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Sample records for s1-like nuclease coded

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

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

    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

  3. Recombinant Cyclophilins Lack Nuclease Activity

    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.

  4. Genome Editing in Rats Using TALE Nucleases.

    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.

  5. A sensitive assay for Staphylococcus aureus nucleases

    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.

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

    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.

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

    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, ...

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

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

    2017-05-15

    algorithm permitting the identification of genomic sequences with unexpected cleavage activity. The GUIDEseq package enables analysis of GUIDE-data from various nuclease platforms for any species with a defined genomic sequence. This software package has been used successfully to analyze several GUIDE-seq datasets. The software, source code and documentation are freely available at http://www.bioconductor.org/packages/release/bioc/html/GUIDEseq.html .

  9. Eukaryotic zinc-dependent multifunctional nuclease I

    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

  10. Origins of Programmable Nucleases for Genome Engineering.

    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

  11. Probing chromatin structure with nuclease sensitivity assays.

    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.

  12. TALE nucleases and next generation GM crops.

    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. Hybrid nanosensor for colorimetric and ultrasensitive detection of nuclease contaminations

    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.

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

    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.

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

    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.

  16. Halophilic Nuclease from a Moderately Halophilic Micrococcus varians

    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

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

    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...

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

    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.

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

    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

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

    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

  1. Antitumor Effects and Cytotoxicity of Recombinant Plant Nucleases

    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

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

    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.)

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

    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

  4. Phylogenomic analysis of the GIY-YIG nuclease superfamily

    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.

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

    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.

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

    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

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

    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...

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

    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 ...

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

    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.

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

    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...

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

    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...

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

    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.

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

    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.

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

    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.

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

    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

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

    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...

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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. ∗.

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

    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.

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

    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...

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

    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)

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

    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)

  8. Mung Bean nuclease mapping of RNAs 3' end

    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.

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

    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.

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

    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

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

    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...

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

    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.

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

    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...

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

    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...

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

    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

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

    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...

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

    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

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

    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.

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

    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

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

    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

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

    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

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

    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.

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

    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....

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

    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....

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

    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

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

    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

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

    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....

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

    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

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

    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.

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

    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

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

    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.

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

    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.

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

    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

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

    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.

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

    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.

  16. Code Cactus; Code Cactus

    Fajeau, M; Nguyen, L T; Saunier, J [Commissariat a l' Energie Atomique, Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France)

    1966-09-01

    This code handles the following problems: -1) Analysis of thermal experiments on a water loop at high or low pressure; steady state or transient behavior; -2) Analysis of thermal and hydrodynamic behavior of water-cooled and moderated reactors, at either high or low pressure, with boiling permitted; fuel elements are assumed to be flat plates: - Flowrate in parallel channels coupled or not by conduction across plates, with conditions of pressure drops or flowrate, variable or not with respect to time is given; the power can be coupled to reactor kinetics calculation or supplied by the code user. The code, containing a schematic representation of safety rod behavior, is a one dimensional, multi-channel code, and has as its complement (FLID), a one-channel, two-dimensional code. (authors) [French] Ce code permet de traiter les problemes ci-dessous: 1. Depouillement d'essais thermiques sur boucle a eau, haute ou basse pression, en regime permanent ou transitoire; 2. Etudes thermiques et hydrauliques de reacteurs a eau, a plaques, a haute ou basse pression, ebullition permise: - repartition entre canaux paralleles, couples on non par conduction a travers plaques, pour des conditions de debit ou de pertes de charge imposees, variables ou non dans le temps; - la puissance peut etre couplee a la neutronique et une representation schematique des actions de securite est prevue. Ce code (Cactus) a une dimension d'espace et plusieurs canaux, a pour complement Flid qui traite l'etude d'un seul canal a deux dimensions. (auteurs)

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

    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.

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

    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.

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

    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.

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

    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

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

    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

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

    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.

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

    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

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

    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

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

    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.

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

    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.

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

    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

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

    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

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

    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

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

    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.

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

    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.

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

    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.

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

    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.

  14. Identification of ‘safe harbor’ loci in indica rice genome by harnessing the property of zinc-finger nucleases to induce DNA damage and repair.

    Christian eCantos

    2014-06-01

    Full Text Available Zinc-finger nucleases (ZFNs have proved to be successful tools for targeted genome manipulation in several organisms. Their main property is the induction of double-strand breaks (DSBs at specific sites, which are further repaired through homologous recombination (HR or non-homologous end joining (NHEJ. However, for the appropriate integration of genes at specific chromosomal locations, proper sites for gene integration need to be identified. These regions, hereby named safe harbor loci, must be localized in non-coding regions and possess high gene expression. In the present study, three different ZFN constructs (pZFN1, pZFN2, pZFN3, harboring β-glucuronidase (GUS as a reporter gene, were used to identify safe harbor loci regions on rice chromosomes. The constructs were delivered into IR64 rice by using an improved Agrobacterium-mediated transformation protocol, based on the use of immature embryos. Gene expression was measured by histochemical GUS activity and the flanking regions were determined through thermal-asymmetric interlaced polymerase chain reaction (TAIL PCR. Following sequencing, 28 regions were identified as putative sites for safe integration, but only one was localized in a non-coding region and it also possessed high GUS expression. These findings have significant applicability to create crops with new and valuable traits, since the site can be subsequently used to stably introduce one or more genes in a targeted manner.

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

    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

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

    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

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

    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

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

    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

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

    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

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

    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

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

    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

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

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

    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.

  16. Coding Partitions

    Fabio Burderi

    2007-05-01

    Full Text Available Motivated by the study of decipherability conditions for codes weaker than Unique Decipherability (UD, we introduce the notion of coding partition. Such a notion generalizes that of UD code and, for codes that are not UD, allows to recover the ``unique decipherability" at the level of the classes of the partition. By tacking into account the natural order between the partitions, we define the characteristic partition of a code X as the finest coding partition of X. This leads to introduce the canonical decomposition of a code in at most one unambiguouscomponent and other (if any totally ambiguouscomponents. In the case the code is finite, we give an algorithm for computing its canonical partition. This, in particular, allows to decide whether a given partition of a finite code X is a coding partition. This last problem is then approached in the case the code is a rational set. We prove its decidability under the hypothesis that the partition contains a finite number of classes and each class is a rational set. Moreover we conjecture that the canonical partition satisfies such a hypothesis. Finally we consider also some relationships between coding partitions and varieties of codes.

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

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

    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

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

    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

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

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

    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

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

    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

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

    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.

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

    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)

  5. Suppression of HBV replication by the expression of nickase- and nuclease dead-Cas9.

    Kurihara, Takeshi; Fukuhara, Takasuke; Ono, Chikako; Yamamoto, Satomi; Uemura, Kentaro; Okamoto, Toru; Sugiyama, Masaya; Motooka, Daisuke; Nakamura, Shota; Ikawa, Masato; Mizokami, Masashi; Maehara, Yoshihiko; Matsuura, Yoshiharu

    2017-07-21

    Complete removal of hepatitis B virus (HBV) DNA from nuclei is difficult by the current therapies. Recent reports have shown that a novel genome-editing tool using Cas9 with a single-guide RNA (sgRNA) system can cleave the HBV genome in vitro and in vivo. However, induction of a double-strand break (DSB) on the targeted genome by Cas9 risks undesirable off-target cleavage on the host genome. Nickase-Cas9 cleaves a single strand of DNA, and thereby two sgRNAs are required for inducing DSBs. To avoid Cas9-induced off-target mutagenesis, we examined the effects of the expressions of nickase-Cas9 and nuclease dead Cas9 (d-Cas9) with sgRNAs on HBV replication. The expression of nickase-Cas9 with a pair of sgRNAs cleaved the target HBV genome and suppressed the viral-protein expression and HBV replication in vitro. Moreover, nickase-Cas9 with the sgRNA pair cleaved the targeted HBV genome in mouse liver. Interestingly, d-Cas9 expression with the sgRNAs also suppressed HBV replication in vitro without cleaving the HBV genome. These results suggest the possible use of nickase-Cas9 and d-Cas9 with a pair of sgRNAs for eliminating HBV DNA from the livers of chronic hepatitis B patients with low risk of undesirable off-target mutation on the host genome.

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

    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.

  7. DNA replication restart and cellular dynamics of Hef helicase/nuclease protein in Haloferax volcanii.

    Lestini, Roxane; Delpech, Floriane; Myllykallio, Hannu

    2015-11-01

    Understanding how frequently spontaneous replication arrests occur and how archaea deal with these arrests are very interesting and challenging research topics. Here we will described how genetic and imaging studies have revealed the central role of the archaeal helicase/nuclease Hef belonging to the XPF/MUS81/FANCM family of endonucleases in repair of arrested replication forks. Special focus will be on description of a recently developed combination of genetic and imaging tools to study the dynamic localization of a functional Hef::GFP (Green Fluorescent Protein) fusion protein in the living cells of halophilic archaea Haloferax volcanii. As Archaea provide an excellent and unique model for understanding how DNA replication is regulated to allow replication of a circular DNA molecule either from single or multiple replication origins, we will also summarize recent studies that have revealed peculiar features regarding DNA replication, particularly in halophilic archaea. We strongly believe that fundamental knowledge of our on-going studies will shed light on the evolutionary history of the DNA replication machinery and will help to establish general rules concerning replication restart and the key role of recombination proteins not only in bacteria, yeast and higher eukaryotes but also in archaea. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

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

    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.

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

    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.

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

    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.

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

    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.

  12. Speaking Code

    Cox, Geoff

    Speaking Code begins by invoking the “Hello World” convention used by programmers when learning a new language, helping to establish the interplay of text and code that runs through the book. Interweaving the voice of critical writing from the humanities with the tradition of computing and software...

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

    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

  14. Coding Labour

    Anthony McCosker

    2014-03-01

    Full Text Available As well as introducing the Coding Labour section, the authors explore the diffusion of code across the material contexts of everyday life, through the objects and tools of mediation, the systems and practices of cultural production and organisational management, and in the material conditions of labour. Taking code beyond computation and software, their specific focus is on the increasingly familiar connections between code and labour with a focus on the codification and modulation of affect through technologies and practices of management within the contemporary work organisation. In the grey literature of spreadsheets, minutes, workload models, email and the like they identify a violence of forms through which workplace affect, in its constant flux of crisis and ‘prodromal’ modes, is regulated and governed.

  15. AAV-mediated delivery of zinc finger nucleases targeting hepatitis B virus inhibits active replication.

    Nicholas D Weber

    Full Text Available Despite an existing effective vaccine, hepatitis B virus (HBV remains a major public health concern. There are effective suppressive therapies for HBV, but they remain expensive and inaccessible to many, and not all patients respond well. Furthermore, HBV can persist as genomic covalently closed circular DNA (cccDNA that remains in hepatocytes even during otherwise effective therapy and facilitates rebound in patients after treatment has stopped. Therefore, the need for an effective treatment that targets active and persistent HBV infections remains. As a novel approach to treat HBV, we have targeted the HBV genome for disruption to prevent viral reactivation and replication. We generated 3 zinc finger nucleases (ZFNs that target sequences within the HBV polymerase, core and X genes. Upon the formation of ZFN-induced DNA double strand breaks (DSB, imprecise repair by non-homologous end joining leads to mutations that inactivate HBV genes. We delivered HBV-specific ZFNs using self-complementary adeno-associated virus (scAAV vectors and tested their anti-HBV activity in HepAD38 cells. HBV-ZFNs efficiently disrupted HBV target sites by inducing site-specific mutations. Cytotoxicity was seen with one of the ZFNs. scAAV-mediated delivery of a ZFN targeting HBV polymerase resulted in complete inhibition of HBV DNA replication and production of infectious HBV virions in HepAD38 cells. This effect was sustained for at least 2 weeks following only a single treatment. Furthermore, high specificity was observed for all ZFNs, as negligible off-target cleavage was seen via high-throughput sequencing of 7 closely matched potential off-target sites. These results show that HBV-targeted ZFNs can efficiently inhibit active HBV replication and suppress the cellular template for HBV persistence, making them promising candidates for eradication therapy.

  16. Efficacy of a marine bacterial nuclease against biofilm forming microorganisms isolated from chronic rhinosinusitis.

    Robert C Shields

    Full Text Available BACKGROUND: The persistent colonization of paranasal sinus mucosa by microbial biofilms is a major factor in the pathogenesis of chronic rhinosinusitis (CRS. Control of microorganisms within biofilms is hampered by the presence of viscous extracellular polymers of host or microbial origin, including nucleic acids. The aim of this study was to investigate the role of extracellular DNA in biofilm formation by bacteria associated with CRS. METHODS/PRINCIPAL FINDINGS: Obstructive mucin was collected from patients during functional endoscopic sinus surgery. Examination of the mucous by transmission electron microscopy revealed an acellular matrix punctuated occasionally with host cells in varying states of degradation. Bacteria were observed in biofilms on mucosal biopsies, and between two and six different species were isolated from each of 20 different patient samples. In total, 16 different bacterial genera were isolated, of which the most commonly identified organisms were coagulase-negative staphylococci, Staphylococcus aureus and α-haemolytic streptococci. Twenty-four fresh clinical isolates were selected for investigation of biofilm formation in vitro using a microplate model system. Biofilms formed by 14 strains, including all 9 extracellular nuclease-producing bacteria, were significantly disrupted by treatment with a novel bacterial deoxyribonuclease, NucB, isolated from a marine strain of Bacillus licheniformis. Extracellular biofilm matrix was observed in untreated samples but not in those treated with NucB and extracellular DNA was purified from in vitro biofilms. CONCLUSION/SIGNIFICANCE: Our data demonstrate that bacteria associated with CRS form robust biofilms which can be reduced by treatment with matrix-degrading enzymes such as NucB. The dispersal of bacterial biofilms with NucB may offer an additional therapeutic target for CRS sufferers.

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

    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.

  18. Targeted mutagenesis using zinc-finger nucleases in perennial fruit trees.

    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.

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

    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.

  20. Gene repair of an Usher syndrome causing mutation by zinc-finger nuclease mediated homologous recombination.

    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.

  1. Speech coding

    Ravishankar, C., Hughes Network Systems, Germantown, MD

    1998-05-08

    Speech is the predominant means of communication between human beings and since the invention of the telephone by Alexander Graham Bell in 1876, speech services have remained to be the core service in almost all telecommunication systems. Original analog methods of telephony had the disadvantage of speech signal getting corrupted by noise, cross-talk and distortion Long haul transmissions which use repeaters to compensate for the loss in signal strength on transmission links also increase the associated noise and distortion. On the other hand digital transmission is relatively immune to noise, cross-talk and distortion primarily because of the capability to faithfully regenerate digital signal at each repeater purely based on a binary decision. Hence end-to-end performance of the digital link essentially becomes independent of the length and operating frequency bands of the link Hence from a transmission point of view digital transmission has been the preferred approach due to its higher immunity to noise. The need to carry digital speech became extremely important from a service provision point of view as well. Modem requirements have introduced the need for robust, flexible and secure services that can carry a multitude of signal types (such as voice, data and video) without a fundamental change in infrastructure. Such a requirement could not have been easily met without the advent of digital transmission systems, thereby requiring speech to be coded digitally. The term Speech Coding is often referred to techniques that represent or code speech signals either directly as a waveform or as a set of parameters by analyzing the speech signal. In either case, the codes are transmitted to the distant end where speech is reconstructed or synthesized using the received set of codes. A more generic term that is applicable to these techniques that is often interchangeably used with speech coding is the term voice coding. This term is more generic in the sense that the

  2. Optimal codes as Tanner codes with cyclic component codes

    Høholdt, Tom; Pinero, Fernando; Zeng, Peng

    2014-01-01

    In this article we study a class of graph codes with cyclic code component codes as affine variety codes. Within this class of Tanner codes we find some optimal binary codes. We use a particular subgraph of the point-line incidence plane of A(2,q) as the Tanner graph, and we are able to describe ...

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

    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...

  4. Aztheca Code

    Quezada G, S.; Espinosa P, G.; Centeno P, J.; Sanchez M, H.

    2017-09-01

    This paper presents the Aztheca code, which is formed by the mathematical models of neutron kinetics, power generation, heat transfer, core thermo-hydraulics, recirculation systems, dynamic pressure and level models and control system. The Aztheca code is validated with plant data, as well as with predictions from the manufacturer when the reactor operates in a stationary state. On the other hand, to demonstrate that the model is applicable during a transient, an event occurred in a nuclear power plant with a BWR reactor is selected. The plant data are compared with the results obtained with RELAP-5 and the Aztheca model. The results show that both RELAP-5 and the Aztheca code have the ability to adequately predict the behavior of the reactor. (Author)

  5. Vocable Code

    Soon, Winnie; Cox, Geoff

    2018-01-01

    a computational and poetic composition for two screens: on one of these, texts and voices are repeated and disrupted by mathematical chaos, together exploring the performativity of code and language; on the other, is a mix of a computer programming syntax and human language. In this sense queer code can...... be understood as both an object and subject of study that intervenes in the world’s ‘becoming' and how material bodies are produced via human and nonhuman practices. Through mixing the natural and computer language, this article presents a script in six parts from a performative lecture for two persons...

  6. NSURE code

    Rattan, D.S.

