-selected DNA sequence and generate site-specific genomic double-strand DNA breaks. TALE-based hybrid nucleases hold much promise as powerful molecular tools for gene targeting applications.

  5. The involvement of nuclear nucleases in rat thymocyte DNA degradation after γ-irradiation

    International Nuclear Information System (INIS)

    Nikonova, L.V.; Nelipovich, P.A.; Umansky, S.R.

    1982-01-01

    Possible mechanisms of internucleosomal DNA fragmentation in thymocytes of irradiated rats were studied. It was shown that thymocyte nuclei contain at least two nucleases that cleave DNA between nucleosomes - a Ca 2+ /Mg 2+ -dependent nuclease and an acidic one which does not depend on bivalent ions. 2 and 3 h after irradiation at a dose of 10 Gy the initial rate of DNA cleavage by Ca 2+ /Mg 2+ -dependent nuclease in isolated nuclei increased three and seven times, respectively, but the kinetics of DNA digestion by acidic nuclease did not change. The experiments with cycloheximide indicated that Ca 2+ /Mg 2+ -dependent endonuclease turns over at a high rate. The activity of the cytoplasmic acidic and Mg 2+ -dependent nucleases was shown to increase (by 40 and 50%, respectively) 3h after irradiation. The effect is caused by the de novo synthesis of the nucleases. At the same time the activity of nuclear nucleases did not essentially change. The chromatin isolated from rat thymocytes 3 h after irradiation did not differ in its sensitivity to some exogenic nucleases (DNAase I, micrococcal nuclease and nuclease from Serratia marcescens) from the control. Thus, Ca 2+ /Mg 2+ -dependent endonuclease seems to be responsible for the postirradiation internucleosomal DNA fragmentation in dying thymocytes. (Auth.)

  6. Intra and extracellular nuclease production by Aspergillus niger and Aspergillus nidulans

    Directory of Open Access Journals (Sweden)

    Ferreira Adlane V. B.

    1998-01-01

    Full Text Available Intra and extracellular nuclease production by strains of Aspergillus niger and Aspergillus nidulans was estimated using a modified DNAse test agar and cell-free extract assays. Differences in the production of nucleases by A. niger and A. nidulans were observed. These observations suggest that the DNAse test agar can be helpful for a quick screening for some types of nucleases in filamentous fungi. The assays using cell-free extracts can also be useful for initial characterization of other types of nucleases.

  7. Eukaryotic zinc-dependent multifunctional nuclease I

    Czech Academy of Sciences Publication Activity Database

    Koval, Tomáš; Lipovová, P.; Podzimek, T.; Matoušek, Jaroslav; Stránský, Jan; Dušková, Jarmila; Fejfarová, Karla; Skálová, Tereza; Hašek, Jindřich; Dohnálek, Jan

    2014-01-01

    Roč. 70, Supplement /August/ (2014), C211 ISSN 0108-7673. [Congress and General Assembly of the International Union of Crystallography /23./ - IUCr 2014. 05.08.2014-12.08.2014, Montreal] R&D Projects: GA MŠk(CZ) EE2.3.30.0029; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 ; RVO:86652036 ; RVO:60077344 Keywords : nuclease * tomato * crystal structure Subject RIV: CE - Biochemistry

  8. Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1

    Energy Technology Data Exchange (ETDEWEB)

    Gwon, Gwang Hyeon; Kim, Youngran; Liu, Yaqi; Watson, Adam T.; Jo, Aera; Etheridge, Thomas J.; Yuan, Fenghua; Zhang, Yanbin; Kim, YoungChang; Carr, Anthony M.; Cho, Yunje

    2014-10-15

    Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI–FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5' flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5' flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.

  9. Structural characterization of the virulence factor nuclease A from Streptococcus agalactiae.

    Science.gov (United States)

    Moon, Andrea F; Gaudu, Philippe; Pedersen, Lars C

    2014-11-01

    The group B pathogen Streptococcus agalactiae commonly populates the human gut and urogenital tract, and is a major cause of infection-based mortality in neonatal infants and in elderly or immunocompromised adults. Nuclease A (GBS_NucA), a secreted DNA/RNA nuclease, serves as a virulence factor for S. agalactiae, facilitating bacterial evasion of the human innate immune response. GBS_NucA efficiently degrades the DNA matrix component of neutrophil extracellular traps (NETs), which attempt to kill and clear invading bacteria during the early stages of infection. In order to better understand the mechanisms of DNA substrate binding and catalysis of GBS_NucA, the high-resolution structure of a catalytically inactive mutant (H148G) was solved by X-ray crystallography. Several mutants on the surface of GBS_NucA which might influence DNA substrate binding and catalysis were generated and evaluated using an imidazole chemical rescue technique. While several of these mutants severely inhibited nuclease activity, two mutants (K146R and Q183A) exhibited significantly increased activity. These structural and biochemical studies have greatly increased our understanding of the mechanism of action of GBS_NucA in bacterial virulence and may serve as a foundation for the structure-based drug design of antibacterial compounds targeted to S. agalactiae.

  10. Design of a colicin E7 based chimeric zinc-finger nuclease

    Science.gov (United States)

    Németh, Eszter; Schilli, Gabriella K.; Nagy, Gábor; Hasenhindl, Christoph; Gyurcsik, Béla; Oostenbrink, Chris

    2014-08-01

    Colicin E7 is a natural bacterial toxin. Its nuclease domain (NColE7) enters the target cell and kills it by digesting the nucleic acids. The HNH-motif as the catalytic centre of NColE7 at the C-terminus requires the positively charged N-terminal loop for the nuclease activity—offering opportunities for allosteric control in a NColE7-based artificial nuclease. Accordingly, four novel zinc finger nucleases were designed by computational methods exploiting the special structural features of NColE7. The constructed models were subjected to MD simulations. The comparison of structural stability and functional aspects showed that these models may function as safely controlled artificial nucleases. This study was complemented by random mutagenesis experiments identifying potentially important residues for NColE7 function outside the catalytic region.

  11. Generation of knockout rabbits using transcription activator-like effector nucleases

    OpenAIRE

    Wang, Yu; Fan, Nana; Song, Jun; Zhong, Juan; Guo, Xiaogang; Tian, Weihua; Zhang, Quanjun; Cui, Fenggong; Li, Li; Newsome, Philip N; Frampton, Jon; Esteban, Miguel A; Lai, Liangxue

    2014-01-01

    Zinc-finger nucleases and transcription activator-like effector nucleases are novel gene-editing platforms contributing to redefine the boundaries of modern biological research. They are composed of a non-specific cleavage domain and a tailor made DNA-binding module, which enables a broad range of genetic modifications by inducing efficient DNA double-strand breaks at desired loci. Among other remarkable uses, these nucleases have been employed to produce gene knockouts in mid-size and large ...

  12. Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis

    Czech Academy of Sciences Publication Activity Database

    Koval, Tomáš; Lipovová, P.; Podzimek, T.; Matoušek, Jaroslav; Dušková, Jarmila; Skálová, Tereza; Štěpánková, Andrea; Hašek, Jindřich; Dohnálek, Jan

    2013-01-01

    Roč. 69, č. 2 (2013), s. 213-226 ISSN 0907-4449 R&D Projects: GA MŠk EE2.3.30.0029; GA ČR GAP302/11/0855; GA ČR GA310/09/1407; GA ČR GA521/09/1214 Grant - others:AV ČR(CZ) AP0802 Program:Akademická prémie - Praemium Academiae Institutional support: RVO:61389013 ; RVO:60077344 Keywords : plant nucleases * catalytic zinc cluster * glycoproteins Subject RIV: CE - Biochemistry; EB - Genetics ; Molecular Biology (BC-A) Impact factor: 7.232, year: 2013

  13. Automated 5 ' nuclease assay for detection of virulence factors in porcine Escherichia coli

    DEFF Research Database (Denmark)

    Frydendahl, K.; Imberechts, H.; Lehmann, S.

    2001-01-01

    (STa, STb, EAST1) and heat labile LT) enterotoxins and the verocytotoxin variant 2e (VT2e). To correctly identify false negative results, an endogenous internal control targeting the E. coil 16S rRNA gene was incorporated in each test tube. The assay was evaluated using a collection of E. coil...... reference strains which have previously been examined with phenotypical assays or DNA hybridization. Furthermore, the assay was evaluated by testing porcine E. coil field strains, previously characterized. The 5' nuclease assay correctly detected the presence of virulence genes in all reference strains....... When testing field strains there was generally excellent agreement with results obtained by laboratories in Belgium and Germany. In conclusion, the 5' nuclease assay developed is a fast and specific tool for detection of E. coli virulence genes in the veterinary diagnostic laboratory....

  14. Generation of knockout rabbits using transcription activator-like effector nucleases.

    Science.gov (United States)

    Wang, Yu; Fan, Nana; Song, Jun; Zhong, Juan; Guo, Xiaogang; Tian, Weihua; Zhang, Quanjun; Cui, Fenggong; Li, Li; Newsome, Philip N; Frampton, Jon; Esteban, Miguel A; Lai, Liangxue

    2014-01-01

    Zinc-finger nucleases and transcription activator-like effector nucleases are novel gene-editing platforms contributing to redefine the boundaries of modern biological research. They are composed of a non-specific cleavage domain and a tailor made DNA-binding module, which enables a broad range of genetic modifications by inducing efficient DNA double-strand breaks at desired loci. Among other remarkable uses, these nucleases have been employed to produce gene knockouts in mid-size and large animals, such as rabbits and pigs, respectively. This approach is cost effective, relatively quick, and can produce invaluable models for human disease studies, biotechnology or agricultural purposes. Here we describe a protocol for the efficient generation of knockout rabbits using transcription activator-like effector nucleases, and a perspective of the field.

  15. Generation of knockout rabbits using transcription activator-like effector nucleases

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2014-01-01

    Full Text Available Zinc-finger nucleases and transcription activator-like effector nucleases are novel gene-editing platforms contributing to redefine the boundaries of modern biological research. They are composed of a non-specific cleavage domain and a tailor made DNA-binding module, which enables a broad range of genetic modifications by inducing efficient DNA double-strand breaks at desired loci. Among other remarkable uses, these nucleases have been employed to produce gene knockouts in mid-size and large animals, such as rabbits and pigs, respectively. This approach is cost effective, relatively quick, and can produce invaluable models for human disease studies, biotechnology or agricultural purposes. Here we describe a protocol for the efficient generation of knockout rabbits using transcription activator-like effector nucleases, and a perspective of the field.

  16. Genetic correction using engineered nucleases for gene therapy applications.

    Science.gov (United States)

    Li, Hongmei Lisa; Nakano, Takao; Hotta, Akitsu

    2014-01-01

    Genetic mutations in humans are associated with congenital disorders and phenotypic traits. Gene therapy holds the promise to cure such genetic disorders, although it has suffered from several technical limitations for decades. Recent progress in gene editing technology using tailor-made nucleases, such as meganucleases (MNs), zinc finger nucleases (ZFNs), TAL effector nucleases (TALENs) and, more recently, CRISPR/Cas9, has significantly broadened our ability to precisely modify target sites in the human genome. In this review, we summarize recent progress in gene correction approaches of the human genome, with a particular emphasis on the clinical applications of gene therapy. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

  17. Chemical Approach to Biological Safety: Molecular-Level Control of an Integrated Zinc Finger Nuclease

    DEFF Research Database (Denmark)

    Németh, Eszter; Asaka, Masamitsu N; Kato, Kohsuke

    2018-01-01

    circular dichroism spectroscopy, and nano-electrospray ionisation mass spectrometry. In situ intramolecular activation of the nuclease domain was observed, resulting in specific cleavage of DNA with moderate activity. This study represents a new approach to AN design through integrated nucleases consisting......Application of artificial nucleases (ANs) in genome editing is still hindered by their cytotoxicity related to off-target cleavages. This problem can be targeted by regulation of the nuclease domain. Here, we provide an experimental survey of computationally designed integrated zinc finger...... nucleases, constructed by linking the inactivated catalytic centre and the allosteric activator sequence of the colicin E7 nuclease domain to the two opposite termini of a zinc finger array. DNA specificity and metal binding were confirmed by electrophoretic mobility shift assays, synchrotron radiation...

  18. Cell wall-anchored nuclease of Streptococcus sanguinis contributes to escape from neutrophil extracellular trap-mediated bacteriocidal activity.

    Directory of Open Access Journals (Sweden)

    Chisato Morita

    Full Text Available Streptococcus sanguinis, a member of the commensal mitis group of streptococci, is a primary colonizer of the tooth surface, and has been implicated in infectious complications including bacteremia and infective endocarditis. During disease progression, S. sanguinis may utilize various cell surface molecules to evade the host immune system to survive in blood. In the present study, we discovered a novel cell surface nuclease with a cell-wall anchor domain, termed SWAN (streptococcal wall-anchored nuclease, and investigated its contribution to bacterial resistance against the bacteriocidal activity of neutrophil extracellular traps (NETs. Recombinant SWAN protein (rSWAN digested multiple forms of DNA including NET DNA and human RNA, which required both Mg(2+ and Ca(2+ for optimum activity. Furthermore, DNase activity of S. sanguinis was detected around growing colonies on agar plates containing DNA. In-frame deletion of the swan gene mostly reduced that activity. These findings indicated that SWAN is a major nuclease displayed on the surface, which was further confirmed by immuno-detection of SWAN in the cell wall fraction. The sensitivity of S. sanguinis to NET killing was reduced by swan gene deletion. Moreover, heterologous expression of the swan gene rendered a Lactococcus lactis strain more resistant to NET killing. Our results suggest that the SWAN nuclease on the bacterial surface contributes to survival in the potential situation of S. sanguinis encountering NETs during the course of disease progression.

  19. Cell wall-anchored nuclease of Streptococcus sanguinis contributes to escape from neutrophil extracellular trap-mediated bacteriocidal activity.

    Science.gov (United States)

    Morita, Chisato; Sumioka, Ryuichi; Nakata, Masanobu; Okahashi, Nobuo; Wada, Satoshi; Yamashiro, Takashi; Hayashi, Mikako; Hamada, Shigeyuki; Sumitomo, Tomoko; Kawabata, Shigetada

    2014-01-01

    Streptococcus sanguinis, a member of the commensal mitis group of streptococci, is a primary colonizer of the tooth surface, and has been implicated in infectious complications including bacteremia and infective endocarditis. During disease progression, S. sanguinis may utilize various cell surface molecules to evade the host immune system to survive in blood. In the present study, we discovered a novel cell surface nuclease with a cell-wall anchor domain, termed SWAN (streptococcal wall-anchored nuclease), and investigated its contribution to bacterial resistance against the bacteriocidal activity of neutrophil extracellular traps (NETs). Recombinant SWAN protein (rSWAN) digested multiple forms of DNA including NET DNA and human RNA, which required both Mg(2+) and Ca(2+) for optimum activity. Furthermore, DNase activity of S. sanguinis was detected around growing colonies on agar plates containing DNA. In-frame deletion of the swan gene mostly reduced that activity. These findings indicated that SWAN is a major nuclease displayed on the surface, which was further confirmed by immuno-detection of SWAN in the cell wall fraction. The sensitivity of S. sanguinis to NET killing was reduced by swan gene deletion. Moreover, heterologous expression of the swan gene rendered a Lactococcus lactis strain more resistant to NET killing. Our results suggest that the SWAN nuclease on the bacterial surface contributes to survival in the potential situation of S. sanguinis encountering NETs during the course of disease progression.

  20. Probing chromatin structure with nuclease sensitivity assays.

    Science.gov (United States)

    Gregory, R I; Khosla, S; Feil, R

    2001-01-01

    To further our understanding of genomic imprinting it will be essential to identify key control elements, and to investigate their regulation by both epigenetic modifications (such as DNA methylation) and trans-acting factors. So far, sequence elements that regulate parental allele-specific gene expression have been identified in a number of imprinted loci, either because of their differential DNA methylation or through functional studies in transgenic mice (1,2). A systematic search for allele-specific chromatin features constitutes an alternative strategy to identify elements that regulate imprinting. The validity of such an in vivo chromatin approach derives from the fact that in several known imprinting control-elements, a specialized organization of chromatin characterized by nuclease hypersensitivity is present on only one of the two parental chromosome (3). For example, the differentially methylated 5 -portion of the human SNRPN gene-a sequence element that controls imprinting in the Prader-Willi and Angelman syndromes' domain on chromosome 15q11- q13-has strong DNase-I hypersensitive sites on the unmethylated paternal chromosome (4). A differentially methylated region that regulates the imprinting of H19 and that of the neighboring insulin-like growth factor-2 gene on mouse chromosome 7 was also found to have parental chromosome-specific hypersensitive sites (5,6). The precise nature of the allelic nuclease hypersensitivity in these and other imprinted loci remains to be determined in more detail, for example, by applying complementary chromatin methodologies (7,8). However, it is commonly observed that a nuclease hypersensitive site corresponds to a small region where nucleosomes are absent or partially disrupted.

  1. Staphylococcus aureus Nuc2 is a functional, surface-attached extracellular nuclease.

    Directory of Open Access Journals (Sweden)

    Megan R Kiedrowski

    Full Text Available Staphylococcus aureus is a prominent bacterial pathogen that causes a diverse range of acute and chronic infections. Recently, it has been demonstrated that the secreted nuclease (Nuc enzyme is a virulence factor in multiple models of infection, and in vivo expression of nuc has facilitated the development of an infection imaging approach based on Nuc-activatable probes. Interestingly, S. aureus strains encode a second nuclease (Nuc2 that has received limited attention. With the growing interest in bacterial nucleases, we sought to characterize Nuc2 in more detail through localization, expression, and biochemical studies. Fluorescence microscopy and alkaline phosphatase localization approaches using Nuc2-GFP and Nuc2-PhoA fusions, respectively, demonstrated that Nuc2 is membrane bound with the C-terminus facing the extracellular environment, indicating it is a signal-anchored Type II membrane protein. Nuc2 enzyme activity was detectable on the S. aureus cell surface using a fluorescence resonance energy transfer (FRET assay, and in time courses, both nuc2 transcription and enzyme activity peaked in early logarithmic growth and declined in stationary phase. Using a mouse model of S. aureus pyomyositis, Nuc2 activity was detected with activatable probes in vivo in nuc mutant strains, demonstrating that Nuc2 is produced during infections. To assess Nuc2 biochemical properties, the protein was purified and found to cleave both single- and double-stranded DNA, and it exhibited thermostability and calcium dependence, paralleling the properties of Nuc. Purified Nuc2 prevented biofilm formation in vitro and modestly decreased biomass in dispersal experiments. Altogether, our findings confirm that S. aureus encodes a second, surface-attached and functional DNase that is expressed during infections and displays similar biochemical properties to the secreted Nuc enzyme.

  2. Targeted genome editing by lentiviral protein transduction of zinc-finger and TAL-effector nucleases.

    Science.gov (United States)

    Cai, Yujia; Bak, Rasmus O; Mikkelsen, Jacob Giehm

    2014-04-24

    Future therapeutic use of engineered site-directed nucleases, like zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), relies on safe and effective means of delivering nucleases to cells. In this study, we adapt lentiviral vectors as carriers of designer nuclease proteins, providing efficient targeted gene disruption in vector-treated cell lines and primary cells. By co-packaging pairs of ZFN proteins with donor RNA in 'all-in-one' lentiviral particles, we co-deliver ZFN proteins and the donor template for homology-directed repair leading to targeted DNA insertion and gene correction. Comparative studies of ZFN activity in a predetermined target locus and a known nearby off-target locus demonstrate reduced off-target activity after ZFN protein transduction relative to conventional delivery approaches. Additionally, TALEN proteins are added to the repertoire of custom-designed nucleases that can be delivered by protein transduction. Altogether, our findings generate a new platform for genome engineering based on efficient and potentially safer delivery of programmable nucleases.DOI: http://dx.doi.org/10.7554/eLife.01911.001. Copyright © 2014, Cai et al.

  3. Improved somatic mutagenesis in zebrafish using transcription activator-like effector nucleases (TALENs.

    Directory of Open Access Journals (Sweden)

    Finola E Moore

    Full Text Available Zinc Finger Nucleases (ZFNs made by Context-Dependent Assembly (CoDA and Transcription Activator-Like Effector Nucleases (TALENs provide robust and user-friendly technologies for efficiently inactivating genes in zebrafish. These designer nucleases bind to and cleave DNA at particular target sites, inducing error-prone repair that can result in insertion or deletion mutations. Here, we assess the relative efficiencies of these technologies for inducing somatic DNA mutations in mosaic zebrafish. We find that TALENs exhibited a higher success rate for obtaining active nucleases capable of inducing mutations than compared with CoDA ZFNs. For example, all six TALENs tested induced DNA mutations at genomic target sites while only a subset of CoDA ZFNs exhibited detectable rates of mutagenesis. TALENs also exhibited higher mutation rates than CoDA ZFNs that had not been pre-screened using a bacterial two-hybrid assay, with DNA mutation rates ranging from 20%-76.8% compared to 1.1%-3.3%. Furthermore, the broader targeting range of TALENs enabled us to induce mutations at the methionine translation start site, sequences that were not targetable using the CoDA ZFN platform. TALENs exhibited similar toxicity to CoDA ZFNs, with >50% of injected animals surviving to 3 days of life. Taken together, our results suggest that TALEN technology provides a robust alternative to CoDA ZFNs for inducing targeted gene-inactivation in zebrafish, making it a preferred technology for creating targeted knockout mutants in zebrafish.

  4. Aggregation of fragmented chromatin associated with the appearance of products of its nuclease treatment

    International Nuclear Information System (INIS)

    Lobanenkov, V.V.; Mironov, N.M.; Kupriyanova, E.I.; Shapot, V.S.

    1986-01-01

    Isolated cell nuclei were incubated with nucleases, and then the chromatin was extracted with a low-salt buffer. When degradation of the nuclear chromatin DNase I or micrococcal nuclease is intensified, solubilization of the deoxyribonucleoprotein (DNP) in low-salt buffer at first increases, reaching a maximum in the case of hydrolysis of 2-4% of the nuclear DNA, but after intensive treatment with nucleases, it decreases sharply. Soluble fragmented chromatin is aggregated during treatment with DNase I. The addition of exogenous products of nuclease treatment of isolated nuclei to a preparation of gelatinous chromatin induces its aggregation. Pretreatment of nuclear chromatin with RNase prevents the solubilization of DNP by solutions with low ionic strength. Certain experimental data obtained using rigorous nuclease treatment are discussed; for their interpretation it is necessary to consider the effect of aggregation of fragmented chromatin by products of its nuclease degradation

  5. Origins of Programmable Nucleases for Genome Engineering.

    Science.gov (United States)

    Chandrasegaran, Srinivasan; Carroll, Dana

    2016-02-27

    Genome engineering with programmable nucleases depends on cellular responses to a targeted double-strand break (DSB). The first truly targetable reagents were the zinc finger nucleases (ZFNs) showing that arbitrary DNA sequences could be addressed for cleavage by protein engineering, ushering in the breakthrough in genome manipulation. ZFNs resulted from basic research on zinc finger proteins and the FokI restriction enzyme (which revealed a bipartite structure with a separable DNA-binding domain and a non-specific cleavage domain). Studies on the mechanism of cleavage by 3-finger ZFNs established that the preferred substrates were paired binding sites, which doubled the size of the target sequence recognition from 9 to 18bp, long enough to specify a unique genomic locus in plant and mammalian cells. Soon afterwards, a ZFN-induced DSB was shown to stimulate homologous recombination in cells. Transcription activator-like effector nucleases (TALENs) that are based on bacterial TALEs fused to the FokI cleavage domain expanded this capability. The fact that ZFNs and TALENs have been used for genome modification of more than 40 different organisms and cell types attests to the success of protein engineering. The most recent technology platform for delivering a targeted DSB to cellular genomes is that of the RNA-guided nucleases, which are based on the naturally occurring Type II prokaryotic CRISPR-Cas9 system. Unlike ZFNs and TALENs that use protein motifs for DNA sequence recognition, CRISPR-Cas9 depends on RNA-DNA recognition. The advantages of the CRISPR-Cas9 system-the ease of RNA design for new targets and the dependence on a single, constant Cas9 protein-have led to its wide adoption by research laboratories around the world. These technology platforms have equipped scientists with an unprecedented ability to modify cells and organisms almost at will, with wide-ranging implications across biology and medicine. However, these nucleases have also been shown to cut

  6. Solving RNA's structural secrets: interaction with antibodies and crystal structure of a nuclease resistant RNA

    International Nuclear Information System (INIS)

    Wallace, S.T.

    1998-10-01

    This Ph.D. thesis concerns the structural characterization of RNA. The work is split into two sections: 1) in vitro selection and characterization of RNAs which bind antibiotics and 2) crystal structure of a nuclease resistant RNA molecule used in antisense applications. Understanding antibiotic-RNA interactions is crucial in aiding rational drug design. We were interested in studying antibiotic interactions with RNAs small enough to characterize at the molecular and possibly at the atomic level. In order to do so, we previously performed in vitro selection to find small RNAs which bind to the peptide antibiotic viomycin and the aminoglycoside antibiotic streptomycin. The characterization of the viomycin-binding RNAs revealed the necessity of a pseudoknot-structure in order to interact with the antibiotic. The RNAs which were selected to interact with streptomycin require the presence of magnesium to bind the antibiotic. One of the RNAs, upon interacting with streptomycin undergoes a significant conformational change spanning the entire RNA sequence needed to bind the antibiotic. In a quest to design oligodeoxynucleotides (ODNs) which are able to specifically bid and inactivate the mRNA of a gene, it is necessary to fulfill two criteria: 1) increase binding affinity between the ODN and the target RNA and 2) increase the ODN's resistance to nuclease degradation. An ODN with an aminopropyl modification at the 2' position of its ribose has emerged as the most successful candidate at fulfilling both criteria. It is the most nuclease resistant modification known to date. We were interested in explaining how this modification is able to circumvent degradation by nucleases. A dodecamer containing a single 2'-O-aminopropyl modified nucleotide was crystallized and the structure was solved to a resolution of 1.6 A. In an attempt to explain the nuclease resistance, the crystal coordinates were modeled into the active exonuclease site of DNA polymerase I. We propose the

  7. Hybrid nanosensor for colorimetric and ultrasensitive detection of nuclease contaminations

    Science.gov (United States)

    Cecere, Paola; Valentini, Paola; Pompa, Pier Paolo

    2016-04-01

    Nucleases are ubiquitous enzymes that degrade DNA or RNA, thus they can prejudice the good outcome of molecular biology experiments involving nucleic acids. We propose a colorimetric test for the naked-eye detection of nuclease contaminations. The system uses an hybrid nanosensor, based on gold nanoparticles functionalized with DNA probes. Our assay is rapid, instrument-free, simple and low-cost. Moreover, it reaches sensitivity equal or better than those of commercial kits, and presents a lot of advantageous aspects. Therefore, it is very competitive, with a real market potential. This test will be relevant in routine process monitoring in scientific laboratories, and in quality control in clinical laboratories and industrial processes, allowing the simultaneous detection of nucleases with different substrate specificities and large-scale screening.

  8. TT2014 meeting report on the 12th Transgenic Technology meeting in Edinburgh: new era of transgenic technologies with programmable nucleases in the foreground

    Czech Academy of Sciences Publication Activity Database

    Beck, Inken; Sedláček, Radislav

    2015-01-01

    Roč. 24, č. 1 (2015), s. 179-183 ISSN 0962-8819 Institutional support: RVO:68378050 Keywords : Transgenic * Nuclease * Gene Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.054, year: 2015

  9. Analysis of pyrimidine dimer content of isolated DNA by nuclease digestion

    International Nuclear Information System (INIS)

    Farland, W.H.; Sutherland, B.M.

    1980-01-01

    Isolated DNA is highly susceptible to degradation by exogenous nucleases. Complete digestion is possible with a number of well-characterized enzymes from a variety of sources. Treatment of DNA with a battery of enzymes including both phosphodiesterase and phosphatase activities yields a mixture of nucleosides and inorganic phosphate (P/sub i/) as a final product. Unlike native DNA, ultraviolet-irradiated DNA is resistant to complete digestion. Setlow et al. demonstrated that the structural changes in the DNA responsible for the nuclease resistance were the formation of cyclobutyl pyrimidine dimers, the major photoproduct in UV-irradiated DNA. Using venom phosphodiesterase, they demonstrated that UV irradiation of DNA affected both the rate and extent of enzymatic hydrolysis. In addition, it was demonstrated that the major nuclease-resistant product of this hydrolysis was an oligonucleotide containing dimerized pyrimidines. Treatment of the DNA to split the dimers, either photochemically or photoenzymatically, rendered the polymer more susceptible to hydrolysis by the phosphodiesterase. The specificity of photoreactivating enzyme for pyrimidine dimers lends support to the role of these structures in conferring nuclease resistance to UV-irradiated DNA. The nuclease resistance of DNA containing dimers has been the basis of several assays for the measurement of these photoproducts. Sutherland and Chamberlin reported the development of a rapid and sensitive assay for dimers in 32 P-labeled DNA

  10. Investigation of a redox-sensitive predictive model of mouse embryonic stem cells differentiation using quantitative nuclease protection assays and glutathione redox status

    Science.gov (United States)

    Investigation of a redox-sensitive predictive model of mouse embryonic stem cell differentiation via quantitative nuclease protection assays and glutathione redox status Chandler KJ,Hansen JM, Knudsen T,and Hunter ES 1. U.S. Environmental Protection Agency, Research Triangl...

  11. Recognition and repair of the CC-1065-(N3-Adenine)-DNA adduct by the UVRABC nuclease

    International Nuclear Information System (INIS)

    Tang, M.; Lee, C.S.; Doisy, R.; Ross, L.; Needham-VanDevanter, D.R.; Hurley, L.H.

    1988-01-01

    The recognition and repair of the helix-stabilizing and relatively nondistortive CC-1065-(N3-adenine)-DNA adduct by UVRABC nuclease has been investigated both in vivo with phi X174RFI DNA by a transfection assay and in vitro by a site-directed adduct in a 117 base pair fragment from M13mp1. CC-1065 is a potent antitumor antibiotic produced by Streptomyces zelensis which binds within the minor groove of DNA through N3 of adenine. In contrast to the helix-destabilizing and distortive modifications of DNA caused by ultraviolet light or N-acetoxy-2-(acetylamino)fluorene, CC-1065 increases the melting point of DNA and decreases the S1 nuclease activity. Using a viral DNA-Escherichia coli transfection system, the authors have found that the uvrA, uvrB, and uvrC genes, which code for the major excision repair proteins for UV- and NAAAF-induced DNA damage, are also involved in the repair of CC-1065-DNA adducts. In contrast, the uvrD gene product, which has been found to be involved in the repair of UV damage, has no effect in repairing CC-1065-DNA adducts. Purified UVRA, UVRB, and UVRC proteins must work in concert to incise the drug-modified phi X174RFI DNA. Using a site-directed and multiple CC-1065 modified (MspI-BstNI) 117 base pair fragment from M13mp1, they have found that UVRABC nuclease incises at the eight phosphodiester bond on the 5' side of the CC-1065-DNA adduct on the drug-modified strand. The enzymes do not cut the noncovalently modified strand. The DNA sequence and/or helix-stabilizing effect of multiple adducts may determine the recognition and/or incision of the drug-DNA adduct by UVRABC nuclease. These results are discussed in relation to the structure of the CC-1065-DNA adduct and the effect of drug binding on local DNA structure

  12. Nucleases from Prevotella intermedia can degrade neutrophil extracellular traps.

    Science.gov (United States)

    Doke, M; Fukamachi, H; Morisaki, H; Arimoto, T; Kataoka, H; Kuwata, H

    2017-08-01

    Periodontitis is an inflammatory disease caused by periodontal bacteria in subgingival plaque. These bacteria are able to colonize the periodontal region by evading the host immune response. Neutrophils, the host's first line of defense against infection, use various strategies to kill invading pathogens, including neutrophil extracellular traps (NETs). These are extracellular net-like fibers comprising DNA and antimicrobial components such as histones, LL-37, defensins, myeloperoxidase, and neutrophil elastase from neutrophils that disarm and kill bacteria extracellularly. Bacterial nuclease degrades the NETs to escape NET killing. It has now been shown that extracellular nucleases enable bacteria to evade this host antimicrobial mechanism, leading to increased pathogenicity. Here, we compared the DNA degradation activity of major Gram-negative periodontopathogenic bacteria, Porphyromonas gingivalis, Prevotella intermedia, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. We found that Pr. intermedia showed the highest DNA degradation activity. A genome search of Pr. intermedia revealed the presence of two genes, nucA and nucD, putatively encoding secreted nucleases, although their enzymatic and biological activities are unknown. We cloned nucA- and nucD-encoding nucleases from Pr. intermedia ATCC 25611 and characterized their gene products. Recombinant NucA and NucD digested DNA and RNA, which required both Mg 2+ and Ca 2+ for optimal activity. In addition, NucA and NucD were able to degrade the DNA matrix comprising NETs. © 2016 The Authors Molecular Oral Microbiology Published by John Wiley & Sons Ltd.

  13. Erasure of Tet-Oxidized 5-Methylcytosine by a SRAP Nuclease

    Directory of Open Access Journals (Sweden)

    Soo-Mi Kweon

    2017-10-01

    Full Text Available Enzymatic oxidation of 5-methylcytosine (5mC in DNA by the Tet dioxygenases reprograms genome function in embryogenesis and postnatal development. Tet-oxidized derivatives of 5mC such as 5-hydroxymethylcytosine (5hmC act as transient intermediates in DNA demethylation or persist as durable marks, yet how these alternative fates are specified at individual CpGs is not understood. Here, we report that the SOS response-associated peptidase (SRAP domain protein Srap1, the mammalian ortholog of an ancient protein superfamily associated with DNA damage response operons in bacteria, binds to Tet-oxidized forms of 5mC in DNA and catalyzes turnover of these bases to unmodified cytosine by an autopeptidase-coupled nuclease. Biallelic inactivation of murine Srap1 causes embryonic sublethality associated with widespread accumulation of ectopic 5hmC. These findings establish a function for a class of DNA base modification-selective nucleases and position Srap1 as a determinant of 5mC demethylation trajectories during mammalian embryonic development.

  14. Rapid and Sensitive Detection of Breast Cancer Cells in Patient Blood with Nuclease-Activated Probe Technology

    Directory of Open Access Journals (Sweden)

    Sven Kruspe

    2017-09-01

    Full Text Available A challenge for circulating tumor cell (CTC-based diagnostics is the development of simple and inexpensive methods that reliably detect the diverse cells that make up CTCs. CTC-derived nucleases are one category of proteins that could be exploited to meet this challenge. Advantages of nucleases as CTC biomarkers include: (1 their elevated expression in many cancer cells, including cells implicated in metastasis that have undergone epithelial-to-mesenchymal transition; and (2 their enzymatic activity, which can be exploited for signal amplification in detection methods. Here, we describe a diagnostic assay based on quenched fluorescent nucleic acid probes that detect breast cancer CTCs via their nuclease activity. This assay exhibited robust performance in distinguishing breast cancer patients from healthy controls, and it is rapid, inexpensive, and easy to implement in most clinical labs. Given its broad applicability, this technology has the potential to have a substantive impact on the diagnosis and treatment of many cancers. Keywords: cancer, circulating tumor cells, diagnostic nucleic acids, nucleases, diagnostic markers, breast cancer, liquid biopsy

  15. Repair of DNA-polypeptide crosslinks by human excision nuclease

    Science.gov (United States)

    Reardon, Joyce T.; Sancar, Aziz

    2006-03-01

    DNA-protein crosslinks are relatively common DNA lesions that form during the physiological processing of DNA by replication and recombination proteins, by side reactions of base excision repair enzymes, and by cellular exposure to bifunctional DNA-damaging agents such as platinum compounds. The mechanism by which pathological DNA-protein crosslinks are repaired in humans is not known. In this study, we investigated the mechanism of recognition and repair of protein-DNA and oligopeptide-DNA crosslinks by the human excision nuclease. Under our assay conditions, the human nucleotide excision repair system did not remove a 16-kDa protein crosslinked to DNA at a detectable level. However, 4- and 12-aa-long oligopeptides crosslinked to the DNA backbone were recognized by some of the damage recognition factors of the human excision nuclease with moderate selectivity and were excised from DNA at relatively efficient rates. Our data suggest that, if coupled with proteolytic degradation of the crosslinked protein, the human excision nuclease may be the major enzyme system for eliminating protein-DNA crosslinks from the genome. damage recognition | nucleotide excision repair

  16. The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once.

    Science.gov (United States)

    Tsutakawa, Susan E; Lafrance-Vanasse, Julien; Tainer, John A

    2014-07-01

    To avoid genome instability, DNA repair nucleases must precisely target the correct damaged substrate before they are licensed to incise. Damage identification is a challenge for all DNA damage response proteins, but especially for nucleases that cut the DNA and necessarily create a cleaved DNA repair intermediate, likely more toxic than the initial damage. How do these enzymes achieve exquisite specificity without specific sequence recognition or, in some cases, without a non-canonical DNA nucleotide? Combined structural, biochemical, and biological analyses of repair nucleases are revealing their molecular tools for damage verification and safeguarding against inadvertent incision. Surprisingly, these enzymes also often act on RNA, which deserves more attention. Here, we review protein-DNA structures for nucleases involved in replication, base excision repair, mismatch repair, double strand break repair (DSBR), and telomere maintenance: apurinic/apyrimidinic endonuclease 1 (APE1), Endonuclease IV (Nfo), tyrosyl DNA phosphodiesterase (TDP2), UV Damage endonuclease (UVDE), very short patch repair endonuclease (Vsr), Endonuclease V (Nfi), Flap endonuclease 1 (FEN1), exonuclease 1 (Exo1), RNase T and Meiotic recombination 11 (Mre11). DNA and RNA structure-sensing nucleases are essential to life with roles in DNA replication, repair, and transcription. Increasingly these enzymes are employed as advanced tools for synthetic biology and as targets for cancer prognosis and interventions. Currently their structural biology is most fully illuminated for DNA repair, which is also essential to life. How DNA repair enzymes maintain genome fidelity is one of the DNA double helix secrets missed by James Watson and Francis Crick, that is only now being illuminated though structural biology and mutational analyses. Structures reveal motifs for repair nucleases and mechanisms whereby these enzymes follow the old carpenter adage: measure twice, cut once. Furthermore, to measure

  17. Caffeine impairs resection during DNA break repair by reducing the levels of nucleases Sae2 and Dna2

    Science.gov (United States)

    Tsabar, Michael; Eapen, Vinay V.; Mason, Jennifer M.; Memisoglu, Gonen; Waterman, David P.; Long, Marcus J.; Bishop, Douglas K.; Haber, James E.

    2015-01-01

    In response to chromosomal double-strand breaks (DSBs), eukaryotic cells activate the DNA damage checkpoint, which is orchestrated by the PI3 kinase-like protein kinases ATR and ATM (Mec1 and Tel1 in budding yeast). Following DSB formation, Mec1 and Tel1 phosphorylate histone H2A on serine 129 (known as γ-H2AX). We used caffeine to inhibit the checkpoint kinases after DSB induction. We show that prolonged phosphorylation of H2A-S129 does not require continuous Mec1 and Tel1 activity. Unexpectedly, caffeine treatment impaired homologous recombination by inhibiting 5′ to 3′ end resection, independent of Mec1 and Tel1 inhibition. Caffeine treatment led to the rapid loss, by proteasomal degradation, of both Sae2, a nuclease that plays a role in early steps of resection, and Dna2, a nuclease that facilitates one of two extensive resection pathways. Sae2's instability is evident in the absence of DNA damage. A similar loss is seen when protein synthesis is inhibited by cycloheximide. Caffeine treatment had similar effects on irradiated HeLa cells, blocking the formation of RPA and Rad51 foci that depend on 5′ to 3′ resection of broken chromosome ends. Our findings provide insight toward the use of caffeine as a DNA damage-sensitizing agent in cancer cells. PMID:26019182

  18. Efficient Genome Editing in Induced Pluripotent Stem Cells with Engineered Nucleases In Vitro.

    Science.gov (United States)

    Termglinchan, Vittavat; Seeger, Timon; Chen, Caressa; Wu, Joseph C; Karakikes, Ioannis

    2017-01-01

    Precision genome engineering is rapidly advancing the application of the induced pluripotent stem cells (iPSCs) technology for in vitro disease modeling of cardiovascular diseases. Targeted genome editing using engineered nucleases is a powerful tool that allows for reverse genetics, genome engineering, and targeted transgene integration experiments to be performed in a precise and predictable manner. However, nuclease-mediated homologous recombination is an inefficient process. Herein, we describe the development of an optimized method combining site-specific nucleases and the piggyBac transposon system for "seamless" genome editing in pluripotent stem cells with high efficiency and fidelity in vitro.

  19. A novel mitochondrial nuclease-associated protein: a major executor of the programmed nuclear death in Tetrahymena thermophila.

    Science.gov (United States)

    Osada, Eriko; Akematsu, Takahiko; Asano, Tomoya; Endoh, Hiroshi

    2014-03-01

    Programmed nuclear death (PND) in the ciliate Tetrahymena is an apoptosis-like phenomenon that occurs in a restricted space of cytoplasm during conjugation. In the process, only the parental macronucleus is selectively eliminated from the progeny cytoplasm, in conjunction with differentiation of new macronuclei for the next generation. For the last decade, mitochondria have been elucidated to be a crucial executioner like apoptosis: apoptosis-inducing factor and yet-unidentified nucleases localised in mitochondria are major factors for PND. To identify such nucleases, we performed a DNase assay in a PAGE (SDS-DNA-PAGE) using total mitochondrial proteins. Some proteins showed DNase activity, but particularly a 17 kDa protein exhibited the highest and predominant activity. Mass spectrometric analysis revealed a novel mitochondrial nuclease, named TMN1, whose homologue has been discovered only in the ciliate Paramecium tetraurelia, but not in other eukaryotes. Gene disruption of TMN1 led to a drastic reduction of mitochondrial nuclease activity and blocked nuclear degradation during conjugation, but did not affect accumulation of autophagic and lysosomal machinery around the parental macronucleus. These observations strongly suggest that the mitochondrial nuclease-associated protein plays a key role in PND as a major executor. Taking the novel protein specific to ciliates in consideration, Tetrahymena would have diverted a different protein from common apoptotic factors shared in eukaryotes to PND in the course of ciliate evolution. © 2014 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

  20. Comprehensive analysis of the specificity of transcription activator-like effector nucleases

    DEFF Research Database (Denmark)

    Juillerat, Alexandre; Dubois, Gwendoline; Valton, Julien

    2014-01-01

    A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within...... their target site. The ability to predict the specificity of targeting is thus highly desirable. Here, we describe the first comprehensive experimental study focused on the specificity of the four commonly used repeat variable diresidues (RVDs; NI:A, HD:C, NN:G and NG:T) incorporated in transcription activator......-like effector nucleases (TALEN). The analysis of >15 500 unique TALEN/DNA cleavage profiles allowed us to monitor the specificity gradient of the RVDs along a TALEN/DNA binding array and to present a specificity scoring matrix for RVD/nucleotide association. Furthermore, we report that TALEN can only...

  1. Paired D10A Cas9 nickases are sometimes more efficient than individual nucleases for gene disruption.

    Science.gov (United States)

    Gopalappa, Ramu; Suresh, Bharathi; Ramakrishna, Suresh; Kim, Hyongbum Henry

    2018-03-23

    The use of paired Cas9 nickases instead of Cas9 nuclease drastically reduces off-target effects. Because both nickases must function for a nickase pair to make a double-strand break, the efficiency of paired nickases can intuitively be expected to be lower than that of either corresponding nuclease alone. Here, we carefully compared the gene-disrupting efficiency of Cas9 paired nickases with that of nucleases. Interestingly, the T7E1 assay and deep sequencing showed that on-target efficiency of paired D10A Cas9 nickases was frequently comparable, but sometimes higher than that of either corresponding nucleases in mammalian cells. As the underlying mechanism, we found that the HNH domain, which is preserved in the D10A Cas9 nickase, has higher activity than the RuvC domain in mammalian cells. In this study, we showed: (i) the in vivo cleavage efficiency of the HNH domain of Cas9 in mammalian cells is higher than that of the RuvC domain, (ii) paired Cas9 nickases are sometimes more efficient than individual nucleases for gene disruption. We envision that our findings which were overlooked in previous reports will serve as a new potential guideline for tool selection for CRISPR-Cas9-mediated gene disruption, facilitating efficient and precise genome editing.

  2. Engineering nucleases for gene targeting: safety and regulatory considerations.

    Science.gov (United States)

    Pauwels, Katia; Podevin, Nancy; Breyer, Didier; Carroll, Dana; Herman, Philippe

    2014-01-25

    Nuclease-based gene targeting (NBGT) represents a significant breakthrough in targeted genome editing since it is applicable from single-celled protozoa to human, including several species of economic importance. Along with the fast progress in NBGT and the increasing availability of customized nucleases, more data are available about off-target effects associated with the use of this approach. We discuss how NBGT may offer a new perspective for genetic modification, we address some aspects crucial for a safety improvement of the corresponding techniques and we also briefly relate the use of NBGT applications and products to the regulatory oversight. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. A metal-free DNA nuclease based on a cyclic peptide scaffold

    Czech Academy of Sciences Publication Activity Database

    Alkhader, S.; Ezra, A.; Kašpárková, Jana; Brabec, Viktor; Yavin, E.

    2010-01-01

    Roč. 21, č. 8 (2010), s. 1425-1431 ISSN 1043-1802 R&D Projects: GA AV ČR(CZ) IAA400040803; GA MŠk(CZ) LC06030; GA MŠk(CZ) ME08017; GA MŠk(CZ) OC08003; GA AV ČR(CZ) KAN200200651 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA * cleavage * chemical nuclease Subject RIV: BO - Biophysics Impact factor: 5.002, year: 2010

  4. Modular Nuclease-Responsive DNA Three-Way Junction-Based Dynamic Assembly of a DNA Device and Its Sensing Application.

    Science.gov (United States)

    Zhu, Jing; Wang, Lei; Xu, Xiaowen; Wei, Haiping; Jiang, Wei

    2016-04-05

    Here, we explored a modular strategy for rational design of nuclease-responsive three-way junctions (TWJs) and fabricated a dynamic DNA device in a "plug-and-play" fashion. First, inactivated TWJs were designed, which contained three functional domains: the inaccessible toehold and branch migration domains, the specific sites of nucleases, and the auxiliary complementary sequence. The actions of different nucleases on their specific sites in TWJs caused the close proximity of the same toehold and branch migration domains, resulting in the activation of the TWJs and the formation of a universal trigger for the subsequent dynamic assembly. Second, two hairpins (H1 and H2) were introduced, which could coexist in a metastable state, initially to act as the components for the dynamic assembly. Once the trigger initiated the opening of H1 via TWJs-driven strand displacement, the cascade hybridization of hairpins immediately switched on, resulting in the formation of the concatemers of H1/H2 complex appending numerous integrated G-quadruplexes, which were used to obtain label-free signal readout. The inherent modularity of this design allowed us to fabricate a flexible DNA dynamic device and detect multiple nucleases through altering the recognition pattern slightly. Taking uracil-DNA glycosylase and CpG methyltransferase M.SssI as models, we successfully realized the butt joint between the uracil-DNA glycosylase and M.SssI recognition events and the dynamic assembly process. Furthermore, we achieved ultrasensitive assay of nuclease activity and the inhibitor screening. The DNA device proposed here will offer an adaptive and flexible tool for clinical diagnosis and anticancer drug discovery.

  5. Improving Fab' fragment retention in an autonucleolytic Escherichia coli strain by swapping periplasmic nuclease translocation signal from OmpA to DsbA.

    Science.gov (United States)

    Schofield, Desmond M; Sirka, Ernestas; Keshavarz-Moore, Eli; Ward, John M; Nesbeth, Darren N

    2017-12-01

    To reduce unwanted Fab' leakage from an autonucleolytic Escherichia coli strain, which co-expresses OmpA-signalled Staphylococcal nuclease and Fab' fragment in the periplasm, by substituting in Serratial nuclease and the DsbA periplasm translocation signal as alternatives. We attempted to genetically fuse a nuclease from Serratia marcescens to the OmpA signal peptide but plasmid construction failed, possibly due to toxicity of the resultant nuclease. Combining Serratial nuclease to the DsbA signal peptide was successful. The strain co-expressing this nuclease and periplasmic Fab' grew in complex media and exhibited nuclease activity detectable by DNAse agar plate but its growth in defined medium was retarded. Fab' coexpression with Staphylococcal nuclease fused to the DsbA signal peptide resulted in cells exhibiting nuclease activity and growth in defined medium. In cultivation to high cell density in a 5 l bioreactor, DsbA-fused Staphylococcal nuclease co-expression coincided with reduced Fab' leakage relative to the original autonucleolytic Fab' strain with OmpA-fused staphylococcal nuclease. We successfully rescued Fab' leakage back to acceptable levels and established a basis for future investigation of the linkage between periplasmic nuclease expression and leakage of co-expressed periplasmic Fab' fragment to the surrounding growth media.

  6. Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.

    Science.gov (United States)

    Zhou, Chun; Pourmal, Sergei; Pavletich, Nikola P

    2015-11-02

    The Dna2 nuclease-helicase maintains genomic integrity by processing DNA double-strand breaks, Okazaki fragments and stalled replication forks. Dna2 requires ssDNA ends, and is dependent on the ssDNA-binding protein Rpa, which controls cleavage polarity. Here we present the 2.3 Å structure of intact mouse Dna2 bound to a 15-nucleotide ssDNA. The nuclease active site is embedded in a long, narrow tunnel through which the DNA has to thread. The helicase domain is required for DNA binding but not threading. We also present the structure of a flexibly-tethered Dna2-Rpa interaction that recruits Dna2 to Rpa-coated DNA. We establish that a second Dna2-Rpa interaction is mutually exclusive with Rpa-DNA interactions and mediates the displacement of Rpa from ssDNA. This interaction occurs at the nuclease tunnel entrance and the 5' end of the Rpa-DNA complex. Hence, it only displaces Rpa from the 5' but not 3' end, explaining how Rpa regulates cleavage polarity.

  7. QoS mapping algorithm for ETE QoS provisioning

    Science.gov (United States)

    Wu, Jian J.; Foster, Gerry

    2002-08-01

    End-to-End (ETE) Quality of Service (QoS) is critical for next generation wireless multimedia communication systems. To meet the ETE QoS requirements, Universal Mobile Telecommunication System (UMTS) requires not only meeting the 3GPP QoS requirements [1-2] but also mapping external network QoS classes to UMTS QoS classes. There are four Quality of Services (QoS) classes in UMTS; they are Conversational, Streaming, Interactive and Background. There are eight QoS classes for LAN in IEEE 802.1 (one reserved). ATM has four QoS categories. They are Constant Bit Rate (CBR) - highest priority, short queue for strict Cell Delay Variation (CDV), Variable Bit Rate (VBR) - second highest priority, short queues for real time, longer queues for non-real time, Guaranteed Frame Rate (GFR)/ Unspecified Bit Rate (UBR) with Minimum Desired Cell Rate (MDCR) - intermediate priority, dependent on service provider UBR/ Available Bit Rate (ABR) - lowest priority, long queues, large delay variation. DiffServ (DS) has six-bit DS codepoint (DSCP) available to determine the datagram's priority relative to other datagrams and therefore, up to 64 QoS classes are available from the IPv4 and IPv6 DSCP. Different organisations have tried to solve the QoS issues from their own perspective. However, none of them has a full picture for end-to-end QoS classes and how to map them among all QoS classes. Therefore, a universal QoS needs to be created and a new set of QoS classes to enable end-to-end (ETE) QoS provisioning is required. In this paper, a new set of ETE QoS classes is proposed and a mappings algorithm for different QoS classes that are proposed by different organisations is given. With our proposal, ETE QoS mapping and control can be implemented.

  8. Activity-associated miRNA are packaged in Map1b-enriched exosomes released from depolarized neurons.

    Science.gov (United States)

    Goldie, Belinda J; Dun, Matthew D; Lin, Minjie; Smith, Nathan D; Verrills, Nicole M; Dayas, Christopher V; Cairns, Murray J

    2014-08-01

    Rapid input-restricted change in gene expression is an important aspect of synaptic plasticity requiring complex mechanisms of post-transcriptional mRNA trafficking and regulation. Small non-coding miRNA are uniquely poised to support these functions by providing a nucleic-acid-based specificity component for universal-sequence-dependent RNA binding complexes. We investigated the subcellular distribution of these molecules in resting and potassium chloride depolarized human neuroblasts, and found both selective enrichment and depletion in neurites. Depolarization was associated with a neurite-restricted decrease in miRNA expression; a subset of these molecules was recovered from the depolarization medium in nuclease resistant extracellular exosomes. These vesicles were enriched with primate specific miRNA and the synaptic-plasticity-associated protein MAP1b. These findings further support a role for miRNA as neural plasticity regulators, as they are compartmentalized in neurons and undergo activity-associated redistribution or release into the extracellular matrix. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Phylogenomic analysis of the GIY-YIG nuclease superfamily

    Directory of Open Access Journals (Sweden)

    Bujnicki Janusz M

    2006-04-01

    Full Text Available Abstract Background The GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons and in enzymes involved in DNA repair and recombination. However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported. Results We carried out database searches to identify all members of known GIY-YIG nuclease families. Multiple sequence alignments together with predicted secondary structures of identified families were represented as Hidden Markov Models (HMM and compared by the HHsearch method to the uncharacterized protein families gathered in the COG, KOG, and PFAM databases. This analysis allowed for extending the GIY-YIG superfamily to include members of COG3680 and a number of proteins not classified in COGs and to predict that these proteins may function as nucleases, potentially involved in DNA recombination and/or repair. Finally, all old and new members of the GIY-YIG superfamily were compared and analyzed to infer the phylogenetic tree. Conclusion An evolutionary classification of the GIY-YIG superfamily is presented for the very first time, along with the structural annotation of all (subfamilies. It provides a comprehensive picture of sequence-structure-function relationships in this superfamily of nucleases, which will help to design experiments to study the mechanism of action of known members (especially the uncharacterized ones and will facilitate the prediction of function for the newly discovered ones.

  10. Efficient gene targeting by homology-directed repair in rat zygotes using TALE nucleases.

    Science.gov (United States)

    Remy, Séverine; Tesson, Laurent; Menoret, Séverine; Usal, Claire; De Cian, Anne; Thepenier, Virginie; Thinard, Reynald; Baron, Daniel; Charpentier, Marine; Renaud, Jean-Baptiste; Buelow, Roland; Cost, Gregory J; Giovannangeli, Carine; Fraichard, Alexandre; Concordet, Jean-Paul; Anegon, Ignacio

    2014-08-01

    The generation of genetically modified animals is important for both research and commercial purposes. The rat is an important model organism that until recently lacked efficient genetic engineering tools. Sequence-specific nucleases, such as ZFNs, TALE nucleases, and CRISPR/Cas9 have allowed the creation of rat knockout models. Genetic engineering by homology-directed repair (HDR) is utilized to create animals expressing transgenes in a controlled way and to introduce precise genetic modifications. We applied TALE nucleases and donor DNA microinjection into zygotes to generate HDR-modified rats with large new sequences introduced into three different loci with high efficiency (0.62%-5.13% of microinjected zygotes). Two of these loci (Rosa26 and Hprt1) are known to allow robust and reproducible transgene expression and were targeted for integration of a GFP expression cassette driven by the CAG promoter. GFP-expressing embryos and four Rosa26 GFP rat lines analyzed showed strong and widespread GFP expression in most cells of all analyzed tissues. The third targeted locus was Ighm, where we performed successful exon exchange of rat exon 2 for the human one. At all three loci we observed HDR only when using linear and not circular donor DNA. Mild hypothermic (30°C) culture of zygotes after microinjection increased HDR efficiency for some loci. Our study demonstrates that TALE nuclease and donor DNA microinjection into rat zygotes results in efficient and reproducible targeted donor integration by HDR. This allowed creation of genetically modified rats in a work-, cost-, and time-effective manner. © 2014 Remy et al.; Published by Cold Spring Harbor Laboratory Press.

  11. Synthesis, characterisation, nuclease and cytotoxic activity of ...

    Indian Academy of Sciences (India)

    GULZAR A BHAT

    2018-02-07

    Feb 7, 2018 ... 2 were evaluated for their nuclease and in vitro anti-tumor activities against human breast and colorectal cancer cell lines. The DNA ... tive chemotherapeutic agent for the treatment of ovarian, lung, testicular, colon, and neck ... coma, leukemia, Hodgkin's lymphoma, brain tumours and cancer of the cervix, ...

  12. Activity of some nucleases of cotton sorts and species of various radiosensitivity

    International Nuclear Information System (INIS)

    Nazirov, N.N.; Arslanova, S.B.

    1979-01-01

    The activity of some nucleases under the effect of gamma rays was studied on cotton varieties and species differing in radiosensitivity. It was found that acid nuclease was more active in wild cotton forms as compared to the cultivated varieties, whereas with alkaline DNA-ase it was opposite. At the radiation dose of 30 kR the activity of alkaline DNA-ase activated in 26-chromosome wild cotton G. arboreum ssp. alfusifalium and 52-chromosome S.h.ssp.mexicanum, while the activity of acid DNA-ase somewhat decreased. Under irradiating AN-402 variety (produced from ssp. mexicanum by irradiation) the activity of alkaline DNA-ase increased noticeably when budding, whereas the activity of acid DNA-ase was at the level of control. The activity of the alkaline DNA-ase form normalized in the phase of blooming. In C-70-59 variety (G.arboreum) the activity of both DNA-ases increased after irradiation in the phase of blooming. The activity of acid DNA-ase and RNA-ase drastically activated in guza 183 (G. herbaceum) under gamma irradiation, whereas that of alkaline ones remained unchanged

  13. De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks

    KAUST Repository

    Mahfouz, Magdy M.

    2011-01-24

    Site-specific and rare cutting nucleases are valuable tools for genome engineering. The generation of double-strand DNA breaks (DSBs) promotes homologous recombination in eukaryotes and can facilitate gene targeting, additions, deletions, and inactivation. Zinc finger nucleases have been used to generate DSBs and subsequently, for genome editing but with low efficiency and reproducibility. The transcription activator-like family of type III effectors (TALEs) contains a central domain of tandem repeats that could be engineered to bind specific DNA targets. Here, we report the generation of a Hax3-based hybrid TALE nuclease with a user-selected DNA binding specificity. We show that the engineered TALE nuclease can bind to its target sequence in vitro and that the homodimeric TALE nuclease can cleave double-stranded DNA in vitro if the DNA binding sites have the proper spacing and orientation. Transient expression assays in tobacco leaves suggest that the hybrid nuclease creates DSB in its target sequence, which is subsequently repaired by nonhomologous end-joining repair. Taken together, our data show the feasibility of engineering TALE-based hybrid nucleases capable of generating site-specific DSBs and the great potential for site-specific genome modification in plants and eukaryotes in general.

  14. Nuclease Target Site Selection for Maximizing On-target Activity and Minimizing Off-target Effects in Genome Editing

    Science.gov (United States)

    Lee, Ciaran M; Cradick, Thomas J; Fine, Eli J; Bao, Gang

    2016-01-01

    The rapid advancement in targeted genome editing using engineered nucleases such as ZFNs, TALENs, and CRISPR/Cas9 systems has resulted in a suite of powerful methods that allows researchers to target any genomic locus of interest. A complementary set of design tools has been developed to aid researchers with nuclease design, target site selection, and experimental validation. Here, we review the various tools available for target selection in designing engineered nucleases, and for quantifying nuclease activity and specificity, including web-based search tools and experimental methods. We also elucidate challenges in target selection, especially in predicting off-target effects, and discuss future directions in precision genome editing and its applications. PMID:26750397

  15. Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes.

    Science.gov (United States)

    Zhao, Junhua; Wang, Guliang; Del Mundo, Imee M; McKinney, Jennifer A; Lu, Xiuli; Bacolla, Albino; Boulware, Stephen B; Zhang, Changsheng; Zhang, Haihua; Ren, Pengyu; Freudenreich, Catherine H; Vasquez, Karen M

    2018-01-30

    Sequences with the capacity to adopt alternative DNA structures have been implicated in cancer etiology; however, the mechanisms are unclear. For example, H-DNA-forming sequences within oncogenes have been shown to stimulate genetic instability in mammals. Here, we report that H-DNA-forming sequences are enriched at translocation breakpoints in human cancer genomes, further implicating them in cancer etiology. H-DNA-induced mutations were suppressed in human cells deficient in the nucleotide excision repair nucleases, ERCC1-XPF and XPG, but were stimulated in cells deficient in FEN1, a replication-related endonuclease. Further, we found that these nucleases cleaved H-DNA conformations, and the interactions of modeled H-DNA with ERCC1-XPF, XPG, and FEN1 proteins were explored at the sub-molecular level. The results suggest mechanisms of genetic instability triggered by H-DNA through distinct structure-specific, cleavage-based replication-independent and replication-dependent pathways, providing critical evidence for a role of the DNA structure itself in the etiology of cancer and other human diseases. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Isolating DNA from sexual assault cases: a comparison of standard methods with a nuclease-based approach

    Science.gov (United States)

    2012-01-01

    Background Profiling sperm DNA present on vaginal swabs taken from rape victims often contributes to identifying and incarcerating rapists. Large amounts of the victim’s epithelial cells contaminate the sperm present on swabs, however, and complicate this process. The standard method for obtaining relatively pure sperm DNA from a vaginal swab is to digest the epithelial cells with Proteinase K in order to solubilize the victim’s DNA, and to then physically separate the soluble DNA from the intact sperm by pelleting the sperm, removing the victim’s fraction, and repeatedly washing the sperm pellet. An alternative approach that does not require washing steps is to digest with Proteinase K, pellet the sperm, remove the victim’s fraction, and then digest the residual victim’s DNA with a nuclease. Methods The nuclease approach has been commercialized in a product, the Erase Sperm Isolation Kit (PTC Labs, Columbia, MO, USA), and five crime laboratories have tested it on semen-spiked female buccal swabs in a direct comparison with their standard methods. Comparisons have also been performed on timed post-coital vaginal swabs and evidence collected from sexual assault cases. Results For the semen-spiked buccal swabs, Erase outperformed the standard methods in all five laboratories and in most cases was able to provide a clean male profile from buccal swabs spiked with only 1,500 sperm. The vaginal swabs taken after consensual sex and the evidence collected from rape victims showed a similar pattern of Erase providing superior profiles. Conclusions In all samples tested, STR profiles of the male DNA fractions obtained with Erase were as good as or better than those obtained using the standard methods. PMID:23211019

  17. The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain

    Science.gov (United States)

    Hilbert, Brendan J.; Hayes, Janelle A.; Stone, Nicholas P.; Xu, Rui-Gang

    2017-01-01

    Abstract Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the adenosine triphosphatase (ATPase) that powers DNA translocation and an endonuclease that cleaves the concatemeric genome at both initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage remains mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in the nuclease active site. We screened a large panel of TerL variants for defects in binding and DNA cleavage, revealing that the ATPase domain is the primary site for DNA binding, and is required for nuclease activity. The nuclease domain is dispensable for DNA binding but residues lining the active site guide DNA for cleavage. Kinetic analysis of DNA cleavage suggests flexible tethering of the nuclease domains during DNA cleavage. We propose that interactions with the procapsid during DNA translocation conformationally restrict the nuclease domain, inhibiting cleavage; TerL release from the capsid upon completion of packaging unlocks the nuclease domains to cleave DNA. PMID:28082398

  18. Functional Interplay of the Mre11 Nuclease and Ku in the Response to Replication-Associated DNA Damage ▿

    Science.gov (United States)

    Foster, Steven S.; Balestrini, Alessia; Petrini, John H. J.

    2011-01-01

    The Mre11 complex is a central component of the DNA damage response, with roles in damage sensing, molecular bridging, and end resection. We have previously shown that in Saccharomyces cerevisiae, Ku70 (yKu70) deficiency reduces the ionizing radiation sensitivity of mre11Δ mutants. In this study, we show that yKu70 deficiency suppressed the camptothecin (CPT) and methyl methanesulfonate (MMS) sensitivity of nuclease-deficient mre11-3 and sae2Δ mutants in an Exo1-dependent manner. CPT-induced G2/M arrest, γ-H2AX persistence, and chromosome breaks were elevated in mre11-3 mutants. These outcomes were reduced by yKu70 deficiency. Given that the genotoxic effects of CPT are manifest during DNA replication, these data suggest that Ku limits Exo1-dependent double-strand break (DSB) resection during DNA replication, inhibiting the initial processing steps required for homology-directed repair. We propose that Mre11 nuclease- and Sae2-dependent DNA end processing, which initiates DSB resection prevents Ku from engaging DSBs, thus promoting Exo1-dependent resection. In agreement with this idea, we show that Ku affinity for binding to short single-stranded overhangs is much lower than for blunt DNA ends. Collectively, the data define a nonhomologous end joining (NHEJ)-independent, S-phase-specific function of the Ku heterodimer. PMID:21876003

  19. Coincident resection at both ends of random, γ-induced double-strand breaks requires MRX (MRN, Sae2 (Ctp1, and Mre11-nuclease.

    Directory of Open Access Journals (Sweden)

    James W Westmoreland

    2013-03-01

    Full Text Available Resection is an early step in homology-directed recombinational repair (HDRR of DNA double-strand breaks (DSBs. Resection enables strand invasion as well as reannealing following DNA synthesis across a DSB to assure efficient HDRR. While resection of only one end could result in genome instability, it has not been feasible to address events at both ends of a DSB, or to distinguish 1- versus 2-end resections at random, radiation-induced "dirty" DSBs or even enzyme-induced "clean" DSBs. Previously, we quantitatively addressed resection and the role of Mre11/Rad50/Xrs2 complex (MRX at random DSBs in circular chromosomes within budding yeast based on reduced pulsed-field gel electrophoretic mobility ("PFGE-shift". Here, we extend PFGE analysis to a second dimension and demonstrate unique patterns associated with 0-, 1-, and 2-end resections at DSBs, providing opportunities to examine coincidence of resection. In G2-arrested WT, Δrad51 and Δrad52 cells deficient in late stages of HDRR, resection occurs at both ends of γ-DSBs. However, for radiation-induced and I-SceI-induced DSBs, 1-end resections predominate in MRX (MRN null mutants with or without Ku70. Surprisingly, Sae2 (Ctp1/CtIP and Mre11 nuclease-deficient mutants have similar responses, although there is less impact on repair. Thus, we provide direct molecular characterization of coincident resection at random, radiation-induced DSBs and show that rapid and coincident initiation of resection at γ-DSBs requires MRX, Sae2 protein, and Mre11 nuclease. Structural features of MRX complex are consistent with coincident resection being due to an ability to interact with both DSB ends to directly coordinate resection. Interestingly, coincident resection at clean I-SceI-induced breaks is much less dependent on Mre11 nuclease or Sae2, contrary to a strong dependence on MRX complex, suggesting different roles for these functions at "dirty" and clean DSB ends. These approaches apply to resection at

  20. CRISPR/Cas9 nuclease-mediated gene knock-in in bovine-induced pluripotent cells.

    Science.gov (United States)

    Heo, Young Tae; Quan, Xiaoyuan; Xu, Yong Nan; Baek, Soonbong; Choi, Hwan; Kim, Nam-Hyung; Kim, Jongpil

    2015-02-01

    Efficient and precise genetic engineering in livestock such as cattle holds great promise in agriculture and biomedicine. However, techniques that generate pluripotent stem cells, as well as reliable tools for gene targeting in livestock, are still inefficient, and thus not routinely used. Here, we report highly efficient gene targeting in the bovine genome using bovine pluripotent cells and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 nuclease. First, we generate induced pluripotent stem cells (iPSCs) from bovine somatic fibroblasts by the ectopic expression of yamanaka factors and GSK3β and MEK inhibitor (2i) treatment. We observed that these bovine iPSCs are highly similar to naïve pluripotent stem cells with regard to gene expression and developmental potential in teratomas. Moreover, CRISPR/Cas9 nuclease, which was specific for the bovine NANOG locus, showed highly efficient editing of the bovine genome in bovine iPSCs and embryos. To conclude, CRISPR/Cas9 nuclease-mediated homologous recombination targeting in bovine pluripotent cells is an efficient gene editing method that can be used to generate transgenic livestock in the future.

  1. Staphylococcal nuclease active-site amino acids: pH dependence of tyrosines and arginines by 13C NMR and correlation with kinetic studies

    International Nuclear Information System (INIS)

    Grissom, C.G.; Markley, J.L.