    1993-11-01

    NSURE stands for Near-Surface Repository code. NSURE is a performance assessment code. developed for the safety assessment of near-surface disposal facilities for low-level radioactive waste (LLRW). Part one of this report documents the NSURE model, governing equations and formulation of the mathematical models, and their implementation under the SYVAC3 executive. The NSURE model simulates the release of nuclides from an engineered vault, their subsequent transport via the groundwater and surface water pathways tot he biosphere, and predicts the resulting dose rate to a critical individual. Part two of this report consists of a User's manual, describing simulation procedures, input data preparation, output and example test cases

  7. Zinc Finger Nuclease: A New Approach to Overcome Beta-Lactam Antibiotic Resistance

    Shahbazi Dastjerdeh, Mansoureh; Kouhpayeh, Shirin; Sabzehei, Faezeh; Khanahmad, Hossein; Salehi, Mansour; Mohammadi, Zahra; Shariati, Laleh; Hejazi, Zahra; Rabiei, Parisa; Manian, Mostafa

    2016-01-01

    Background: The evolution of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) has been accelerated recently by the indiscriminate application of antibiotics. Antibiotic resistance has challenged the success of medical interventions and therefore is considered a hazardous threat to human health. Objectives: The present study aimed to describe the use of zinc finger nuclease (ZFN) technology to target and disrupt a plasmid-encoded β-lactamase, which prevents horizontal gene transfer-mediated evolution of ARBs. Materials and Methods: An engineered ZFN was designed to target a specific sequence in the ampicillin resistance gene (ampR) of the pTZ57R plasmid. The Escherichia coli bacteria already contained the pZFN kanamycin-resistant (kanaR) plasmid as the case or the pP15A, kanaR empty vector as the control, were transformed with the pTZ57R; the ability of the designed ZFN to disrupt the β-lactamase gene was evaluated with the subsequent disturbed ability of the bacteria to grow on ampicillin (amp) and ampicillin-kanamycin (amp-kana)-containing media. The effect of mild hypothermia on the ZFN gene targeting efficiency was also evaluated. Results: The growth of bacteria in the case group on the amp and amp-kana-containing media was significantly lower compared with the control group at 37°C (P < 0.001). Despite being more efficient in hypothermic conditions at 30°C (P < 0.001), there were no significant associations between the incubation temperature and the ZFN gene targeting efficiency. Conclusions: Our findings revealed that the ZFN technology could be employed to overcome ampicillin resistance by the targeted disruption of the ampicillin resistance gene, which leads to inactivation of β-lactam synthesis. Therefore, ZFN technology could be engaged to decrease the antibiotic resistance issue with the construction of a ZFN archive against different ARGs. To tackle the resistance issue at the environmental level, recombinant phages

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

    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

  9. The Aster code; Code Aster

    Delbecq, J.M

    1999-07-01

    The Aster code is a 2D or 3D finite-element calculation code for structures developed by the R and D direction of Electricite de France (EdF). This dossier presents a complete overview of the characteristics and uses of the Aster code: introduction of version 4; the context of Aster (organisation of the code development, versions, systems and interfaces, development tools, quality assurance, independent validation); static mechanics (linear thermo-elasticity, Euler buckling, cables, Zarka-Casier method); non-linear mechanics (materials behaviour, big deformations, specific loads, unloading and loss of load proportionality indicators, global algorithm, contact and friction); rupture mechanics (G energy restitution level, restitution level in thermo-elasto-plasticity, 3D local energy restitution level, KI and KII stress intensity factors, calculation of limit loads for structures), specific treatments (fatigue, rupture, wear, error estimation); meshes and models (mesh generation, modeling, loads and boundary conditions, links between different modeling processes, resolution of linear systems, display of results etc..); vibration mechanics (modal and harmonic analysis, dynamics with shocks, direct transient dynamics, seismic analysis and aleatory dynamics, non-linear dynamics, dynamical sub-structuring); fluid-structure interactions (internal acoustics, mass, rigidity and damping); linear and non-linear thermal analysis; steels and metal industry (structure transformations); coupled problems (internal chaining, internal thermo-hydro-mechanical coupling, chaining with other codes); products and services. (J.S.)

  10. Coding Class

    Ejsing-Duun, Stine; Hansbøl, Mikala

    Denne rapport rummer evaluering og dokumentation af Coding Class projektet1. Coding Class projektet blev igangsat i skoleåret 2016/2017 af IT-Branchen i samarbejde med en række medlemsvirksomheder, Københavns kommune, Vejle Kommune, Styrelsen for IT- og Læring (STIL) og den frivillige forening...... Coding Pirates2. Rapporten er forfattet af Docent i digitale læringsressourcer og forskningskoordinator for forsknings- og udviklingsmiljøet Digitalisering i Skolen (DiS), Mikala Hansbøl, fra Institut for Skole og Læring ved Professionshøjskolen Metropol; og Lektor i læringsteknologi, interaktionsdesign......, design tænkning og design-pædagogik, Stine Ejsing-Duun fra Forskningslab: It og Læringsdesign (ILD-LAB) ved Institut for kommunikation og psykologi, Aalborg Universitet i København. Vi har fulgt og gennemført evaluering og dokumentation af Coding Class projektet i perioden november 2016 til maj 2017...

  11. Uplink Coding

    Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

    2007-01-01

    This slide presentation reviews the objectives, meeting goals and overall NASA goals for the NASA Data Standards Working Group. The presentation includes information on the technical progress surrounding the objective, short LDPC codes, and the general results on the Pu-Pw tradeoff.

  12. ANIMAL code

    Lindemuth, I.R.

    1979-01-01

    This report describes ANIMAL, a two-dimensional Eulerian magnetohydrodynamic computer code. ANIMAL's physical model also appears. Formulated are temporal and spatial finite-difference equations in a manner that facilitates implementation of the algorithm. Outlined are the functions of the algorithm's FORTRAN subroutines and variables

  13. Network Coding

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Network Coding. K V Rashmi Nihar B Shah P Vijay Kumar. General Article Volume 15 Issue 7 July 2010 pp 604-621. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/015/07/0604-0621 ...

  14. MCNP code

    Cramer, S.N.

    1984-01-01

    The MCNP code is the major Monte Carlo coupled neutron-photon transport research tool at the Los Alamos National Laboratory, and it represents the most extensive Monte Carlo development program in the United States which is available in the public domain. The present code is the direct descendent of the original Monte Carlo work of Fermi, von Neumaum, and Ulam at Los Alamos in the 1940s. Development has continued uninterrupted since that time, and the current version of MCNP (or its predecessors) has always included state-of-the-art methods in the Monte Carlo simulation of radiation transport, basic cross section data, geometry capability, variance reduction, and estimation procedures. The authors of the present code have oriented its development toward general user application. The documentation, though extensive, is presented in a clear and simple manner with many examples, illustrations, and sample problems. In addition to providing the desired results, the output listings give a a wealth of detailed information (some optional) concerning each state of the calculation. The code system is continually updated to take advantage of advances in computer hardware and software, including interactive modes of operation, diagnostic interrupts and restarts, and a variety of graphical and video aids

  15. Expander Codes

    Home; Journals; Resonance – Journal of Science Education; Volume 10; Issue 1. Expander Codes - The Sipser–Spielman Construction. Priti Shankar. General Article Volume 10 ... Author Affiliations. Priti Shankar1. Department of Computer Science and Automation, Indian Institute of Science Bangalore 560 012, India.

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

    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

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

    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.

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

    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

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

    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.

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

    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

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

    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.

  2. Panda code

    Altomare, S.; Minton, G.

    1975-02-01

    PANDA is a new two-group one-dimensional (slab/cylinder) neutron diffusion code designed to replace and extend the FAB series. PANDA allows for the nonlinear effects of xenon, enthalpy and Doppler. Fuel depletion is allowed. PANDA has a completely general search facility which will seek criticality, maximize reactivity, or minimize peaking. Any single parameter may be varied in a search. PANDA is written in FORTRAN IV, and as such is nearly machine independent. However, PANDA has been written with the present limitations of the Westinghouse CDC-6600 system in mind. Most computation loops are very short, and the code is less than half the useful 6600 memory size so that two jobs can reside in the core at once. (auth)

  3. CANAL code

    Gara, P.; Martin, E.

    1983-01-01

    The CANAL code presented here optimizes a realistic iron free extraction channel which has to provide a given transversal magnetic field law in the median plane: the current bars may be curved, have finite lengths and cooling ducts and move in a restricted transversal area; terminal connectors may be added, images of the bars in pole pieces may be included. A special option optimizes a real set of circular coils [fr

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

    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...

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

    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.

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

    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.

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

    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...

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

    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.

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

    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...

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

    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.

  11. From concatenated codes to graph codes

    Justesen, Jørn; Høholdt, Tom

    2004-01-01

    We consider codes based on simple bipartite expander graphs. These codes may be seen as the first step leading from product type concatenated codes to more complex graph codes. We emphasize constructions of specific codes of realistic lengths, and study the details of decoding by message passing...

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

    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.

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

    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

  14. Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

    Matvienko, Marta; Kozik, Alexander; Froenicke, Lutz; Lavelle, Dean; Martineau, Belinda; Perroud, Bertrand; Michelmore, Richard

    2013-01-01

    Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.

  15. Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride.

    Marta Matvienko

    Full Text Available Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC, which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.

  16. Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities

    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....

  17. Probing force-induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding

    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

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

    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.

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

    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.

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

    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

  1. Automatic coding method of the ACR Code

    Park, Kwi Ae; Ihm, Jong Sool; Ahn, Woo Hyun; Baik, Seung Kook; Choi, Han Yong; Kim, Bong Gi

    1993-01-01

    The authors developed a computer program for automatic coding of ACR(American College of Radiology) code. The automatic coding of the ACR code is essential for computerization of the data in the department of radiology. This program was written in foxbase language and has been used for automatic coding of diagnosis in the Department of Radiology, Wallace Memorial Baptist since May 1992. The ACR dictionary files consisted of 11 files, one for the organ code and the others for the pathology code. The organ code was obtained by typing organ name or code number itself among the upper and lower level codes of the selected one that were simultaneous displayed on the screen. According to the first number of the selected organ code, the corresponding pathology code file was chosen automatically. By the similar fashion of organ code selection, the proper pathologic dode was obtained. An example of obtained ACR code is '131.3661'. This procedure was reproducible regardless of the number of fields of data. Because this program was written in 'User's Defined Function' from, decoding of the stored ACR code was achieved by this same program and incorporation of this program into program in to another data processing was possible. This program had merits of simple operation, accurate and detail coding, and easy adjustment for another program. Therefore, this program can be used for automation of routine work in the department of radiology

  2. Error-correction coding

    Hinds, Erold W. (Principal Investigator)

    1996-01-01

    This report describes the progress made towards the completion of a specific task on error-correcting coding. The proposed research consisted of investigating the use of modulation block codes as the inner code of a concatenated coding system in order to improve the overall space link communications performance. The study proposed to identify and analyze candidate codes that will complement the performance of the overall coding system which uses the interleaved RS (255,223) code as the outer code.

  3. Dynamic Shannon Coding

    Gagie, Travis

    2005-01-01

    We present a new algorithm for dynamic prefix-free coding, based on Shannon coding. We give a simple analysis and prove a better upper bound on the length of the encoding produced than the corresponding bound for dynamic Huffman coding. We show how our algorithm can be modified for efficient length-restricted coding, alphabetic coding and coding with unequal letter costs.

  4. Fundamentals of convolutional coding

    Johannesson, Rolf

    2015-01-01

    Fundamentals of Convolutional Coding, Second Edition, regarded as a bible of convolutional coding brings you a clear and comprehensive discussion of the basic principles of this field * Two new chapters on low-density parity-check (LDPC) convolutional codes and iterative coding * Viterbi, BCJR, BEAST, list, and sequential decoding of convolutional codes * Distance properties of convolutional codes * Includes a downloadable solutions manual

  5. Codes Over Hyperfields

    Atamewoue Surdive

    2017-12-01

    Full Text Available In this paper, we define linear codes and cyclic codes over a finite Krasner hyperfield and we characterize these codes by their generator matrices and parity check matrices. We also demonstrate that codes over finite Krasner hyperfields are more interesting for code theory than codes over classical finite fields.

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

    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

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

    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

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

    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

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

    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...

  10. Vector Network Coding Algorithms

    Ebrahimi, Javad; Fragouli, Christina

    2010-01-01

    We develop new algebraic algorithms for scalar and vector network coding. In vector network coding, the source multicasts information by transmitting vectors of length L, while intermediate nodes process and combine their incoming packets by multiplying them with L x L coding matrices that play a similar role as coding c in scalar coding. Our algorithms for scalar network jointly optimize the employed field size while selecting the coding coefficients. Similarly, for vector coding, our algori...

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

    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.

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

    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

  13. Homological stabilizer codes

    Anderson, Jonas T., E-mail: jonastyleranderson@gmail.com

    2013-03-15

    In this paper we define homological stabilizer codes on qubits which encompass codes such as Kitaev's toric code and the topological color codes. These codes are defined solely by the graphs they reside on. This feature allows us to use properties of topological graph theory to determine the graphs which are suitable as homological stabilizer codes. We then show that all toric codes are equivalent to homological stabilizer codes on 4-valent graphs. We show that the topological color codes and toric codes correspond to two distinct classes of graphs. We define the notion of label set equivalencies and show that under a small set of constraints the only homological stabilizer codes without local logical operators are equivalent to Kitaev's toric code or to the topological color codes. - Highlights: Black-Right-Pointing-Pointer We show that Kitaev's toric codes are equivalent to homological stabilizer codes on 4-valent graphs. Black-Right-Pointing-Pointer We show that toric codes and color codes correspond to homological stabilizer codes on distinct graphs. Black-Right-Pointing-Pointer We find and classify all 2D homological stabilizer codes. Black-Right-Pointing-Pointer We find optimal codes among the homological stabilizer codes.

  14. Diagnostic Coding for Epilepsy.

    Williams, Korwyn; Nuwer, Marc R; Buchhalter, Jeffrey R

    2016-02-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  15. Coding of Neuroinfectious Diseases.

    Barkley, Gregory L

    2015-12-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  16. Inactivation of Phaeodactylum tricornutum urease gene using transcription activator-like effector nuclease-based targeted mutagenesis.

    Weyman, Philip D; Beeri, Karen; Lefebvre, Stephane C; Rivera, Josefa; McCarthy, James K; Heuberger, Adam L; Peers, Graham; Allen, Andrew E; Dupont, Christopher L

    2015-05-01

    Diatoms are unicellular photosynthetic algae with promise for green production of fuels and other chemicals. Recent genome-editing techniques have greatly improved the potential of many eukaryotic genetic systems, including diatoms, to enable knowledge-based studies and bioengineering. Using a new technique, transcription activator-like effector nucleases (TALENs), the gene encoding the urease enzyme in the model diatom, Phaeodactylum tricornutum, was targeted for interruption. The knockout cassette was identified within the urease gene by PCR and Southern blot analyses of genomic DNA. The lack of urease protein was confirmed by Western blot analyses in mutant cell lines that were unable to grow on urea as the sole nitrogen source. Untargeted metabolomic analysis revealed a build-up of urea, arginine and ornithine in the urease knockout lines. All three intermediate metabolites are upstream of the urease reaction within the urea cycle, suggesting a disruption of the cycle despite urea production. Numerous high carbon metabolites were enriched in the mutant, implying a breakdown of cellular C and N repartitioning. The presented method improves the molecular toolkit for diatoms and clarifies the role of urease in the urea cycle. © 2014 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  17. Human lactoferrin efficiently targeted into caprine beta-lactoglobulin locus with transcription activator-like effector nucleases

    Yu-Guo Yuan

    2017-08-01

    Full Text Available Objective To create genetically modified goat as a biopharming source of recombinant human lacotoferrin (hLF with transcription activator-like effector nucleases. Methods TALENs and targeting vector were transferred into cultured fibroblasts to insert hLF cDNA in the goat beta-lactoglobulin (BLG locus with homology-directed repair. The gene targeted efficiency was checked using sequencing and TE7I assay. The bi-allelic gene targeted colonies were isolated and confirmed with polymerase chain reaction, and used as donor cells for somatic cell nuclear transfer (SCNT. Results The targeted efficiency for BLG gene was approximately 10%. Among 12 Bi-allelic gene targeted colonies, five were used in first round SCNT and 4 recipients (23% were confirmed pregnant at 30 d. In second round SCNT, 7 (53%, 4 (31%, and 3 (23% recipients were confirmed to be pregnant by ultrasound on 30 d, 60 d, and 90 d. Conclusion This finding signifies the combined use of TALENs and SCNT can generate bi-allelic knock-in fibroblasts that can be cloned in a fetus. Therefore, it might lay the foundation for transgenic hLF goat generation and possible use of their mammary gland as a bioreactor for large-scale production of recombinant hLF.

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

    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

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

    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.

  1. Generation of knockout rats with X-linked severe combined immunodeficiency (X-SCID using zinc-finger nucleases.

    Tomoji Mashimo

    Full Text Available BACKGROUND: Although the rat is extensively used as a laboratory model, the inability to utilize germ line-competent rat embryonic stem (ES cells has been a major drawback for studies that aim to elucidate gene functions. Recently, zinc-finger nucleases (ZFNs were successfully used to create genome-specific double-stranded breaks and thereby induce targeted gene mutations in a wide variety of organisms including plants, drosophila, zebrafish, etc. METHODOLOGY/PRINCIPAL FINDINGS: We report here on ZFN-induced gene targeting of the rat interleukin 2 receptor gamma (Il2rg locus, where orthologous human and mouse mutations cause X-linked severe combined immune deficiency (X-SCID. Co-injection of mRNAs encoding custom-designed ZFNs into the pronucleus of fertilized oocytes yielded genetically modified offspring at rates greater than 20%, which possessed a wide variety of deletion/insertion mutations. ZFN-modified founders faithfully transmitted their genetic changes to the next generation along with the severe combined immune deficiency phenotype. CONCLUSIONS AND SIGNIFICANCE: The efficient and rapid generation of gene knockout rats shows that using ZFN technology is a new strategy for creating gene-targeted rat models of human diseases. In addition, the X-SCID rats that were established in this study will be valuable in vivo tools for evaluating drug treatment or gene therapy as well as model systems for examining the treatment of xenotransplanted malignancies.

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

    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.

  3. Substrate overlap and functional competition between human nucleotide excision repair and Escherichia coli photolyase and (A)BC excision nuclease

    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

  4. A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations.

    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.

  5. Vector Network Coding

    Ebrahimi, Javad; Fragouli, Christina

    2010-01-01

    We develop new algebraic algorithms for scalar and vector network coding. In vector network coding, the source multicasts information by transmitting vectors of length L, while intermediate nodes process and combine their incoming packets by multiplying them with L X L coding matrices that play a similar role as coding coefficients in scalar coding. Our algorithms for scalar network jointly optimize the employed field size while selecting the coding coefficients. Similarly, for vector co...

  6. Entropy Coding in HEVC

    Sze, Vivienne; Marpe, Detlev

    2014-01-01

    Context-Based Adaptive Binary Arithmetic Coding (CABAC) is a method of entropy coding first introduced in H.264/AVC and now used in the latest High Efficiency Video Coding (HEVC) standard. While it provides high coding efficiency, the data dependencies in H.264/AVC CABAC make it challenging to parallelize and thus limit its throughput. Accordingly, during the standardization of entropy coding for HEVC, both aspects of coding efficiency and throughput were considered. This chapter describes th...

  7. Generalized concatenated quantum codes

    Grassl, Markus; Shor, Peter; Smith, Graeme; Smolin, John; Zeng Bei

    2009-01-01

    We discuss the concept of generalized concatenated quantum codes. This generalized concatenation method provides a systematical way for constructing good quantum codes, both stabilizer codes and nonadditive codes. Using this method, we construct families of single-error-correcting nonadditive quantum codes, in both binary and nonbinary cases, which not only outperform any stabilizer codes for finite block length but also asymptotically meet the quantum Hamming bound for large block length.

  8. Rateless feedback codes

    Sørensen, Jesper Hemming; Koike-Akino, Toshiaki; Orlik, Philip

    2012-01-01

    This paper proposes a concept called rateless feedback coding. We redesign the existing LT and Raptor codes, by introducing new degree distributions for the case when a few feedback opportunities are available. We show that incorporating feedback to LT codes can significantly decrease both...... the coding overhead and the encoding/decoding complexity. Moreover, we show that, at the price of a slight increase in the coding overhead, linear complexity is achieved with Raptor feedback coding....

  9. Advanced video coding systems

    Gao, Wen

    2015-01-01

    This comprehensive and accessible text/reference presents an overview of the state of the art in video coding technology. Specifically, the book introduces the tools of the AVS2 standard, describing how AVS2 can help to achieve a significant improvement in coding efficiency for future video networks and applications by incorporating smarter coding tools such as scene video coding. Topics and features: introduces the basic concepts in video coding, and presents a short history of video coding technology and standards; reviews the coding framework, main coding tools, and syntax structure of AV

  10. Coding for dummies

    Abraham, Nikhil

    2015-01-01

    Hands-on exercises help you learn to code like a pro No coding experience is required for Coding For Dummies,your one-stop guide to building a foundation of knowledge inwriting computer code for web, application, and softwaredevelopment. It doesn't matter if you've dabbled in coding or neverwritten a line of code, this book guides you through the basics.Using foundational web development languages like HTML, CSS, andJavaScript, it explains in plain English how coding works and whyit's needed. Online exercises developed by Codecademy, a leading online codetraining site, help hone coding skill

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

    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

  12. NanoRNase from Aeropyrum pernix shows nuclease activity on ssDNA and ssRNA.

    Deng, Yong-Jie; Feng, Lei; Zhou, Huan; Xiao, Xiang; Wang, Feng-Ping; Liu, Xi-Peng

    2018-05-01

    In cells, degrading DNA and RNA by various nucleases is very important. These processes are strictly controlled and regulated to maintain DNA integrity and to mature or recycle various RNAs. NanoRNase (Nrn) is a 3'-exonuclease that specifically degrades nanoRNAs shorter than 5 nucleotides. Several Nrns have been identified and characterized in bacteria, mainly in Firmicutes. Archaea often grow in extreme environments and might be subjected to more damage to DNA/RNA, so DNA repair and recycling of damaged RNA are very important in archaea. There is no report on the identification and characterization of Nrn in archaea. Aeropyrum pernix encodes three potential Nrns: NrnA (Ape1437), NrnB (Ape0124), and an Nrn-like protein Ape2190. Biochemical characterization showed that only Ape0124 could degrade ssDNA and ssRNA from the 3'-end in the presence of Mn 2+ . Interestingly, unlike bacterial Nrns, Ape0124 prefers ssDNA, including short nanoDNA, and degrades nanoRNA with lower efficiency. The 3'-DNA backbone was found to be required for efficiently hydrolyzing the phosphodiester bonds. In addition, Ape0124 also degrads the 3'-overhang of double-stranded DNA. Interestingly, Ape0124 could hydrolyze pAp into AMP, which is a feature of bacterial NrnA, not NrnB. Our results indicate that Ape0124 is a novel Nrn with a combined substrate profile of bacterial NrnA and NrnB. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Role for Artemis nuclease in the repair of radiation-induced DNA double strand breaks by alternative end joining.

    Moscariello, Mario; Wieloch, Radi; Kurosawa, Aya; Li, Fanghua; Adachi, Noritaka; Mladenov, Emil; Iliakis, George

    2015-07-01

    Exposure of cells to ionizing radiation or radiomimetic drugs generates DNA double-strand breaks that are processed either by homologous recombination repair (HRR), or by canonical, DNA-PKcs-dependent non-homologous end-joining (C-NHEJ). Chemical or genetic inactivation of factors involved in C-NHEJ or HRR, but also their local failure in repair proficient cells, promotes an alternative, error-prone end-joining pathway that serves as backup (A-EJ). There is evidence for the involvement of Artemis endonuclease, a protein deficient in a human radiosensitivity syndrome associated with severe immunodeficiency (RS-SCID), in the processing of subsets of DSBs by HRR or C-NHEJ. It is thought that within HRR or C-NHEJ Artemis processes DNA termini at complex DSBs. Whether Artemis has a role in A-EJ remains unknown. Here, we analyze using pulsed-field gel electrophoresis (PFGE) and specialized reporter assays, DSB repair in wild-type pre-B NALM-6 lymphocytes, as well as in their Artemis(-/-), DNA ligase 4(-/-) (LIG4(-/-)), and LIG4(-/-)/Artemis(-/-) double mutant counterparts, under conditions allowing evaluation of A-EJ. Our results substantiate the suggested roles of Artemis in C-NHEJ and HRR, but also demonstrate a role for the protein in A-EJ that is confirmed in Artemis deficient normal human fibroblasts. We conclude that Artemis is a nuclease participating in DSB repair by all major repair pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Generation of SNCA Cell Models Using Zinc Finger Nuclease (ZFN) Technology for Efficient High-Throughput Drug Screening.

    Dansithong, Warunee; Paul, Sharan; Scoles, Daniel R; Pulst, Stefan M; Huynh, Duong P

    2015-01-01

    Parkinson's disease (PD) is a progressive neurodegenerative disorder caused by loss of dopaminergic neurons of the substantia nigra. The hallmark of PD is the appearance of neuronal protein aggregations known as Lewy bodies and Lewy neurites, of which α-synuclein forms a major component. Familial PD is rare and is associated with missense mutations of the SNCA gene or increases in gene copy number resulting in SNCA overexpression. This suggests that lowering SNCA expression could be therapeutic for PD. Supporting this hypothesis, SNCA reduction was neuroprotective in cell line and rodent PD models. We developed novel cell lines expressing SNCA fused to the reporter genes luciferase (luc) or GFP with the objective to enable high-throughput compound screening (HTS) for small molecules that can lower SNCA expression. Because SNCA expression is likely regulated by far-upstream elements (including the NACP-REP1 located at 8852 bp upstream of the transcription site), we employed zinc finger nuclease (ZFN) genome editing to insert reporter genes in-frame downstream of the SNCA gene in order to retain native SNCA expression control. This ensured full retention of known and unknown up- and downstream genetic elements controlling SNCA expression. Treatment of cells with the histone deacetylase inhibitor valproic acid (VPA) resulted in significantly increased SNCA-luc and SNCA-GFP expression supporting the use of our cell lines for identifying small molecules altering complex modes of expression control. Cells expressing SNCA-luc treated with a luciferase inhibitor or SNCA siRNA resulted in Z'-scores ≥ 0.75, suggesting the suitability of these cell lines for use in HTS. This study presents a novel use of genome editing for the creation of cell lines expressing α-synuclein fusion constructs entirely under native expression control. These cell lines are well suited for HTS for compounds that lower SNCA expression directly or by acting at long-range sites to the SNCA

  15. Targeted gene disruption by use of transcription activator-like effector nuclease (TALEN) in the water flea Daphnia pulex.

    Hiruta, Chizue; Ogino, Yukiko; Sakuma, Tetsushi; Toyota, Kenji; Miyagawa, Shinichi; Yamamoto, Takashi; Iguchi, Taisen

    2014-11-18

    The cosmopolitan microcrustacean Daphnia pulex provides a model system for both human health research and monitoring ecosystem integrity. It is the first crustacean to have its complete genome sequenced, an unprecedented ca. 36% of which has no known homologs with any other species. Moreover, D. pulex is ideally suited for experimental manipulation because of its short reproductive cycle, large numbers of offspring, synchronization of oocyte maturation, and other life history characteristics. However, existing gene manipulation techniques are insufficient to accurately define gene functions. Although our previous investigations developed an RNA interference (RNAi) system in D. pulex, the possible time period of functional analysis was limited because the effectiveness of RNAi is transient. Thus, in this study, we developed a genome editing system for D. pulex by first microinjecting transcription activator-like effector nuclease (TALEN) mRNAs into early embryos and then evaluating TALEN activity and mutation phenotypes. We assembled a TALEN construct specific to the Distal-less gene (Dll), which is a homeobox transcription factor essential for distal limb development in invertebrates and vertebrates, and evaluated its activity in vitro by single-strand annealing assay. Then, we injected TALEN mRNAs into eggs within 1 hour post-ovulation. Injected embryos presented with defects in the second antenna and altered appendage development, and indel mutations were detected in Dll loci, indicating that this technique successfully knocked out the target gene. We succeeded, for the first time in D. pulex, in targeted mutagenesis by use of Platinum TALENs. This genome editing technique makes it possible to conduct reverse genetic analysis in D. pulex, making this species an even more appropriate model organism for environmental, evolutionary, and developmental genomics.

  16. Establishment of pten knockout medaka with transcription activator-like effector nucleases (TALENs as a model of PTEN deficiency disease.

    Yuriko Matsuzaki

    Full Text Available Phosphatase and tensin homolog (PTEN is a lipid and protein phosphatase that antagonizes signaling by the phosphatidylinositol 3-kinase (PI3K-AKT signaling pathway. The PTEN gene is a major tumor suppressor, with mutations of this gene occurring frequently in tumors of humans and mice. We have now developed mutant medaka deficient in PTEN with the use of transcription activator-like effector nuclease (TALEN technology. Medaka possesses two pten genes, ptena and ptenb, similar to zebrafish. We established 16 ptena mutant lines and two ptenb mutant lines. Homozygous single pten mutants were found to be viable and fertile. In contrast, pten double-knockout (dko embryos manifested severe abnormalities in vasculogenesis, eye size, and tail development at 72 hours post fertilization(hpf and died before hatching. Immunoblot analysis revealed that the ratio of phosphorylated to total forms of AKT (pAKT/AKT in pten dko embryos was four times that in wild-type embryos, indicative of up-regulation of signaling by the PI3K-AKT pathway. Treatment of pten dko embryos with the PI3K inhibitor LY294002 reduced the pAKT/AKT ratio by about one-half and partially rescued the defect in vasculogenesis. Additional inhibitors of the PI3K-AKT pathway, including rapamycin and N-α-tosyl-L-phenylalanyl chloromethyl ketone, also partially restored vasculogenesis in the dko embryos. Our model system thus allows pten dko embryos to be readily distinguished from wild-type embryos at an early stage of development and is suitable for the screening of drugs able to compensate for PTEN deficiency.

  17. Direct stacking of sequence-specific nuclease-induced mutations to produce high oleic and low linolenic soybean oil.

    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. Discussion on LDPC Codes and Uplink Coding

    Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

    2007-01-01

    This slide presentation reviews the progress that the workgroup on Low-Density Parity-Check (LDPC) for space link coding. The workgroup is tasked with developing and recommending new error correcting codes for near-Earth, Lunar, and deep space applications. Included in the presentation is a summary of the technical progress of the workgroup. Charts that show the LDPC decoder sensitivity to symbol scaling errors are reviewed, as well as a chart showing the performance of several frame synchronizer algorithms compared to that of some good codes and LDPC decoder tests at ESTL. Also reviewed is a study on Coding, Modulation, and Link Protocol (CMLP), and the recommended codes. A design for the Pseudo-Randomizer with LDPC Decoder and CRC is also reviewed. A chart that summarizes the three proposed coding systems is also presented.

  19. Locally orderless registration code

    2012-01-01

    This is code for the TPAMI paper "Locally Orderless Registration". The code requires intel threadding building blocks installed and is provided for 64 bit on mac, linux and windows.......This is code for the TPAMI paper "Locally Orderless Registration". The code requires intel threadding building blocks installed and is provided for 64 bit on mac, linux and windows....

  20. Decoding Codes on Graphs

    Shannon limit of the channel. Among the earliest discovered codes that approach the. Shannon limit were the low density parity check (LDPC) codes. The term low density arises from the property of the parity check matrix defining the code. We will now define this matrix and the role that it plays in decoding. 2. Linear Codes.

  1. Manually operated coded switch

    Barnette, J.H.

    1978-01-01

    The disclosure related to a manually operated recodable coded switch in which a code may be inserted, tried and used to actuate a lever controlling an external device. After attempting a code, the switch's code wheels must be returned to their zero positions before another try is made

  2. Coding in Muscle Disease.

    Jones, Lyell K; Ney, John P

    2016-12-01

    Accurate coding is critically important for clinical practice and research. Ongoing changes to diagnostic and billing codes require the clinician to stay abreast of coding updates. Payment for health care services, data sets for health services research, and reporting for medical quality improvement all require accurate administrative coding. This article provides an overview of administrative coding for patients with muscle disease and includes a case-based review of diagnostic and Evaluation and Management (E/M) coding principles in patients with myopathy. Procedural coding for electrodiagnostic studies and neuromuscular ultrasound is also reviewed.

  3. QR Codes 101

    Crompton, Helen; LaFrance, Jason; van 't Hooft, Mark

    2012-01-01

    A QR (quick-response) code is a two-dimensional scannable code, similar in function to a traditional bar code that one might find on a product at the supermarket. The main difference between the two is that, while a traditional bar code can hold a maximum of only 20 digits, a QR code can hold up to 7,089 characters, so it can contain much more…

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

    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.

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

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

    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

  7. Codes and curves

    Walker, Judy L

    2000-01-01

    When information is transmitted, errors are likely to occur. Coding theory examines efficient ways of packaging data so that these errors can be detected, or even corrected. The traditional tools of coding theory have come from combinatorics and group theory. Lately, however, coding theorists have added techniques from algebraic geometry to their toolboxes. In particular, by re-interpreting the Reed-Solomon codes, one can see how to define new codes based on divisors on algebraic curves. For instance, using modular curves over finite fields, Tsfasman, Vladut, and Zink showed that one can define a sequence of codes with asymptotically better parameters than any previously known codes. This monograph is based on a series of lectures the author gave as part of the IAS/PCMI program on arithmetic algebraic geometry. Here, the reader is introduced to the exciting field of algebraic geometric coding theory. Presenting the material in the same conversational tone of the lectures, the author covers linear codes, inclu...

  8. In Vivo Zinc Finger Nuclease-mediated Targeted Integration of a Glucose-6-phosphatase Transgene Promotes Survival in Mice With Glycogen Storage Disease Type IA

    Landau, Dustin J; Brooks, Elizabeth Drake; Perez-Pinera, Pablo; Amarasekara, Hiruni; Mefferd, Adam; Li, Songtao; Bird, Andrew; Gersbach, Charles A; Koeberl, Dwight D

    2016-01-01

    Glycogen storage disease type Ia (GSD Ia) is caused by glucose-6-phosphatase (G6Pase) deficiency in association with severe, life-threatening hypoglycemia that necessitates lifelong dietary therapy. Here we show that use of a zinc-finger nuclease (ZFN) targeted to the ROSA26 safe harbor locus and a ROSA26-targeting vector containing a G6PC donor transgene, both delivered with adeno-associated virus (AAV) vectors, markedly improved survival of G6Pase knockout (G6Pase-KO) mice compared with mice receiving the donor vector alone (P Ia, as compared with normal littermates, at 8 months following vector administration (P Ia. PMID:26865405

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

    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

  10. Distribution of nuclease attack sites and complexity of DNA in the products of post-irradiation degradiation of rat thymus chromatin

    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. Influence of some exo nucleases in response to the induced genetic damage in Escherichia coli by alpha radiation

    Aguilar M, M.