    1989-01-01

    The pH and temperature dependence of the kinetic parameters of staphylococcal nuclease have been examined with three p-nitrophenyl phosphate containing DNA analogues that vary as to 3'-substituent. With wild-type (Foggi variant) nuclease (nuclease wt) and the substrates thymidine 3'-phosphate 5'-(p-nitrophenyl phosphate) (PNPdTp), thymidine 3'-methylphosphonate 5'-(p-nitrophenyl phosphate) (PNPdTp Me), and thymidine 5'-(p-nitrophenyl phosphate) (PNPdT), k cat remains nearly constant at 13 min -1 . However, k cat /k m with nuclease wt varies considerably. The data suggests that the inflection k cat /K m with pK a at 9.67 arises from ionization of tyrosine-85, which hydrogen bonds to the divalent 3'-phosphomonester of substrates with this substituent. The enthalpy of ionization of both deprotonation steps in the k cat /K m versus pH profile is 5 kcal/mol. 13 C NMR has been used to determine the pK a values of the arginine and tyrosine residues. The results do not rule out arginine as a candidate for the acidic catalyst that protonates the 5'-ribose alkoxide prior to product release. The phenolic hydroxyl carbon of tyrosine-85 has been assigned by comparing the 13 C NMR spectrum of nuclease wt and nuclease Y85F. This correlation between pK a values along with the absence of other candidates indicates that the ionization of tyrosine-85 is the pK a seen in the k cat /K m vs pH profile for substrates with a divalent 3'-phosphomonester. This conclusion is consistent with the proposed role of tyrosine-85 as a hydrogen-bond donor to the 3'-phosphomonoester of substrates poised for exonucleolytic hydrolysis

  2. TRF2 Recruits RTEL1 to Telomeres in S Phase to Promote T-Loop Unwinding

    OpenAIRE

    Sarek, Grzegorz; Vannier, Jean-Baptiste; Panier, Stephanie; Petrini, John?H.J.; Boulton, Simon?J.

    2015-01-01

    Summary The helicase RTEL1 promotes t-loop unwinding and suppresses telomere fragility to maintain the integrity of vertebrate telomeres. An interaction between RTEL1 and PCNA is important to prevent telomere fragility, but how RTEL1 engages with the telomere to promote t-loop unwinding is unclear. Here, we establish that the shelterin protein TRF2 recruits RTEL1 to telomeres in S phase, which is required to?prevent catastrophic t-loop processing by structure-specific nucleases. We show that ...

  3. Leishmania infantum EndoG is an endo/exo-nuclease essential for parasite survival.

    Directory of Open Access Journals (Sweden)

    Eva Rico

    Full Text Available EndoG, a member of the DNA/RNA non-specific ββα-metal family of nucleases, has been demonstrated to be present in many organisms, including Trypanosomatids. This nuclease participates in the apoptotic program in these parasites by migrating from the mitochondrion to the nucleus, where it takes part in the degradation of genomic DNA that characterizes this process. We now demonstrate that Leishmania infantum EndoG (LiEndoG is an endo-exonuclease that has a preferential 5' exonuclease activity on linear DNA. Regardless of its role during apoptotic cell death, this enzyme seems to be necessary during normal development of the parasites as indicated by the reduced growth rates observed in LiEndoG hemi-knockouts and their poor infectivity in differentiated THP-1 cells. The pro-life role of this protein is also corroborated by the higher survival rates of parasites that over-express this protein after treatment with the LiEndoG inhibitor Lei49. Taken together, our results demonstrate that this enzyme plays essential roles in both survival and death of Leishmania parasites.

  4. Development of synthetic selfish elements based on modular nucleases in Drosophila melanogaster.

    Science.gov (United States)

    Simoni, Alekos; Siniscalchi, Carla; Chan, Yuk-Sang; Huen, David S; Russell, Steven; Windbichler, Nikolai; Crisanti, Andrea

    2014-06-01

    Selfish genes are DNA elements that increase their rate of genetic transmission at the expense of other genes in the genome and can therefore quickly spread within a population. It has been suggested that selfish elements could be exploited to modify the genome of entire populations for medical and ecological applications. Here we report that transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) can be engineered into site-specific synthetic selfish elements (SSEs) and demonstrate their transmission of up to 70% in the Drosophila germline. We show here that SSEs can spread via DNA break-induced homologous recombination, a process known as 'homing' similar to that observed for homing endonuclease genes (HEGs), despite their fundamentally different modes of DNA binding and cleavage. We observed that TALEN and ZFN have a reduced capability of secondary homing compared to HEG as their repetitive structure had a negative effect on their genetic stability. The modular architecture of ZFNs and TALENs allows for the rapid design of novel SSEs against specific genomic sequences making them potentially suitable for the genetic engineering of wild-type populations of animals and plants, in applications such as gene replacement or population suppression of pest species. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease.

    Science.gov (United States)

    Doetschman, Thomas; Georgieva, Teodora

    2017-03-03

    Genetic engineering of model organisms and cultured cells has for decades provided important insights into the mechanisms underlying cardiovascular development and disease. In the past few years the development of several nuclease systems has broadened the range of model/cell systems that can be engineered. Of these, the CRISPR (clustered regularly interspersed short palindromic repeats)/Cas9 (CRISPR-associated protein 9) system has become the favorite for its ease of application. Here we will review this RNA-guided nuclease system for gene editing with respect to its usefulness for cardiovascular studies and with an eye toward potential therapy. Studies on its off-target activity, along with approaches to minimize this activity will be given. The advantages of gene editing versus gene targeting in embryonic stem cells, including the breadth of species and cell types to which it is applicable, will be discussed. We will also cover its use in iPSC for research and possible therapeutic purposes; and we will review its use in muscular dystrophy studies where considerable progress has been made toward dystrophin correction in mice. The CRISPR/Ca9s system is also being used for high-throughput screening of genes, gene regulatory regions, and long noncoding RNAs. In addition, the CRISPR system is being used for nongene-editing purposes such as activation and inhibition of gene expression, as well as for fluorescence tagging of chromosomal regions and individual mRNAs to track their cellular location. Finally, an approach to circumvent the inability of post-mitotic cells to support homologous recombination-based gene editing will be presented. In conclusion, applications of the CRISPR/Cas system are expanding at a breath-taking pace and are revolutionizing approaches to gain a better understanding of human diseases. © 2017 American Heart Association, Inc.

  6. Glycoengineering of Human Cell Lines Using Zinc Finger Nuclease Gene Targeting

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Bennett, Eric Paul; Clausen, Henrik

    2013-01-01

    Lectin affinity chromatography is a powerful technique for isolation of glycoproteins carrying a specific glycan structure of interest. However, the enormous diversity of glycans present on the cell surface, as well as on individual proteins, makes it difficult to isolate an entire glycoproteome...... with one or even a series of lectins. Here we present a technique to generate cell lines with homogenous truncated O-glycans using zinc finger nuclease gene targeting. Because of their simplified O-glycoproteome, the cells have been named SimpleCells. Glycoproteins from SimpleCells can be isolated...... in a single purification step by lectin chromatography performed on a long lectin column. This protocol describes Zinc finger nuclease gene targeting of human cells to simplify the glycoproteome, as well as lectin chromatography and isolation of glycopeptides from total cell lysates of SimpleCells....

  7. Tsetse salivary gland proteins 1 and 2 are high affinity nucleic acid binding proteins with residual nuclease activity.

    Directory of Open Access Journals (Sweden)

    Guy Caljon

    Full Text Available Analysis of the tsetse fly salivary gland EST database revealed the presence of a highly enriched cluster of putative endonuclease genes, including tsal1 and tsal2. Tsal proteins are the major components of tsetse fly (G. morsitans morsitans saliva where they are present as monomers as well as high molecular weight complexes with other saliva proteins. We demonstrate that the recombinant tsetse salivary gland proteins 1&2 (Tsal1&2 display DNA/RNA non-specific, high affinity nucleic acid binding with K(D values in the low nanomolar range and a non-exclusive preference for duplex. These Tsal proteins exert only a residual nuclease activity with a preference for dsDNA in a broad pH range. Knockdown of Tsal expression by in vivo RNA interference in the tsetse fly revealed a partially impaired blood digestion phenotype as evidenced by higher gut nucleic acid, hematin and protein contents.

  8. Crystallization and preliminary crystallographic analysis of an Escherichia coli-selected mutant of the nuclease domain of the metallonuclease colicin E7

    International Nuclear Information System (INIS)

    Czene, Anikó; Tóth, Eszter; Gyurcsik, Béla; Otten, Harm; Poulsen, Jens-Christian N.; Lo Leggio, Leila; Larsen, Sine; Christensen, Hans E. M.; Nagata, Kyosuke

    2013-01-01

    An N-terminally truncated mutant of the colicin E7 nuclease domain was crystallized and diffraction data set was collected to 1.6 Å resolution. The metallonuclease colicin E7 is a member of the HNH family of endonucleases. It serves as a bacterial toxin in Escherichia coli, protecting the host cell from other related bacteria and bacteriophages by degradation of their chromosomal DNA under environmental stress. Its cell-killing activity is attributed to the nonspecific nuclease domain (NColE7), which possesses the catalytic ββα-type metal ion-binding HNH motif at its C-terminus. Mutations affecting the positively charged amino acids at the N-terminus of NColE7 (444–576) surprisingly showed no or significantly reduced endonuclease activity [Czene et al. (2013 ▶), J. Biol. Inorg. Chem.18, 309–321]. The necessity of the N-terminal amino acids for the function of the C-terminal catalytic centre poses the possibility of allosteric activation within the enzyme. Precise knowledge of the intramolecular interactions of these residues that affect the catalytic activity could turn NColE7 into a novel platform for artificial nuclease design. In this study, the N-terminal deletion mutant ΔN4-NColE7-C* of the nuclease domain of colicin E7 selected by E. coli was overexpressed and crystallized at room temperature by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 1.6 Å resolution and could be indexed and averaged in the trigonal space group P3 1 21 or P3 2 21, with unit-cell parameters a = b = 55.4, c = 73.1 Å. Structure determination by molecular replacement is in progress

  9. Nuclease-like activity of some Cu(II) complexes

    International Nuclear Information System (INIS)

    Durackova, Z.; Fenikova, L.; Svorenova, L.; Labudova, O.; Kollarova, M.; Labuda, J.

    1995-01-01

    The nuclease reaction of a copper complex with the macrocyclic Schiff base ligand tetrabenzo[b,f,j,n][a,3,9,13]tetraaza cyclohexadecine (TAAB) at the cleavage of DNA in aerobic conditions and the presence of ascorbic acid has been investigated and compared with that of the copper phenanthroline complex. The AT specifity of the Cu(TAAB) 2+ for both single-stranded and double-stranded DNA templates was observed. (authors), 4 figs., 6 refs

  10. Evaluation of 5 ' nuclease assay for detection of Actinobacillus pleuropneumoniae

    DEFF Research Database (Denmark)

    Angen, Øystein; Jensen, J.; Lavritsen, D. T.

    2001-01-01

    Sequence detection by the 5' nuclease TaqMan assay uses online detection of internal fluorogenic probes in closed PCR tubes. Primers and probe were chosen from a part of the omlA gene common to all serotypes of Actinobacillus pleuropneumoniae, which gave an amplicon of 92 bp, The test was evaluat...

  11. The adnAB Locus, Encoding a Putative Helicase-Nuclease Activity, Is Essential in Streptomyces

    Science.gov (United States)

    Zhang, Lingli; Nguyen, Hoang Chuong; Chipot, Ludovic; Piotrowski, Emilie; Bertrand, Claire

    2014-01-01

    Homologous recombination is a crucial mechanism that repairs a wide range of DNA lesions, including the most deleterious ones, double-strand breaks (DSBs). This multistep process is initiated by the resection of the broken DNA ends by a multisubunit helicase-nuclease complex exemplified by Escherichia coli RecBCD, Bacillus subtilis AddAB, and newly discovered Mycobacterium tuberculosis AdnAB. Here we show that in Streptomyces, neither recBCD nor addAB homologues could be detected. The only putative helicase-nuclease-encoding genes identified were homologous to M. tuberculosis adnAB genes. These genes are conserved as a single copy in all sequenced genomes of Streptomyces. The disruption of adnAB in Streptomyces ambofaciens and Streptomyces coelicolor could not be achieved unless an ectopic copy was provided, indicating that adnAB is essential for growth. Both adnA and adnB genes were shown to be inducible in response to DNA damage (mitomycin C) and to be independently transcribed. Introduction of S. ambofaciens adnAB genes in an E. coli recB mutant restored viability and resistance to UV light, suggesting that Streptomyces AdnAB could be a functional homologue of RecBCD and be involved in DNA damage resistance. PMID:24837284

  12. Cleavage of influenza RNA by using a human PUF-based artificial RNA-binding protein–staphylococcal nuclease hybrid

    International Nuclear Information System (INIS)

    Mori, Tomoaki; Nakamura, Kento; Masaoka, Keisuke; Fujita, Yusuke; Morisada, Ryosuke; Mori, Koichi; Tobimatsu, Takamasa; Sera, Takashi

    2016-01-01

    Various viruses infect animals and humans and cause a variety of diseases, including cancer. However, effective methodologies to prevent virus infection have not yet been established. Therefore, development of technologies to inactivate viruses is highly desired. We have already demonstrated that cleavage of a DNA virus genome was effective to prevent its replication. Here, we expanded this methodology to RNA viruses. In the present study, we used staphylococcal nuclease (SNase) instead of the PIN domain (PilT N-terminus) of human SMG6 as an RNA-cleavage domain and fused the SNase to a human Pumilio/fem-3 binding factor (PUF)-based artificial RNA-binding protein to construct an artificial RNA restriction enzyme with enhanced RNA-cleavage rates for influenzavirus. The resulting SNase-fusion nuclease cleaved influenza RNA at rates 120-fold greater than the corresponding PIN-fusion nuclease. The cleaving ability of the PIN-fusion nuclease was not improved even though the linker moiety between the PUF and RNA-cleavage domain was changed. Gel shift assays revealed that the RNA-binding properties of the PUF derivative used was not as good as wild type PUF. Improvement of the binding properties or the design method will allow the SNase-fusion nuclease to cleave an RNA target in mammalian animal cells and/or organisms. - Highlights: • A novel RNA restriction enzyme using SNase was developed tor cleave viral RNA. • Our enzyme cleaved influenza RNA with rates >120-fold higher rates a PIN-fusion one. • Our artificial enzyme with the L5 linker showed the highest RNA cleavage rate. • Our artificial enzyme site-selectively cleaved influenza RNA in vitro.

  13. Zinc finger nuclease: a new approach for excising HIV-1 proviral DNA from infected human T cells.

    Science.gov (United States)

    Qu, Xiying; Wang, Pengfei; Ding, Donglin; Wang, Xiaohui; Zhang, Gongmin; Zhou, Xin; Liu, Lin; Zhu, Xiaoli; Zeng, Hanxian; Zhu, Huanzhang

    2014-09-01

    A major reason that Acquired Immune Deficiency Syndrome (AIDS) cannot be completely cured is the human immunodeficiency virus 1 (HIV-1) provirus integrated into the human genome. Though existing therapies can inhibit replication of HIV-1, they cannot eradicate it. A molecular therapy gains popularity due to its specifically targeting to HIV-1 infected cells and effectively removing the HIV-1, regardless of viral genes being active or dormant. Now, we propose a new method which can excellently delete the HIV provirus from the infected human T cell genome. First, we designed zinc-finger nucleases (ZFNs) that target a sequence within the long terminal repeat (LTR) U3 region that is highly conserved in whole clade. Then, we screened out one pair of ZFN and named it as ZFN-U3. We discovered that ZFN-U3 can exactly target and eliminate the full-length HIV-1 proviral DNA after the infected human cell lines treated with it, and the frequency of its excision was about 30 % without cytotoxicity. These results prove that ZFN-U3 can efficiently excise integrated HIV-1 from the human genome in infected cells. This method to delete full length HIV-1 in human genome can therefore provide a novel approach to cure HIV-infected individuals in the future.

  14. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system.

    Science.gov (United States)

    Sinkunas, Tomas; Gasiunas, Giedrius; Fremaux, Christophe; Barrangou, Rodolphe; Horvath, Philippe; Siksnys, Virginijus

    2011-04-06

    Clustered regularly interspaced short palindromic repeat (CRISPR) is a recently discovered adaptive prokaryotic immune system that provides acquired immunity against foreign nucleic acids by utilizing small guide crRNAs (CRISPR RNAs) to interfere with invading viruses and plasmids. In Escherichia coli, Cas3 is essential for crRNA-guided interference with virus proliferation. Cas3 contains N-terminal HD phosphohydrolase and C-terminal Superfamily 2 (SF2) helicase domains. Here, we provide the first report of the cloning, expression, purification and in vitro functional analysis of the Cas3 protein of the Streptococcus thermophilus CRISPR4 (Ecoli subtype) system. Cas3 possesses a single-stranded DNA (ssDNA)-stimulated ATPase activity, which is coupled to unwinding of DNA/DNA and RNA/DNA duplexes. Cas3 also shows ATP-independent nuclease activity located in the HD domain with a preference for ssDNA substrates. To dissect the contribution of individual domains, Cas3 separation-of-function mutants (ATPase(+)/nuclease(-) and ATPase(-)/nuclease(+)) were obtained by site-directed mutagenesis. We propose that the Cas3 ATPase/helicase domain acts as a motor protein, which assists delivery of the nuclease activity to Cascade-crRNA complex targeting foreign DNA.

  15. The space of harmonic maps of S2 into S4

    International Nuclear Information System (INIS)

    Loo, B.

    1989-05-01

    Every branched superminimal surface of area 4πd in S 4 is shown to arise from a pair of meromorphic functions (f 1 ,f 2 ) of bidegree (d,d) such that f 1 and f 2 have the same ramification divisor. Conditions under which branched superminimal surfaces can be generated from such pairs of functions are derived. For each d ≥ 1 the space of harmonic maps (i.e branched superminimal immersions) of S 2 into S 4 of harmonic degree d is shown to be a connected space of complex dimension 2d+4. (author). 18 refs

  16. HETEROGENEITY OF POLYCLONAL IMMUNOGLOBULINS NUCLEASE ACTIVITY IN RHEUMATOID AND REACTIVE ARTHRITIS

    Directory of Open Access Journals (Sweden)

    M. V. Volkova

    2017-01-01

    Full Text Available Catalytic properties of immunoglobulins are widely studied within recent years. It was found that nuclease activity of immunoglobulins is increased in systemic autoimmune diseases. Given some pathogenetic features of rheumatoid arthritis and reactive arthritis, it is appropriate to clarify the nature of nuclease activity in these diseases. Determination of DNAse activity of immunoglobulins with different DNA substrates, and search for specific substrates for distinct clinical entities could serve these purposes. The aim of present work is to determine DNase activity of the polyclonal class G immunoglobulins in rheumatoid and reactive arthritis using various methods.Different methods are used to evaluate nuclease activity. In this paper we present newly developed and modified techniques for determination of DNAse activity of polyclonal IgGs. Particular attention was paid to the electrophoretic method of DNase activity assessment. Polyclonal IgG isolated from blood serum of patients with rheumatoid arthritis and reactive arthritis were used for assays. In this study, we demonstrated the presence of an inhomogeneous DNase activity of immunoglobulins in relation to different substrates.Along with calf thymus DNA, we used bacterial plasmid DNA and PCR products based on bacterial gene sequences. Levels of DNase activity by rivanol clot method with calf thymus DNA as substrate proved to be higher in patients with rheumatoid arthritis than the control values (p < 0.01. DNase abzyme activity in patients with rheumatoid arthritis was elevated, as compared to the patients with reactive arthritis (p < 0.01.When examining ability of the IgG to hydrolyze procaryotic DNA (bacterial plasmid DNA and PCR products, based on bacterial genes, we obtained heterogeneous results. Different Ig samples showed varying degrees of DNA hydrolysis. Abzyme hydrolysis of DNA substrates longer than 700 bp was more pronounced, as compared to short DNA substrates (100 base pairs

  17. Mapping DNA cleavage by the Type ISP restriction-modification enzymes following long-range communication between DNA sites in different orientations

    Science.gov (United States)

    van Aelst, Kara; Saikrishnan, Kayarat; Szczelkun, Mark D.

    2015-01-01

    The prokaryotic Type ISP restriction-modification enzymes are single-chain proteins comprising an Mrr-family nuclease, a superfamily 2 helicase-like ATPase, a coupler domain, a methyltransferase, and a DNA-recognition domain. Upon recognising an unmodified DNA target site, the helicase-like domain hydrolyzes ATP to cause site release (remodeling activity) and to then drive downstream translocation consuming 1–2 ATP per base pair (motor activity). On an invading foreign DNA, double-strand breaks are introduced at random wherever two translocating enzymes form a so-called collision complex following long-range communication between a pair of target sites in inverted (head-to-head) repeat. Paradoxically, structural models for collision suggest that the nuclease domains are too far apart (>30 bp) to dimerise and produce a double-strand DNA break using just two strand-cleavage events. Here, we examined the organisation of different collision complexes and how these lead to nuclease activation. We mapped DNA cleavage when a translocating enzyme collides with a static enzyme bound to its site. By following communication between sites in both head-to-head and head-to-tail orientations, we could show that motor activity leads to activation of the nuclease domains via distant interactions of the helicase or MTase-TRD. Direct nuclease dimerization is not required. To help explain the observed cleavage patterns, we also used exonuclease footprinting to demonstrate that individual Type ISP domains can swing off the DNA. This study lends further support to a model where DNA breaks are generated by multiple random nicks due to mobility of a collision complex with an overall DNA-binding footprint of ∼30 bp. PMID:26507855

  18. Mining the O-glycoproteome using zinc-finger nuclease-glycoengineered SimpleCell lines

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Vakhrushev, Sergey Y; Vester-Christensen, Malene B

    2011-01-01

    Zinc-finger nuclease (ZFN) gene targeting is emerging as a versatile tool for engineering of multiallelic gene deficiencies. A longstanding obstacle for detailed analysis of glycoproteomes has been the extensive heterogeneities in glycan structures and attachment sites. Here we applied ZFN target...

  19. sUAS Facility Map - Download dataset

    Data.gov (United States)

    Department of Transportation — sUAS Facility Maps (UASFM) that indicate “pre-approved fly altitudes.” Within each grid on the map, FAA would identify maximum altitudes at which flight is permitted...

  20. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases

    DEFF Research Database (Denmark)

    Chen, Fuqiang; Pruett-Miller, Shondra M; Huang, Yuping

    2011-01-01

    Zinc-finger nucleases (ZFNs) have enabled highly efficient gene targeting in multiple cell types and organisms. Here we describe methods for using simple ssDNA oligonucleotides in tandem with ZFNs to efficiently produce human cell lines with three distinct genetic outcomes: (i) targeted point...

  1. Crystallization and preliminary X-ray characterization of two thermostable DNA nucleases

    International Nuclear Information System (INIS)

    Kuettner, E. Bartholomeus; Pfeifer, Sven; Keim, Antje; Greiner-Stöffele, Thomas; Sträter, Norbert

    2006-01-01

    Two thermostable DNA nucleases from archaea were crystallized in different space groups; the crystals were suitable for X-ray analysis. Temperature-tolerant organisms are an important source to enhance the stability of enzymes used in biotechnological processes. The DNA-cleaving enzyme exonuclease III from Escherichia coli is used in several applications in gene technology. A thermostable variant could expand the applicability of the enzyme in these methods. Two homologous nucleases from Archaeoglobus fulgidus (ExoAf) and Methanothermobacter thermoautrophicus (ExoMt) were studied for this purpose. Both enzymes were crystallized in different space groups using (poly)ethylene glycols, 2,4-methyl pentandiol, dioxane, ethanol or 2-propanol as precipitants. The addition of a 10-mer DNA oligonucleotide was important to obtain monoclinic crystals of ExoAf and ExoMt that diffracted to resolutions better than 2 Å using synchrotron radiation. The crystal structures of the homologous proteins can serve as templates for genetic engineering of the E. coli exonuclease III and will aid in understanding the different catalytic properties of the enzymes

  2. Genome editing in mouse spermatogonial stem/progenitor cells using engineered nucleases.

    Directory of Open Access Journals (Sweden)

    Danielle A Fanslow

    Full Text Available Editing the genome to create specific sequence modifications is a powerful way to study gene function and promises future applicability to gene therapy. Creation of precise modifications requires homologous recombination, a very rare event in most cell types that can be stimulated by introducing a double strand break near the target sequence. One method to create a double strand break in a particular sequence is with a custom designed nuclease. We used engineered nucleases to stimulate homologous recombination to correct a mutant gene in mouse "GS" (germline stem cells, testicular derived cell cultures containing spermatogonial stem cells and progenitor cells. We demonstrated that gene-corrected cells maintained several properties of spermatogonial stem/progenitor cells including the ability to colonize following testicular transplantation. This proof of concept for genome editing in GS cells impacts both cell therapy and basic research given the potential for GS cells to be propagated in vitro, contribute to the germline in vivo following testicular transplantation or become reprogrammed to pluripotency in vitro.

  3. Automated 5 ' nuclease PCR assay for identification of Salmonella enterica

    DEFF Research Database (Denmark)

    Hoorfar, Jeffrey; Ahrens, Peter; Rådström, P.

    2000-01-01

    -point fluorescence (FAM) signals for the samples and positive control (TET) signals (relative sensitivity [Delta Rn], >0.6). The diagnostic specificity of the method was assessed using 120 non-Salmonella strains, which all resulted in negative FAM signals (Delta Rn, less than or equal to 0.5). All 100 rough...... Salmonella strains tested resulted in positive FAM and TET signals. In addition, it was found that the complete PCR mixture, predispensed in microwell plates, could be stored for up to 3 months at -20 degrees C, Thus, the diagnostic TaqMan assay developed can be a useful and simple alternative method......A simple and ready-to-go test based on a 5' nuclease (TaqMan) PCR technique was developed for identification of presumptive Salmonella enterica isolates. The results were compared with those of conventional methods. The TaqMan assay was evaluated for its ability to accurately detect 210 S. enterica...

  4. An Intracellular Peptidyl-Prolyl cis/trans Isomerase Is Required for Folding and Activity of the Staphylococcus aureus Secreted Virulence Factor Nuclease.

    Science.gov (United States)

    Wiemels, Richard E; Cech, Stephanie M; Meyer, Nikki M; Burke, Caleb A; Weiss, Andy; Parks, Anastacia R; Shaw, Lindsey N; Carroll, Ronan K

    2017-01-01

    Staphylococcus aureus is an important human pathogen that relies on a large repertoire of secreted and cell wall-associated proteins for pathogenesis. Consequently, the ability of the organism to cause disease is absolutely dependent on its ability to synthesize and successfully secrete these proteins. In this study, we investigate the role of peptidyl-prolyl cis/trans isomerases (PPIases) on the activity of the S. aureus secreted virulence factor nuclease (Nuc). We identify a staphylococcal cyclophilin-type PPIase (PpiB) that is required for optimal activity of Nuc. Disruption of ppiB results in decreased nuclease activity in culture supernatants; however, the levels of Nuc protein are not altered, suggesting that the decrease in activity results from misfolding of Nuc in the absence of PpiB. We go on to demonstrate that PpiB exhibits PPIase activity in vitro, is localized to the bacterial cytosol, and directly interacts with Nuc in vitro to accelerate the rate of Nuc refolding. Finally, we demonstrate an additional role for PpiB in S. aureus hemolysis and demonstrate that the S. aureus parvulin-type PPIase PrsA also plays a role in the activity of secreted virulence factors. The deletion of prsA leads to a decrease in secreted protease and phospholipase activity, similar to that observed in other Gram-positive pathogens. Together, these results demonstrate, for the first time to our knowledge, that PPIases play an important role in the secretion of virulence factors in S. aureus IMPORTANCE: Staphylococcus aureus is a highly dangerous bacterial pathogen capable of causing a variety of infections throughout the human body. The ability of S. aureus to cause disease is largely due to an extensive repertoire of secreted and cell wall-associated proteins, including adhesins, toxins, exoenzymes, and superantigens. These virulence factors, once produced, are typically transported across the cell membrane by the secretory (Sec) system in a denatured state. Consequently

  5. A Biochemical Approach to Understanding the Fanconi Anemia Pathway-Regulated Nucleases in Genome Maintenance for Preventing Bone Marrow Failure and Cancer

    Science.gov (United States)

    2014-04-01

    the Fanconi Anemia Pathway- Regulated Nucleases in Genome Maintenance for Preventing Bone Marrow Failure and Cancer PRINCIPAL INVESTIGATOR...GRANT NUMBER 4. TITLE AND SUBTITLE A Biochemical Approach to Understanding the Fanconi Anemia Pathway-Regulated Nucleases in Genome Maintenance for...Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Fanconi anemia is the most prevalent inherited BMF syndromes, caused by mutations in

  6. Engineering HIV-resistant human CD4+ T cells with CXCR4-specific zinc-finger nucleases.

    Directory of Open Access Journals (Sweden)

    Craig B Wilen

    2011-04-01

    Full Text Available HIV-1 entry requires the cell surface expression of CD4 and either the CCR5 or CXCR4 coreceptors on host cells. Individuals homozygous for the ccr5Δ32 polymorphism do not express CCR5 and are protected from infection by CCR5-tropic (R5 virus strains. As an approach to inactivating CCR5, we introduced CCR5-specific zinc-finger nucleases into human CD4+ T cells prior to adoptive transfer, but the need to protect cells from virus strains that use CXCR4 (X4 in place of or in addition to CCR5 (R5X4 remains. Here we describe engineering a pair of zinc finger nucleases that, when introduced into human T cells, efficiently disrupt cxcr4 by cleavage and error-prone non-homologous DNA end-joining. The resulting cells proliferated normally and were resistant to infection by X4-tropic HIV-1 strains. CXCR4 could also be inactivated in ccr5Δ32 CD4+ T cells, and we show that such cells were resistant to all strains of HIV-1 tested. Loss of CXCR4 also provided protection from X4 HIV-1 in a humanized mouse model, though this protection was lost over time due to the emergence of R5-tropic viral mutants. These data suggest that CXCR4-specific ZFNs may prove useful in establishing resistance to CXCR4-tropic HIV for autologous transplant in HIV-infected individuals.

  7. Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

    Science.gov (United States)

    Kleinstiver, Benjamin P; Prew, Michelle S; Tsai, Shengdar Q; Topkar, Ved V; Nguyen, Nhu T; Zheng, Zongli; Gonzales, Andrew P W; Li, Zhuyun; Peterson, Randall T; Yeh, Jing-Ruey Joanna; Aryee, Martin J; Joung, J Keith

    2015-07-23

    Although CRISPR-Cas9 nucleases are widely used for genome editing, the range of sequences that Cas9 can recognize is constrained by the need for a specific protospacer adjacent motif (PAM). As a result, it can often be difficult to target double-stranded breaks (DSBs) with the precision that is necessary for various genome-editing applications. The ability to engineer Cas9 derivatives with purposefully altered PAM specificities would address this limitation. Here we show that the commonly used Streptococcus pyogenes Cas9 (SpCas9) can be modified to recognize alternative PAM sequences using structural information, bacterial selection-based directed evolution, and combinatorial design. These altered PAM specificity variants enable robust editing of endogenous gene sites in zebrafish and human cells not currently targetable by wild-type SpCas9, and their genome-wide specificities are comparable to wild-type SpCas9 as judged by GUIDE-seq analysis. In addition, we identify and characterize another SpCas9 variant that exhibits improved specificity in human cells, possessing better discrimination against off-target sites with non-canonical NAG and NGA PAMs and/or mismatched spacers. We also find that two smaller-size Cas9 orthologues, Streptococcus thermophilus Cas9 (St1Cas9) and Staphylococcus aureus Cas9 (SaCas9), function efficiently in the bacterial selection systems and in human cells, suggesting that our engineering strategies could be extended to Cas9s from other species. Our findings provide broadly useful SpCas9 variants and, more importantly, establish the feasibility of engineering a wide range of Cas9s with altered and improved PAM specificities.

  8. Distribution of ultraviolet-induced DNA repair synthesis in nuclease sensitive and resistant regions of human chromatin

    International Nuclear Information System (INIS)

    Smerdon, M.J.; Tlsty, T.D.; Lieberman, M.W.

    1978-01-01

    The distribution of ultraviolet radiation (uv) induced DNA repair synthesis within chromatin was examined in cultured human diploid fibroblasts (IMR-90). Measurement of the time course of repair synthesis yielded two distinct phases: An initial rapid phase (fast repair) which occurs during the first 2 to 3 h after damage and a slower phase (slow repair) associated with a tenfold decrease in the rate of nucleotide incorporation, which persists for at least 35 h after damage. Staphylococcal nuclease digests of nuclei from cells damaged with uv and labeled during the fast-repair phase revealed a marked preference of fast-repair synthesis for the nuclease-sensitive regions. A new method was developed to analyze the digestion data and showed that approximately 50% of the nucleotides incorporated during the fast-repair phase are located in staphylococcal nuclease-sensitive regions, which comprise about 30% of the genome. Calculations from these data indicate that in the staphylococcal nuclease-sensitive regions the number of newly inserted nucleotides per unit DNA is about twice that of resistant regions. These results were supported by electrophoresis studies which demonstrated a decreased representation of fast-repair synthesis in core particle DNA. In contrast, the distribution within chromatin of nucleotides incorporated during the slow-repair phase was found to be much more homogeneous with about 30% of the repair sites located in 25% of the genome. Digestion studieswith DNase I indicated a slight preference of repair synthesis for regions sensitive to this enzyme; however, no marked difference between the distributions of fast- and slow-repair synthesis was observed. This study provides evidence that the structural constraints placed upon DNA in chromatin also place constraints upon uv-induced DNA repair synthesis in human cells

  9. Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease

    Science.gov (United States)

    Flowers, G. Parker; Timberlake, Andrew T.; Mclean, Kaitlin C.; Monaghan, James R.; Crews, Craig M.

    2014-01-01

    Among tetrapods, only urodele salamanders, such as the axolotl Ambystoma mexicanum, can completely regenerate limbs as adults. The mystery of why salamanders, but not other animals, possess this ability has for generations captivated scientists seeking to induce this phenomenon in other vertebrates. Although many recent advances in molecular biology have allowed limb regeneration and tissue repair in the axolotl to be investigated in increasing detail, the molecular toolkit for the study of this process has been limited. Here, we report that the CRISPR-Cas9 RNA-guided nuclease system can efficiently create mutations at targeted sites within the axolotl genome. We identify individual animals treated with RNA-guided nucleases that have mutation frequencies close to 100% at targeted sites. We employ this technique to completely functionally ablate EGFP expression in transgenic animals and recapitulate developmental phenotypes produced by loss of the conserved gene brachyury. Thus, this advance allows a reverse genetic approach in the axolotl and will undoubtedly provide invaluable insight into the mechanisms of salamanders' unique regenerative ability. PMID:24764077

  10. Dynamics and denaturation of a protein. Simulations and neutron scattering on staphylococcus nuclease

    International Nuclear Information System (INIS)

    Goupil-Lamy, Anne

    1997-01-01

    This research thesis reports simulations and experiments of inelastic scattering on the whole frequency spectrum to analyse the vibrations of the staphylococcus nuclease and its fragment, in order to study protein folding. Based on these experiments, information on eigenvectors which describe vibration modes can be directly obtained. Inelastic intensities are indeed fully determined by nuclear cross sections and the mean square displacement of each atom. Some experimentally noticed peaks are then explained by calculating a theoretical spectrum from an analysis of normal modes. The studied fragment is made of 136 c-terminal residues. The fragment structure obtained by molecular dynamics simulation is compared with available experimental data. Then, experiments of neutron scattering on the nuclease of staphylococcus and its fragment have been performed. Quasi elastic scattering spectra have been measured. The author then used simulations to try to reproduce the quasi-elastic spectrum. Experiments of inelastic scattering have then been performed [fr

  11. Mapping of Epitopes Occurring in Bovine α(s1)-Casein Variants by Peptide Microarray Immunoassay.

    Science.gov (United States)

    Lisson, Maria; Erhardt, Georg

    2016-01-01

    Immunoglobulin E epitope mapping of milk proteins reveals important information about their immunologic properties. Genetic variants of αS1-casein, one of the major allergens in bovine milk, are until now not considered when discussing the allergenic potential. Here we describe the complete procedure to assess the allergenicity of αS1-casein variants B and C, which are frequent in most breeds, starting from milk with identification and purification of casein variants by isoelectric focusing (IEF) and anion-exchange chromatography, followed by in vitro gastrointestinal digestion of the casein variants, identification of the resulting peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), in silico analysis of the variant-specific peptides as allergenic epitopes, and determination of their IgE-binding properties by microarray immunoassay with cow's milk allergic human sera.

  12. High-efficiency genome editing via 2A-coupled co-expression of fluorescent proteins and zinc finger nucleases or CRISPR/Cas9 nickase pairs

    DEFF Research Database (Denmark)

    Duda, Katarzyna; Lonowski, Lindsey A; Kofoed-Nielsen, Michael

    2014-01-01

    Targeted endonucleases including zinc finger nucleases (ZFNs) and clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas9 are increasingly being used for genome editing in higher species. We therefore devised a broadly applicable and versatile method for increasing editing...... higher genome editing rates. For ZFNs, this approach, combined with delivery of donors as single-stranded oligodeoxynucleotides and nucleases as messenger ribonucleic acid, enabled high knockin efficiencies in demanding applications, including biallelic codon conversion frequencies reaching 30......-70% at high transfection efficiencies and ∼2% at low transfection efficiencies, simultaneous homozygous knockin mutation of two genes with ∼1.5% efficiency as well as generation of cell pools with almost complete codon conversion via three consecutive targeting and FACS events. Observed off-target effects...

  13. Supersymmetric extension of Hopf maps: N = 4 {sigma}-models and the S{sup 3} {yields} S{sup 2} fibration

    Energy Technology Data Exchange (ETDEWEB)

    Carvalho, L. Faria; Toppan, F., E-mail: leofc@cbpf.b, E-mail: toppan@cbpf.b [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil); Kuznetsova, Z., E-mail: zhanna.kuznetsova@ufabc.edu.b [Universidade Federal do ABC (UFABC), Santo Andre, SP (Brazil)

    2009-07-01

    We discuss four off-shell N = 4 D = 1 supersymmetry transformations, their associated one-dimensional -models and their mutual relations. They are given by I - the (4, 4){sub lin} linear 'root' supermultiplet (supersymmetric extension of R{sup 4}), II - the (3, 4, 1){sub lin} linear supermultiplet (supersymmetric extension of R3), III - the (3, 4, 1){sub nl} non-linear supermultiplet living on S{sup 3} and IV - the (2, 4, 2){sub nl} non-linear supermultiplet living on S{sup 2}. The I {yields} II map is the supersymmetric extension of the R4 {yields} R3 bilinear map, while the II {yields} IV map is the supersymmetric extension of the S{sup 3} {yields} S{sup 2} first Hopf fibration. The restrictions on the S{sup 3}, S{sup 2} spheres are expressed in terms of the stereo graphic projections. The non-linear supermultiplets, whose super transformations are local differential polynomials, are not equivalent to the linear supermultiplets with the same field content. The -models are determined in terms of an unconstrained pre potential of the target coordinates. The Uniformization Problem requires solving an inverse problem for the pre potential. The basic features of the supersymmetric extension of the second and third Hopf maps are briefly sketched. Finally, the Schur's lemma (i.e. the real, complex or quaternionic property) is extended to all minimal linear supermultiplets up to N {<=} 8. (author)

  14. Fine mapping of Best`s macular dystrophy localises the gene in close proximity to, but distinct from, the D115480/ROM1

    Energy Technology Data Exchange (ETDEWEB)

    Graff, C.; Ahlbom, B.E.; Anneren, G. [University Hospital, Uppsala (Sweden)] [and others

    1994-09-01

    Best`s macular dystrophy (BMD) is an autosomal dominant disease characterized by accumulation of lipofuscin beneath the pigment epithelium of the macula, leading to early-onset impairment of central vision. The gene has previously been mapped to 11q13. Based on DNA from 191 people from a large 12-generation family, the gene now has been mapped to a 1.5 cM interval between the markers Fc{epsilon}RI and D11S480/ROM1. By disequilibrium analysis the gene was estimated to be 0.321 cM centromeric to the marker D11S480. Since this on average corresponds to 300 kb, the gene may be at a distance contained in YAC molecules. To physically characterize this region, YAC clones positive for markers flanking BMD have been identified. Sequence analysis of the candidate gene ROM1 did not reveal any mutation. However, one recombination between intragenic ROM1 polymorphisms and BMD was detected, which make it highly unlikely that mutations in ROM1 are causing BMD.

  15. Functional identification of the non-specific nuclease from white spot syndrome virus

    International Nuclear Information System (INIS)

    Li Li; Lin Shumei; Yanga Feng

    2005-01-01

    The product encoded by the wsv191 gene from shrimp white spot syndrome virus (WSSV) is homologous with non-specific nucleases (NSN) of other organisms. To functionally identify the protein, the wsv191 gene was expressed in Escherichia coli as a glutathione S-transferase (GST) fusion protein with 6His-tag at C-terminal. The fusion protein (termed as rWSSV-NSN) was purified using Ni-NTA affinity chromatography under denatured conditions, renatured and characterized by three methods. The results showed that rWSSV-NSN could hydrolyze both DNA and RNA. 5'-RACE result revealed that the transcription initiation site of the wsv191 gene was located at nucleotide residue G of the predicted ATG triplet. Therefore, we concluded that the next ATG should be the genuine translation initiation codon of the wsv191 gene. Western blot analysis revealed that the molecular mass of natural WSSV-NSN was 37 kDa

  16. Selection-independent generation of gene knockout mouse embryonic stem cells using zinc-finger nucleases.

    Directory of Open Access Journals (Sweden)

    Anna Osiak

    Full Text Available Gene knockout in murine embryonic stem cells (ESCs has been an invaluable tool to study gene function in vitro or to generate animal models with altered phenotypes. Gene targeting using standard techniques, however, is rather inefficient and typically does not exceed frequencies of 10(-6. In consequence, the usage of complex positive/negative selection strategies to isolate targeted clones has been necessary. Here, we present a rapid single-step approach to generate a gene knockout in mouse ESCs using engineered zinc-finger nucleases (ZFNs. Upon transient expression of ZFNs, the target gene is cleaved by the designer nucleases and then repaired by non-homologous end-joining, an error-prone DNA repair process that introduces insertions/deletions at the break site and therefore leads to functional null mutations. To explore and quantify the potential of ZFNs to generate a gene knockout in pluripotent stem cells, we generated a mouse ESC line containing an X-chromosomally integrated EGFP marker gene. Applying optimized conditions, the EGFP locus was disrupted in up to 8% of ESCs after transfection of the ZFN expression vectors, thus obviating the need of selection markers to identify targeted cells, which may impede or complicate downstream applications. Both activity and ZFN-associated cytotoxicity was dependent on vector dose and the architecture of the nuclease domain. Importantly, teratoma formation assays of selected ESC clones confirmed that ZFN-treated ESCs maintained pluripotency. In conclusion, the described ZFN-based approach represents a fast strategy for generating gene knockouts in ESCs in a selection-independent fashion that should be easily transferrable to other pluripotent stem cells.

  17. Characterization of a major late herpes simplex virus type 1 mRNA.

    Science.gov (United States)

    Costa, R H; Devi, B G; Anderson, K P; Gaylord, B H; Wagner, E K

    1981-05-01

    A major, late 6-kilobase (6-kb) mRNa mapping in the large unique region of herpes simplex virus type 1 (HSV-1) was characterized by using two recombinant DNA clones, one containing EcoRI fragment G (0.190 to 0.30 map units) in lambda. WES.B (L. Enquist, M. Madden, P. Schiop-Stansly, and G. Vandl Woude, Science 203:541-544, 1979) and one containing HindIII fragment J (0.181 to 0.259 map units) in pBR322. This 6-kb mRNA had its 3' end to the left of 0.231 on the prototypical arrangement of the HSV-1 genome and was transcribed from right to left. It was bounded on both sides by regions containing a large number of distinct mRNA species, and its 3' end was partially colinear with a 1.5-kb mRNA which encoded a 35,000-dalton polypeptide. The 6-kb mRNA encoded a 155,000-dalton polypeptide which was shown to be the only one of this size detectable by hybrid-arrested translation encoded by late polyadenylated polyribosomal RNA. The S1 nuclease mapping experiments indicated that there were no introns in the coding sequence for this mRNA and that its 3' end mapped approximately 800 nucleotides to the left of the BglII site at 0.231, whereas its 5' end extended very close to the BamHI site at 0.266.

  18. Transcription activator-like effector nucleases mediated metabolic engineering for enhanced fatty acids production in Saccharomyces cerevisiae

    KAUST Repository

    Aouida, Mustapha; Li, Lixin; Mahjoub, Ali; Alshareef, Sahar; Ali, Zahir; Piatek, Agnieszka Anna; Mahfouz, Magdy M.

    2015-01-01

    Targeted engineering of microbial genomes holds much promise for diverse biotechnological applications. Transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/Cas9 systems are capable of efficiently editing microbial genomes, including that of Saccharomyces cerevisiae. Here, we demonstrate the use of TALENs to edit the genome of S.cerevisiae with the aim of inducing the overproduction of fatty acids. Heterodimeric TALENs were designed to simultaneously edit the FAA1 and FAA4 genes encoding acyl-CoA synthetases in S.cerevisiae. Functional yeast double knockouts generated using these TALENs over-produce large amounts of free fatty acids into the cell. This study demonstrates the use of TALENs for targeted engineering of yeast and demonstrates that this technology can be used to stimulate the enhanced production of free fatty acids, which are potential substrates for biofuel production. This proof-of-principle study extends the utility of TALENs as excellent genome editing tools and highlights their potential use for metabolic engineering of yeast and other organisms, such as microalgae and plants, for biofuel production. © 2015 The Society for Biotechnology, Japan.

  19. Transcription activator-like effector nucleases mediated metabolic engineering for enhanced fatty acids production in Saccharomyces cerevisiae

    KAUST Repository

    Aouida, Mustapha

    2015-04-01

    Targeted engineering of microbial genomes holds much promise for diverse biotechnological applications. Transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/Cas9 systems are capable of efficiently editing microbial genomes, including that of Saccharomyces cerevisiae. Here, we demonstrate the use of TALENs to edit the genome of S.cerevisiae with the aim of inducing the overproduction of fatty acids. Heterodimeric TALENs were designed to simultaneously edit the FAA1 and FAA4 genes encoding acyl-CoA synthetases in S.cerevisiae. Functional yeast double knockouts generated using these TALENs over-produce large amounts of free fatty acids into the cell. This study demonstrates the use of TALENs for targeted engineering of yeast and demonstrates that this technology can be used to stimulate the enhanced production of free fatty acids, which are potential substrates for biofuel production. This proof-of-principle study extends the utility of TALENs as excellent genome editing tools and highlights their potential use for metabolic engineering of yeast and other organisms, such as microalgae and plants, for biofuel production. © 2015 The Society for Biotechnology, Japan.

  20. Genome Editing with Engineered Nucleases in Economically Important Animals and Plants: State of the Art in the Research Pipeline.

    Science.gov (United States)

    Sovová, Tereza; Kerins, Gerard; Demnerová, Kateřina; Ovesná, Jaroslava

    2017-01-01

    After induced mutagenesis and transgenesis, genome editing is the next step in the development of breeding techniques. Genome editing using site-directed nucleases - including meganucleases, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the CRISPR/Cas9 system - is based on the mechanism of double strand breaks. The nuclease is directed to cleave the DNA at a specific place of the genome which is then repaired by natural repair mechanisms. Changes are introduced during the repair that are either accidental or can be targeted if a DNA template with the desirable sequence is provided. These techniques allow making virtually any change to the genome including specific DNA sequence changes, gene insertion, replacements or deletions with unprecedented precision and specificity while being less laborious and more straightforward compared to traditional breeding techniques or transgenesis. Therefore, the research in this field is developing quickly and, apart from model species, multiple studies have focused on economically important species and agronomically important traits that were the key subjects of this review. In plants, studies have been undertaken on disease resistance, herbicide tolerance, nutrient metabolism and nutritional value. In animals, the studies have mainly focused on disease resistance, meat production and allergenicity of milk. However, none of the promising studies has led to commercialization despite several patent applications. The uncertain legal status of genome-editing methods is one of the reasons for poor commercial development, as it is not clear whether the products would fall under the GMO regulation. We believe this issue should be clarified soon in order to allow promising methods to reach their full potential.

  1. Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis

    DEFF Research Database (Denmark)

    Lonowski, Lindsey A; Narimatsu, Yoshiki; Riaz, Anjum

    2017-01-01

    , FACS enrichment of cells expressing nucleases linked to fluorescent proteins can be used to maximize knockout or knock-in editing efficiencies or to balance editing efficiency and toxic/off-target effects. The two methods can be combined to form a pipeline for cell-line editing that facilitates...

  2. A 'new lease of life': FnCpf1 possesses DNA cleavage activity for genome editing in human cells.

    Science.gov (United States)

    Tu, Mengjun; Lin, Li; Cheng, Yilu; He, Xiubin; Sun, Huihui; Xie, Haihua; Fu, Junhao; Liu, Changbao; Li, Jin; Chen, Ding; Xi, Haitao; Xue, Dongyu; Liu, Qi; Zhao, Junzhao; Gao, Caixia; Song, Zongming; Qu, Jia; Gu, Feng

    2017-11-02

    Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in precision site-specific human genome editing, the range of sequences that AsCpf1 and LbCpf1 can recognize is limited due to the size of this PAM. To address this limitation, we sought to identify a novel Cpf1 nuclease with simpler PAM requirements. Specifically, here we sought to test and engineer FnCpf1, one reported Cpf1 nuclease (FnCpf1) only requires 5'-TTN-3' as a PAM but does not exhibit detectable levels of nuclease-induced indels at certain locus in human cells. Surprisingly, we found that FnCpf1 possesses DNA cleavage activity in human cells at multiple loci. We also comprehensively and quantitatively examined various FnCpf1 parameters in human cells, including spacer sequence, direct repeat sequence and the PAM sequence. Our study identifies FnCpf1 as a new member of the Cpf1 family for human genome editing with distinctive characteristics, which shows promise as a genome editing tool with the potential for both research and therapeutic applications. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. OpenStreetMap Collaborative Prototype, Phase 1

    Science.gov (United States)

    Wolf, Eric B.; Matthews, Greg D.; McNinch, Kevin; Poore, Barbara S.

    2011-01-01

    Phase One of the OpenStreetMap Collaborative Prototype (OSMCP) attempts to determine if the open source software developed for the OpenStreetMap (OSM, http://www.openstreetmap.org) can be used for data contributions and improvements that meet or exceed the requirements for integration into The National Map (http://www.nationalmap.gov). OpenStreetMap Collaborative Prototype Phase One focused on road data aggregated at the state level by the Kansas Data Access and Support Center (DASC). Road data from the DASC were loaded into a system hosted by the U.S. Geological Survey (USGS) National Geospatial Technical Operations Center (NGTOC) in Rolla, Missouri. U.S. Geological Survey editing specifications were developed by NGTOC personnel (J. Walters and G. Matthews, USGS, unpub. report, 2010). Interstate and U.S. Highways in the dataset were edited to the specifications by NGTOC personnel while State roads were edited by DASC personnel. Resulting data were successfully improved to meet standards for The National Map once the system and specifications were in place. The OSM software proved effective in providing a usable platform for collaborative data editing

  4. Osteosarcoma: correlation of T1 map and histology map

    International Nuclear Information System (INIS)

    Suh, Jin Suck; Yun, Mi Jin; Jeong, Eun Kee; Shin, Kyoo Ho; Yang, Woo Ick

    1999-01-01

    To determine whether T1 mapping shows regional differences between viable and necrotic regions of osteosarcomas after anticancer chemotherapy and to assess whether this mapping is able to express the characteristics of various intramural tissue components. Eleven of 20 osteosarcomas were included in this study, while the remaining nine were excluded because the tumor site was inappropriate for comparison of T1 map and tumor macrosection. All patients underwent MR imaging for the purpose of T1 mapping, followed by pre-operative chemotherapy and subsequent limb-salvage surgery. Spin echo pulse sequencing was used with varying TR (100, 200, 400, 800, 1600, and 2400 msec) and a constant TE of 20 msec. Using a C-language software program, T1 relaxation time was calculated on a pixel-by-pixel basis and then a T1 map was generated by using a post-processing program, NIH Image. We attempted correlation of the T1 map and histologic findings, particularly in regions of interest(ROI) if certain areas were different from other regions on either the T1 or histologic map. Value was expressed as an average of the ratio of T1 of ROI and T1 of fat tissue, and this was used as an internal reference for normalization of the measurement. Tumor necrosis was 100 %(Grade IV) in six specimens, and over 90 % (Grade III) in five. Viable tumor cells were found mostly in regions with chondroid matrix and seldom in regions with osteoid matrix. Regardless of cell viability, values ranged from 0.9 to 9.87(mean, 4.02) in tumor necrotic area with osteoid matrices, and from 3.04 to 3.9(mean, 3.55) in areas with chondroid matrices. Other regions with fibrous tissue proliferation, hemorrhage, and fatty necrosis showed values of 2.92-9.83(mean, 7.20), 2.65-5.96(mean,3.59), and 1.43-3.11(mean, 2.68) respectively. The values of various tissues overlapped. No statistically significant difference was found between regions in which tumors were viable and those with tumor necrosis. Although we hypothesized

  5. Mung bean nuclease treatment increases capture specificity of microdroplet-PCR based targeted DNA enrichment.

    Directory of Open Access Journals (Sweden)

    Zhenming Yu

    Full Text Available Targeted DNA enrichment coupled with next generation sequencing has been increasingly used for interrogation of select sub-genomic regions at high depth of coverage in a cost effective manner. Specificity measured by on-target efficiency is a key performance metric for target enrichment. Non-specific capture leads to off-target reads, resulting in waste of sequencing throughput on irrelevant regions. Microdroplet-PCR allows simultaneous amplification of up to thousands of regions in the genome and is among the most commonly used strategies for target enrichment. Here we show that carryover of single-stranded template genomic DNA from microdroplet-PCR constitutes a major contributing factor for off-target reads in the resultant libraries. Moreover, treatment of microdroplet-PCR enrichment products with a nuclease specific to single-stranded DNA alleviates off-target load and improves enrichment specificity. We propose that nuclease treatment of enrichment products should be incorporated in the workflow of targeted sequencing using microdroplet-PCR for target capture. These findings may have a broad impact on other PCR based applications for which removal of template DNA is beneficial.

  6. Mislocalization of XPF-ERCC1 nuclease contributes to reduced DNA repair in XP-F patients.

    Directory of Open Access Journals (Sweden)

    Anwaar Ahmad

    2010-03-01

    Full Text Available Xeroderma pigmentosum (XP is caused by defects in the nucleotide excision repair (NER pathway. NER removes helix-distorting DNA lesions, such as UV-induced photodimers, from the genome. Patients suffering from XP exhibit exquisite sun sensitivity, high incidence of skin cancer, and in some cases neurodegeneration. The severity of XP varies tremendously depending upon which NER gene is mutated and how severely the mutation affects DNA repair capacity. XPF-ERCC1 is a structure-specific endonuclease essential for incising the damaged strand of DNA in NER. Missense mutations in XPF can result not only in XP, but also XPF-ERCC1 (XFE progeroid syndrome, a disease of accelerated aging. In an attempt to determine how mutations in XPF can lead to such diverse symptoms, the effects of a progeria-causing mutation (XPF(R153P were compared to an XP-causing mutation (XPF(R799W in vitro and in vivo. Recombinant XPF harboring either mutation was purified in a complex with ERCC1 and tested for its ability to incise a stem-loop structure in vitro. Both mutant complexes nicked the substrate indicating that neither mutation obviates catalytic activity of the nuclease. Surprisingly, differential immunostaining and fractionation of cells from an XFE progeroid patient revealed that XPF-ERCC1 is abundant in the cytoplasm. This was confirmed by fluorescent detection of XPF(R153P-YFP expressed in Xpf mutant cells. In addition, microinjection of XPF(R153P-ERCC1 into the nucleus of XPF-deficient human cells restored nucleotide excision repair of UV-induced DNA damage. Intriguingly, in all XPF mutant cell lines examined, XPF-ERCC1 was detected in the cytoplasm of a fraction of cells. This demonstrates that at least part of the DNA repair defect and symptoms associated with mutations in XPF are due to mislocalization of XPF-ERCC1 into the cytoplasm of cells, likely due to protein misfolding. Analysis of these patient cells therefore reveals a novel mechanism to potentially

  7. Combinatorial regulation of meiotic holliday junction resolution in C. elegans by HIM-6 (BLM) helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 nucleases.

    Science.gov (United States)

    Agostinho, Ana; Meier, Bettina; Sonneville, Remi; Jagut, Marlène; Woglar, Alexander; Blow, Julian; Jantsch, Verena; Gartner, Anton

    2013-01-01

    Holliday junctions (HJs) are cruciform DNA structures that are created during recombination events. It is a matter of considerable importance to determine the resolvase(s) that promote resolution of these structures. We previously reported that C. elegans GEN-1 is a symmetrically cleaving HJ resolving enzyme required for recombinational repair, but we could not find an overt role in meiotic recombination. Here we identify C. elegans proteins involved in resolving meiotic HJs. We found no evidence for a redundant meiotic function of GEN-1. In contrast, we discovered two redundant HJ resolution pathways likely coordinated by the SLX-4 scaffold protein and also involving the HIM-6/BLM helicase. SLX-4 associates with the SLX-1, MUS-81 and XPF-1 nucleases and has been implicated in meiotic recombination in C. elegans. We found that C. elegans [mus-81; xpf-1], [slx-1; xpf-1], [mus-81; him-6] and [slx-1; him-6] double mutants showed a similar reduction in survival rates as slx-4. Analysis of meiotic diakinesis chromosomes revealed a distinct phenotype in these double mutants. Instead of wild-type bivalent chromosomes, pairs of "univalents" linked by chromatin bridges occur. These linkages depend on the conserved meiosis-specific transesterase SPO-11 and can be restored by ionizing radiation, suggesting that they represent unresolved meiotic HJs. This suggests the existence of two major resolvase activities, one provided by XPF-1 and HIM-6, the other by SLX-1 and MUS-81. In all double mutants crossover (CO) recombination is reduced but not abolished, indicative of further redundancy in meiotic HJ resolution. Real time imaging revealed extensive chromatin bridges during the first meiotic division that appear to be eventually resolved in meiosis II, suggesting back-up resolution activities acting at or after anaphase I. We also show that in HJ resolution mutants, the restructuring of chromosome arms distal and proximal to the CO still occurs, suggesting that CO initiation

  8. Cholesterol-Containing Nuclease-Resistant siRNA Accumulates in Tumors in a Carrier-free Mode and Silences MDR1 Gene

    Directory of Open Access Journals (Sweden)

    Ivan V. Chernikov

    2017-03-01

    Full Text Available Chemical modifications are an effective way to improve the therapeutic properties of small interfering RNAs (siRNAs, making them more resistant to degradation in serum and ensuring their delivery to target cells and tissues. Here, we studied the carrier-free biodistribution and biological activity of a nuclease-resistant anti-MDR1 cholesterol-siRNA conjugate in healthy and tumor-bearing severe combined immune deficiency (SCID mice. The attachment of cholesterol to siRNA provided its efficient accumulation in the liver and in tumors, and reduced its retention in the kidneys after intravenous and intraperitoneal injection. The major part of cholesterol-siRNA after intramuscular and subcutaneous injections remained in the injection place. Confocal microscopy data demonstrated that cholesterol-siRNA spread deep in the tissue and was present in the cytoplasm of almost all the liver and tumor cells. The reduction of P-glycoprotein level in human KB-8-5 xenograft overexpressing the MDR1 gene by 60% was observed at days 5–6 after injection. Then, its initial level recovered by the eighth day. The data showed that, regardless of the mode of administration (intravenous, intraperitoneal, or peritumoral, cholesterol-siMDR efficiently reduced the P-glycoprotein level in tumors. The designed anti-MDR1 conjugate has potential as an adjuvant therapeutic for the reversal of multiple drug resistance of cancer cells.

  9. Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa).

    Science.gov (United States)

    Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

    2017-05-12

    The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

  10. Contig Maps and Genomic Sequencing Identify Candidate Genes in the Usher 1C Locus

    Science.gov (United States)

    Higgins, Michael J.; Day, Colleen D.; Smilinich, Nancy J.; Ni, L.; Cooper, Paul R.; Nowak, Norma J.; Davies, Chris; de Jong, Pieter J.; Hejtmancik, Fielding; Evans, Glen A.; Smith, Richard J.H.; Shows, Thomas B.

    1998-01-01

    Usher syndrome 1C (USH1C) is a congenital condition manifesting profound hearing loss, the absence of vestibular function, and eventual retinal degeneration. The USH1C locus has been mapped genetically to a 2- to 3-cM interval in 11p14–15.1 between D11S899 and D11S861. In an effort to identify the USH1C disease gene we have isolated the region between these markers in yeast artificial chromosomes (YACs) using a combination of STS content mapping and Alu–PCR hybridization. The YAC contig is ∼3.5 Mb and has located several other loci within this interval, resulting in the order CEN-LDHA-SAA1-TPH-D11S1310-(D11S1888/KCNC1)-MYOD1-D11S902D11S921-D11S1890-TEL. Subsequent haplotyping and homozygosity analysis refined the location of the disease gene to a 400-kb interval between D11S902 and D11S1890 with all affected individuals being homozygous for the internal marker D11S921. To facilitate gene identification, the critical region has been converted into P1 artificial chromosome (PAC) clones using sequence-tagged sites (STSs) mapped to the YAC contig, Alu–PCR products generated from the YACs, and PAC end probes. A contig of >50 PAC clones has been assembled between D11S1310 and D11S1890, confirming the order of markers used in haplotyping. Three PAC clones representing nearly two-thirds of the USH1C critical region have been sequenced. PowerBLAST analysis identified six clusters of expressed sequence tags (ESTs), two known genes (BIR,SUR1) mapped previously to this region, and a previously characterized but unmapped gene NEFA (DNA binding/EF hand/acidic amino-acid-rich). GRAIL analysis identified 11 CpG islands and 73 exons of excellent quality. These data allowed the construction of a transcription map for the USH1C critical region, consisting of three known genes and six or more novel transcripts. Based on their map location, these loci represent candidate disease loci for USH1C. The NEFA gene was assessed as the USH1C locus by the sequencing of an amplified NEFA

  11. Genetic maps of polymorphic DNA loci on rat chromosome 1

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Yan-Ping; Remmers, E.F.; Longman, R.E. [National Institutes of Health, Bethesda, MD (United States)] [and others

    1996-09-01

    Genetic linkage maps of loci defined by polymorphic DNA markers on rat chromosome 1 were constructed by genotyping F2 progeny of F344/N x LEW/N, BN/SsN x LEW/N, and DA/Bkl x F344/Hsd inbred rat strains. In total, 43 markers were mapped, of which 3 were restriction fragment length polymorphisms and the others were simple sequence length polymorphisms. Nineteen of these markers were associated with genes. Six markers for five genes, {gamma}-aminobutyric acid receptor {beta}3 (Gabrb3), syntaxin 2 (Stx2), adrenergic receptor {beta}3 (Gabrb3), syntaxin 2 (Stx2), adrenergic receptor {beta}1 (Adrb1), carcinoembryonic antigen gene family member 1 (Cgm1), and lipogenic protein S14 (Lpgp), and 20 anonymous loci were not previously reported. Thirteen gene loci (Myl2, Aldoa, Tnt, Igf2, Prkcg, Cgm4, Calm3, Cgm3, Psbp1, Sa, Hbb, Ins1, and Tcp1) were previously mapped. Comparative mapping analysis indicated that the large portion of rat chromosome 1 is homologous to mouse chromosome 7, although the homologous to mouse chromosome 7, although the homologs of two rat genes are located on mouse chromosomes 17 and 19. Homologs of the rat chromosome 1 genes that we mapped are located on human chromosomes 6, 10, 11, 12, 15, 16, and 19. 38 refs., 1 fig., 3 tabs.

  12. TALE nucleases and next generation GM crops.

    KAUST Repository

    Mahfouz, Magdy M.

    2011-04-01

    Site-specific and adaptable DNA binding domains are essential modules to develop genome engineering technologies for crop improvement. Transcription activator-like effectors (TALEs) proteins are used to provide a highly specific and adaptable DNA binding modules. TALE chimeric nucleases (TALENs) were used to generate site-specific double strand breaks (DSBs) in vitro and in yeast, Caenorhabditis elegans, mammalian and plant cells. The genomic DSBs can be generated at predefined and user-selected loci and repaired by either the non-homologous end joining (NHEJ) or homology dependent repair (HDR). Thus, TALENs can be used to achieve site-specific gene addition, stacking, deletion or inactivation. TALE-based genome engineering tools should be powerful to develop new agricultural biotechnology approaches for crop improvement. Here, we discuss the recent research and the potential applications of TALENs to accelerate the generation of genomic variants through targeted mutagenesis and to produce a non-transgenic GM crops with the desired phenotype.

  13. T1 and T2 Mapping in Cardiology: "Mapping the Obscure Object of Desire".

    Science.gov (United States)

    Mavrogeni, Sophie; Apostolou, Dimitris; Argyriou, Panayiotis; Velitsista, Stella; Papa, Lilika; Efentakis, Stelios; Vernardos, Evangelos; Kanoupaki, Mikela; Kanoupakis, George; Manginas, Athanassios

    The increasing use of cardiovascular magnetic resonance (CMR) is based on its capability to perform biventricular function assessment and tissue characterization without radiation and with high reproducibility. The use of late gadolinium enhancement (LGE) gave the potential of non-invasive biopsy for fibrosis quantification. However, LGE is unable to detect diffuse myocardial disease. Native T1 mapping and extracellular volume fraction (ECV) provide knowledge about pathologies affecting both the myocardium and interstitium that is otherwise difficult to identify. Changes of myocardial native T1 reflect cardiac diseases (acute coronary syndromes, infarction, myocarditis, and diffuse fibrosis, all with high T1) and systemic diseases such as cardiac amyloid (high T1), Anderson-Fabry disease (low T1), and siderosis (low T1). The ECV, an index generated by native and post-contrast T1 mapping, measures the cellular and extracellular interstitial matrix (ECM) compartments. This myocyte-ECM dichotomy has important implications for identifying specific therapeutic targets of great value for heart failure treatment. On the other hand, T2 mapping is superior compared with myocardial T1 and ECM for assessing the activity of myocarditis in recent-onset heart failure. Although these indices can significantly affect the clinical decision making, multicentre studies and a community-wide approach (including MRI vendors, funding, software, contrast agent manufacturers, and clinicians) are still missing. © 2017 S. Karger AG, Basel.

  14. Geologic mapping of Kentucky; a history and evaluation of the Kentucky Geological Survey--U.S. Geological Survey Mapping Program, 1960-1978

    Science.gov (United States)

    Cressman, Earle Rupert; Noger, Martin C.

    1981-01-01

    In 1960, the U.S. Geological Survey and the Kentucky Geological Survey began a program to map the State geologically at a scale of 1:24,000 and to publish the maps as 707 U.S. Geological Survey Geologic Quadrangle Maps. Fieldwork was completed by the spring of 1977, and all maps were published by December 1978. Geologic mapping of the State was proposed by the Kentucky Society of Professional Engineers in 1959. Wallace W. Hagan, Director and State Geologist of the Kentucky Geological Survey, and Preston McGrain, Assistant State Geologist, promoted support for the proposal among organizations such as Chambers of Commerce, industrial associations, professional societies, and among members of the State government. It was also arranged for the U.S. Geological Survey to supply mapping personnel and to publish the maps; the cost would be shared equally by the two organizations. Members of the U.S. Geological Survey assigned to the program were organized as the Branch of Kentucky Geology. Branch headquarters, including an editorial staff, was at Lexington, Ky., but actual mapping was conducted from 18 field offices distributed throughout the State. The Publications Division of the U.S. Geological Survey established a cartographic office at Lexington to prepare the maps for publication. About 260 people, including more than 200 professionals, were assigned to the Branch of Kentucky Geology by the U.S. Geological Survey at one time or another. The most geologists assigned any one year was 61. To complete the mapping and ancillary studies, 661 professional man-years were required, compared with an original estimate of 600 man-years. A wide variety of field methods were used, but most geologists relied on the surveying altimeter to obtain elevations. Surface data were supplemented by drill-hole records, and several dozen shallow diamond-drill holes were drilled to aid the mapping. Geologists generally scribed their own maps, with a consequent saving of publication costs

  15. User’s guide for MapMark4GUI—A graphical user interface for the MapMark4 R package

    Science.gov (United States)

    Shapiro, Jason

    2018-05-29

    MapMark4GUI is an R graphical user interface (GUI) developed by the U.S. Geological Survey to support user implementation of the MapMark4 R statistical software package. MapMark4 was developed by the U.S. Geological Survey to implement probability calculations for simulating undiscovered mineral resources in quantitative mineral resource assessments. The GUI provides an easy-to-use tool to input data, run simulations, and format output results for the MapMark4 package. The GUI is written and accessed in the R statistical programming language. This user’s guide includes instructions on installing and running MapMark4GUI and descriptions of the statistical output processes, output files, and test data files.

  16. USGS Map Indices Overlay Map Service from The National Map

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Map Indices service from The National Map (TNM) consists of 1x1 Degree, 30x60 Minute (100K), 15 Minute (63K), 7.5 Minute (24K), and 3.75 Minute grid...

  17. De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks

    KAUST Repository

    Mahfouz, Magdy M.; Li, Lixin; Shamimuzzaman, Md.; Wibowo, Anjar Tri; Fang, Xiaoyun; Zhu, Jian-Kang

    2011-01-01

    Site-specific and rare cutting nucleases are valuable tools for genome engineering. The generation of double-strand DNA breaks (DSBs) promotes homologous recombination in eukaryotes and can facilitate gene targeting, additions, deletions

  18. Distinct properties of proteases and nucleases in the gut, salivary gland and saliva of southern green stink bug, Nezara viridula

    Science.gov (United States)

    Lomate, Purushottam R.; Bonning, Bryony C.

    2016-01-01

    Stink bugs negatively impact numerous plant species of agricultural and horticultural importance. While efforts to develop effective control measures are underway, the unique digestive physiology of these pests presents a significant hurdle for either protein- or nucleotide-based management options. Here we report the comparative biochemical and proteomic characterization of proteases and nucleases from the gut, salivary gland and saliva of the southern green stink bug, Nezara viridula. The pH optimum for protease activity was acidic (5 to 6) in the gut with the primary proteases being cysteine proteases, and alkaline (8 to 9) in the saliva and salivary gland with the primary proteases being serine proteases. The serine proteases in saliva differ biochemically from trypsin and chymotrypsin, and the cathepsins in the gut and saliva showed distinct properties in inhibitor assays. Nuclease activity (DNase, RNase, dsRNase) was concentrated in the salivary gland and saliva with negligible activity in the gut. The most abundant proteins of the gut (530) and salivary gland (631) identified by proteomic analysis included four gut proteases along with eight proteases and one nuclease from the salivary gland. Understanding of N. viridula digestive physiology will facilitate the design of new strategies for management of this significant pest. PMID:27282882

  19. Zinc Finger Nuclease induced DNA double stranded breaks and rearrangements in MLL

    International Nuclear Information System (INIS)

    Do, To Uyen; Ho, Bay; Shih, Shyh-Jen; Vaughan, Andrew

    2012-01-01

    Highlights: ► A Zinc Finger Nuclease (ZFN) targeting a leukemogenic hot spot for rearrangement in MLL is created. ► The novel ZFN efficiently cleaves MLL exon 13. ► Despite MLL cleavage and evidence of mis-repair, no leukemogenic translocations were produced. ► MLL cleavage alone is insufficient to generate leukemogenic translocations. - Abstract: Radiation treatment or chemotherapy has been linked with a higher risk of secondary cancers such as therapy related Acute Myeloid Leukemia (tAML). Several of these cancers have been shown to be correlated to the introduction of double stranded breaks (DSB) and rearrangements within the Mixed Lineage Leukemia (MLL) gene. We used Zinc Finger Nucleases (ZFNs) to introduce precise cuts within MLL to examine how a single DNA DSB might lead to chromosomal rearrangements. A ZFN targeting exon 13 within the Breakpoint Cluster Region of MLL was transiently expressed in a human lymphoblast cell line originating from a CML patient. Although FISH analysis showed ZFN DSB at this region increased the rate of MLL fragmentation, we were unable to detect leukemogenic rearrangements or translocations via inverse PCR. Interestingly, gene fragmentation as well as small interstitial deletions, insertions and base substitutions increased with the inhibition of DNA-PK, suggesting repair of this particular DSB is linked to non-homologous end joining (NHEJ). Although mis-repair of DSBs may be necessary for the initiation of leukemogenic translocations, a MLL targeted DNA break alone is insufficient

  20. Zinc Finger Nuclease induced DNA double stranded breaks and rearrangements in MLL

    Energy Technology Data Exchange (ETDEWEB)

    Do, To Uyen [Graduate Group in Immunology, University of California Davis, Davis, CA 95616 (United States); Department of Radiation Oncology, University of California Davis, Sacramento CA 95817 (United States); Ho, Bay; Shih, Shyh-Jen [Department of Radiation Oncology, University of California Davis, Sacramento CA 95817 (United States); Vaughan, Andrew, E-mail: Andrew.vaughan@ucdmc.ucdavis.edu [Graduate Group in Immunology, University of California Davis, Davis, CA 95616 (United States); Department of Radiation Oncology, University of California Davis, Sacramento CA 95817 (United States)

    2012-12-15

    Highlights: ► A Zinc Finger Nuclease (ZFN) targeting a leukemogenic hot spot for rearrangement in MLL is created. ► The novel ZFN efficiently cleaves MLL exon 13. ► Despite MLL cleavage and evidence of mis-repair, no leukemogenic translocations were produced. ► MLL cleavage alone is insufficient to generate leukemogenic translocations. - Abstract: Radiation treatment or chemotherapy has been linked with a higher risk of secondary cancers such as therapy related Acute Myeloid Leukemia (tAML). Several of these cancers have been shown to be correlated to the introduction of double stranded breaks (DSB) and rearrangements within the Mixed Lineage Leukemia (MLL) gene. We used Zinc Finger Nucleases (ZFNs) to introduce precise cuts within MLL to examine how a single DNA DSB might lead to chromosomal rearrangements. A ZFN targeting exon 13 within the Breakpoint Cluster Region of MLL was transiently expressed in a human lymphoblast cell line originating from a CML patient. Although FISH analysis showed ZFN DSB at this region increased the rate of MLL fragmentation, we were unable to detect leukemogenic rearrangements or translocations via inverse PCR. Interestingly, gene fragmentation as well as small interstitial deletions, insertions and base substitutions increased with the inhibition of DNA-PK, suggesting repair of this particular DSB is linked to non-homologous end joining (NHEJ). Although mis-repair of DSBs may be necessary for the initiation of leukemogenic translocations, a MLL targeted DNA break alone is insufficient.

  1. Nature’s Benefit Mapping User Guide

    Science.gov (United States)

    Nature’s benefit mapping provides a way to quickly get an idea of where the beneficial aspects of ecosystems can be found. When trying to communicate the value of natural areas to policy makers, members of a community, or another group, it can help to provide an intuitive visual....

  2. ZFNGenome: A comprehensive resource for locating zinc finger nuclease target sites in model organisms

    Directory of Open Access Journals (Sweden)

    Voytas Daniel F

    2011-01-01

    Full Text Available Abstract Background Zinc Finger Nucleases (ZFNs have tremendous potential as tools to facilitate genomic modifications, such as precise gene knockouts or gene replacements by homologous recombination. ZFNs can be used to advance both basic research and clinical applications, including gene therapy. Recently, the ability to engineer ZFNs that target any desired genomic DNA sequence with high fidelity has improved significantly with the introduction of rapid, robust, and publicly available techniques for ZFN design such as the Oligomerized Pool ENgineering (OPEN method. The motivation for this study is to make resources for genome modifications using OPEN-generated ZFNs more accessible to researchers by creating a user-friendly interface that identifies and provides quality scores for all potential ZFN target sites in the complete genomes of several model organisms. Description ZFNGenome is a GBrowse-based tool for identifying and visualizing potential target sites for OPEN-generated ZFNs. ZFNGenome currently includes a total of more than 11.6 million potential ZFN target sites, mapped within the fully sequenced genomes of seven model organisms; S. cerevisiae, C. reinhardtii, A. thaliana, D. melanogaster, D. rerio, C. elegans, and H. sapiens and can be visualized within the flexible GBrowse environment. Additional model organisms will be included in future updates. ZFNGenome provides information about each potential ZFN target site, including its chromosomal location and position relative to transcription initiation site(s. Users can query ZFNGenome using several different criteria (e.g., gene ID, transcript ID, target site sequence. Tracks in ZFNGenome also provide "uniqueness" and ZiFOpT (Zinc Finger OPEN Targeter "confidence" scores that estimate the likelihood that a chosen ZFN target site will function in vivo. ZFNGenome is dynamically linked to ZiFDB, allowing users access to all available information about zinc finger reagents, such as the

  3. TRF2 recruits RTEL1 to telomeres in S phase to promote t-loop unwinding.

    Science.gov (United States)

    Sarek, Grzegorz; Vannier, Jean-Baptiste; Panier, Stephanie; Petrini, John H J; Boulton, Simon J

    2015-02-19

    The helicase RTEL1 promotes t-loop unwinding and suppresses telomere fragility to maintain the integrity of vertebrate telomeres. An interaction between RTEL1 and PCNA is important to prevent telomere fragility, but how RTEL1 engages with the telomere to promote t-loop unwinding is unclear. Here, we establish that the shelterin protein TRF2 recruits RTEL1 to telomeres in S phase, which is required to prevent catastrophic t-loop processing by structure-specific nucleases. We show that the TRF2-RTEL1 interaction is mediated by a metal-coordinating C4C4 motif in RTEL1, which is compromised by the Hoyeraal-Hreidarsson syndrome (HHS) mutation, RTEL1(R1264H). Conversely, we define a TRF2(I124D) substitution mutation within the TRFH domain of TRF2, which eliminates RTEL1 binding and phenocopies the RTEL1(R1264H) mutation, giving rise to aberrant t-loop excision, telomere length heterogeneity, and loss of the telomere as a circle. These results implicate TRF2 in the recruitment of RTEL1 to facilitate t-loop disassembly at telomeres in S phase. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  4. Recognition and repair of 2-aminofluorene- and 2-(acetylamino)fluorene-DNA adducts by UVRABC nuclease

    International Nuclear Information System (INIS)

    Pierce, J.R.; Case, R.; Tang, Moonshong

    1989-01-01

    Recognition of damage induced by N-hydroxy-2-aminofluorene (N-OH-AF) and N-acetoxy-2-(acetylamino)fluorene (NAAAF) in both φX174 RFI supercoiled DNA and a linear DNA fragment by purified UVRA, UVRB, and UVRC proteins was investigated. The authors have previously demonstrated that N-OH-AF and NAAAF treatments produce N-(deoxyguanosin-8-yl)-2-aminofluorene (dG-C8-AF) and N-(deoxyguanosin-8-yl)-2-(acetylamino)fluorene (dG-C8-AAF), respectively, in DNA. Using a piperidine cleavage method and DNA sequence analysis, they have found that all guanine residues can be modified by N-OH-AF and NAAAF. These two kinds of adducts have different impacts on the DNA helix structure; while dG-C8-AF maintains the anti configuration, dG-C8-AAF is in the syn form. φX174 RF DNA-Escherichia coli transfection results indicate that while the uvrA, uvrB, and uvrC gene products are needed to repair dG-C8-AAF, the uvrC, but not the uvrA or uvrB gene products, is needed for repair of dG-C8-Af. However, they have found that in vitro the UVRA, UVRB, and UVRC proteins must work in concert to nick both dG-C8-AF and dG-C8-AAF. In general, the reactions of UVRABC nuclease toward dG-C8-AF are similar to those toward dG-C8-AAF; it incises seven to eight nucleotides from the 5' side and three to four nucleotides from the 3' side of the DNA adduct. Evidence is presented to suggest that hydrolysis on the 3' and 5' sides of the damaged base by UVRABC nuclease is not simultaneous and that at least occasionally hydrolysis occurs only on the 3' side or on the 5' side of the damage site. The possible mechanisms of UVRABC nuclease incision for AF-DNA are discussed

  5. Inhibition of DNA2 nuclease as a therapeutic strategy targeting replication stress in cancer cells.

    Science.gov (United States)

    Kumar, S; Peng, X; Daley, J; Yang, L; Shen, J; Nguyen, N; Bae, G; Niu, H; Peng, Y; Hsieh, H-J; Wang, L; Rao, C; Stephan, C C; Sung, P; Ira, G; Peng, G

    2017-04-17

    Replication stress is a characteristic feature of cancer cells, which is resulted from sustained proliferative signaling induced by activation of oncogenes or loss of tumor suppressors. In cancer cells, oncogene-induced replication stress manifests as replication-associated lesions, predominantly double-strand DNA breaks (DSBs). An essential mechanism utilized by cells to repair replication-associated DSBs is homologous recombination (HR). In order to overcome replication stress and survive, cancer cells often require enhanced HR repair capacity. Therefore, the key link between HR repair and cellular tolerance to replication-associated DSBs provides us with a mechanistic rationale for exploiting synthetic lethality between HR repair inhibition and replication stress. DNA2 nuclease is an evolutionarily conserved essential enzyme in replication and HR repair. Here we demonstrate that DNA2 is overexpressed in pancreatic cancers, one of the deadliest and more aggressive forms of human cancers, where mutations in the KRAS are present in 90-95% of cases. In addition, depletion of DNA2 significantly reduces pancreatic cancer cell survival and xenograft tumor growth, suggesting the therapeutic potential of DNA2 inhibition. Finally, we develop a robust high-throughput biochemistry assay to screen for inhibitors of the DNA2 nuclease activity. The top inhibitors were shown to be efficacious against both yeast Dna2 and human DNA2. Treatment of cancer cells with DNA2 inhibitors recapitulates phenotypes observed upon DNA2 depletion, including decreased DNA double strand break end resection and attenuation of HR repair. Similar to genetic ablation of DNA2, chemical inhibition of DNA2 selectively attenuates the growth of various cancer cells with oncogene-induced replication stress. Taken together, our findings open a new avenue to develop a new class of anticancer drugs by targeting druggable nuclease DNA2. We propose DNA2 inhibition as new strategy in cancer therapy by targeting

  6. A Dream of the Perfect Map – Calvino’s Invisible Cities

    Directory of Open Access Journals (Sweden)

    Mario Vrbančić

    2012-06-01

    Full Text Available The cartographer’s dream is that of a perfect map: a map that perfectly represents a territory, a dream of Divine knowledge; a map that has haunted the ideology of representation throughout history; a map so detailed that it coincides with real space. In a short parable, ‘Museum, on Exactitude in Science’, Borges describes the mysterious gild of cartographers which charts such a map. Although Borges’ narrative finishes with a nostalgic conclusion about a superfluous and forgotten discipline, the cartographer’s dream of a perfect map has never ceased: it has merely varied throughout history. For medieval cartographers the perfect map included the physical cosmos and the spiritual one. In Dante’s time the European ‘mappa mundi’ depicted one single landmass, the Northern Hemisphere, with Jerusalem in the middle and the world is variously shown as dominated or held by God. In the Psalter mappa mundi, which is surmounted by an illustration of the Last Judgement, God holds a little dark red ball, the size of a golf ball – the world. Its size reminds us of the world’s shrinkage due to the advancing technology of transport and communications of the 20th century. Borges’ mystical Aleph on the other hand contains the whole cosmos within its confines (no bigger than the globe held by God on the Hereford map. In a sense the Aleph is a goal of cartography, its theology. Instead of God’s gaze into the unknown distance (as on the Hereford map, Renaissance cartographers imagined the Ptolemaic human gaze looking down on the Earth. The cartographer’s ‘organ of sight’ began to shift from the inner eye of the soul to the physical eye of the body: the idea of the globe as a whole observed by a ‘roving human eye’ is connected to the Renaissance idea of perspectivism. In many respects Renaissance concepts of space laid the foundations for the Enlightenment project. Maps were stripped of spiritual space, of their angels and their

  7. LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis.

    Science.gov (United States)

    Hong, Ye; Sonneville, Remi; Wang, Bin; Scheidt, Viktor; Meier, Bettina; Woglar, Alexander; Demetriou, Sarah; Labib, Karim; Jantsch, Verena; Gartner, Anton

    2018-02-20

    Faithful chromosome segregation and genome maintenance requires the removal of all DNA bridges that physically link chromosomes before cells divide. Using C. elegans embryos we show that the LEM-3/Ankle1 nuclease defines a previously undescribed genome integrity mechanism by processing DNA bridges right before cells divide. LEM-3 acts at the midbody, the structure where abscission occurs at the end of cytokinesis. LEM-3 localization depends on factors needed for midbody assembly, and LEM-3 accumulation is increased and prolonged when chromatin bridges are trapped at the cleavage plane. LEM-3 locally processes chromatin bridges that arise from incomplete DNA replication, unresolved recombination intermediates, or the perturbance of chromosome structure. Proper LEM-3 midbody localization and function is regulated by AIR-2/Aurora B kinase. Strikingly, LEM-3 acts cooperatively with the BRC-1/BRCA1 homologous recombination factor to promote genome integrity. These findings provide a molecular basis for the suspected role of the LEM-3 orthologue Ankle1 in human breast cancer.

  8. Volumetric B1 (+) mapping of the brain at 7T using DREAM.

    Science.gov (United States)

    Nehrke, Kay; Versluis, Maarten J; Webb, Andrew; Börnert, Peter

    2014-01-01

    To tailor and optimize the Dual Refocusing Echo Acquisition Mode (DREAM) approach for volumetric B1 (+) mapping of the brain at 7T. A new DREAM echo timing scheme based on the virtual stimulated echo was derived to minimize potential effects of transverse relaxation. Furthermore, the DREAM B1 (+) mapping performance was investigated in simulations and experimentally in phantoms and volunteers for volumetric applications, studying and optimizing the accuracy of the sequence with respect to saturation effects, slice profile imperfections, and T1 and T2 relaxation. Volumetric brain protocols were compiled for different isotropic resolutions (5-2.5 mm) and SENSE factors, and were studied in vivo for different RF drive modes (circular/linear polarization) and the application of dielectric pads. Volumetric B1 (+) maps with good SNR at 2.5 mm isotropic resolution were acquired in about 20 s or less. The specific absorption rate was well below the safety limits for all scans. Mild flow artefacts were observed in the large vessels. Moreover, a slight contrast in the ventricle was observed in the B1 (+) maps, which could be attributed to T1 and T2 relaxation effects. DREAM enables safe, very fast, and robust volumetric B1 (+) mapping of the brain at ultrahigh fields. Copyright © 2013 Wiley Periodicals, Inc.

  9. A Nuclease from Streptococcus mutans Facilitates Biofilm Dispersal and Escape from Killing by Neutrophil Extracellular Traps.

    Science.gov (United States)

    Liu, Jia; Sun, Luping; Liu, Wei; Guo, Lihong; Liu, Zhaohui; Wei, Xi; Ling, Junqi

    2017-01-01

    Streptococcus mutans is the primary etiologic agent of dental caries and occasionally infective endocarditis, with the ability to form biofilms and disperse cells into distal sites to exacerbate and spread infection. In this study, we identified a nuclease (DeoC) as a S. mutans biofilm dispersal modulating factor through microarray analysis. In vitro assays revealed a dispersal defect of a deoC deletion mutant, and functional studies with purified protein were indicative of the biofilm dispersal activity of DeoC. Neutrophils are a key host response factor restraining bacterial spreading through the formation of neutrophil extracellular traps (NETs), which consist of a nuclear DNA backbone associated with antimicrobial peptides. Therefore, we hypothesized that the dispersed S. mutans might utilize DeoC to degrade NETs and escape killing by the immune system. It was found that S. mutans induced NET formation upon contact with neutrophils, while the presence of NETs in turn enhanced the deoC expression of S. mutans . Fluorescence microscopy inspection showed that deoC deletion resulted in a decreased NET degradation ability of S. mutans and enhanced susceptibility to neutrophil killing. Data obtained from this study assigned two important roles for DeoC in S. mutans : contributing to the spread of infection through mediating biofilm dispersal, and facilitating the escape of S. mutans from neutrophil killing through NET degradation.

  10. Landslides density map of S. Miguel Island, Azores archipelago

    Science.gov (United States)

    Valadão, P.; Gaspar, J. L.; Queiroz, G.; Ferreira, T.

    The Azores archipelago is located in the Atlantic Ocean and is composed of nine volcanic islands. S. Miguel, the largest one, is formed by three active, E-W trending, trachytic central volcanoes with caldera (Sete Cidades, Fogo and Furnas). Chains of basaltic cinder cones link those major volcanic structures. An inactive trachytic central volcano (Povoação) and an old basaltic volcanic complex (Nordeste) comprise the easternmost part of the island. Since the settlement of the island early in the 15th century, several destructive landslides triggered by catastrophic rainfall episodes, earthquakes and volcanic eruptions occurred in different areas of S. Miguel. One unique event killed thousands of people in 1522. Houses and bridges were destroyed, roads were cut, communications, water and energy supply systems became frequently disrupted and areas of fertile land were often buried by mud. Based on (1) historical documents, (2) aerial photographs and (3) field observations, landslide sites were plotted on a topographic map, in order to establish a landslide density map for the island. Data obtained showed that landslide hazard is higher on (1) the main central volcanoes where the thickness of unconsolidated pyroclastic deposits is considerable high and (2) the old basaltic volcanic complex, marked by deep gullies developed on thick sequences of lava flows. In these areas, caldera walls, fault scarps, steep valley margins and sea cliffs are potentially hazardous.

  11. The NMDAR subunit NR3A interacts with microtubule-associated protein 1S in the brain

    DEFF Research Database (Denmark)

    Eriksson, Maria; Samuelsson, Helena; Samuelsson, Eva-Britt

    2007-01-01

    -proximal part of the NR3A C-terminus. MAP1S belongs to the same family as MAP1A and MAP1B, and was found to be abundant in both postnatal and adult rat brain. In hippocampal neurons the distribution-pattern of MAP1S resembled that of beta-tubulin III, but a fraction of the protein colocalized with synaptic...

  12. Thioredoxin-1 promotes survival in cells exposed to S-nitrosoglutathione: Correlation with reduction of intracellular levels of nitrosothiols and up-regulation of the ERK1/2 MAP Kinases

    International Nuclear Information System (INIS)

    Arai, Roberto J.; Ogata, Fernando T.; Batista, Wagner L.; Masutani, Hiroshi; Yodoi, Junji; Debbas, Victor; Augusto, Ohara; Stern, Arnold; Monteiro, Hugo P.

    2008-01-01

    Accumulating evidence indicates that post-translational protein modifications by nitric oxide and its derived species are critical effectors of redox signaling in cells. These protein modifications are most likely controlled by intracellular reductants. Among them, the importance of the 12 kDa dithiol protein thioredoxin-1 (TRX-1) has been increasingly recognized. However, the effects of TRX-1 in cells exposed to exogenous nitrosothiols remain little understood. We investigated the levels of intracellular nitrosothiols and survival signaling in HeLa cells over-expressing TRX-1 and exposed to S-nitrosoglutahione (GSNO). A role for TRX-1 expression on GSNO catabolism and cell viability was demonstrated by the concentration-dependent effects of GSNO on decreasing TRX-1 expression, activation of caspase-3, and increasing cell death. The over-expression of TRX-1 in HeLa cells partially attenuated caspase-3 activation and enhanced cell viability upon GSNO treatment. This was correlated with reduction of intracellular levels of nitrosothiols and increasing levels of nitrite and nitrotyrosine. The involvement of ERK, p38 and JNK pathways were investigated in parental cells treated with GSNO. Activation of ERK1/2 MAP kinases was shown to be critical for survival signaling. In cells over-expressing TRX-1, basal phosphorylation levels of ERK1/2 MAP kinases were higher and further increased after GSNO treatment. These results indicate that the enhanced cell viability promoted by TRX-1 correlates with its capacity to regulate the levels of intracellular nitrosothiols and to up-regulate the survival signaling pathway mediated by the ERK1/2 MAP kinases

  13. Comparative high-resolution mapping of the wax inhibitors Iw1 and Iw2 in hexaploid wheat.

    Directory of Open Access Journals (Sweden)

    Haibin Wu

    Full Text Available The wax (glaucousness on wheat leaves and stems is mainly controlled by two sets of genes: glaucousness loci (W1 and W2 and non-glaucousness loci (Iw1 and Iw2. The non-glaucousness (Iw loci act as inhibitors of the glaucousness loci (W. High-resolution comparative genetic linkage maps of the wax inhibitors Iw1 originating from Triticum dicoccoides, and Iw2 from Aegilops tauschii were developed by comparative genomics analyses of Brachypodium, sorghum and rice genomic sequences corresponding to the syntenic regions of the Iw loci in wheat. Eleven Iw1 and eight Iw2 linked EST markers were developed and mapped to linkage maps on the distal regions of chromosomes 2BS and 2DS, respectively. The Iw1 locus mapped within a 0.96 cM interval flanked by the BE498358 and CA499581 EST markers that are collinear with 122 kb, 202 kb, and 466 kb genomic regions in the Brachypodium 5S chromosome, the sorghum 6S chromosome and the rice 4S chromosome, respectively. The Iw2 locus was located in a 4.1 to 5.4-cM interval in chromosome 2DS that is flanked by the CJ886319 and CJ519831 EST markers, and this region is collinear with a 2.3 cM region spanning the Iw1 locus on chromosome 2BS. Both Iw1 and Iw2 co-segregated with the BF474014 and CJ876545 EST markers, indicating they are most likely orthologs on 2BS and 2DS. These high-resolution maps can serve as a framework for chromosome landing, physical mapping and map-based cloning of the wax inhibitors in wheat.

  14. Disabling a Type I-E CRISPR-Cas Nuclease with a Bacteriophage-Encoded Anti-CRISPR Protein

    Directory of Open Access Journals (Sweden)

    April Pawluk

    2017-12-01

    Full Text Available CRISPR (clustered regularly interspaced short palindromic repeat-Cas adaptive immune systems are prevalent defense mechanisms in bacteria and archaea. They provide sequence-specific detection and neutralization of foreign nucleic acids such as bacteriophages and plasmids. One mechanism by which phages and other mobile genetic elements are able to overcome the CRISPR-Cas system is through the expression of anti-CRISPR proteins. Over 20 different families of anti-CRISPR proteins have been described, each of which inhibits a particular type of CRISPR-Cas system. In this work, we determined the structure of type I-E anti-CRISPR protein AcrE1 by X-ray crystallography. We show that AcrE1 binds to the CRISPR-associated helicase/nuclease Cas3 and that the C-terminal region of the anti-CRISPR protein is important for its inhibitory activity. We further show that AcrE1 can convert the endogenous type I-E CRISPR system into a programmable transcriptional repressor.

  15. Optomagnetic Detection of MicroRNA Based on Duplex-Specific Nuclease-Assisted Target Recycling and Multilayer Core-Satellite Magnetic Superstructures

    DEFF Research Database (Denmark)

    Tian, Bo; Ma, Jing; Qiu, Zhen

    2017-01-01

    -efficiency, and potential for bioresponsive multiplexing. Herein, we demonstrate a sensitive and rapid miRNA detection method based on optomagnetic read-out, duplex-specific nuclease (DSN)-assisted target recycling, and the use of multilayer core-satellite magnetic superstructures. Triggered by the presence of target mi...

  16. Geology and resource assessment of Costa Rica at 1:500,000 scale; a digital representation of maps of the U.S. Geological Survey's 1987 folio I-1865

    Science.gov (United States)

    Schruben, Paul G.

    1997-01-01

    This CD-ROM contains digital versions of the geology and resource assessment maps of Costa Rica originally published in USGS Folio I-1865 (U.S. Geological Survey, the Direccion General de Geologia, Minas e Hidrocarburos, and the Universidad de Costa Rica, 1987) at a scale of 1:500,000. The following layers are available on the CD-ROM: geology and faults; favorable domains for selected deposit types; Bouguer gravity data; isostatic gravity contours; mineral deposits, prospects, and occurrences; and rock geochemistry sample points. For DOS users, the CD-ROM contains MAPPER, a user-friendly map display program. Some of the maps are also provided in the following additional formats on the CD-ROM: (1) ArcView 1 and 3, (2) ARC/INFO 6.1.2 Export, (3) Digital Line Graph (DLG) Optional, and (4) Drawing Exchange File (DXF.)

  17. Phosphorylation sites of Arabidopsis MAP Kinase Substrate 1 (MKS1)

    DEFF Research Database (Denmark)

    Caspersen, M.B.; Qiu, J.-L.; Zhang, X.

    2007-01-01

    The Arabidopsis MAP kinase 4 (MPK4) substrate MKS1 was expressed in Escherichia coli and purified, full-length, 6x histidine (His)-tagged MKS1 was phosphorylated in vitro by hemagglutinin (HA)-tagged MPK4 immuno-precipitated from plants. MKS1 phosphorylation was initially verified by electrophore......The Arabidopsis MAP kinase 4 (MPK4) substrate MKS1 was expressed in Escherichia coli and purified, full-length, 6x histidine (His)-tagged MKS1 was phosphorylated in vitro by hemagglutinin (HA)-tagged MPK4 immuno-precipitated from plants. MKS1 phosphorylation was initially verified...... phosphopeptide detection. As MAP kinases generally phosphorylate serine or threonine followed by proline (Ser/Thr-Pro), theoretical masses of potentially phosphorylated peptides were calculated and mass spectrometric peaks matching these masses were fragmented and searched for a neutral-loss signal...... at approximately 98 Da indicative of phosphorylation. Additionally, mass spectrometric peaks present in the MPK4-treated MKS1, but not in the control peptide map of untreated MKS1, were fragmented. Fragmentation spectra were subjected to a MASCOT database search which identified three of the twelve Ser-Pro serine...

  18. High-resolution physical map for chromosome 16q12.1-q13, the Blau syndrome locus

    Directory of Open Access Journals (Sweden)

    Bonavita Gina

    2002-08-01

    Full Text Available Abstract Background The Blau syndrome (MIM 186580, an autosomal dominant granulomatous disease, was previously mapped to chromosome 16p12-q21. However, inconsistent physical maps of the region and consequently an unknown order of microsatellite markers, hampered us from further refining the genetic locus for the Blau syndrome. To address this problem, we constructed our own high-resolution physical map for the Blau susceptibility region. Results We generated a high-resolution physical map that provides more than 90% coverage of a refined Blau susceptibility region. The map consists of four contigs of sequence tagged site-based bacterial artificial chromosomes with a total of 124 bacterial artificial chromosomes, and spans approximately 7.5 Mbp; however, three gaps still exist in this map with sizes of 425, 530 and 375 kbp, respectively, estimated from radiation hybrid mapping. Conclusions Our high-resolution map will assist genetic studies of loci in the interval from D16S3080, near D16S409, and D16S408 (16q12.1 to 16q13.

  19. Efficient methods for targeted mutagenesis in zebrafish using zinc-finger nucleases: data from targeting of nine genes using CompoZr or CoDA ZFNs.

    Directory of Open Access Journals (Sweden)

    Raman Sood

    Full Text Available Recently, it has been shown that targeted mutagenesis using zinc-finger nucleases (ZFNs and transcription activator-like effector nucleases (TALENs can be used to generate knockout zebrafish lines for analysis of their function and/or developing disease models. A number of different methods have been developed for the design and assembly of gene-specific ZFNs and TALENs, making them easily available to most zebrafish researchers. Regardless of the choice of targeting nuclease, the process of generating mutant fish is similar. It is a time-consuming and multi-step process that can benefit significantly from development of efficient high throughput methods. In this study, we used ZFNs assembled through either the CompoZr (Sigma-Aldrich or the CoDA (context-dependent assembly platforms to generate mutant zebrafish for nine genes. We report our improved high throughput methods for 1 evaluation of ZFNs activity by somatic lesion analysis using colony PCR, eliminating the need for plasmid DNA extractions from a large number of clones, and 2 a sensitive founder screening strategy using fluorescent PCR with PIG-tailed primers that eliminates the stutter bands and accurately identifies even single nucleotide insertions and deletions. Using these protocols, we have generated multiple mutant alleles for seven genes, five of which were targeted with CompoZr ZFNs and two with CoDA ZFNs. Our data also revealed that at least five-fold higher mRNA dose was required to achieve mutagenesis with CoDA ZFNs than with CompoZr ZFNs, and their somatic lesion frequency was lower (<5% when compared to CopmoZr ZFNs (9-98%. This work provides high throughput protocols for efficient generation of zebrafish mutants using ZFNs and TALENs.

  20. Modeling of 5 ' nuclease real-time responses for optimization of a high-throughput enrichment PCR procedure for Salmonella enterica

    DEFF Research Database (Denmark)

    Knutsson, R.; Löfström, Charlotta; Grage, H.

    2002-01-01

    The performance of a 5' nuclease real-time PCR assay was studied to optimize an automated method of detection of preenriched Salmonella enterica cells in buffered peptone water (BPW). The concentrations and interactions of the PCR reagents were evaluated on the basis of two detection responses, t...

  1. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency.

    Science.gov (United States)

    Song, Jun; Yang, Dongshan; Xu, Jie; Zhu, Tianqing; Chen, Y Eugene; Zhang, Jifeng

    2016-01-28

    Zinc-finger nuclease, transcription activator-like effector nuclease and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) are becoming major tools for genome editing. Importantly, knock-in in several non-rodent species has been finally achieved thanks to these customizable nucleases; yet the rates remain to be further improved. We hypothesize that inhibiting non-homologous end joining (NHEJ) or enhancing homology-directed repair (HDR) will improve the nuclease-mediated knock-in efficiency. Here we show that the in vitro application of an HDR enhancer, RS-1, increases the knock-in efficiency by two- to five-fold at different loci, whereas NHEJ inhibitor SCR7 has minimal effects. We then apply RS-1 for animal production and have achieved multifold improvement on the knock-in rates as well. Our work presents tools to nuclease-mediated knock-in animal production, and sheds light on improving gene-targeting efficiencies on pluripotent stem cells.

  2. RS-1 enhances CRISPR/Cas9- and TALEN-mediated knock-in efficiency

    Science.gov (United States)

    Song, Jun; Yang, Dongshan; Xu, Jie; Zhu, Tianqing; Chen, Y. Eugene; Zhang, Jifeng

    2016-01-01

    Zinc-finger nuclease, transcription activator-like effector nuclease and CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) are becoming major tools for genome editing. Importantly, knock-in in several non-rodent species has been finally achieved thanks to these customizable nucleases; yet the rates remain to be further improved. We hypothesize that inhibiting non-homologous end joining (NHEJ) or enhancing homology-directed repair (HDR) will improve the nuclease-mediated knock-in efficiency. Here we show that the in vitro application of an HDR enhancer, RS-1, increases the knock-in efficiency by two- to five-fold at different loci, whereas NHEJ inhibitor SCR7 has minimal effects. We then apply RS-1 for animal production and have achieved multifold improvement on the knock-in rates as well. Our work presents tools to nuclease-mediated knock-in animal production, and sheds light on improving gene-targeting efficiencies on pluripotent stem cells. PMID:26817820

  3. Ground motion models used in the 2014 U.S. National Seismic Hazard Maps

    Science.gov (United States)

    Rezaeian, Sanaz; Petersen, Mark D.; Moschetti, Morgan P.

    2015-01-01

    The National Seismic Hazard Maps (NSHMs) are an important component of seismic design regulations in the United States. This paper compares hazard using the new suite of ground motion models (GMMs) relative to hazard using the suite of GMMs applied in the previous version of the maps. The new source characterization models are used for both cases. A previous paper (Rezaeian et al. 2014) discussed the five NGA-West2 GMMs used for shallow crustal earthquakes in the Western United States (WUS), which are also summarized here. Our focus in this paper is on GMMs for earthquakes in stable continental regions in the Central and Eastern United States (CEUS), as well as subduction interface and deep intraslab earthquakes. We consider building code hazard levels for peak ground acceleration (PGA), 0.2-s, and 1.0-s spectral accelerations (SAs) on uniform firm-rock site conditions. The GMM modifications in the updated version of the maps created changes in hazard within 5% to 20% in WUS; decreases within 5% to 20% in CEUS; changes within 5% to 15% for subduction interface earthquakes; and changes involving decreases of up to 50% and increases of up to 30% for deep intraslab earthquakes for most U.S. sites. These modifications were combined with changes resulting from modifications in the source characterization models to obtain the new hazard maps.

  4. MR relaxometry in chronic liver diseases: Comparison of T1 mapping, T2 mapping, and diffusion-weighted imaging for assessing cirrhosis diagnosis and severity

    Energy Technology Data Exchange (ETDEWEB)

    Cassinotto, Christophe, E-mail: christophe.cassinotto@chu-bordeaux.fr [Department of Diagnostic and Interventional Imaging, Hôpital Haut-Lévêque, Centre Hospitalier Universitaire et Université de Bordeaux, 1 Avenue de Magellan, 33604 Pessac (France); INSERM U1053, Université Bordeaux, Bordeaux (France); Feldis, Matthieu, E-mail: matthieu.feldis@chu-bordeaux.fr [Department of Diagnostic and Interventional Imaging, Hôpital Haut-Lévêque, Centre Hospitalier Universitaire et Université de Bordeaux, 1 Avenue de Magellan, 33604 Pessac (France); Vergniol, Julien, E-mail: julien.vergniol@chu-bordeaux.fr [Centre D’investigation de la Fibrose Hépatique, Hôpital Haut-Lévêque, Centre Hospitalier Universitaire de Bordeaux, 1 Avenue de Magellan, 33604 Pessac (France); Mouries, Amaury, E-mail: amaury.mouries@chu-bordeaux.fr [Department of Diagnostic and Interventional Imaging, Hôpital Haut-Lévêque, Centre Hospitalier Universitaire et Université de Bordeaux, 1 Avenue de Magellan, 33604 Pessac (France); Cochet, Hubert, E-mail: hubert.cochet@chu-bordeaux.fr [Department of Diagnostic and Interventional Imaging, Hôpital Haut-Lévêque, Centre Hospitalier Universitaire et Université de Bordeaux, 1 Avenue de Magellan, 33604 Pessac (France); and others

    2015-08-15

    Highlights: • The use of MR to classify cirrhosis in different stages is a new interesting field. • We compared liver and spleen T1 mapping, T2 mapping and diffusion-weighted imaging. • MR relaxometry using liver T1 mapping is accurate for the diagnosis of cirrhosis. • Liver T1 mapping shows that values increase with the severity of cirrhosis. • Diffusion-weighted imaging is less accurate than T1 mapping while T2 mapping is not reliable. - Abstract: Background: MR relaxometry has been extensively studied in the field of cardiac diseases, but its contribution to liver imaging is unclear. We aimed to compare liver and spleen T1 mapping, T2 mapping, and diffusion-weighted MR imaging (DWI) for assessing the diagnosis and severity of cirrhosis. Methods: We prospectively included 129 patients with normal (n = 40) and cirrhotic livers (n = 89) from May to September 2014. Non-enhanced liver T1 mapping, splenic T2 mapping, and liver and splenic DWI were measured and compared for assessing cirrhosis severity using Child-Pugh score, MELD score, and presence or not of large esophageal varices (EVs) and liver stiffness measurements using Fibroscan{sup ®} as reference. Results: Liver T1 mapping was the only variable demonstrating significant differences between normal patients (500 ± 79 ms), Child-Pugh A patients (574 ± 84 ms) and Child-Pugh B/C patients (690 ± 147 ms; all p-values <0.00001). Liver T1 mapping had a significant correlation with Child-Pugh score (Pearson's correlation coefficient of 0.46), MEDL score (0.30), and liver stiffness measurement (0.52). Areas under the receiver operating characteristic curves of liver T1 mapping for the diagnosis of cirrhosis (O.85; 95% confidence intervals (CI), 0.77–0.91), Child-Pugh B/C cirrhosis (0.87; 95%CI, 0.76–0.93), and large EVs (0.75; 95%CI, 0.63–0.83) were greater than that of spleen T2 mapping, liver and spleen DWI (all p-values < 0.01). Conclusion: Liver T1 mapping is a promising new diagnostic

  5. MR relaxometry in chronic liver diseases: Comparison of T1 mapping, T2 mapping, and diffusion-weighted imaging for assessing cirrhosis diagnosis and severity

    International Nuclear Information System (INIS)

    Cassinotto, Christophe; Feldis, Matthieu; Vergniol, Julien; Mouries, Amaury; Cochet, Hubert

    2015-01-01

    Highlights: • The use of MR to classify cirrhosis in different stages is a new interesting field. • We compared liver and spleen T1 mapping, T2 mapping and diffusion-weighted imaging. • MR relaxometry using liver T1 mapping is accurate for the diagnosis of cirrhosis. • Liver T1 mapping shows that values increase with the severity of cirrhosis. • Diffusion-weighted imaging is less accurate than T1 mapping while T2 mapping is not reliable. - Abstract: Background: MR relaxometry has been extensively studied in the field of cardiac diseases, but its contribution to liver imaging is unclear. We aimed to compare liver and spleen T1 mapping, T2 mapping, and diffusion-weighted MR imaging (DWI) for assessing the diagnosis and severity of cirrhosis. Methods: We prospectively included 129 patients with normal (n = 40) and cirrhotic livers (n = 89) from May to September 2014. Non-enhanced liver T1 mapping, splenic T2 mapping, and liver and splenic DWI were measured and compared for assessing cirrhosis severity using Child-Pugh score, MELD score, and presence or not of large esophageal varices (EVs) and liver stiffness measurements using Fibroscan ® as reference. Results: Liver T1 mapping was the only variable demonstrating significant differences between normal patients (500 ± 79 ms), Child-Pugh A patients (574 ± 84 ms) and Child-Pugh B/C patients (690 ± 147 ms; all p-values <0.00001). Liver T1 mapping had a significant correlation with Child-Pugh score (Pearson's correlation coefficient of 0.46), MEDL score (0.30), and liver stiffness measurement (0.52). Areas under the receiver operating characteristic curves of liver T1 mapping for the diagnosis of cirrhosis (O.85; 95% confidence intervals (CI), 0.77–0.91), Child-Pugh B/C cirrhosis (0.87; 95%CI, 0.76–0.93), and large EVs (0.75; 95%CI, 0.63–0.83) were greater than that of spleen T2 mapping, liver and spleen DWI (all p-values < 0.01). Conclusion: Liver T1 mapping is a promising new diagnostic tool for

  6. Chinese HJ-1C SAR And Its Wind Mapping Capability

    Science.gov (United States)

    Huang, Weigen; Chen, Fengfeng; Yang, Jingsong; Fu, Bin; Chen, Peng; Zhang, Chan

    2010-04-01

    Chinese Huan Jing (HJ)-1C synthetic aperture radar (SAR) satellite has been planed to be launched in 2010. HJ-1C satellite will fly in a sun-synchronous polar orbit of 500-km altitude. SAR will be the only sensor on board the satellite. It operates in S band with VV polarization. Its image mode has the incidence angles 25°and 47°at the near and far sides of the swath respectively. There are two selectable SAR modes of operation, which are fine resolution beams and standard beams respectively. The sea surface wind mapping capability of the SAR has been examined using M4S radar imaging model developed by Romeiser. The model is based on Bragg scattering theory in a composite surface model expansion. It accounts for contributions of the full ocean wave spectrum to the radar backscatter from ocean surface. The model reproduces absolute normalized radar cross section (NRCS) values for wide ranges of wind speeds. The model results of HJ-1C SAR have been compared with the model results of Envisat ASAR. It shows that HJ-1C SAR is as good as Envisat ASAR at sea surface wind mapping.

  7. Knockout of exogenous EGFP gene in porcine somatic cells using zinc-finger nucleases

    International Nuclear Information System (INIS)

    Watanabe, Masahito; Umeyama, Kazuhiro; Matsunari, Hitomi; Takayanagi, Shuko; Haruyama, Erika; Nakano, Kazuaki; Fujiwara, Tsukasa; Ikezawa, Yuka; Nakauchi, Hiromitsu

    2010-01-01

    Research highlights: → EGFP gene integrated in porcine somatic cells could be knocked out using the ZFN-KO system. → ZFNs induced targeted mutations in porcine primary cultured cells. → Complete absence of EGFP fluorescence was confirmed in ZFN-treated cells. -- Abstract: Zinc-finger nucleases (ZFNs) are expected as a powerful tool for generating gene knockouts in laboratory and domestic animals. Currently, it is unclear whether this technology can be utilized for knocking-out genes in pigs. Here, we investigated whether knockout (KO) events in which ZFNs recognize and cleave a target sequence occur in porcine primary cultured somatic cells that harbor the exogenous enhanced green fluorescent protein (EGFP) gene. ZFN-encoding mRNA designed to target the EGFP gene was introduced by electroporation into the cell. Using the Surveyor nuclease assay and flow cytometric analysis, we confirmed ZFN-induced cleavage of the target sequence and the disappearance of EGFP fluorescence expression in ZFN-treated cells. In addition, sequence analysis revealed that ZFN-induced mutations such as base substitution, deletion, or insertion were generated in the ZFN cleavage site of EGFP-expression negative cells that were cloned from ZFN-treated cells, thereby showing it was possible to disrupt (i.e., knock out) the function of the EGFP gene in porcine somatic cells. To our knowledge, this study provides the first evidence that the ZFN-KO system can be applied to pigs. These findings may open a new avenue to the creation of gene KO pigs using ZFN-treated cells and somatic cell nuclear transfer.

  8. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases.

    Science.gov (United States)

    Citorik, Robert J; Mimee, Mark; Lu, Timothy K

    2014-11-01

    Current antibiotics tend to be broad spectrum, leading to indiscriminate killing of commensal bacteria and accelerated evolution of drug resistance. Here, we use CRISPR-Cas technology to create antimicrobials whose spectrum of activity is chosen by design. RNA-guided nucleases (RGNs) targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation. The DNA targets of RGNs can be undesirable genes or polymorphisms, including antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli. Delivery of RGNs significantly improves survival in a Galleria mellonella infection model. We also show that RGNs enable modulation of complex bacterial populations by selective knockdown of targeted strains based on genetic signatures. RGNs constitute a class of highly discriminatory, customizable antimicrobials that enact selective pressure at the DNA level to reduce the prevalence of undesired genes, minimize off-target effects and enable programmable remodeling of microbiota.

  9. Q-S synchronization in 3D Henon-like map and generalized Henon map via a scalar controller

    International Nuclear Information System (INIS)

    Yan Zhenya

    2005-01-01

    In this Letter, a generalized, systematic and automatic backstepping scheme is developed to investigate the Q-S synchronization of two identical 3a discrete-time dynamical systems and two different 3D discrete-time dynamical systems. With the aid of symbolic-numeric computation, we use the proposed scheme to illustrate chaos synchronization between two identical 3D generalized Henon map and Q-S synchronization between two different 3D generalized Henon map and Henon-like map via a scalar controller, respectively. Moreover numerical simulations are used to verify the effectiveness of the proposed scheme. In addition, the scheme can be also applied to investigate the tracking problem in the discrete-time systems and to generate automatically the scalar controller in computer with the aid of symbolic-numeric computation

  10. Temperature Map of Tempel 1

    Science.gov (United States)

    2005-01-01

    A temperature map of the nucleus with different spatial resolutions. The context image (in black and white) is a HRIVIS image taken just before impact. The color bar in the middle gives temperature in Kelvins. The sun is to the right in all images. These data were acquired with the IR spectrometer using signal between 1.8 and 2.2 um and modeled to contain both a reflected and an emitted component. After this model is applied, the resulting number is a temperature which is represented by different colors with red being the highest and purple the coldest. The derived temperature varies from 260 +/- 6K to 329 +/- 8K. Shadows are the coolest temperatures, and the point directly below the sun is hottest. These temperatures indicate that the thermal inertia of the surface (the quality of the surface describing the ability to conduct and store heat) is low. In other words, on Tempel 1, it is hot in the sun and cold in the shadows. A value for thermal inertia is estimated at 2/s1/2.

  11. DAWN GRAND MAP CERES HYDROGEN MAP V1.0

    Data.gov (United States)

    National Aeronautics and Space Administration — A global map of the concentration of hydrogen within the regolith of asteroid 1 Ceres on twenty-degree quasi-equal-area pixels is provided. Hydrogen concentrations...

  12. Specification for the U.S. Geological Survey Historical Topographic Map Collection

    Science.gov (United States)

    Allord, Gregory J.; Walter, Jennifer L.; Fishburn, Kristin A.; Shea, Gale A.

    2014-01-01

    This document provides the detailed requirements for producing, archiving, and disseminating a comprehensive digital collection of topographic maps for the U.S. Geological Survey (USGS) Historical Topographic Map Collection (HTMC). The HTMC is a digital archive of about 190,000 printed topographic maps published by the USGS from the inception of the topographic mapping program in 1884 until the last paper topographic map using lithographic printing technology was published in 2006. The HTMC provides a comprehensive digital repository of all scales and all editions of USGS printed topographic maps that is easily discovered, browsed, and downloaded by the public at no cost. The HTMC provides ready access to maps that are no longer available for distribution in print. A digital file representing the original paper historical topographic map is produced for each historical map in the HTMC in georeferenced PDF (GeoPDF) format (a portable document format [PDF] with a geospatial extension).

  13. Blanding’s Turtle (Emydoidea blandingii Potential Habitat Mapping Using Aerial Orthophotographic Imagery and Object Based Classification

    Directory of Open Access Journals (Sweden)

    Douglas J. King

    2012-01-01

    Full Text Available Blanding’s turtle (Emydoidea blandingii is a threatened species under Canada’s Species at Risk Act. In southern Québec, field based inventories are ongoing to determine its abundance and potential habitat. The goal of this research was to develop means for mapping of potential habitat based on primary habitat attributes that can be detected with high-resolution remotely sensed imagery. Using existing spring leaf-off 20 cm resolution aerial orthophotos of a portion of Gatineau Park where some Blanding’s turtle observations had been made, habitat attributes were mapped at two scales: (1 whole wetlands; (2 within wetland habitat features of open water, vegetation (used for camouflage and thermoregulation, and logs (used for spring sun-basking. The processing steps involved initial pixel-based classification to eliminate most areas of non-wetland, followed by object-based segmentations and classifications using a customized rule sequence to refine the wetland map and to map the within wetland habitat features. Variables used as inputs to the classifications were derived from the orthophotos and included image brightness, texture, and segmented object shape and area. Independent validation using field data and visual interpretation showed classification accuracy for all habitat attributes to be generally over 90% with a minimum of 81.5% for the producer’s accuracy of logs. The maps for each attribute were combined to produce a habitat suitability map for Blanding’s turtle. Of the 115 existing turtle observations, 92.3% were closest to a wetland of the two highest suitability classes. High-resolution imagery combined with object-based classification and habitat suitability mapping methods such as those presented provide a much more spatially explicit representation of detailed habitat attributes than can be obtained through field work alone. They can complement field efforts to document and track turtle activities and can contribute to

  14. High Density Nodes in the Chaotic Region of 1D Discrete Maps

    Directory of Open Access Journals (Sweden)

    George Livadiotis

    2018-01-01

    Full Text Available We report on the definition and characteristics of nodes in the chaotic region of bifurcation diagrams in the case of 1D mono-parametrical and S-unimodal maps, using as guiding example the logistic map. We examine the arrangement of critical curves, the identification and arrangement of nodes, and the connection between the periodic windows and nodes in the chaotic zone. We finally present several characteristic features of nodes, which involve their convergence and entropy.

  15. Wet Snow Mapping in Southern Ontario with Sentinel-1A Observations

    Science.gov (United States)

    Chen, H.; Kelly, R. E. J.

    2017-12-01

    Wet snow is defined as snow with liquid water present in an ice-water mix. It is can be an indicator for the onset of the snowmelt period. Knowledge about the extent of wet snow area can be of great importance for the monitoring of seasonal snowmelt runoff with climate-induced changes in snowmelt duration having implications for operational hydrological and ecological applications. Spaceborne microwave remote sensing has been used to observe seasonal snow under all-weather conditions. Active microwave observations of snow at C-band are sensitive to wet snow due to the high dielectric contrast with non-wet snow surfaces and synthetic aperture radar (SAR) is now openly available to identify and map the wet snow areas globally at relatively fine spatial resolutions ( 100m). In this study, a semi-automated workflow is developed from the change detection method of Nagler et al. (2016) using multi-temporal Sentinel-1A (S1A) dual-polarization observations of Southern Ontario. Weather station data and visible-infrared satellite observations are used to refine the wet snow area estimates. Wet snow information from National Operational Hydrologic Remote Sensing Center (NOHRSC) is used to compare with the S1A estimates. A time series of wet snow maps shows the variations in backscatter from wet snow on a pixel basis. Different land cover types in Southern Ontario are assessed with respect to their impacts on wet snow estimates. While forests and complex land surfaces can impact the ability to map wet snow, the approach taken is robust and illustrates the strong sensitivity of the approach to wet snow backscattering characteristics. The results indicate the feasibility of the change detection method on non-mountainous large areas and address the usefulness of Sentinel-1A data for wet snow mapping.

  16. DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair.

    Science.gov (United States)

    de Laat, W L; Appeldoorn, E; Sugasawa, K; Weterings, E; Jaspers, N G; Hoeijmakers, J H

    1998-08-15

    The human single-stranded DNA-binding replication A protein (RPA) is involved in various DNA-processing events. By comparing the affinity of hRPA for artificial DNA hairpin structures with 3'- or 5'-protruding single-stranded arms, we found that hRPA binds ssDNA with a defined polarity; a strong ssDNA interaction domain of hRPA is positioned at the 5' side of its binding region, a weak ssDNA-binding domain resides at the 3' side. Polarity appears crucial for positioning of the excision repair nucleases XPG and ERCC1-XPF on the DNA. With the 3'-oriented side of hRPA facing a duplex ssDNA junction, hRPA interacts with and stimulates ERCC1-XPF, whereas the 5'-oriented side of hRPA at a DNA junction allows stable binding of XPG to hRPA. Our data pinpoint hRPA to the undamaged strand during nucleotide excision repair. Polarity of hRPA on ssDNA is likely to contribute to the directionality of other hRPA-dependent processes as well.

  17. Emydid herpesvirus 1 infection in northern map turtles (Graptemys geographica) and painted turtles (Chrysemys picta).

    Science.gov (United States)

    Ossiboff, Robert J; Newton, Alisa L; Seimon, Tracie A; Moore, Robert P; McAloose, Denise

    2015-05-01

    A captive, juvenile, female northern map turtle (Graptemys geographica) was found dead following a brief period of weakness and nasal discharge. Postmortem examination identified pneumonia with necrosis and numerous epithelial, intranuclear viral inclusion bodies, consistent with herpesviral pneumonia. Similar intranuclear inclusions were also associated with foci of hepatocellular and splenic necrosis. Polymerase chain reaction (PCR) screening of fresh, frozen liver for the herpesviral DNA-dependent DNA polymerase gene yielded an amplicon with 99.2% similarity to recently described emydid herpesvirus 1 (EmyHV-1). Molecular screening of turtles housed in enclosures that shared a common circulation system with the affected map turtle identified 4 asymptomatic, EmyHV-1 PCR-positive painted turtles (Chrysemys picta) and 1 asymptomatic northern map turtle. Herpesvirus transmission between painted and map turtles has been previously suggested, and our report provides the molecular characterization of a herpesvirus in asymptomatic painted turtles that can cause fatal herpesvirus-associated disease in northern map turtles. © 2015 The Author(s).

  18. [In vitro study of joint intervention of E-cad and Bmi-1 mediated by transcription activator-like effector nuclease in nasopharyngeal carcinoma].

    Science.gov (United States)

    Luo, Tingting; Yan, Aifen; Liu, Lian; Jiang, Hong; Feng, Cuilan; Liu, Guannan; Liu, Fang; Tang, Dongsheng; Zhou, Tianhong

    2018-03-28

    To explore the effect of intervention of E-cadherin (E-cad) and B-lymphoma Moloney murine leukemia virus insertion region-1 (Bmi-1) mediated by transcription activator-like effector nuclease (TALEN) on the biological behaviors of nasopharyngeal carcinoma cells.
 Methods: Multi-locus gene targeting vectors pUC-DS1-CMV-E-cad-2A-Neo-DS2 and pUC-DS1-Bmi-1 shRNA-Zeo-DS2 were constructed, and the E-cad and Bmi-1 targeting vectors were transferred with TALEN plasmids to CNE-2 cells individually or simultaneously. The integration of target genes were detected by PCR, the expressions of E-cad and Bmi-1 were detected by Western blot. The changes of cell proliferation were detected by cell counting kit-8 (CCK-8) assay. The cell cycle and apoptosis were detected by flow cytometry. The cell migration and invasion were detected by Transwell assay.
 Results: The E-cad and Bmi-1 shRNA expression elements were successfully integrated into the genome of CNE-2 cells, the protein expression level of E-cad was up-regulated, and the protein expression level of Bmi-1 was down-regulated. The intervention of E-cad and Bmi-1 didn't affect the proliferation, cell cycle and apoptosis of CNE-2 cells, but it significantly inhibited the migration and invasion ability of CNE-2 cells. Furthermore, the intervention of E-cad and Bmi-1 together significantly inhibited the migration ability of nasopharyngeal carcinoma cells compared with the intervention of E-cad or Bmi-1 alone (all Pcad and Bmi-1 mediated by TALEN can effectively inhibit the migration and invasion of nasopharyngeal carcinoma cells in vitro, which may lay the preliminary experimental basis for gene therapy of human cancer.

  19. Application of halophilic nuclease H of Micrococcus varians subsp. halophilus to commercial production of flavoring agent 5'-GMP.

    Science.gov (United States)

    Kamekura, M; Hamakawa, T; Onishi, H

    1982-01-01

    RNA was degraded at 60 degrees C for 24 h by halophilic nuclease H in supernatants from broth cultures of Micrococcus varians subsp. halophilus containing 12% NaCl. Since contaminating 5'-nucleotidase exhibited almost no activity under these conditions, the 5'-GMP formed could be recovered from the reaction mixture, and the yield was 805 mg from 5 g of RNA. PMID:6184020

  20. Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition

    Czech Academy of Sciences Publication Activity Database

    Koval, Tomáš; Ostergaard, L. H.; Lehmbeck, J.; Norgaard, A.; Lipovová, P.; Dušková, Jarmila; Skálová, Tereza; Trundová, Mária; Kolenko, Petr; Fejfarová, Karla; Stránský, Jan; Švecová, Leona; Hašek, Jindřich; Dohnálek, Jan

    2016-01-01

    Roč. 11, č. 12 (2016), č. článku e0168832. E-ISSN 1932-6203 R&D Projects: GA ČR GA15-05228S; GA MŠk LG14009; GA MŠk(CZ) LM2015043 Grant - others:GA MŠk(CZ) CZ.1.05/1.1.00/02.0109 Institutional support: RVO:86652036 Keywords : macromolecular crystallography * crystal-structures * resolution * p1 Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 2.806, year: 2016

  1. The 1:3M geologic map of Mercury: progress and updates

    Science.gov (United States)

    Galluzzi, Valentina; Guzzetta, Laura; Mancinelli, Paolo; Giacomini, Lorenza; Malliband, Christopher C.; Mosca, Alessandro; Wright, Jack; Ferranti, Luigi; Massironi, Matteo; Pauselli, Cristina; Rothery, David A.; Palumbo, Pasquale

    2017-04-01

    02), Mercury. J. Maps, 12, 226-238. Giacomini L. et al. (2017). Geological mapping of the Kuiper quadrangle (H06) of Mercury. EGU General Assembly 2017, Abs. #14574. Guzzetta L. et al. (2016). Geologic map of the Shakespeare Quadrangle (H03) of Mercury. 88th Congress of the Italian Geological Society, 7-9 Sep 2016, Naples. Malliband C.C. et al. (2017). Preliminary results of 1:3million geological mapping of the Mercury quadrangle H-10 (Derain). XLVIII LPSC Abs., #1476. Mancinelli P. et al. (2016). Geology of the Raditladi Quadrangle, Mercury (H04). J. Maps, 12, 190-202. Prockter L. M. et al. (2016). The First Global Geological Map of Mercury. XLVII LPSC., Abs. #1245. Rothery D. A. et al. (2017). Geological mapping of the Hokusai (H05) quadrangle of Mercury. XLVIII LPSC, Abs. #1406. Spudis P. D. and Guest J. E. (1988). Stratigraphy and geologic history of Mercury. In: Vilas F., Chapman, C. R. and Matthews M. S. Eds., Mercury, 118-164. The University of Arizona Press, Tucson.

  2. Generalna karta Bosne i Hercegovine razmjere 1:150 000 : General map of Bosnia and Herzegovina at scale 1:150 000

    Directory of Open Access Journals (Sweden)

    Nedim Tuno

    2015-12-01

    Full Text Available Generalna karta Bosne i Hercegovine razmjere 1:150 000 u izdanju Vojnogeografskog instituta u Beču predstavlja jednu od najznačajnijih karata izrađenih na osnovu prvog sistematskog geodetskog premjera BiH. Temeljem analize izvornih kartografskih dokumenata i ostalih dostupnih podataka, u radu su izneseni najbitniji detalji koji karakterišu ovu kartu. Poslije kratkog historijskog osvrta na okolnosti koje su dovele do njenog nastanka, detaljno su analizirani elementi karte. Data je i kratka uporedba primijenjenih rješenja na spomenutoj karti s onima na ranijoj karti razmjere 1:300 000. Na osnovi provedenih istraživanja zaključuje se da je generalna karta BiH prva prava moderna topografska karta te zemlje, koja predstavlja izuzetno vrijednu kartografsku baštinu. : General map of Bosnia and Herzegovina at scale 1:150 000 published by the Military Geographical Institute of Vienna. is one of the most important maps made on the basis of the first systematic geodetic survey of B&H. Based on the analysis of the original cartographic documents and other available data, the paper presents the most important details that characterize this map. The elements of the map are analyzed in details after a brief historical review of the circumstances that led to the creation of the map. A brief comparison of solutions adopted on this map, with those of the previous 1: 300 000 scale map, is also given in the paper. Based on the conducted research it was concluded that the General map of Bosnia and Herzegovina is the first true modern topographic map of the country. This map is a cartographic heritage of exceptional value.

  3. Cerebrovascular-Reactivity Mapping Using MRI: Considerations for Alzheimer’s Disease

    Directory of Open Access Journals (Sweden)

    J. J. Chen

    2018-06-01

    Full Text Available Alzheimer’s disease (AD is associated with well-established macrostructural and cellular markers, including localized brain atrophy and deposition of amyloid. However, there is growing recognition of the link between cerebrovascular dysfunction and AD, supported by continuous experimental evidence in the animal and human literature. As a result, neuroimaging studies of AD are increasingly aiming to incorporate vascular measures, exemplified by measures of cerebrovascular reactivity (CVR. CVR is a measure that is rooted in clinical practice, and as non-invasive CVR-mapping techniques become more widely available, routine CVR mapping may open up new avenues of investigation into the development of AD. This review focuses on the use of MRI to map CVR, paying specific attention to recent developments in MRI methodology and on the emerging stimulus-free approaches to CVR mapping. It also summarizes the biological basis for the vascular contribution to AD, and provides critical perspective on the choice of CVR-mapping techniques amongst frail populations.

  4. PRMT1 methylates the single Argonaute of Toxoplasma gondii and is important for the recruitment of Tudor nuclease for target RNA cleavage by antisense guide RNA

    Science.gov (United States)

    Musiyenko, Alla; Majumdar, Tanmay; Andrews, Joel; Adams, Brian; Barik, Sailen

    2013-01-01

    Summary Argonaute (Ago) plays a central role in RNA interference in metazoans, but its status in lower organisms remains ill-defined. We report on the Ago complex of the unicellular protozoan, Toxoplasma gondii (Tg), an obligatory pathogen of mammalian hosts. The PIWI-like domain of TgAgo lacked the canonical DDE/H catalytic triad, explaining its weak target RNA cleavage activity. However, TgAgo associated with a stronger RNA slicer, a Tudor staphylococcal nuclease (TSN), and with a protein Arg methyl transferase, PRMT1. Mutational analysis suggested that the N-terminal RGG-repeat domain of TgAgo was methylated by PRMT1, correlating with the recruitment of TSN. The slicer activity of TgAgo was Mg2+-dependent and required perfect complementarity between the guide RNA and the target. In contrast, the TSN activity was Ca2+-dependent and required an imperfectly paired guide RNA. Ago knockout parasites showed essentially normal growth, but in contrast, the PRMT1 knockouts grew abnormally. Chemical inhibition of Arg-methylation also had an anti-parasitic effect. These results suggest that the parasitic PRMT1 plays multiple roles, and its loss affects the recruitment of a more potent second slicer to the parasitic RNA silencing complex, the exact mechanism of which remains to be determined. PMID:22309152

  5. Mapping of transport sensitive areas - Task 3.1

    DEFF Research Database (Denmark)

    Münier, Bernd

    and retrieval of data available for pan European mapping exercises revealed a considerable number of high resolution maps suitable for production of map examples. The results have been documented as a spreadsheet, containing essential sets of metadata. Furthermore, it could be realised that the number...... and related sensitive areas in the EU deals with the operationalisation of the criteria for transport sensitivity and impacts, as defined in D2. This paper reports the findings of task 3.1, a Review on spatial approaches, mapping examples and available data sets at EU level. The outcomes of this task...... and quality of map data available is constantly increasing, both with regard to coverage of existing maps and the release of new maps or maps harmonised from national mapping tasks. Main data gaps seem to be within data on meteorology and air quality, as they only exist in rather coarse spatial resolution...

  6. DAWN GRAND MAP CERES SMOOTHED HYDROGEN MAP V1.0

    Data.gov (United States)

    National Aeronautics and Space Administration — A smoothed, global map of the concentration of hydrogen within the regolith of asteroid 1 Ceres on two-degree equal-angle pixels is provided. Hydrogen concentrations...

  7. Hazard Map of the Poás Volcano

    Directory of Open Access Journals (Sweden)

    Gustavo Barrantes Castillo

    2015-07-01

    Full Text Available The Poás volcano presents a series of hazards to the lives and activities of the communities in its surroundings; these hazards include ash fall, volcanic gases, ballistic projection, pyroclastic flows, lahars and lava flows. In the study described in this article, risks were zoned and integrated to form combined hazard maps for later use in territorial planning processes. With respect to methodology, the study was based on a heuristic approximation, which was supported with cartographic, geomorphological, and historical impact criteria to achieve a suitable product in terms of scale and ease of interpretation. These maps present greater detail and integration than other works and cartographies of volcanic hazards in Costa Rica.

  8. Cartilage quality in rheumatoid arthritis: comparison of T2* mapping, native T1 mapping, dGEMRIC, ΔR1 and value of pre-contrast imaging

    International Nuclear Information System (INIS)

    Buchbender, Christian; Scherer, Axel; Kroepil, Patric; Quentin, Michael; Reichelt, Dorothea C.; Lanzman, Rotem S.; Mathys, Christian; Blondin, Dirk; Wittsack, Hans-Joerg; Antoch, Gerald; Miese, Falk; Koerbl, Birthe; Bittersohl, Bernd; Zilkens, Christoph; Hofer, Matthias; Schneider, Matthias; Ostendorf, Benedikt

    2012-01-01

    To prospectively evaluate four non-invasive markers of cartilage quality - T2* mapping, native T1 mapping, dGEMRIC and ΔR1 - in healthy volunteers and rheumatoid arthritis (RA) patients. Cartilage of metacarpophalangeal (MCP) joints II were imaged in 28 consecutive subjects: 12 healthy volunteers [9 women, mean (SD) age 52.67 (9.75) years, range 30-66] and 16 RA patients with MCP II involvement [12 women, mean (SD) age 58.06 (12.88) years, range 35-76]. Sagittal T2* mapping was performed with a multi-echo gradient-echo on a 3 T MRI scanner. For T1 mapping the dual flip angle method was applied prior to native T1 mapping and 40 min after gadolinium application (delayed gadolinium-enhanced MRI of cartilage, dGEMRIC, T1 Gd ). The difference in the longitudinal relaxation rate induced by gadolinium (ΔR1) was calculated. The area under the receiver operating characteristic curve (AROC) was used to test for differentiation of RA patients from healthy volunteers. dGEMRIC (AUC 0.81) and ΔR1 (AUC 0.75) significantly differentiated RA patients from controls. T2* mapping (AUC 0.66) and native T1 mapping (AUC 0.66) were not significantly different in RA patients compared to controls. The data support the use of dGEMRIC for the assessment of MCP joint cartilage quality in RA. T2* and native T1 mapping are of low diagnostic value. Pre-contrast T1 mapping for the calculation of ΔR1 does not increase the diagnostic value of dGEMRIC. (orig.)