    2005-01-01

    Within the strategies with those that E. coli counts to overcome to the genetic damage there is the SOS response, a group of genes that participate in repair and/or tolerance that it confers to the bacteria major opportunities of surviving. These genes are repressed and its only are expressed when it happens genetic damage. So that this system is activated it is necessary that DNA of a band exists and in this sense the double ruptures (RDB) its are not able to induce this response unless there is a previous processing. In stumps with defects in certain genes that have to do with repair of RDB (as recO, recJ and xonA) the activity of SOS is smaller than in a wild stump what suggests that these participate in the previous processes to the activation of the response. The ionizing radiation produce among other many lesions, RDB in greater or smaller proportion, depending on the ionization capacity. A parameter to evaluate this capacity is the lineal energy transfer (LET), defined as the average energy given by unit of distance travelled. In general the LET of the corpuscular radiations is a lot but high that of the electromagnetic one, for what produces bigger quantity of ionizations inside a restricted zone and it increases by this way the probability that RDB has been generated. This work has for object to infer the participation of xonA and recJ in this response and to evaluate the damage produced by ionizing radiation of different LET (alpha particles of different energies) in a stump with all the functional repair mechanisms. Its were considered two parameters: the survival and the activity of SOS evaluated by means of the chromo test. The results indicate that the activity of these exo nucleases is necessary for the repair of RDB as well as for the processing of lesions foresaw to the activation of SOS. As for the treatment with alphas of different energies is observed that so much the survival like the activity of SOS vary as the LET of the radiation changes

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

    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

  13. The materiality of Code

    Soon, Winnie

    2014-01-01

    This essay studies the source code of an artwork from a software studies perspective. By examining code that come close to the approach of critical code studies (Marino, 2006), I trace the network artwork, Pupufu (Lin, 2009) to understand various real-time approaches to social media platforms (MSN......, Twitter and Facebook). The focus is not to investigate the functionalities and efficiencies of the code, but to study and interpret the program level of code in order to trace the use of various technological methods such as third-party libraries and platforms’ interfaces. These are important...... to understand the socio-technical side of a changing network environment. Through the study of code, including but not limited to source code, technical specifications and other materials in relation to the artwork production, I would like to explore the materiality of code that goes beyond technical...

  14. Coding for optical channels

    Djordjevic, Ivan; Vasic, Bane

    2010-01-01

    This unique book provides a coherent and comprehensive introduction to the fundamentals of optical communications, signal processing and coding for optical channels. It is the first to integrate the fundamentals of coding theory and optical communication.

  15. SEVERO code - user's manual

    Sacramento, A.M. do.

    1989-01-01

    This user's manual contains all the necessary information concerning the use of SEVERO code. This computer code is related to the statistics of extremes = extreme winds, extreme precipitation and flooding hazard risk analysis. (A.C.A.S.)

  16. Synthesizing Certified Code

    Whalen, Michael; Schumann, Johann; Fischer, Bernd

    2002-01-01

    Code certification is a lightweight approach for formally demonstrating software quality. Its basic idea is to require code producers to provide formal proofs that their code satisfies certain quality properties. These proofs serve as certificates that can be checked independently. Since code certification uses the same underlying technology as program verification, it requires detailed annotations (e.g., loop invariants) to make the proofs possible. However, manually adding annotations to th...

  17. FERRET data analysis code

    Schmittroth, F.

    1979-09-01

    A documentation of the FERRET data analysis code is given. The code provides a way to combine related measurements and calculations in a consistent evaluation. Basically a very general least-squares code, it is oriented towards problems frequently encountered in nuclear data and reactor physics. A strong emphasis is on the proper treatment of uncertainties and correlations and in providing quantitative uncertainty estimates. Documentation includes a review of the method, structure of the code, input formats, and examples

  18. Stylize Aesthetic QR Code

    Xu, Mingliang; Su, Hao; Li, Yafei; Li, Xi; Liao, Jing; Niu, Jianwei; Lv, Pei; Zhou, Bing

    2018-01-01

    With the continued proliferation of smart mobile devices, Quick Response (QR) code has become one of the most-used types of two-dimensional code in the world. Aiming at beautifying the appearance of QR codes, existing works have developed a series of techniques to make the QR code more visual-pleasant. However, these works still leave much to be desired, such as visual diversity, aesthetic quality, flexibility, universal property, and robustness. To address these issues, in this paper, we pro...

  19. Enhancing QR Code Security

    Zhang, Linfan; Zheng, Shuang

    2015-01-01

    Quick Response code opens possibility to convey data in a unique way yet insufficient prevention and protection might lead into QR code being exploited on behalf of attackers. This thesis starts by presenting a general introduction of background and stating two problems regarding QR code security, which followed by a comprehensive research on both QR code itself and related issues. From the research a solution taking advantages of cloud and cryptography together with an implementation come af...

  20. Opening up codings?

    Steensig, Jakob; Heinemann, Trine

    2015-01-01

    doing formal coding and when doing more “traditional” conversation analysis research based on collections. We are more wary, however, of the implication that coding-based research is the end result of a process that starts with qualitative investigations and ends with categories that can be coded...

  1. Gauge color codes

    Bombin Palomo, Hector

    2015-01-01

    Color codes are topological stabilizer codes with unusual transversality properties. Here I show that their group of transversal gates is optimal and only depends on the spatial dimension, not the local geometry. I also introduce a generalized, subsystem version of color codes. In 3D they allow...

  2. Refactoring test code

    A. van Deursen (Arie); L.M.F. Moonen (Leon); A. van den Bergh; G. Kok

    2001-01-01

    textabstractTwo key aspects of extreme programming (XP) are unit testing and merciless refactoring. Given the fact that the ideal test code / production code ratio approaches 1:1, it is not surprising that unit tests are being refactored. We found that refactoring test code is different from

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

    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.

  4. Software Certification - Coding, Code, and Coders

    Havelund, Klaus; Holzmann, Gerard J.

    2011-01-01

    We describe a certification approach for software development that has been adopted at our organization. JPL develops robotic spacecraft for the exploration of the solar system. The flight software that controls these spacecraft is considered to be mission critical. We argue that the goal of a software certification process cannot be the development of "perfect" software, i.e., software that can be formally proven to be correct under all imaginable and unimaginable circumstances. More realistically, the goal is to guarantee a software development process that is conducted by knowledgeable engineers, who follow generally accepted procedures to control known risks, while meeting agreed upon standards of workmanship. We target three specific issues that must be addressed in such a certification procedure: the coding process, the code that is developed, and the skills of the coders. The coding process is driven by standards (e.g., a coding standard) and tools. The code is mechanically checked against the standard with the help of state-of-the-art static source code analyzers. The coders, finally, are certified in on-site training courses that include formal exams.

  5. The network code

    1997-01-01

    The Network Code defines the rights and responsibilities of all users of the natural gas transportation system in the liberalised gas industry in the United Kingdom. This report describes the operation of the Code, what it means, how it works and its implications for the various participants in the industry. The topics covered are: development of the competitive gas market in the UK; key points in the Code; gas transportation charging; impact of the Code on producers upstream; impact on shippers; gas storage; supply point administration; impact of the Code on end users; the future. (20 tables; 33 figures) (UK)

  6. Coding for Electronic Mail

    Rice, R. F.; Lee, J. J.

    1986-01-01

    Scheme for coding facsimile messages promises to reduce data transmission requirements to one-tenth current level. Coding scheme paves way for true electronic mail in which handwritten, typed, or printed messages or diagrams sent virtually instantaneously - between buildings or between continents. Scheme, called Universal System for Efficient Electronic Mail (USEEM), uses unsupervised character recognition and adaptive noiseless coding of text. Image quality of resulting delivered messages improved over messages transmitted by conventional coding. Coding scheme compatible with direct-entry electronic mail as well as facsimile reproduction. Text transmitted in this scheme automatically translated to word-processor form.

  7. NAGRADATA. Code key. Geology

    Mueller, W.H.; Schneider, B.; Staeuble, J.

    1984-01-01

    This reference manual provides users of the NAGRADATA system with comprehensive keys to the coding/decoding of geological and technical information to be stored in or retreaved from the databank. Emphasis has been placed on input data coding. When data is retreaved the translation into plain language of stored coded information is done automatically by computer. Three keys each, list the complete set of currently defined codes for the NAGRADATA system, namely codes with appropriate definitions, arranged: 1. according to subject matter (thematically) 2. the codes listed alphabetically and 3. the definitions listed alphabetically. Additional explanation is provided for the proper application of the codes and the logic behind the creation of new codes to be used within the NAGRADATA system. NAGRADATA makes use of codes instead of plain language for data storage; this offers the following advantages: speed of data processing, mainly data retrieval, economies of storage memory requirements, the standardisation of terminology. The nature of this thesaurian type 'key to codes' makes it impossible to either establish a final form or to cover the entire spectrum of requirements. Therefore, this first issue of codes to NAGRADATA must be considered to represent the current state of progress of a living system and future editions will be issued in a loose leave ringbook system which can be updated by an organised (updating) service. (author)

  8. XSOR codes users manual

    Jow, Hong-Nian; Murfin, W.B.; Johnson, J.D.

    1993-11-01

    This report describes the source term estimation codes, XSORs. The codes are written for three pressurized water reactors (Surry, Sequoyah, and Zion) and two boiling water reactors (Peach Bottom and Grand Gulf). The ensemble of codes has been named ''XSOR''. The purpose of XSOR codes is to estimate the source terms which would be released to the atmosphere in severe accidents. A source term includes the release fractions of several radionuclide groups, the timing and duration of releases, the rates of energy release, and the elevation of releases. The codes have been developed by Sandia National Laboratories for the US Nuclear Regulatory Commission (NRC) in support of the NUREG-1150 program. The XSOR codes are fast running parametric codes and are used as surrogates for detailed mechanistic codes. The XSOR codes also provide the capability to explore the phenomena and their uncertainty which are not currently modeled by the mechanistic codes. The uncertainty distributions of input parameters may be used by an. XSOR code to estimate the uncertainty of source terms

  9. Reactor lattice codes

    Kulikowska, T.

    1999-01-01

    The present lecture has a main goal to show how the transport lattice calculations are realised in a standard computer code. This is illustrated on the example of the WIMSD code, belonging to the most popular tools for reactor calculations. Most of the approaches discussed here can be easily modified to any other lattice code. The description of the code assumes the basic knowledge of reactor lattice, on the level given in the lecture on 'Reactor lattice transport calculations'. For more advanced explanation of the WIMSD code the reader is directed to the detailed descriptions of the code cited in References. The discussion of the methods and models included in the code is followed by the generally used homogenisation procedure and several numerical examples of discrepancies in calculated multiplication factors based on different sources of library data. (author)

  10. DLLExternalCode

    2014-05-14

    DLLExternalCode is the a general dynamic-link library (DLL) interface for linking GoldSim (www.goldsim.com) with external codes. The overall concept is to use GoldSim as top level modeling software with interfaces to external codes for specific calculations. The DLLExternalCode DLL that performs the linking function is designed to take a list of code inputs from GoldSim, create an input file for the external application, run the external code, and return a list of outputs, read from files created by the external application, back to GoldSim. Instructions for creating the input file, running the external code, and reading the output are contained in an instructions file that is read and interpreted by the DLL.

  11. Toric Varieties and Codes, Error-correcting Codes, Quantum Codes, Secret Sharing and Decoding

    Hansen, Johan Peder

    We present toric varieties and associated toric codes and their decoding. Toric codes are applied to construct Linear Secret Sharing Schemes (LSSS) with strong multiplication by the Massey construction. Asymmetric Quantum Codes are obtained from toric codes by the A.R. Calderbank P.W. Shor and A.......M. Steane construction of stabilizer codes (CSS) from linear codes containing their dual codes....

  12. An Optimal Linear Coding for Index Coding Problem

    Pezeshkpour, Pouya

    2015-01-01

    An optimal linear coding solution for index coding problem is established. Instead of network coding approach by focus on graph theoric and algebraic methods a linear coding program for solving both unicast and groupcast index coding problem is presented. The coding is proved to be the optimal solution from the linear perspective and can be easily utilize for any number of messages. The importance of this work is lying mostly on the usage of the presented coding in the groupcast index coding ...

  13. The Aesthetics of Coding

    Andersen, Christian Ulrik

    2007-01-01

    Computer art is often associated with computer-generated expressions (digitally manipulated audio/images in music, video, stage design, media facades, etc.). In recent computer art, however, the code-text itself – not the generated output – has become the artwork (Perl Poetry, ASCII Art, obfuscated...... code, etc.). The presentation relates this artistic fascination of code to a media critique expressed by Florian Cramer, claiming that the graphical interface represents a media separation (of text/code and image) causing alienation to the computer’s materiality. Cramer is thus the voice of a new ‘code...... avant-garde’. In line with Cramer, the artists Alex McLean and Adrian Ward (aka Slub) declare: “art-oriented programming needs to acknowledge the conditions of its own making – its poesis.” By analysing the Live Coding performances of Slub (where they program computer music live), the presentation...

  14. Majorana fermion codes

    Bravyi, Sergey; Terhal, Barbara M; Leemhuis, Bernhard

    2010-01-01

    We initiate the study of Majorana fermion codes (MFCs). These codes can be viewed as extensions of Kitaev's one-dimensional (1D) model of unpaired Majorana fermions in quantum wires to higher spatial dimensions and interacting fermions. The purpose of MFCs is to protect quantum information against low-weight fermionic errors, that is, operators acting on sufficiently small subsets of fermionic modes. We examine to what extent MFCs can surpass qubit stabilizer codes in terms of their stability properties. A general construction of 2D MFCs is proposed that combines topological protection based on a macroscopic code distance with protection based on fermionic parity conservation. Finally, we use MFCs to show how to transform any qubit stabilizer code to a weakly self-dual CSS code.

  15. Theory of epigenetic coding.

    Elder, D

    1984-06-07

    The logic of genetic control of development may be based on a binary epigenetic code. This paper revises the author's previous scheme dealing with the numerology of annelid metamerism in these terms. Certain features of the code had been deduced to be combinatorial, others not. This paradoxical contrast is resolved here by the interpretation that these features relate to different operations of the code; the combinatiorial to coding identity of units, the non-combinatorial to coding production of units. Consideration of a second paradox in the theory of epigenetic coding leads to a new solution which further provides a basis for epimorphic regeneration, and may in particular throw light on the "regeneration-duplication" phenomenon. A possible test of the model is also put forward.

  16. DISP1 code

    Vokac, P.

    1999-12-01

    DISP1 code is a simple tool for assessment of the dispersion of the fission product cloud escaping from a nuclear power plant after an accident. The code makes it possible to tentatively check the feasibility of calculations by more complex PSA3 codes and/or codes for real-time dispersion calculations. The number of input parameters is reasonably low and the user interface is simple enough to allow a rapid processing of sensitivity analyses. All input data entered through the user interface are stored in the text format. Implementation of dispersion model corrections taken from the ARCON96 code enables the DISP1 code to be employed for assessment of the radiation hazard within the NPP area, in the control room for instance. (P.A.)

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

    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

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

    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

  19. Phonological coding during reading.

    Leinenger, Mallorie

    2014-11-01

    The exact role that phonological coding (the recoding of written, orthographic information into a sound based code) plays during silent reading has been extensively studied for more than a century. Despite the large body of research surrounding the topic, varying theories as to the time course and function of this recoding still exist. The present review synthesizes this body of research, addressing the topics of time course and function in tandem. The varying theories surrounding the function of phonological coding (e.g., that phonological codes aid lexical access, that phonological codes aid comprehension and bolster short-term memory, or that phonological codes are largely epiphenomenal in skilled readers) are first outlined, and the time courses that each maps onto (e.g., that phonological codes come online early [prelexical] or that phonological codes come online late [postlexical]) are discussed. Next the research relevant to each of these proposed functions is reviewed, discussing the varying methodologies that have been used to investigate phonological coding (e.g., response time methods, reading while eye-tracking or recording EEG and MEG, concurrent articulation) and highlighting the advantages and limitations of each with respect to the study of phonological coding. In response to the view that phonological coding is largely epiphenomenal in skilled readers, research on the use of phonological codes in prelingually, profoundly deaf readers is reviewed. Finally, implications for current models of word identification (activation-verification model, Van Orden, 1987; dual-route model, e.g., M. Coltheart, Rastle, Perry, Langdon, & Ziegler, 2001; parallel distributed processing model, Seidenberg & McClelland, 1989) are discussed. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

  20. The aeroelastic code FLEXLAST

    Visser, B. [Stork Product Eng., Amsterdam (Netherlands)

    1996-09-01

    To support the discussion on aeroelastic codes, a description of the code FLEXLAST was given and experiences within benchmarks and measurement programmes were summarized. The code FLEXLAST has been developed since 1982 at Stork Product Engineering (SPE). Since 1992 FLEXLAST has been used by Dutch industries for wind turbine and rotor design. Based on the comparison with measurements, it can be concluded that the main shortcomings of wind turbine modelling lie in the field of aerodynamics, wind field and wake modelling. (au)

  1. MORSE Monte Carlo code

    Cramer, S.N.

    1984-01-01

    The MORSE code is a large general-use multigroup Monte Carlo code system. Although no claims can be made regarding its superiority in either theoretical details or Monte Carlo techniques, MORSE has been, since its inception at ORNL in the late 1960s, the most widely used Monte Carlo radiation transport code. The principal reason for this popularity is that MORSE is relatively easy to use, independent of any installation or distribution center, and it can be easily customized to fit almost any specific need. Features of the MORSE code are described

  2. QR codes for dummies

    Waters, Joe

    2012-01-01

    Find out how to effectively create, use, and track QR codes QR (Quick Response) codes are popping up everywhere, and businesses are reaping the rewards. Get in on the action with the no-nonsense advice in this streamlined, portable guide. You'll find out how to get started, plan your strategy, and actually create the codes. Then you'll learn to link codes to mobile-friendly content, track your results, and develop ways to give your customers value that will keep them coming back. It's all presented in the straightforward style you've come to know and love, with a dash of humor thrown

  3. Tokamak Systems Code

    Reid, R.L.; Barrett, R.J.; Brown, T.G.

    1985-03-01

    The FEDC Tokamak Systems Code calculates tokamak performance, cost, and configuration as a function of plasma engineering parameters. This version of the code models experimental tokamaks. It does not currently consider tokamak configurations that generate electrical power or incorporate breeding blankets. The code has a modular (or subroutine) structure to allow independent modeling for each major tokamak component or system. A primary benefit of modularization is that a component module may be updated without disturbing the remainder of the systems code as long as the imput to or output from the module remains unchanged

  4. Efficient Coding of Information: Huffman Coding -RE ...

    to a stream of equally-likely symbols so as to recover the original stream in the event of errors. The for- ... The source-coding problem is one of finding a mapping from U to a ... probability that the random variable X takes the value x written as ...

  5. NR-code: Nonlinear reconstruction code

    Yu, Yu; Pen, Ue-Li; Zhu, Hong-Ming

    2018-04-01

    NR-code applies nonlinear reconstruction to the dark matter density field in redshift space and solves for the nonlinear mapping from the initial Lagrangian positions to the final redshift space positions; this reverses the large-scale bulk flows and improves the precision measurement of the baryon acoustic oscillations (BAO) scale.

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

    Beck, Inken M; Sedlacek, Radislav

    2015-02-01

    The 12th Transgenic Technology meeting was held in Edinburgh on 6th-8th October 2014 and interest to participate in the meeting overcame all expectations. The TT2014 was the largest meeting ever with more than 540 scientists, technicians, and students from all over the world. The meeting had an excellent scientific program that brought information on the latest ground-breaking technologies for gene targeting and genome editing using programmable nucleases into the foreground. These presentations were well balanced with several highlights over viewing topics in embryonic stem cell research, embryogenesis, disease models, and animals in agriculture. Ample space was reserved also for short talks presenting technical development and for highlighting posters contributions. A highlight of the meeting was the award of the 10th International Society of Transgenic Technologies Prize to Janet Rossant for her outstanding contributions in the field of mouse embryogenesis.

  7. Nuclease-mediated double-strand break (DSB) enhancement of small fragment homologous recombination (SFHR) gene modification in human-induced pluripotent stem cells (hiPSCs).

    Sargent, R Geoffrey; Suzuki, Shingo; Gruenert, Dieter C

    2014-01-01

    Recent developments in methods to specifically modify genomic DNA using sequence-specific endonucleases and donor DNA have opened the door to a new therapeutic paradigm for cell and gene therapy of inherited diseases. Sequence-specific endonucleases, in particular transcription activator-like (TAL) effector nucleases (TALENs), have been coupled with polynucleotide small/short DNA fragments (SDFs) to correct the most common mutation in the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene, a 3-base-pair deletion at codon 508 (delF508), in induced pluripotent stem (iPS) cells. The studies presented here describe the generation of candidate TALENs and their co-transfection with wild-type (wt) CFTR-SDFs into CF-iPS cells homozygous for the delF508 mutation. Using an allele-specific PCR (AS-PCR)-based cyclic enrichment protocol, clonal populations of corrected CF-iPS cells were isolated and expanded.

  8. Molecular Imaging of Human Embryonic Stem Cells Stably Expressing Human PET Reporter Genes After Zinc Finger Nuclease-Mediated Genome Editing.

    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.

  9. Synthesizing Certified Code

    Whalen, Michael; Schumann, Johann; Fischer, Bernd

    2002-01-01

    Code certification is a lightweight approach to demonstrate software quality on a formal level. Its basic idea is to require producers to provide formal proofs that their code satisfies certain quality properties. These proofs serve as certificates which can be checked independently. Since code certification uses the same underlying technology as program verification, it also requires many detailed annotations (e.g., loop invariants) to make the proofs possible. However, manually adding theses annotations to the code is time-consuming and error-prone. We address this problem by combining code certification with automatic program synthesis. We propose an approach to generate simultaneously, from a high-level specification, code and all annotations required to certify generated code. Here, we describe a certification extension of AUTOBAYES, a synthesis tool which automatically generates complex data analysis programs from compact specifications. AUTOBAYES contains sufficient high-level domain knowledge to generate detailed annotations. This allows us to use a general-purpose verification condition generator to produce a set of proof obligations in first-order logic. The obligations are then discharged using the automated theorem E-SETHEO. We demonstrate our approach by certifying operator safety for a generated iterative data classification program without manual annotation of the code.

  10. Code of Ethics

    Division for Early Childhood, Council for Exceptional Children, 2009

    2009-01-01

    The Code of Ethics of the Division for Early Childhood (DEC) of the Council for Exceptional Children is a public statement of principles and practice guidelines supported by the mission of DEC. The foundation of this Code is based on sound ethical reasoning related to professional practice with young children with disabilities and their families…

  11. Interleaved Product LDPC Codes

    Baldi, Marco; Cancellieri, Giovanni; Chiaraluce, Franco

    2011-01-01

    Product LDPC codes take advantage of LDPC decoding algorithms and the high minimum distance of product codes. We propose to add suitable interleavers to improve the waterfall performance of LDPC decoding. Interleaving also reduces the number of low weight codewords, that gives a further advantage in the error floor region.

  12. Insurance billing and coding.

    Napier, Rebecca H; Bruelheide, Lori S; Demann, Eric T K; Haug, Richard H

    2008-07-01

    The purpose of this article is to highlight the importance of understanding various numeric and alpha-numeric codes for accurately billing dental and medically related services to private pay or third-party insurance carriers. In the United States, common dental terminology (CDT) codes are most commonly used by dentists to submit claims, whereas current procedural terminology (CPT) and International Classification of Diseases, Ninth Revision, Clinical Modification (ICD.9.CM) codes are more commonly used by physicians to bill for their services. The CPT and ICD.9.CM coding systems complement each other in that CPT codes provide the procedure and service information and ICD.9.CM codes provide the reason or rationale for a particular procedure or service. These codes are more commonly used for "medical necessity" determinations, and general dentists and specialists who routinely perform care, including trauma-related care, biopsies, and dental treatment as a result of or in anticipation of a cancer-related treatment, are likely to use these codes. Claim submissions for care provided can be completed electronically or by means of paper forms.

  13. Error Correcting Codes

    Science and Automation at ... the Reed-Solomon code contained 223 bytes of data, (a byte ... then you have a data storage system with error correction, that ..... practical codes, storing such a table is infeasible, as it is generally too large.

  14. Scrum Code Camps

    Pries-Heje, Lene; Pries-Heje, Jan; Dalgaard, Bente

    2013-01-01

    is required. In this paper we present the design of such a new approach, the Scrum Code Camp, which can be used to assess agile team capability in a transparent and consistent way. A design science research approach is used to analyze properties of two instances of the Scrum Code Camp where seven agile teams...

  15. RFQ simulation code

    Lysenko, W.P.

    1984-04-01

    We have developed the RFQLIB simulation system to provide a means to systematically generate the new versions of radio-frequency quadrupole (RFQ) linac simulation codes that are required by the constantly changing needs of a research environment. This integrated system simplifies keeping track of the various versions of the simulation code and makes it practical to maintain complete and up-to-date documentation. In this scheme, there is a certain standard version of the simulation code that forms a library upon which new versions are built. To generate a new version of the simulation code, the routines to be modified or added are appended to a standard command file, which contains the commands to compile the new routines and link them to the routines in the library. The library itself is rarely changed. Whenever the library is modified, however, this modification is seen by all versions of the simulation code, which actually exist as different versions of the command file. All code is written according to the rules of structured programming. Modularity is enforced by not using COMMON statements, simplifying the relation of the data flow to a hierarchy diagram. Simulation results are similar to those of the PARMTEQ code, as expected, because of the similar physical model. Different capabilities, such as those for generating beams matched in detail to the structure, are available in the new code for help in testing new ideas in designing RFQ linacs

  16. Error Correcting Codes

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 3. Error Correcting Codes - Reed Solomon Codes. Priti Shankar. Series Article Volume 2 Issue 3 March ... Author Affiliations. Priti Shankar1. Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560 012, India ...

  17. 78 FR 18321 - International Code Council: The Update Process for the International Codes and Standards

    2013-03-26

    ... Energy Conservation Code. International Existing Building Code. International Fire Code. International... Code. International Property Maintenance Code. International Residential Code. International Swimming Pool and Spa Code International Wildland-Urban Interface Code. International Zoning Code. ICC Standards...

  18. Validation of thermalhydraulic codes

    Wilkie, D.

    1992-01-01

    Thermalhydraulic codes require to be validated against experimental data collected over a wide range of situations if they are to be relied upon. A good example is provided by the nuclear industry where codes are used for safety studies and for determining operating conditions. Errors in the codes could lead to financial penalties, to the incorrect estimation of the consequences of accidents and even to the accidents themselves. Comparison between prediction and experiment is often described qualitatively or in approximate terms, e.g. ''agreement is within 10%''. A quantitative method is preferable, especially when several competing codes are available. The codes can then be ranked in order of merit. Such a method is described. (Author)

  19. Fracture flow code

    Dershowitz, W; Herbert, A.; Long, J.

    1989-03-01

    The hydrology of the SCV site will be modelled utilizing discrete fracture flow models. These models are complex, and can not be fully cerified by comparison to analytical solutions. The best approach for verification of these codes is therefore cross-verification between different codes. This is complicated by the variation in assumptions and solution techniques utilized in different codes. Cross-verification procedures are defined which allow comparison of the codes developed by Harwell Laboratory, Lawrence Berkeley Laboratory, and Golder Associates Inc. Six cross-verification datasets are defined for deterministic and stochastic verification of geometric and flow features of the codes. Additional datasets for verification of transport features will be documented in a future report. (13 figs., 7 tabs., 10 refs.) (authors)

  20. Huffman coding in advanced audio coding standard

    Brzuchalski, Grzegorz

    2012-05-01

    This article presents several hardware architectures of Advanced Audio Coding (AAC) Huffman noiseless encoder, its optimisations and working implementation. Much attention has been paid to optimise the demand of hardware resources especially memory size. The aim of design was to get as short binary stream as possible in this standard. The Huffman encoder with whole audio-video system has been implemented in FPGA devices.

  1. Report number codes

    Nelson, R.N. (ed.)

    1985-05-01

    This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name.

  2. Report number codes

    Nelson, R.N.

    1985-05-01

    This publication lists all report number codes processed by the Office of Scientific and Technical Information. The report codes are substantially based on the American National Standards Institute, Standard Technical Report Number (STRN)-Format and Creation Z39.23-1983. The Standard Technical Report Number (STRN) provides one of the primary methods of identifying a specific technical report. The STRN consists of two parts: The report code and the sequential number. The report code identifies the issuing organization, a specific program, or a type of document. The sequential number, which is assigned in sequence by each report issuing entity, is not included in this publication. Part I of this compilation is alphabetized by report codes followed by issuing installations. Part II lists the issuing organization followed by the assigned report code(s). In both Parts I and II, the names of issuing organizations appear for the most part in the form used at the time the reports were issued. However, for some of the more prolific installations which have had name changes, all entries have been merged under the current name

  3. Cryptography cracking codes

    2014-01-01

    While cracking a code might seem like something few of us would encounter in our daily lives, it is actually far more prevalent than we may realize. Anyone who has had personal information taken because of a hacked email account can understand the need for cryptography and the importance of encryption-essentially the need to code information to keep it safe. This detailed volume examines the logic and science behind various ciphers, their real world uses, how codes can be broken, and the use of technology in this oft-overlooked field.

  4. Coded Splitting Tree Protocols

    Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...

  5. Transport theory and codes

    Clancy, B.E.

    1986-01-01

    This chapter begins with a neutron transport equation which includes the one dimensional plane geometry problems, the one dimensional spherical geometry problems, and numerical solutions. The section on the ANISN code and its look-alikes covers problems which can be solved; eigenvalue problems; outer iteration loop; inner iteration loop; and finite difference solution procedures. The input and output data for ANISN is also discussed. Two dimensional problems such as the DOT code are given. Finally, an overview of the Monte-Carlo methods and codes are elaborated on

  6. Gravity inversion code

    Burkhard, N.R.

    1979-01-01

    The gravity inversion code applies stabilized linear inverse theory to determine the topography of a subsurface density anomaly from Bouguer gravity data. The gravity inversion program consists of four source codes: SEARCH, TREND, INVERT, and AVERAGE. TREND and INVERT are used iteratively to converge on a solution. SEARCH forms the input gravity data files for Nevada Test Site data. AVERAGE performs a covariance analysis on the solution. This document describes the necessary input files and the proper operation of the code. 2 figures, 2 tables

  7. Fulcrum Network Codes

    2015-01-01

    Fulcrum network codes, which are a network coding framework, achieve three objectives: (i) to reduce the overhead per coded packet to almost 1 bit per source packet; (ii) to operate the network using only low field size operations at intermediate nodes, dramatically reducing complexity...... in the network; and (iii) to deliver an end-to-end performance that is close to that of a high field size network coding system for high-end receivers while simultaneously catering to low-end ones that can only decode in a lower field size. Sources may encode using a high field size expansion to increase...... the number of dimensions seen by the network using a linear mapping. Receivers can tradeoff computational effort with network delay, decoding in the high field size, the low field size, or a combination thereof....

  8. Supervised Convolutional Sparse Coding

    Affara, Lama Ahmed; Ghanem, Bernard; Wonka, Peter

    2018-01-01

    coding, which aims at learning discriminative dictionaries instead of purely reconstructive ones. We incorporate a supervised regularization term into the traditional unsupervised CSC objective to encourage the final dictionary elements

  9. SASSYS LMFBR systems code

    Dunn, F.E.; Prohammer, F.G.; Weber, D.P.

    1983-01-01

    The SASSYS LMFBR systems analysis code is being developed mainly to analyze the behavior of the shut-down heat-removal system and the consequences of failures in the system, although it is also capable of analyzing a wide range of transients, from mild operational transients through more severe transients leading to sodium boiling in the core and possible melting of clad and fuel. The code includes a detailed SAS4A multi-channel core treatment plus a general thermal-hydraulic treatment of the primary and intermediate heat-transport loops and the steam generators. The code can handle any LMFBR design, loop or pool, with an arbitrary arrangement of components. The code is fast running: usually faster than real time

  10. OCA Code Enforcement

    Montgomery County of Maryland — The Office of the County Attorney (OCA) processes Code Violation Citations issued by County agencies. The citations can be viewed by issued department, issued date...

  11. The fast code

    Freeman, L.N.; Wilson, R.E. [Oregon State Univ., Dept. of Mechanical Engineering, Corvallis, OR (United States)

    1996-09-01

    The FAST Code which is capable of determining structural loads on a flexible, teetering, horizontal axis wind turbine is described and comparisons of calculated loads with test data are given at two wind speeds for the ESI-80. The FAST Code models a two-bladed HAWT with degrees of freedom for blade bending, teeter, drive train flexibility, yaw, and windwise and crosswind tower motion. The code allows blade dimensions, stiffnesses, and weights to differ and models tower shadow, wind shear, and turbulence. Additionally, dynamic stall is included as are delta-3 and an underslung rotor. Load comparisons are made with ESI-80 test data in the form of power spectral density, rainflow counting, occurrence histograms, and azimuth averaged bin plots. It is concluded that agreement between the FAST Code and test results is good. (au)

  12. Code Disentanglement: Initial Plan

    Wohlbier, John Greaton [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kelley, Timothy M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rockefeller, Gabriel M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Calef, Matthew Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-01-27

    The first step to making more ambitious changes in the EAP code base is to disentangle the code into a set of independent, levelized packages. We define a package as a collection of code, most often across a set of files, that provides a defined set of functionality; a package a) can be built and tested as an entity and b) fits within an overall levelization design. Each package contributes one or more libraries, or an application that uses the other libraries. A package set is levelized if the relationships between packages form a directed, acyclic graph and each package uses only packages at lower levels of the diagram (in Fortran this relationship is often describable by the use relationship between modules). Independent packages permit independent- and therefore parallel|development. The packages form separable units for the purposes of development and testing. This is a proven path for enabling finer-grained changes to a complex code.

  13. Induction technology optimization code

    Caporaso, G.J.; Brooks, A.L.; Kirbie, H.C.

    1992-01-01

    A code has been developed to evaluate relative costs of induction accelerator driver systems for relativistic klystrons. The code incorporates beam generation, transport and pulsed power system constraints to provide an integrated design tool. The code generates an injector/accelerator combination which satisfies the top level requirements and all system constraints once a small number of design choices have been specified (rise time of the injector voltage and aspect ratio of the ferrite induction cores, for example). The code calculates dimensions of accelerator mechanical assemblies and values of all electrical components. Cost factors for machined parts, raw materials and components are applied to yield a total system cost. These costs are then plotted as a function of the two design choices to enable selection of an optimum design based on various criteria. (Author) 11 refs., 3 figs

  14. VT ZIP Code Areas

    Vermont Center for Geographic Information — (Link to Metadata) A ZIP Code Tabulation Area (ZCTA) is a statistical geographic entity that approximates the delivery area for a U.S. Postal Service five-digit...