  9. Cartilage quality in rheumatoid arthritis: comparison of T2* mapping, native T1 mapping, dGEMRIC, {delta}R1 and value of pre-contrast imaging

    Energy Technology Data Exchange (ETDEWEB)

    Buchbender, Christian; Scherer, Axel; Kroepil, Patric; Quentin, Michael; Reichelt, Dorothea C.; Lanzman, Rotem S.; Mathys, Christian; Blondin, Dirk; Wittsack, Hans-Joerg; Antoch, Gerald; Miese, Falk [University Duesseldorf, Department of Diagnostic and Interventional Radiology, Medical Faculty, Duesseldorf (Germany); Koerbl, Birthe [Heinrich-Heine-University, Department of Endocrinology, Diabetology and Rheumatology, Medical Faculty, Duesseldorf (Germany); Heinrich-Heine-University, Leibniz Centre for Diabetes Research, Institute of Biometrics and Epidemiology, German Diabetes Centre, Duesseldorf (Germany); Bittersohl, Bernd; Zilkens, Christoph [Heinrich-Heine-University, Department of Orthopaedics, Medical Faculty, Duesseldorf (Germany); Hofer, Matthias [Heinrich-Heine-University, Medical Education Group, Medical School, Duesseldorf (Germany); Schneider, Matthias; Ostendorf, Benedikt [Heinrich-Heine-University, Department of Endocrinology, Diabetology and Rheumatology, Medical Faculty, Duesseldorf (Germany)

    2012-06-15

    To prospectively evaluate four non-invasive markers of cartilage quality - T2* mapping, native T1 mapping, dGEMRIC and {delta}R1 - in healthy volunteers and rheumatoid arthritis (RA) patients. Cartilage of metacarpophalangeal (MCP) joints II were imaged in 28 consecutive subjects: 12 healthy volunteers [9 women, mean (SD) age 52.67 (9.75) years, range 30-66] and 16 RA patients with MCP II involvement [12 women, mean (SD) age 58.06 (12.88) years, range 35-76]. Sagittal T2* mapping was performed with a multi-echo gradient-echo on a 3 T MRI scanner. For T1 mapping the dual flip angle method was applied prior to native T1 mapping and 40 min after gadolinium application (delayed gadolinium-enhanced MRI of cartilage, dGEMRIC, T1{sub Gd}). The difference in the longitudinal relaxation rate induced by gadolinium ({delta}R1) was calculated. The area under the receiver operating characteristic curve (AROC) was used to test for differentiation of RA patients from healthy volunteers. dGEMRIC (AUC 0.81) and {delta}R1 (AUC 0.75) significantly differentiated RA patients from controls. T2* mapping (AUC 0.66) and native T1 mapping (AUC 0.66) were not significantly different in RA patients compared to controls. The data support the use of dGEMRIC for the assessment of MCP joint cartilage quality in RA. T2* and native T1 mapping are of low diagnostic value. Pre-contrast T1 mapping for the calculation of {delta}R1 does not increase the diagnostic value of dGEMRIC. (orig.)

  10. Map of calculated radioactivity of fission product, (1)

    International Nuclear Information System (INIS)

    Takeda, Tsuneo

    1977-02-01

    In this work, the radioactivities of fission products were calculated and summarized in contour maps and tables depending on irradiation and cooling times. The irradiation condition and other parameters used for the present calculation are shown in the followings. Neutron flux (N sub(th)): 3x10 13 n/sec/cm 2 Atom number of uranium: 1 mole (6x10 23 , ca. 271 gUO 2 ) Enrichment of U-235: 2.7% Range of irradiation time: 60-6x10 7 sec (ca. 1.9 y) Range of cooling time: 60-6x10 7 sec (ca. 1.9 y). Values of the neutron flux and the enrichment treated here are representative for common LWRs. The maps and tables of 560 nuclides are divided and compiled into the following three volumes. Vol. I Maps of radioactivity of overall total, element total and each nuclide (Ni - Zr) Vol. II Maps of radioactivity of each nuclide (Nb - Sb) Vol. III Maps of radioactivity of each nuclide (Te - Tm) (auth.)

  11. Structural analysis of the 5' flanking region of the β-globin gene in African sickle cell anemia patients: Further evidence for three origins of the sickle cell mutation in Africa

    International Nuclear Information System (INIS)

    Chebloune, Y.; Pagnier, J.; Trabuchet, G.; Faure, C.; Verdier, G.; Labie, D.; Nigon, V.

    1988-01-01

    Haplotype analysis of the β-globin gene cluster shows two regions of DNA characterized by nonrandom association of restriction site polymorphisms. These regions are separated by a variable segment containing the repeated sequences (ATTTT) n and (AT) x T y , which might be involved in recombinational events. Studies of haplotypes linked to the sickle cell gene in Africa provide strong argument for three origins of the mutation: Benin, Senegal, and the Central African Republic. The structure of the variable segment in the three African populations was studied by S1 nuclease mapping of genomic DNA, which allows a comparison of several samples. A 1080-base-pair DNA segment was sequenced for one sample from each population. S1 nuclease mapping confirmed the homogeneity of each population with regard to both (ATTTT) n and (AT) x T y repeats. The authors found three additional structures for (AT) x T y correlating with the geographic origin of the patients. Ten other nucleotide positions, 5' and 3' to the (AT) x T y copies, were found to be variable when compared to homologous sequences from human and monkey DNAs. These results allow us to propose an evolutionary scheme for the polymorphisms in the 5' flanking region of the β-globin gene. The results strongly support the hypothesis of three origins for the sickle mutation in Africa

  12. USGS Imagery Only Base Map Service from The National Map

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — USGS Imagery Only is a tile cache base map of orthoimagery in The National Map visible to the 1:18,000 scale. Orthoimagery data are typically high resolution images...

  13. Knockout of Myostatin by Zinc-finger Nuclease in Sheep Fibroblasts and Embryos

    Directory of Open Access Journals (Sweden)

    Xuemei Zhang

    2016-10-01

    Full Text Available Myostatin (MSTN can negatively regulate the growth and development of skeletal muscle, and natural mutations can cause “double-muscling” trait in animals. In order to block the inhibiting effect of MSTN on muscle growth, we transferred zinc-finger nucleases (ZFN which targeted sheep MSTN gene into cultured fibroblasts. Gene targeted colonies were isolated from transfected fibroblasts by serial dilution culture and screened by sequencing. Two colonies were identified with mono-allele mutation and one colony with bi-allelic deletion. Further, we introduced the MSTN-ZFN mRNA into sheep embryos by microinjection. Thirteen of thirty-seven parthenogenetic embryos were targeted by ZFN, with the efficiency of 35%. Our work established the technical foundation for generation of MSTN gene editing sheep by somatic cloning and microinjection ZFN into embryos.

  14. Mapping the Thermal Inertia of Saturn’s Rings with Cassini CIRS

    Science.gov (United States)

    Brooks, Shawn M.; Spilker, L. J.; PIlorz, S. H.; Showalter, M. R.

    2013-10-01

    We use data from Cassini's Composite Infrared Spectrometer to map out the thermal response of Saturn's ring particles passing through Saturn's shadow and to determine variations in ring thermal inertia. CIRS records far infrared radiation in three separate detectors, each of which covers a distinct wavelength range. In this work, we analyze rings spectra recorded at focal plane 1 (FP1), as its wavelength response (16.7-1000 microns) is well suited to detecting direct thermal emission from Saturn's rings. The thermal budget of the rings is typically dominated by solar radiation. When ring particles enter Saturn’s shadow this source of energy is abruptly cut off with a consequential drop in ring temperature. Likewise, temperatures rebound when particles exit the shadow. To characterize these heating and cooling events, FP1 was repeatedly scanned across the main rings. Each scan was offset from either the ingress or egress shadow boundary by an amount corresponding to a fraction of a Keplerian orbit. By resampling these scans onto a common radial grid, we can map out the rings’ response to the abrupt changes in insolation at shadow ingress and egress. Periods near equinox represent a unique situation. During this time the Sun's disk crosses the ring plane and its rays strike the rings at zero incidence. Solar heating is virtually absent, and thermal radiation from Saturn and sunlight reflected by Saturn dominate the thermal environment. While ring temperature variations at equinox are much more subtle, they represent temperature contrasts that vary at the unique timescale corresponding to variations in Saturn contributions to the rings’ thermal budget. By analyzing CIRS data at a variety of locations and epochs, we will map out thermal inertia across the rings and attempt to tease out structural information about the particles which comprise Saturn’s rings. This presentation will report upon our progress towards these ends. This research was carried out at the

  15. Children’s Non-symbolic, Symbolic Addition and Their Mapping Capacity at 4–7 Years Old

    Directory of Open Access Journals (Sweden)

    Yanjun Li

    2017-07-01

    Full Text Available The study aimed to examine the developmental trajectories of non-symbolic and symbolic addition capacities in children and the mapping ability between these two. We assessed 106 4- to 7-year-old children and found that 4-year-olds were able to do non-symbolic addition but not symbolic addition. Five-year-olds and older were able to do symbolic addition and their performance in symbolic addition exceeded non-symbolic addition in grade 1 (approximate age 7. These results suggested non-symbolic addition ability emerges earlier and is less affected by formal mathematical education than symbolic addition. Meanwhile, we tested children’s bi-directional mapping ability using a novel task and found that children were able to map between symbolic and non-symbolic representations of number at age 5. Their ability in mapping non-symbolic to symbolic number became more proficient in grade 1 (approximate age 7. This suggests children at age 7 have developed a relatively mature symbolic representation system.

  16. Dynamic Quantitative T1 Mapping in Orthotopic Brain Tumor Xenografts

    Directory of Open Access Journals (Sweden)

    Kelsey Herrmann

    2016-04-01

    Full Text Available Human brain tumors such as glioblastomas are typically detected using conventional, nonquantitative magnetic resonance imaging (MRI techniques, such as T2-weighted and contrast enhanced T1-weighted MRI. In this manuscript, we tested whether dynamic quantitative T1 mapping by MRI can localize orthotopic glioma tumors in an objective manner. Quantitative T1 mapping was performed by MRI over multiple time points using the conventional contrast agent Optimark. We compared signal differences to determine the gadolinium concentration in tissues over time. The T1 parametric maps made it easy to identify the regions of contrast enhancement and thus tumor location. Doubling the typical human dose of contrast agent resulted in a clearer demarcation of these tumors. Therefore, T1 mapping of brain tumors is gadolinium dose dependent and improves detection of tumors by MRI. The use of T1 maps provides a quantitative means to evaluate tumor detection by gadolinium-based contrast agents over time. This dynamic quantitative T1 mapping technique will also enable future quantitative evaluation of various targeted MRI contrast agents.

  17. Serum Soluble Fms-Like Tyrosine Kinase 1 (sFlt-1 Predicts the Severity of Acute Pancreatitis

    Directory of Open Access Journals (Sweden)

    Paulina Dumnicka

    2016-12-01

    Full Text Available Organ failure is the most important determinant of the severity of acute pancreatitis (AP. Soluble fms-like tyrosine kinase 1 (sFlt-1 is positively associated with organ failure in sepsis. Our aim was to evaluate the diagnostic utility of automated sFlt-1 measurements for early prediction of AP severity. Adult patients (66 with AP were recruited, including 46 with mild (MAP, 15 with moderately-severe (MSAP and 5 with severe AP (SAP. Serum and urine samples were collected twice. Serum sFlt-1 was measured with automated electrochemiluminescence immunoassay. Serum concentrations of sFlt-1 were significantly higher in patients with MSAP and SAP as compared to MAP. SAP patients had the highest concentrations. At 24 and 48 h, sFlt-1 positively correlated with inflammatory markers (leukocyte count, C-reactive protein, kidney function (creatinine, urea, cystatin C, serum and urine neutrophil gelatinase-associated lipocalin, urine albumin/creatinine ratio, D-dimer and angiopoietin-2. sFlt-1 positively correlated with the bedside index of severity in AP (BISAP score and the duration of hospital stay. Serum sFlt-1 above 139 pg/mL predicted more severe AP (MSAP + SAP. In the early phase of AP, sFlt-1 is positively associated with the severity of AP and predicts organ failure, in particular kidney failure. Serum sFlt-1 may be a practical way to improve early assessment of AP severity.

  18. Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification.

    Science.gov (United States)

    Li, Lixin; Piatek, Marek J; Atef, Ahmed; Piatek, Agnieszka; Wibowo, Anjar; Fang, Xiaoyun; Sabir, J S M; Zhu, Jian-Kang; Mahfouz, Magdy M

    2012-03-01

    Transcription activator-like effectors (TALEs) can be used as DNA-targeting modules by engineering their repeat domains to dictate user-selected sequence specificity. TALEs have been shown to function as site-specific transcriptional activators in a variety of cell types and organisms. TALE nucleases (TALENs), generated by fusing the FokI cleavage domain to TALE, have been used to create genomic double-strand breaks. The identity of the TALE repeat variable di-residues, their number, and their order dictate the DNA sequence specificity. Because TALE repeats are nearly identical, their assembly by cloning or even by synthesis is challenging and time consuming. Here, we report the development and use of a rapid and straightforward approach for the construction of designer TALE (dTALE) activators and nucleases with user-selected DNA target specificity. Using our plasmid set of 100 repeat modules, researchers can assemble repeat domains for any 14-nucleotide target sequence in one sequential restriction-ligation cloning step and in only 24 h. We generated several custom dTALEs and dTALENs with new target sequence specificities and validated their function by transient expression in tobacco leaves and in vitro DNA cleavage assays, respectively. Moreover, we developed a web tool, called idTALE, to facilitate the design of dTALENs and the identification of their genomic targets and potential off-targets in the genomes of several model species. Our dTALE repeat assembly approach along with the web tool idTALE will expedite genome-engineering applications in a variety of cell types and organisms including plants.

  19. Mapping the three-dimensional dust extinction towards the supernova remnant S147 - the S147 dust cloud

    Science.gov (United States)

    Chen, B.-Q.; Liu, X.-W.; Ren, J.-J.; Yuan, H.-B.; Huang, Y.; Yu, B.; Xiang, M.-S.; Wang, C.; Tian, Z.-J.; Zhang, H.-W.

    2017-12-01

    We present a three-dimensional (3D) extinction analysis in the region towards the supernova remnant (SNR) S147 (G180.0-1.7) using multiband photometric data from the Xuyi Schmidt Telescope Photometric Survey of the Galactic Anticentre (XSTPS-GAC), 2MASS and WISE. We isolate a previously unrecognized dust structure likely to be associated with SNR S147. The structure, which we term as 'S147 dust cloud', is estimated to have a distance d = 1.22 ± 0.21 kpc, consistent with the conjecture that S147 is associated with pulsar PSR J0538 + 2817. The cloud includes several dense clumps of relatively high extinction that locate on the radio shell of S147 and coincide spatially with the CO and gamma-ray emission features. We conclude that the usage of CO measurements to trace the SNR associated MCs is unavoidably limited by the detection threshold, dust depletion and the difficulty of distance estimates in the outer Galaxy. 3D dust extinction mapping may provide a better way to identify and study SNR-MC interactions.

  20. Parametric techniques for characterizing myocardial tissue by magnetic resonance imaging (part 1): T1 mapping.

    Science.gov (United States)

    Perea Palazón, R J; Ortiz Pérez, J T; Prat González, S; de Caralt Robira, T M; Cibeira López, M T; Solé Arqués, M

    2016-01-01

    The development of myocardial fibrosis is a common process in the appearance of ventricular dysfunction in many heart diseases. Magnetic resonance imaging makes it possible to accurately evaluate the structure and function of the heart, and its role in the macroscopic characterization of myocardial fibrosis by late enhancement techniques has been widely validated clinically. Recent studies have demonstrated that T1-mapping techniques can quantify diffuse myocardial fibrosis and the expansion of the myocardial extracellular space in absolute terms. However, further studies are necessary to validate the usefulness of this technique in the early detection of tissue remodeling at a time when implementing early treatment would improve a patient's prognosis. This article reviews the state of the art for T1 mapping of the myocardium, its clinical applications, and its limitations. Copyright © 2016 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

  1. THE ARIZONA RADIO OBSERVATORY CO MAPPING SURVEY OF GALACTIC MOLECULAR CLOUDS. II. THE W3 REGION IN CO J = 2-1, 13CO J = 2-1, AND CO J = 3-2 EMISSION

    International Nuclear Information System (INIS)

    Bieging, John H.; Peters, William L.

    2011-01-01

    We present fully sampled 38'' resolution maps of the CO and 13 CO J = 2-1 lines in the molecular clouds toward the H II region complex W3. The maps cover a 2. 0 0 x 1. 0 67 section of the galactic plane and span -70 to -20 km s -1 (LSR) in velocity with a resolution of ∼1.3 km s -1 . The velocity range of the images includes all the gas in the Perseus spiral arm. We also present maps of CO J = 3-2 emission for a 0. 0 5 x 0. 0 33 area containing the H II regions W3 Main and W3(OH). The J = 3-2 maps have velocity resolution of 0.87 km s -1 and 24'' angular resolution. Color figures display the peak line brightness temperature, the velocity-integrated intensity, and velocity channel maps for all three lines, and also the (CO/ 13 CO) J = 2-1 line intensity ratios as a function of velocity. The line intensity image cubes are made available in standard FITS format as electronically readable files. We compare our molecular line maps with the 1.1 mm continuum image from the BOLOCAM Galactic Plane Survey (BGPS). From our 13 CO image cube, we derive kinematic information for the 65 BGPS sources in the mapped field, in the form of Gaussian component fits.

  2. Mass spectroscopic phosphoprotein mapping of Ral binding protein 1 (RalBP1/Rip1/RLIP76)

    International Nuclear Information System (INIS)

    Herlevsen, Mikael C.; Theodorescu, Dan

    2007-01-01

    RalBP1, a multifunctional protein implicated in cancer cell proliferation, radiation and chemoresistance, and ligand dependent receptor internalization, is upregulated in bladder cancer and is a downstream effector of RalB, a GTPase associated with metastasis. RalBP1 can be regulated by phosphorylation by protein kinase C (PKC). No studies have comprehensively mapped RalBP1 phosphorylation sites or whether RalB affects these. We identified 14 phosphorylation sites of RalBP1 in human bladder carcinoma UMUC-3 and embryonic kidney derived 293T cells. The phosphorylated residues are concentrated at the N-terminus. Ten of the first 100 amino acids of the primary structure were phosphorylated. Nine were serine residues, and one a threonine. We evaluated the effect of RalB overexpression on RalBP1 phosphorylation and found the largest change in phosphorylation status at S463 and S645. Further characterization of these sites will provide novel insights on RalBP1 biology, its functional relationship to RalB and possible avenues for therapeutic intervention

  3. Anticonvulsant activity of a mGlu(4alpha) receptor selective agonist, (1S,3R,4S)-1-aminocyclopentane-1,2,4-tricarboxylic acid.

    Science.gov (United States)

    Chapman, A G; Talebi, A; Yip, P K; Meldrum, B S

    2001-07-20

    The metabotropic Group III agonist, (1S,3R,4S)-1-aminocyclopentane-1,2,4-tricarboxylic acid (ACPT-1), selective for the mGlu(4alpha) receptor, suppresses sound-induced seizures in DBA/2 mice following its intracerebroventricular (i.c.v.) administration (ED(50) 5.6 [2.9-10.7], nmol i.c.v., 15 min, clonic phase) and in genetically epilepsy-prone (GEP) rats following focal administration into the inferior colliculus (ED(50) 0.08 [0.01-0.50], nmol, 60 min, clonic phase). ACPT-1 also protects against clonic seizures induced in DBA/2 mice by the Group I agonist, (RS)-3,5-dihydroxyphenylglycine (3,5-DHPG) (ED(50) 0.60 [0.29-1.2], nmol i.c.v.) and by the Group III antagonist, (RS)-alpha-methylserine-O-phosphate (MSOP) (ED(50) 49.3 [37.9-64.1], nmol i.c.v.). Another Group III agonist, (RS)-4-phosphonophenyl-glycine (PPG), preferentially activating the mGlu(8) receptor, previously shown to protect against sound-induced seizures in DBA/2 mice and GEP rats, also protects against seizures induced in DBA/2 by 3,5-DHPG (ED(50) 3.7 [2.4-5.7], nmol i.c.v.) and by the Group III antagonist, MSOP (ED(50) 40.2 [21.0-77.0], nmol i.c.v.). At very high doses (500 nmol i.c.v. and above), Group III antagonists have pro-convulsant and convulsant activity. The anticonvulsant protection against sound-induced seizures in DBA/2 mice provided by a fully protective dose (20 nmol, i.c.v.) of the mGlu(4) receptor agonist ACPT-1, is partially reversed by the co-administration of the Group III antagonists, MSOP, (RS)-alpha-methyl-4-phosphonophenylglycine (MPPG) or (S)-2-amino-2-methyl-4-phosphonobutanoic acid (MAP4), in the 20-50 nmol dose range. At doses of 50-200 nmol, MPPG and MAP4 cause further reversal of the ACPT-1 anticonvulsant protection, while the MSOP effect on ACPT-1 protection is abolished at higher doses. In contrast, the anticonvulsant protection against sound-induced seizures in DBA/2 mice provided by a fully protective dose (20 nmol, i.c.v.) of the mGlu(8) receptor agonist PPG, is not

  4. Global Rural-Urban Mapping Project, Version 1 (GRUMPv1): Coastlines

    Data.gov (United States)

    National Aeronautics and Space Administration — The Global Rural-Urban Mapping Project, Version 1 (GRUMPv1) consists of estimates of human population for the years 1990, 1995, and 2000 by 30 arc-second (1km) grid...

  5. U.S. Environmental Protection Agency Office of Enforcement and Compliance Assurance New Mapping Tool for Enforcement Cases

    Data.gov (United States)

    U.S. Environmental Protection Agency — The new mapping tool shows facilities in the United States where the EPA concluded formal environmental enforcement actions between October 1, 2008 and September 30,...

  6. Genetic mapping and validation of the loci controlling 7S α' and 11S A-type storage protein subunits in soybean [Glycine max (L.) Merr.].

    Science.gov (United States)

    Boehm, Jeffrey D; Nguyen, Vi; Tashiro, Rebecca M; Anderson, Dale; Shi, Chun; Wu, Xiaoguang; Woodrow, Lorna; Yu, Kangfu; Cui, Yuhai; Li, Zenglu

    2018-03-01

    Four soybean storage protein subunit QTLs were mapped using bulked segregant analysis and an F 2 population, which were validated with an F 5 RIL population. The storage protein globulins β-conglycinin (7S subunit) and glycinin (11S subunits) can affect the quantity and quality of proteins found in soybean seeds and account for more than 70% of the total soybean protein. Manipulating the storage protein subunits to enhance soymeal nutrition and for desirable tofu manufacturing characteristics are two end-use quality goals in soybean breeding programs. To aid in developing soybean cultivars with desired seed composition, an F 2 mapping population (n = 448) and an F 5 RIL population (n = 180) were developed by crossing high protein cultivar 'Harovinton' with the breeding line SQ97-0263_3-1a, which lacks the 7S α', 11S A 1 , 11S A 2 , 11S A 3 and 11S A 4 subunits. The storage protein composition of each individual in the F 2 and F 5 populations were profiled using SDS-PAGE. Based on the presence/absence of the subunits, genomic DNA bulks were formed among the F 2 plants to identify genomic regions controlling the 7S α' and 11S protein subunits. By utilizing polymorphic SNPs between the bulks characterized with Illumina SoySNP50K iSelect BeadChips at targeted genomic regions, KASP assays were designed and used to map QTLs causing the loss of the subunits. Soybean storage protein QTLs were identified on Chromosome 3 (11S A 1 ), Chromosome 10 (7S α' and 11S A 4 ), and Chromosome 13 (11S A 3 ), which were also validated in the F 5 RIL population. The results of this research could allow for the deployment of marker-assisted selection for desired storage protein subunits by screening breeding populations using the SNPs linked with the subunits of interest.

  7. Sea-Ice Feature Mapping using JERS-1 Imagery

    Science.gov (United States)

    Maslanik, James; Heinrichs, John

    1994-01-01

    JERS-1 SAR and OPS imagery are examined in combination with other data sets to investigate the utility of the JERS-1 sensors for mapping fine-scale sea ice conditions. Combining ERS-1 C band and JERS-1 L band SAR aids in discriminating multiyear and first-year ice. Analysis of OPS imagery for a field site in the Canadian Archipelago highlights the advantages of OPS's high spatial and spectral resolution for mapping ice structure, melt pond distribution, and surface albedo.

  8. Proviral HIV-genome-wide and pol-gene specific Zinc Finger Nucleases: Usability for targeted HIV gene therapy

    Directory of Open Access Journals (Sweden)

    Wayengera Misaki

    2011-07-01

    Full Text Available Abstract Background Infection with HIV, which culminates in the establishment of a latent proviral reservoir, presents formidable challenges for ultimate cure. Building on the hypothesis that ex-vivo or even in-vivo abolition or disruption of HIV-gene/genome-action by target mutagenesis or excision can irreversibly abrogate HIV's innate fitness to replicate and survive, we previously identified the isoschizomeric bacteria restriction enzymes (REases AcsI and ApoI as potent cleavers of the HIV-pol gene (11 and 9 times in HIV-1 and 2, respectively. However, both enzymes, along with others found to cleave across the entire HIV-1 genome, slice (SX at palindromic sequences that are prevalent within the human genome and thereby pose the risk of host genome toxicity. A long-term goal in the field of R-M enzymatic therapeutics has thus been to generate synthetic restriction endonucleases with longer recognition sites limited in specificity to HIV. We aimed (i to assemble and construct zinc finger arrays and nucleases (ZFN with either proviral-HIV-pol gene or proviral-HIV-1 whole-genome specificity respectively, and (ii to advance a model for pre-clinically testing lentiviral vectors (LV that deliver and transduce either ZFN genotype. Methods and Results First, we computationally generated the consensus sequences of (a 114 dsDNA-binding zinc finger (Zif arrays (ZFAs or ZifHIV-pol and (b two zinc-finger nucleases (ZFNs which, unlike the AcsI and ApoI homeodomains, possess specificity to >18 base-pair sequences uniquely present within the HIV-pol gene (ZifHIV-polFN. Another 15 ZFNs targeting >18 bp sequences within the complete HIV-1 proviral genome were constructed (ZifHIV-1FN. Second, a model for constructing lentiviral vectors (LVs that deliver and transduce a diploid copy of either ZifHIV-polFN or ZifHIV-1FN chimeric genes (termed LV- 2xZifHIV-polFN and LV- 2xZifHIV-1FN, respectively is proposed. Third, two preclinical models for controlled testing of

  9. Proviral HIV-genome-wide and pol-gene specific zinc finger nucleases: usability for targeted HIV gene therapy.

    Science.gov (United States)

    Wayengera, Misaki

    2011-07-22

    Infection with HIV, which culminates in the establishment of a latent proviral reservoir, presents formidable challenges for ultimate cure. Building on the hypothesis that ex-vivo or even in-vivo abolition or disruption of HIV-gene/genome-action by target mutagenesis or excision can irreversibly abrogate HIV's innate fitness to replicate and survive, we previously identified the isoschizomeric bacteria restriction enzymes (REases) AcsI and ApoI as potent cleavers of the HIV-pol gene (11 and 9 times in HIV-1 and 2, respectively). However, both enzymes, along with others found to cleave across the entire HIV-1 genome, slice (SX) at palindromic sequences that are prevalent within the human genome and thereby pose the risk of host genome toxicity. A long-term goal in the field of R-M enzymatic therapeutics has thus been to generate synthetic restriction endonucleases with longer recognition sites limited in specificity to HIV. We aimed (i) to assemble and construct zinc finger arrays and nucleases (ZFN) with either proviral-HIV-pol gene or proviral-HIV-1 whole-genome specificity respectively, and (ii) to advance a model for pre-clinically testing lentiviral vectors (LV) that deliver and transduce either ZFN genotype. First, we computationally generated the consensus sequences of (a) 114 dsDNA-binding zinc finger (Zif) arrays (ZFAs or ZifHIV-pol) and (b) two zinc-finger nucleases (ZFNs) which, unlike the AcsI and ApoI homeodomains, possess specificity to >18 base-pair sequences uniquely present within the HIV-pol gene (ZifHIV-polFN). Another 15 ZFNs targeting >18 bp sequences within the complete HIV-1 proviral genome were constructed (ZifHIV-1FN). Second, a model for constructing lentiviral vectors (LVs) that deliver and transduce a diploid copy of either ZifHIV-polFN or ZifHIV-1FN chimeric genes (termed LV- 2xZifHIV-polFN and LV- 2xZifHIV-1FN, respectively) is proposed. Third, two preclinical models for controlled testing of the safety and efficacy of either of these

  10. Linking retinotopic fMRI mapping and anatomical probability maps of human occipital areas V1 and V2.

    Science.gov (United States)

    Wohlschläger, A M; Specht, K; Lie, C; Mohlberg, H; Wohlschläger, A; Bente, K; Pietrzyk, U; Stöcker, T; Zilles, K; Amunts, K; Fink, G R

    2005-05-15

    Using functional MRI, we characterized field sign maps of the occipital cortex and created three-dimensional maps of these areas. By averaging the individual maps into group maps, probability maps of functionally defined V1 or V2 were determined and compared to anatomical probability maps of Brodmann areas BA17 and BA18 derived from cytoarchitectonic analysis (Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., Zilles, K., 2000. Brodmann's areas 17 and 18 brought into stereotaxic space-where and how variable? NeuroImage 11, 66-84). Comparison of areas BA17/V1 and BA18/V2 revealed good agreement of the anatomical and functional probability maps. Taking into account that our functional stimulation (due to constraints of the visual angle of stimulation achievable in the MR scanner) only identified parts of V1 and V2, for statistical evaluation of the spatial correlation of V1 and BA17, or V2 and BA18, respectively, the a priori measure kappa was calculated testing the hypothesis that a region can only be part of functionally defined V1 or V2 if it is also in anatomically defined BA17 or BA18, respectively. kappa = 1 means the hypothesis is fully true, kappa = 0 means functionally and anatomically defined visual areas are independent. When applying this measure to the probability maps, kappa was equal to 0.84 for both V1/BA17 and V2/BA18. The data thus show a good correspondence of functionally and anatomically derived segregations of early visual processing areas and serve as a basis for employing anatomical probability maps of V1 and V2 in group analyses to characterize functional activations of early visual processing areas.

  11. Mapping the global land surface using 1 km AVHRR data

    Science.gov (United States)

    Lauer, D.T.; Eidenshink, J.C.

    1998-01-01

    The scientific requirements for mapping the global land surface using 1 km advanced very high resolution radiometer (AVHRR) data have been set forth by the U.S. Global Change Research Program; the International Geosphere Biosphere Programme (IGBP); The United Nations; the National Oceanic and Atmospheric Administration (NOAA); the Committee on Earth Observations Satellites; and the National Aeronautics and Space Administration (NASA) mission to planet Earth (MTPE) program. Mapping the global land surface using 1 km AVHRR data is an international effort to acquire, archive, process, and distribute 1 km AVHRR data to meet the needs of the international science community. A network of AVHRR receiving stations, along with data recorded by NOAA, has been acquiring daily global land coverage since April 1, 1992. A data set of over 70,000 AVHRR images is archived and distributed by the United States Geological Survey (USGS) EROS Data Center, and the European Space Agency. Under the guidance of the IGBP, processing standards have been developed for calibration, atmospheric correction, geometric registration, and the production of global 10-day maximum normalized difference vegetation index (NDVI) composites. The major uses of the composites are for the study of surface vegetation condition, mapping land cover, and deriving biophysical characteristics of terrestrial ecosystems. A time-series of 54 10-day global vegetation index composites for the period of April 1, 1992 through September 1993 has been produced. The production of a time-series of 33 10-day global vegetation index composites using NOAA-14 data for the period of February 1, 1995 through December 31, 1995 is underway. The data products are available from the USGS, in cooperation with NASA's MTPE program and other international organizations.

  12. MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease.

    Science.gov (United States)

    Gunner, M R; Zhu, Xuyu; Klein, Max C

    2011-12-01

    The pK(a)s of 96 acids and bases introduced into buried sites in the staphylococcal nuclease protein (SNase) were calculated using the multiconformation continuum electrostatics (MCCE) program and the results compared with experimental values. The pK(a)s are obtained by Monte Carlo sampling of coupled side chain protonation and position as a function of pH. The dependence of the results on the protein dielectric constant (ε(prot)) in the continuum electrostatics analysis and on the Lennard-Jones non-electrostatics parameters was evaluated. The pK(a)s of the introduced residues have a clear dependence on ε(prot,) whereas native ionizable residues do not. The native residues have electrostatic interactions with other residues in the protein favoring ionization, which are larger than the desolvation penalty favoring the neutral state. Increasing ε(prot) scales both terms, which for these residues leads to small changes in pK(a). The introduced residues have a larger desolvation penalty and negligible interactions with residues in the protein. For these residues, changing ε(prot) has a large influence on the calculated pK(a). An ε(prot) of 8-10 and a Lennard-Jones scaling of 0.25 is best here. The X-ray crystal structures of the mutated proteins are found to provide somewhat better results than calculations carried out on mutations made in silico. Initial relaxation of the in silico mutations by Gromacs and extensive side chain rotamer sampling within MCCE can significantly improve the match with experiment. Copyright © 2011 Wiley-Liss, Inc.

  13. Zinc finger nuclease-mediated precision genome editing of an endogenous gene in hexaploid bread wheat (Triticum aestivum) using a DNA repair template.

    Science.gov (United States)

    Ran, Yidong; Patron, Nicola; Kay, Pippa; Wong, Debbie; Buchanan, Margaret; Cao, Ying-Ying; Sawbridge, Tim; Davies, John P; Mason, John; Webb, Steven R; Spangenberg, German; Ainley, William M; Walsh, Terence A; Hayden, Matthew J

    2018-05-07

    Sequence-specific nucleases have been used to engineer targeted genome modifications in various plants. While targeted gene knockouts resulting in loss of function have been reported with relatively high rates of success, targeted gene editing using an exogenously supplied DNA repair template and site-specific transgene integration has been more challenging. Here, we report the first application of zinc finger nuclease (ZFN)-mediated, nonhomologous end-joining (NHEJ)-directed editing of a native gene in allohexaploid bread wheat to introduce, via a supplied DNA repair template, a specific single amino acid change into the coding sequence of acetohydroxyacid synthase (AHAS) to confer resistance to imidazolinone herbicides. We recovered edited wheat plants having the targeted amino acid modification in one or more AHAS homoalleles via direct selection for resistance to imazamox, an AHAS-inhibiting imidazolinone herbicide. Using a cotransformation strategy based on chemical selection for an exogenous marker, we achieved a 1.2% recovery rate of edited plants having the desired amino acid change and a 2.9% recovery of plants with targeted mutations at the AHAS locus resulting in a loss-of-function gene knockout. The latter results demonstrate a broadly applicable approach to introduce targeted modifications into native genes for nonselectable traits. All ZFN-mediated changes were faithfully transmitted to the next generation. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  14. Children’s Mapping between Non-Symbolic and Symbolic Numerical Magnitudes and Its Association with Timed and Untimed Tests of Mathematics Achievement

    Science.gov (United States)

    Brankaer, Carmen; Ghesquière, Pol; De Smedt, Bert

    2014-01-01

    The ability to map between non-symbolic numerical magnitudes and Arabic numerals has been put forward as a key factor in children’s mathematical development. This mapping ability has been mainly examined indirectly by looking at children’s performance on a symbolic magnitude comparison task. The present study investigated mapping in a more direct way by using a task in which children had to choose which of two choice quantities (Arabic digits or dot arrays) matched the target quantity (dot array or Arabic digit), thereby focusing on small quantities ranging from 1 to 9. We aimed to determine the development of mapping over time and its relation to mathematics achievement. Participants were 36 first graders (M = 6 years 8 months) and 46 third graders (M = 8 years 8 months) who all completed mapping tasks, symbolic and non-symbolic magnitude comparison tasks and standardized timed and untimed tests of mathematics achievement. Findings revealed that children are able to map between non-symbolic and symbolic representations and that this mapping ability develops over time. Moreover, we found that children’s mapping ability is related to timed and untimed measures of mathematics achievement, over and above the variance accounted for by their numerical magnitude comparison skills. PMID:24699664

  15. Comparative FISH mapping of BMPR1B, BMP15 and GDF9 ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 92; Issue 3. Comparative FISH mapping of BMPR1B, BMP15 and GDF9 fecundity genes on cattle, river buffalo, sheep and goat chromosomes. A. Farhadi V. Genualdo A. Perucatti S. H. Hafezian G. Rahimi-Mianji L. De Lorenzi P. Parma L. Iannuzzi A. Iannuzzi. Research Note ...

  16. Mapping of novel powdery mildew resistance gene(s) from Agropyron cristatum chromosome 2P.

    Science.gov (United States)

    Li, Huanhuan; Jiang, Bo; Wang, Jingchang; Lu, Yuqing; Zhang, Jinpeng; Pan, Cuili; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

    2017-01-01

    A physical map of Agropyron cristatum 2P chromosome was constructed for the first time and the novel powdery mildew resistance gene(s) from chromosome 2P was(were) also mapped. Agropyron cristatum (L.) Gaertn. (2n = 28, PPPP), a wild relative of common wheat, is highly resistant to powdery mildew. Previous studies showed that wheat-A. cristatum 2P disomic addition line II-9-3 displayed high resistance to powdery mildew, and the resistance was attributable to A. cristatum chromosome 2P. To utilize and physically map the powdery mildew resistance gene(s), 15 wheat-A. cristatum 2P translocation lines and three A. cristatum 2P deletion lines with different chromosomal segment sizes, obtained from II-9-3 using 60 Co-γ ray irradiation, were characterized using cytogenetic and molecular marker analysis. A. cristatum 2P chromosomal segments in the translocations were translocated to different wheat chromosomes, including 1A, 4A, 5A, 6A, 7A, 1B, 2B, 3B, 7B, 3D, 4D, and 6D. A physical map of the 2P chromosome was constructed with 82 STS markers, consisting of nine bins with 34 markers on 2PS and eight bins with 48 markers on 2PL. The BC 1 F 2 populations of seven wheat-A. cristatum 2P translocation lines (2PT-3, 2PT-4, 2PT-5, 2PT-6, 2PT-8, 2PT-9, and 2PT-10) were developed by self-pollination, tested with powdery mildew and genotyped with 2P-specific STS markers. From these results, the gene(s) conferring powdery mildew resistance was(were) located on 2PL bin FL 0.66-0.86 and 19 2P-specific markers were identified in this bin. Moreover, two new powdery mildew-resistant translocation lines (2PT-4 and 2PT-5) with small 2PL chromosome segments were obtained. The newly developed wheat lines with powdery mildew resistance and the closely linked molecular markers will be valuable for wheat disease breeding in the future.

  17. RICE CROP MAPPING USING SENTINEL-1A PHENOLOGICAL METRICS

    Directory of Open Access Journals (Sweden)

    C. F. Chen

    2016-06-01

    Full Text Available Rice is the most important food crop in Vietnam, providing food more than 90 million people and is considered as an essential source of income for majority of rural populations. Monitoring rice-growing areas is thus important to developing successful strategies for food security in the country. This paper aims to develop an approach for crop acreage estimation from multi-temporal Sentinel-1A data. We processed the data for two main cropping seasons (e.g., winter–spring, summer–autumn in the Mekong River Delta (MRD, Vietnam through three main steps: (1 data pre-processing, (3 rice classification based on crop phenological metrics, and (4 accuracy assessment of the mapping results. The classification results compared with the ground reference data indicated the overall accuracy of 86.2% and Kappa coefficient of 0.72. These results were reaffirmed by close correlation between the government’s rice area statistics for such crops (R2 > 0.95. The values of relative error in area obtained for the winter–spring and summer–autumn were -3.6% and 6.7%, respectively. This study demonstrates the potential application of multi-temporal Sentinel-1A data for rice crop mapping using information of crop phenology in the study region.

  18. Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification

    KAUST Repository

    Li, Lixin

    2012-01-22

    Transcription activator-like effectors (TALEs) can be used as DNA-targeting modules by engineering their repeat domains to dictate user-selected sequence specificity. TALEs have been shown to function as site-specific transcriptional activators in a variety of cell types and organisms. TALE nucleases (TALENs), generated by fusing the FokI cleavage domain to TALE, have been used to create genomic double-strand breaks. The identity of the TALE repeat variable di-residues, their number, and their order dictate the DNA sequence specificity. Because TALE repeats are nearly identical, their assembly by cloning or even by synthesis is challenging and time consuming. Here, we report the development and use of a rapid and straightforward approach for the construction of designer TALE (dTALE) activators and nucleases with user-selected DNA target specificity. Using our plasmid set of 100 repeat modules, researchers can assemble repeat domains for any 14-nucleotide target sequence in one sequential restriction-ligation cloning step and in only 24 h. We generated several custom dTALEs and dTALENs with new target sequence specificities and validated their function by transient expression in tobacco leaves and in vitro DNA cleavage assays, respectively. Moreover, we developed a web tool, called idTALE, to facilitate the design of dTALENs and the identification of their genomic targets and potential off-targets in the genomes of several model species. Our dTALE repeat assembly approach along with the web tool idTALE will expedite genome-engineering applications in a variety of cell types and organisms including plants. © 2012 Springer Science+Business Media B.V.

  19. A gene for late-onset fundus flavimaculatus with macular dystrophy maps to chromosome 1p13

    Energy Technology Data Exchange (ETDEWEB)

    Gerber, S.; Rozet, J.M.; Bonneau, D.; Souied, E.; Camuzat, A.; Munnich, A.; Kaplan, J. [Hopital des Enfants Malades, Paris (France); Dufier, J.L. [Hopital Laeennec, Paris (France); Amalric, P. [Consultation d`Ophtalmologie, Albi (France); Weissenbach, J. [Genethon, Evry (France)

    1995-02-01

    Fundus flavimaculatus with macular dystrophy is an autosomal recessive disease responsible for a progressive loss of visual acuity in adulthood, with pigmentary changes of the macula, perimacular flecks, and atrophy of the retinal pigmentary epithelium. Since this condition shares several clinical features with Stargardt disease, which has been mapped to chromosome 1p21-p13, we tested the disease for linkage to chromosome 1p. We report the mapping of the disease locus to chromosome 1p13-p21, in the genetic interval defined by loci D1S435 and D1S415, in four multiplex families (maximum lod score 4.79 at recombination fraction 0 for probe AFM217xb2 at locus D1S435). Thus, despite differences in the age at onset, clinical course, and severity, fundus flavimaculatus with macular dystrophy and Stargardt disease are probably allelic disorders. This result supports the view that allelic mutations produce a continuum of macular dystrophies, with onset in early childhood to late adulthood. 16 refs., 3 figs., 1 tab.

  20. Syntheses of prodrug-type phosphotriester oligonucleotides responsive to intracellular reducing environment for improvement of cell membrane permeability and nuclease resistance.

    Science.gov (United States)

    Hayashi, Junsuke; Samezawa, Yusuke; Ochi, Yosuke; Wada, Shun-Ichi; Urata, Hidehito

    2017-07-15

    We synthesized prodrug-type phosphotriester (PTE) oligonucleotides containing the six-membered cyclic disulfide moiety by using phosphoramidite chemistry. Prodrug-type oligonucleotides named "Reducing-Environment-Dependent Uncatalyzed Chemical Transforming (REDUCT) PTE oligonucleotides" were converted into natural oligonucleotides under cytosol-mimetic reductive condition. Furthermore, the REDUCT PTE oligonucleotides were robust to nuclease digestion and exhibited good cell membrane permeability. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Mapping sense(s) of place

    DEFF Research Database (Denmark)

    Skovse, Astrid Ravn; Hovy, Dirk; Johannsen, Anders Trærup

    2016-01-01

    , the question of how to tap into this constitutes a methodological challenge to researchers (Latham 2003, Hall 2009). This paper presents an experimental method aimed at eliciting data on sense of place and everyday mobility in a feasible and low-tech manner through the use of mental maps and mobility maps...... for answering questions about the relationship between places, speakers and linguistic practice....

  2. A ‘new lease of life’: FnCpf1 possesses DNA cleavage activity for genome editing in human cells

    Science.gov (United States)

    Tu, Mengjun; Lin, Li; Cheng, Yilu; He, Xiubin; Sun, Huihui; Xie, Haihua; Fu, Junhao; Liu, Changbao; Li, Jin; Chen, Ding; Xi, Haitao; Xue, Dongyu; Liu, Qi; Zhao, Junzhao; Gao, Caixia; Song, Zongming; Qu, Jia

    2017-01-01

    Abstract Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5′-TTTN-3′ protospacer adjacent motif (PAM) at the 5′ end of the protospacer for genome editing. For widespread application in precision site-specific human genome editing, the range of sequences that AsCpf1 and LbCpf1 can recognize is limited due to the size of this PAM. To address this limitation, we sought to identify a novel Cpf1 nuclease with simpler PAM requirements. Specifically, here we sought to test and engineer FnCpf1, one reported Cpf1 nuclease (FnCpf1) only requires 5′-TTN-3′ as a PAM but does not exhibit detectable levels of nuclease-induced indels at certain locus in human cells. Surprisingly, we found that FnCpf1 possesses DNA cleavage activity in human cells at multiple loci. We also comprehensively and quantitatively examined various FnCpf1 parameters in human cells, including spacer sequence, direct repeat sequence and the PAM sequence. Our study identifies FnCpf1 as a new member of the Cpf1 family for human genome editing with distinctive characteristics, which shows promise as a genome editing tool with the potential for both research and therapeutic applications. PMID:28977650

  3. Ocjena točnosti državne topografske karte mjerila 1 : 25 000 : Evaluation of accuracy of state topographic map scale 1:25 000

    Directory of Open Access Journals (Sweden)

    Slobodanka Ključanin

    2011-03-01

    Full Text Available U Bosni i Hecegovini 2002. godine, pokrenut je projekt - izrada digitalne topografske karte M=1:25000 (TK 25 uz financijsku i stručnu pomoć Japanske agencije za međunarodnu saradnju (JICA. Projekt je završen krajem 2005. godine. Federalna uprava za geodeteske i imovinsko-pravne poslove, 2007. godine započela je s projektom ažuriranja postojećih TK25. Projekt teče sporo i sukcesivno (zavisno od prikupljenih financijskih sredstava. Do danas ni jedan list TK25 nije u potpunosti završen (od četiri lista koja su u procesu ažuriranja, niti je izvedena ocjena točnosti jednog lista TK25. U ovom članku obrađena je prethodna (a priori i stvarna (a poseteriori ocjena točnosti jenog lista TK25 (Žepče 093-1-1. : Bosnia and Herzegovina initiated the project in year 2002 to make digital topographic maps M = 1:25000 (TK 25, with financial and technical assistanceof the Japan‘s International Cooperation Agency (JICA. The project was completed in late 2005. In year 2007 Federal Geodetic Administration started project updates to existing TK25. The project is going slowly and successively (depending on the collected funds. To date, no have fully completed map TK25 (four maps that are in the process of updating, or made estimation of accuracy of any maps TK25. This article deals with the preliminary (a priori and actual (a poseteriori rating accuracy map TK25 (Zepce 093-1-1.

  4. FISH-mapping of the 5S rDNA locus in chili peppers (Capsicum-Solanaceae).

    Science.gov (United States)

    Aguilera, Patricia M; Debat, Humberto J; Scaldaferro, Marisel A; Martí, Dardo A; Grabiele, Mauro

    2016-03-01

    We present here the physical mapping of the 5S rDNA locus in six wild and five cultivated taxa of Capsicum by means of a genus-specific FISH probe. In all taxa, a single 5S locus per haploid genome that persistently mapped onto the short arm of a unique metacentric chromosome pair at intercalar position, was found. 5S FISH signals of almost the same size and brightness intensity were observed in all the analyzed taxa. This is the first cytological characterization of the 5S in wild taxa of Capsicum by using a genus-derived probe, and the most exhaustive and comprehensive in the chili peppers up to now. The information provided here will aid the cytomolecular characterization of pepper germplasm to evaluate variability and can be instrumental to integrate physical, genetic and genomic maps already generated in the genus.

  5. The modification of siRNA with 3' cholesterol to increase nuclease protection and suppression of native mRNA by select siRNA polyplexes.

    Science.gov (United States)

    Ambardekar, Vishakha V; Han, Huai-Yun; Varney, Michelle L; Vinogradov, Serguei V; Singh, Rakesh K; Vetro, Joseph A

    2011-02-01

    Polymer-siRNA complexes (siRNA polyplexes) are being actively developed to improve the therapeutic application of siRNA. A major limitation for many siRNA polyplexes, however, is insufficient mRNA suppression. Given that modifying the sense strand of siRNA with 3' cholesterol (chol-siRNA) increases the activity of free nuclease-resistant siRNA in vitro and in vivo, we hypothesized that complexation of chol-siRNA can increase mRNA suppression by siRNA polyplexes. In this study, the characteristics and siRNA activity of self assembled polyplexes formed with chol-siRNA or unmodified siRNA were compared using three types of conventional, positively charged polymers: (i) biodegradable, cross-linked nanogels (BDNG) (ii) graft copolymers (PEI-PEG), and (iii) linear block copolymers (PLL10-PEG, and PLL50-PEG). Chol-siRNA did not alter complex formation or the resistance of polyplexes to siRNA displacement by heparin but increased nuclease protection by BDNG, PLL10-PEG, and PLL50-PEG polyplexes over polyplexes with unmodified siRNA. Chol-CYPB siRNA increased suppression of native CYPB mRNA in mammary microvascular endothelial cells (MVEC) by BDNG polyplexes (35%) and PLL10-PEG polyplexes (69%) over comparable CYPB siRNA polyplexes but had no effect on PEI-PEG or PLL50-PEG polyplexes. Overall, these results indicate that complexation of chol-siRNA increases nuclease protection and mRNA suppression by select siRNA polyplexes. These results also suggest that polycationic block length is an important factor in increasing mRNA suppression by PLL-PEG chol-siRNA polyplexes in mammary MVEC. Copyright © 2010 Elsevier Ltd. All rights reserved.

  6. A de novo 1.58 Mb deletion, including MAP2K6 and mapping 1.28 Mb upstream to SOX9, identified in a patient with Pierre Robin sequence and osteopenia with multiple fractures.

    Science.gov (United States)

    Smyk, Marta; Roeder, Elizabeth; Cheung, Sau Wai; Szafranski, Przemyslaw; Stankiewicz, Paweł

    2015-08-01

    Defects of long-range regulatory elements of dosage-sensitive genes represent an under-recognized mechanism underlying genetic diseases. Haploinsufficiency of SOX9, the gene essential for development of testes and differentiation of chondrocytes, results in campomelic dysplasia, a skeletal malformation syndrome often associated with sex reversal. Chromosomal rearrangements with breakpoints mapping up to 1.6 Mb up- and downstream to SOX9, and disrupting its distant cis-regulatory elements, have been described in patients with milder forms of campomelic dysplasia, Pierre Robin sequence, and sex reversal. We present an ∼1.58 Mb deletion mapping1.28 Mb upstream to SOX9 that encompasses its putative long-range cis-regulatory element(s) and MAP2K6 in a patient with Pierre Robin sequence and osteopenia with multiple fractures. Low bone mass panel testing using massively parallel sequencing of 23 nuclear genes, including COL1A1 and COL1A2 was negative. Based on the previous mouse model of Map2k6, suggesting that Sox9 is likely a downstream target of the p38 MAPK pathway, and our previous chromosome conformation capture-on-chip (4C) data showing potential interactions between SOX9 promoter and MAP2K6, we hypothesize that deletion of MAP2K6 might have affected SOX9 expression and contributed to our patient's phenotype. © 2015 Wiley Periodicals, Inc.

  7. A note on Verhulst's logistic equation and related logistic maps

    Energy Technology Data Exchange (ETDEWEB)

    Gutierrez, M Ranferi; Reyes, M A [Depto de Fisica, Universidad de Guanajuato, Apdo. Postal E143, 37150 Leon, Gto. (Mexico); Rosu, H C, E-mail: hcr@ipicyt.edu.m [IPICyT, Instituto Potosino de Investigacion Cientifica y Tecnologica, Apdo Postal 3-74 Tangamanga, 78231 San Luis PotosI (Mexico)

    2010-05-21

    We consider the Verhulst logistic equation and a couple of forms of the corresponding logistic maps. For the case of the logistic equation we show that using the general Riccati solution only changes the initial conditions of the equation. Next, we consider two forms of corresponding logistic maps reporting the following results. For the map x{sub n+1} = rx{sub n}(1 - x{sub n}) we propose a new way to write the solution for r = -2 which allows better precision of the iterative terms, while for the map x{sub n+1} - x{sub n} = rx{sub n}(1 - x{sub n+1}) we show that it behaves identically to the logistic equation from the standpoint of the general Riccati solution, which is also provided herein for any value of the parameter r.

  8. Interaction of avian infectious bronchitis virus S1 protein with heat ...

    African Journals Online (AJOL)

    The interaction between S1 and HSP47 was verified by colocalization experiment and co-immunoprecipitation of HeLa cell lysates expressing both proteins. The mapping studies localized the critical S1 sequences for this interaction to amino acids 340-470. Based on these results, we speculate that HSP47 is a functional ...

  9. Northern Circumpolar Soils Map, Version 1

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set consists of a circumpolar map of dominant soil characteristics, with a scale of 1:10,000,000, covering the United States, Canada, Greenland, Iceland,...

  10. Australia’s National Health Programs: An Ontological Mapping

    Directory of Open Access Journals (Sweden)

    Arkalgud Ramaprasad

    2016-11-01

    Full Text Available Australia has a large number of health program initiatives whose comprehensive assessment will help refine and redefine priorities by highlighting areas of emphasis, under-emphasis, and non-emphasis. The objectives of our research are to: (a systematically map all the programs onto an ontological framework, and (b systemically analyse their relative emphases at different levels of granularity. We mapped all the health program initiatives onto an ontology with five dimensions, namely: (a Policy-scope, (b Policy-focus, (c Outcomes, (d Type of care, and (e Population served. Each dimension is expanded into a taxonomy of its constituent elements. Each combination of elements from the five dimensions is a possible policy initiative component. There are 30,030 possible components encapsulated in the ontology. It includes, for example: (a National financial policies on accessibility of preventive care for family, and (b Local-urban regulatory policies on cost of palliative care for individual-aged. Four of the authors mapped all of Australia’s health programs and initiatives on to the ontology. Visualizations of the data are used to highlight the relative emphases in the program initiatives. The dominant emphasis of the program initiatives is: [National] [educational, personnel-physician, information] policies on [accessibility, quality] of [preventive, wellness] care for the [community]. However, although (a information is emphasized technology is not; and (b accessibility and quality are emphasized cost, satisfaction, and quality are not. The ontology and the results of the mapping can help systematically reassess and redirect the relative emphases of the programs and initiatives from a systemic perspective.

  11. Landsat Image Map Production Methods at the U. S. Geological Survey

    Science.gov (United States)

    Kidwell, R.D.; Binnie, D.R.; Martin, S.

    1987-01-01

    To maintain consistently high quality in satellite image map production, the U. S. Geological Survey (USGS) has developed standard procedures for the photographic and digital production of Landsat image mosaics, and for lithographic printing of multispectral imagery. This paper gives a brief review of the photographic, digital, and lithographic procedures currently in use for producing image maps from Landsat data. It is shown that consistency in the printing of image maps is achieved by standardizing the materials and procedures that affect the image detail and color balance of the final product. Densitometric standards are established by printing control targets using the pressplates, inks, pre-press proofs, and paper to be used for printing.

  12. Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1

    KAUST Repository

    Sobhy, M.; Joudeh, L.; Huang, X.; Takahashi, Masateru; Hamdan, S.

    2013-01-01

    Human flap endonuclease 1 (FEN1), one of the structure-specific 5' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5' nuclease mechanisms. This is achieved by coordinating threading of the 5' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection ofDNA junctions from nonspecific bending and cleavage. 2013 The Authors.

  13. Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1

    KAUST Repository

    Sobhy, M.

    2013-06-06

    Human flap endonuclease 1 (FEN1), one of the structure-specific 5\\' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5\\' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5\\' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5\\' nuclease mechanisms. This is achieved by coordinating threading of the 5\\' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5\\' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection ofDNA junctions from nonspecific bending and cleavage. 2013 The Authors.

  14. Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease

    DEFF Research Database (Denmark)

    Francis, C. J.; Lindorff-Larsen, Kresten; Best, R. B.

    2006-01-01

    dynamics simulations to characterise the residual structure of the 131 fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that 131 under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild......The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular...

  15. The Mapping X-ray Fluorescence Spectrometer (MapX)

    Science.gov (United States)

    Sarrazin, P.; Blake, D. F.; Marchis, F.; Bristow, T.; Thompson, K.

    2017-12-01

    Many planetary surface processes leave traces of their actions as features in the size range 10s to 100s of microns. The Mapping X-ray Fluorescence Spectrometer (MapX) will provide elemental imaging at 100 micron spatial resolution, yielding elemental chemistry at a scale where many relict physical, chemical, or biological features can be imaged and interpreted in ancient rocks on planetary bodies and planetesimals. MapX is an arm-based instrument positioned on a rock or regolith with touch sensors. During an analysis, an X-ray source (tube or radioisotope) bombards the sample with X-rays or alpha-particles / gamma-rays, resulting in sample X-ray Fluorescence (XRF). X-rays emitted in the direction of an X-ray sensitive CCD imager pass through a 1:1 focusing lens (X-ray micro-pore Optic (MPO)) that projects a spatially resolved image of the X-rays onto the CCD. The CCD is operated in single photon counting mode so that the energies and positions of individual X-ray photons are recorded. In a single analysis, several thousand frames are both stored and processed in real-time. Higher level data products include single-element maps with a lateral spatial resolution of 100 microns and quantitative XRF spectra from ground- or instrument- selected Regions of Interest (ROI). XRF spectra from ROI are compared with known rock and mineral compositions to extrapolate the data to rock types and putative mineralogies. When applied to airless bodies and implemented with an appropriate radioisotope source for alpha-particle excitation, MapX will be able to analyze biogenic elements C, N, O, P, S, in addition to the cations of the rock-forming elements >Na, accessible with either X-ray or gamma-ray excitation. The MapX concept has been demonstrated with a series of lab-based prototypes and is currently under refinement and TRL maturation.

  16. Functionalized bioengineered spider silk spheres improve nuclease resistance and activity of oligonucleotide therapeutics providing a strategy for cancer treatment.

    Science.gov (United States)

    Kozlowska, Anna Karolina; Florczak, Anna; Smialek, Maciej; Dondajewska, Ewelina; Mackiewicz, Andrzej; Kortylewski, Marcin; Dams-Kozlowska, Hanna

    2017-09-01

    Cell-selective delivery and sensitivity to serum nucleases remain major hurdles to the clinical application of RNA-based oligonucleotide therapeutics, such as siRNA. Spider silk shows great potential as a biomaterial due to its biocompatibility and biodegradability. Self-assembling properties of silk proteins allow for processing into several different morphologies such as fibers, scaffolds, films, hydrogels, capsules and spheres. Moreover, bioengineering of spider silk protein sequences can functionalize silk by adding peptide moieties with specific features including binding or cell recognition domains. We demonstrated that modification of silk protein by adding the nucleic acid binding domain enabled the development of a novel oligonucleotide delivery system that can be utilized to improve pharmacokinetics of RNA-based therapeutics, such as CpG-siRNA. The MS2 bioengineered silk was functionalized with poly-lysine domain (KN) to generate hybrid silk MS2KN. CpG-siRNA efficiently bound to MS2KN in contrary to control MS2. Both MS2KN complexes and spheres protected CpG-siRNA from degradation by serum nucleases. CpG-siRNA molecules encapsulated into MS2KN spheres were efficiently internalized and processed by TLR9-positive macrophages. Importantly, CpG-STAT3siRNA loaded in silk spheres showed delayed and extended target gene silencing compared to naked oligonucleotides. The prolonged Stat3 silencing resulted in the more pronounced downregulation of interleukin 6 (IL-6), a proinflammatory cytokine and upstream activator of STAT3, which limits the efficacy of TLR9 immunostimulation. Our results demonstrate the feasibility of using spider silk spheres as a carrier of therapeutic nucleic acids. Moreover, the modified kinetic and activity of the CpG-STAT3siRNA embedded into silk spheres is likely to improve immunotherapeutic effects in vivo. We demonstrated that modification of silk protein by adding the nucleic acid binding domain enabled the development of a novel

  17. Identification of a new family of putative PD-(D/EXK nucleases with unusual phylogenomic distribution and a new type of the active site

    Directory of Open Access Journals (Sweden)

    Bujnicki Janusz M

    2005-02-01

    Full Text Available Abstract Background Prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the cornerstones of genomics. Theoretical assignment of three-dimensional folds and prediction of protein function even at a very general level can facilitate the experimental determination of the molecular mechanism of action and the role that members of a given protein family fulfill in the cell. Here, we predict the three-dimensional fold and study the phylogenomic distribution of members of a large family of uncharacterized proteins classified in the Clusters of Orthologous Groups database as COG4636. Results Using protein fold-recognition we found that members of COG4636 are remotely related to Holliday junction resolvases and other nucleases from the PD-(D/EXK superfamily. Structure modeling and sequence analyses suggest that most members of COG4636 exhibit a new, unusual variant of the putative active site, in which the catalytic Lys residue migrated in the sequence, but retained similar spatial position with respect to other functionally important residues. Sequence analyses revealed that members of COG4636 and their homologs are found mainly in Cyanobacteria, but also in other bacterial phyla. They undergo horizontal transfer and extensive proliferation in the colonized genomes; for instance in Gloeobacter violaceus PCC 7421 they comprise over 2% of all protein-encoding genes. Thus, members of COG4636 appear to be a new type of selfish genetic elements, which may fulfill an important role in the genome dynamics of Cyanobacteria and other species they invaded. Our analyses provide a platform for experimental determination of the molecular and cellular function of members of this large protein family. Conclusion After submission of this manuscript, a crystal structure of one of the COG4636 members was released in the Protein Data Bank (code 1wdj

  18. Alignment and referencing of maps and aerial photographs

    International Nuclear Information System (INIS)

    Cullings, Harry M.; Fujita, Shoichiro; Hoshi, Masaharu; Egbert, Stephen D.; Kerr, George D.

    2005-01-01

    Documentation of survivor locations as well as sample collection sites for dosimetry-related measurements requires reference to suitable maps. The maps traditionally used at RERF for these purposes are the U.S. Army maps that date from circa 1945 (see Chapter 1). In later years, some use has been made of Japanese city plan maps, which are much newer (1979 in Hiroshima and 1981 in Nagasaki) and of larger scale (1:2,500 vs. 1:12,500 for the U.S. Army maps). Even before the publication of DS86, efforts were made to reconcile the locations of buildings and other features of interest on these two sets of maps. Beyond the simple desire to compare two different sources of map information, it was thought that a better standard of accuracy for technical reasons could be achieved with the use of the newer maps. The U.S. Army maps were compiled under wartime conditions from an assortment of older Japanese maps and other sources, including aerial photographs of limited quality, using the best methods available at the time. The newer Japanese maps had the benefit of 34 years of improvement in cartographic methods and were made with extensive new survey information. Because of their larger scale, they are also more detailed than the U.S. Army maps. (J.P.N.)

  19. High specific radioactivity (1R,2S)-4-[18F]fluorometaraminol: a PET radiotracer for mapping sympathetic nerves of the heart

    International Nuclear Information System (INIS)

    Langer, Oliver; Valette, Heric; Dolle, Frederic; Halldin, Christer; Loc'h, Christian; Fuseau, Chantal; Coulon, Christine; Ottaviani, Michele; Bottlaender, Michel; Maziere, Bernard; Crouzel, Christian

    2000-01-01

    The radiolabeled catecholamine analogue (1R,2S)-6-[ 18 F]fluorometaraminol (6-[ 18 F]FMR) is a substrate for the neuronal norepinephrine transporter. It has been used as a positron emission tomography (PET) ligand to map sympathetic nerves in dog heart. 6-[ 18 F]FMR could be only synthesized with low specific radioactivity, which precluded its use in human subjects. We have recently prepared (1R,2S)-4-[ 18 F]fluorometaraminol (4-[ 18 F]FMR), a new fluoro-analogue of metaraminol, with high specific radioactivity (56-106 GBq/μmol). In the present study, we demonstrate in rats that 4-[ 18 F]FMR possesses similar affinity toward myocardial norepinephrine transport mechanisms as 6-[ 18 F]FMR. When compared with control animals, an 80% and 76% reduction in myocardial uptake was observed in animals pretreated with desipramine (an inhibitor of the neuronal norepinephrine transporter) and with reserpine (a blocker of the vesicular storage of monoamines), respectively. The entire radioactivity in rat myocardium represented unmetabolized parent tracer as determined by high performance liquid chromatography analysis of tissue extracts. In dogs, myocardial kinetics of 4-[ 18 F]FMR were assessed using PET. A rapid and high uptake was observed, followed by prolonged cardiac retention. A heart-to-lung ratio of 15 was reached 10 min after injection of the radiotracer. Pretreatment with desipramine reduced the heart half-life of 4-[ 18 F]FMR by 90% compared with control. Moreover, an infusion of tyramine caused a rapid decline of radioactivity in the heart. This demonstrates that 4-[ 18 F]FMR specifically visualizes sympathetic neurons in dog heart. High specific radioactivity 4-[ 18 F]FMR is a promising alternative to 6-[ 18 F]FMR for myocardial neuronal mapping with PET in humans

  20. Dark Energy Survey Year 1 results: curved-sky weak lensing mass map

    Science.gov (United States)

    Chang, C.; Pujol, A.; Mawdsley, B.; Bacon, D.; Elvin-Poole, J.; Melchior, P.; Kovács, A.; Jain, B.; Leistedt, B.; Giannantonio, T.; Alarcon, A.; Baxter, E.; Bechtol, K.; Becker, M. R.; Benoit-Lévy, A.; Bernstein, G. M.; Bonnett, C.; Busha, M. T.; Rosell, A. Carnero; Castander, F. J.; Cawthon, R.; da Costa, L. N.; Davis, C.; De Vicente, J.; DeRose, J.; Drlica-Wagner, A.; Fosalba, P.; Gatti, M.; Gaztanaga, E.; Gruen, D.; Gschwend, J.; Hartley, W. G.; Hoyle, B.; Huff, E. M.; Jarvis, M.; Jeffrey, N.; Kacprzak, T.; Lin, H.; MacCrann, N.; Maia, M. A. G.; Ogando, R. L. C.; Prat, J.; Rau, M. M.; Rollins, R. P.; Roodman, A.; Rozo, E.; Rykoff, E. S.; Samuroff, S.; Sánchez, C.; Sevilla-Noarbe, I.; Sheldon, E.; Troxel, M. A.; Varga, T. N.; Vielzeuf, P.; Vikram, V.; Wechsler, R. H.; Zuntz, J.; Abbott, T. M. C.; Abdalla, F. B.; Allam, S.; Annis, J.; Bertin, E.; Brooks, D.; Buckley-Geer, E.; Burke, D. L.; Kind, M. Carrasco; Carretero, J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; Desai, S.; Diehl, H. T.; Dietrich, J. P.; Doel, P.; Estrada, J.; Neto, A. Fausti; Fernandez, E.; Flaugher, B.; Frieman, J.; García-Bellido, J.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; James, D. J.; Jeltema, T.; Johnson, M. W. G.; Johnson, M. D.; Kent, S.; Kirk, D.; Krause, E.; Kuehn, K.; Kuhlmann, S.; Lahav, O.; Li, T. S.; Lima, M.; March, M.; Martini, P.; Menanteau, F.; Miquel, R.; Mohr, J. J.; Neilsen, E.; Nichol, R. C.; Petravick, D.; Plazas, A. A.; Romer, A. K.; Sako, M.; Sanchez, E.; Scarpine, V.; Schubnell, M.; Smith, M.; Smith, R. C.; Soares-Santos, M.; Sobreira, F.; Suchyta, E.; Tarle, G.; Thomas, D.; Tucker, D. L.; Walker, A. R.; Wester, W.; Zhang, Y.

    2018-04-01

    We construct the largest curved-sky galaxy weak lensing mass map to date from the DES first-year (DES Y1) data. The map, about 10 times larger than the previous work, is constructed over a contiguous ≈1500 deg2, covering a comoving volume of ≈10 Gpc3. The effects of masking, sampling, and noise are tested using simulations. We generate weak lensing maps from two DES Y1 shear catalogues, METACALIBRATION and IM3SHAPE, with sources at redshift 0.2 < z < 1.3, and in each of four bins in this range. In the highest signal-to-noise map, the ratio between the mean signal to noise in the E-mode map and the B-mode map is ˜1.5 (˜2) when smoothed with a Gaussian filter of σG = 30 (80) arcmin. The second and third moments of the convergence κ in the maps are in agreement with simulations. We also find no significant correlation of κ with maps of potential systematic contaminants. Finally, we demonstrate two applications of the mass maps: (1) cross-correlation

  1. Linkage mapping of the gene for Type III collagen (COL3A1) to human chromosome 2q using a VNTR polymorphism

    Energy Technology Data Exchange (ETDEWEB)

    Tiller, G.E.; Polumbo, P.A.; Summar, M.L. (Vanderbilt Univ. Medical Center, Nashville, TN (United States))

    1994-03-15

    The gene for the [alpha]1(III) chain of type III collagen, COL3A1, has been previously mapped to human chromosome 2q24.3-q31 by in situ hybridization. Physical mapping by pulsed-field gel electrophoresis has demonstrated that COL3A1 lies within 35 kb of COL5A2. The authors genotyped the CEPH families at the COL3A2 locus using a pentanucleotide repeat polymorphism within intron 25. They demonstrated significant linkage to 18 anonymous markers as well as the gene for carbamyl phosphate synthetase (CPSI), which had been previously mapped to this region. No recombination was seen between COL3A1 and COL5A2 (Z = 9.93 at [theta] = 0) or D2S24 (Z = 10.55 at [theta] = 0). The locus order is (D2S32-D2S138-D2S148)-(D2S24-COL5A2-COL3A1)-(D2S118-D2S161), with odds of 1:2300 for the next most likely order. These relationships are consistent with the physical mapping of COL3A1 to the distal portion of 2q and place it proximal to CPSI by means of multipoint analysis. These linkage relationships should prove useful in further studies of Ehlers-Danlos syndrome type IV and carbamyl phosphate synthetase I deficiency and provide an additional framework for localizing other genes in this region. 13 refs., 2 figs., 1 tab.