  15. Bandwidth efficient coding

    Anderson, John B

    2017-01-01

    Bandwidth Efficient Coding addresses the major challenge in communication engineering today: how to communicate more bits of information in the same radio spectrum. Energy and bandwidth are needed to transmit bits, and bandwidth affects capacity the most. Methods have been developed that are ten times as energy efficient at a given bandwidth consumption as simple methods. These employ signals with very complex patterns and are called "coding" solutions. The book begins with classical theory before introducing new techniques that combine older methods of error correction coding and radio transmission in order to create narrowband methods that are as efficient in both spectrum and energy as nature allows. Other topics covered include modulation techniques such as CPM, coded QAM and pulse design.

  16. Reactor lattice codes

    Kulikowska, T.

    2001-01-01

    The description of reactor lattice codes is carried out on the example of the WIMSD-5B code. The WIMS code in its various version is the most recognised lattice code. It is used in all parts of the world for calculations of research and power reactors. The version WIMSD-5B is distributed free of charge by NEA Data Bank. The description of its main features given in the present lecture follows the aspects defined previously for lattice calculations in the lecture on Reactor Lattice Transport Calculations. The spatial models are described, and the approach to the energy treatment is given. Finally the specific algorithm applied in fuel depletion calculations is outlined. (author)

  17. Critical Care Coding for Neurologists.

    Nuwer, Marc R; Vespa, Paul M

    2015-10-01

    Accurate coding is an important function of neurologic practice. This contribution to Continuum is part of an ongoing series that presents helpful coding information along with examples related to the issue topic. Tips for diagnosis coding, Evaluation and Management coding, procedure coding, or a combination are presented, depending on which is most applicable to the subject area of the issue.

  18. Lattice Index Coding

    Natarajan, Lakshmi; Hong, Yi; Viterbo, Emanuele

    2014-01-01

    The index coding problem involves a sender with K messages to be transmitted across a broadcast channel, and a set of receivers each of which demands a subset of the K messages while having prior knowledge of a different subset as side information. We consider the specific case of noisy index coding where the broadcast channel is Gaussian and every receiver demands all the messages from the source. Instances of this communication problem arise in wireless relay networks, sensor networks, and ...

  19. Towards advanced code simulators

    Scriven, A.H.

    1990-01-01

    The Central Electricity Generating Board (CEGB) uses advanced thermohydraulic codes extensively to support PWR safety analyses. A system has been developed to allow fully interactive execution of any code with graphical simulation of the operator desk and mimic display. The system operates in a virtual machine environment, with the thermohydraulic code executing in one virtual machine, communicating via interrupts with any number of other virtual machines each running other programs and graphics drivers. The driver code itself does not have to be modified from its normal batch form. Shortly following the release of RELAP5 MOD1 in IBM compatible form in 1983, this code was used as the driver for this system. When RELAP5 MOD2 became available, it was adopted with no changes needed in the basic system. Overall the system has been used for some 5 years for the analysis of LOBI tests, full scale plant studies and for simple what-if studies. For gaining rapid understanding of system dependencies it has proved invaluable. The graphical mimic system, being independent of the driver code, has also been used with other codes to study core rewetting, to replay results obtained from batch jobs on a CRAY2 computer system and to display suitably processed experimental results from the LOBI facility to aid interpretation. For the above work real-time execution was not necessary. Current work now centers on implementing the RELAP 5 code on a true parallel architecture machine. Marconi Simulation have been contracted to investigate the feasibility of using upwards of 100 processors, each capable of a peak of 30 MIPS to run a highly detailed RELAP5 model in real time, complete with specially written 3D core neutronics and balance of plant models. This paper describes the experience of using RELAP5 as an analyzer/simulator, and outlines the proposed methods and problems associated with parallel execution of RELAP5

  20. Cracking the Gender Codes

    Rennison, Betina Wolfgang

    2016-01-01

    extensive work to raise the proportion of women. This has helped slightly, but women remain underrepresented at the corporate top. Why is this so? What can be done to solve it? This article presents five different types of answers relating to five discursive codes: nature, talent, business, exclusion...... in leadership management, we must become more aware and take advantage of this complexity. We must crack the codes in order to crack the curve....

  1. PEAR code review

    De Wit, R.; Jamieson, T.; Lord, M.; Lafortune, J.F.

    1997-07-01

    As a necessary component in the continuous improvement and refinement of methodologies employed in the nuclear industry, regulatory agencies need to periodically evaluate these processes to improve confidence in results and ensure appropriate levels of safety are being achieved. The independent and objective review of industry-standard computer codes forms an essential part of this program. To this end, this work undertakes an in-depth review of the computer code PEAR (Public Exposures from Accidental Releases), developed by Atomic Energy of Canada Limited (AECL) to assess accidental releases from CANDU reactors. PEAR is based largely on the models contained in the Canadian Standards Association (CSA) N288.2-M91. This report presents the results of a detailed technical review of the PEAR code to identify any variations from the CSA standard and other supporting documentation, verify the source code, assess the quality of numerical models and results, and identify general strengths and weaknesses of the code. The version of the code employed in this review is the one which AECL intends to use for CANDU 9 safety analyses. (author)

  2. KENO-V code

    Cramer, S.N.

    1984-01-01

    The KENO-V code is the current release of the Oak Ridge multigroup Monte Carlo criticality code development. The original KENO, with 16 group Hansen-Roach cross sections and P 1 scattering, was one ot the first multigroup Monte Carlo codes and it and its successors have always been a much-used research tool for criticality studies. KENO-V is able to accept large neutron cross section libraries (a 218 group set is distributed with the code) and has a general P/sub N/ scattering capability. A supergroup feature allows execution of large problems on small computers, but at the expense of increased calculation time and system input/output operations. This supergroup feature is activated automatically by the code in a manner which utilizes as much computer memory as is available. The primary purpose of KENO-V is to calculate the system k/sub eff/, from small bare critical assemblies to large reflected arrays of differing fissile and moderator elements. In this respect KENO-V neither has nor requires the many options and sophisticated biasing techniques of general Monte Carlo codes

  3. Code, standard and specifications

    Abdul Nassir Ibrahim; Azali Muhammad; Ab. Razak Hamzah; Abd. Aziz Mohamed; Mohamad Pauzi Ismail

    2008-01-01

    Radiography also same as the other technique, it need standard. This standard was used widely and method of used it also regular. With that, radiography testing only practical based on regulations as mentioned and documented. These regulation or guideline documented in code, standard and specifications. In Malaysia, level one and basic radiographer can do radiography work based on instruction give by level two or three radiographer. This instruction was produced based on guideline that mention in document. Level two must follow the specifications mentioned in standard when write the instruction. From this scenario, it makes clearly that this radiography work is a type of work that everything must follow the rule. For the code, the radiography follow the code of American Society for Mechanical Engineer (ASME) and the only code that have in Malaysia for this time is rule that published by Atomic Energy Licensing Board (AELB) known as Practical code for radiation Protection in Industrial radiography. With the existence of this code, all the radiography must follow the rule or standard regulated automatically.

  4. Fast Coding Unit Encoding Mechanism for Low Complexity Video Coding

    Gao, Yuan; Liu, Pengyu; Wu, Yueying; Jia, Kebin; Gao, Guandong

    2016-01-01

    In high efficiency video coding (HEVC), coding tree contributes to excellent compression performance. However, coding tree brings extremely high computational complexity. Innovative works for improving coding tree to further reduce encoding time are stated in this paper. A novel low complexity coding tree mechanism is proposed for HEVC fast coding unit (CU) encoding. Firstly, this paper makes an in-depth study of the relationship among CU distribution, quantization parameter (QP) and content ...

  5. SPECTRAL AMPLITUDE CODING OCDMA SYSTEMS USING ENHANCED DOUBLE WEIGHT CODE

    F.N. HASOON

    2006-12-01

    Full Text Available A new code structure for spectral amplitude coding optical code division multiple access systems based on double weight (DW code families is proposed. The DW has a fixed weight of two. Enhanced double-weight (EDW code is another variation of a DW code family that can has a variable weight greater than one. The EDW code possesses ideal cross-correlation properties and exists for every natural number n. A much better performance can be provided by using the EDW code compared to the existing code such as Hadamard and Modified Frequency-Hopping (MFH codes. It has been observed that theoretical analysis and simulation for EDW is much better performance compared to Hadamard and Modified Frequency-Hopping (MFH codes.

  6. Nuclear code abstracts (1975 edition)

    Akanuma, Makoto; Hirakawa, Takashi

    1976-02-01

    Nuclear Code Abstracts is compiled in the Nuclear Code Committee to exchange information of the nuclear code developments among members of the committee. Enlarging the collection, the present one includes nuclear code abstracts obtained in 1975 through liaison officers of the organizations in Japan participating in the Nuclear Energy Agency's Computer Program Library at Ispra, Italy. The classification of nuclear codes and the format of code abstracts are the same as those in the library. (auth.)

  7. Some new ternary linear codes

    Rumen Daskalov

    2017-07-01

    Full Text Available Let an $[n,k,d]_q$ code be a linear code of length $n$, dimension $k$ and minimum Hamming distance $d$ over $GF(q$. One of the most important problems in coding theory is to construct codes with optimal minimum distances. In this paper 22 new ternary linear codes are presented. Two of them are optimal. All new codes improve the respective lower bounds in [11].

  8. ACE - Manufacturer Identification Code (MID)

    Department of Homeland Security — The ACE Manufacturer Identification Code (MID) application is used to track and control identifications codes for manufacturers. A manufacturer is identified on an...

  9. Algebraic and stochastic coding theory

    Kythe, Dave K

    2012-01-01

    Using a simple yet rigorous approach, Algebraic and Stochastic Coding Theory makes the subject of coding theory easy to understand for readers with a thorough knowledge of digital arithmetic, Boolean and modern algebra, and probability theory. It explains the underlying principles of coding theory and offers a clear, detailed description of each code. More advanced readers will appreciate its coverage of recent developments in coding theory and stochastic processes. After a brief review of coding history and Boolean algebra, the book introduces linear codes, including Hamming and Golay codes.

  10. Optical coding theory with Prime

    Kwong, Wing C

    2013-01-01

    Although several books cover the coding theory of wireless communications and the hardware technologies and coding techniques of optical CDMA, no book has been specifically dedicated to optical coding theory-until now. Written by renowned authorities in the field, Optical Coding Theory with Prime gathers together in one volume the fundamentals and developments of optical coding theory, with a focus on families of prime codes, supplemented with several families of non-prime codes. The book also explores potential applications to coding-based optical systems and networks. Learn How to Construct

  11. The Aster code

    Delbecq, J.M.

    1999-01-01

    The Aster code is a 2D or 3D finite-element calculation code for structures developed by the R and D direction of Electricite de France (EdF). This dossier presents a complete overview of the characteristics and uses of the Aster code: introduction of version 4; the context of Aster (organisation of the code development, versions, systems and interfaces, development tools, quality assurance, independent validation); static mechanics (linear thermo-elasticity, Euler buckling, cables, Zarka-Casier method); non-linear mechanics (materials behaviour, big deformations, specific loads, unloading and loss of load proportionality indicators, global algorithm, contact and friction); rupture mechanics (G energy restitution level, restitution level in thermo-elasto-plasticity, 3D local energy restitution level, KI and KII stress intensity factors, calculation of limit loads for structures), specific treatments (fatigue, rupture, wear, error estimation); meshes and models (mesh generation, modeling, loads and boundary conditions, links between different modeling processes, resolution of linear systems, display of results etc..); vibration mechanics (modal and harmonic analysis, dynamics with shocks, direct transient dynamics, seismic analysis and aleatory dynamics, non-linear dynamics, dynamical sub-structuring); fluid-structure interactions (internal acoustics, mass, rigidity and damping); linear and non-linear thermal analysis; steels and metal industry (structure transformations); coupled problems (internal chaining, internal thermo-hydro-mechanical coupling, chaining with other codes); products and services. (J.S.)

  12. Adaptive distributed source coding.

    Varodayan, David; Lin, Yao-Chung; Girod, Bernd

    2012-05-01

    We consider distributed source coding in the presence of hidden variables that parameterize the statistical dependence among sources. We derive the Slepian-Wolf bound and devise coding algorithms for a block-candidate model of this problem. The encoder sends, in addition to syndrome bits, a portion of the source to the decoder uncoded as doping bits. The decoder uses the sum-product algorithm to simultaneously recover the source symbols and the hidden statistical dependence variables. We also develop novel techniques based on density evolution (DE) to analyze the coding algorithms. We experimentally confirm that our DE analysis closely approximates practical performance. This result allows us to efficiently optimize parameters of the algorithms. In particular, we show that the system performs close to the Slepian-Wolf bound when an appropriate doping rate is selected. We then apply our coding and analysis techniques to a reduced-reference video quality monitoring system and show a bit rate saving of about 75% compared with fixed-length coding.

  13. Speech coding code- excited linear prediction

    Bäckström, Tom

    2017-01-01

    This book provides scientific understanding of the most central techniques used in speech coding both for advanced students as well as professionals with a background in speech audio and or digital signal processing. It provides a clear connection between the whys hows and whats thus enabling a clear view of the necessity purpose and solutions provided by various tools as well as their strengths and weaknesses in each respect Equivalently this book sheds light on the following perspectives for each technology presented Objective What do we want to achieve and especially why is this goal important Resource Information What information is available and how can it be useful and Resource Platform What kind of platforms are we working with and what are their capabilities restrictions This includes computational memory and acoustic properties and the transmission capacity of devices used. The book goes on to address Solutions Which solutions have been proposed and how can they be used to reach the stated goals and ...

  14. Spatially coded backscatter radiography

    Thangavelu, S.; Hussein, E.M.A.

    2007-01-01

    Conventional radiography requires access to two opposite sides of an object, which makes it unsuitable for the inspection of extended and/or thick structures (airframes, bridges, floors etc.). Backscatter imaging can overcome this problem, but the indications obtained are difficult to interpret. This paper applies the coded aperture technique to gamma-ray backscatter-radiography in order to enhance the detectability of flaws. This spatial coding method involves the positioning of a mask with closed and open holes to selectively permit or block the passage of radiation. The obtained coded-aperture indications are then mathematically decoded to detect the presence of anomalies. Indications obtained from Monte Carlo calculations were utilized in this work to simulate radiation scattering measurements. These simulated measurements were used to investigate the applicability of this technique to the detection of flaws by backscatter radiography

  15. Aztheca Code; Codigo Aztheca

    Quezada G, S.; Espinosa P, G. [Universidad Autonoma Metropolitana, Unidad Iztapalapa, San Rafael Atlixco No. 186, Col. Vicentina, 09340 Ciudad de Mexico (Mexico); Centeno P, J.; Sanchez M, H., E-mail: sequga@gmail.com [UNAM, Facultad de Ingenieria, Ciudad Universitaria, Circuito Exterior s/n, 04510 Ciudad de Mexico (Mexico)

    2017-09-15

    This paper presents the Aztheca code, which is formed by the mathematical models of neutron kinetics, power generation, heat transfer, core thermo-hydraulics, recirculation systems, dynamic pressure and level models and control system. The Aztheca code is validated with plant data, as well as with predictions from the manufacturer when the reactor operates in a stationary state. On the other hand, to demonstrate that the model is applicable during a transient, an event occurred in a nuclear power plant with a BWR reactor is selected. The plant data are compared with the results obtained with RELAP-5 and the Aztheca model. The results show that both RELAP-5 and the Aztheca code have the ability to adequately predict the behavior of the reactor. (Author)

  16. The Coding Question.

    Gallistel, C R

    2017-07-01

    Recent electrophysiological results imply that the duration of the stimulus onset asynchrony in eyeblink conditioning is encoded by a mechanism intrinsic to the cerebellar Purkinje cell. This raises the general question - how is quantitative information (durations, distances, rates, probabilities, amounts, etc.) transmitted by spike trains and encoded into engrams? The usual assumption is that information is transmitted by firing rates. However, rate codes are energetically inefficient and computationally awkward. A combinatorial code is more plausible. If the engram consists of altered synaptic conductances (the usual assumption), then we must ask how numbers may be written to synapses. It is much easier to formulate a coding hypothesis if the engram is realized by a cell-intrinsic molecular mechanism. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Revised SRAC code system

    Tsuchihashi, Keichiro; Ishiguro, Yukio; Kaneko, Kunio; Ido, Masaru.

    1986-09-01

    Since the publication of JAERI-1285 in 1983 for the preliminary version of the SRAC code system, a number of additions and modifications to the functions have been made to establish an overall neutronics code system. Major points are (1) addition of JENDL-2 version of data library, (2) a direct treatment of doubly heterogeneous effect on resonance absorption, (3) a generalized Dancoff factor, (4) a cell calculation based on the fixed boundary source problem, (5) the corresponding edit required for experimental analysis and reactor design, (6) a perturbation theory calculation for reactivity change, (7) an auxiliary code for core burnup and fuel management, etc. This report is a revision of the users manual which consists of the general description, input data requirements and their explanation, detailed information on usage, mathematics, contents of libraries and sample I/O. (author)

  18. Code query by example

    Vaucouleur, Sebastien

    2011-02-01

    We introduce code query by example for customisation of evolvable software products in general and of enterprise resource planning systems (ERPs) in particular. The concept is based on an initial empirical study on practices around ERP systems. We motivate our design choices based on those empirical results, and we show how the proposed solution helps with respect to the infamous upgrade problem: the conflict between the need for customisation and the need for upgrade of ERP systems. We further show how code query by example can be used as a form of lightweight static analysis, to detect automatically potential defects in large software products. Code query by example as a form of lightweight static analysis is particularly interesting in the context of ERP systems: it is often the case that programmers working in this field are not computer science specialists but more of domain experts. Hence, they require a simple language to express custom rules.

  19. The correspondence between projective codes and 2-weight codes

    Brouwer, A.E.; Eupen, van M.J.M.; Tilborg, van H.C.A.; Willems, F.M.J.

    1994-01-01

    The hyperplanes intersecting a 2-weight code in the same number of points obviously form the point set of a projective code. On the other hand, if we have a projective code C, then we can make a 2-weight code by taking the multiset of points E PC with multiplicity "Y(w), where W is the weight of

  20. Visualizing code and coverage changes for code review

    Oosterwaal, Sebastiaan; van Deursen, A.; De Souza Coelho, R.; Sawant, A.A.; Bacchelli, A.

    2016-01-01

    One of the tasks of reviewers is to verify that code modifications are well tested. However, current tools offer little support in understanding precisely how changes to the code relate to changes to the tests. In particular, it is hard to see whether (modified) test code covers the changed code.

  1. Turbo-Gallager Codes: The Emergence of an Intelligent Coding ...

    Today, both turbo codes and low-density parity-check codes are largely superior to other code families and are being used in an increasing number of modern communication systems including 3G standards, satellite and deep space communications. However, the two codes have certain distinctive characteristics that ...

  2. Code of Medical Ethics

    . SZD-SZZ

    2017-03-01

    Full Text Available Te Code was approved on December 12, 1992, at the 3rd regular meeting of the General Assembly of the Medical Chamber of Slovenia and revised on April 24, 1997, at the 27th regular meeting of the General Assembly of the Medical Chamber of Slovenia. The Code was updated and harmonized with the Medical Association of Slovenia and approved on October 6, 2016, at the regular meeting of the General Assembly of the Medical Chamber of Slovenia.

  3. Supervised Convolutional Sparse Coding

    Affara, Lama Ahmed

    2018-04-08

    Convolutional Sparse Coding (CSC) is a well-established image representation model especially suited for image restoration tasks. In this work, we extend the applicability of this model by proposing a supervised approach to convolutional sparse coding, which aims at learning discriminative dictionaries instead of purely reconstructive ones. We incorporate a supervised regularization term into the traditional unsupervised CSC objective to encourage the final dictionary elements to be discriminative. Experimental results show that using supervised convolutional learning results in two key advantages. First, we learn more semantically relevant filters in the dictionary and second, we achieve improved image reconstruction on unseen data.

  4. CONCEPT computer code

    Delene, J.

    1984-01-01

    CONCEPT is a computer code that will provide conceptual capital investment cost estimates for nuclear and coal-fired power plants. The code can develop an estimate for construction at any point in time. Any unit size within the range of about 400 to 1300 MW electric may be selected. Any of 23 reference site locations across the United States and Canada may be selected. PWR, BWR, and coal-fired plants burning high-sulfur and low-sulfur coal can be estimated. Multiple-unit plants can be estimated. Costs due to escalation/inflation and interest during construction are calculated

  5. Principles of speech coding

    Ogunfunmi, Tokunbo

    2010-01-01

    It is becoming increasingly apparent that all forms of communication-including voice-will be transmitted through packet-switched networks based on the Internet Protocol (IP). Therefore, the design of modern devices that rely on speech interfaces, such as cell phones and PDAs, requires a complete and up-to-date understanding of the basics of speech coding. Outlines key signal processing algorithms used to mitigate impairments to speech quality in VoIP networksOffering a detailed yet easily accessible introduction to the field, Principles of Speech Coding provides an in-depth examination of the

  6. Evaluation Codes from an Affine Veriety Code Perspective

    Geil, Hans Olav

    2008-01-01

    Evaluation codes (also called order domain codes) are traditionally introduced as generalized one-point geometric Goppa codes. In the present paper we will give a new point of view on evaluation codes by introducing them instead as particular nice examples of affine variety codes. Our study...... includes a reformulation of the usual methods to estimate the minimum distances of evaluation codes into the setting of affine variety codes. Finally we describe the connection to the theory of one-pointgeometric Goppa codes. Contents 4.1 Introduction...... . . . . . . . . . . . . . . . . . . . . . . . 171 4.9 Codes form order domains . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173 4.10 One-point geometric Goppa codes . . . . . . . . . . . . . . . . . . . . . . . . 176 4.11 Bibliographical Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178 References...

  7. Characterization of Genomic Deletion Efficiency Mediated by Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 Nuclease System in Mammalian Cells*♦

    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

  8. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells.

    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.

  9. 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

    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

  10. Comparison of the solution and crystal structures of staphylococcal nuclease with 13C and 15N chemical shifts used as structural fingerprints

    Cole, H.B.R.; Sparks, S.W.; Torchia, D.A.

    1988-01-01

    The authors report high-resolution 13 C and 15 N NMR spectra of crystalline staphylococcal nuclease (Nase) complexed to thymidine 3',5'-diphosphate and Ca 2+ . High sensitivity and resolution are obtained by applying solid-state NMR techniques-high power proton decoupling and cross-polarization magic angle sample spinning (CPMASS)-to protein samples that have been efficiently synthesized and labeled by an overproducing strain of Escherichia coli. A comparison of CPMASS and solution spectra of Nase labeled with either [methyl- 13 C]methionine or [ 15 ]valine shows that the chemical shifts in the crystalline and solution states are virtually identical. This result is strong evidence that the protein conformations in the solution and crystalline states are nearly the same. Because of the close correspondence of the crystal and solution chemical shifts, sequential assignments obtained in solution apply to the crystal spectra. It should therefore be possible to study the molecular structure and dynamics of many sequentially assigned atomic sites in Nase crystals. Similar experiments are applicable to the growing number of proteins that can be obtained from efficient expression systems

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

    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.

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

    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...

  13. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

    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.

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

    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

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

    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.

  16. Dual Coding in Children.

    Burton, John K.; Wildman, Terry M.

    The purpose of this study was to test the applicability of the dual coding hypothesis to children's recall performance. The hypothesis predicts that visual interference will have a small effect on the recall of visually presented words or pictures, but that acoustic interference will cause a decline in recall of visually presented words and…

  17. Physical layer network coding

    Fukui, Hironori; Popovski, Petar; Yomo, Hiroyuki

    2014-01-01

    Physical layer network coding (PLNC) has been proposed to improve throughput of the two-way relay channel, where two nodes communicate with each other, being assisted by a relay node. Most of the works related to PLNC are focused on a simple three-node model and they do not take into account...

  18. Radioactive action code

    Anon.

    1988-01-01

    A new coding system, 'Hazrad', for buildings and transportation containers for alerting emergency services personnel to the presence of radioactive materials has been developed in the United Kingdom. The hazards of materials in the buildings or transport container, together with the recommended emergency action, are represented by a number of codes which are marked on the building or container and interpreted from a chart carried as a pocket-size guide. Buildings would be marked with the familiar yellow 'radioactive' trefoil, the written information 'Radioactive materials' and a list of isotopes. Under this the 'Hazrad' code would be written - three symbols to denote the relative radioactive risk (low, medium or high), the biological risk (also low, medium or high) and the third showing the type of radiation emitted, alpha, beta or gamma. The response cards indicate appropriate measures to take, eg for a high biological risk, Bio3, the wearing of a gas-tight protection suit is advised. The code and its uses are explained. (U.K.)

  19. Building Codes and Regulations.

    Fisher, John L.

    The hazard of fire is of great concern to libraries due to combustible books and new plastics used in construction and interiors. Building codes and standards can offer architects and planners guidelines to follow but these standards should be closely monitored, updated, and researched for fire prevention. (DS)

  20. Physics of codes

    Cooper, R.K.; Jones, M.E.

    1989-01-01

    The title given this paper is a bit presumptuous, since one can hardly expect to cover the physics incorporated into all the codes already written and currently being written. The authors focus on those codes which have been found to be particularly useful in the analysis and design of linacs. At that the authors will be a bit parochial and discuss primarily those codes used for the design of radio-frequency (rf) linacs, although the discussions of TRANSPORT and MARYLIE have little to do with the time structures of the beams being analyzed. The plan of this paper is first to describe rather simply the concepts of emittance and brightness, then to describe rather briefly each of the codes TRANSPORT, PARMTEQ, TBCI, MARYLIE, and ISIS, indicating what physics is and is not included in each of them. It is expected that the vast majority of what is covered will apply equally well to protons and electrons (and other particles). This material is intended to be tutorial in nature and can in no way be expected to be exhaustive. 31 references, 4 figures

  1. Reliability and code level

    Kasperski, M.; Geurts, C.P.W.

    2005-01-01

    The paper describes the work of the IAWE Working Group WBG - Reliability and Code Level, one of the International Codification Working Groups set up at ICWE10 in Copenhagen. The following topics are covered: sources of uncertainties in the design wind load, appropriate design target values for the

  2. Ready, steady… Code!

    Anaïs Schaeffer

    2013-01-01

    This summer, CERN took part in the Google Summer of Code programme for the third year in succession. Open to students from all over the world, this programme leads to very successful collaborations for open source software projects.   Image: GSoC 2013. Google Summer of Code (GSoC) is a global programme that offers student developers grants to write code for open-source software projects. Since its creation in 2005, the programme has brought together some 6,000 students from over 100 countries worldwide. The students selected by Google are paired with a mentor from one of the participating projects, which can be led by institutes, organisations, companies, etc. This year, CERN PH Department’s SFT (Software Development for Experiments) Group took part in the GSoC programme for the third time, submitting 15 open-source projects. “Once published on the Google Summer for Code website (in April), the projects are open to applications,” says Jakob Blomer, one of the o...

  3. CERN Code of Conduct

    Department, HR

    2010-01-01

    The Code is intended as a guide in helping us, as CERN contributors, to understand how to conduct ourselves, treat others and expect to be treated. It is based around the five core values of the Organization. We should all become familiar with it and try to incorporate it into our daily life at CERN.

  4. Nuclear safety code study

    Hu, H.H.; Ford, D.; Le, H.; Park, S.; Cooke, K.L.; Bleakney, T.; Spanier, J.; Wilburn, N.P.; O' Reilly, B.; Carmichael, B.

    1981-01-01

    The objective is to analyze an overpower accident in an LMFBR. A simplified model of the primary coolant loop was developed in order to understand the instabilities encountered with the MELT III and SAS codes. The computer programs were translated for switching to the IBM 4331. Numerical methods were investigated for solving the neutron kinetics equations; the Adams and Gear methods were compared. (DLC)

  5. Revised C++ coding conventions

    Callot, O

    2001-01-01

    This document replaces the note LHCb 98-049 by Pavel Binko. After a few years of practice, some simplification and clarification of the rules was needed. As many more people have now some experience in writing C++ code, their opinion was also taken into account to get a commonly agreed set of conventions

  6. Corporate governance through codes

    Haxhi, I.; Aguilera, R.V.; Vodosek, M.; den Hartog, D.; McNett, J.M.

    2014-01-01

    The UK's 1992 Cadbury Report defines corporate governance (CG) as the system by which businesses are directed and controlled. CG codes are a set of best practices designed to address deficiencies in the formal contracts and institutions by suggesting prescriptions on the preferred role and

  7. Error Correcting Codes -34 ...

    information and coding theory. A large scale relay computer had failed to deliver the expected results due to a hardware fault. Hamming, one of the active proponents of computer usage, was determined to find an efficient means by which computers could detect and correct their own faults. A mathematician by train-.

  8. Broadcast Coded Slotted ALOHA

    Ivanov, Mikhail; Brännström, Frederik; Graell i Amat, Alexandre

    2016-01-01

    We propose an uncoordinated medium access control (MAC) protocol, called all-to-all broadcast coded slotted ALOHA (B-CSA) for reliable all-to-all broadcast with strict latency constraints. In B-CSA, each user acts as both transmitter and receiver in a half-duplex mode. The half-duplex mode gives ...

  9. Software Defined Coded Networking

    Di Paola, Carla; Roetter, Daniel Enrique Lucani; Palazzo, Sergio

    2017-01-01

    the quality of each link and even across neighbouring links and using simulations to show that an additional reduction of packet transmission in the order of 40% is possible. Second, to advocate for the use of network coding (NC) jointly with software defined networking (SDN) providing an implementation...

  10. New code of conduct

    Laëtitia Pedroso

    2010-01-01

    During his talk to the staff at the beginning of the year, the Director-General mentioned that a new code of conduct was being drawn up. What exactly is it and what is its purpose? Anne-Sylvie Catherin, Head of the Human Resources (HR) Department, talked to us about the whys and wherefores of the project.   Drawing by Georges Boixader from the cartoon strip “The World of Particles” by Brian Southworth. A code of conduct is a general framework laying down the behaviour expected of all members of an organisation's personnel. “CERN is one of the very few international organisations that don’t yet have one", explains Anne-Sylvie Catherin. “We have been thinking about introducing a code of conduct for a long time but lacked the necessary resources until now”. The call for a code of conduct has come from different sources within the Laboratory. “The Equal Opportunities Advisory Panel (read also the "Equal opportuni...

  11. (Almost) practical tree codes

    Khina, Anatoly

    2016-08-15

    We consider the problem of stabilizing an unstable plant driven by bounded noise over a digital noisy communication link, a scenario at the heart of networked control. To stabilize such a plant, one needs real-time encoding and decoding with an error probability profile that decays exponentially with the decoding delay. The works of Schulman and Sahai over the past two decades have developed the notions of tree codes and anytime capacity, and provided the theoretical framework for studying such problems. Nonetheless, there has been little practical progress in this area due to the absence of explicit constructions of tree codes with efficient encoding and decoding algorithms. Recently, linear time-invariant tree codes were proposed to achieve the desired result under maximum-likelihood decoding. In this work, we take one more step towards practicality, by showing that these codes can be efficiently decoded using sequential decoding algorithms, up to some loss in performance (and with some practical complexity caveats). We supplement our theoretical results with numerical simulations that demonstrate the effectiveness of the decoder in a control system setting.

  12. Decoding Codes on Graphs

    having a probability Pi of being equal to a 1. Let us assume ... equal to a 0/1 has no bearing on the probability of the. It is often ... bits (call this set S) whose individual bits add up to zero ... In the context of binary error-correct~ng codes, specifi-.

  13. The Redox Code.

    Jones, Dean P; Sies, Helmut

    2015-09-20

    The redox code is a set of principles that defines the positioning of the nicotinamide adenine dinucleotide (NAD, NADP) and thiol/disulfide and other redox systems as well as the thiol redox proteome in space and time in biological systems. The code is richly elaborated in an oxygen-dependent life, where activation/deactivation cycles involving O₂ and H₂O₂ contribute to spatiotemporal organization for differentiation, development, and adaptation to the environment. Disruption of this organizational structure during oxidative stress represents a fundamental mechanism in system failure and disease. Methodology in assessing components of the redox code under physiological conditions has progressed, permitting insight into spatiotemporal organization and allowing for identification of redox partners in redox proteomics and redox metabolomics. Complexity of redox networks and redox regulation is being revealed step by step, yet much still needs to be learned. Detailed knowledge of the molecular patterns generated from the principles of the redox code under defined physiological or pathological conditions in cells and organs will contribute to understanding the redox component in health and disease. Ultimately, there will be a scientific basis to a modern redox medicine.

  14. Z₂-double cyclic codes

    Borges, J.

    2014-01-01

    A binary linear code C is a Z2-double cyclic code if the set of coordinates can be partitioned into two subsets such that any cyclic shift of the coordinates of both subsets leaves invariant the code. These codes can be identified as submodules of the Z2[x]-module Z2[x]/(x^r − 1) × Z2[x]/(x^s − 1). We determine the structure of Z2-double cyclic codes giving the generator polynomials of these codes. The related polynomial representation of Z2-double cyclic codes and its duals, and the relation...

  15. Coding for urologic office procedures.

    Dowling, Robert A; Painter, Mark

    2013-11-01

    This article summarizes current best practices for documenting, coding, and billing common office-based urologic procedures. Topics covered include general principles, basic and advanced urologic coding, creation of medical records that support compliant coding practices, bundled codes and unbundling, global periods, modifiers for procedure codes, when to bill for evaluation and management services during the same visit, coding for supplies, and laboratory and radiology procedures pertinent to urology practice. Detailed information is included for the most common urology office procedures, and suggested resources and references are provided. This information is of value to physicians, office managers, and their coding staff. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Essential idempotents and simplex codes

    Gladys Chalom

    2017-01-01

    Full Text Available We define essential idempotents in group algebras and use them to prove that every mininmal abelian non-cyclic code is a repetition code. Also we use them to prove that every minimal abelian code is equivalent to a minimal cyclic code of the same length. Finally, we show that a binary cyclic code is simplex if and only if is of length of the form $n=2^k-1$ and is generated by an essential idempotent.

  17. Rate-adaptive BCH codes for distributed source coding

    Salmistraro, Matteo; Larsen, Knud J.; Forchhammer, Søren

    2013-01-01

    This paper considers Bose-Chaudhuri-Hocquenghem (BCH) codes for distributed source coding. A feedback channel is employed to adapt the rate of the code during the decoding process. The focus is on codes with short block lengths for independently coding a binary source X and decoding it given its...... strategies for improving the reliability of the decoded result are analyzed, and methods for estimating the performance are proposed. In the analysis, noiseless feedback and noiseless communication are assumed. Simulation results show that rate-adaptive BCH codes achieve better performance than low...... correlated side information Y. The proposed codes have been analyzed in a high-correlation scenario, where the marginal probability of each symbol, Xi in X, given Y is highly skewed (unbalanced). Rate-adaptive BCH codes are presented and applied to distributed source coding. Adaptive and fixed checking...