  2. Global maps of the magnetic thickness and magnetization of the Earth’s lithosphere

    OpenAIRE

    Foteini Vervelidou; Erwan Thébault

    2015-01-01

    We have constructed global maps of the large-scale magnetic thickness and magnetization of Earth’s lithosphere. Deriving such large-scale maps based on lithospheric magnetic field measurements faces the challenge of the masking effect of the core field. In this study, the maps were obtained through analyses in the spectral domain by means of a new regional spatial power spectrum based on the Revised Spherical Cap Harmonic Analysis (R-SCHA) formalism. A series of regional spectral analyses wer...

  3. Dark Energy Survey Year 1 Results: Curved-Sky Weak Lensing Mass Map

    Energy Technology Data Exchange (ETDEWEB)

    Chang, C.; et al.

    2017-08-04

    We construct the largest curved-sky galaxy weak lensing mass map to date from the DES first-year (DES Y1) data. The map, about 10 times larger than previous work, is constructed over a contiguous $\\approx1,500 $deg$^2$, covering a comoving volume of $\\approx10 $Gpc$^3$. The effects of masking, sampling, and noise are tested using simulations. We generate weak lensing maps from two DES Y1 shear catalogs, Metacalibration and Im3shape, with sources at redshift $0.21.3,$ and in each of four bins in this range. In the highest signal-to-noise map, the ratio between the mean signal-to-noise in the E-mode and the B-mode map is $\\sim$1.5 ($\\sim$2) when smoothed with a Gaussian filter of $\\sigma_{G}=30$ (80) arcminutes. The second and third moments of the convergence $\\kappa$ in the maps are in agreement with simulations. We also find no significant correlation of $\\kappa$ with maps of potential systematic contaminants. Finally, we demonstrate two applications of the mass maps: (1) cross-correlation with different foreground tracers of mass and (2) exploration of the largest peaks and voids in the maps.

  4. Strong Convergence for Hybrid Implicit S-Iteration Scheme of Nonexpansive and Strongly Pseudocontractive Mappings

    Directory of Open Access Journals (Sweden)

    Shin Min Kang

    2014-01-01

    Full Text Available Let K be a nonempty closed convex subset of a real Banach space E, let S:K→K be nonexpansive, and let  T:K→K be Lipschitz strongly pseudocontractive mappings such that p∈FS∩FT=x∈K:Sx=Tx=x and x-Sy≤Sx-Sy and x-Ty≤Tx-Ty for all x, y∈K. Let βn be a sequence in 0, 1 satisfying (i ∑n=1∞βn=∞; (ii limn→∞⁡βn=0. For arbitrary x0∈K, let xn be a sequence iteratively defined by xn=Syn, yn=1-βnxn-1+βnTxn, n≥1. Then the sequence xn converges strongly to a common fixed point p of S and T.

  5. Design, construction, and analysis of specific zinc finger nucleases for microphthalmia - associate transcription factor

    Directory of Open Access Journals (Sweden)

    Wenwen Wang

    2012-08-01

    Full Text Available This work studied the design, construction, and cleavage analysis of zinc finger nucleases (ZFNs that could cut the specific sequences within microphthalmia - associate transcription factor (mitfa of zebra fish. The target site and ZFPs were selected and designed with zinc finger tools, while the ZFPs were synthesized using DNAWorks and two-step PCR. The ZFNs were constructed, expressed, purified, and analyzed in vitro. As expected, the designed ZFNs could create a double-stand break (DSB at the target site in vitro. The DNAWorks, two-step PCR, and an optimized process of protein expression were firstly induced in the construction of ZFNs successfully, which was an effective and simplified protocol. These results could be useful for further application of ZFNs - mediated gene targeting.

  6. Genetic characterization and fine mapping of S25, a hybrid male sterility gene, on rice chromosome 12.

    Science.gov (United States)

    Kubo, Takahiko; Yoshimura, Atsushi; Kurata, Nori

    2018-02-10

    Hybrid male sterility genes are important factors in creating postzygotic reproductive isolation barriers in plants. One such gene, S25, is known to cause severe transmission ratio distortion in inter-subspecific progeny of cultivated rice Oryza sativa ssp. indica and japonica. To further characterize the S25 gene, we fine-mapped and genetically characterized the S25 gene using near-isogenic lines with reciprocal genetic backgrounds. We mapped the S25 locus within the 0.67-1.02 Mb region on rice chromosome 12. Further genetic analyses revealed that S25 substantially reduced male fertility in the japonica background, but not in the indica background. In first-generation hybrid progeny, S25 had a milder effect than it had in the japonica background. These results suggest that the expression of S25 is epistatically regulated by at least one partially dominant gene present in the indica genome. This finding supports our previous studies showing that hybrid male sterility due to pollen killer genes results from epistatic interaction with other genes that are hidden in the genetic background.

  7. A novel method of S-box design based on chaotic map and composition method

    International Nuclear Information System (INIS)

    Lambić, Dragan

    2014-01-01

    Highlights: • Novel chaotic S-box generation method is presented. • Presented S-box has better cryptographic properties than other examples of chaotic S-boxes. • The advantages of the proposed method are the low complexity and large key space. -- Abstract: An efficient algorithm for obtaining random bijective S-boxes based on chaotic maps and composition method is presented. The proposed method is based on compositions of S-boxes from a fixed starting set. The sequence of the indices of starting S-boxes used is obtained by using chaotic maps. The results of performance test show that the S-box presented in this paper has good cryptographic properties. The advantages of the proposed method are the low complexity and the possibility to achieve large key space

  8. The Modification of siRNA with 3′ Cholesterol to Increase Nuclease Protection and Suppression of Native mRNA by Select siRNA Polyplexes

    Science.gov (United States)

    Ambardekar, Vishakha V.; Han, Huai-Yun; Varney, Michelle L.; Vinogradov, Serguei V.; Singh, Rakesh K.; Vetro, Joseph A.

    2010-01-01

    Polymer-siRNA complexes (siRNA polyplexes) are being actively developed to improve the therapeutic application of siRNA. A major limitation for many siRNA polyplexes, however, is insufficient mRNA suppression. Given that modifying the sense strand of siRNA with 3′ cholesterol (chol-siRNA) increases the activity of free nuclease-resistant siRNA in vitro and in vivo, we hypothesized that complexation of chol-siRNA can increase mRNA suppression by siRNA polyplexes. In this study, the characteristics and siRNA activity of self assembled polyplexes formed with chol-siRNA or unmodified siRNA were compared using three types of conventional, positively charged polymers: (i) biodegradable, cross-linked nanogels (BDNG) (ii) graft copolymers (PEI-PEG), and (iii) linear block copolymers (PLL10-PEG, and PLL50-PEG). Chol-siRNA did not alter complex formation or the resistance of polyplexes to siRNA displacement by heparin but increased nuclease protection by BDNG, PLL10-PEG, and PLL50-PEG polyplexes over polyplexes with unmodified siRNA. Chol-CYPB siRNA increased suppression of native CYPB mRNA in mammary microvascular endothelial cells (MVEC) by BDNG polyplexes (35%) and PLL10-PEG polyplexes (69%) over comparable CYPB siRNA polyplexes but had no effect on PEI-PEG or PLL50-PEG polyplexes. Overall, these results indicate that complexation of chol-siRNA increases nuclease protection and mRNA suppression by select siRNA polyplexes. These results also suggest that polycationic block length is an important factor in increasing mRNA suppression by PLL-PEG chol-siRNA polyplexes in mammary MVEC. PMID:21047680

  9. Evolution of primary and secondary structures in 5S and 5.8S rRNA

    International Nuclear Information System (INIS)

    Curtiss, W.C.

    1986-01-01

    The secondary structure of Bombyx mori 5S rRNA was studied using the sing-strand specific S1 nuclease and the base pair specific cobra venom ribonuclease. The RNA was end-labeled with [ 32 P] at either the 5' or 3' end and sequenced using enzymatic digestion techniques. These enzymatic data coupled with thermodynamic structure prediction were used to generate a secondary structure for 5S rRNA. A computer algorithm has been implemented to aid in the comparison of a large set of homologous RNAs. Eukaryotic 5S rRNA sequences from thirty four diverse species were compared by (1) alignment or the sequences, (2) the positions of substitutions were located with respect to the aligned sequence and secondary structure, and (3) the R-Y model of base stacking was used to study stacking pattern relationships in the structure. Eukaryotic 5S rRNA was found to have significant sequence variation throughout much of the molecule while maintaining a relatively constant secondary structure. A detailed analysis of the sequence and structure variability in each region of the molecule is presented

  10. Fast T1 mapping of the brain at high field using Look-Locker and fast imaging.

    Science.gov (United States)

    Jiang, Ke; Zhu, Yanjie; Jia, Sen; Wu, Yin; Liu, Xin; Chung, Yiu-Cho

    2017-02-01

    This study aims to develop and evaluate a new method for fast high resolution T1 mapping of the brain based on the Look-Locker technique. Single-shot turboflash sequence with high temporal acceleration is used to sample the recovery of inverted magnetization. Multi-slice interleaved acquisition within one inversion slab is used to reduce the number of inversion pulses and hence SAR. Accuracy of the proposed method was studied using simulation and validated in phantoms. It was then evaluated in healthy volunteers and stroke patients. In-vivo results were compared to values obtained by inversion recovery fast spin echo (IR-FSE) and literatures. With the new method, T 1 values in phantom experiments agreed with reference values with median error map was acquired in 3.35s and the T1 maps of the whole brain were acquired in 2min with two-slice interleaving, with a spatial resolution of 1.1×1.1×4mm 3 . The T 1 values obtained were comparable to those measured with IR-FSE and those reported in literatures. These results demonstrated the feasibility of the proposed method for fast T1 mapping of the brain in both healthy volunteers and stroke patients at 3T. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Historical Topographic Map Collection bookmark

    Science.gov (United States)

    Fishburn, Kristin A.; Allord, Gregory J.

    2017-06-29

    The U.S. Geological Survey (USGS) National Geospatial Program is scanning published USGS 1:250,000-scale and larger topographic maps printed between 1884, the inception of the topographic mapping program, and 2006. The goal of this project, which began publishing the historical scanned maps in 2011, is to provide a digital repository of USGS topographic maps, available to the public at no cost. For more than 125 years, USGS topographic maps have accurately portrayed the complex geography of the Nation. The USGS is the Nation’s largest producer of printed topographic maps, and prior to 2006, USGS topographic maps were created using traditional cartographic methods and printed using a lithographic printing process. As the USGS continues the release of a new generation of topographic maps (US Topo) in electronic form, the topographic map remains an indispensable tool for government, science, industry, land management planning, and leisure.

  12. Digital Mapping of Soil Drainage Classes Using Multitemporal RADARSAT-1 and ASTER Images and Soil Survey Data

    Directory of Open Access Journals (Sweden)

    Mohamed Abou Niang

    2012-01-01

    Full Text Available Discriminant analysis classification (DAC and decision tree classifiers (DTC were used for digital mapping of soil drainage in the Bras-d’Henri watershed (QC, Canada using earth observation data (RADARSAT-1 and ASTER and soil survey dataset. Firstly, a forward stepwise selection was applied to each land use type identified by ASTER image in order to derive an optimal subset of soil drainage class predictors. The classification models were then applied to these subsets for each land use and merged to obtain a digital soil drainage map for the whole watershed. The DTC method provided better classification accuracies (29 to 92% than the DAC method (33 to 79% according to the land use type. A similarity measure (S was used to compare the best digital soil drainage map (DTC to the conventional soil drainage map. Medium to high similarities (0.6≤S<0.9 were observed for 83% (187 km2 of the study area while 3% of the study area showed very good agreement (S≥0.9. Few soil polygons showed very weak similarities (S<0.3. This study demonstrates the efficiency of combining radar and optical remote sensing data with a representative soil dataset for producing digital maps of soil drainage.

  13. A topographic feature taxonomy for a U.S. national topographic mapping ontology

    Science.gov (United States)

    Varanka, Dalia E.

    2013-01-01

    Using legacy feature lists from the U.S. National Topographic Mapping Program of the twentieth century, a taxonomy of features is presented for purposes of developing a national topographic feature ontology for geographic mapping and analysis. After reviewing published taxonomic classifications, six basic classes are suggested; terrain, surface water, ecological regimes, built-up areas, divisions, and events. Aspects of ontology development are suggested as the taxonomy is described.

  14. Historical Map & Chart Collection of NOAA's Nautical Charts, Hydrographic Surveys, Topographic Surveys, Geodetic Surveys, City Plans, and Civil War Battle Maps Starting from the mid 1700's

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Historical Map and Chart Collection of the Office of Coast Survey contains over 20000 historical maps and charts from the mid 1700s through the late 1900s. These...

  15. A quantitative multiplex nuclease protection assay reveals immunotoxicity gene expression profiles in the rabbit model for vaginal drug safety evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Fichorova, Raina N., E-mail: rfichorova@rics.bwh.harvard.edu [Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States); Mendonca, Kevin; Yamamoto, Hidemi S.; Murray, Ryan [Laboratory of Genital Tract Biology, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women' s Hospital and Harvard Medical School, Boston, MA (United States); Chandra, Neelima; Doncel, Gustavo F. [CONRAD, Department of Obstetrics and Gynecology, Eastern Virginia Medical School, Norfolk, VA (United States)

    2015-06-15

    Any vaginal product that alters the mucosal environment and impairs the immune barrier increases the risk of sexually transmitted infections, especially HIV infection, which thrives on mucosal damage and inflammation. The FDA-recommended rabbit vaginal irritation (RVI) model serves as a first line selection tool for vaginal products; however, for decades it has been limited to histopathology scoring, insufficient to select safe anti-HIV microbicides. In this study we incorporate to the RVI model a novel quantitative nuclease protection assay (qNPA) to quantify mRNA levels of 25 genes representing leukocyte differentiation markers, toll-like receptors (TLR), cytokines, chemokines, epithelial repair, microbicidal and vascular markers, by designing two multiplex arrays. Tissue sections were obtained from 36 rabbits (6 per treatment arm) after 14 daily applications of a placebo gel, saline, 4% nonoxynol-9 (N-9), and three combinations of the anti-HIV microbicides tenofovir (TFV) and UC781 in escalating concentrations (highest: 10% TFV + 2.5%UC781). Results showed that increased expression levels of toll-like receptor (TLR)-4, interleukin (IL)-1β, CXCL8, epithelial membrane protein (EMP)-1 (P < 0.05), and decreased levels of TLR2 (P < 0.05), TLR3 and bactericidal permeability increasing protein (BPI) (P < 0.001) were associated with cervicovaginal mucosal alteration (histopathology). Seven markers showed a significant linear trend predicting epithelial damage (up with CD4, IL-1β, CXCL8, CCL2, CCL21, EMP1 and down with BPI). Despite the low tissue damage RVI scores, the high-dose microbicide combination gel caused activation of HIV host cells (SLC and CD4) while N-9 caused proinflammatory gene upregulation (IL-8 and TLR4) suggesting a potential for increasing risk of HIV via different mechanisms depending on the chemical nature of the test product. - Highlights: • A transcriptome nuclease protection assay assessed microbicides for vaginal safety. • Biomarkers were

  16. A quantitative multiplex nuclease protection assay reveals immunotoxicity gene expression profiles in the rabbit model for vaginal drug safety evaluation

    International Nuclear Information System (INIS)

    Fichorova, Raina N.; Mendonca, Kevin; Yamamoto, Hidemi S.; Murray, Ryan; Chandra, Neelima; Doncel, Gustavo F.

    2015-01-01

    Any vaginal product that alters the mucosal environment and impairs the immune barrier increases the risk of sexually transmitted infections, especially HIV infection, which thrives on mucosal damage and inflammation. The FDA-recommended rabbit vaginal irritation (RVI) model serves as a first line selection tool for vaginal products; however, for decades it has been limited to histopathology scoring, insufficient to select safe anti-HIV microbicides. In this study we incorporate to the RVI model a novel quantitative nuclease protection assay (qNPA) to quantify mRNA levels of 25 genes representing leukocyte differentiation markers, toll-like receptors (TLR), cytokines, chemokines, epithelial repair, microbicidal and vascular markers, by designing two multiplex arrays. Tissue sections were obtained from 36 rabbits (6 per treatment arm) after 14 daily applications of a placebo gel, saline, 4% nonoxynol-9 (N-9), and three combinations of the anti-HIV microbicides tenofovir (TFV) and UC781 in escalating concentrations (highest: 10% TFV + 2.5%UC781). Results showed that increased expression levels of toll-like receptor (TLR)-4, interleukin (IL)-1β, CXCL8, epithelial membrane protein (EMP)-1 (P < 0.05), and decreased levels of TLR2 (P < 0.05), TLR3 and bactericidal permeability increasing protein (BPI) (P < 0.001) were associated with cervicovaginal mucosal alteration (histopathology). Seven markers showed a significant linear trend predicting epithelial damage (up with CD4, IL-1β, CXCL8, CCL2, CCL21, EMP1 and down with BPI). Despite the low tissue damage RVI scores, the high-dose microbicide combination gel caused activation of HIV host cells (SLC and CD4) while N-9 caused proinflammatory gene upregulation (IL-8 and TLR4) suggesting a potential for increasing risk of HIV via different mechanisms depending on the chemical nature of the test product. - Highlights: • A transcriptome nuclease protection assay assessed microbicides for vaginal safety. • Biomarkers were

  17. Implementation of fast macromolecular proton fraction mapping on 1.5 and 3 Tesla clinical MRI scanners: preliminary experience

    Science.gov (United States)

    Yarnykh, V.; Korostyshevskaya, A.

    2017-08-01

    Macromolecular proton fraction (MPF) is a biophysical parameter describing the amount of macromolecular protons involved into magnetization exchange with water protons in tissues. MPF represents a significant interest as a magnetic resonance imaging (MRI) biomarker of myelin for clinical applications. A recent fast MPF mapping method enabled clinical translation of MPF measurements due to time-efficient acquisition based on the single-point constrained fit algorithm. However, previous MPF mapping applications utilized only 3 Tesla MRI scanners and modified pulse sequences, which are not commonly available. This study aimed to test the feasibility of MPF mapping implementation on a 1.5 Tesla clinical scanner using standard manufacturer’s sequences and compare the performance of this method between 1.5 and 3 Tesla scanners. MPF mapping was implemented on 1.5 and 3 Tesla MRI units of one manufacturer with either optimized custom-written or standard product pulse sequences. Whole-brain three-dimensional MPF maps obtained from a single volunteer were compared between field strengths and implementation options. MPF maps demonstrated similar quality at both field strengths. MPF values in segmented brain tissues and specific anatomic regions appeared in close agreement. This experiment demonstrates the feasibility of fast MPF mapping using standard sequences on 1.5 T and 3 T clinical scanners.

  18. A tailored biocatalyst achieved by the rational anchoring of imidazole groups on a natural polymer: furnishing a potential artificial nuclease by sustainable materials engineering.

    Science.gov (United States)

    Ferreira, José G L; Grein-Iankovski, Aline; Oliveira, Marco A S; Simas-Tosin, Fernanda F; Riegel-Vidotti, Izabel C; Orth, Elisa S

    2015-04-11

    Foreseeing the development of artificial enzymes by sustainable materials engineering, we rationally anchored reactive imidazole groups on gum arabic, a natural biocompatible polymer. The tailored biocatalyst GAIMZ demonstrated catalytic activity (>10(5)-fold) in dephosphorylation reactions with recyclable features and was effective in cleaving plasmid DNA, comprising a potential artificial nuclease.

  19. Cowichan Valley energy mapping and modelling. Report 1 - GIS mapping of potential renewable energy resources in the CVRD. Final report. [Vancouver Island, Canada

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-06-15

    The driving force behind the Integrated Energy Mapping and Analysis project was the identification and analysis of a suite of pathways that the Cowichan Valley Regional District (CVRD) can utilise to increase its energy resilience, as well as reduce energy consumption and GHG emissions, with a primary focus on the residential sector. Mapping and analysis undertaken will support provincial energy and GHG reduction targets, and the suite of pathways outlined will address a CVRD internal target that calls for 75% of the region's energy within the residential sector to come from locally sourced renewables by 2050. The target has been developed as a mechanism to meet resilience and climate action target. The maps and findings produced are to be integrated as part of a regional policy framework currently under development. The first task in the project was the production of a series of thematic GIS maps and associated databases of potential renewable energy resources in the CVRD. The renewable energy sources mapped were solar, wind, micro hydro, and biomass (residues and waste). Other sources were also discussed (e.g. geothermal heat) but not mapped due to lack of spatially explicit input data. The task 1 findings are detailed in this report. (LN)

  20. Digital geologic map in the scale 1:50 000

    International Nuclear Information System (INIS)

    Kacer, S.; Antalik, M.

    2005-01-01

    In this presentation authors present preparation of new digital geologic map of the Slovak Republic. This map is prepared by the State Geological Institute of Dionyz Stur as a part of the project Geological information system GeoIS. One of the basic information geologic layers, which will be accessible on the web-site will be digital geologic map of the Slovak Republic in the scale 1: 50 000

  1. AutoMap User’s Guide 2011

    Science.gov (United States)

    2011-06-13

    the Generalization Thesaurus but leaves all other concepts intact. If useThesauriContentOnly="y" then AutoMap replaces concepts but removes all...crf.sourceforge.net/ google-collect- 1.0-rc1.jar Guava http://code.google.com/p/ guava -libraries/ The Apache Software License, Version 2.0 htmlparser.jar...He lives on a dairy farm. He considers it a good life. Would he ever consider leaving ? Direct Adjacency Ted lives United States America. He lives

  2. Cloning, purification, and functional characterization of Carocin S2, a ribonuclease bacteriocin produced by Pectobacterium carotovorum

    Directory of Open Access Journals (Sweden)

    Tzeng Kuo-Ching

    2011-05-01

    Full Text Available Abstract Background Most isolates of Pectobacterium carotovorum subsp. carotovorum (Pcc produce bacteriocins. In this study, we have determined that Pcc strain F-rif-18 has a chromosomal gene encoding the low-molecular-weight bacteriocin, Carocin S2, and that this bacteriocin inhibits the growth of a closely related strain. Carocin S2 is inducible by ultraviolet radiation but not by mutagenic agents such as mitomycin C. Results A carocin S2-defective mutant, TF1-2, was obtained by Tn5 insertional mutagenesis using F-rif-18. A 5706-bp DNA fragment was detected by Southern blotting, selected from a genomic DNA library, and cloned to the vector, pMS2KI. Two adjacent complete open reading frames within pMS2KI were sequenced, characterized, and identified as caroS2K and caroS2I, which respectively encode the killing protein and immunity protein. Notably, carocin S2 could be expressed not only in the mutant TF1-2 but also in Escherichia coli DH5α after entry of the plasmid pMS2KI. Furthermore, the C-terminal domain of CaroS2K was homologous to the nuclease domains of colicin D and klebicin D. Moreover, SDS-PAGE analysis showed that the relative mass of CaroS2K was 85 kDa and that of CaroS2I was 10 kDa. Conclusion This study shown that another nuclease type of bacteriocin was found in Pectobacterium carotovorum. This new type of bacteriocin, Carocin S2, has the ribonuclease activity of CaroS2K and the immunity protein activity of CaroS2I.

  3. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

    KAUST Repository

    Rashid, Fahad

    2017-02-23

    Human flap endonuclease 1 (FEN1) and related structure-specific 5\\'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5\\'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually \\'locks\\' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.

  4. Efficient immunoglobulin gene disruption and targeted replacement in rabbit using zinc finger nucleases.

    Directory of Open Access Journals (Sweden)

    Tatiana Flisikowska

    Full Text Available Rabbits are widely used in biomedical research, yet techniques for their precise genetic modification are lacking. We demonstrate that zinc finger nucleases (ZFNs introduced into fertilized oocytes can inactivate a chosen gene by mutagenesis and also mediate precise homologous recombination with a DNA gene-targeting vector to achieve the first gene knockout and targeted sequence replacement in rabbits. Two ZFN pairs were designed that target the rabbit immunoglobulin M (IgM locus within exons 1 and 2. ZFN mRNAs were microinjected into pronuclear stage fertilized oocytes. Founder animals carrying distinct mutated IgM alleles were identified and bred to produce offspring. Functional knockout of the immunoglobulin heavy chain locus was confirmed by serum IgM and IgG deficiency and lack of IgM(+ and IgG(+ B lymphocytes. We then tested whether ZFN expression would enable efficient targeted sequence replacement in rabbit oocytes. ZFN mRNA was co-injected with a linear DNA vector designed to replace exon 1 of the IgM locus with ∼1.9 kb of novel sequence. Double strand break induced targeted replacement occurred in up to 17% of embryos and in 18% of fetuses analyzed. Two major goals have been achieved. First, inactivation of the endogenous IgM locus, which is an essential step for the production of therapeutic human polyclonal antibodies in the rabbit. Second, establishing efficient targeted gene manipulation and homologous recombination in a refractory animal species. ZFN mediated genetic engineering in the rabbit and other mammals opens new avenues of experimentation in immunology and many other research fields.

  5. USGS Elevation Contours Overlay Map Service from The National Map

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Elevation Contours service from The National Map (TNM) consists of contours generated for the conterminous United States from 1- and 1/3 arc-second...

  6. Lunar Geologic Mapping: A Preliminary Map of a Portion of the LQ-10 ("Marius") Quadrangle

    Science.gov (United States)

    Gregg, T. K. P.; Yingst, R. A.

    2009-01-01

    Since the first lunar mapping program ended in the 1970s, new topographical, multispectral, elemental and albedo imaging datasets have become available (e.g., Clementine, Lunar Prospector, Galileo). Lunar science has also advanced within the intervening time period. A new systematic lunar geologic mapping effort endeavors to build on the success of earlier mapping programs by fully integrating the many disparate datasets using GIS software and bringing to bear the most current understanding of lunar geologic history. As part of this program, we report on a 1:2,500,000-scale preliminary map of a subset of Lunar Quadrangle 10 ("LQ-10" or the "Marius Quadrangle," see Figures 1 and 2), and discuss the first-order science results. By generating a geologic map of this region, we can constrain the stratigraphic and geologic relationships between features, revealing information about the Moon s chemical and thermal evolution.

  7. Damage-induced BRCA1 phosphorylation by Chk2 contributes to the timing of end resection.

    Science.gov (United States)

    Parameswaran, Balaji; Chiang, Huai-Chin; Lu, Yunzhe; Coates, Julia; Deng, Chu-Xia; Baer, Richard; Lin, Hui-Kuan; Li, Rong; Paull, Tanya T; Hu, Yanfen

    2015-01-01

    The BRCA1 tumor suppressor plays an important role in homologous recombination (HR)-mediated DNA double-strand-break (DSB) repair. BRCA1 is phosphorylated by Chk2 kinase upon γ-irradiation, but the role of Chk2 phosphorylation is not understood. Here, we report that abrogation of Chk2 phosphorylation on BRCA1 delays end resection and the dispersion of BRCA1 from DSBs but does not affect the assembly of Mre11/Rad50/NBS1 (MRN) and CtIP at DSBs. Moreover, we show that BRCA1 is ubiquitinated by SCF(Skp2) and that abrogation of Chk2 phosphorylation impairs its ubiquitination. Our study suggests that BRCA1 is more than a scaffold protein to assemble HR repair proteins at DSBs, but that Chk2 phosphorylation of BRCA1 also serves as a built-in clock for HR repair of DSBs. BRCA1 is known to inhibit Mre11 nuclease activity. SCF(Skp2) activity appears at late G1 and peaks at S/G2, and is known to ubiquitinate phosphodegron motifs. The removal of BRCA1 from DSBs by SCF(Skp2)-mediated degradation terminates BRCA1-mediated inhibition of Mre11 nuclease activity, allowing for end resection and restricting the initiation of HR to the S/G2 phases of the cell cycle.

  8. High specific radioactivity (1R,2S)-4-[{sup 18}F]fluorometaraminol: a PET radiotracer for mapping sympathetic nerves of the heart

    Energy Technology Data Exchange (ETDEWEB)

    Langer, Oliver; Valette, Heric; Dolle, Frederic E-mail: dolle@dsvidf.cea.fr; Halldin, Christer; Loc' h, Christian; Fuseau, Chantal; Coulon, Christine; Ottaviani, Michele; Bottlaender, Michel; Maziere, Bernard; Crouzel, Christian

    2000-04-01

    The radiolabeled catecholamine analogue (1R,2S)-6-[{sup 18}F]fluorometaraminol (6-[{sup 18}F]FMR) is a substrate for the neuronal norepinephrine transporter. It has been used as a positron emission tomography (PET) ligand to map sympathetic nerves in dog heart. 6-[{sup 18}F]FMR could be only synthesized with low specific radioactivity, which precluded its use in human subjects. We have recently prepared (1R,2S)-4-[{sup 18}F]fluorometaraminol (4-[{sup 18}F]FMR), a new fluoro-analogue of metaraminol, with high specific radioactivity (56-106 GBq/{mu}mol). In the present study, we demonstrate in rats that 4-[{sup 18}F]FMR possesses similar affinity toward myocardial norepinephrine transport mechanisms as 6-[{sup 18}F]FMR. When compared with control animals, an 80% and 76% reduction in myocardial uptake was observed in animals pretreated with desipramine (an inhibitor of the neuronal norepinephrine transporter) and with reserpine (a blocker of the vesicular storage of monoamines), respectively. The entire radioactivity in rat myocardium represented unmetabolized parent tracer as determined by high performance liquid chromatography analysis of tissue extracts. In dogs, myocardial kinetics of 4-[{sup 18}F]FMR were assessed using PET. A rapid and high uptake was observed, followed by prolonged cardiac retention. A heart-to-lung ratio of 15 was reached 10 min after injection of the radiotracer. Pretreatment with desipramine reduced the heart half-life of 4-[{sup 18}F]FMR by 90% compared with control. Moreover, an infusion of tyramine caused a rapid decline of radioactivity in the heart. This demonstrates that 4-[{sup 18}F]FMR specifically visualizes sympathetic neurons in dog heart. High specific radioactivity 4-[{sup 18}F]FMR is a promising alternative to 6-[{sup 18}F]FMR for myocardial neuronal mapping with PET in humans.

  9. Roles of sphingosine-1-phosphate (S1P) receptors in malignant behavior of glioma cells. Differential effects of S1P2 on cell migration and invasiveness

    International Nuclear Information System (INIS)

    Young, Nicholas; Van Brocklyn, James R.

    2007-01-01

    Sphingosine-1-phosphate (S1P) is a bioactive lipid that signals through a family of five G-protein-coupled receptors, termed S1P 1-5 . S1P stimulates growth and invasiveness of glioma cells, and high expression levels of the enzyme that forms S1P, sphingosine kinase-1, correlate with short survival of glioma patients. In this study we examined the mechanism of S1P stimulation of glioma cell proliferation and invasion by either overexpressing or knocking down, by RNA interference, S1P receptor expression in glioma cell lines. S1P 1 , S1P 2 and S1P 3 all contribute positively to S1P-stimulated glioma cell proliferation, with S1P 1 being the major contributor. Stimulation of glioma cell proliferation by these receptors correlated with activation of ERK MAP kinase. S1P 5 blocks glioma cell proliferation, and inhibits ERK activation. S1P 1 and S1P 3 enhance glioma cell migration and invasion. S1P 2 inhibits migration through Rho activation, Rho kinase signaling and stress fiber formation, but unexpectedly, enhances glioma cell invasiveness by stimulating cell adhesion. S1P 2 also potently enhances expression of the matricellular protein CCN1/Cyr61, which has been implicated in tumor cell adhesion, and invasion as well as tumor angiogenesis. A neutralizing antibody to CCN1 blocked S1P 2 -stimulated glioma invasion. Thus, while S1P 2 decreases glioma cell motility, it may enhance invasion through induction of proteins that modulate glioma cell interaction with the extracellular matrix

  10. Auxin molecular field maps define AUX1 selectivity: many auxin herbicides are not substrates

    Czech Academy of Sciences Publication Activity Database

    Hoyerová, Klára; Hošek, Petr; Quareshy, M.; Li, J.; Klíma, Petr; Kubeš, Martin; Yemm, A. A.; Neve, P.; Tripathi, A.; Bennett, M.J.; Napier, R. M.

    2018-01-01

    Roč. 217, č. 4 (2018), s. 1625-1639 ISSN 0028-646X R&D Projects: GA ČR(CZ) GA16-19557S; GA MŠk LD15137 Grant - others:OPPK(XE) CZ.2.16/3.1.00/21519 Institutional support: RVO:61389030 Keywords : auxin transport * cheminformatics * herbicide * herbicide resistance * molecular field maps * pharmacophore * structure–activity relationship * uptake carrier Subject RIV: ED - Physiology OBOR OECD: Cell biology Impact factor: 7.330, year: 2016

  11. Dylan Thomas’s The Map of Love: The Poetic Licence

    Directory of Open Access Journals (Sweden)

    S. Bharadwaj

    2015-09-01

    Full Text Available In the early poetry, 18 Poems and 25 Poems, Dylan Thomas speaks of his awareness of the artistic heritage and also of his poetic freedom resulting in a poetic force.The Map of Love vindicates, while mapping out the continuous process of exploiting poetic licence in his works, that the poetry of the past cannot fully serve the demands of the present. Apparently, the third book offers a comparative estimate of  the time-conscientious poets, Cecil Day Lewis, Stephen Spender, and Louis MacNeice and the life-conscious War poets, Roy Fuller, Alan  Rook, and Keidrych Rhys.The issues involved are wider and cover the whole range of aesthetic transcendence and historic sense of Auden. Thomas, “refusing to fall in love with God … gave himself to the love of created things … accepting only what he could see” and created his own poetic design, “an ideal surely which … here if anywhere is feasible.” This explains why Thomas’s earth-concentric poetic licence is deeper than Auden’s ideology-centric poetic justice. The War poets heaved a sigh of relief as the world-concentric Thomas’s 18 Poems offers a hope for poetry, “life-blood” for their poetic mind fumbling around Auden’s structural consciousness. The poetic licence developed in The Map of Love is, therefore, central to an understanding of Thomas’s entire poetic ouvre, more particularly, of the maturer poetry of the later phase carving out a road taken already to immortality. In the literary study of this collection, Walford Davies and John Ackerman refer to Thomas’s “querying the nature” of  his own “earlier adolescent attitudes.” However, as their study remains limited to general or literal statements, denotative or elucidative meaning of a few individual poems, they fail to render the core of the poem, the totality of its meaning. The poetic language of this transitional  poem is endowed with implications, suggestions, and modifications. Hence, this paper

  12. Planimetric Features Generalization for the Production of Small-Scale Map by Using Base Maps and the Existing Algorithms

    Directory of Open Access Journals (Sweden)

    M. Modiri

    2014-10-01

    Full Text Available Cartographic maps are representations of the Earth upon a flat surface in the smaller scale than it’s true. Large scale maps cover relatively small regions in great detail and small scale maps cover large regions such as nations, continents and the whole globe. Logical connection between the features and scale map must be maintained by changing the scale and it is important to recognize that even the most accurate maps sacrifice a certain amount of accuracy in scale to deliver a greater visual usefulness to its user. Cartographic generalization, or map generalization, is the method whereby information is selected and represented on a map in a way that adapts to the scale of the display medium of the map, not necessarily preserving all intricate geographical or other cartographic details. Due to the problems facing small-scale map production process and the need to spend time and money for surveying, today’s generalization is used as executive approach. The software is proposed in this paper that converted various data and information to certain Data Model. This software can produce generalization map according to base map using the existing algorithm. Planimetric generalization algorithms and roles are described in this article. Finally small-scale maps with 1:100,000, 1:250,000 and 1:500,000 scale are produced automatically and they are shown at the end.

  13. Processing parameters for the mechanical working of 9 Cr-1 Mo steel: processing maps approach

    Energy Technology Data Exchange (ETDEWEB)

    Sivaprasad, P.V.; Mannan, S.L.; Prasad, Y.V.R.K. [Indira Ghandi Centre for Atomic Research, Tamilnadu (India)

    2004-12-15

    Processing and instability maps using a dynamic materials model have been developed for 9Cr-1Mo steel in the temperature range 850 to 1200{sup o}C and strain rate range 0.001-100 s{sup -1} with a view to optimising its hot workability. The efficiency of power dissipation increased with increase in temperature and decrease in strain rate. The 9Cr-1Mo material exhibited two dynamic recrystallisation domains, one with a peak efficiency of 37% occurring at 950{sup o}C and 0.001 s{sup -1} and the other with a peak efficiency of 35% occurring at 1200{sup o}C and 0.1 s{sup -1}. These results are in good agreement with those found in industry. (author)

  14. A novel method for designing S-boxes based on chaotic maps

    International Nuclear Information System (INIS)

    Tang Guoping; Liao Xiaofeng; Chen Yong

    2005-01-01

    A method for obtaining cryptographically strong 8 x 8 S-boxes based on chaotic maps is presented and the cryptographical properties such as bijection, nonlinearity, strict avalanche criterion, output bits independence criterion and equiprobable input/output XOR distribution of these S-boxes are analyzed in detail. The results of numerical analysis also show that the S-boxes proposed are of the above properties and can resist the differential attack. Furthermore, our approach is suitable for practical application in designing cryptosystem

  15. Crystal Structure and Functional Characterization of the Complement Regulator Mannose-binding Lectin (MBL)/Ficolin-associated Protein-1 (MAP-1)

    DEFF Research Database (Denmark)

    Skjoedt, M.-o.; Roversi, P.; Hummelshoj, T.

    2012-01-01

    .5 nM, respectively. We studied structural aspects of MAP-1 and could show by multi-angle laser light scattering that MAP-1 forms a calcium-dependent homo-dimer in solution. We were able to determine the crystal structure of MAP-1, which also contains a head-to-tail dimer approximately 146 Angstrom...... long. This structure of MAP-1 also enables modeling and assembly of the MASP-1 molecule in its entirety. Finally we found that MAP-1 competes with all three MASPs for ligand binding and is able to mediate a strong dose dependent inhibitory effect on the lectin pathway activation, as measured by levels...

  16. Knockdown of MAP4 and DNAL1 produces a post-fusion and pre-nuclear translocation impairment in HIV-1 replication

    International Nuclear Information System (INIS)

    Gallo, Daniel E.; Hope, Thomas J.

    2012-01-01

    DNAL1 and MAP4 are both microtubule-associated proteins. These proteins were identified as HIV-1 dependency factors in a screen with wild-type HIV-1. In this study we demonstrate that knockdown using DNAL1 and MAP4 siRNAs and shRNAs inhibits HIV-1 infection regardless of envelope. Using a fusion assay, we show that DNAL1 and MAP4 do not impact fusion. By assaying for late reverse transcripts and 2-LTR circles, we show that DNAL1 and MAP4 inhibit both by approximately 50%. These results demonstrate that DNAL1 and MAP4 impact reverse transcription but not nuclear translocation. DNAL1 and MAP4 knockdown cells do not display cytoskeletal defects. Together these experiments indicate that DNAL1 and MAP4 may exert their functions in the HIV life cycle at reverse transcription, prior to nuclear translocation.

  17. Electron velocity map imaging and theoretical study on CuXH (X = O and S) anions

    Science.gov (United States)

    Qin, Zhengbo; Wang, Hui; Ren, Yangdi; Zheng, Xianfeng; Cui, Zhifeng; Tang, Zichao

    2018-01-01

    Vibrationally resolved photoelectron spectra of CuOH- and CuSH- have been determined via velocity map imaging method to investigate the transitions of X1A‧ ← X2A‧ at 532 nm. Adiabatic detachment energies of CuOH- and CuSH- are assigned to 0.995(12) and 1.098(12) eV, respectively. Combined theoretical calculations with Franck-Condon simulations, it allows extracting the vibrational frequencies in neutral, which yields 629(32) cm-1 with Cusbnd O stretching mode and 387(24) cm-1 with Cusbnd S stretching mode for CuXH (X = O and S). Parallel transition properties of photoelectron angular distributions (PADs) for both species are correlated to the photodetachment of SOMO orbitals, which mainly involved in the Cu atom s orbital and partial s orbital in other atoms. Based on chemical bonding analyses (Wiberg, NAO, Mayer, NRT, and ELF), it is suggested that a trend is observed with a subtle variation of covalent component from weak covalent behavior between Cusbnd O in CuOH-1/0 to stronger covalent bonding between Cusbnd S in CuSH-1/0 (especially for non-ignorable covalent component in CuSH species) though ionic bonding dominates both in Cusbnd O and Cusbnd S bonds for the two systems.

  18. The geological map of Canelones Department scale 1:1000.000

    International Nuclear Information System (INIS)

    Spoturno, J.; Oyhantcabal, P.; Goso, C.; Aubet, N.; Cazaux; S; Huelmo, S.; Morales, E.; Loureiro, J.

    2004-01-01

    The geological map of Canelones Department (Uruguay), scale 1:100.000 is presented. This map shows the distribution of the proterozoic, mesozoic and cenozoic lithological units. A stratigraphic division of this region is included [es

  19. The geological map of Montevideo Department scale 1:50.000

    International Nuclear Information System (INIS)

    Spoturno, J.; Oyhantcabal, P.; Goso, C.; Aubet, N.; Cazaux; S; Huelmo, S.; Morales, E.; Loureiro, J.

    2004-01-01

    The geological map of Montevideo Department (Uruguay), scale 1:50.000 is presented. This map shows the distribution of the proterozoic, mesozoic and cenozoic lithological units. A stratigraphic division of this region is included [es

  20. The map-1 gene family in root-knot nematodes, Meloidogyne spp.: a set of taxonomically restricted genes specific to clonal species.

    Directory of Open Access Journals (Sweden)

    Iva Tomalova

    Full Text Available Taxonomically restricted genes (TRGs, i.e., genes that are restricted to a limited subset of phylogenetically related organisms, may be important in adaptation. In parasitic organisms, TRG-encoded proteins are possible determinants of the specificity of host-parasite interactions. In the root-knot nematode (RKN Meloidogyne incognita, the map-1 gene family encodes expansin-like proteins that are secreted into plant tissues during parasitism, thought to act as effectors to promote successful root infection. MAP-1 proteins exhibit a modular architecture, with variable number and arrangement of 58 and 13-aa domains in their central part. Here, we address the evolutionary origins of this gene family using a combination of bioinformatics and molecular biology approaches. Map-1 genes were solely identified in one single member of the phylum Nematoda, i.e., the genus Meloidogyne, and not detected in any other nematode, thus indicating that the map-1 gene family is indeed a TRG family. A phylogenetic analysis of the distribution of map-1 genes in RKNs further showed that these genes are specifically present in species that reproduce by mitotic parthenogenesis, with the exception of M. floridensis, and could not be detected in RKNs reproducing by either meiotic parthenogenesis or amphimixis. These results highlight the divergence between mitotic and meiotic RKN species as a critical transition in the evolutionary history of these parasites. Analysis of the sequence conservation and organization of repeated domains in map-1 genes suggests that gene duplication(s together with domain loss/duplication have contributed to the evolution of the map-1 family, and that some strong selection mechanism may be acting upon these genes to maintain their functional role(s in the specificity of the plant-RKN interactions.

  1. Mineral mapping in the western Kunlun Mountains using Tiangong-1 hyperspectral imagery

    Science.gov (United States)

    Ge, W.; Cheng, Q.; Jing, L.; Chen, Y.; Guo, X.; Ding, H.; Liu, Q.

    2016-04-01

    The unmanned Chinese space module Tiangong-1 was launched in September 2011 with a hyperspectral sensor on board. The sensor combines high spatial and spectral resolution suitable for mineral mapping. In this study, Tiangong-1 hyperspectral data were employed for mineral mapping in the western Kunlun Mountains, an important metallogenic belt in China. A Spectral Hourglass Wizard method was applied to detect common minerals from the Tiangong- 1 shortwave infrared data with reference to a set of spectral libraries. Spectral information on minerals, such as zoisite, mica, quartz, sodalite, dolomite, and actinolite, was extracted from the data. The resulting mineral interpretation maps were highly correlated with the reference geological maps and information from ASTER satellite imagery, suggesting that the hyperspectral data are suitable for mineral mapping.

  2. Size and frequency of gaps in newly synthesized DNA of xeroderma pigmentosum human cells irradiated with ultraviolet light

    International Nuclear Information System (INIS)

    Meneghini, R.; Cordeiro-Stone, M.; Schumacher, R.I.

    1981-01-01

    Native newly synthesized DNA from human cells (xeroderma pigmentosum type) irradiated with ultraviolet light releases short pieces of DNA (L-DNA) when incubated with the single-strand specific S 1 nuclease. This is not observed in the case of unirradiated cells. Previous experiments had shown that the L-DNA resulted from the action of S 1 nuclease upon gaps, i.e., single-stranded DNA discontinuities in larger pieces of double-stranded DNA. We verified that the duplex L-DNA, that arises from the inter-gap regions upon S 1 nuclease treatment, has a size which approximates the distance between two pyrimidine dimers on the same strand. A method was devised to measure the size of the gaps. These parameters have been considered in the proposition of a model for DNA synthesis on a template containing pyrimidine dimers

  3. 7 Tesla quantitative hip MRI: T1, T2 and T2* mapping of hip cartilage in healthy volunteers

    Energy Technology Data Exchange (ETDEWEB)

    Lazik, Andrea; Theysohn, Jens M.; Geis, Christina [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); Johst, Soeren; Kraff, Oliver [University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); Ladd, Mark E. [University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); German Cancer Research Center (DKFZ), Medical Physics in Radiology, Heidelberg (Germany); Quick, Harald H. [University of Duisburg-Essen, Erwin L. Hahn Institute for Magnetic Resonance Imaging, Essen (Germany); University Hospital Essen, High Field and Hybrid MR Imaging, Essen (Germany)

    2016-05-15

    To evaluate the technical feasibility and applicability of quantitative MR techniques (delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), T2 mapping, T2* mapping) at 7 T MRI for assessing hip cartilage. Hips of 11 healthy volunteers were examined at 7 T MRI with an 8-channel radiofrequency transmit/receive body coil using multi-echo sequences for T2 and T2* mapping and a dual flip angle gradient-echo sequence before (T1{sub 0}) and after intravenous contrast agent administration (T1{sub Gd}; 0.2 mmol/kg Gd-DTPA{sup 2-} followed by 0.5 h of walking and 0.5 h of rest) for dGEMRIC. Relaxation times of cartilage were measured manually in 10 regions of interest. Pearson's correlations between R1{sub delta} = 1/T1{sub Gd} - 1/T1{sub 0} and T1{sub Gd} and between T2 and T2* were calculated. Image quality and the delineation of acetabular and femoral cartilage in the relaxation time maps were evaluated using discrete rating scales. High correlations were found between R1{sub delta} and T1{sub Gd} and between T2 and T2* relaxation times (all p < 0.01). All techniques delivered diagnostic image quality, with best delineation of femoral and acetabular cartilage in the T2* maps (mean 3.2 out of a maximum of 4 points). T1, T2 and T2* mapping of hip cartilage with diagnostic image quality is feasible at 7 T. To perform dGEMRIC at 7 T, pre-contrast T1 mapping can be omitted. (orig.)

  4. Targeted Editing of Myostatin Gene in Sheep by Transcription Activator-like Effector Nucleases

    Directory of Open Access Journals (Sweden)

    Xinxia Zhao

    2016-03-01

    Full Text Available Myostatin (MSTN is a secreted growth factor expressed in skeletal muscle and adipose tissue that negatively regulates skeletal muscle mass. Gene knockout of MSTN can result in increasing muscle mass in sheep. The objectives were to investigate whether myostatin gene can be edited in sheep by transcription activator-like effector nucleases (TALENs in tandem with single-stranded DNA oligonucleotides (ssODNs. We designed a pair of TALENs to target a highly conserved sequence in the coding region of the sheep MSTN gene. The activity of the TALENs was verified by using luciferase single-strand annealing reporter assay in HEK 293T cell line. Co-transfection of TALENs and ssODNs oligonucleotides induced precise gene editing of myostatin gene in sheep primary fibroblasts. MSTN gene-edited cells were successfully used as nuclear donors for generating cloned embryos. TALENs combined with ssDNA oligonucleotides provide a useful approach for precise gene modification in livestock animals.

  5. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Science.gov (United States)

    Bi, Yanwei; Sun, Le; Gao, Dandan; Ding, Chen; Li, Zhihua; Li, Yadong; Cun, Wei; Li, Qihan

    2014-05-01

    A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas)) RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ) and homology-directed repair (HDR) pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  6. High-efficiency targeted editing of large viral genomes by RNA-guided nucleases.

    Directory of Open Access Journals (Sweden)

    Yanwei Bi

    2014-05-01

    Full Text Available A facile and efficient method for the precise editing of large viral genomes is required for the selection of attenuated vaccine strains and the construction of gene therapy vectors. The type II prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats (CRISPR-associated (Cas RNA-guided nuclease system can be introduced into host cells during viral replication. The CRISPR-Cas9 system robustly stimulates targeted double-stranded breaks in the genomes of DNA viruses, where the non-homologous end joining (NHEJ and homology-directed repair (HDR pathways can be exploited to introduce site-specific indels or insert heterologous genes with high frequency. Furthermore, CRISPR-Cas9 can specifically inhibit the replication of the original virus, thereby significantly increasing the abundance of the recombinant virus among progeny virus. As a result, purified recombinant virus can be obtained with only a single round of selection. In this study, we used recombinant adenovirus and type I herpes simplex virus as examples to demonstrate that the CRISPR-Cas9 system is a valuable tool for editing the genomes of large DNA viruses.

  7. ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

    Science.gov (United States)

    Fooshee, David; Andronico, Alessio; Baldi, Pierre

    2013-11-25

    Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu .

  8. CdS nanorods/organic hybrid LED array and the piezo-phototronic effect of the device for pressure mapping.

    Science.gov (United States)

    Bao, Rongrong; Wang, Chunfeng; Dong, Lin; Shen, Changyu; Zhao, Kun; Pan, Caofeng

    2016-04-21

    As widely applied in light-emitting diodes and optical devices, CdS has attracted the attention of many researchers due to its nonlinear properties and piezo-electronic effect. Here, we demonstrate a LED array composed of PSS and CdS nanorods and research the piezo-photonic effect of the array device. The emission intensity of the device depends on the electron-hole recombination at the interface of the p-n junction which can be adjusted using the piezo-phototronic effect and can be used to map the pressure applied on the surface of the device with spatial resolution as high as 1.5 μm. A flexible LED device array has been prepared using a CdS nanorod array on a Au/Cr/kapton substrate. This device may be used in the field of strain mapping using its high pressure spatial-resolution and flexibility.

  9. Constellation and Mapping Optimization of APSK Modulations used in DVB-S2

    Directory of Open Access Journals (Sweden)

    L. Jordanova

    2014-10-01

    Full Text Available This article represents the algorithms of APSK constellation and mapping optimization. The dependencies of the symbol error probability Ps on the parameters of the 16APSK and 32APSK constellations are examined and several options that satisfy the requirements to the minimum value of Ps are selected. Mapping optimization is carried out for the selected APSK constellations. BER characteristics of the satellite DVB-S2 channels are represented when using optimized and standard 16APSK and 32APSK constellations and a comparative analysis of the results achieved is made.

  10. Evaluation of MRI sequences for quantitative T1 brain mapping

    Science.gov (United States)

    Tsialios, P.; Thrippleton, M.; Glatz, A.; Pernet, C.

    2017-11-01

    T1 mapping constitutes a quantitative MRI technique finding significant application in brain imaging. It allows evaluation of contrast uptake, blood perfusion, volume, providing a more specific biomarker of disease progression compared to conventional T1-weighted images. While there are many techniques for T1-mapping there is a wide range of reported T1-values in tissues, raising the issue of protocols reproducibility and standardization. The gold standard for obtaining T1-maps is based on acquiring IR-SE sequence. Widely used alternative sequences are IR-SE-EPI, VFA (DESPOT), DESPOT-HIFI and MP2RAGE that speed up scanning and fitting procedures. A custom MRI phantom was used to assess the reproducibility and accuracy of the different methods. All scans were performed using a 3T Siemens Prisma scanner. The acquired data processed using two different codes. The main difference was observed for VFA (DESPOT) which grossly overestimated T1 relaxation time by 214 ms [126 270] compared to the IR-SE sequence. MP2RAGE and DESPOT-HIFI sequences gave slightly shorter time than IR-SE (~20 to 30ms) and can be considered as alternative and time-efficient methods for acquiring accurate T1 maps of the human brain, while IR-SE-EPI gave identical result, at a cost of a lower image quality.

  11. B1 mapping for bias-correction in quantitative T1 imaging of the brain at 3T using standard pulse sequences.

    Science.gov (United States)

    Boudreau, Mathieu; Tardif, Christine L; Stikov, Nikola; Sled, John G; Lee, Wayne; Pike, G Bruce

    2017-12-01

    B 1 mapping is important for many quantitative imaging protocols, particularly those that include whole-brain T 1 mapping using the variable flip angle (VFA) technique. However, B 1 mapping sequences are not typically available on many magnetic resonance imaging (MRI) scanners. The aim of this work was to demonstrate that B 1 mapping implemented using standard scanner product pulse sequences can produce B 1 (and VFA T 1 ) maps comparable in quality and acquisition time to advanced techniques. Six healthy subjects were scanned at 3.0T. An interleaved multislice spin-echo echo planar imaging double-angle (EPI-DA) B 1 mapping protocol, using a standard product pulse sequence, was compared to two alternative methods (actual flip angle imaging, AFI, and Bloch-Siegert shift, BS). Single-slice spin-echo DA B 1 maps were used as a reference for comparison (Ref. DA). VFA flip angles were scaled using each B 1 map prior to fitting T 1 ; the nominal flip angle case was also compared. The pooled-subject voxelwise correlation (ρ) for B 1 maps (BS/AFI/EPI-DA) relative to the reference B 1 scan (Ref. DA) were ρ = 0.92/0.95/0.98. VFA T 1 correlations using these maps were ρ = 0.86/0.88/0.96, much better than without B 1 correction (ρ = 0.53). The relative error for each B 1 map (BS/AFI/EPI-DA/Nominal) had 95 th percentiles of 5/4/3/13%. Our findings show that B 1 mapping implemented using product pulse sequences can provide excellent quality B 1 (and VFA T 1 ) maps, comparable to other custom techniques. This fast whole-brain measurement (∼2 min) can serve as an excellent alternative for researchers without access to advanced B 1 pulse sequences. 1 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2017;46:1673-1682. © 2017 International Society for Magnetic Resonance in Medicine.

  12. Creation of next generation U.S. Geological Survey topographic maps

    Science.gov (United States)

    Craun, Kari J.

    2010-01-01

    The U.S. Geological Survey (USGS) is 2 years into a 3-year cycle to create new digital topographic map products for the conterminous United States from data acquired and maintained as part of The National Map databases. These products are in the traditional, USGS topographic quadrangle, 7.5-minute (latitude and longitude) cell format. The 3-year cycle was conceived to follow the acquisition of National Aerial Imagery Program (NAIP) orthorectified imagery, a key layer in the new product. In fiscal year (FY) 2009 (ending September 30, 2009), the first year of the 3-year cycle, the USGS produced 13,200 products. These initial products of the “Digital MapBeta” series had limited feature content, including only the NAIP image, some roads, geographic names, and grid and collar information. The products were created in layered georegistered Portable Document Format (PDF) files, allowing users with freely available Adobe® Reader® software to view, print, and perform simple Geographic Information System-like functions. In FY 2010 (ending September 30, 2010), the USGS produced 20,380 products. These products of the “US Topo” series added hydrography (surface water features), contours, and some boundaries. In FY 2011 (ending September 30, 2011), the USGS will complete the initial coverage with US Topo products and will add additional feature content to the maps. The design, development, and production associated with the US Topo products provide management and technical challenges for the USGS and its public and private sector partners. One challenge is the acquisition and maintenance of nationally consistent base map data from multiple sources. Another is the use of these data to create a consistent, current series of cartographic products that can be used by the broad spectrum of traditional topographic map users. Although the USGS and its partners have overcome many of these challenges, many, such as establishing and funding a sustainable base data

  13. Late-onset Stargardt-like macular dystrophy maps to chromosome 1p13

    Energy Technology Data Exchange (ETDEWEB)

    Kaplan, J.; Gerber, S.; Rozet, J.M. [Hopital des Enfants Malades, Paris (France)] [and others

    1994-09-01

    Stargardt`s disease (MIM 248200), originally described in 1909, is an autosomal recessive condition of childhood, characterized by a sudden and bilateral loss of central vision. Typically, it has an early onset (7 to 12 years), a rapidly progressive course and a poor final outcome. The central area of the retina (macula) displays pigmentary changes in a ring form with depigmentation and atrophy of the retinal pigmentary epithelium (RPE). Perimacular yellowish spots, termed fundus flavimaculatus, are observed in a high percentage of patients. We have recently reported the genetic mapping of Stargardt`s disease to chromosome 1p13. On the other hand, considering that fundus flavimaculatus (MIM 230100) is another form of fleck fundus disease, with a Stargardt-like retinal aspect but with a late-onset and a more progressive course, we decided to test the hypothesis of allelism between typical Stargardt`s disease and late-onset autosomal recessive fundus flavimaculatus. Significant pairwise lod scores were obtained in each of four multiplex families (11 affected individuals, 12 relatives) with four markers of the 1p13 region (Z = 4.79, 4.64, 3.07, 3.16 at loci D1S435, D1S424, D1S236, and D1S415, respectively at {theta} = 0). Multipoint analysis showed that the best estimate for location of the disease gene is between D1S424 and D1S236 (maximum lod score of 5.20) as also observed in Stargardt`s disease. Our results are consistent with the location of the gene responsible of the late-onset Stargardt-like macular dystrophy in the 1p13 region and raise the hypothesis of either allelic mutational events or contiguous genes in this chromosomal region. The question of possible relationship with some age-related macular dystrophies in now open to debate.

  14. CONSTRAINING THE MILKY WAY POTENTIAL WITH A SIX-DIMENSIONAL PHASE-SPACE MAP OF THE GD-1 STELLAR STREAM

    International Nuclear Information System (INIS)

    Koposov, Sergey E.; Rix, Hans-Walter; Hogg, David W.

    2010-01-01

    The narrow GD-1 stream of stars, spanning 60 0 on the sky at a distance of ∼10 kpc from the Sun and ∼15 kpc from the Galactic center, is presumed to be debris from a tidally disrupted star cluster that traces out a test-particle orbit in the Milky Way halo. We combine Sloan Digital Sky Survey (SDSS) photometry, USNO-B astrometry, and SDSS and Calar Alto spectroscopy to construct a complete, empirical six-dimensional (6D) phase-space map of the stream. We find that an eccentric orbit in a flattened isothermal potential describes this phase-space map well. Even after marginalizing over the stream orbital parameters and the distance from the Sun to the Galactic center, the orbital fit to GD-1 places strong constraints on the circular velocity at the Sun's radius V c = 224 ± 13 km s -1 and total potential flattening q Φ = 0.87 +0.07 -0.04 . When we drop any informative priors on V c , the GD-1 constraint becomes V c = 221 ± 18 km s -1 . Our 6D map of GD-1, therefore, yields the best current constraint on V c and the only strong constraint on q Φ at Galactocentric radii near R ∼ 15 kpc. Much, if not all, of the total potential flattening may be attributed to the mass in the stellar disk, so the GD-1 constraints on the flattening of the halo itself are weak: q Φ,halo > 0.89 at 90% confidence. The greatest uncertainty in the 6D map and the orbital analysis stems from the photometric distances, which will be obviated by GAIA.

  15. A Novel Image Cryptosystem Based on S-AES and Chaotic Map

    Directory of Open Access Journals (Sweden)

    Bai Lan

    2015-01-01

    Full Text Available This paper proposes a novel scheme based on simplified advanced encryption standard (S-AES for image encryption. Modified Arnold Map applied as diffusion technique for an image, and the key and dynamic S-box of encryption is generated by PWLCM. The goal is to balance rapidity and security of encryption. Experimental implementation has been done. This light encryption scheme shows resistance against chosen-plaintext attack and is suitable for sensor networks and IoT.

  16. Meta-analysis of the research impact of Baddeley’s multicomponent working memory model and Cowan’s embedded-processes model of working memory : a bibliometric mapping approach

    OpenAIRE

    Gruszka-Gosiewska, Aleksandra; Orzechowski, Jarosław

    2016-01-01

    In this study bibliometric mapping method was employed to visualise the current research trends and the impact of the two most influential models of working memory, namely: A. D. Baddeley and G. J. Hitch’s (1974) multicomponent working memory model and N. Cowan’s (1988) embedded-processes model of working memory. Using VOSviewer software two maps were generated based on the index-term words extracted from the research papers citing Baddeley (2000) and Cowan (2001), respectively. The maps repr...

  17. USGS Topo Base Map from The National Map

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Topographic Base Map from The National Map. This tile cached web map service combines the most current data services (Boundaries, Names, Transportation,...

  18. Engineering customized TALE nucleases (TALENs) and TALE transcription factors by fast ligation-based automatable solid-phase high-throughput (FLASH) assembly.

    Science.gov (United States)

    Reyon, Deepak; Maeder, Morgan L; Khayter, Cyd; Tsai, Shengdar Q; Foley, Jonathan E; Sander, Jeffry D; Joung, J Keith

    2013-07-01

    Customized DNA-binding domains made using transcription activator-like effector (TALE) repeats are rapidly growing in importance as widely applicable research tools. TALE nucleases (TALENs), composed of an engineered array of TALE repeats fused to the FokI nuclease domain, have been used successfully for directed genome editing in various organisms and cell types. TALE transcription factors (TALE-TFs), consisting of engineered TALE repeat arrays linked to a transcriptional regulatory domain, have been used to up- or downregulate expression of endogenous genes in human cells and plants. This unit describes a detailed protocol for the recently described fast ligation-based automatable solid-phase high-throughput (FLASH) assembly method. FLASH enables automated high-throughput construction of engineered TALE repeats using an automated liquid handling robot or manually using a multichannel pipet. Using the automated approach, a single researcher can construct up to 96 DNA fragments encoding TALE repeat arrays of various lengths in a single day, and then clone these to construct sequence-verified TALEN or TALE-TF expression plasmids in a week or less. Plasmids required for FLASH are available by request from the Joung lab (http://eGenome.org). This unit also describes improvements to the Zinc Finger and TALE Targeter (ZiFiT Targeter) web server (http://ZiFiT.partners.org) that facilitate the design and construction of FLASH TALE repeat arrays in high throughput. © 2013 by John Wiley & Sons, Inc.

  19. The MAP, M/G1,G2/1 queue with preemptive priority

    Directory of Open Access Journals (Sweden)

    Bong Dae Choi

    1997-01-01

    Full Text Available We consider the MAP, M/G1,G2/1 queue with preemptive resume priority, where low priority customers arrive to the system according to a Markovian arrival process (MAP and high priority customers according to a Poisson process. The service time density function of low (respectively: high priority customers is g1(x (respectively: g2(x. We use the supplementary variable method with Extended Laplace Transforms to obtain the joint transform of the number of customers in each priority queue, as well as the remaining service time for the customer in service in the steady state. We also derive the probability generating function for the number of customers of low (respectively, high priority in the system just after the service completion epochs for customers of low (respectively, high priority.

  20. Detailed geomorphological map sheet Bela Palanka at scale 1:100,000

    Directory of Open Access Journals (Sweden)

    Menković Ljubomir

    2011-01-01

    Full Text Available The Geomorphological Map Sheet Bela Palanka is a graphical representation of landforms in the area covered by the Topographical Map Sheet Bela Palanka at scale 1:100,000. The map is published in 2008 by the Serbian Academy of Sciences and Arts (SASA and the SASA Geodynamics Board. It is the first detailed geomorphological map edited in Serbia. This paper presents the methods used in preparing the geomorphological map, the contents and the mode of data presentation, geologic structure, genetic types of landforms and the subtypes, and the geomorphological history since the Neogene.

  1. Determination of alpha(s)(M(tau)(2)): conformal mapping approach

    Czech Academy of Sciences Publication Activity Database

    Caprini, I.; Fischer, Jan

    2011-01-01

    Roč. 218, - (2011), s. 128-133 ISSN 0920-5632. [11th International Workshop on Tau Lepton Physics. Manchester, 13.09.2010-17.09.2010] R&D Projects: GA MŠk LC527; GA MŠk LA08015 Institutional research plan: CEZ:AV0Z10100502 Keywords : perturbative QCD expansion * conformal mapping * hadronic decay of the tau lepton Subject RIV: BF - Elementary Particles and High Energy Physics

  2. A Novel Prokaryotic Green Fluorescent Protein Expression System for Testing Gene Editing Tools Activity Like Zinc Finger Nuclease.

    Science.gov (United States)

    Sabzehei, Faezeh; Kouhpayeh, Shirin; Dastjerdeh, Mansoureh Shahbazi; Khanahmad, Hossein; Salehi, Rasoul; Naderi, Shamsi; Taghizadeh, Razieh; Rabiei, Parisa; Hejazi, Zahra; Shariati, Laleh

    2017-01-01

    Gene editing technology has created a revolution in the field of genome editing. The three of the most famous tools in gene editing technology are zinc finger nucleases (ZFNs), transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated systems. As their predictable nature, it is necessary to assess their efficiency. There are some methods for this purpose, but most of them are time labor and complicated. Here, we introduce a new prokaryotic reporter system, which makes it possible to evaluate the efficiency of gene editing tools faster, cheaper, and simpler than previous methods. At first, the target sites of a custom ZFN, which is designed against a segment of ampicillin resistance gene, were cloned on both sides of green fluorescent protein (GFP) gene to construct pPRO-GFP. Then pPRO-GFP was transformed into Escherichia coli TOP10F' that contains pZFN (contains expression cassette of a ZFN against ampicillin resistant gene), or p15A-KanaR as a negative control. The transformed bacteria were cultured on three separate media that contained ampicillin, kanamycin, and ampicillin + kanamycin; then the resulted colonies were assessed by flow cytometry. The results of flow cytometry showed a significant difference between the case (bacteria contain pZFN) and control (bacteria contain p15A, KanaR) in MFI (Mean Fluorescence Intensity) ( P < 0.0001). According to ZFN efficiency, it can bind and cut the target sites, the bilateral cutting can affect the intensity of GFP fluorescence. Our flow cytometry results showed that this ZFN could reduce the intensity of GFP color and colony count of bacteria in media containing amp + kana versus control sample.

  3. U.S. Federal Mapping Coordination

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Sandy Emergency Supplemental appropriations contained funds for federal and state agencies that will go to ocean and coastal mapping data acquisition. These data...

  4. Gene repair of an Usher syndrome causing mutation by zinc-finger nuclease mediated homologous recombination.

    Science.gov (United States)

    Overlack, Nora; Goldmann, Tobias; Wolfrum, Uwe; Nagel-Wolfrum, Kerstin

    2012-06-26

    Human Usher syndrome (USH) is the most frequent cause of inherited deaf-blindness. It is clinically and genetically heterogeneous, assigned to three clinical types of which the most severe type is USH1. No effective treatment for the ophthalmic component of USH exists. Gene augmentation is an attractive strategy for hereditary retinal diseases. However, several USH genes, like USH1C, are expressed in various isoforms, hampering gene augmentation. As an alternative treatment strategy, we applied the zinc-finger nuclease (ZFN) technology for targeted gene repair of an USH1C, causing mutation by homologous recombination. We designed ZFNs customized for the p.R31X nonsense mutation in Ush1c. We evaluated ZFNs for DNA cleavage capability and analyzed ZFNs biocompatibilities by XTT assays. We demonstrated ZFNs mediated gene repair on genomic level by digestion assays and DNA sequencing, and on protein level by indirect immunofluorescence and Western blot analyses. The specifically designed ZFNs did not show cytotoxic effects in a p.R31X cell line. We demonstrated that ZFN induced cleavage of their target sequence. We showed that simultaneous application of ZFN and rescue DNA induced gene repair of the disease-causing mutation on the genomic level, resulting in recovery of protein expression. In our present study, we analyzed for the first time ZFN-activated gene repair of an USH gene. The data highlight the ability of ZFNs to induce targeted homologous recombination and mediate gene repair in USH. We provide further evidence that the ZFN technology holds great potential to recover disease-causing mutations in inherited retinal disorders.

  5. Assessment of myocardial fibrosis with T1 mapping MRI

    International Nuclear Information System (INIS)

    Everett, R.J.; Stirrat, C.G.; Semple, S.I.R.; Newby, D.E.; Dweck, M.R.; Mirsadraee, S.

    2016-01-01

    Myocardial fibrosis can arise from a range of pathological processes and its presence correlates with adverse clinical outcomes. Cardiac magnetic resonance (CMR) can provide a non-invasive assessment of cardiac structure, function, and tissue characteristics, which includes late gadolinium enhancement (LGE) techniques to identify focal irreversible replacement fibrosis with a high degree of accuracy and reproducibility. Importantly the presence of LGE is consistently associated with adverse outcomes in a range of common cardiac conditions; however, LGE techniques are qualitative and unable to detect diffuse myocardial fibrosis, which is an earlier form of fibrosis preceding replacement fibrosis that may be reversible. Novel T1 mapping techniques allow quantitative CMR assessment of diffuse myocardial fibrosis with the two most common measures being native T1 and extracellular volume (ECV) fraction. Native T1 differentiates normal from infarcted myocardium, is abnormal in hypertrophic cardiomyopathy, and may be particularly useful in the diagnosis of Anderson–Fabry disease and amyloidosis. ECV is a surrogate measure of the extracellular space and is equivalent to the myocardial volume of distribution of the gadolinium-based contrast medium. It is reproducible and correlates well with fibrosis on histology. ECV is abnormal in patients with cardiac failure and aortic stenosis, and is associated with functional impairment in these groups. T1 mapping techniques promise to allow earlier detection of disease, monitor disease progression, and inform prognosis; however, limitations remain. In particular, reference ranges are lacking for T1 mapping values as these are influenced by specific CMR techniques and magnetic field strength. In addition, there is significant overlap between T1 mapping values in healthy controls and most disease states, particularly using native T1, limiting the clinical application of these techniques at present.

  6. Assessment of myocardial fibrosis with T1 mapping MRI.

    Science.gov (United States)

    Everett, R J; Stirrat, C G; Semple, S I R; Newby, D E; Dweck, M R; Mirsadraee, S

    2016-08-01

    Myocardial fibrosis can arise from a range of pathological processes and its presence correlates with adverse clinical outcomes. Cardiac magnetic resonance (CMR) can provide a non-invasive assessment of cardiac structure, function, and tissue characteristics, which includes late gadolinium enhancement (LGE) techniques to identify focal irreversible replacement fibrosis with a high degree of accuracy and reproducibility. Importantly the presence of LGE is consistently associated with adverse outcomes in a range of common cardiac conditions; however, LGE techniques are qualitative and unable to detect diffuse myocardial fibrosis, which is an earlier form of fibrosis preceding replacement fibrosis that may be reversible. Novel T1 mapping techniques allow quantitative CMR assessment of diffuse myocardial fibrosis with the two most common measures being native T1 and extracellular volume (ECV) fraction. Native T1 differentiates normal from infarcted myocardium, is abnormal in hypertrophic cardiomyopathy, and may be particularly useful in the diagnosis of Anderson-Fabry disease and amyloidosis. ECV is a surrogate measure of the extracellular space and is equivalent to the myocardial volume of distribution of the gadolinium-based contrast medium. It is reproducible and correlates well with fibrosis on histology. ECV is abnormal in patients with cardiac failure and aortic stenosis, and is associated with functional impairment in these groups. T1 mapping techniques promise to allow earlier detection of disease, monitor disease progression, and inform prognosis; however, limitations remain. In particular, reference ranges are lacking for T1 mapping values as these are influenced by specific CMR techniques and magnetic field strength. In addition, there is significant overlap between T1 mapping values in healthy controls and most disease states, particularly using native T1, limiting the clinical application of these techniques at present. Copyright © 2016 The Royal College

  7. Probing force-induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding

    International Nuclear Information System (INIS)

    Ishii, Takaaki; Murayama, Yoshihiro; Katano, Atsuto; Maki, Kosuke; Kuwajima, Kunihiro; Sano, Masaki

    2008-01-01

    Single-molecule manipulation techniques have given experimental access to unfolding intermediates of proteins that are inaccessible in conventional experiments. A detailed characterization of the intermediates is a challenging problem that provides new possibilities for directly probing the energy landscape of proteins. We investigated single-molecule mechanical unfolding of a small globular protein, staphylococcal nuclease (SNase), using atomic force microscopy. The unfolding trajectories of the protein displayed sub-molecular and stochastic behavior with typical lengths corresponding to the size of the unfolded substructures. Our results support the view that the single protein unfolds along multiple pathways as suggested in recent theoretical studies. Moreover, we found the drastic change, caused by the ligand and inhibitor bindings, in the mechanical unfolding dynamics

  8. THE DESIGN AND PRODUCT OF NATIONAL 1:1000000 CARTOGRAPHIC DATA OF TOPOGRAPHIC MAP

    Directory of Open Access Journals (Sweden)

    G. Wang

    2016-06-01

    Full Text Available National administration of surveying, mapping and geoinformation started to launch the project of national fundamental geographic information database dynamic update in 2012. Among them, the 1:50000 database was updated once a year, furthermore the 1:250000 database was downsized and linkage-updated on the basis. In 2014, using the latest achievements of 1:250000 database, comprehensively update the 1:1000000 digital line graph database. At the same time, generate cartographic data of topographic map and digital elevation model data. This article mainly introduce national 1:1000000 cartographic data of topographic map, include feature content, database structure, Database-driven Mapping technology, workflow and so on.

  9. Geologic map of the east half of the Lime Hills 1:250,000-scale quadrangle, Alaska

    Science.gov (United States)

    Gamble, Bruce M.; Reed, Bruce L.; Richter, Donald H.; Lanphere, Marvin A.

    2013-01-01

    This map is compiled from geologic mapping conducted between 1985 and 1992 by the U.S. Geological Survey as part of the Alaska Mineral Resource Assessment Program. That mapping built upon previous USGS work (1963–1988) unraveling the magmatic history of the Alaska–Aleutian Range batholith. Quaternary unit contacts depicted on this map are derived largely from aerial-photograph interpretation. K-Ar ages made prior to this study have been recalculated using 1977 decay constants. The east half of the Lime Hills 1:250,000-scale quadrangle includes part of the Alaska–Aleutian Range batholith and several sequences of sedimentary rocks or mixed sedimentary and volcanic rocks. The Alaska–Aleutian Range batholith contains rocks that represent three major igneous episodes, (1) Early and Middle Jurassic, (2) Late Cretaceous and early Tertiary, and (3) middle Tertiary; only rocks from the latter two episodes are found in this map area. The map area is one of very steep and rugged terrain; elevations range from a little under 1,000 ft (305 m) to 9,828 ft (2,996 m). Foot traverses are generally restricted to lowermost elevations. Areas suitable for helicopter landings can be scarce at higher elevations. Most of the area was mapped from the air, supplemented by direct examination of rocks where possible. This restricted access greatly complicates understanding some of the more complex geologic units. For example, we know there are plutons whose compositions vary from gabbro to granodiorite, but we have little insight as to how these phases are distributed and what their relations might be to each other. It is also possible that some of what we have described as compositionally complex plutons might actually be several distinct intrusions.

  10. Distribution of nuclease attack sites and complexity of DNA in the products of post-irradiation degradiation of rat thymus chromatin

    International Nuclear Information System (INIS)

    Zvonareva, N.B.; Zhivotovsky, B.D.; Hanson, K.P.

    1983-01-01

    The distribution of nuclease attack sites in chromatin has been studied on the basis of the quantitative relationship of the single- and double-stranded fragments of various lengths in the products of post-irradiation degradation of chromatin (PDN). It has been shown that in irradiated thymocytes internucleosome degradation of chromatin occurs and the products of the enzymic digestion of chromatin derive from randomly distributed genome areas accumulate. Analysis of the reassociation curves has not shown any differences in the complexity of the PDN fractions and total DNA. (author)

  11. Application of processing maps in the optimization of the parameters of a hot working process. Part 2. Processing maps of a microalloyed medium carbon steel

    International Nuclear Information System (INIS)

    Al Omar, A.; Cabrera, J.M.; Prado, J.M.

    1997-01-01

    Part 1 of this work presents a revision of the general characteristics of the so called dynamic materials model on which processing maps are developed. In this part following the methodology described in part 1, processing maps of a microalloyed medium carbon steel are developed over a temperature range varying from 900 to 1.150 degree centigree at different true strain rates ranging from 10''-4 to 10s''-1. The analysis of these maps revealed a domain of dynamic recrystallization centred at about 1.1.50 degree centigree and strain rate 10 s''-1 and a domain of dynamic recovery centred at 900 degree centigree and 0,1 s''-1. (Author) 20 refs

  12. Molecular Imaging of Human Embryonic Stem Cells Stably Expressing Human PET Reporter Genes After Zinc Finger Nuclease-Mediated Genome Editing.

    Science.gov (United States)

    Wolfs, Esther; Holvoet, Bryan; Ordovas, Laura; Breuls, Natacha; Helsen, Nicky; Schönberger, Matthias; Raitano, Susanna; Struys, Tom; Vanbilloen, Bert; Casteels, Cindy; Sampaolesi, Maurilio; Van Laere, Koen; Lambrichts, Ivo; Verfaillie, Catherine M; Deroose, Christophe M

    2017-10-01

    Molecular imaging is indispensable for determining the fate and persistence of engrafted stem cells. Standard strategies for transgene induction involve the use of viral vectors prone to silencing and insertional mutagenesis or the use of nonhuman genes. Methods: We used zinc finger nucleases to induce stable expression of human imaging reporter genes into the safe-harbor locus adeno-associated virus integration site 1 in human embryonic stem cells. Plasmids were generated carrying reporter genes for fluorescence, bioluminescence imaging, and human PET reporter genes. Results: In vitro assays confirmed their functionality, and embryonic stem cells retained differentiation capacity. Teratoma formation assays were performed, and tumors were imaged over time with PET and bioluminescence imaging. Conclusion: This study demonstrates the application of genome editing for targeted integration of human imaging reporter genes in human embryonic stem cells for long-term molecular imaging. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

  13. Meta-analysis of the research impact of Baddeley’s multicomponent working memory model and Cowan’s embedded-processes model of working memory: A bibliometric mapping approach

    Directory of Open Access Journals (Sweden)

    Gruszka Aleksandra

    2016-04-01

    Full Text Available In this study bibliometric mapping method was employed to visualise the current research trends and the impact of the two most influential models of working memory, namely: A. D. Baddeley and G. J. Hitch’s (1974 multicomponent working memory model and N. Cowan’s (1988 embedded-processes model of working memory. Using VOSviewer software two maps were generated based on the index-term words extracted from the research papers citing Baddeley (2000 and Cowan (2001, respectively. The maps represent networks of co-occurrences of index terms and can be interpreted as an indication of the main research fields related to the examined models of WM. The results of the analysis revealed that the spheres of influence of the two main conceptualisations of WM are rather different than similar. Although the first two clusters, i.e. “brain mapping” and “higher-level cognition and development” are present in both maps, their relative importance varies. The remaining clusters are unique to each map. Baddeley’s theory seems to have a greater influence on “neuropsychology”, while Cowan’s theory - on basic research on “biological systems”, including the nervous system in humans and animals. The second difference between these theories concerns their relations to functions and dysfunctions associated with particular sensory modalities: in Baddelay’s theory with the “auditory modality” cluster, and in Cowan’s - with the “visual modality” one.

  14. Automated mapping of persistent ice and snow cover across the western U.S. with Landsat

    Science.gov (United States)

    Selkowitz, David J.; Forster, Richard R.

    2016-01-01

    We implemented an automated approach for mapping persistent ice and snow cover (PISC) across the conterminous western U.S. using all available Landsat TM and ETM+ scenes acquired during the late summer/early fall period between 2010 and 2014. Two separate validation approaches indicate this dataset provides a more accurate representation of glacial ice and perennial snow cover for the region than either the U.S. glacier database derived from US Geological Survey (USGS) Digital Raster Graphics (DRG) maps (based on aerial photography primarily from the 1960s–1980s) or the National Land Cover Database 2011 perennial ice and snow cover class. Our 2010–2014 Landsat-derived dataset indicates 28% less glacier and perennial snow cover than the USGS DRG dataset. There are larger differences between the datasets in some regions, such as the Rocky Mountains of Northwest Wyoming and Southwest Montana, where the Landsat dataset indicates 54% less PISC area. Analysis of Landsat scenes from 1987–1988 and 2008–2010 for three regions using a more conventional, semi-automated approach indicates substantial decreases in glaciers and perennial snow cover that correlate with differences between PISC mapped by the USGS DRG dataset and the automated Landsat-derived dataset. This suggests that most of the differences in PISC between the USGS DRG and the Landsat-derived dataset can be attributed to decreases in PISC, as opposed to differences between mapping techniques. While the dataset produced by the automated Landsat mapping approach is not designed to serve as a conventional glacier inventory that provides glacier outlines and attribute information, it allows for an updated estimate of PISC for the conterminous U.S. as well as for smaller regions. Additionally, the new dataset highlights areas where decreases in PISC have been most significant over the past 25–50 years.

  15. Uruguay Hydrogeological map scale 1/1.000.000

    International Nuclear Information System (INIS)

    Heinzen, W.; Carrion, R.; Massa, E.; Pena, S.; Stapff, M.

    2003-06-01

    Between the main items the Uruguayan Hydrogeological map show us: aquifers productivity, geographical references, well information, depth, level, caudal, dry waste, from Hydrologic unit cuaternario differenced, Villa Soriano, Chuy, Raigon, Salto, Cretacico Superior, Tacuarembo, Las Arenas, Del Terciario, Cretacico Superior, Tres Islas, Cerrezuelo, Arapey, Neoproterozoico, Paleoproterozoico. It shows a brief map about Guarani Aquifer

  16. Subsea Permafrost Mapped Across the U.S. Beaufort Sea Using Multichannel Seismic Data

    Science.gov (United States)

    Brothers, L.; Hart, P. E.; Ruppel, C. D.

    2011-12-01

    Circum-Arctic continental shelves at water depths less than ~100 m were subaerial permafrost prior to the onset of sea-level rise starting in the late Pleistocene. Rapid transgression and the resulting temperature increase at the sediment surface have led to thawing of the inundated permafrost, landward retreat of the leading edge of the permafrost, and dissociation of permafrost-associated gas hydrates. Past numerical modeling has shown that gas hydrate dissociation is particularly pronounced at the permafrost-to-no permafrost transition offshore. On the U.S. Beaufort margin, subsea permafrost has never been systematically mapped, and the best insights about permafrost and associated gas hydrate have been based on a limited number of offshore boreholes and numerical studies, with sometimes contrasting predictions of the permafrost's seaward extent. We bring together 5370 km of multichannel seismic (MCS) data acquired during various proprietary exploration industry and public domain government surveys between 1977 and 1992 to map a velocity anomaly diagnostic of submerged permafrost along 500 km of the US Beaufort coastline. These high-velocity (>~2.8 km/s) refractions (HVR), which are evident in prestack MCS shot records, reveal laterally continuous layers of shallow, ice-bonded, coarse-grained sediments beneath the inner continental shelf. The HVR occur in less than 5% of the tracklines, and calculated HVR depths range from 60 to 350 m below seafloor. The velocity anomaly is not observed seaward of the 20 m isobath, and is only found within 30 km of the current shoreline. These results can be used to: 1) create a map of the minimum distribution of remaining US Beaufort shelf subsea permafrost; 2) reconcile discrepancies between model-predicted and borehole-verified offshore permafrost distribution; and 3) constrain where to expect hydrate dissociation.

  17. Synthesis of in vitro Co1E1 transcripts with 5'-terminal ribonucleotides that exhibit noncomplementarity with the DNA template

    International Nuclear Information System (INIS)

    Parker, R.C.

    1986-01-01

    A region that forms the S1 nuclease site in Co1E1 DNA is shown to code for an in vitro transcript, called S1 RNA-B, which contains a 5'-terminal GTP residue that exhibits noncomplementarity with the template's DNA sequence. The synthesis of S1 RNA-B initiates four bases upstream from the start point for S1 RNA-C. The initial four bases in S1 RNA-B and S1 RNA-C are identical. The relative synthesis of S1 RNA-B to S1 RNA-C is sensitive to the concentration of GTP, a substrate that is required for elongation past the +4 position in S1 RNA-C. Dinucleotides that are expected to only initiate synthesis of S1 RNA-C yield two transcripts that appear to initiate from the S1 RNA-C and S1 RNA-B start sites. In vitro studies involving other Co1E1 transcripts, RNA-B and RNA-C, provide similar observations concerning the noncomplementary initiation phenomenon. A model involving transcriptional slippage is suggested to explain the noncomplementary initiation phenomenon. The model proposes that the cycling reaction of Escherichia coli RNA polymerase produces tetranucleotides that are transposed to nearby upstream sequences for priming transcription

  18. Substrate overlap and functional competition between human nucleotide excision repair and Escherichia coli photolyase and (A)BC excision nuclease

    International Nuclear Information System (INIS)

    Sibghat-Ullah; Sancar, Z.

    1990-01-01

    Human cell free extract prepared by the method of Manley et al. carries out repair synthesis on UV-irradiated DNA. Removal of pyrimidine dimers by photoreactivation with DNA photolyase reduces repair synthesis by about 50%. With excess enzyme in the reaction mixture photolyase reduced the repair signal by the same amount even in the absence of photoreactivating light, presumably by binding to pyrimidine dimers and interfering with the binding of human damage recognition protein. Similarly, the UvrB subunit of Escherichia coli (A)BC excinuclease when loaded onto UV-irradiated or psoralen-adducted DNA inhibited repair synthesis by cell-free extract by 75-80%. The opposite was true also as HeLa cell free extract specifically inhibited the photorepair of a thymine dimer by DNA photolyase and its removal by (A)BC excinuclease. Cell-free extracts from xeroderma pigmentosum (XP) complementation groups A and C were equally effective in blocking the E. coli repair proteins, while extracts from complementation groups D and E were ineffective in blocking the E. coli enzyme. These results suggest that XP-D and XP-E cells are defective in the damage recognition subunits(s) of human excision nuclease

  19. The National Map - Orthoimagery

    Science.gov (United States)

    Mauck, James; Brown, Kim; Carswell, William J.

    2009-01-01

    Orthorectified digital aerial photographs and satellite images of 1-meter (m) pixel resolution or finer make up the orthoimagery component of The National Map. The process of orthorectification removes feature displacements and scale variations caused by terrain relief and sensor geometry. The result is a combination of the image characteristics of an aerial photograph or satellite image and the geometric qualities of a map. These attributes allow users to: *Measure distance *Calculate areas *Determine shapes of features *Calculate directions *Determine accurate coordinates *Determine land cover and use *Perform change detection *Update maps The standard digital orthoimage is a 1-m or finer resolution, natural color or color infra-red product. Most are now produced as GeoTIFFs and accompanied by a Federal Geographic Data Committee (FGDC)-compliant metadata file. The primary source for 1-m data is the National Agriculture Imagery Program (NAIP) leaf-on imagery. The U.S. Geological Survey (USGS) utilizes NAIP imagery as the image layer on its 'Digital- Map' - a new generation of USGS topographic maps (http://nationalmap.gov/digital_map). However, many Federal, State, and local governments and organizations require finer resolutions to meet a myriad of needs. Most of these images are leaf-off, natural-color products at resolutions of 1-foot (ft) or finer.

  20. An integrated genetic, physical, and transcriptional map of chromosome 13

    Energy Technology Data Exchange (ETDEWEB)

    Scheffer, H.; Kooy, R.F.; Wijngaard, A. [Univ. of Groningen (Netherlands)] [and others

    1994-09-01

    In this study a genetic map containing 20 markers and typed in 40 CEPH families is presented. It includes 7 thusfar untyped microsatellite markers, 7 that have previously been mapped on a subset of 8 CEPH families, one reference marker, D13S71, and three telomeric VNTR markers. Also, 4 intragenic RB1 markers were typed. The markers have an average heterozygosity of 73% (80%, excluding the three RFLPs). The total sex average length of the map is 140 cM. The mean female to male ratio is 1.54. For the non-telomeric part of the chromosome between the markers D13S221 in 13q12 and D13S173 in 13q33-q34, this ratio is 1.99. This ratio is reversed in the telomeric part of the chromosome between D13S173 and D13S234 in distal 13q34, where it is 0.47. A high new mutation frequency of 1% was detected in the (CTTT(T)){sub n} repeat in intron 20 of the RB1 gene. The map has been integrated with 7 microsatellite markers and 2 RFLP markers from CEPH database version 7.0, resulting in a map with 32 markers (28 loci) of chromosome 13q. In addition, a deletion hybrid breakpoint map ordering 50 markers in 18 intervals is constructed. It includes 32 microsatellite markers, 4 genes, 5 STSs, and 9 ESTs. Each of 18 intervals contains at least one microsatellite marker included in the extended genetic map. These data allow a correlation between the genetic and physical map of chromosome 13. New ESTs are currently being identified and localized at this integrated map.

  1. Introduction to SNPP/VIIRS Flood Mapping Software Version 1.0

    Science.gov (United States)

    Li, S.; Sun, D.; Goldberg, M.; Sjoberg, W.; Santek, D.; Hoffman, J.

    2017-12-01

    Near real-time satellite-derived flood maps are invaluable to river forecasters and decision-makers for disaster monitoring and relief efforts. With support from the JPSS (Joint Polar Satellite System) Proving Ground and Risk Reduction (PGRR) Program, flood detection software has been developed using Suomi-NPP/VIIRS (Suomi National Polar-orbiting Partnership/Visible Infrared Imaging Radiometer Suite) imagery to automatically generate near real-time flood maps for National Weather Service (NWS) River Forecast Centers (RFC) in the USA. The software, which is called VIIRS NOAA GMU Flood Version 1.0 (hereafter referred to as VNG Flood V1.0), consists of a series of algorithms that include water detection, cloud shadow removal, terrain shadow removal, minor flood detection, water fraction retrieval, and floodwater determination. The software is designed for flood detection in any land region between 80°S and 80°N, and it has been running routinely with direct broadcast SNPP/VIIRS data at the Space Science and Engineering Center at the University of Wisconsin-Madison (UW/SSEC) and the Geographic Information Network of Alaska at the University of Alaska-Fairbanks (UAF/GINA) since 2014. Near real-time flood maps are distributed via the Unidata Local Data Manager (LDM), reviewed by river forecasters in AWIPS-II (the second generation of the Advanced Weather Interactive Processing System) and applied in flood operations. Initial feedback from operational forecasters on the product accuracy and performance has been largely positive. The software capability has also been extended to areas outside of the USA via a case-driven mode to detect major floods all over the world. Offline validation efforts include the visual inspection of over 10,000 VIIRS false-color composite images, an inter-comparison with MODIS automatic flood products and a quantitative evaluation using Landsat imagery. The steady performance from the 3-year routine process and the promising validation results

  2. Nucleolin forms a specific complex with a fragment of the viral (minus) strand of minute virus of mice DNA.

    Science.gov (United States)

    Barrijal, S; Perros, M; Gu, Z; Avalosse, B L; Belenguer, P; Amalric, F; Rommelaere, J

    1992-01-01

    Nucleolin, a major nucleolar protein, forms a specific complex with the genome (a single-stranded DNA molecule of minus polarity) of parvovirus MVMp in vitro. By means of South-western blotting experiments, we mapped the binding site to a 222-nucleotide motif within the non-structural transcription unit, referred to as NUBE (nucleolin-binding element). The specificity of the interaction was confirmed by competitive gel retardation assays. DNaseI and nuclease S1 probing showed that NUBE folds into a secondary structure, in agreement with a computer-assisted conformational prediction. The whole NUBE may be necessary for the interaction with nucleolin, as suggested by the failure of NUBE subfragments to bind the protein and by the nuclease footprinting experiments. The present work extends the previously reported ability of nucleolin to form a specific complex with ribosomal RNA, to a defined DNA substrate. Considering the tropism of MVMp DNA replication for host cell nucleoli, these data raise the possibility that nucleolin may contribute to the regulation of the parvoviral life-cycle. Images PMID:1408821

  3. Fat fraction bias correction using T1 estimates and flip angle mapping.

    Science.gov (United States)

    Yang, Issac Y; Cui, Yifan; Wiens, Curtis N; Wade, Trevor P; Friesen-Waldner, Lanette J; McKenzie, Charles A

    2014-01-01

    To develop a new method of reducing T1 bias in proton density fat fraction (PDFF) measured with iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL). PDFF maps reconstructed from high flip angle IDEAL measurements were simulated and acquired from phantoms and volunteer L4 vertebrae. T1 bias was corrected using a priori T1 values for water and fat, both with and without flip angle correction. Signal-to-noise ratio (SNR) maps were used to measure precision of the reconstructed PDFF maps. PDFF measurements acquired using small flip angles were then compared to both sets of corrected large flip angle measurements for accuracy and precision. Simulations show similar results in PDFF error between small flip angle measurements and corrected large flip angle measurements as long as T1 estimates were within one standard deviation from the true value. Compared to low flip angle measurements, phantom and in vivo measurements demonstrate better precision and accuracy in PDFF measurements if images were acquired at a high flip angle, with T1 bias corrected using T1 estimates and flip angle mapping. T1 bias correction of large flip angle acquisitions using estimated T1 values with flip angle mapping yields fat fraction measurements of similar accuracy and superior precision compared to low flip angle acquisitions. Copyright © 2013 Wiley Periodicals, Inc.

  4. S1P in HDL promotes interaction between SR-BI and S1PR1 and activates S1PR1-mediated biological functions: calcium flux and S1PR1 internalization[S

    Science.gov (United States)

    Lee, Mi-Hye; Appleton, Kathryn M.; El-Shewy, Hesham M.; Sorci-Thomas, Mary G.; Thomas, Michael J.; Lopes-Virella, Maria F.; Luttrell, Louis M.; Hammad, Samar M.; Klein, Richard L.

    2017-01-01

    HDL normally transports about 50–70% of plasma sphingosine 1-phosphate (S1P), and the S1P in HDL reportedly mediates several HDL-associated biological effects and signaling pathways. The HDL receptor, SR-BI, as well as the cell surface receptors for S1P (S1PRs) may be involved partially and/or completely in these HDL-induced processes. Here we investigate the nature of the HDL-stimulated interaction between the HDL receptor, SR-BI, and S1PR1 using a protein-fragment complementation assay and confocal microscopy. In both primary rat aortic vascular smooth muscle cells and HEK293 cells, the S1P content in HDL particles increased intracellular calcium concentration, which was mediated by S1PR1. Mechanistic studies performed in HEK293 cells showed that incubation of cells with HDL led to an increase in the physical interaction between the SR-BI and S1PR1 receptors that mainly occurred on the plasma membrane. Model recombinant HDL (rHDL) particles formed in vitro with S1P incorporated into the particle initiated the internalization of S1PR1, whereas rHDL without supplemented S1P did not, suggesting that S1P transported in HDL can selectively activate S1PR1. In conclusion, these data suggest that S1P in HDL stimulates the transient interaction between SR-BI and S1PRs that can activate S1PRs and induce an elevation in intracellular calcium concentration. PMID:27881715

  5. THE ARIZONA RADIO OBSERVATORY CO MAPPING SURVEY OF GALACTIC MOLECULAR CLOUDS. I. THE W51 REGION IN CO AND 13CO J = 2-1 EMISSION

    International Nuclear Information System (INIS)

    Bieging, John H.; Peters, William L.; Kang, Miju

    2010-01-01

    We present 38'' resolution maps of the CO and 13 CO J = 2-1 lines in the molecular clouds toward the H II region complex W51. The maps cover a 1. 0 25 x 1 0 section of the galactic plane and span +30 to +85 km s -1 (LSR) in velocity. The spectral resolution is ∼1.3 km s -1 . The velocity range of the images includes all the gas in the Sagittarius spiral arm. Color figures display the peak line brightness temperature, the velocity-integrated intensity, and 2 km s -1 channel-averaged maps for both isotopologs, and also the CO/ 13 CO J = 2-1 line intensity ratio as a function of velocity. The CO and 13 CO line intensity image cubes are made available in standard FITS format as electronically readable tables. We compare our molecular line maps with the 1.1 mm continuum image from the BOLOCAM Galactic Plane Survey. From our 13 CO image cube, we derive kinematic information for the 99 BGPS sources in the mapped field in the form of Gaussian component fits. The integrated 13 CO line intensity and the 1.1 mm source flux density show only a modest degree of correlation for the 99 sources, likely due to a range of dust and gas physical conditions within the sources. However, the 1.1 mm continuum surface brightness and the integrated 13 CO line intensity for small regions containing single BGPS sources and molecular clouds show very good correlations in many cases. Differences in the shapes of these correlations from one spatial region to another probably result from different physical conditions or structure in the clouds.

  6. Transplantation of Gene-Edited Hepatocyte-like Cells Modestly Improves Survival of Arginase-1-Deficient Mice

    Directory of Open Access Journals (Sweden)

    Yuan Yan Sin

    2018-03-01

    Full Text Available Progress in gene editing research has been accelerated by utilizing engineered nucleases in combination with induced pluripotent stem cell (iPSC technology. Here, we report transcription activator-like effector nuclease (TALEN-mediated reincorporation of Arg1 exons 7 and 8 in iPSCs derived from arginase-1-deficient mice possessing Arg1Δ alleles lacking these terminal exons. The edited cells could be induced to differentiate into hepatocyte-like cells (iHLCs in vitro and were subsequently used for transplantation into our previously described (Sin et al., PLoS ONE 2013 tamoxifen-inducible Arg1-Cre arginase-1-deficient mouse model. While successful gene-targeted repair was achieved in iPSCs containing Arg1Δ alleles, only minimal restoration of urea cycle function could be observed in the iHLC-transplanted mice compared to control mice, and survival in this lethal model was extended by up to a week in some mice. The partially rescued phenotype may be due to inadequate regenerative capacity of arginase-1-expressing cells in the correct metabolic zones. Technical hurdles exist and will need to be overcome for gene-edited iPSC to iHLC rescue of arginase-1 deficiency, a rare urea cycle disorder.

  7. Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density

    International Nuclear Information System (INIS)

    Terwilliger, Thomas C.; Berendzen, Joel

    1999-01-01

    The correlation of local r.m.s. density is shown to be a good measure of the presence of distinct solvent and macromolecule regions in macromolecular electron-density maps. It has recently been shown that the standard deviation of local r.m.s. electron density is a good indicator of the presence of distinct regions of solvent and protein in macromolecular electron-density maps [Terwilliger & Berendzen (1999 ▶). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a complementary measure, the correlation of local r.m.s. density in adjacent regions on the unit cell, is also a good measure of the presence of distinct solvent and protein regions. The correlation of local r.m.s. density is essentially a measure of how contiguous the solvent (and protein) regions are in the electron-density map. This statistic can be calculated in real space or in reciprocal space and has potential uses in evaluation of heavy-atom solutions in the MIR and MAD methods as well as for evaluation of trial phase sets in ab initio phasing procedures

  8. Entropic Phase Maps in Discrete Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Benjamin F. Dribus

    2017-06-01

    Full Text Available Path summation offers a flexible general approach to quantum theory, including quantum gravity. In the latter setting, summation is performed over a space of evolutionary pathways in a history configuration space. Discrete causal histories called acyclic directed sets offer certain advantages over similar models appearing in the literature, such as causal sets. Path summation defined in terms of these histories enables derivation of discrete Schrödinger-type equations describing quantum spacetime dynamics for any suitable choice of algebraic quantities associated with each evolutionary pathway. These quantities, called phases, collectively define a phase map from the space of evolutionary pathways to a target object, such as the unit circle S 1 ⊂ C , or an analogue such as S 3 or S 7 . This paper explores the problem of identifying suitable phase maps for discrete quantum gravity, focusing on a class of S 1 -valued maps defined in terms of “structural increments” of histories, called terminal states. Invariants such as state automorphism groups determine multiplicities of states, and induce families of natural entropy functions. A phase map defined in terms of such a function is called an entropic phase map. The associated dynamical law may be viewed as an abstract combination of Schrödinger’s equation and the second law of thermodynamics.

  9. Cadastral map supersession acording new instructions

    Directory of Open Access Journals (Sweden)

    Alena Berková

    2009-11-01

    Full Text Available Digital form o cadastral map exists on 36 % of cadastral areas of the Czech republic. Contemporary rate of dogitalizationis 2-3 % of total number cadastral areas anually. In Jule 2007 was approved by goverment decree N. 871/2007 document of Czechoffice for surveying, mapping and cadstre, that assesments deadline of cadstral maps digitalization in the year 2015. Financingof digitalization has to solve amendent of act N. 634/2004 Sb. of administrative charges. As interium solution offered COSMC Parcelorientation maps, that are free available on internet from March 2008. There are rastr images of cadastral maps in datum S-JTSKsuccesive complemented with parcel defonition points. One of reason insufficient rate of digitalization was uncertainty of reworkingtechnology of maps. These maps cover about 70 % territory of the Czech republic. From 1.1.2008 stands the new instruction, thatestablishs technology approach for cadastral map supersession. The article descibes curiosity, where was find erreneouslydetermination of property boundry, without solving next relationships.

  10. ESI-V1 Frederiksted, St. Croix., U.S. Virgin Islands 2000 (Environmental Sensitivity Index Map)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Environmental Sensitivity Index (ESI) maps are an integral component in oil-spill contingency planning and assessment. They serve as a source of information in the...

  11. MAP3S precipitation chemistry network: fourth periodic summary report (1980)

    Energy Technology Data Exchange (ETDEWEB)

    1981-12-01

    This, the fourth in a series of summary reports, contains complete field and chemical data from the MAP3S/RAINE (Multistate Atmospheric Power Production Pollution Studies) Precipitation Chemistry Network for the year 1980. The 1980 data were added to the previous data base, and an update of the previous statistical summary completed. Included are basic statistics, time trend analyses, and monthly averages.

  12. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

    Science.gov (United States)

    Mulepati, Sabin; Bailey, Scott

    2011-09-09

    RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.

  13. S-Boxes Based on Affine Mapping and Orbit of Power Function

    Science.gov (United States)

    Khan, Mubashar; Azam, Naveed Ahmed

    2015-06-01

    The demand of data security against computational attacks such as algebraic, differential, linear and interpolation attacks has been increased as a result of rapid advancement in the field of computation. It is, therefore, necessary to develop such cryptosystems which can resist current cryptanalysis and more computational attacks in future. In this paper, we present a multiple S-boxes scheme based on affine mapping and orbit of the power function used in Advanced Encryption Standard (AES). The proposed technique results in 256 different S-boxes named as orbital S-boxes. Rigorous tests and comparisons are performed to analyse the cryptographic strength of each of the orbital S-boxes. Furthermore, gray scale images are encrypted by using multiple orbital S-boxes. Results and simulations show that the encryption strength of the orbital S-boxes against computational attacks is better than that of the existing S-boxes.

  14. Cloning, expression, and mapping of allergenic determinants of alphaS1-casein, a major cow's milk allergen.

    Science.gov (United States)

    Schulmeister, Ulrike; Hochwallner, Heidrun; Swoboda, Ines; Focke-Tejkl, Margarete; Geller, Beate; Nystrand, Mats; Härlin, Annika; Thalhamer, Josef; Scheiblhofer, Sandra; Keller, Walter; Niggemann, Bodo; Quirce, Santiago; Ebner, Christoph; Mari, Adriano; Pauli, Gabrielle; Herz, Udo; Valenta, Rudolf; Spitzauer, Susanne

    2009-06-01

    Milk is one of the first components introduced into human diet. It also represents one of the first allergen sources, which induces IgE-mediated allergies in childhood ranging from gastrointestinal, skin, and respiratory manifestations to severe life-threatening manifestations, such as anaphylaxis. Here we isolated a cDNA coding for a major cow's milk allergen, alphaS1-casein, from a bovine mammary gland cDNA library with allergic patients' IgE Abs. Recombinant alphaS1-casein was expressed in Escherichia coli, purified, and characterized by circular dichroism as a folded protein. IgE epitopes of alphaS1-casein were determined with recombinant fragments and synthetic peptides spanning the alphaS1-casein sequence using microarrayed components and sera from 66 cow's milk-sensitized patients. The allergenic activity of ralphaS1-casein and the alphaS1-casein-derived peptides was determined using rat basophil leukemia cells transfected with human FcepsilonRI, which had been loaded with the patients' serum IgE. Our results demonstrate that ralphaS1-casein as well as alphaS1-casein-derived peptides exhibit IgE reactivity, but mainly the intact ralphaS1-casein induced strong basophil degranulation. These results suggest that primarily intact alphaS1-casein or larger IgE-reactive portions thereof are responsible for IgE-mediated symptoms of food allergy. Recombinant alphaS1-casein as well as alphaS1-casein-derived peptides may be used in clinical studies to further explore pathomechanisms of food allergy as well as for the development of new diagnostic and therapeutic strategies for milk allergy.

  15. KINETIC TOMOGRAPHY. I. A METHOD FOR MAPPING THE MILKY WAY’S INTERSTELLAR MEDIUM IN FOUR DIMENSIONS

    Energy Technology Data Exchange (ETDEWEB)

    Tchernyshyov, Kirill [The Johns Hopkins University (United States); Peek, J. E. G. [Space Telescope Science Institute (United States)

    2017-01-01

    We have developed a method for deriving the distribution of the Milky Way’s interstellar medium as a function of longitude, latitude, distance, and line-of-sight velocity. This method takes as input maps of reddening as a function of longitude, latitude, distance, and maps of line emission as a function of longitude, latitude, and line-of-sight velocity. We have applied this method to data sets covering much of the Galactic plane. The output of this method correctly reproduces the line-of-sight velocities of high-mass star-forming regions with known distances from Reid et al. and qualitatively agrees with results from the Milky Way kinematics literature. These maps will be useful for measuring flows of gas around the Milky Way’s spiral arms and into and out of giant molecular clouds.

  16. Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

    Energy Technology Data Exchange (ETDEWEB)

    Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd [School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia); Johari, Norazfa [Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor (Malaysia)

    2014-09-03

    Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved from 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively.

  17. Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

    International Nuclear Information System (INIS)

    Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd; Johari, Norazfa

    2014-01-01

    Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved from 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively

  18. FAN1 acts with FANCI-FANCD2 to promote DNA interstrand cross-link repair.

    Science.gov (United States)

    Liu, Ting; Ghosal, Gargi; Yuan, Jingsong; Chen, Junjie; Huang, Jun

    2010-08-06

    Fanconi anemia (FA) is caused by mutations in 13 Fanc genes and renders cells hypersensitive to DNA interstrand cross-linking (ICL) agents. A central event in the FA pathway is mono-ubiquitylation of the FANCI-FANCD2 (ID) protein complex. Here, we characterize a previously unrecognized nuclease, Fanconi anemia-associated nuclease 1 (FAN1), that promotes ICL repair in a manner strictly dependent on its ability to accumulate at or near sites of DNA damage and that relies on mono-ubiquitylation of the ID complex. Thus, the mono-ubiquitylated ID complex recruits the downstream repair protein FAN1 and facilitates the repair of DNA interstrand cross-links.

  19. Weakly Compatible Mappings along with $CLR_{S}$ property in Fuzzy Metric Spaces

    Directory of Open Access Journals (Sweden)

    Saurabh Manro

    2013-11-01

    Full Text Available The aim of this work is to use newly introduced property, which is so called common limit in the range $(CLR_{S}$ for four self-mappings, and prove some theorems which satisfy this property. Moreover, we establish some new existence of a common fixed point theorem for generalized contractive mappings in fuzzy metric spaces by using this new property and give some examples to support our results. Ours results does not require condition of closeness of range and so our theorems generalize, unify, and extend many results in literature. Our results improve and extend the results of Cho et al. [4], Pathak et al. [20] and Imdad et. al. [10] besides several known results.

  20. Predictive Mapping of the Biotic Condition of Conterminous U.S. Rivers and Streams

    Science.gov (United States)

    Understanding and mapping the spatial variations in the biological condition of streams could provide an important tool for assessment and restoration of stream ecosystems. The US EPA’s National Rivers and Streams Assessment (NRSA) summarizes the percent of stream lengths within ...

  1. High-resolution mapping of the S-locus in Turnera leads to the discovery of three genes tightly associated with the S-alleles.

    Science.gov (United States)

    Labonne, Jonathan J D; Goultiaeva, Alina; Shore, Joel S

    2009-06-01

    While the breeding system known as distyly has been used as a model system in genetics, and evolutionary biology for over a century, the genes determining this system remain unknown. To positionally clone genes determining distyly, a high-resolution map of the S-locus region of Turnera has been constructed using segregation data from 2,013 backcross progeny. We discovered three putative genes tightly linked with the S-locus. An N-acetyltransferase (TkNACE) flanks the S-locus at 0.35 cM while a sulfotransferase (TkST1) and a non-LTR retroelement (TsRETRO) show complete linkage to the S-locus. An assay of population samples of six species revealed that TsRETRO, initially discovered in diploid Turnera subulata, is also associated with the S-allele in tetraploid T. subulata and diploid Turnera scabra. The sulfotransferase gene shows some level of differential expression in long versus short styles, indicating it might be involved in some aspect of distyly. The complete linkage of TkST1 and TsRETRO to the S-locus suggests that both genes may reside within, or in the immediate vicinity of the S-locus. Chromosome walking has been initiated using one of the genes discovered in the present study to identify the genes determining distyly.

  2. Characterization of Genomic Deletion Efficiency Mediated by Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 Nuclease System in Mammalian Cells*♦

    Science.gov (United States)

    Canver, Matthew C.; Bauer, Daniel E.; Dass, Abhishek; Yien, Yvette Y.; Chung, Jacky; Masuda, Takeshi; Maeda, Takahiro; Paw, Barry H.; Orkin, Stuart H.

    2014-01-01

    The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 nuclease system has provided a powerful tool for genome engineering. Double strand breaks may trigger nonhomologous end joining repair, leading to frameshift mutations, or homology-directed repair using an extrachromosomal template. Alternatively, genomic deletions may be produced by a pair of double strand breaks. The efficiency of CRISPR/Cas9-mediated genomic deletions has not been systematically explored. Here, we present a methodology for the production of deletions in mammalian cells, ranging from 1.3 kb to greater than 1 Mb. We observed a high frequency of intended genomic deletions. Nondeleted alleles are nonetheless often edited with inversions or small insertion/deletions produced at CRISPR recognition sites. Deleted alleles also typically include small insertion/deletions at predicted deletion junctions. We retrieved cells with biallelic deletion at a frequency exceeding that of probabilistic expectation. We demonstrate an inverse relationship between deletion frequency and deletion size. This work suggests that CRISPR/Cas9 is a robust system to produce a spectrum of genomic deletions to allow investigation of genes and genetic elements. PMID:24907273

  3. Structure of period-2 step-1 accelerator island in area preserving maps

    International Nuclear Information System (INIS)

    Hirose, K.; Ichikawa, Y.H.; Saito, S.

    1996-03-01

    Since the multi-periodic accelerator modes manifest their contribution even in the region of small stochastic parameters, analysis of such regular motion appears to be critical to explore the stochastic properties of the Hamiltonian system. Here, structure of period-2 step-1 accelerator mode is analyzed for the systems described by the Harper map and by the standard map. The stability criterions have been analyzed in detail in comparison with numerical analyses. The period-3 squeezing around the period-2 step-1 islands is identified in the standard map. (author)

  4. Phenology-based Spartina alterniflora mapping in coastal wetland of the Yangtze Estuary using time series of GaoFen satellite no. 1 wide field of view imagery

    Science.gov (United States)

    Ai, Jinquan; Gao, Wei; Gao, Zhiqiang; Shi, Runhe; Zhang, Chao

    2017-04-01

    Spartina alterniflora is an aggressive invasive plant species that replaces native species, changes the structure and function of the ecosystem across coastal wetlands in China, and is thus a major conservation concern. Mapping the spread of its invasion is a necessary first step for the implementation of effective ecological management strategies. The performance of a phenology-based approach for S. alterniflora mapping is explored in the coastal wetland of the Yangtze Estuary using a time series of GaoFen satellite no. 1 wide field of view camera (GF-1 WFV) imagery. First, a time series of the normalized difference vegetation index (NDVI) was constructed to evaluate the phenology of S. alterniflora. Two phenological stages (the senescence stage from November to mid-December and the green-up stage from late April to May) were determined as important for S. alterniflora detection in the study area based on NDVI temporal profiles, spectral reflectance curves of S. alterniflora and its coexistent species, and field surveys. Three phenology feature sets representing three major phenology-based detection strategies were then compared to map S. alterniflora: (1) the single-date imagery acquired within the optimal phenological window, (2) the multitemporal imagery, including four images from the two important phenological windows, and (3) the monthly NDVI time series imagery. Support vector machines and maximum likelihood classifiers were applied on each phenology feature set at different training sample sizes. For all phenology feature sets, the overall results were produced consistently with high mapping accuracies under sufficient training samples sizes, although significantly improved classification accuracies (10%) were obtained when the monthly NDVI time series imagery was employed. The optimal single-date imagery had the lowest accuracies of all detection strategies. The multitemporal analysis demonstrated little reduction in the overall accuracy compared with the

  5. Global Rural-Urban Mapping Project, Version 1 (GRUMPv1): Urban Extent Polygons, Revision 01

    Data.gov (United States)

    National Aeronautics and Space Administration — The primary output of the Global Rural Urban Mapping Project, Version 1 (GRUMPv1) are a series of grids representing estimated population counts and density for the...

  6. Circum-North Pacific tectonostratigraphic terrane map

    Science.gov (United States)

    Nokleberg, Warren J.; Parfenov, Leonid M.; Monger, James W.H.; Baranov, Boris B.; Byalobzhesky, Stanislav G.; Bundtzen, Thomas K.; Feeney, Tracey D.; Fujita, Kazuya; Gordey, Steven P.; Grantz, Arthur; Khanchuk, Alexander I.; Natal'in, Boris A.; Natapov, Lev M.; Norton, Ian O.; Patton, William W.; Plafker, George; Scholl, David W.; Sokolov, Sergei D.; Sosunov, Gleb M.; Stone, David B.; Tabor, Rowland W.; Tsukanov, Nickolai V.; Vallier, Tracy L.; Wakita, Koji

    1994-01-01

    The companion tectonostratigraphic terrane and overlap assemblage of map the Circum-North Pacific presents a modern description of the major geologic and tectonic units of the region. The map illustrates both the onshore terranes and overlap volcanic assemblages of the region, and the major offshore geologic features. The map is the first collaborative compilation of the geology of the region at a scale of 1:5,000,000 by geologists of the Russian Far East, Japanese, Alaskan, Canadian, and U.S.A. Pacific Northwest. The map is designed to be a source of geologic information for all scientists interested in the region, and is designed to be used for several purposes, including regional tectonic analyses, mineral resource and metallogenic analyses (Nokleberg and others, 1993, 1994a), petroleum analyses, neotectonic analyses, and analyses of seismic hazards and volcanic hazards. This text contains an introduction, tectonic definitions, acknowledgments, descriptions of postaccretion stratified rock units, descriptions and stratigraphic columns for tectonostratigraphic terranes in onshore areas, and references for the companion map (Sheets 1 to 5). This map is the result of extensive geologic mapping and associated tectonic studies in the Russian Far East, Hokkaido Island of Japan, Alaska, the Canadian Cordillera, and the U.S.A. Pacific Northwest in the last few decades. Geologic mapping suggests that most of this region can be interpreted as a collage of fault-bounded tectonostratigraphic terranes that were accreted onto continental margins around the Circum-

  7. Maximum Historical Seismic Intensity Map of S. Miguel Island (azores)

    Science.gov (United States)

    Silveira, D.; Gaspar, J. L.; Ferreira, T.; Queiroz, G.

    The Azores archipelago is situated in the Atlantic Ocean where the American, African and Eurasian lithospheric plates meet. The so-called Azores Triple Junction located in the area where the Terceira Rift, a NW-SE to WNW-ESE fault system with a dextral component, intersects the Mid-Atlantic Ridge, with an approximate N-S direction, dominates its geological setting. S. Miguel Island is located in the eastern segment of the Terceira Rift, showing a high diversity of volcanic and tectonic structures. It is the largest Azorean island and includes three active trachytic central volcanoes with caldera (Sete Cidades, Fogo and Furnas) placed in the intersection of the NW-SE Ter- ceira Rift regional faults with an E-W deep fault system thought to be a relic of a Mid-Atlantic Ridge transform fault. N-S and NE-SW faults also occur in this con- text. Basaltic cinder cones emplaced along NW-SE fractures link that major volcanic structures. The easternmost part of the island comprises an inactive trachytic central volcano (Povoação) and an old basaltic volcanic complex (Nordeste). Since the settle- ment of the island, early in the XV century, several destructive earthquakes occurred in the Azores region. At least 11 events hit S. Miguel Island with high intensity, some of which caused several deaths and significant damages. The analysis of historical documents allowed reconstructing the history and the impact of all those earthquakes and new intensity maps using the 1998 European Macrosseismic Scale were produced for each event. The data was then integrated in order to obtain the maximum historical seismic intensity map of S. Miguel. This tool is regarded as an important document for hazard assessment and risk mitigation taking in account that indicates the location of dangerous seismogenic zones and provides a comprehensive set of data to be applied in land-use planning, emergency planning and building construction.

  8. Superstring field theories on super-flag manifolds: superdiff S1/S1 and superdiff S1/super S1

    International Nuclear Information System (INIS)

    Zhao Zhiyong; Wu, Ke; Saito, Takesi

    1987-01-01

    We generalize the geometric approach of Bowick and Rajeev [BR] to superstring field theories. The anomaly is identified with nonvanishing of the Ricci curvature of the super-flag manifold. We explicitly calculate the curvatures of superdiff S 1 /S 1 and superdiff S 1 /superS 1 using super-Toeplitz operator techniques. No regularization is needed in this formalism. The critical dimension D=10 is rediscovered as a result of vanishing curvature of the product bundle over the super-flag manifold. (orig.)

  9. A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations.

    Science.gov (United States)

    Comeron, Josep M; Reed, Jordan; Christie, Matthew; Jacobs, Julia S; Dierdorff, Jason; Eberl, Daniel F; Manak, J Robert

    2016-04-05

    Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1) genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2) identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3) screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv) gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.

  10. MAP17 and SGLT1 protein expression levels as prognostic markers for cervical tumor patient survival.

    Directory of Open Access Journals (Sweden)

    Marco Perez

    Full Text Available MAP17 is a membrane-associated protein that is overexpressed in human tumors. Because the expression of MAP17 increases reactive oxygen species (ROS generation through SGLT1 in cancer cells, in the present work, we investigated whether MAP17 and/or SGLT1 might be markers for the activity of treatments involving oxidative stress, such as cisplatin or radiotherapy. First, we confirmed transcriptional alterations in genes involved in the oxidative stress induced by MAP17 expression in HeLa cervical tumor cells and found that Hela cells expressing MAP17 were more sensitive to therapies that induce ROS than were parental cells. Furthermore, MAP17 increased glucose uptake through SGLT receptors. We then analyzed MAP17 and SGLT1 expression levels in cervical tumors treated with cisplatin plus radiotherapy and correlated the expression levels with patient survival. MAP17 and SGLT1 were expressed in approximately 70% and 50% of cervical tumors of different types, respectively, but they were not expressed in adenoma tumors. Furthermore, there was a significant correlation between MAP17 and SGLT1 expression levels. High levels of either MAP17 or SGLT1 correlated with improved patient survival after treatment. However, the patients with high levels of both MAP17 and SGLT1 survived through the end of this study. Therefore, the combination of high MAP17 and SGLT1 levels is a marker for good prognosis in patients with cervical tumors after cisplatin plus radiotherapy treatment. These results also suggest that the use of MAP17 and SGLT1 markers may identify patients who are likely to exhibit a better response to treatments that boost oxidative stress in other cancer types.

  11. White Oak Creek Watershed topographic map and related materials

    International Nuclear Information System (INIS)

    Farrow, N.D.

    1981-04-01

    On March 22, 1978 a contract was let to Accu-Air Surveys, Inc., of Seymour, Indiana, to produce a topographic map of the White Oak Creek Watershed. Working from photography and ground control surveys, Accu-Air produced a map to ORNL's specifications. The map is in four sections (N.W., N.E., S.W., S.E.) at a scale of 1:2400. Contour intervals are 5 ft (1.5 m) with accented delineations every 25 ft (7.6 m). The scribe method was used for the finished map. Planimetric features, roads, major fence lines, drainage features, and tree lines are included. The ORNL grid is the primary coordinate system which is superimposed on the state plain coordinates

  12. Forsmark Bedrock mapping. Stage 1 (2002) - Outcrop data including fracture data

    Energy Technology Data Exchange (ETDEWEB)

    Stephens, M.B.; Bergman, T.; Andersson, J.; Hermansson, T.; Wahlgren, C.H.; Albrecht, L.; Mikko, H. [Geological Survey of Sweden, Uppsala (Sweden)

    2003-02-01

    Infra-red aerial photographs over the study area, taken at a height of 2700 m, were interpreted in order to locate either the position of outcrops where the bedrock is exposed at the Earth's surface or sites where the bedrock lies beneath a thin (< 50 cm) cover of Quaternary deposits. These data were critical for the planning and execution of the field activities. It was aimed to map all the outcrops in the mainland part of the study area during stage 1 of the project. These data will be integrated with both bedrock analytical data and the interpretations obtained from the study of airborne geophysical data in order to produce a bedrock map over the study area. In order to gain some information on the regional variation in the frequency and orientation of fractures over the candidate area, a documentation of the position and strike and dip of fractures longer than 100 cm was carried out at 44 outcrops. This work will also help in the selection of outcrops where detailed fracture analysis will be carried out during a later stage of the site investigation programme. Field work associated with stage 1 of the project initiated in the candidate area during June 2002. Field activities then continued in the coastal area to the northeast, in the area north of 6700000 N to the northwest of the candidate area and in the inland area to the southwest. Field activities ceased during September 2002. Both descriptive and numerical data from the 1054 observation points have been included in an outcrop database. Primarily on account of the complexity of the outcrops visited and, as a consequence, the longer time required for the field activities, a large part of the area south of road 76 was not mapped during 2002.

  13. Geologic map of Mészáros revisited: Pioneering tectonic mapping of the Transdanubian Range in the early 1980s

    Science.gov (United States)

    Zámolyi, A.; Horváth, F.; Kovács, G.; Timár, G.; Székely, B.

    2009-04-01

    the faults mapped by Mészáros (1983) coincide fairly well with their microtectonic measurements. TR is nowadays interpreted as the uppermost Cretaceous thrust sheet of the Alpine nappes based on the interpretation of seismic surveys (Rumpler & Horváth, 1988; Horváth, 1993) and microtectonic measurements (Kiss & Fodor, 2007). We integrated the map into a GIS environment in order to evaluate the spatial accuracy of tectonic features and deformation style in the study area. Georeferencing was based upon control points applying rubber sheeting. Geological formations were digitized as polygons with their respective attributes (colour- or numerically coded). Three different categories of bounding elements are represented on the map: established, supposed and covered by younger geologic formations. Mészáros put a major emphasis on tectonic features, using 21 different line-types for representation. Digital terrain analysis methods using a 10 m DTM reveal a good correlation of the fault pattern with geomorphologic features, especially in the category of confirmed strike-slip faults. The connection of tectonic elements with the topography is a very anticipatory way of thinking for the early 1980s that became widely accepted by the end of the century. Csontos, L., Tari, G., Bergerat, F., Fodor, L. 1991. Tectonophysics, 199, 73-91. Horváth, F. 1993. In: Cloething, S., Sassi, W. & Horváth, F. (eds.) Tectonophysics, 226, 333-358. Kiss, A., Fodor, L. I. 2007. Geologica Carpathica, 58(5), 465-475. Mészáros, J. 1983. Ann. Rep. Hung. Geol. Inst. 1981, 485-502. Prinz, Gy. 1926. Danubia könyvkiadó, Pécs, 202 p. Rumpler, J., Horváth, F. 1988. In: L.H. Royden and F. Horváth (eds.) AAPG Mem. 45, Tulsa, Okl., 153-169p. Uhlig, V. 1907. Sitz. Ber. Akad. Wiss., math.- nat., Kl. 116(1), 871-982.

  14. GIS integration of the 1:75,000 Romanian topographic map series from the World War I

    Science.gov (United States)

    Timár, G.; Mugnier, C. J.

    2009-04-01

    During the WWI, the Kingdom of Romania developed a 1:75,000 topographic map series, covering not only the actual territory of the country (the former Danube Principalities and Dobrogea) but also Bessarabia (now the Republic of Moldova), which was under Russian rule. The map sheets were issued between 1914 and 1917. The whole map consists of two zones; Columns A-F are the western zone, while Columns G-Q are belonging to the eastern one. To integrate the scanned map sheets to a geographic information system (GIS), the parameters of the map projection and the geodetic datum should be defined as well as the sheet labelling system. The sheets have no grid lines indicated; most of them have latitude and longitude lines but some of them have no coordinate descriptions. The sheets, however, can be rectified using their four corners as virtual control points, and using the following grid and datum parameters: Eastern zone: • Projection type: Bonne. • Projection center: latitude=46d 30m; longitude=27d 20m 13.35s (from Greenwich). • Base ellipsoid: Bessel 1841 • Datum parameters (from local to WGS84): dX=+875 m; dY=-119 m; dZ=+313 m. • Sheet size: 40*40 kilometers, projection center is the NW corner of the 779 (Column L; Row VII) sheet. Western zone: • Projection type: Bonne. • Projection center: latitude=45d; longitude=26d 6m 41.18s (from Greenwich); • Base ellipsoid: Bessel 1841 • Datum parameters (from local to WGS84): dX=+793 m; dY=+364 m; dZ=+173 m. • Sheet size: 0.6*0.4 grad (new degrees), except Column F, which is wider to east to fill the territory to the zone boundary. In Columns E and F geographic coordinates are indicated in new degrees, with the prime meridian of Bucharest. Apart from the system of columns and rows, each sheet has its own label of three or four digit. The last two digit correspond to the column number (69 for Column A going up to 84 for Column Q) while the first digit(s) refer directly to row number (1-15). During the

  15. Mapping the backbone of science.

    Energy Technology Data Exchange (ETDEWEB)

    Klavans, Richard (Indiana University, Bloomington, IN); BÞorner, Katy (Strategies for Science & Technology, Incorporation, Berwyn, PA); Boyack, Kevin W.

    2004-11-01

    This paper presents a new map representing the structure of all of science, based on journal articles, including both the natural and social sciences. Similar to cartographic maps of our world, the map of science provides a bird's eye view of today's scientific landscape. It can be used to visually identify major areas of science, their size, similarity, and interconnectedness. In order to be useful, the map needs to be accurate on a local and on a global scale. While our recent work has focused on the former aspect, this paper summarizes results on how to achieve structural accuracy. Eight alternative measures of journal similarity were applied to a data set of 7,121 journals covering over 1 million documents in the combined Science Citation and Social Science Citation Indexes. For each journal similarity measure we generated two-dimensional spatial layouts using the force-directed graph layout tool, VxOrd. Next, mutual information values were calculated for each graph at different clustering levels to give a measure of structural accuracy for each map. The best co-citation and inter-citation maps according to local and structural accuracy were selected and are presented and characterized. These two maps are compared to establish robustness. The inter-citation map is then used to examine linkages between disciplines. Biochemistry appears as the most interdisciplinary discipline in science.

  16. Mapping Women’s and Gender Studies in the Academic Field in Slovenia

    Directory of Open Access Journals (Sweden)

    Milica Antić Gaber

    2017-06-01

    Full Text Available The aim of the present paper is to map the development of women’s and gender studies (WGS in the academic field in Slovenia. Slovenia is the first of the former Yugoslav state republics in which WGS have succeeded in entering the academic field and becoming part of institutionalised university study. In this paper we will ask the following questions: How, when and why did this happen? How was this connected to women’s and feminist movements and politics regarding women’s issues and demands? What were the obstacles in this process? Who were the agents and what were the factors that supported demands for the incorporation of WGS in academia? How has the field evolved in the last few decades? What were the phases of this development? Which fields were the forerunners, which were the late-comers and which are still left aside? What are the thematic scopes taught in WGS courses? In which degrees are the courses offered and what are their modules? Who teaches them? The mapping in this paper is mainly based on primary sources of university programmes and their curricula at faculties of the University of Ljubljana, as well as on interviews with important agents in the field.

  17. Direct stacking of sequence-specific nuclease-induced mutations to produce high oleic and low linolenic soybean oil.

    Science.gov (United States)

    Demorest, Zachary L; Coffman, Andrew; Baltes, Nicholas J; Stoddard, Thomas J; Clasen, Benjamin M; Luo, Song; Retterath, Adam; Yabandith, Ann; Gamo, Maria Elena; Bissen, Jeff; Mathis, Luc; Voytas, Daniel F; Zhang, Feng

    2016-10-13

    The ability to modulate levels of individual fatty acids within soybean oil has potential to increase shelf-life and frying stability and to improve nutritional characteristics. Commodity soybean oil contains high levels of polyunsaturated linoleic and linolenic acid, which contribute to oxidative instability - a problem that has been addressed through partial hydrogenation. However, partial hydrogenation increases levels of trans-fatty acids, which have been associated with cardiovascular disease. Previously, we generated soybean lines with knockout mutations within fatty acid desaturase 2-1A (FAD2-1A) and FAD2-1B genes, resulting in oil with increased levels of monounsaturated oleic acid (18:1) and decreased levels of linoleic (18:2) and linolenic acid (18:3). Here, we stack mutations within FAD2-1A and FAD2-1B with mutations in fatty acid desaturase 3A (FAD3A) to further decrease levels of linolenic acid. Mutations were introduced into FAD3A by directly delivering TALENs into fad2-1a fad2-1b soybean plants. Oil from fad2-1a fad2-1b fad3a plants had significantly lower levels of linolenic acid (2.5 %), as compared to fad2-1a fad2-1b plants (4.7 %). Furthermore, oil had significantly lower levels of linoleic acid (2.7 % compared to 5.1 %) and significantly higher levels of oleic acid (82.2 % compared to 77.5 %). Transgene-free fad2-1a fad2-1b fad3a soybean lines were identified. The methods presented here provide an efficient means for using sequence-specific nucleases to stack quality traits in soybean. The resulting product comprised oleic acid levels above 80 % and linoleic and linolenic acid levels below 3 %.

  18. Global Geological Map of Venus

    Science.gov (United States)

    Ivanov, M. A.

    2008-09-01

    Introduction: The Magellan SAR images provide sufficient data to compile a geological map of nearly the entire surface of Venus. Such a global and selfconsistent map serves as the base to address the key questions of the geologic history of Venus. 1) What is the spectrum of units and structures that makes up the surface of Venus [1-3]? 2) What volcanic/tectonic processes do they characterize [4-7]? 3) Did these processes operated locally, regionally, or globally [8- 11]? 4) What are the relationships of relative time among the units [8]? 5) At which length-scale these relationships appear to be consistent [8-10]? 6) What is the absolute timing of formation of the units [12-14]? 7) What are the histories of volcanism, tectonics and the long-wavelength topography on Venus? 7) What model(s) of heat loss and lithospheric evolution [15-21] do these histories correspond to? The ongoing USGS program of Venus mapping has already resulted in a series of published maps at the scale 1:5M [e.g. 22-30]. These maps have a patch-like distribution, however, and are compiled by authors with different mapping philosophy. This situation not always results in perfect agreement between the neighboring areas and, thus, does not permit testing geological hypotheses that could be addressed with a self-consistent map. Here the results of global geological mapping of Venus at the scale 1:10M is presented. The map represents a contiguous area extending from 82.5oN to 82.5oS and comprises ~99% of the planet. Mapping procedure: The map was compiled on C2- MIDR sheets, the resolution of which permits identifying the basic characteristics of previously defined units. The higher resolution images were used during the mapping to clarify geologic relationships. When the map was completed, its quality was checked using published USGS maps [e.g., 22-30] and the catalogue of impact craters [31]. The results suggest that the mapping on the C2-base provided a highquality map product. Units and

  19. Introduction to "Mapping Vietnameseness"

    Directory of Open Access Journals (Sweden)

    Hue-Tam Ho Tai

    2016-09-01

    Full Text Available Vietnam and China are currently engaged in a map war, with each country using ancient maps to buttress its claims to territorial sovereignty over some uninhabited islands in the South China Sea (in Chinese terminology, also known as the Eastern Sea (in Vietnamese. But what do maps in fact represent? What is meant by “territory”? How are territorial limits conceived? These questions were raised in a May 2015 workshop inspired by Thongchai Winichakul’s Siam Mapped: A History of the Geo-Body of a Nation (1994, a groundbreaking book that traces the transformation of Thai geographical consciousness as a result of Siam’s encounter with Western powers in the nineteenth century. While many of Thongchai’s insights apply to the Vietnamese case, as the first of the three articles included in this special issue of Cross-Currents shows, some of the 2015 workshop participants’ conclusions departed from his, especially regarding the formation of a Vietnamese geographical consciousness before the colonial period.[i] This is true of the other two papers, which focus specifically on the construction of borders and the associated production of maps in the nineteenth century before French colonial conquest... Notes 1 Thanks are due to the Max Planck Institute for the Study of Religious and Ethnic Change in Gottingen, Germany, for its gracious hosting and generous funding of the conference, together with the Asia Center of Harvard University.

  20. Curvature of super Diff(S1)/S1

    International Nuclear Information System (INIS)

    Oh, P.; Ramond, P.

    1987-01-01

    Motivated by the work of Bowick and Rajeev, we calculate the curvature of the infinite-dimensional flag manifolds Diff(S 1 )/S 1 and Super Diff(S 1 )/S 1 using standard finite-dimensional coset space techniques. We regularize the infinite by ζ-function regularization and recover the conformal and superconformal anomalies respectively for a specific choice of the torsion. (orig.)

  1. Mapping the Extent of M82's outlfows with VIRUS-P

    Science.gov (United States)

    Indahl, Briana; Hill, Gary J.; Drory, Niv; McLinden, Emily

    2017-06-01

    Starburst-driven outflows (SBDOs) and other feedback processes play a critical role in the evolution of galaxies through the regulation and disruption of star formation. However, our ability to observe and quantify feedback from SBDOs directly has been limited by the inability to obtain the spectroscopy needed for physical diagnostics over the large areas of local SBDOs. We present integral field spectroscopy taken with the George and Cynthia Mitchell Spectrograph (VIRUS-P) on the 2.7 meter Harlan J. Smith Telescope at McDonald Observatory mapping the full extent of M82’s northern outflow out to ~12kpc covering ~139 square arcminutes. We measured line ratios ([OIII]/Hβ, [OI]/Hα, [NII]/Hα), [SII]/Hα) for each spaxel in our fields. Using Ionization Diagnostic Diagrams (IDDs) we spatially map shock dominated regions which we show trace the biconical structure of the outflow. M82 is a local galaxy (z~0.000677) and the classical example of a starburst galaxy with vigorous outflows. As a result it has been comprehensively studied for nearly 50 years. However, we present the most sensitive and extensive map of the warm ionized gas to date from the disk to the Hα cap at ~12kpc.

  2. FISH and AgNor mapping of the 45S and 5S rRNA genes in wild and cultivated species of Capsicum (Solananceae).

    Science.gov (United States)

    Scaldaferro, Marisel A; da Cruz, M Victoria Romero; Cecchini, Nicolás M; Moscone, Eduardo A

    2016-02-01

    Chromosome number and position of rDNA were studied in 12 wild and cultivated species of the genus Capsicum with chromosome numbers x = 12 and x = 13 (22 samples). For the first time in these species, the 5S and 45S rRNA loci were localized and physically mapped using two-color fluorescence in situ hybridization and AgNOR banding. We focused on the comparison of the results obtained with both methods with the aim of accurately revealing the real functional rRNA genes. The analyzes were based on a previous work that reported that the 18S-5.8S-25S loci mostly coincide with GC-rich heterochromatic regions and likely have given rise to satellite DNAs, which are not active genes. These data show the variability of rDNA within karyotypes of the genus Capsicum, providing anchor points for (comparative) genetic maps. In addition, the obtained information might be useful for studies on evolution of repetitive DNA.

  3. Preliminary Geologic Map of the Cook Inlet Region, Alaska-Including Parts of the Talkeetna, Talkeetna Mountains, Tyonek, Anchorage, Lake Clark, Kenai, Seward, Iliamna, Seldovia, Mount Katmai, and Afognak 1:250,000-scale Quadrangles

    Science.gov (United States)

    Wilson, Frederic H.; Hults, Chad P.; Schmoll, Henry R.; Haeussler, Peter J.; Schmidt, Jeanine M.; Yehle, Lynn A.; Labay, Keith A.; Shew, Nora B.

    2009-01-01

    The growth in the use of Geographic Information Systems (GIS) has highlighted the need for digital geologic maps that have been attributed with information about age and lithology. Such maps can be conveniently used to generate derivative maps for manifold special purposes such as mineral-resource assessment, metallogenic studies, tectonic studies, and environmental research. This report is part of a series of integrated geologic map databases that cover the entire United States. Three national-scale geologic maps that portray most or all of the United States already exist; for the conterminous U.S., King and Beikman (1974a,b) compiled a map at a scale of 1:2,500,000, Beikman (1980) compiled a map for Alaska at 1:2,500,000 scale, and for the entire U.S., Reed and others (2005a,b) compiled a map at a scale of 1:5,000,000. A digital version of the King and Beikman map was published by Schruben and others (1994). Reed and Bush (2004) produced a digital version of the Reed and others (2005a) map for the conterminous U.S. The present series of maps is intended to provide the next step in increased detail. State geologic maps that range in scale from 1:100,000 to 1:1,000,000 are available for most of the country, and digital versions of these state maps are the basis of this product. The digital geologic maps presented here are in a standardized format as ARC/INFO export files and as ArcView shape files. The files named __geol contain geologic polygons and line (contact) attributes; files named __fold contain fold axes; files named __lin contain lineaments; and files named __dike contain dikes as lines. Data tables that relate the map units to detailed lithologic and age information accompany these GIS files. The map is delivered as a set 1:250,000-scale quadrangle files. To the best of our ability, these quadrangle files are edge-matched with respect to geology. When the maps are merged, the combined attribute tables can be used directly with the merged maps to make

  4. A surface plasmon resonance assay for characterisation and epitope mapping of anti-GLP-1 antibodies.

    Science.gov (United States)

    Thomsen, Lasse; Gurevich, Leonid

    2018-04-19

    The incretin hormone glucagon-like peptide-1 (GLP-1) has been subject to substantial pharmaceutical research regarding the treatment of type 2 diabetes mellitus. However, quantification of GLP-1 levels remains complicated due to the low circulation concentration and concurrent existence of numerous metabolites, homologous peptides, and potentially introduced GLP-1 receptor agonists. Surface plasmon resonance (SPR) facilitates real-time monitoring allowing a more detailed characterisation of the interaction compared with conventional enzyme-linked immunosorbent assays (ELISA). In this paper, we describe the development of the first SPR assays for characterisation of anti-GLP-1 antibodies for ELISA purposes. Binding responses were obtained on covalently immobilised anti-GLP-1 antibodies at 12°C, 25°C, and 40°C and fitted to a biomolecular (1:1) interaction model showing association rates of 1.01 × 10 3 to 4.54 × 10 3  M -1  s -1 and dissociation rates of 3.56 × 10 -5 to 1.56 × 10 -3  s -1 leading to affinities of 35.2 to 344 nM, depending on the temperature. Determination of thermodynamic properties revealed an enthalpy driven interaction (ΔH polar amino acids (ΔC p  < 0). Pair-wise epitope mapping was performed on captured anti-GLP-1 antibodies followed by subsequent interaction with GLP-1 (7-36) and other anti-GLP-1 antibodies. A global evaluation of every binding response led to an epitope map elucidating the potential of various anti-GLP-1 antibody pairs for sandwich ELISA and hence pinpointing the optimal antibody combinations. The SPR assays proved capable of providing vital information for ELISA development endorsing it as a useful optimisation tool. Copyright © 2018 John Wiley & Sons, Ltd.

  5. Zebrafish Model of NF1 for Structure-Function Analysis, Mechanisms of Glial Tumorigenesis, and Chemical Biology

    Science.gov (United States)

    2015-08-01

    models. Zinc-finger nucleases (ZFNs) are chimeric fusions between a zinc-finger protein (ZFP) and the nuclease domain of FokI (Urnov et al., 2010). ZFNs...reference line. Once a target site is chosen, the user can click on the ZFN entry (QueryID; see Fig. 4B) for details about each construct (Fig. 4C...Zhong, Y. (1997). Requirement of Drosophila NF1 for activation of adenylyl cyclase by PACAP38-like neuro- peptides . Science 276, 795–798.ports 8, 1265

  6. DATA QUALIFICATION REPORT: DATA QUALIFICATION REPORT FOR 1991 1:1200 TOPOGRAPHIC MAPS FOR USE ON THE YUCCA MOUNTAIN PROJECT

    International Nuclear Information System (INIS)

    Knop, M.F.; Grant, T.A.; Bonisolli, R.W.

    2005-01-01

    This Data Qualification Report (DQR) is prepared in accordance with the provisions of AP-SIII.2Q, Rev. 0, ICN 3, Qualification of Unqualified Data and the Documentation of Rationale for Accepted Data and Data Qualification Plan for 1991 Topographic Maps 1:1200 Scale for use on the Yucca Mountain Project, DQP-WHS-CI-000001, Rev. 00 (BSC 2002a). This DQR presents an evaluation of a set of 90 topographic sheets at 1:1200 scale (and an associated electronic file) that covers an approximate 18 square mile area surrounding the proposed Yucca Mountain Project repository surface facilities location in Midway Valley, Nevada. These maps, that require qualification, are now being used to determine the physical characteristics of watershed sub-areas, interconnecting channels, and drainage channel cross-sections for hydrologic engineering studies of the north portal pad and vicinity. The result of this effort is to qualify one data tracking number (DTN) containing the electronic version of the mapping data. This DTN is: M09906COV98462.000. Coverage: TOP02FTS. The underlying quality assurance (QA) issue associated with these topographic maps is that the maps were originally designated as not for use in the design of items important to safety, waste isolation, and/or of programmatic importance. The maps were therefore generated outside the U.S. Department of Energy Office of Civilian Radioactive Waste Management (OCRWM) QA program. Based on a comparison with corroborating information, this report concludes that the topographic maps are qualified. The comparison found that the mapping was reasonably accurate when compared with other mapping and survey data within the coverage area of the maps. Relative map accuracy was found to be very good and suitable for the hydrologic engineering studies being considered. Absolute accuracy is good but could not be demonstrated to comply with national map accuracy standards. Point locations that require high absolute accuracy should be

  7. The mapping and preparation of human resources for NPP’S operation and maintenance in Indonesia

    International Nuclear Information System (INIS)

    Moch-Djoko Birmano; Yohanes Dwi Anggoro

    2013-01-01

    The preparation of the competent human resources (HRs) is one of the basic infrastructure of NPP’s development. IAEA recommends that at the initial activity in preparation of human resources for NPP is doing Business Process Mapping by identifying the knowledge, skills and abilities of required human resources to carry out the operation and maintenance of NPPs. This study aims to mapping and preparing of human resources for NPP’s operation and maintenance in Indonesia. The method used are mapping business processes at operation and maintenance stage of NPP, identifying positions, conducting surveys with questionnaires and calculations, and data analysis. Surveys and questionnaires to determine the level of technical competence of personnel in BATAN at operation and maintenance stage. Analysis using the Method of Gap Analysis with human resources Competency Standards Criteria based on technical competence qualifications. This study uses the assumption that the nuclear power plant will be built 2 units (twin) and start operation in 2027. The results showed that from the aspect of education, BATAN able to meet the needs of human resources at 53.64 to 73.75%. While from the aspect of training and specific work experience, participation level of BATAN’s human resources is still very low of IAEA requirements. This case caused because young human resources in BATAN who have educational qualifications, experience, training and technical certifications in the field of operation and maintenance of nuclear power plants is still limited. Based on this, there should be preparation of NPP’s human resources with establish NPP’s human resources development program based on required qualifications. (author)

  8. S1P in HDL promotes interaction between SR-BI and S1PR1 and activates S1PR1-mediated biological functions: calcium flux and S1PR1 internalization.

    Science.gov (United States)

    Lee, Mi-Hye; Appleton, Kathryn M; El-Shewy, Hesham M; Sorci-Thomas, Mary G; Thomas, Michael J; Lopes-Virella, Maria F; Luttrell, Louis M; Hammad, Samar M; Klein, Richard L

    2017-02-01

    HDL normally transports about 50-70% of plasma sphingosine 1-phosphate (S1P), and the S1P in HDL reportedly mediates several HDL-associated biological effects and signaling pathways. The HDL receptor, SR-BI, as well as the cell surface receptors for S1P (S1PRs) may be involved partially and/or completely in these HDL-induced processes. Here we investigate the nature of the HDL-stimulated interaction between the HDL receptor, SR-BI, and S1PR1 using a protein-fragment complementation assay and confocal microscopy. In both primary rat aortic vascular smooth muscle cells and HEK293 cells, the S1P content in HDL particles increased intracellular calcium concentration, which was mediated by S1PR1. Mechanistic studies performed in HEK293 cells showed that incubation of cells with HDL led to an increase in the physical interaction between the SR-BI and S1PR1 receptors that mainly occurred on the plasma membrane. Model recombinant HDL (rHDL) particles formed in vitro with S1P incorporated into the particle initiated the internalization of S1PR1, whereas rHDL without supplemented S1P did not, suggesting that S1P transported in HDL can selectively activate S1PR1. In conclusion, these data suggest that S1P in HDL stimulates the transient interaction between SR-BI and S1PRs that can activate S1PRs and induce an elevation in intracellular calcium concentration.

  9. Solving topological field theories on mapping tori

    International Nuclear Information System (INIS)

    Blau, M.; Jermyn, I.; Thompson, G.

    1996-05-01

    Using gauge theory and functional integral methods, we derive concrete expressions for the partition functions of BF theory and the U(1 modul 1) model of Rozansky and Saleur on Σ x S 1 , both directly and using equivalent two-dimensional theories. We also derive the partition function on a certain non-abelian generalization of the U(1 modul 1) model on mapping tori and hence obtain explicit expressions for the Ray-Singer torsion on these manifolds. Extensions of these results to BF and Chern-Simons theories on mapping tori are also discussed. The topological field theory actions of the equivalent two- dimensional theories we find have the interesting property of depending explicitly on the diffeomorphism defining the mapping torus while the quantum field theory is sensitive only to its isomorphism class defining the mapping torus as a smooth manifold. (author). 20 refs

  10. Usability Assessment of the Missouri Cancer Registry’s Published Interactive Mapping Reports: Round One

    Science.gov (United States)

    Jackson-Thompson, Jeannette; Schmaltz, Chester Lee

    2017-01-01

    Background  Many users of spatial data have difficulty interpreting information in health-related spatial reports. The Missouri Cancer Registry and Research Center (MCR-ARC) has produced interactive reports for several years. These reports have never been tested for usability. Objective  The aims of this study were to: (1) conduct a multi-approach usability testing study to understand ease of use (user friendliness) and user satisfaction; and (2) evaluate the usability of MCR-ARC’s published InstantAtlas reports. Methods   An institutional review board (IRB) approved mixed methodology usability testing study using a convenience sample of health professionals. A recruiting email was sent to faculty in the Master of Public Health program and to faculty and staff in the Department of Health Management and Informatics at the University of Missouri-Columbia. The study included 7 participants. The test included a pretest questionnaire, a multi-task usability test, and the System Usability Scale (SUS). Also, the researchers collected participants’ comments about the tested maps immediately after every trial. Software was used to record the computer screen during the trial and the participants’ spoken comments. Several performance and usability metrics were measured to evaluate the usability of MCR-ARC’s published mapping reports. Results Of the 10 assigned tasks, 6 reached a 100% completion success rate, and this outcome was relative to the complexity of the tasks. The simple tasks were handled more efficiently than the complicated tasks. The SUS score ranged between 20-100 points, with an average of 62.7 points and a median of 50.5 points. The tested maps’ effectiveness outcomes were better than the efficiency and satisfaction outcomes. There was a statistically significant relationship between the subjects’ performance on the study test and the users’ previous experience with geographic information system (GIS) tools (P=.03). There were no

  11. Topographic mapping

    Science.gov (United States)

    ,

    2008-01-01

    The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

  12. Disagreement between splenic switch-off and myocardial T1-mapping after caffeine intake.

    Science.gov (United States)

    Kuijpers, Dirkjan; van Dijk, Randy; van Assen, Marly; Kaandorp, Theodorus A M; van Dijkman, Paul R M; Vliegenthart, Rozemarijn; van der Harst, Pim; Oudkerk, Matthijs

    2018-04-01

    Caffeine is an adenosine receptor antagonist and a possible cause of inadequate stress perfusion. Splenic switch-off (SSO) and splenic rest-stress T1-mapping have been proposed as indicators of stress adequacy during perfusion cardiac magnetic resonance (CMR). We compared myocardial rest-stress T1-mapping with SSO and splenic rest-stress T1-mapping in patients with and without recent coffee intake. We analyzed 344 consecutive patients suspected of myocardial ischemia with adenosine perfusion CMR. All 146 normal CMR studies with a normal T1-rest of the myocardium, used as standard of reference, were included and divided in two groups. 22 patients accidentally ingested coffee < 4 h before CMR, compared to control group of 124 patients without self-reported coffee intake. Two independent readers graded SSO visually. T1-reactivity (ΔT1) was defined as percentual difference in T1-rest and T1-stress. Follow-up data were extracted from electronic patients records. In patients with recent coffee intake SSO was identified in 96%, which showed no significant difference with SSO in controls (94%, p = 0.835), however event rates were significantly different (13.6 and 0.8%, respectively (p < 0.001), median FU 17 months). Myocardial ΔT1 in the coffee group (- 5.2%) was significantly lower compared to control (+ 4.0%, p < 0.001), in contrast to the splenic ΔT1 (- 3.7 and - 4.0%, p = 0.789). The splenic T1-mapping results failed to predict false negative results. SSO and splenic rest-stress T1-mapping are not reliable indicators of stress adequacy in patients with recent coffee intake. Therefore, the dark spleen sign does not indicate adequate myocardial stress in patients with recent caffeine intake. Myocardial rest-stress T1-mapping is an excellent indicator of stress adequacy during adenosine perfusion CMR.

  13. Curriculum Mapping of the Master’s Program in Pharmacy in Slovenia with the PHAR-QA Competency Framework

    Science.gov (United States)

    Gmeiner, Tanja; Horvat, Nejc; Kos, Mitja; Obreza, Aleš; Vovk, Tomaž; Grabnar, Iztok; Božič, Borut

    2017-01-01

    This article presents the results of mapping the Slovenian pharmacy curriculum to evaluate the adequacy of the recently developed and validated European Pharmacy Competences Framework (EPCF). The mapping was carried out and evaluated progressively by seven members of the teaching staff at the University of Ljubljana’s Faculty of Pharmacy. Consensus was achieved by using a two-round modified Delphi technique to evaluate the coverage of competences in the current curriculum. The preliminary results of the curriculum mapping showed that all of the competences as defined by the EPCF are covered in Ljubljana’s academic program. However, because most EPCF competences cover healthcare-oriented pharmacy practice, a lack of competences was observed for the drug development and production perspectives. Both of these perspectives are important because a pharmacist is (or should be) responsible for the entire process, from the development and production of medicines to pharmaceutical care in contact with patients. Nevertheless, Ljubljana’s graduates are employed in both of these pharmaceutical professions in comparable proportions. The Delphi study revealed that the majority of differences in scoring arise from different perspectives on the pharmacy profession (e.g., community, hospital, industrial, etc.). Nevertheless, it can be concluded that curriculum mapping using the EPCF is very useful for evaluating and recognizing weak and strong points of the curriculum. However, the competences of the framework should address various fields of the pharmacist’s profession in a more balanced way. PMID:28970436

  14. Mixed ligand complexes of Cu(II)/Zn(II) ions containing (m-)/(p-) carboxylato phenyl azo pentane 2,4-dione and 2,2'-bipyridine/1,10 phenanthroline: Synthesis, characterization, DNA binding, nuclease and topoisomerase I inhibitory activity.

    Science.gov (United States)

    Hasan, Md Amin; Kumari, Niraj; Singh, Kanhaiya; Singh, Kiran; Mishra, Lallan

    2016-01-05

    Metal complexes of type [Cu(L1H)2(bpy)] (1), [Zn(L1H)2(bpy)] (2), [Cu(L2H)2(bpy)] (3) and [Cu(L2H)2(Phen)] (4) (L1H2=3-[N'-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, L2H2=4-[N'-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, bpy=2,2'-bipyridine, Phen=1,10 phenanthroline) are synthesized and characterized using spectroscopic techniques (FT-IR, (1)H NMR, (13)C NMR, electronic absorption and emission) and elemental analysis data. The assembly of the complexes involving intramolecular H-bonding is displayed using corresponding crystal structure. Binding of the complexes separately with Calf Thymus DNA is monitored using UV-vis spectral titrations. The displacement of ethidium bromide (EB) bound to DNA by the complexes, in phosphate buffer solution (pH∼7.2) is monitored using fluorescence spectral titrations. Nuclease activity of the complexes follow the order 4>3>1>2. The gel electrophoretic mobility assay measurement in presence of minor groove binder 4',6-diamidino-2-phenylindole (DAPI), suggests that complexes preferably bind with the minor groove of DNA. Topoisomerase I inhibitory activity of the complexes 3 and 4 inhibit topoisomerase I activity with IC50 values of 112 and 87μM respectively. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Participation of the Pennsylvania State University in the MAP3S precipitation chemistry network

    International Nuclear Information System (INIS)

    Lamb, D.; de Pena, R.G.

    1991-04-01

    The Meteorology Department of the Pennsylvania State University collected precipitation in central Pennsylvania for more than 14 years on behalf of the Multistate Atmospheric Power Production Pollution Study (MAP3S). The MAP3S protocol, based on the sampling of precipitation from individual meteorological events over a long period of time, has allowed both for the development of a chemical climatology of precipitation in the eastern region of the United States and for a vastly improved understanding of the atmospheric processes responsible for wet acidic deposition. The precipitation chemistry data from the Penn State MAP3S site provide evidence of links to the anthropogenic emissions of sulfur dioxide and oxidant precursors. There is now little doubt that the free acidity in the precipitation of the region is due to the presence of unneutralized sulfate in the aqueous phase. In the absence of significant sources of this sulfur species and in view of supplemental enrichment studies, it is concluded that the sulfate enters cloud and rain water primarily through the aqueous-phase oxidation of sulfur dioxide emitted into the air within the geographical region of deposition. Within the source region the local abundances of sulfur dioxide often exceed those of the oxidants, so the depositions of sulfate and free acidity tend to be modulated by the availability of the strong oxidants. As a consequence, the deposition of sulfate exhibits a very strong seasonal dependence and little response to changes in the emissions of sulfur dioxide

  16. Assessment of acute kidney injury with T1 mapping MRI following solid organ transplantation

    Energy Technology Data Exchange (ETDEWEB)

    Peperhove, Matti; Vo Chieu, Van Dai; Gutberlet, Marcel; Hartung, Dagmar; Tewes, Susanne; Wacker, Frank; Hueper, Katja [Hannover Medical School, Diagnostic and Interventional Radiology, Hannover (Germany); Jang, Mi-Sun; Gwinner, Wilfried; Haller, Hermann; Gueler, Faikah [Nephrology, Hannover Medical School, Hannover (Germany); Warnecke, Gregor; Fegbeutel, Christiane; Haverich, Axel [Hannover Medical School, Cardiothoracic, Transplantation and Vascular Surgery, Hannover (Germany); Lehner, Frank [Hannover Medical School, General, Abdominal and Transplant Surgery, Hannover (Germany); Braesen, Jan Hinrich [Pathology, Hannover Medical School, Hannover (Germany)

    2018-01-15

    To evaluate T1 mapping as a non-invasive, functional MRI biomarker in patients shortly after solid organ transplantation to detect acute postsurgical kidney damage and to correlate T1 times with renal function. 101 patients within 2 weeks after solid organ transplantation (49 kidney transplantation, 52 lung transplantation) and 14 healthy volunteers were examined by MRI between July 2012 and April 2015 using the modified Look-Locker inversion recovery (MOLLI) sequence. T1 times in renal cortex and medulla and the corticomedullary difference were compared between groups using one-way ANOVA adjusted for multiple comparison with the Tukey test, and T1 times were correlated with renal function using Pearson's correlation. Compared to healthy volunteers T1 times were significantly increased after solid organ transplantation in the renal cortex (healthy volunteers 987 ± 102 ms; kidney transplantation 1299 ± 101 ms, p < 0.001; lung transplantation 1058 ± 96 ms, p < 0.05) and to a lesser extent in the renal medulla. Accordingly, the corticomedullary difference was diminished shortly after solid organ transplantation. T1 changes were more pronounced following kidney compared to lung transplantation, were associated with the stage of renal impairment and significantly correlated with renal function. T1 mapping may be helpful for early non-invasive assessment of acute kidney injury and renal pathology following major surgery such as solid organ transplantation. (orig.)

  17. Assessment of acute kidney injury with T1 mapping MRI following solid organ transplantation

    International Nuclear Information System (INIS)

    Peperhove, Matti; Vo Chieu, Van Dai; Gutberlet, Marcel; Hartung, Dagmar; Tewes, Susanne; Wacker, Frank; Hueper, Katja; Jang, Mi-Sun; Gwinner, Wilfried; Haller, Hermann; Gueler, Faikah; Warnecke, Gregor; Fegbeutel, Christiane; Haverich, Axel; Lehner, Frank; Braesen, Jan Hinrich

    2018-01-01

    To evaluate T1 mapping as a non-invasive, functional MRI biomarker in patients shortly after solid organ transplantation to detect acute postsurgical kidney damage and to correlate T1 times with renal function. 101 patients within 2 weeks after solid organ transplantation (49 kidney transplantation, 52 lung transplantation) and 14 healthy volunteers were examined by MRI between July 2012 and April 2015 using the modified Look-Locker inversion recovery (MOLLI) sequence. T1 times in renal cortex and medulla and the corticomedullary difference were compared between groups using one-way ANOVA adjusted for multiple comparison with the Tukey test, and T1 times were correlated with renal function using Pearson's correlation. Compared to healthy volunteers T1 times were significantly increased after solid organ transplantation in the renal cortex (healthy volunteers 987 ± 102 ms; kidney transplantation 1299 ± 101 ms, p < 0.001; lung transplantation 1058 ± 96 ms, p < 0.05) and to a lesser extent in the renal medulla. Accordingly, the corticomedullary difference was diminished shortly after solid organ transplantation. T1 changes were more pronounced following kidney compared to lung transplantation, were associated with the stage of renal impairment and significantly correlated with renal function. T1 mapping may be helpful for early non-invasive assessment of acute kidney injury and renal pathology following major surgery such as solid organ transplantation. (orig.)

  18. ORF Alignment: NC_000913 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available junction ... nuclease; resolution of structures; repair; Holliday ... junction nuclease [Esche...richia coli K12] gb|AAG56853.1| ... Holliday junction nuclease; resolution of structures...|NP_288300.1| Holliday junction nuclease; ... resolution of structures; repair [Escherichia coli ...

  19. ORF Alignment: NC_002695 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available junction ... nuclease; resolution of structures; repair; Holliday ... junction nuclease [Esche...richia coli K12] gb|AAG56853.1| ... Holliday junction nuclease; resolution of structures...|NP_288300.1| Holliday junction nuclease; ... resolution of structures; repair [Escherichia coli ...

  20. ORF Alignment: NC_004431 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available junction ... nuclease; resolution of structures; repair; Holliday ... junction nuclease [Esche...richia coli K12] gb|AAG56853.1| ... Holliday junction nuclease; resolution of structures...|NP_288300.1| Holliday junction nuclease; ... resolution of structures; repair [Escherichia coli ...

  1. ORF Alignment: NC_002655 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available junction ... nuclease; resolution of structures; repair; Holliday ... junction nuclease [Esche...richia coli K12] gb|AAG56853.1| ... Holliday junction nuclease; resolution of structures...|NP_288300.1| Holliday junction nuclease; ... resolution of structures; repair [Escherichia coli ...

  2. Native T1 mapping of the heart - a pictorial review.

    Science.gov (United States)

    Germain, Philippe; El Ghannudi, Soraya; Jeung, Mi-Young; Ohlmann, Patrick; Epailly, Eric; Roy, Catherine; Gangi, Afshin

    2014-01-01

    T1 mapping is now a clinically feasible method, providing pixel-wise quantification of the cardiac structure's T1 values. Beyond focal lesions, well depicted by late gadolinium enhancement sequences, it has become possible to discriminate diffuse myocardial alterations, previously not assessable by noninvasive means. The strength of this method includes the high reproducibility and immediate clinical applicability, even without the use of contrast media injection (native or pre-contrast T1). The two most important determinants of native T1 augmentation are (1) edema related to tissue water increase (recent infarction or inflammation) and (2) interstitial space increase related to fibrosis (infarction scar, cardiomyopathy) or to amyloidosis. Conversely, lipid (Anderson-Fabry) or iron overload diseases are responsible for T1 reduction. In this pictorial review, the main features provided by native T1 mapping are discussed and illustrated, with a special focus on the awaited clinical purpose of this unique, promising new method.

  3. Global statistical maps of extreme-event magnetic observatory 1 min first differences in horizontal intensity

    Science.gov (United States)

    Love, Jeffrey J.; Coisson, Pierdavide; Pulkkinen, Antti

    2016-01-01

    Analysis is made of the long-term statistics of three different measures of ground level, storm time geomagnetic activity: instantaneous 1 min first differences in horizontal intensity ΔBh, the root-mean-square of 10 consecutive 1 min differences S, and the ramp change R over 10 min. Geomagnetic latitude maps of the cumulative exceedances of these three quantities are constructed, giving the threshold (nT/min) for which activity within a 24 h period can be expected to occur once per year, decade, and century. Specifically, at geomagnetic 55°, we estimate once-per-century ΔBh, S, and R exceedances and a site-to-site, proportional, 1 standard deviation range [1 σ, lower and upper] to be, respectively, 1000, [690, 1450]; 500, [350, 720]; and 200, [140, 280] nT/min. At 40°, we estimate once-per-century ΔBh, S, and R exceedances and 1 σ values to be 200, [140, 290]; 100, [70, 140]; and 40, [30, 60] nT/min.

  4. Madagascar’s Mangroves: Quantifying Nation-Wide and Ecosystem Specific Dynamics, and Detailed Contemporary Mapping of Distinct Ecosystems

    Directory of Open Access Journals (Sweden)

    Trevor G. Jones

    2016-01-01

    Full Text Available Mangrove ecosystems help mitigate climate change, are highly biodiverse, and provide critical goods and services to coastal communities. Despite their importance, anthropogenic activities are rapidly degrading and deforesting mangroves world-wide. Madagascar contains 2% of the world’s mangroves, many of which have undergone or are starting to exhibit signs of widespread degradation and deforestation. Remotely sensed data can be used to quantify mangrove loss and characterize remaining distributions, providing detailed, accurate, timely and updateable information. We use USGS maps produced from Landsat data to calculate nation-wide dynamics for Madagascar’s mangroves from 1990 to 2010, and examine change more closely by partitioning the national distribution in to primary (i.e., >1000 ha ecosystems; with focus on four Areas of Interest (AOIs: Ambaro-Ambanja Bays (AAB, Mahajamba Bay (MHJ, Tsiribihina Manombolo Delta (TMD and Bay des Assassins (BdA. Results indicate a nation–wide net-loss of 21% (i.e., 57,359 ha from 1990 to 2010, with dynamics varying considerably among primary mangrove ecosystems. Given the limitations of national-level maps for certain localized applications (e.g., carbon stock inventories, building on two previous studies for AAB and MHJ, we employ Landsat data to produce detailed, contemporary mangrove maps for TMD and BdA. These contemporary, AOI-specific maps provide improved detail and accuracy over the USGS national-level maps, and are being applied to conservation and restoration initiatives through the Blue Ventures’ Blue Forests programme and WWF Madagascar West Indian Ocean Programme Office’s work in the region.

  5. PCR-RFLPs, linkage and RH mapping of the porcine TGFB1 and TGFBR1 genes

    Czech Academy of Sciences Publication Activity Database

    Kopečný, Michal; Stratil, Antonín; Van Poucke, M.; Bartenschlager, H.; Geldermann, H.; Peelman, L. J.

    2004-01-01

    Roč. 35, - (2004), s. 253-255 ISSN 0268-9146 R&D Projects: GA ČR GP523/01/P124; GA ČR GA523/03/0858; GA AV ČR KSK5052113 Institutional research plan: CEZ:AV0Z5045916 Keywords : gene mapping Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.108, year: 2004

  6. INVESTIGATION OF 1 : 1,000 SCALE MAP GENERATION BY STEREO PLOTTING USING UAV IMAGES

    Directory of Open Access Journals (Sweden)

    S. Rhee

    2017-08-01

    Full Text Available Large scale maps and image mosaics are representative geospatial data that can be extracted from UAV images. Map drawing using UAV images can be performed either by creating orthoimages and digitizing them, or by stereo plotting. While maps generated by digitization may serve the need for geospatial data, many institutions and organizations require map drawing using stereoscopic vision on stereo plotting systems. However, there are several aspects to be checked for UAV images to be utilized for stereo plotting. The first aspect is the accuracy of exterior orientation parameters (EOPs generated through automated bundle adjustment processes. It is well known that GPS and IMU sensors mounted on a UAV are not very accurate. It is necessary to adjust initial EOPs accurately using tie points. For this purpose, we have developed a photogrammetric incremental bundle adjustment procedure. The second aspect is unstable shooting conditions compared to aerial photographing. Unstable image acquisition may bring uneven stereo coverage, which will result in accuracy loss eventually. Oblique stereo pairs will create eye fatigue. The third aspect is small coverage of UAV images. This aspect will raise efficiency issue for stereo plotting of UAV images. More importantly, this aspect will make contour generation from UAV images very difficult. This paper will discuss effects relate to these three aspects. In this study, we tried to generate 1 : 1,000 scale map from the dataset using EOPs generated from software developed in-house. We evaluated Y-disparity of the tie points extracted automatically through the photogrammetric incremental bundle adjustment process. We could confirm that stereoscopic viewing is possible. Stereoscopic plotting work was carried out by a professional photogrammetrist. In order to analyse the accuracy of the map drawing using stereoscopic vision, we compared the horizontal and vertical position difference between adjacent models after

  7. Investigation of 1 : 1,000 Scale Map Generation by Stereo Plotting Using Uav Images

    Science.gov (United States)

    Rhee, S.; Kim, T.

    2017-08-01

    Large scale maps and image mosaics are representative geospatial data that can be extracted from UAV images. Map drawing using UAV images can be performed either by creating orthoimages and digitizing them, or by stereo plotting. While maps generated by digitization may serve the need for geospatial data, many institutions and organizations require map drawing using stereoscopic vision on stereo plotting systems. However, there are several aspects to be checked for UAV images to be utilized for stereo plotting. The first aspect is the accuracy of exterior orientation parameters (EOPs) generated through automated bundle adjustment processes. It is well known that GPS and IMU sensors mounted on a UAV are not very accurate. It is necessary to adjust initial EOPs accurately using tie points. For this purpose, we have developed a photogrammetric incremental bundle adjustment procedure. The second aspect is unstable shooting conditions compared to aerial photographing. Unstable image acquisition may bring uneven stereo coverage, which will result in accuracy loss eventually. Oblique stereo pairs will create eye fatigue. The third aspect is small coverage of UAV images. This aspect will raise efficiency issue for stereo plotting of UAV images. More importantly, this aspect will make contour generation from UAV images very difficult. This paper will discuss effects relate to these three aspects. In this study, we tried to generate 1 : 1,000 scale map from the dataset using EOPs generated from software developed in-house. We evaluated Y-disparity of the tie points extracted automatically through the photogrammetric incremental bundle adjustment process. We could confirm that stereoscopic viewing is possible. Stereoscopic plotting work was carried out by a professional photogrammetrist. In order to analyse the accuracy of the map drawing using stereoscopic vision, we compared the horizontal and vertical position difference between adjacent models after drawing a specific

  8. Characterizing and Mapping of Ecosystem Services (CMESs) Literature Database Version 1.0

    Science.gov (United States)

    Ecosystem services (ESs) represent an ecosystem’s capacity for satisfying essential human needs, directly or indirectly, above that required to maintain ecosystem integrity (structure, function and processes). The spatial characterization and mapping of ESs is an essential first ...

  9. Theory and praxis pf map analsys in CHEF part 1: Linear normal form

    Energy Technology Data Exchange (ETDEWEB)

    Michelotti, Leo; /Fermilab

    2008-10-01

    This memo begins a series which, put together, could comprise the 'CHEF Documentation Project' if there were such a thing. The first--and perhaps only--three will telegraphically describe theory, algorithms, implementation and usage of the normal form map analysis procedures encoded in CHEF's collection of libraries. [1] This one will begin the sequence by explaining the linear manipulations that connect the Jacobian matrix of a symplectic mapping to its normal form. It is a 'Reader's Digest' version of material I wrote in Intermediate Classical Dynamics (ICD) [2] and randomly scattered across technical memos, seminar viewgraphs, and lecture notes for the past quarter century. Much of its content is old, well known, and in some places borders on the trivial.1 Nevertheless, completeness requires their inclusion. The primary objective is the 'fundamental theorem' on normalization written on page 8. I plan to describe the nonlinear procedures in a subsequent memo and devote a third to laying out algorithms and lines of code, connecting them with equations written in the first two. Originally this was to be done in one short paper, but I jettisoned that approach after its first section exceeded a dozen pages. The organization of this document is as follows. A brief description of notation is followed by a section containing a general treatment of the linear problem. After the 'fundamental theorem' is proved, two further subsections discuss the generation of equilibrium distributions and issue of 'phase'. The final major section reviews parameterizations--that is, lattice functions--in two and four dimensions with a passing glance at the six-dimensional version. Appearances to the contrary, for the most part I have tried to restrict consideration to matters needed to understand the code in CHEF's libraries.

  10. Böttner’s Inventory and Other Finding Aids for the Grimani Maps Collection from the State Archive in Zadar

    Directory of Open Access Journals (Sweden)

    Lena Mirošević

    2010-06-01

    Full Text Available The paper briefly describes the development of cadastre in Dalmatia, with a special emphasis on the 18th century and the period of Governor Francesco Grimani’s rule. His Provision on Land Restructuring in Dalmatia from 1756 was appropriately named after him, the Grimani Law, just like the cadastre of this period was named the Grimani Cadastre and the integral cadastral plans the Grimani Maps. However, as time went by, the title Grimani Maps started being used for some 17th and 18th century cadastral plans, which did not originate from Francesco Grimani’s reform. Therefore, authors describe available archival finding aids from the State Archive in Zadar which may help in analysing cartographic material known as the Grimani Maps. The oldest finding aid is Böttner’s handwritten inventory, which provides systematization for 800 maps, plans and drawings kept in the Archive. It has been paid special attention in this paper, even though it does not specifically mention the Grimani maps. However, it should be taken into consideration since it is still in use, despite being the oldest one. Appendix A contains basic information about E. Böttner’s life and work. Afterwards, the Tabularium journal, which was published in the period 1901–1904 is analysed in detail. A review of archival material from the Zadar State Archive was published in its first issue. The material is associated with the present Grimani Maps Collection and paid considerable attention in this paper. It represents the first printed summarised inventory of the Zadar Archive. The entire content of all Tabularium issues is presented in Appendix B for the first time. A description of internal inventory of the State Archive in Zadar follows and for the first time it presents a collection of cadastral maps titled Grimani Maps. The description is followed by an analysis of a Review of Archival Funds and Collections of the Republic of Croatia from 2006, as well as the latest network

  11. Explicative memory of the geologic map of Uruguay. Esc. 1.500.000

    International Nuclear Information System (INIS)

    Preciozzi Porta, F.; Spoturno, J.; Rossi, P.; Heinzen, W.

    1985-01-01

    The Geological Map of Uruguay Esc. 1.500.000 is part of the Geological Map Programme developed by the Institute Geologic during the years 1977 - 1980. Its memory describe the geography, the lit ho stratigraphy and the crystalline area in the soil of Uruguay.

  12. Comparative study and grouping of nonstructural (NS1)proteins of influenza A viruses by the method of oligopeptide mapping

    International Nuclear Information System (INIS)

    Sokolov, B.P.; Rudneva, I.A.; Zhdanov, V.M.

    1983-01-01

    Oligopeptide mapping of 35 S-methionine labeled non-stuctural (NS1) proteins of 23 influenza A virus strains showed the presence of both common and variable oligopeptides. Analysis of the oligopeptide maps revealed at least four groups of NS1 proteins. The first group includes NS1 proteins of several human H1N1 influenza viruses (that were designated as H0N1 according to the old classification). The second group is composed of NS1 proteins of H1N1 and H2N2 viruses. The third group includes NS1 proteins of H3N2 human influenza viruses. The fourth group is composed of NS1 proteins of five avian influenza viruses and an equine (H3N8) influenza virus. Two animal influenza viruses A/equi/Prague/56 (H7N7) and A/duck/England/56 (H11N6) contain NS1 proteins that belong to the second group. (Author)

  13. NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1

    International Nuclear Information System (INIS)

    Dexheimer, Thomas S.; Carey, Steven S.; Zuohe, Song; Gokhale, Vijay M.; Hu, Xiaohui; Murata, Lauren B.; Maes, Estelle M.; Weichsel, Andrzej; Sun, Daekyu; Meuillet, Emmanuelle J.; Montfort, William R.; Hurley, Laurence H.

    2009-01-01

    The formation of G-quadruplex structures within the nuclease hypersensitive element (NHE) III 1 region of the c-myc promoter and the ability of these structures to repress c-myc transcription have been well established. However, just how these extremely stable DNA secondary structures are transformed to activate c-myc transcription is still unknown. NM23-H2/nucleoside diphosphate kinase B has been recognized as an activator of c-myc transcription via interactions with the NHE III 1 region of the c-myc gene promoter. Through the use of RNA interference, we confirmed the transcriptional regulatory role of NM23-H2. In addition, we find that further purification of NM23-H2 results in loss of the previously identified DNA strand cleavage activity, but retention of its DNA binding activity. NM23-H2 binds to both single-stranded guanine- and cytosine-rich strands of the c-myc NHE III 1 and, to a lesser extent, to a random single-stranded DNA template. However, it does not bind to or cleave the NHE III 1 in duplex form. Significantly, potassium ions and compounds that stabilize the G-quadruplex and i-motif structures have an inhibitory effect on NM23-H2 DNA-binding activity. Mutation of Arg 88 to Ala 88 (R88A) reduced both DNA and nucleotide binding but had minimal effect on the NM23-H2 crystal structure. On the basis of these data and molecular modeling studies, we have proposed a stepwise trapping-out of the NHE III 1 region in a single-stranded form, thus allowing single-stranded transcription factors to bind and activate c-myc transcription. Furthermore, this model provides a rationale for how the stabilization of the G-quadruplex or i-motif structures formed within the c-myc gene promoter region can inhibit NM23-H2 from activating c-myc gene expression.

  14. Reverberation mapping of the Seyfert 1 galaxy NGC 7469

    International Nuclear Information System (INIS)

    Peterson, B. M.; Grier, C. J.; Pogge, R. W.; De Rosa, G.; Denney, K. D.; Martini, Paul; Zu, Y.; Kochanek, C. S.; Shappee, B.; Araya Salvo, C.; Beatty, T. G.; Bird, J. C.; Horne, Keith; Bentz, M. C.; Sergeev, S. G.; Borman, G. A.; Kaspi, S.; Minezaki, T.; Siverd, R. J.; Bord, D. J.

    2014-01-01

    A large reverberation-mapping study of the Seyfert 1 galaxy NGC 7469 has yielded emission-line lags for Hβ λ4861 and He II λ4686 and a central black hole mass measurement M BH ≈ 1 × 10 7 M ☉ , consistent with previous measurements. A very low level of variability during the monitoring campaign precluded meeting our original goal of recovering velocity-delay maps from the data, but with the new Hβ measurement, NGC 7469 is no longer an outlier in the relationship between the size of the Hβ-emitting broad-line region and the luminosity of the active galactic nucleus. It was necessary to detrend the continuum and Hβ and He II λ4686 line light curves and those from archival UV data for different time-series analysis methods to yield consistent results.

  15. Reverberation mapping of the Seyfert 1 galaxy NGC 7469

    Energy Technology Data Exchange (ETDEWEB)

    Peterson, B. M.; Grier, C. J.; Pogge, R. W.; De Rosa, G.; Denney, K. D.; Martini, Paul; Zu, Y.; Kochanek, C. S.; Shappee, B.; Araya Salvo, C.; Beatty, T. G.; Bird, J. C. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Horne, Keith [SUPA Physics and Astronomy, University of St. Andrews, Fife KY16 9SS (United Kingdom); Bentz, M. C. [Department of Physics and Astronomy, Georgia State University, Astronomy Offices, 25 Park Place, Suite 605, Atlanta, GA 30303 (United States); Sergeev, S. G.; Borman, G. A. [Crimean Astrophysical Observatory, P/O Nauchny Crimea 298409 (Russian Federation); Kaspi, S. [School of Physics and Astronomy, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel); Minezaki, T. [Institute of Astronomy, School of Science, University of Tokyo, 2-21-1, Osawa, Mitaka, 181-0015 Tokyo (Japan); Siverd, R. J. [Department of Physics and Astronomy, Vanderbilt University, 6301 Stevenson Center, Nashville, TN 37235 (United States); Bord, D. J., E-mail: peterson.12@osu.edu [Department of Natural Sciences, The University of Michigan—Dearborn, 4901 Evergreen Road, Dearborn, MI 48128 (United States); and others

    2014-11-10

    A large reverberation-mapping study of the Seyfert 1 galaxy NGC 7469 has yielded emission-line lags for Hβ λ4861 and He II λ4686 and a central black hole mass measurement M {sub BH} ≈ 1 × 10{sup 7} M {sub ☉}, consistent with previous measurements. A very low level of variability during the monitoring campaign precluded meeting our original goal of recovering velocity-delay maps from the data, but with the new Hβ measurement, NGC 7469 is no longer an outlier in the relationship between the size of the Hβ-emitting broad-line region and the luminosity of the active galactic nucleus. It was necessary to detrend the continuum and Hβ and He II λ4686 line light curves and those from archival UV data for different time-series analysis methods to yield consistent results.

  16. hydrogeological map of kabo sheet 80 nw topographical sheet 1

    African Journals Online (AJOL)

    DR. AMINU

    Figure 1: Geologic Map of Kabo and its environs (Solid geology). .... Explanation: 1- Surface water in Kusalla Dam, Munkimau and Kurma rivers, the last two are seasonal ones; 2-Ground .... effluent, i.e. recharges are from water shed flowing to.

  17. Sphingosine-1-phosphate (S1P) displays sustained S1P1 receptor agonism and signaling through S1P lyase-dependent receptor recycling.

    Science.gov (United States)

    Gatfield, John; Monnier, Lucile; Studer, Rolf; Bolli, Martin H; Steiner, Beat; Nayler, Oliver

    2014-07-01

    The sphingosine-1-phosphate (S1P) type 1 receptor (S1P1R) is a novel therapeutic target in lymphocyte-mediated autoimmune diseases. S1P1 receptor desensitization caused by synthetic S1P1 receptor agonists prevents T-lymphocyte egress from secondary lymphoid organs into the circulation. The selective S1P1 receptor agonist ponesimod, which is in development for the treatment of autoimmune diseases, efficiently reduces peripheral lymphocyte counts and displays efficacy in animal models of autoimmune disease. Using ponesimod and the natural ligand S1P, we investigated the molecular mechanisms leading to different signaling, desensitization and trafficking behavior of S1P1 receptors. In recombinant S1P1 receptor-expressing cells, ponesimod and S1P triggered Gαi protein-mediated signaling and β-arrestin recruitment with comparable potency and efficiency, but only ponesimod efficiently induced intracellular receptor accumulation. In human umbilical vein endothelial cells (HUVEC), ponesimod and S1P triggered translocation of the endogenous S1P1 receptor to the Golgi compartment. However, only ponesimod treatment caused efficient surface receptor depletion, receptor accumulation in the Golgi and degradation. Impedance measurements in HUVEC showed that ponesimod induced only short-lived Gαi protein-mediated signaling followed by resistance to further stimulation, whereas S1P induced sustained Gαi protein-mediated signaling without desensitization. Inhibition of S1P lyase activity in HUVEC rendered S1P an efficient S1P1 receptor internalizing compound and abrogated S1P-mediated sustained signaling. This suggests that S1P lyase - by facilitating S1P1 receptor recycling - is essential for S1P-mediated sustained signaling, and that synthetic agonists are functional antagonists because they are not S1P lyase substrates. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Spatial Digital Database for the Geologic Map of Oregon

    Science.gov (United States)

    Walker, George W.; MacLeod, Norman S.; Miller, Robert J.; Raines, Gary L.; Connors, Katherine A.

    2003-01-01

    Introduction This report describes and makes available a geologic digital spatial database (orgeo) representing the geologic map of Oregon (Walker and MacLeod, 1991). The original paper publication was printed as a single map sheet at a scale of 1:500,000, accompanied by a second sheet containing map unit descriptions and ancillary data. A digital version of the Walker and MacLeod (1991) map was included in Raines and others (1996). The dataset provided by this open-file report supersedes the earlier published digital version (Raines and others, 1996). This digital spatial database is one of many being created by the U.S. Geological Survey as an ongoing effort to provide geologic information for use in spatial analysis in a geographic information system (GIS). This database can be queried in many ways to produce a variety of geologic maps. This database is not meant to be used or displayed at any scale larger than 1:500,000 (for example, 1:100,000). This report describes the methods used to convert the geologic map data into a digital format, describes the ArcInfo GIS file structures and relationships, and explains how to download the digital files from the U.S. Geological Survey public access World Wide Web site on the Internet. Scanned images of the printed map (Walker and MacLeod, 1991), their correlation of map units, and their explanation of map symbols are also available for download.

  19. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells.

    Science.gov (United States)

    Canver, Matthew C; Bauer, Daniel E; Dass, Abhishek; Yien, Yvette Y; Chung, Jacky; Masuda, Takeshi; Maeda, Takahiro; Paw, Barry H; Orkin, Stuart H

    2014-08-01

    The clustered regularly interspaced short [corrected] palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 nuclease system has provided a powerful tool for genome engineering. Double strand breaks may trigger nonhomologous end joining repair, leading to frameshift mutations, or homology-directed repair using an extrachromosomal template. Alternatively, genomic deletions may be produced by a pair of double strand breaks. The efficiency of CRISPR/Cas9-mediated genomic deletions has not been systematically explored. Here, we present a methodology for the production of deletions in mammalian cells, ranging from 1.3 kb to greater than 1 Mb. We observed a high frequency of intended genomic deletions. Nondeleted alleles are nonetheless often edited with inversions or small insertion/deletions produced at CRISPR recognition sites. Deleted alleles also typically include small insertion/deletions at predicted deletion junctions. We retrieved cells with biallelic deletion at a frequency exceeding that of probabilistic expectation. We demonstrate an inverse relationship between deletion frequency and deletion size. This work suggests that CRISPR/Cas9 is a robust system to produce a spectrum of genomic deletions to allow investigation of genes and genetic elements. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Blocking S1P interaction with S1P1 receptor by a novel competitive S1P1-selective antagonist inhibits angiogenesis

    International Nuclear Information System (INIS)

    Fujii, Yasuyuki; Ueda, Yasuji; Ohtake, Hidenori; Ono, Naoya; Takayama, Tetsuo; Nakazawa, Kiyoshi; Igarashi, Yasuyuki; Goitsuka, Ryo

    2012-01-01

    Highlights: ► The effect of a newly developed S1P 1 -selective antagonist on angiogenic responses. ► S1P 1 is a critical component of VEGF-related angiogenic responses. ► S1P 1 -selective antagonist showed in vitro activity to inhibit angiogenesis. ► S1P 1 -selective antagonist showed in vivo activity to inhibit angiogenesis. ► The efficacy of S1P 1 -selective antagonist for anti-cancer therapies. -- Abstract: Sphingosine 1-phosphate receptor type 1 (S1P 1 ) was shown to be essential for vascular maturation during embryonic development and it has been demonstrated that substantial crosstalk exists between S1P 1 and other pro-angiogenic growth factors, such as vascular endothelial growth factor (VEGF) and basic fibroblast growth factor. We developed a novel S1P 1 -selective antagonist, TASP0277308, which is structurally unrelated to S1P as well as previously described S1P 1 antagonists. TASP0277308 inhibited S1P- as well as VEGF-induced cellular responses, including migration and proliferation of human umbilical vein endothelial cells. Furthermore, TASP0277308 effectively blocked a VEGF-induced tube formation in vitro and significantly suppressed tumor cell-induced angiogenesis in vivo. These findings revealed that S1P 1 is a critical component of VEGF-related angiogenic responses and also provide evidence for the efficacy of TASP0277308 for anti-cancer therapies.

  1. Mixed ligand complexes of Cu(II)/Zn(II) ions containing (m-)/(p-) carboxylato phenyl azo pentane 2,4-dione and 2,2‧-bipyridine/1,10 phenanthroline: Synthesis, characterization, DNA binding, nuclease and topoisomerase I inhibitory activity

    Science.gov (United States)

    Hasan, Md. Amin; Kumari, Niraj; Singh, Kanhaiya; Singh, Kiran; Mishra, Lallan

    2016-01-01

    Metal complexes of type [Cu(L1H)2(bpy)] (1), [Zn(L1H)2(bpy)] (2), [Cu(L2H)2(bpy)] (3) and [Cu(L2H)2(Phen)] (4) (L1H2 = 3-[N‧-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, L2H2 = 4-[N‧-(1-acetyl-2-oxo-propylidene)-hydrazino]-benzoic acid, bpy = 2,2‧-bipyridine, Phen = 1,10 phenanthroline) are synthesized and characterized using spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, electronic absorption and emission) and elemental analysis data. The assembly of the complexes involving intramolecular H-bonding is displayed using corresponding crystal structure. Binding of the complexes separately with Calf Thymus DNA is monitored using UV-vis spectral titrations. The displacement of ethidium bromide (EB) bound to DNA by the complexes, in phosphate buffer solution (pH ∼ 7.2) is monitored using fluorescence spectral titrations. Nuclease activity of the complexes follow the order 4 > 3 > 1 > 2. The gel electrophoretic mobility assay measurement in presence of minor groove binder 4‧,6-diamidino-2-phenylindole (DAPI), suggests that complexes preferably bind with the minor groove of DNA. Topoisomerase I inhibitory activity of the complexes 3 and 4 inhibit topoisomerase I activity with IC50 values of 112 and 87 μM respectively.

  2. A map of the universe

    Energy Technology Data Exchange (ETDEWEB)

    Gott III, J. Richard; Juric, Mario; Schlegel, David; Hoyle, Fiona; Vogeley, Michael; Tegmark, Max; Bahcall, Neta; Brinkmann, Jon

    2003-10-20

    We have produced a new conformal map of the universe illustrating recent discoveries, ranging from Kuiper belt objects in the Solar system, to the galaxies and quasars from the Sloan Digital Sky Survey. This map projection, based on the logarithm map of the complex plane, preserves shapes locally, and yet is able to display the entire range of astronomical scales from the Earth s neighborhood to the cosmic microwave background. The conformal nature of the projection, preserving shapes locally, may be of particular use for analyzing large scale structure. Prominent in the map is a Sloan Great Wall of galaxies 1.37 billion light years long, 80 percent longer than the Great Wall discovered by Geller and Huchra and therefore the largest observed structure in the universe.

  3. Targeted mutagenesis using zinc-finger nucleases in perennial fruit trees.

    Science.gov (United States)

    Peer, Reut; Rivlin, Gil; Golobovitch, Sara; Lapidot, Moshe; Gal-On, Amit; Vainstein, Alexander; Tzfira, Tzvi; Flaishman, Moshe A

    2015-04-01

    Targeting a gene in apple or fig with ZFN, introduced by transient or stable transformation, should allow genome editing with high precision to advance basic science and breeding programs. Genome editing is a powerful tool for precise gene manipulation in any organism; it has recently been shown to be of great value for annual plants. Classical breeding strategies using conventional cross-breeding and induced mutations have played an important role in the development of new cultivars in fruit trees. However, fruit-tree breeding is a lengthy process with many limitations. Efficient and widely applied methods for targeted modification of fruit-tree genomes are not yet available. In this study, transgenic apple and fig lines carrying a zinc-finger nuclease (ZFNs) under the control of a heat-shock promoter were developed. Editing of a mutated uidA gene, following expression of the ZFN genes by heat shock, was confirmed by GUS staining and PCR product sequencing. Finally, whole plants with a repaired uidA gene due to deletion of a stop codon were regenerated. The ZFN-mediated gene modifications were stable and passed onto regenerants from ZFN-treated tissue cultures. This is the first demonstration of efficient and precise genome editing, using ZFN at a specific genomic locus, in two different perennial fruit trees-apple and fig. We conclude that targeting a gene in apple or fig with a ZFN introduced by transient or stable transformation should allow knockout of a gene of interest. Using this technology for genome editing allows for marker gene-independent and antibiotic selection-free genome engineering with high precision in fruit trees to advance basic science as well as nontransgenic breeding programs.

  4. The MAP kinase Pmk1 and protein kinase A are required for rotenone resistance in the fission yeast, Schizosaccharomyces pombe

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yiwei; Gulis, Galina; Buckner, Scott; Johnson, P. Connor; Sullivan, Daniel [Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 (United States); Busenlehner, Laura [Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487 (United States); Marcus, Stevan, E-mail: smarcus@bama.ua.edu [Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487 (United States)

    2010-08-20

    Research highlights: {yields} Rotenone induces generation of ROS and mitochondrial fragmentation in fission yeast. {yields} The MAPK Pmk1 and PKA are required for rotenone resistance in fission yeast. {yields} Pmk1 and PKA are required for ROS clearance in rotenone treated fission yeast cells. {yields} PKA plays a role in ROS clearance under normal growth conditions in fission yeast. -- Abstract: Rotenone is a widely used pesticide that induces Parkinson's disease-like symptoms in rats and death of dopaminergic neurons in culture. Although rotenone is a potent inhibitor of complex I of the mitochondrial electron transport chain, it can induce death of dopaminergic neurons independently of complex I inhibition. Here we describe effects of rotenone in the fission yeast, Schizosaccharomyces pombe, which lacks complex I and carries out rotenone-insensitive cellular respiration. We show that rotenone induces generation of reactive oxygen species (ROS) as well as fragmentation of mitochondrial networks in treated S. pombe cells. While rotenone is only modestly inhibitory to growth of wild type S. pombe cells, it is strongly inhibitory to growth of mutants lacking the ERK-type MAP kinase, Pmk1, or protein kinase A (PKA). In contrast, cells lacking the p38 MAP kinase, Spc1, exhibit modest resistance to rotenone. Consistent with these findings, we provide evidence that Pmk1 and PKA, but not Spc1, are required for clearance of ROS in rotenone treated S. pombe cells. Our results demonstrate the usefulness of S. pombe for elucidating complex I-independent molecular targets of rotenone as well as mechanisms conferring resistance to the toxin.

  5. Understanding the Future Market for NovaSAR-S Flood Mapping Products Using Data Mining and Simulation

    Science.gov (United States)

    Lavender, Samantha; Haria, Kajal; Cooksley, Geraint; Farman, Alex; Beaton, Thomas

    2016-08-01

    The aim was to understand a future market for NovaSAR-S, with a particular focus on flood mapping, through developing a simple Synthetic Aperture Radar (SAR) simulator that can be used in advance of NovaSAR-S data becoming available.The return signal was determined from a combination of a terrain or elevation model, Envisat S-Band Radar Altimeter (RA)-2, Landsat and CORINE land cover information; allowing for a simulation of a SAR image that's influenced by both the geometry and surface type. The test sites correspond to data from the 2014 AirSAR campaign, and validation is performed by using AirSAR together with Envisat Advanced (ASAR) and Advanced Land Observing Satellite "Daichi" (ALOS) Phased Array type L-Band Synthetic Aperture Radar (PALSAR) data.It's envisaged that the resulting simulated data, and the simulator, will not only aid early understanding of NovaSAR-S, but will also aid the development of flood mapping applications.

  6. Maps of surface activity of 137Cs of Slovakia on scale 1:200 000

    International Nuclear Information System (INIS)

    Gluch, A.

    2005-05-01

    The present set of maps (13 maps) arose from the geological project 'Re-ambulation of 137 Cs radioactivity map of Slovakia at scales 1:200 000 and 1:500 000' in phase of indicative geological survey of environmental factors. Maps document the state of contamination of the territory of Slovakia by one of the radioisotopes cesium-137 at the reference date 01.01.2005. In solving of geological tasks were used all available relevant data on measurements of 137 Cs activity from the whole territory of the Slovak Republic for the period from 1990 to 2003 from results of air and ground gamma spectrometric measurements. (authors)

  7. Geopan AT@S: a Brokering Based Gateway to Georeferenced Historical Maps for Risk Analysis

    Science.gov (United States)

    Previtali, M.

    2017-08-01

    Importance of ancient and historical maps is nowadays recognized in many applications (e.g., urban planning, landscape valorisation and preservation, land changes identification, etc.). In the last years a great effort has been done by different institutions, such as Geographical Institutes, Public Administrations, and collaborative communities, for digitizing and publishing online collections of historical maps. In spite of this variety and availability of data, information overload makes difficult their discovery and management: without knowing the specific repository where the data are stored, it is difficult to find the information required. In addition, problems of interconnection between different data sources and their restricted interoperability may arise. This paper describe a new brokering based gateway developed to assure interoperability between data, in particular georeferenced historical maps and geographic data, gathered from different data providers, with various features and referring to different historical periods. The developed approach is exemplified by a new application named GeoPAN Atl@s that is aimed at linking in Northern Italy area land changes with risk analysis (local seismicity amplification and flooding risk) by using multi-temporal data sources and historic maps.

  8. Myocardial T1 and T2 mapping: Techniques and clinical applications

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Pan Ki; Hong, Yoo Jin; Im, Dong Jin [Dept. of Radiology and Research Institute of Radiological Science, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); and others

    2017-01-15

    Cardiac magnetic resonance (CMR) imaging is widely used in various medical fields related to cardiovascular diseases. Rapid technological innovations in magnetic resonance imaging in recent times have resulted in the development of new techniques for CMR imaging. T1 and T2 image mapping sequences enable the direct quantification of T1, T2, and extracellular volume fraction (ECV) values of the myocardium, leading to the progressive integration of these sequences into routine CMR settings. Currently, T1, T2, and ECV values are being recognized as not only robust biomarkers for diagnosis of cardiomyopathies, but also predictive factors for treatment monitoring and prognosis. In this study, we have reviewed various T1 and T2 mapping sequence techniques and their clinical applications.

  9. Solar Maps | Geospatial Data Science | NREL

    Science.gov (United States)

    Solar Maps Solar Maps These solar maps provide average daily total solar resource information on disability, contact the Geospatial Data Science Team. U.S. State Solar Resource Maps Access state maps of MT NE NV NH NJ NM NY NC ND OH OK OR PA RI SC SD TN TX UT VT VA WA WV WI WY × U.S. Solar Resource

  10. Sensitivity mapping for oil spill response. V. 1

    International Nuclear Information System (INIS)

    1997-01-01

    Making and updating sensitivity maps are key activities in the oil spill contingency planning process. These maps convey essential information to spill responders by showing where the different coastal resources are, and by indicating environmentally sensitive areas. The making of a map involves assembling information on resources and deciding on what guidelines for spill response should be included, through consultation with relevant organizations. This can be done regardless of whether or not the benefits of computerized Geographic Information Systems and databases are available. Uses of sensitivity maps range from planning practical site-specific shore protection and clean-up to strategic planning for large remote areas. This report provides information and guidelines on different map types, categories of information to be included, and symbols, with reference to the different users and their requirements. (UK)

  11. Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities

    DEFF Research Database (Denmark)

    Guo, Yang; Kragelund, Birthe Brandt; White, Malcolm F.

    2015-01-01

    encoding proteins of unknown function and forming an operon with ORF207 (gp19). SIRV2 gp17 was found to be a single-stranded DNA (ssDNA) binding protein different in structure from all previously characterized ssDNA binding proteins. Mutagenesis of a few conserved basic residues suggested a U......-shaped binding path for ssDNA. The recombinant gp18 showed an ssDNA annealing activity often associated with helicases and recombinases. To gain insight into the biological role of the entire operon, we characterized SIRV2 gp19 and showed it to possess a 5'→3' ssDNA exonuclease activity, in addition...... for rudiviruses and the close interaction among the ssDNA binding, annealing and nuclease proteins strongly point to a role of the gene operon in genome maturation and/or DNA recombination that may function in viral DNA replication/repair....

  12. Cryptanalysis of a family of 1D unimodal maps

    Science.gov (United States)

    Md Said, Mohamad Rushdan; Hina, Aliyu Danladi; Banerjee, Santo

    2017-07-01

    In this paper, we proposed a topologically conjugate map, equivalent to the well known logistic map. This constructed map is defined on the integer domain [0, 2n) with a view to be used as a random number generator (RNG) based on an integer domain as is the required in classical cryptography. The maps were found to have a one to one correspondence between points in their respective defining intervals defined on an n-bits precision. The dynamics of the proposed map similar with that of the logistic map, in terms of the Lyapunov exponents with the control parameter. This similarity between the curves indicates topological conjugacy between the maps. With a view to be applied in cryptography as a Pseudo-Random number generator (PRNG), the complexity of the constructed map as a source of randomness is determined using both the permutation entropy (PE) and the Lempel-Ziv (LZ-76) complexity measures, and the results are compared with numerical simulations.

  13. Transcription of human 7S K DNA in vitro and in vivo is exclusively controlled by an upstream promoter

    Energy Technology Data Exchange (ETDEWEB)

    Kleinert, H.; Benecke, B.J.

    1988-02-25

    The authors have analyzed the transcription of a recently isolated human 7S K RNA gene in vitro and in vivo. In contrast to hitherto characterized class III genes (genes transcribed by RNA polymerase III), the coding sequence of this gene is not required for faithful and efficient transcription by RNA polymerase III. In fact, a procaryotic vector DNA sequence was efficiently transcribed by RNA polymerase III under the control of the 7S K RNA gene upstream sequence in vitro and in vivo. S/sub 1/-nuclease protection analyses confirmed that the 7S K 5'flanking sequence was sufficient for accurate transcription initiation. These data demonstrate that 7S K DNA represents a novel class III gene, the promoter elements of which are located outside the coding sequence.

  14. The map of chromosome 1 of man

    NARCIS (Netherlands)

    W.G. Burgerhout (Wim)

    1977-01-01

    textabstractMaking maps is an essential procedure in the exploration of new territories. In the field of genetics, many basic concepts concerning the structure of a genome and the regulation of gene activity have emerged from regional mapping studies on the chromosomes of e.g. Escherichia coli

  15. Endonuclease from Gram-Negative Bacteria Serratia marcescens Is as Effective as Pulmozyme in the Hydrolysis of DNA in Sputum

    Science.gov (United States)

    Vafina, Gulnaz; Zainutdinova, Elmira; Bulatov, Emil; Filimonova, Maria N.

    2018-01-01

    One of the approaches to effective airway cleansing is the degradation of DNA into smaller fragments. For this purpose Pulmozyme® is used with high efficacy because it contains recombinant DNase I as its active component. The aim of the study was to comparatively analyze DNase activity of Pulmozyme® and the nuclease from gram-negative bacteria Serratia marcescens, because at optimal conditions the catalytic efficiency of the nuclease is much higher than the efficiency of DNase I. Highly polymerized DNA and purulent-mucous sputum were used as substrates. The examination showed that both S. marcescens nuclease and Pulmozyme® hydrolyzed DNA in sputum. Also S. marcescens nuclease was found capable of hydrolyzing DNA in conditions that are standard for Pulmozyme® and suitable for its therapeutic application. For manifesting the similar hydrolytic activity the nuclease amount in the assay mixture containing highly polymerized DNA or the sonicated sputum and NaCl together with calcium- or magnesium- cations can be about 10- time lower than that of the recombinant DNase I. In the presence of magnesium cations the DNase activity of both S. marcescens nuclease and Pulmozyme® was higher than in the presence of calcium cations. PMID:29503617

  16. Mapping Vinyl Cyanide and Other Nitriles in Titan’s Atmosphere Using ALMA

    Science.gov (United States)

    Lai, J. C.-Y.; Cordiner, M. A.; Nixon, C. A.; Achterberg, R. K.; Molter, E. M.; Teanby, N. A.; Palmer, M. Y.; Charnley, S. B.; Lindberg, J. E.; Kisiel, Z.; Mumma, M. J.; Irwin, P. G. J.

    2017-11-01

    Vinyl cyanide (C2H3CN) is theorized to form in Titan’s atmosphere via high-altitude photochemistry and is of interest regarding the astrobiology of cold planetary surfaces due to its predicted ability to form cell membrane-like structures (azotosomes) in liquid methane. In this work, we follow up on the initial spectroscopic detection of C2H3CN on Titan by Palmer et al. with the detection of three new C2H3CN rotational emission lines at submillimeter frequencies. These new, high-resolution detections have allowed for the first spatial distribution mapping of C2H3CN on Titan. We present simultaneous observations of C2H5CN, HC3N, and CH3CN emission, and obtain the first (tentative) detection of C3H8 (propane) at radio wavelengths. We present disk-averaged vertical abundance profiles, two-dimensional spatial maps, and latitudinal flux profiles for the observed nitriles. Similarly to HC3N and C2H5CN, which are theorized to be short-lived in Titan’s atmosphere, C2H3CN is most abundant over the southern (winter) pole, whereas the longer-lived CH3CN is more concentrated in the north. This abundance pattern is consistent with the combined effects of high-altitude photochemical production, poleward advection, and the subsequent reversal of Titan’s atmospheric circulation system following the recent transition from northern to southern winter. We confirm that C2H3CN and C2H5CN are most abundant at altitudes above 200 km. Using a 300 km step model, the average abundance of C2H3CN is found to be 3.03 ± 0.29 ppb, with a C2H5CN/C2H3CN abundance ratio of 2.43 ± 0.26. Our HC3N and CH3CN spectra can be accurately modeled using abundance gradients above the tropopause, with fractional scale-heights of 2.05 ± 0.16 and 1.63 ± 0.02, respectively.

  17. Physical and transcript map of the region between D6S264 and D6S149 on chromosome 6q27, the minimal region of allele loss in sporadic epithelial ovarian cancer

    DEFF Research Database (Denmark)

    Liu, Ying; Emilion, Gracy; Mungall, Andrew J

    2002-01-01

    We have previously shown a high frequency of allele loss at D6S193 (62%) on chromosomal arm 6q27 in ovarian tumours and mapped the minimal region of allele loss between D6S297 and D6S264 (3 cM). We isolated and mapped a single non-chimaeric YAC (17IA12, 260-280 kb) containing D6S193 and D6S297...

  18. Variable flip angle 3D ultrashort echo time (UTE) T1 mapping of mouse lung: A repeatability assessment.

    Science.gov (United States)

    Alamidi, Daniel F; Smailagic, Amir; Bidar, Abdel W; Parker, Nicole S; Olsson, Marita; Hockings, Paul D; Lagerstrand, Kerstin M; Olsson, Lars E

    2018-03-08

    Lung T 1 is a potential translational biomarker of lung disease. The precision and repeatability of variable flip angle (VFA) T 1 mapping using modern 3D ultrashort echo time (UTE) imaging of the whole lung needs to be established before it can be used to assess response to disease and therapy. To evaluate the feasibility of regional lung T 1 quantification with VFA 3D-UTE and to investigate long- and short-term T 1 repeatability in the lungs of naive mice. Prospective preclinical animal study. Eight naive mice and phantoms. 3D free-breathing radial UTE (8 μs) at 4.7T. VFA 3D-UTE T 1 calculations were validated against T 1 values measured with inversion recovery (IR) in phantoms. Lung T 1 and proton density (S 0 ) measurements of whole lung and muscle were repeated five times over 1 month in free-breathing naive mice. Two consecutive T 1 measurements were performed during one of the imaging sessions. Agreement in T 1 between VFA 3D-UTE and IR in phantoms was assessed using Bland-Altman and Pearson 's correlation analysis. The T 1 repeatability in mice was evaluated using coefficient of variation (CV), repeated-measures analysis of variance (ANOVA), and paired t-test. Good T 1 agreement between the VFA 3D-UTE and IR methods was found in phantoms. T 1 in lung and muscle showed a 5% and 3% CV (1255 ± 63 msec and 1432 ± 42 msec, respectively, mean ± SD) with no changes in T 1 or S 0 over a month. Consecutive measurements resulted in an increase of 2% in both lung T 1 and S 0 . VFA 3D-UTE shows promise as a reliable T 1 mapping method that enables full lung coverage, high signal-to-noise ratio (∼25), and spatial resolution (300 μm) in freely breathing animals. The precision of the VFA 3D-UTE method will enable better design and powering of studies. 1 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

  19. First-order shallow aquifer characteristics across Europe: The International Hydrogeological Map of Europe at scale 1:1.5 Million (IHME1500)

    Science.gov (United States)

    Günther, Andreas; Duscher, Klaus; Broda, Stefan; Clos, Patrick; Reichling, Jörg

    2017-04-01

    Since the mid of the last century, pan-European hydrogeological overview-mapping is conducted at the scale 1 : 1.5 Million following common standards and guidelines to interpret suitable geologic mapping units in terms of potential uppermost aquifer (or non-aquifer) characteristics. These comprises potential aquifer productivities and general hydrogeological aquifer conditions (fissured vs. porous). The printed IHME1500 dataset successively elaborated and published from 1970 - 2013 consists of 25 individual map sheets. Besides the potential aquifer characterization grouped in six classes, IHME1500 offers a complete coverage of lithological material properties of potential shallow aquifer assemblages, and tracelines of major fault structures. Regional information on groundwater surfaces, aquifer thicknesses and depths, locations and characteristics of groundwater springs and other punctual information related to European groundwater resources is present for some areas in selected map sheets, however not digitally available. Synoptic IHME1500 vector data consists of a topographically corrected, seamless and harmonized polygon layer with attribute information on potential aquifer productivity and lithology. While the standardized aquifer-classification is relatively easy to harmonize across the entire mapped area, the lithological information of IHME1500 is presented using sheet-specific legend information resulting in more than 1000 aquifer lithology classes. An attempt was made to harmonize this information utilizing a specifically developed taxonomic scheme, treating consolidated, partly consolidated and unconsolidated materials separately. The translation of the original lithological information into this scheme allows for a hierarchical grouping of the mapping units into five generalization levels, where the highest aggregation level displays a ternary map showing the distribution of consolidated, partially consolidated and unconsolidated aquifer materials. The

  20. Paenibacillus larvae 16S-23S rDNA intergenic transcribed spacer (ITS) regions: DNA fingerprinting and characterization.

    Science.gov (United States)

    Dingman, Douglas W

    2012-07-01

    Paenibacillus larvae is the causative agent of American foulbrood in honey bee (Apis mellifera) larvae. PCR amplification of the 16S-23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) regions, and agarose gel electrophoresis of the amplified DNA, was performed using genomic DNA collected from 134 P. larvae strains isolated in Connecticut, six Northern Regional Research Laboratory stock strains, four strains isolated in Argentina, and one strain isolated in Chile. Following electrophoresis of amplified DNA, all isolates exhibited a common migratory profile (i.e., ITS-PCR fingerprint pattern) of six DNA bands. This profile represented a unique ITS-PCR DNA fingerprint that was useful as a fast, simple, and accurate procedure for identification of P. larvae. Digestion of ITS-PCR amplified DNA, using mung bean nuclease prior to electrophoresis, characterized only three of the six electrophoresis bands as homoduplex DNA and indicating three true ITS regions. These three ITS regions, DNA migratory band sizes of 915, 1010, and 1474 bp, signify a minimum of three types of rrn operons within P. larvae. DNA sequence analysis of ITS region DNA, using P. larvae NRRL B-3553, identified the 3' terminal nucleotides of the 16S rRNA gene, 5' terminal nucleotides of the 23S rRNA gene, and the complete DNA sequences of the 5S rRNA, tRNA(ala), and tRNA(ile) genes. Gene organization within the three rrn operon types was 16S-23S, 16S-tRNA(ala)-23S, and l6S-5S-tRNA(ile)-tRNA(ala)-23S and these operons were named rrnA, rrnF, and rrnG, respectively. The 23S rRNA gene was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to be present as seven copies. This was suggestive of seven rrn operon copies within the P. larvae genome. Investigation of the 16S-23S rDNA regions of this bacterium has aided the development of a diagnostic procedure and has helped genomic mapping investigations via characterization of the ITS regions. Copyright © 2012 Elsevier Inc

  1. Air Emissions Sources, Charts and Maps

    Data.gov (United States)

    U.S. Environmental Protection Agency — Air Emissions provides (1) interactive charts supporting national, state, or county charts, (2) county maps of criteria air pollutant emissions for a state, and (3)...

  2. A first linkage map of globe artichoke (Cynara cardunculus var. scolymus L.) based on AFLP, S-SAP, M-AFLP and microsatellite markers.

    Science.gov (United States)

    Lanteri, S; Acquadro, A; Comino, C; Mauro, R; Mauromicale, G; Portis, E

    2006-05-01

    We present the first genetic maps of globe artichoke (Cynara cardunculus var. scolymus L. 2n=2x=34), constructed with a two-way pseudo-testcross strategy. A F1 mapping population of 94 individuals was generated between a late-maturing, non-spiny type and an early-maturing spiny type. The 30 AFLP, 13 M-AFLP and 9 S-SAP primer combinations chosen identified, respectively, 352, 38 and 41 polymorphic markers. Of 32 microsatellite primer pairs tested, 12 identified heterozygous loci in one or other parent, and 7 were fully informative as they segregated in both parents. The female parent map comprised 204 loci, spread over 18 linkage groups and spanned 1330.5 cM with a mean marker density of 6.5 cM. The equivalent figures for the male parent map were 180 loci, 17 linkage groups, 1239.4 and 6.9 cM. About 3% of the AFLP and AFLP-derived markers displayed segregation distortion with a P value below 0.01, and were not used for map construction. All the SSR loci were included in the linkage analysis, although one locus did show some segregation distortion. The presence of 78 markers in common to both maps allowed the alignment of 16 linkage groups. The maps generated provide a firm basis for the mapping of agriculturally relevant traits, which will then open the way for the application of a marker-assisted selection breeding strategy in this species.

  3. Benthic Habitat Mapping by Combining Lyzenga’s Optical Model and Relative Water Depth Model in Lintea Island, Southeast Sulawesi

    Science.gov (United States)

    Hafizt, M.; Manessa, M. D. M.; Adi, N. S.; Prayudha, B.

    2017-12-01

    Benthic habitat mapping using satellite data is one challenging task for practitioners and academician as benthic objects are covered by light-attenuating water column obscuring object discrimination. One common method to reduce this water-column effect is by using depth-invariant index (DII) image. However, the application of the correction in shallow coastal areas is challenging as a dark object such as seagrass could have a very low pixel value, preventing its reliable identification and classification. This limitation can be solved by specifically applying a classification process to areas with different water depth levels. The water depth level can be extracted from satellite imagery using Relative Water Depth Index (RWDI). This study proposed a new approach to improve the mapping accuracy, particularly for benthic dark objects by combining the DII of Lyzenga’s water column correction method and the RWDI of Stumpt’s method. This research was conducted in Lintea Island which has a high variation of benthic cover using Sentinel-2A imagery. To assess the effectiveness of the proposed new approach for benthic habitat mapping two different classification procedures are implemented. The first procedure is the commonly applied method in benthic habitat mapping where DII image is used as input data to all coastal area for image classification process regardless of depth variation. The second procedure is the proposed new approach where its initial step begins with the separation of the study area into shallow and deep waters using the RWDI image. Shallow area was then classified using the sunglint-corrected image as input data and the deep area was classified using DII image as input data. The final classification maps of those two areas were merged as a single benthic habitat map. A confusion matrix was then applied to evaluate the mapping accuracy of the final map. The result shows that the new proposed mapping approach can be used to map all benthic objects in

  4. Mapping EBNA-1 Domains Involved in Binding to Metaphase Chromosomes

    Science.gov (United States)

    Marechal, Vincent; Dehee, Axelle; Chikhi-Brachet, Roxane; Piolot, Tristan; Coppey-Moisan, Maité; Nicolas, Jean-Claude

    1999-01-01

    The Epstein-Barr virus (EBV) genome can persist in dividing human B cells as multicopy circular episomes. Viral episomes replicate in synchrony with host cell DNA and are maintained at a relatively constant copy number for a long time. Only two viral elements, the replication origin OriP and the EBNA-1 protein, are required for the persistence of viral genomes during latency. EBNA-1 activates OriP during the S phase and may also contribute to the partition and/or retention of viral genomes during mitosis. Indeed, EBNA-1 has been shown to interact with mitotic chromatin. Moreover, viral genomes are noncovalently associated with metaphase chromosomes. This suggests that EBNA-1 may facilitate the anchorage of viral genomes on cellular chromosomes, thus ensuring proper partition and retention. In the present paper, we have investigated the chromosome-binding activity of EBV EBNA-1, herpesvirus papio (HVP) EBNA-1, and various derivatives of EBV EBNA-1, fused to a variant of the green fluorescent protein. The results show that binding to metaphase chromosomes is a common property of EBV and HVP EBNA-1. Further studies indicated that at least three independent domains (CBS-1, -2, and -3) mediate EBNA-1 binding to metaphase chromosomes. In agreement with the anchorage model, two of these domains mapped to a region that has been previously demonstrated to be required for the long-term persistence of OriP-containing plasmids. PMID:10196336

  5. Mechanism of chromatin degradation in thymocytes of irradiated rats

    International Nuclear Information System (INIS)

    Nikonova, L.V.; Nelipovich, P.A.; Umanskij, S.R.

    1983-01-01

    Chromatin digestion in isolated thymocyte nuclei with DNAase I, micrococcal nuclease and nuclease from Serratia marcescens was studied. It was shown that 3 h after irradiation (10 Gy), the kinetics of accumulation of acid soluble and salt soluble products of DNA degradation, caused by exogenous nucleases, remains unchanged. The administration of cycloheximide does not influence the sensitivity of chromatin to DNAase I and somewhat increases the rate of salt soluble products formation upon the nuclease from S, marcescens treatment

  6. Discussion on the 3D visualizing of 1:200 000 geological map

    Science.gov (United States)

    Wang, Xiaopeng

    2018-01-01

    Using United States National Aeronautics and Space Administration Shuttle Radar Topography Mission (SRTM) terrain data as digital elevation model (DEM), overlap scanned 1:200 000 scale geological map, program using Direct 3D of Microsoft with C# computer language, the author realized the three-dimensional visualization of the standard division geological map. User can inspect the regional geology content with arbitrary angle, rotating, roaming, and can examining the strata synthetical histogram, map section and legend at any moment. This will provide an intuitionistic analyzing tool for the geological practitioner to do structural analysis with the assistant of landform, dispose field exploration route etc.

  7. The MAP kinase Pmk1 and protein kinase A are required for rotenone resistance in the fission yeast, Schizosaccharomyces pombe

    International Nuclear Information System (INIS)

    Wang, Yiwei; Gulis, Galina; Buckner, Scott; Johnson, P. Connor; Sullivan, Daniel; Busenlehner, Laura; Marcus, Stevan

    2010-01-01

    Research highlights: → Rotenone induces generation of ROS and mitochondrial fragmentation in fission yeast. → The MAPK Pmk1 and PKA are required for rotenone resistance in fission yeast. → Pmk1 and PKA are required for ROS clearance in rotenone treated fission yeast cells. → PKA plays a role in ROS clearance under normal growth conditions in fission yeast. -- Abstract: Rotenone is a widely used pesticide that induces Parkinson's disease-like symptoms in rats and death of dopaminergic neurons in culture. Although rotenone is a potent inhibitor of complex I of the mitochondrial electron transport chain, it can induce death of dopaminergic neurons independently of complex I inhibition. Here we describe effects of rotenone in the fission yeast, Schizosaccharomyces pombe, which lacks complex I and carries out rotenone-insensitive cellular respiration. We show that rotenone induces generation of reactive oxygen species (ROS) as well as fragmentation of mitochondrial networks in treated S. pombe cells. While rotenone is only modestly inhibitory to growth of wild type S. pombe cells, it is strongly inhibitory to growth of mutants lacking the ERK-type MAP kinase, Pmk1, or protein kinase A (PKA). In contrast, cells lacking the p38 MAP kinase, Spc1, exhibit modest resistance to rotenone. Consistent with these findings, we provide evidence that Pmk1 and PKA, but not Spc1, are required for clearance of ROS in rotenone treated S. pombe cells. Our results demonstrate the usefulness of S. pombe for elucidating complex I-independent molecular targets of rotenone as well as mechanisms conferring resistance to the toxin.

  8. Multibeam Bathymetry Mapping for U.S. UNCLOS Concerns: A Gold Mine for Marine Geology

    Science.gov (United States)

    Gardner, J. V.; Mayer, L. A.; Armstrong, A.

    2007-12-01

    Since 2003, the University of New Hampshire's Center for Coastal and Ocean Mapping-Joint Hydrographic Center has conducted mapping of several U.S. continental margins in areas where a potential exists for an extended continental shelf as defined under Article 76 of the United Nations Convention on the Law of the Sea. UNH was directed by Congress, through funding to NOAA, to map the bathymetry in areas in the Arctic Ocean, Bering Sea, Gulf of Alaska, Atlantic, Gulf of Mexico, Philippine Sea, and slopes of Kingman Reef and Palmyra Atoll. These new data can be used to accurately locate the 2500-m isobath and to determine the location of the maximum change in gradient at the base of the continental slopes. To achieve these objectives, the area between ~1000 m and ~5000 m isobaths are mapped. The program has mapped >900,000 km2 as of September 2007. The bathymetry data are collected with multibeam echosounders navigated with inertial-aided DGPS and are fully motion compensated. An integral part of the data collection is measurements of the sound-speed profile in the water column to correct for refraction. The data are fully processed at sea. Most cruises also collect 3.5-kHz high-resolution profiles and some have included gravity measurements. All processed bathymetry and associated acoustic backscatter data are immediately available one the web and the raw multibeam datagrams and processed gravity data are archived at NOAA/NGDC. The new data provide a wealth of new information on the geomorphology of the continental margins. The mapping discovered many new features on the U.S. margins, as well as better defined features known to exist but either poorly mapped or mapped with obsolete mapping technology. New features discovered during the surveys include an undiscovered seamount, christened Healy Seamount and a series of huge sediment ridges striking normal to the Barrow margin in the Arctic Ocean; a series of plateaus and ridges north of Bowers Ridge in the Bering Sea

  9. Implementation of NGA-West2 ground motion models in the 2014 U.S. National Seismic Hazard Maps

    Science.gov (United States)

    Rezaeian, Sanaz; Petersen, Mark D.; Moschetti, Morgan P.; Powers, Peter; Harmsen, Stephen C.; Frankel, Arthur D.

    2014-01-01

    The U.S. National Seismic Hazard Maps (NSHMs) have been an important component of seismic design regulations in the United States for the past several decades. These maps present earthquake ground shaking intensities at specified probabilities of being exceeded over a 50-year time period. The previous version of the NSHMs was developed in 2008; during 2012 and 2013, scientists at the U.S. Geological Survey have been updating the maps based on their assessment of the “best available science,” resulting in the 2014 NSHMs. The update includes modifications to the seismic source models and the ground motion models (GMMs) for sites across the conterminous United States. This paper focuses on updates in the Western United States (WUS) due to the use of new GMMs for shallow crustal earthquakes in active tectonic regions developed by the Next Generation Attenuation (NGA-West2) project. Individual GMMs, their weighted combination, and their impact on the hazard maps relative to 2008 are discussed. In general, the combined effects of lower medians and increased standard deviations in the new GMMs have caused only small changes, within 5–20%, in the probabilistic ground motions for most sites across the WUS compared to the 2008 NSHMs.

  10. Accurate atom-mapping computation for biochemical reactions.

    Science.gov (United States)

    Latendresse, Mario; Malerich, Jeremiah P; Travers, Mike; Karp, Peter D

    2012-11-26

    The complete atom mapping of a chemical reaction is a bijection of the reactant atoms to the product atoms that specifies the terminus of each reactant atom. Atom mapping of biochemical reactions is useful for many applications of systems biology, in particular for metabolic engineering where synthesizing new biochemical pathways has to take into account for the number of carbon atoms from a source compound that are conserved in the synthesis of a target compound. Rapid, accurate computation of the atom mapping(s) of a biochemical reaction remains elusive despite significant work on this topic. In particular, past researchers did not validate the accuracy of mapping algorithms. We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric. The metric is based on bond propensity to react and computes biochemically valid atom mappings for a large percentage of biochemical reactions. MWED models can be formulated efficiently as Mixed-Integer Linear Programs (MILPs). We have demonstrated this approach on 7501 reactions of the MetaCyc database for which 87% of the models could be solved in less than 10 s. For 2.1% of the reactions, we found multiple optimal atom mappings. We show that the error rate is 0.9% (22 reactions) by comparing these atom mappings to 2446 atom mappings of the manually curated Kyoto Encyclopedia of Genes and Genomes (KEGG) RPAIR database. To our knowledge, our computational atom-mapping approach is the most accurate and among the fastest published to date. The atom-mapping data will be available in the MetaCyc database later in 2012; the atom-mapping software will be available within the Pathway Tools software later in 2012.

  11. Diagnostic and Prognostic Value of CMR T1-Mapping in Patients With Heart Failure and Preserved Ejection Fraction.

    Science.gov (United States)

    Rommel, Karl-Philipp; Lücke, Christian; Lurz, Philipp

    2017-10-01

    Heart failure with preserved ejection fraction (HFpEF) presents a major challenge in modern cardiology. Although this syndrome is of increasing prevalence and is associated with unfavorable outcomes, treatment trials have failed to establish effective therapies. Currently, solutions to this dilemma are being investigated, including categorizing and characterizing patients more diversely to individualize treatment. In this regard, new imaging techniques might provide important information. Diastolic dysfunction is a diagnostic and pathophysiological cornerstone in HFpEF and is believed to be caused by systemic inflammation with the development of interstitial myocardial fibrosis and myocardial stiffening. Cardiac magnetic resonance (CMR) T 1 -mapping is a novel tool, which allows noninvasive quantification of the extracellular space and diffuse myocardial fibrosis. This review provides an overview of the potential of myocardial tissue characterization with CMR T 1 mapping in HFpEF patients, outlining its diagnostic and prognostic implications and discussing future directions. We conclude that CMR T 1 mapping is potentially an effective tool for patient characterization in large-scale epidemiological, diagnostic, and therapeutic HFpEF trials beyond traditional imaging parameters. Copyright © 2017 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

  12. The Making of the 1:3M Geological Map Series of Mercury: Status and Updates

    Science.gov (United States)

    Galluzzi, V.; Guzzetta, L.; Mancinelli, P.; Giacomini, L.; Lewang, A. M.; Malliband, C.; Mosca, A.; Pegg, D.; Wright, J.; Ferranti, L.; Hiesinger, H.; Massironi, M.; Pauselli, C.; Rothery, D. A.; Palumbo, P.

    2018-05-01

    A complete global series of 1:3M-scale maps of Mercury is being prepared in support to the ESA/JAXA BepiColombo mission. Currently, 35% of Mercury has been mapped and 55% of the planet will be covered soon by the maps in progress.

  13. U.S. Geological Survey ArcMap Sediment Classification tool

    Science.gov (United States)

    O'Malley, John

    2007-01-01

    The U.S. Geological Survey (USGS) ArcMap Sediment Classification tool is a custom toolbar that extends the Environmental Systems Research Institute, Inc. (ESRI) ArcGIS 9.2 Desktop application to aid in the analysis of seabed sediment classification. The tool uses as input either a point data layer with field attributes containing percentage of gravel, sand, silt, and clay or four raster data layers representing a percentage of sediment (0-100%) for the various sediment grain size analysis: sand, gravel, silt and clay. This tool is designed to analyze the percent of sediment at a given location and classify the sediments according to either the Folk (1954, 1974) or Shepard (1954) as modified by Schlee(1973) classification schemes. The sediment analysis tool is based upon the USGS SEDCLASS program (Poppe, et al. 2004).

  14. On retracting properties and covering homotopy theorem for S-maps into Sχ-cofibrations and Sχ-fibrations

    Directory of Open Access Journals (Sweden)

    Amin Saif

    2016-10-01

    Full Text Available In this paper we generalize the retracting property in homotopy theory for topological semigroups by introducing the notions of deformation S-retraction with its weaker forms and ES-homotopy extension property. Furthermore, the covering homotopy theorems for S-maps into Sχ-fibrations and Sχ-cofibrations are introduced and pullbacks for Sχ-fibrations behave properly.

  15. Early macroseismic maps in Central Europe

    Czech Academy of Sciences Publication Activity Database

    Kozák, Jan; Vaněk, Jiří

    2013-01-01

    Roč. 1, č. 2 (2013), s. 43-53 ISSN 2330-1740 Institutional support: RVO:67985530 Keywords : macroseismic maps * intensity scales * Central Europe * 19th century Subject RIV: DC - Siesmology, Volcanology, Earth Structure

  16. A novel method to design S-box based on chaotic map and genetic algorithm

    International Nuclear Information System (INIS)

    Wang, Yong; Wong, Kwok-Wo; Li, Changbing; Li, Yang

    2012-01-01

    The substitution box (S-box) is an important component in block encryption algorithms. In this Letter, the problem of constructing S-box is transformed to a Traveling Salesman Problem and a method for designing S-box based on chaos and genetic algorithm is proposed. Since the proposed method makes full use of the traits of chaotic map and evolution process, stronger S-box is obtained. The results of performance test show that the presented S-box has good cryptographic properties, which justify that the proposed algorithm is effective in generating strong S-boxes. -- Highlights: ► The problem of constructing S-box is transformed to a Traveling Salesman Problem. ► We present a new method for designing S-box based on chaos and genetic algorithm. ► The proposed algorithm is effective in generating strong S-boxes.

  17. A novel method to design S-box based on chaotic map and genetic algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yong, E-mail: wangyong_cqupt@163.com [State Key Laboratory of Power Transmission Equipment and System Security and New Technology, Chongqing University, Chongqing 400044 (China); Key Laboratory of Electronic Commerce and Logistics, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); Wong, Kwok-Wo [Department of Electronic Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong (Hong Kong); Li, Changbing [Key Laboratory of Electronic Commerce and Logistics, Chongqing University of Posts and Telecommunications, Chongqing 400065 (China); Li, Yang [Department of Automatic Control and Systems Engineering, The University of Sheffield, Mapping Street, S1 3DJ (United Kingdom)

    2012-01-30

    The substitution box (S-box) is an important component in block encryption algorithms. In this Letter, the problem of constructing S-box is transformed to a Traveling Salesman Problem and a method for designing S-box based on chaos and genetic algorithm is proposed. Since the proposed method makes full use of the traits of chaotic map and evolution process, stronger S-box is obtained. The results of performance test show that the presented S-box has good cryptographic properties, which justify that the proposed algorithm is effective in generating strong S-boxes. -- Highlights: ► The problem of constructing S-box is transformed to a Traveling Salesman Problem. ► We present a new method for designing S-box based on chaos and genetic algorithm. ► The proposed algorithm is effective in generating strong S-boxes.

  18. White Matter Fiber-based Analysis of T1w/T2w Ratio Map.

    Science.gov (United States)

    Chen, Haiwei; Budin, Francois; Noel, Jean; Prieto, Juan Carlos; Gilmore, John; Rasmussen, Jerod; Wadhwa, Pathik D; Entringer, Sonja; Buss, Claudia; Styner, Martin

    2017-02-01

    To develop, test, evaluate and apply a novel tool for the white matter fiber-based analysis of T1w/T2w ratio maps quantifying myelin content. The cerebral white matter in the human brain develops from a mostly non-myelinated state to a nearly fully mature white matter myelination within the first few years of life. High resolution T1w/T2w ratio maps are believed to be effective in quantitatively estimating myelin content on a voxel-wise basis. We propose the use of a fiber-tract-based analysis of such T1w/T2w ratio data, as it allows us to separate fiber bundles that a common regional analysis imprecisely groups together, and to associate effects to specific tracts rather than large, broad regions. We developed an intuitive, open source tool to facilitate such fiber-based studies of T1w/T2w ratio maps. Via its Graphical User Interface (GUI) the tool is accessible to non-technical users. The framework uses calibrated T1w/T2w ratio maps and a prior fiber atlas as an input to generate profiles of T1w/T2w values. The resulting fiber profiles are used in a statistical analysis that performs along-tract functional statistical analysis. We applied this approach to a preliminary study of early brain development in neonates. We developed an open-source tool for the fiber based analysis of T1w/T2w ratio maps and tested it in a study of brain development.

  19. White matter fiber-based analysis of T1w/T2w ratio map

    Science.gov (United States)

    Chen, Haiwei; Budin, Francois; Noel, Jean; Prieto, Juan Carlos; Gilmore, John; Rasmussen, Jerod; Wadhwa, Pathik D.; Entringer, Sonja; Buss, Claudia; Styner, Martin

    2017-02-01

    Purpose: To develop, test, evaluate and apply a novel tool for the white matter fiber-based analysis of T1w/T2w ratio maps quantifying myelin content. Background: The cerebral white matter in the human brain develops from a mostly non-myelinated state to a nearly fully mature white matter myelination within the first few years of life. High resolution T1w/T2w ratio maps are believed to be effective in quantitatively estimating myelin content on a voxel-wise basis. We propose the use of a fiber-tract-based analysis of such T1w/T2w ratio data, as it allows us to separate fiber bundles that a common regional analysis imprecisely groups together, and to associate effects to specific tracts rather than large, broad regions. Methods: We developed an intuitive, open source tool to facilitate such fiber-based studies of T1w/T2w ratio maps. Via its Graphical User Interface (GUI) the tool is accessible to non-technical users. The framework uses calibrated T1w/T2w ratio maps and a prior fiber atlas as an input to generate profiles of T1w/T2w values. The resulting fiber profiles are used in a statistical analysis that performs along-tract functional statistical analysis. We applied this approach to a preliminary study of early brain development in neonates. Results: We developed an open-source tool for the fiber based analysis of T1w/T2w ratio maps and tested it in a study of brain development.

  20. Twisted Diff S sup 1 -action on loop groups and representations of the Virasoro algebra

    Energy Technology Data Exchange (ETDEWEB)

    Harnad, J [Montreal Univ., Quebec (Canada). Centre de Recherches Mathematiques (CRM); Kupershmidt, B A [Tennessee Univ., Tullahoma (USA). Space Inst.

    1990-05-01

    A modified Hamiltonian action of Diff S{sup 1} on the phase space LG{sup C}/G{sup C}, where LG is a loop group, is defined by twisting the usual action by a left translation in LG. This twisted action is shown to be generated by a nonequivariant moment map, thereby defining a classical Poisson bracket realization of a central extension of the Lie algebra diff{sub C} S{sup 1}. The resulting formula expresses the Diff S{sup 1} generators in terms of the left LG translation generators, giving a shifted modification of both the classical and quantum versions of the Sugawara formula. (orig.).

  1. Identification for the optimal working parameters of Ti-6Al-4V-0.1Ru alloy in a wide deformation condition range by processing maps based on DMM

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Yu-feng; Long, Shuai; Zhou, Yu-ting; Zhao, Jia; Wang, Tian-yu; Zhou, Jie, E-mail: kkyttyls@vip.qq.com [School of Material Science and Engineering, Chongqing University (China)

    2016-11-15

    The hot deformation behaviours of Ti-6Al-4V-0.1Ru alloy were investigated by isothermal hot compression tests in the temperature range of 1023-1423 K and strain rate range of 0.01-10 s{sup -1}. The β transus was determined to be 1198 K by continuous heating method. The values of deformation activation energy Q at the strain of 0.3 were calculated to be 630.01 kJ/mol in dual-phase field and 331.75 kJ/mol in β-phase field. Moreover, the processing maps at the strain of 0.2, 0.4, 0.6 and 0.8 were developed based on dynamic materials model (DMM). To deeply understand the microstructure evolution mechanism during hot deformation processes and to verify the processing maps, the microstructures at different deformation conditions were observed. The stable microstructures (i.e. globularization, dynamic recovery (DRV) and β dynamic recrystallization (β-DRX)) and instable microstructures (i.e. lamellae kinking and flow localization) were obtained. To make it useful in the design of industrial hot working schedules for this material, a microstructural mechanism map was constructed on the basis of processing maps and microstructure observation. Deformation conditions in the vicinity of 1150 K & 0.01 s{sup -1} where globularization occurs and in the vicinity of 1323 K & 0.01 s{sup -1} where β-DRX occurs are recommended. (author)

  2. Blocking S1P interaction with S1P{sub 1} receptor by a novel competitive S1P{sub 1}-selective antagonist inhibits angiogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, Yasuyuki, E-mail: y.fujii@po.rd.taisho.co.jp [Department of Molecular Function and Pharmacology Laboratories, Taisho Pharmaceutical Co. Ltd., 1-403 Saitama, Saitama 331-9530 (Japan); Ueda, Yasuji; Ohtake, Hidenori; Ono, Naoya; Takayama, Tetsuo; Nakazawa, Kiyoshi [Department of Molecular Function and Pharmacology Laboratories, Taisho Pharmaceutical Co. Ltd., 1-403 Saitama, Saitama 331-9530 (Japan); Igarashi, Yasuyuki [Laboratory of Biomembrane and Biofunctional Chemistry, Hokkaido University, Sapporo, Hokkaido 060-0812 (Japan); Goitsuka, Ryo [Division of Development and Aging, Research Institute for Biological Sciences, Tokyo University of Science, Noda, Chiba 278-0022 (Japan)

    2012-03-23

    Highlights: Black-Right-Pointing-Pointer The effect of a newly developed S1P{sub 1}-selective antagonist on angiogenic responses. Black-Right-Pointing-Pointer S1P{sub 1} is a critical component of VEGF-related angiogenic responses. Black-Right-Pointing-Pointer S1P{sub 1}-selective antagonist showed in vitro activity to inhibit angiogenesis. Black-Right-Pointing-Pointer S1P{sub 1}-selective antagonist showed in vivo activity to inhibit angiogenesis. Black-Right-Pointing-Pointer The efficacy of S1P{sub 1}-selective antagonist for anti-cancer therapies. -- Abstract: Sphingosine 1-phosphate receptor type 1 (S1P{sub 1}) was shown to be essential for vascular maturation during embryonic development and it has been demonstrated that substantial crosstalk exists between S1P{sub 1} and other pro-angiogenic growth factors, such as vascular endothelial growth factor (VEGF) and basic fibroblast growth factor. We developed a novel S1P{sub 1}-selective antagonist, TASP0277308, which is structurally unrelated to S1P as well as previously described S1P{sub 1} antagonists. TASP0277308 inhibited S1P- as well as VEGF-induced cellular responses, including migration and proliferation of human umbilical vein endothelial cells. Furthermore, TASP0277308 effectively blocked a VEGF-induced tube formation in vitro and significantly suppressed tumor cell-induced angiogenesis in vivo. These findings revealed that S1P{sub 1} is a critical component of VEGF-related angiogenic responses and also provide evidence for the efficacy of TASP0277308 for anti-cancer therapies.

  3. St. Louis area earthquake hazards mapping project; seismic and liquefaction hazard maps

    Science.gov (United States)

    Cramer, Chris H.; Bauer, Robert A.; Chung, Jae-won; Rogers, David; Pierce, Larry; Voigt, Vicki; Mitchell, Brad; Gaunt, David; Williams, Robert; Hoffman, David; Hempen, Gregory L.; Steckel, Phyllis; Boyd, Oliver; Watkins, Connor M.; Tucker, Kathleen; McCallister, Natasha

    2016-01-01

    We present probabilistic and deterministic seismic and liquefaction hazard maps for the densely populated St. Louis metropolitan area that account for the expected effects of surficial geology on earthquake ground shaking. Hazard calculations were based on a map grid of 0.005°, or about every 500 m, and are thus higher in resolution than any earlier studies. To estimate ground motions at the surface of the model (e.g., site amplification), we used a new detailed near‐surface shear‐wave velocity model in a 1D equivalent‐linear response analysis. When compared with the 2014 U.S. Geological Survey (USGS) National Seismic Hazard Model, which uses a uniform firm‐rock‐site condition, the new probabilistic seismic‐hazard estimates document much more variability. Hazard levels for upland sites (consisting of bedrock and weathered bedrock overlain by loess‐covered till and drift deposits), show up to twice the ground‐motion values for peak ground acceleration (PGA), and similar ground‐motion values for 1.0 s spectral acceleration (SA). Probabilistic ground‐motion levels for lowland alluvial floodplain sites (generally the 20–40‐m‐thick modern Mississippi and Missouri River floodplain deposits overlying bedrock) exhibit up to twice the ground‐motion levels for PGA, and up to three times the ground‐motion levels for 1.0 s SA. Liquefaction probability curves were developed from available standard penetration test data assuming typical lowland and upland water table levels. A simplified liquefaction hazard map was created from the 5%‐in‐50‐year probabilistic ground‐shaking model. The liquefaction hazard ranges from low (60% of area expected to liquefy) in the lowlands. Because many transportation routes, power and gas transmission lines, and population centers exist in or on the highly susceptible lowland alluvium, these areas in the St. Louis region are at significant potential risk from seismically induced liquefaction and associated

  4. Radon risk mapping of the Czech Republic on a scale 1:50000

    International Nuclear Information System (INIS)

    Barnet, I.; Miksova, J.; Tomas, R.; Karenova, J.

    2000-01-01

    A new type of radon risk maps on a scale 1:50000 was published in the Czech Republic. Maps are based on the vectorized contours of' geological units and rock types and field soil gas radon measurements from the radon database. Radon risk is expressed in four categories. More detailed topography enables to predict the radon risk from bedrock in the intravilans of villages and towns. (author)

  5. MRI T2 Mapping of the Knee Articular Cartilage Using Different Acquisition Sequences and Calculation Methods at 1.5 Tesla.

    Science.gov (United States)

    Mars, Mokhtar; Bouaziz, Mouna; Tbini, Zeineb; Ladeb, Fethi; Gharbi, Souha

    2018-06-12

    This study aims to determine how Magnetic Resonance Imaging (MRI) acquisition techniques and calculation methods affect T2 values of knee cartilage at 1.5 Tesla and to identify sequences that can be used for high-resolution T2 mapping in short scanning times. This study was performed on phantom and twenty-nine patients who underwent MRI of the knee joint at 1.5 Tesla. The protocol includes T2 mapping sequences based on Single Echo Spin Echo (SESE), Multi-Echo Spin Echo (MESE), Fast Spin Echo (FSE) and Turbo Gradient Spin Echo (TGSE). The T2 relaxation times were quantified and evaluated using three calculation methods (MapIt, Syngo Offline and monoexponential fit). Signal to Noise Ratios (SNR) were measured in all sequences. All statistical analyses were performed using the t-test. The average T2 values in phantom were 41.7 ± 13.8 ms for SESE, 43.2 ± 14.4 ms for MESE, 42.4 ± 14.1 ms for FSE and 44 ± 14.5 ms for TGSE. In the patient study, the mean differences were 6.5 ± 8.2 ms, 7.8 ± 7.6 ms and 8.4 ± 14.2 ms for MESE, FSE and TGSE compared to SESE respectively; these statistical results were not significantly different (p > 0.05). The comparison between the three calculation methods showed no significant difference (p > 0.05). t-Test showed no significant difference between SNR values for all sequences. T2 values depend not only on the sequence type but also on the calculation method. None of the sequences revealed significant differences compared to the SESE reference sequence. TGSE with its short scanning time can be used for high-resolution T2 mapping. ©2018The Author(s). Published by S. Karger AG, Basel.

  6. 3D Mapping of the SPRY2 domain of ryanodine receptor 1 by single-particle cryo-EM.

    Directory of Open Access Journals (Sweden)

    Alex Perálvarez-Marín

    Full Text Available The type 1 skeletal muscle ryanodine receptor (RyR1 is principally responsible for Ca(2+ release from the sarcoplasmic reticulum and for the subsequent muscle contraction. The RyR1 contains three SPRY domains. SPRY domains are generally known to mediate protein-protein interactions, however the location of the three SPRY domains in the 3D structure of the RyR1 is not known. Combining immunolabeling and single-particle cryo-electron microscopy we have mapped the SPRY2 domain (S1085-V1208 in the 3D structure of RyR1 using three different antibodies against the SPRY2 domain. Two obstacles for the image processing procedure; limited amount of data and signal dilution introduced by the multiple orientations of the antibody bound in the tetrameric RyR1, were overcome by modifying the 3D reconstruction scheme. This approach enabled us to ascertain that the three antibodies bind to the same region, to obtain a 3D reconstruction of RyR1 with the antibody bound, and to map SPRY2 to the periphery of the cytoplasmic domain of RyR1. We report here the first 3D localization of a SPRY2 domain in any known RyR isoform.

  7. The Arizona Radio Observatory CO Mapping Survey of Galactic Molecular Clouds. V. The Sh2-235 Cloud in CO J=2-1, 13CO J=2-1, and CO J=3-2

    Science.gov (United States)

    Bieging, John H.; Patel, Saahil; Peters, William L.; Toth, L. Viktor; Marton, Gábor; Zahorecz, Sarolta

    2016-09-01

    We present the results of a program to map the Sh2-235 molecular cloud complex in the CO and 13CO J = 2 - 1 transitions using the Heinrich Hertz Submillimeter Telescope. The map resolution is 38″ (FWHM), with an rms noise of 0.12 K brightness temperature, for a velocity resolution of 0.34 km s-1. With the same telescope, we also mapped the CO J = 3 - 2 line at a frequency of 345 GHz, using a 64 beam focal plane array of heterodyne mixers, achieving a typical rms noise of 0.5 K brightness temperature with a velocity resolution of 0.23 km s-1. The three spectral line data cubes are available for download. Much of the cloud appears to be slightly sub-thermally excited in the J = 3 level, except for in the vicinity of the warmest and highest column density areas, which are currently forming stars. Using the CO and 13CO J = 2 - 1 lines, we employ an LTE model to derive the gas column density over the entire mapped region. Examining a 125 pc2 region centered on the most active star formation in the vicinity of Sh2-235, we find that the young stellar object surface density scales as approximately the 1.6-power of the gas column density. The area distribution function of the gas is a steeply declining exponential function of gas column density. Comparison of the morphology of ionized and molecular gas suggests that the cloud is being substantially disrupted by expansion of the H II regions, which may be triggering current star formation.

  8. Molecular Mapping of PMR1, a Novel Locus Conferring Resistance to Powdery Mildew in Pepper (Capsicum annuum).

    Science.gov (United States)

    Jo, Jinkwan; Venkatesh, Jelli; Han, Koeun; Lee, Hea-Young; Choi, Gyung Ja; Lee, Hee Jae; Choi, Doil; Kang, Byoung-Cheorl

    2017-01-01

    Powdery mildew, caused by Leveillula taurica , is a major fungal disease affecting greenhouse-grown pepper ( Capsicum annuum ). Powdery mildew resistance has a complex mode of inheritance. In the present study, we investigated a novel powdery mildew resistance locus, PMR1 , using two mapping populations: 102 'VK515' F 2:3 families (derived from a cross between resistant parental line 'VK515R' and susceptible parental line 'VK515S') and 80 'PM Singang' F 2 plants (derived from the F 1 'PM Singang' commercial hybrid). Genetic analysis of the F 2:3 'VK515' and F 2 'PM Singang' populations revealed a single dominant locus for inheritance of the powdery mildew resistance trait. Genetic mapping showed that the PMR1 locus is located on syntenic regions of pepper chromosome 4 in a 4-Mb region between markers CZ2_11628 and HRM4.1.6 in 'VK515R'. Six molecular markers including one SCAR marker and five SNP markers were localized to a region 0 cM from the PMR1 locus. Two putative nucleotide-binding site leucine-rich repeat (NBS-LRR)-type disease resistance genes were identified in this PMR1 region. Genotyping-by-sequencing (GBS) and genetic mapping analysis revealed suppressed recombination in the PMR1 region, perhaps due to alien introgression. In addition, a comparison of species-specific InDel markers as well as GBS-derived SNP markers indicated that C. baccatum represents a possible source of such alien introgression of powdery mildew resistance into 'VK515R'. The molecular markers developed in this study will be especially helpful for marker-assisted selection in pepper breeding programs for powdery mildew resistance.

  9. EX1202L1 Seafloor Mapping Products Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard suite of multibeam survey mapping products generated by the Okeanos Explorer seafloor mapping team on data collected on NOAA Ship Okeanos Explorer during...

  10. EX1605L1 Seafloor Mapping Products Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard suite of multibeam survey mapping products generated by the Okeanos Explorer seafloor mapping team on data collected on NOAA Ship Okeanos Explorer during...

  11. EX1004L1 Seafloor Mapping Products Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard suite of multibeam survey mapping products generated by the Okeanos Explorer seafloor mapping team on data collected on NOAA Ship Okeanos Explorer during...

  12. EX1503L1 Seafloor Mapping Products Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard suite of multibeam survey mapping products generated by the Okeanos Explorer seafloor mapping team on data collected on NOAA Ship Okeanos Explorer during...

  13. EX1205L1 Seafloor Mapping Products Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard suite of multibeam survey mapping products generated by the Okeanos Explorer seafloor mapping team on data collected on NOAA Ship Okeanos Explorer during...

  14. EX1502L1 Seafloor Mapping Products Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard suite of multibeam survey mapping products generated by the Okeanos Explorer seafloor mapping team on data collected on NOAA Ship Okeanos Explorer during...

  15. EX1504L1 Seafloor Mapping Products Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard suite of multibeam survey mapping products generated by the Okeanos Explorer seafloor mapping team on data collected on NOAA Ship Okeanos Explorer during...

  16. EX1404L1 Seafloor Mapping Products Collection

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard suite of multibeam survey mapping products generated by the Okeanos Explorer seafloor mapping team on data collected on NOAA Ship Okeanos Explorer during...

  17. Digital geologic map and Landsat image map of parts of Loralai, Sibi, Quetta, and Khuzar Divisions, Balochistan Province, west-central Pakistan

    Science.gov (United States)

    Maldonado, Florian; Menga, Jan Mohammad; Khan, Shabid Hasan; Thomas, Jean-Claude

    2011-01-01

    This generalized digital geologic map of west-central Pakistan is a product of the Balochistan Coal-Basin Synthesis Study, which was part of a cooperative program of the Geological Survey of Pakistan and the United States Geological Survey. The original nondigital map was published by Maldonado and others (1998). Funding was provided by the Government of Pakistan and the United States Agency for International Development. The sources of geologic map data are primarily 1:253,440-scale geologic maps obtained from Hunting Survey Corporation (1961) and the geologic map of the Muslim Bagh Ophiolite Complex and Bagh Complex area. The geology was modified based on reconnaissance field work and photo interpretation of 1:250,000-scale Landsat Thematic Mapper photo image. The descriptions and thicknesses of map units were based on published and unpublished reports and converted to U.S. Geological Survey format. In the nomenclature of the Geological Survey of Pakistan, there is both an Urak Group and an Urak Formation.

  18. The quantitative determination of metabolites of 6-mercaptopurine in biological materials. VI. Evidence for posttranscriptional modification of 6-thioguanosine residues in RNA from L5178Y cells treated with 6-mercaptopurine.

    Science.gov (United States)

    Breter, H J

    1985-05-24

    Mammalian cells incorporate 6-thioguanosine into their nucleic acids when grown in the presence of 6-mercaptopurine. 35S-labeled total RNA was prepared from L5178Y murine lymphoma cells grown in vitro in the presence of 6-[35S]mercaptopurine. Base analyses of this RNA suggested that 6-thioguanosine residues in RNA molecules undergo posttranscriptional modification. Thus, enzymatic peak-shifting analyses using anion-exchange high-performance liquid chromatography were applied to the hydrolysis products released from total RNA preparations by digestion with nuclease P1 or nuclease P1 plus nucleotide pyrophosphatase. At least eight 35S-labeled, phosphatase-sensitive compounds structurally different from [35S]6thioGMP were found in nuclease P1 digests. Four of these compounds were susceptible to cleavage with nucleotide pyrophosphatase, thus indicating that they contained phosphoric acid anhydride bonds. Individual RNA species were not separately examined, the radiochromatographic data, however, which were obtained from digests of total RNA preparations, present evidence that 6-thioguanosine 5'-diphosphate and 6-thioguanosine 5'-triphosphate exist as 5'-terminal starting nucleotides (in tRNA and rRNA) and that 6-thioguanosine becomes incorporated into the highly modified dinucleoside triphosphate structures (caps) which commonly block the 5'-termini of eukaryotic poly(A)+ mRNA-molecules.

  19. USGS Transportation Overlay Map Service from The National Map

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Transportation service from The National Map (TNM) is based on TIGER/Line data provided through U.S. Census Bureau and road data from U.S. Forest Service....

  20. Mapping the universe.

    Science.gov (United States)

    Geller, M J; Huchra, J P

    1989-11-17

    Maps of the galaxy distribution in the nearby universe reveal large coherent structures. The extent of the largest features is limited only by the size of the survey. Voids with a density typically 20 percent of the mean and with diameters of 5000 km s(-1) are present in every survey large enough to contain them. Many galaxies lie in thin sheet-like structures. The largest sheet detected so far is the "Great Wall" with a minimum extent of 60 h(-1) Mpc x 170 h(-1) Mpc, where h is the Hubble constant in units of 100 km s(-1) Mpc(-1). The frequent occurrence of these structures is one of several serious challenges to our current understanding of the origin and evolution of the large-scale distribution of matter in the universe.

  1. Rapid whole brain myelin water content mapping without an external water standard at 1.5T.

    Science.gov (United States)

    Nguyen, Thanh D; Spincemaille, Pascal; Gauthier, Susan A; Wang, Yi

    2017-06-01

    The objective of this study is to develop rapid whole brain mapping of myelin water content (MWC) at 1.5T. The Fast Acquisition with Spiral Trajectory and T2prep (FAST-T2) pulse sequence originally developed for myelin water fraction (MWF) mapping was modified to obtain fast mapping of T1 and receiver coil sensitivity needed for MWC computation. The accuracy of the proposed T1 mapping was evaluated by comparing with the standard IR-FSE method. Numerical simulations were performed to assess the accuracy and reliability of the proposed MWC mapping. We also compared MWC values obtained with either cerebrospinal fluid (CSF) or an external water tube attached to the subject's head as the water reference. Our results from healthy volunteers show that whole brain MWC mapping is feasible in 7min and provides accurate brain T1 values. Regional brain WC and MWC measurements obtained with the internal CSF-based water standard showed excellent correlation (R>0.99) and negligible bias within narrow limits of agreement compared to those obtained with an external water standard. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. GenProBiS: web server for mapping of sequence variants to protein binding sites.

    Science.gov (United States)

    Konc, Janez; Skrlj, Blaz; Erzen, Nika; Kunej, Tanja; Janezic, Dusanka

    2017-07-03

    Discovery of potentially deleterious sequence variants is important and has wide implications for research and generation of new hypotheses in human and veterinary medicine, and drug discovery. The GenProBiS web server maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein-protein, protein-nucleic acid, protein-compound, and protein-metal ion binding sites. The concept of a protein-compound binding site is understood in the broadest sense, which includes glycosylation and other post-translational modification sites. Binding sites were defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach with new improvements introduced in GenProBiS. Binding site surfaces were generated as three-dimensional grids encompassing the space occupied by predicted ligands. The server allows intuitive visual exploration of comprehensively mapped variants, such as human somatic mis-sense mutations related to cancer and non-synonymous single nucleotide polymorphisms from 21 species, within the predicted binding sites regions for about 80 000 PDB protein structures using fast WebGL graphics. The GenProBiS web server is open and free to all users at http://genprobis.insilab.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Opposing Effects of Zac1 and Curcumin on AP-1-Regulated Expressions of S100A7.

    Directory of Open Access Journals (Sweden)

    Yu-Wen Chu

    Full Text Available ZAC, an encoding gene mapped at chromosome 6q24-q25 within PSORS1, was previously found over-expressed in the lower compartment of the hyperplastic epidermis in psoriatic lesions. Cytokines produced in the inflammatory dermatoses may drive AP-1 transcription factor to induce responsive gene expressions. We demonstrated that mZac1 can enhance AP-1-responsive S100A7 expression of which the encoding gene was located in PSORS4 with HaCaT keratinocytes. However, the mZac1-enhanced AP-1 transcriptional activity was suppressed by curcumin, indicating the anti-inflammatory property of this botanical agent and is exhibited by blocking the AP-1-mediated cross-talk between PSORS1 and PSORS4. Two putative AP-1-binding sites were found and demonstrated to be functionally important in the regulation of S100A7 promoter activity. Moreover, we found curcumin reduced the DNA-binding activity of AP-1 to the recognition element located in the S100A7 promoter. The S100A7 expression was found to be upregulated in the lesioned epidermis of atopic dermatitis and psoriasis, which is where this keratinocyte-derived chemoattractant engaged in the pro-inflammatory feedback loop. Understanding the regulatory mechanism of S100A7 expression will be helpful to develop therapeutic strategies for chronic inflammatory dermatoses via blocking the reciprocal stimuli between the inflammatory cells and keratinocytes.

  4. Geologic Mapping of the Olympus Mons Volcano, Mars

    Science.gov (United States)

    Bleacher, J. E.; Williams, D. A.; Shean, D.; Greeley, R.

    2012-01-01

    We are in the third year of a three-year Mars Data Analysis Program project to map the morphology of the Olympus Mons volcano, Mars, using ArcGIS by ESRI. The final product of this project is to be a 1:1,000,000-scale geologic map. The scientific questions upon which this mapping project is based include understanding the volcanic development and modification by structural, aeolian, and possibly glacial processes. The project s scientific objectives are based upon preliminary mapping by Bleacher et al. [1] along a approx.80-km-wide north-south swath of the volcano corresponding to High Resolution Stereo Camera (HRSC) image h0037. The preliminary project, which covered approx.20% of the volcano s surface, resulted in several significant findings, including: 1) channel-fed lava flow surfaces are areally more abundant than tube-fed surfaces by a ratio of 5:1, 2) channel-fed flows consistently embay tube-fed flows, 3) lava fans appear to be linked to tube-fed flows, 4) no volcanic vents were identified within the map region, and 5) a Hummocky unit surrounds the summit and is likely a combination of non-channelized flows, dust, ash, and/or frozen volatiles. These results led to the suggestion that the volcano had experienced a transition from long-lived tube-forming eruptions to more sporadic and shorter-lived, channel-forming eruptions, as seen at Hawaiian volcanoes between the tholeiitic shield building phase (Kilauea to Mauna Loa) and alkalic capping phase (Hualalai and Mauna Kea).

  5. Grain size effect of monolayer MoS2 transistors characterized by second harmonic generation mapping

    KAUST Repository

    Lin, Chih-Pin

    2015-08-27

    We investigated different CVD-synthesized MoS2 films, aiming to correlate the device characteristics with the grain size. The grain size of MoS2 can be precisely characterized through nondestructive second harmonic generation mapping based on the degree of inversion symmetry. The devices with larger grains at the channel region show improved on/off current ratio, which can be explained by the less carrier scattering caused by the grain boundaries.

  6. Physical mapping of 5S and 18S ribosomal DNA in three species of Agave (Asparagales, Asparagaceae

    Directory of Open Access Journals (Sweden)

    Victor Manuel Gomez-Rodriguez

    2013-08-01

    Full Text Available Agave Linnaeus, 1753 is endemic of America and is considered one of the most important crops in Mexico due to its key role in the country’s economy. Cytogenetic analysis was carried out in A. tequilana Weber, 1902 ‘Azul’, A. cupreata Trelease et Berger, 1915 and A. angustifolia Haworth, 1812. The analysis showed that in all species the diploid chromosome number was 2n = 60, with bimodal karyotypes composed of five pairs of large chromosomes and 25 pairs of small chromosomes. Furthermore, different karyotypical formulae as well as a secondary constriction in a large chromosome pair were found in all species. Fluorescent in situ hybridization (FISH was used for physical mapping of 5S and 18S ribosomal DNA (rDNA. All species analyzed showed that 5S rDNA was located in both arms of a small chromosome pair, while 18S rDNA was associated with the secondary constriction of a large chromosome pair. Data of FISH analysis provides new information about the position and number of rDNA loci and helps for detection of hybrids in breeding programs as well as evolutionary studies.

  7. Crystallization and preliminary crystallographic analysis of an Escherichia coli-selected mutant of the nuclease domain of the metallonuclease colicin E7

    DEFF Research Database (Denmark)

    Czene, Aniko; Toth, Eszter; Gyurcsik, Bela

    2013-01-01

    The metallonuclease colicin E7 is a member of the HNH family of endonucleases. It serves as a bacterial toxin in Escherichia coli, protecting the host cell from other related bacteria and bacteriophages by degradation of their chromosomal DNA under environmental stress. Its cell-killing activity ....... X-ray diffraction data were collected to 1.6 Å resolution and could be indexed and averaged in the trigonal space group P3121 or P3221, with unit-cell parameters a = b = 55.4, c = 73.1 Å. Structure determination by molecular replacement is in progress.......The metallonuclease colicin E7 is a member of the HNH family of endonucleases. It serves as a bacterial toxin in Escherichia coli, protecting the host cell from other related bacteria and bacteriophages by degradation of their chromosomal DNA under environmental stress. Its cell-killing activity...... is attributed to the nonspecific nuclease domain (NColE7), which possesses the catalytic ββα-type metal ion-binding HNH motif at its C-terminus. Mutations affecting the positively charged amino acids at the N-terminus of NColE7 (444-576) surprisingly showed no or significantly reduced endonuclease activity...

  8. US Topo—Topographic maps for the Nation

    Science.gov (United States)

    Fishburn, Kristin A.; Carswell, William J.

    2017-06-23

    Building on the success of 125 years of mapping, the U.S. Geological Survey created US Topo, a georeferenced digital map produced from The National Map data. US Topo maps are designed to be used like the traditional 7.5-minute quadrangle paper topographic maps for which the U.S. Geological Survey is so well known. However, in contrast to paper-based maps, US Topo maps provide modern technological advantages that support faster, wider public distribution and basic, onscreen geospatial analysis, including the georeferencing capability to display the ground coordinate location as the user moves the cursor around the map.

  9. Allelism analysis of BrRfp locus in different restorer lines and map-based cloning of a fertility restorer gene, BrRfp1, for pol CMS in Chinese cabbage (Brassica rapa L.).

    Science.gov (United States)

    Zhang, Huamin; Wu, Junqing; Dai, Zihui; Qin, Meiling; Hao, Lingyu; Ren, Yanjing; Li, Qingfei; Zhang, Lugang

    2017-03-01

    In Chinese cabbage, there are two Rf loci for pol CMS and one of them was mapped to a 12.6-kb region containing a potential candidate gene encoding PPR protein. In Chinese cabbage (Brassica rapa), polima cytoplasmic male sterility (pol CMS) is an important CMS type and is widely used for hybrid breeding. By extensive test crossing in Chinese cabbage, four restorer lines (92s105, 01s325, 00s109, and 88s148) for pol CMS were screened. By analyzing the allelism of the four restorer lines, it was found that 92s105, 01s325, and 00s109 had the same "restorers of fertility" (Rf) locus (designated as BrRfp1), but 88s148 had a different Rf locus (designated as BrRfp2). For fine mapping the BrRfp1 locus of 92s105, a BC 1 F 1 population with 487 individuals and a BC 1 F 2 population with 2485 individuals were successively constructed. Using simple sequence repeat (SSR) markers developed from Brassica rapa reference genome and InDel markers derived from whole-genome resequencing data of 94c9 and 92s105, BrRfp1 was mapped to a 12.6-kb region containing a potential candidate gene encoding pentatricopeptide repeat-containing protein. Based on the nucleotide polymorphisms of the candidate gene sequence between the restoring and nonrestoring alleles, a co-segregating marker SC718 was developed, which would be helpful for hybrid breeding by marker-assisted screening and for detecting new restorer lines.

  10. Agrobacterium: nature’s genetic engineer

    Science.gov (United States)

    Nester, Eugene W.

    2015-01-01

    Agrobacterium was identified as the agent causing the plant tumor, crown gall over 100 years ago. Since then, studies have resulted in many surprising observations. Armin Braun demonstrated that Agrobacterium infected cells had unusual nutritional properties, and that the bacterium was necessary to start the infection but not for continued tumor development. He developed the concept of a tumor inducing principle (TIP), the factor that actually caused the disease. Thirty years later the TIP was shown to be a piece of a tumor inducing (Ti) plasmid excised by an endonuclease. In the next 20 years, most of the key features of the disease were described. The single-strand DNA (T-DNA) with the endonuclease attached is transferred through a type IV secretion system into the host cell where it is likely coated and protected from nucleases by a bacterial secreted protein to form the T-complex. A nuclear localization signal in the endonuclease guides the transferred strand (T-strand), into the nucleus where it is integrated randomly into the host chromosome. Other secreted proteins likely aid in uncoating the T-complex. The T-DNA encodes enzymes of auxin, cytokinin, and opine synthesis, the latter a food source for Agrobacterium. The genes associated with T-strand formation and transfer (vir) map to the Ti plasmid and are only expressed when the bacteria are in close association with a plant. Plant signals are recognized by a two-component regulatory system which activates vir genes. Chromosomal genes with pleiotropic functions also play important roles in plant transformation. The data now explain Braun’s old observations and also explain why Agrobacterium is nature’s genetic engineer. Any DNA inserted between the border sequences which define the T-DNA will be transferred and integrated into host cells. Thus, Agrobacterium has become the major vector in plant genetic engineering. PMID:25610442

  11. Rotational hypersurfaces with $L_r$-pointwise 1-type Gauss map

    Directory of Open Access Journals (Sweden)

    Akram Mohammadpouri

    2018-07-01

    Full Text Available In this paper, we study hypersurfaces in $\\E^{n+1}$ which Gauss map $G$ satisfies the equation $L_rG = f(G + C$ for a smooth function $f$ and a constant vector $C$, where $L_r$ is the linearized operator of the $(r + 1$th mean curvature of the hypersurface, i.e., $L_r(f=tr(P_r\\circ\

  12. Fine Mapping of Two Wheat Powdery Mildew Resistance Genes Located at the Pm1 Cluster

    Directory of Open Access Journals (Sweden)

    Junchao Liang

    2016-07-01

    Full Text Available Powdery mildew caused by (DC. f. sp. ( is a globally devastating foliar disease of wheat ( L.. More than a dozen genes against this disease, identified from wheat germplasms of different ploidy levels, have been mapped to the region surrounding the locus on the long arm of chromosome 7A, which forms a resistance (-gene cluster. and from einkorn wheat ( L. were two of the genes belonging to this cluster. This study was initiated to fine map these two genes toward map-based cloning. Comparative genomics study showed that macrocolinearity exists between L. chromosome 1 (Bd1 and the – region, which allowed us to develop markers based on the wheat sequences orthologous to genes contained in the Bd1 region. With these and other newly developed and published markers, high-resolution maps were constructed for both and using large F populations. Moreover, a physical map of was constructed through chromosome walking with bacterial artificial chromosome (BAC clones and comparative mapping. Eventually, and were restricted to a 0.12- and 0.86-cM interval, respectively. Based on the closely linked common markers, , , and (another powdery mildew resistance gene in the cluster were not allelic to one another. Severe recombination suppression and disruption of synteny were noted in the region encompassing . These results provided useful information for map-based cloning of the genes in the cluster and interpretation of their evolution.

  13. Single-shot T1 mapping of the corpus callosum: A rapid characterization of fiber bundle anatomy

    Directory of Open Access Journals (Sweden)

    Sabine eHofer

    2015-05-01

    Full Text Available Using diffusion-tensor MRI and fiber tractography the topographic organization of the corpus callosum (CC has been described to comprise 5 segments with fibers projecting into prefrontal (I, premotor and supplementary motor (II, primary motor (III, and primary sensory areas (IV, as well as into parietal, temporal, and occipital cortical areas (V. In order to more rapidly characterize the underlying anatomy of these segments, this study used a novel single-shot T1 mapping method to quantitatively determine T1 relaxation times in the human CC. A region-of-interest analysis revealed a tendency for the lowest T1 relaxation times in the genu and the highest T1 relaxation times in the somatomotor region of the CC. This observation separates regions dominated by myelinated fibers with large diameters (somatomotor area from densely packed smaller axonal bundles (genu with less myelin. The results indicate that characteristic T1 relaxation times in callosal profiles provide an additional means to monitor differences in fiber anatomy, fiber density, and gray matter in respective neocortical areas. In conclusion, rapid T1 mapping allows for a characterization of the axonal architecture in an individual CC in less than 10 s. The approach emerges as a valuable means for studying neocortical brain anatomy with possible implications for the diagnosis of neurodegenerative processes.

  14. Mapping Vinyl Cyanide and Other Nitriles in Titan’s Atmosphere Using ALMA

    Energy Technology Data Exchange (ETDEWEB)

    Lai, J. C.-Y.; Cordiner, M. A.; Nixon, C. A.; Achterberg, R. K.; Molter, E. M.; Palmer, M. Y.; Charnley, S. B.; Lindberg, J. E.; Mumma, M. J. [NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, MD 20771 (United States); Teanby, N. A. [School of Earth Sciences, University of Bristol, Wills Memorial Building, Queen’s Road, Bristol, BS8 1RJ (United Kingdom); Kisiel, Z. [Institute of Physics, Polish Academy of Sciences, Al. Lotnikøw 32/46, 02-668 Warszawa (Poland); Irwin, P. G. J., E-mail: martin.cordiner@nasa.gov [Atmospheric, Oceanic and Planetary Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford, OX1 3PU (United Kingdom)

    2017-11-01

    Vinyl cyanide (C{sub 2}H{sub 3}CN) is theorized to form in Titan’s atmosphere via high-altitude photochemistry and is of interest regarding the astrobiology of cold planetary surfaces due to its predicted ability to form cell membrane-like structures (azotosomes) in liquid methane. In this work, we follow up on the initial spectroscopic detection of C{sub 2}H{sub 3}CN on Titan by Palmer et al. with the detection of three new C{sub 2}H{sub 3}CN rotational emission lines at submillimeter frequencies. These new, high-resolution detections have allowed for the first spatial distribution mapping of C{sub 2}H{sub 3}CN on Titan. We present simultaneous observations of C{sub 2}H{sub 5}CN, HC{sub 3}N, and CH{sub 3}CN emission, and obtain the first (tentative) detection of C{sub 3}H{sub 8} (propane) at radio wavelengths. We present disk-averaged vertical abundance profiles, two-dimensional spatial maps, and latitudinal flux profiles for the observed nitriles. Similarly to HC{sub 3}N and C{sub 2}H{sub 5}CN, which are theorized to be short-lived in Titan’s atmosphere, C{sub 2}H{sub 3}CN is most abundant over the southern (winter) pole, whereas the longer-lived CH{sub 3}CN is more concentrated in the north. This abundance pattern is consistent with the combined effects of high-altitude photochemical production, poleward advection, and the subsequent reversal of Titan’s atmospheric circulation system following the recent transition from northern to southern winter. We confirm that C{sub 2}H{sub 3}CN and C{sub 2}H{sub 5}CN are most abundant at altitudes above 200 km. Using a 300 km step model, the average abundance of C{sub 2}H{sub 3}CN is found to be 3.03 ± 0.29 ppb, with a C{sub 2}H{sub 5}CN/C{sub 2}H{sub 3}CN abundance ratio of 2.43 ± 0.26. Our HC{sub 3}N and CH{sub 3}CN spectra can be accurately modeled using abundance gradients above the tropopause, with fractional scale-heights of 2.05 ± 0.16 and 1.63 ± 0.02, respectively.

  15. Biochemical analyses indicate that binding and cleavage specificities define the ordered processing of human Okazaki fragments by Dna2 and FEN1.

    Science.gov (United States)

    Gloor, Jason W; Balakrishnan, Lata; Campbell, Judith L; Bambara, Robert A

    2012-08-01

    In eukaryotic Okazaki fragment processing, the RNA primer is displaced into a single-stranded flap prior to removal. Evidence suggests that some flaps become long before they are cleaved, and that this cleavage involves the sequential action of two nucleases. Strand displacement characteristics of the polymerase show that a short gap precedes the flap during synthesis. Using biochemical techniques, binding and cleavage assays presented here indicate that when the flap is ∼ 30 nt long the nuclease Dna2 can bind with high affinity to the flap and downstream double strand and begin cleavage. When the polymerase idles or dissociates the Dna2 can reorient for additional contacts with the upstream primer region, allowing the nuclease to remain stably bound as the flap is further shortened. The DNA can then equilibrate to a double flap that can bind Dna2 and flap endonuclease (FEN1) simultaneously. When Dna2 shortens the flap even more, FEN1 can displace the Dna2 and cleave at the flap base to make a nick for ligation.

  16. USGS Imagery Topo Large-scale Base Map Service from The National Map

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The USGS Imagery Topo Large service from The National Map (TNM) is a dynamic topographic base map service that combines the best available data (Boundaries,...

  17. Induction of MAP Kinase Homologues during Growth and Morphogenetic Development of Karnal Bunt (Tilletia indica) under the Influence of Host Factor(s) from Wheat Spikes

    Science.gov (United States)

    Gupta, Atul K.; Seneviratne, J. M.; Joshi, G. K.; Kumar, Anil

    2012-01-01

    Signaling pathways that activate different mitogen-activated protein kinases (MAPKs) in response to certain environmental conditions, play important role in mating type switching (Fus3) and pathogenicity (Pmk1) in many fungi. In order to determine the roles of such regulatory genes in Tilletia indica, the causal pathogen of Karnal bunt (KB) of wheat, semi-quantitative and quantitative RT-PCR was carried out to isolate and determine the expression of MAP kinase homologues during fungal growth and development under in vitro culture. Maximum expression of TiFus3 and TiPmk1 genes were observed at 14th and 21st days of culture and decreased thereafter. To investigate whether the fungus alters the expression levels of same kinases upon interaction with plants, cultures were treated with 1% of host factors (extracted from S-2 stage of wheat spikes). Such treatment induced the expression of MAPks in time dependent manner compared to the absence of host factors. These results suggest that host factor(s) provide certain signal(s) which activate TiFus3 and TiPmk1 during morphogenetic development of T. indica. The results also provides a clue about the role of host factors in enhancing the disease potential due to induction of MAP kinases involved in fungal development and pathogenecity. PMID:22547988

  18. Methods in Mapping Usability of Malaysia’s Shopping Centre

    Directory of Open Access Journals (Sweden)

    Abdul Ghani Aida Affina

    2016-01-01

    Full Text Available With more than 200 number of shopping centre in Klang Valley itself, we the consumer actually have vast of choices. Instead of the machineries varieties from the lower class product till the posh one, each of those shopping centres eventually offers the typical product same as others. Those shopping centers are competing with each other and in great endeavour to attract more consumers, to visit and spend. As for the visitor, the typical product and boring ambience seems similar in all malls, and is looking something beyond the standard. Something that promising quality embedded in shopping centre which evokes the various emotions of the user along their journey in malls. This quality is known as usability. Usability; as defined generally is a global user’s experience response with product, environment, service or facilities. It is an assessment in extracting the qualities of shopping centre design. In mapping it, there are a few synthesizing methods to implement it. Therefore, this paper purposely to review the method that been used in usability of Malaysia’s shopping centre research with a few references on previous research done in usability assessment by predecessor’s scholars. With the accentuation on three elements that anchoring what the usability is: effectiveness, efficient and satisfaction, it is hope that this overview can lead other researcher in portraying its relationship with the quality and ‘user friendly’ design of shopping centre.

  19. The Schizosaccharomyces pombe map1 gene encodes an SRF/MCM1-related protein required for P-cell specific gene expression

    DEFF Research Database (Denmark)

    Nielsen, O; Friis, T; Kjaerulff, S

    1996-01-01

    Cells of Schizosaccharomyces pombe undergo mating and meiosis when starved for a nitrogen source. In this process a P and and M cell first mate to generate a diploid zygote, which subsequently enters meiosis and sporulates. The P mating type is controlled by the mat1-Pc gene at the mating type lo...... cerevisiae MCM1. The Mat1-Pc protein contains a motif characteristic for proteins that interact with MADS-box factors, suggesting that Mat-Pc and Map1 may form a heterodimer that activates the P-specific map3 gene....

  20. Molecular Mapping of PMR1, a Novel Locus Conferring Resistance to Powdery Mildew in Pepper (Capsicum annuum

    Directory of Open Access Journals (Sweden)

    Jinkwan Jo

    2017-12-01

    Full Text Available Powdery mildew, caused by Leveillula taurica, is a major fungal disease affecting greenhouse-grown pepper (Capsicum annuum. Powdery mildew resistance has a complex mode of inheritance. In the present study, we investigated a novel powdery mildew resistance locus, PMR1, using two mapping populations: 102 ‘VK515' F2:3 families (derived from a cross between resistant parental line ‘VK515R' and susceptible parental line ‘VK515S' and 80 ‘PM Singang' F2 plants (derived from the F1 ‘PM Singang' commercial hybrid. Genetic analysis of the F2:3 ‘VK515' and F2 ‘PM Singang' populations revealed a single dominant locus for inheritance of the powdery mildew resistance trait. Genetic mapping showed that the PMR1 locus is located on syntenic regions of pepper chromosome 4 in a 4-Mb region between markers CZ2_11628 and HRM4.1.6 in ‘VK515R'. Six molecular markers including one SCAR marker and five SNP markers were localized to a region 0 cM from the PMR1 locus. Two putative nucleotide-binding site leucine-rich repeat (NBS-LRR-type disease resistance genes were identified in this PMR1 region. Genotyping-by-sequencing (GBS and genetic mapping analysis revealed suppressed recombination in the PMR1 region, perhaps due to alien introgression. In addition, a comparison of species-specific InDel markers as well as GBS-derived SNP markers indicated that C. baccatum represents a possible source of such alien introgression of powdery mildew resistance into ‘VK515R'. The molecular markers developed in this study will be especially helpful for marker-assisted selection in pepper breeding programs for powdery mildew resistance.