  18. Entanglement-assisted quantum MDS codes constructed from negacyclic codes

    Chen, Jianzhang; Huang, Yuanyuan; Feng, Chunhui; Chen, Riqing

    2017-12-01

    Recently, entanglement-assisted quantum codes have been constructed from cyclic codes by some scholars. However, how to determine the number of shared pairs required to construct entanglement-assisted quantum codes is not an easy work. In this paper, we propose a decomposition of the defining set of negacyclic codes. Based on this method, four families of entanglement-assisted quantum codes constructed in this paper satisfy the entanglement-assisted quantum Singleton bound, where the minimum distance satisfies q+1 ≤ d≤ n+2/2. Furthermore, we construct two families of entanglement-assisted quantum codes with maximal entanglement.

  19. Efficient convolutional sparse coding

    Wohlberg, Brendt

    2017-06-20

    Computationally efficient algorithms may be applied for fast dictionary learning solving the convolutional sparse coding problem in the Fourier domain. More specifically, efficient convolutional sparse coding may be derived within an alternating direction method of multipliers (ADMM) framework that utilizes fast Fourier transforms (FFT) to solve the main linear system in the frequency domain. Such algorithms may enable a significant reduction in computational cost over conventional approaches by implementing a linear solver for the most critical and computationally expensive component of the conventional iterative algorithm. The theoretical computational cost of the algorithm may be reduced from O(M.sup.3N) to O(MN log N), where N is the dimensionality of the data and M is the number of elements in the dictionary. This significant improvement in efficiency may greatly increase the range of problems that can practically be addressed via convolutional sparse representations.

  20. Coded Network Function Virtualization

    Al-Shuwaili, A.; Simone, O.; Kliewer, J.

    2016-01-01

    Network function virtualization (NFV) prescribes the instantiation of network functions on general-purpose network devices, such as servers and switches. While yielding a more flexible and cost-effective network architecture, NFV is potentially limited by the fact that commercial off......-the-shelf hardware is less reliable than the dedicated network elements used in conventional cellular deployments. The typical solution for this problem is to duplicate network functions across geographically distributed hardware in order to ensure diversity. In contrast, this letter proposes to leverage channel...... coding in order to enhance the robustness on NFV to hardware failure. The proposed approach targets the network function of uplink channel decoding, and builds on the algebraic structure of the encoded data frames in order to perform in-network coding on the signals to be processed at different servers...

  1. The NIMROD Code

    Schnack, D. D.; Glasser, A. H.

    1996-11-01

    NIMROD is a new code system that is being developed for the analysis of modern fusion experiments. It is being designed from the beginning to make the maximum use of massively parallel computer architectures and computer graphics. The NIMROD physics kernel solves the three-dimensional, time-dependent two-fluid equations with neo-classical effects in toroidal geometry of arbitrary poloidal cross section. The NIMROD system also includes a pre-processor, a grid generator, and a post processor. User interaction with NIMROD is facilitated by a modern graphical user interface (GUI). The NIMROD project is using Quality Function Deployment (QFD) team management techniques to minimize re-engineering and reduce code development time. This paper gives an overview of the NIMROD project. Operation of the GUI is demonstrated, and the first results from the physics kernel are given.

  2. Computer code FIT

    Rohmann, D.; Koehler, T.

    1987-02-01

    This is a description of the computer code FIT, written in FORTRAN-77 for a PDP 11/34. FIT is an interactive program to decude position, width and intensity of lines of X-ray spectra (max. length of 4K channels). The lines (max. 30 lines per fit) may have Gauss- or Voigt-profile, as well as exponential tails. Spectrum and fit can be displayed on a Tektronix terminal. (orig.) [de

  3. Discrete Sparse Coding.

    Exarchakis, Georgios; Lücke, Jörg

    2017-11-01

    Sparse coding algorithms with continuous latent variables have been the subject of a large number of studies. However, discrete latent spaces for sparse coding have been largely ignored. In this work, we study sparse coding with latents described by discrete instead of continuous prior distributions. We consider the general case in which the latents (while being sparse) can take on any value of a finite set of possible values and in which we learn the prior probability of any value from data. This approach can be applied to any data generated by discrete causes, and it can be applied as an approximation of continuous causes. As the prior probabilities are learned, the approach then allows for estimating the prior shape without assuming specific functional forms. To efficiently train the parameters of our probabilistic generative model, we apply a truncated expectation-maximization approach (expectation truncation) that we modify to work with a general discrete prior. We evaluate the performance of the algorithm by applying it to a variety of tasks: (1) we use artificial data to verify that the algorithm can recover the generating parameters from a random initialization, (2) use image patches of natural images and discuss the role of the prior for the extraction of image components, (3) use extracellular recordings of neurons to present a novel method of analysis for spiking neurons that includes an intuitive discretization strategy, and (4) apply the algorithm on the task of encoding audio waveforms of human speech. The diverse set of numerical experiments presented in this letter suggests that discrete sparse coding algorithms can scale efficiently to work with realistic data sets and provide novel statistical quantities to describe the structure of the data.

  4. Code of Practice

    Doyle, Colin; Hone, Christopher; Nowlan, N.V.

    1984-05-01

    This Code of Practice introduces accepted safety procedures associated with the use of alpha, beta, gamma and X-radiation in secondary schools (pupils aged 12 to 18) in Ireland, and summarises good practice and procedures as they apply to radiation protection. Typical dose rates at various distances from sealed sources are quoted, and simplified equations are used to demonstrate dose and shielding calculations. The regulatory aspects of radiation protection are outlined, and references to statutory documents are given

  5. Tokamak simulation code manual

    Chung, Moon Kyoo; Oh, Byung Hoon; Hong, Bong Keun; Lee, Kwang Won

    1995-01-01

    The method to use TSC (Tokamak Simulation Code) developed by Princeton plasma physics laboratory is illustrated. In KT-2 tokamak, time dependent simulation of axisymmetric toroidal plasma and vertical stability have to be taken into account in design phase using TSC. In this report physical modelling of TSC are described and examples of application in JAERI and SERI are illustrated, which will be useful when TSC is installed KAERI computer system. (Author) 15 refs., 6 figs., 3 tabs

  6. Status of MARS Code

    N.V. Mokhov

    2003-04-09

    Status and recent developments of the MARS 14 Monte Carlo code system for simulation of hadronic and electromagnetic cascades in shielding, accelerator and detector components in the energy range from a fraction of an electronvolt up to 100 TeV are described. these include physics models both in strong and electromagnetic interaction sectors, variance reduction techniques, residual dose, geometry, tracking, histograming. MAD-MARS Beam Line Build and Graphical-User Interface.

  7. Codes of Good Governance

    Beck Jørgensen, Torben; Sørensen, Ditte-Lene

    2013-01-01

    Good governance is a broad concept used by many international organizations to spell out how states or countries should be governed. Definitions vary, but there is a clear core of common public values, such as transparency, accountability, effectiveness, and the rule of law. It is quite likely......, transparency, neutrality, impartiality, effectiveness, accountability, and legality. The normative context of public administration, as expressed in codes, seems to ignore the New Public Management and Reinventing Government reform movements....

  8. Orthopedics coding and funding.

    Baron, S; Duclos, C; Thoreux, P

    2014-02-01

    The French tarification à l'activité (T2A) prospective payment system is a financial system in which a health-care institution's resources are based on performed activity. Activity is described via the PMSI medical information system (programme de médicalisation du système d'information). The PMSI classifies hospital cases by clinical and economic categories known as diagnosis-related groups (DRG), each with an associated price tag. Coding a hospital case involves giving as realistic a description as possible so as to categorize it in the right DRG and thus ensure appropriate payment. For this, it is essential to understand what determines the pricing of inpatient stay: namely, the code for the surgical procedure, the patient's principal diagnosis (reason for admission), codes for comorbidities (everything that adds to management burden), and the management of the length of inpatient stay. The PMSI is used to analyze the institution's activity and dynamism: change on previous year, relation to target, and comparison with competing institutions based on indicators such as the mean length of stay performance indicator (MLS PI). The T2A system improves overall care efficiency. Quality of care, however, is not presently taken account of in the payment made to the institution, as there are no indicators for this; work needs to be done on this topic. Copyright © 2014. Published by Elsevier Masson SAS.

  9. Code Modernization of VPIC

    Bird, Robert; Nystrom, David; Albright, Brian

    2017-10-01

    The ability of scientific simulations to effectively deliver performant computation is increasingly being challenged by successive generations of high-performance computing architectures. Code development to support efficient computation on these modern architectures is both expensive, and highly complex; if it is approached without due care, it may also not be directly transferable between subsequent hardware generations. Previous works have discussed techniques to support the process of adapting a legacy code for modern hardware generations, but despite the breakthroughs in the areas of mini-app development, portable-performance, and cache oblivious algorithms the problem still remains largely unsolved. In this work we demonstrate how a focus on platform agnostic modern code-development can be applied to Particle-in-Cell (PIC) simulations to facilitate effective scientific delivery. This work builds directly on our previous work optimizing VPIC, in which we replaced intrinsic based vectorisation with compile generated auto-vectorization to improve the performance and portability of VPIC. In this work we present the use of a specialized SIMD queue for processing some particle operations, and also preview a GPU capable OpenMP variant of VPIC. Finally we include a lessons learnt. Work performed under the auspices of the U.S. Dept. of Energy by the Los Alamos National Security, LLC Los Alamos National Laboratory under contract DE-AC52-06NA25396 and supported by the LANL LDRD program.

  10. MELCOR computer code manuals

    Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.; Stuart, D.S.; Thompson, S.L. [Sandia National Labs., Albuquerque, NM (United States); Hodge, S.A.; Hyman, C.R.; Sanders, R.L. [Oak Ridge National Lab., TN (United States)

    1995-03-01

    MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, and combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR`s phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package.

  11. MELCOR computer code manuals

    Summers, R.M.; Cole, R.K. Jr.; Smith, R.C.; Stuart, D.S.; Thompson, S.L.; Hodge, S.A.; Hyman, C.R.; Sanders, R.L.

    1995-03-01

    MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include: thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, and combustion; fission product release and transport; and the impact of engineered safety features on thermal-hydraulic and radionuclide behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications. This publication of the MELCOR computer code manuals corresponds to MELCOR 1.8.3, released to users in August, 1994. Volume 1 contains a primer that describes MELCOR's phenomenological scope, organization (by package), and documentation. The remainder of Volume 1 contains the MELCOR Users Guides, which provide the input instructions and guidelines for each package. Volume 2 contains the MELCOR Reference Manuals, which describe the phenomenological models that have been implemented in each package

  12. Quality Improvement of MARS Code and Establishment of Code Coupling

    Chung, Bub Dong; Jeong, Jae Jun; Kim, Kyung Doo

    2010-04-01

    The improvement of MARS code quality and coupling with regulatory auditing code have been accomplished for the establishment of self-reliable technology based regulatory auditing system. The unified auditing system code was realized also by implementing the CANDU specific models and correlations. As a part of the quality assurance activities, the various QA reports were published through the code assessments. The code manuals were updated and published a new manual which describe the new models and correlations. The code coupling methods were verified though the exercise of plant application. The education-training seminar and technology transfer were performed for the code users. The developed MARS-KS is utilized as reliable auditing tool for the resolving the safety issue and other regulatory calculations. The code can be utilized as a base technology for GEN IV reactor applications

  13. Design of convolutional tornado code

    Zhou, Hui; Yang, Yao; Gao, Hongmin; Tan, Lu

    2017-09-01

    As a linear block code, the traditional tornado (tTN) code is inefficient in burst-erasure environment and its multi-level structure may lead to high encoding/decoding complexity. This paper presents a convolutional tornado (cTN) code which is able to improve the burst-erasure protection capability by applying the convolution property to the tTN code, and reduce computational complexity by abrogating the multi-level structure. The simulation results show that cTN code can provide a better packet loss protection performance with lower computation complexity than tTN code.

  14. Random linear codes in steganography

    Kamil Kaczyński

    2016-12-01

    Full Text Available Syndrome coding using linear codes is a technique that allows improvement in the steganographic algorithms parameters. The use of random linear codes gives a great flexibility in choosing the parameters of the linear code. In parallel, it offers easy generation of parity check matrix. In this paper, the modification of LSB algorithm is presented. A random linear code [8, 2] was used as a base for algorithm modification. The implementation of the proposed algorithm, along with practical evaluation of algorithms’ parameters based on the test images was made.[b]Keywords:[/b] steganography, random linear codes, RLC, LSB

  15. Containment Code Validation Matrix

    Chin, Yu-Shan; Mathew, P.M.; Glowa, Glenn; Dickson, Ray; Liang, Zhe; Leitch, Brian; Barber, Duncan; Vasic, Aleks; Bentaib, Ahmed; Journeau, Christophe; Malet, Jeanne; Studer, Etienne; Meynet, Nicolas; Piluso, Pascal; Gelain, Thomas; Michielsen, Nathalie; Peillon, Samuel; Porcheron, Emmanuel; Albiol, Thierry; Clement, Bernard; Sonnenkalb, Martin; Klein-Hessling, Walter; Arndt, Siegfried; Weber, Gunter; Yanez, Jorge; Kotchourko, Alexei; Kuznetsov, Mike; Sangiorgi, Marco; Fontanet, Joan; Herranz, Luis; Garcia De La Rua, Carmen; Santiago, Aleza Enciso; Andreani, Michele; Paladino, Domenico; Dreier, Joerg; Lee, Richard; Amri, Abdallah

    2014-01-01

    The Committee on the Safety of Nuclear Installations (CSNI) formed the CCVM (Containment Code Validation Matrix) task group in 2002. The objective of this group was to define a basic set of available experiments for code validation, covering the range of containment (ex-vessel) phenomena expected in the course of light and heavy water reactor design basis accidents and beyond design basis accidents/severe accidents. It was to consider phenomena relevant to pressurised heavy water reactor (PHWR), pressurised water reactor (PWR) and boiling water reactor (BWR) designs of Western origin as well as of Eastern European VVER types. This work would complement the two existing CSNI validation matrices for thermal hydraulic code validation (NEA/CSNI/R(1993)14) and In-vessel core degradation (NEA/CSNI/R(2001)21). The report initially provides a brief overview of the main features of a PWR, BWR, CANDU and VVER reactors. It also provides an overview of the ex-vessel corium retention (core catcher). It then provides a general overview of the accident progression for light water and heavy water reactors. The main focus is to capture most of the phenomena and safety systems employed in these reactor types and to highlight the differences. This CCVM contains a description of 127 phenomena, broken down into 6 categories: - Containment Thermal-hydraulics Phenomena; - Hydrogen Behaviour (Combustion, Mitigation and Generation) Phenomena; - Aerosol and Fission Product Behaviour Phenomena; - Iodine Chemistry Phenomena; - Core Melt Distribution and Behaviour in Containment Phenomena; - Systems Phenomena. A synopsis is provided for each phenomenon, including a description, references for further information, significance for DBA and SA/BDBA and a list of experiments that may be used for code validation. The report identified 213 experiments, broken down into the same six categories (as done for the phenomena). An experiment synopsis is provided for each test. Along with a test description

  16. Decoding of concatenated codes with interleaved outer codes

    Justesen, Jørn; Høholdt, Tom; Thommesen, Christian

    2004-01-01

    Recently Bleichenbacher et al. proposed a decoding algorithm for interleaved (N, K) Reed-Solomon codes, which allows close to N-K errors to be corrected in many cases. We discuss the application of this decoding algorithm to concatenated codes.......Recently Bleichenbacher et al. proposed a decoding algorithm for interleaved (N, K) Reed-Solomon codes, which allows close to N-K errors to be corrected in many cases. We discuss the application of this decoding algorithm to concatenated codes....

  17. TASS code topical report. V.1 TASS code technical manual

    Sim, Suk K.; Chang, W. P.; Kim, K. D.; Kim, H. C.; Yoon, H. Y.

    1997-02-01

    TASS 1.0 code has been developed at KAERI for the initial and reload non-LOCA safety analysis for the operating PWRs as well as the PWRs under construction in Korea. TASS code will replace various vendor's non-LOCA safety analysis codes currently used for the Westinghouse and ABB-CE type PWRs in Korea. This can be achieved through TASS code input modifications specific to each reactor type. The TASS code can be run interactively through the keyboard operation. A simimodular configuration used in developing the TASS code enables the user easily implement new models. TASS code has been programmed using FORTRAN77 which makes it easy to install and port for different computer environments. The TASS code can be utilized for the steady state simulation as well as the non-LOCA transient simulations such as power excursions, reactor coolant pump trips, load rejections, loss of feedwater, steam line breaks, steam generator tube ruptures, rod withdrawal and drop, and anticipated transients without scram (ATWS). The malfunctions of the control systems, components, operator actions and the transients caused by the malfunctions can be easily simulated using the TASS code. This technical report describes the TASS 1.0 code models including reactor thermal hydraulic, reactor core and control models. This TASS code models including reactor thermal hydraulic, reactor core and control models. This TASS code technical manual has been prepared as a part of the TASS code manual which includes TASS code user's manual and TASS code validation report, and will be submitted to the regulatory body as a TASS code topical report for a licensing non-LOCA safety analysis for the Westinghouse and ABB-CE type PWRs operating and under construction in Korea. (author). 42 refs., 29 tabs., 32 figs

  18. Construction of new quantum MDS codes derived from constacyclic codes

    Taneja, Divya; Gupta, Manish; Narula, Rajesh; Bhullar, Jaskaran

    Obtaining quantum maximum distance separable (MDS) codes from dual containing classical constacyclic codes using Hermitian construction have paved a path to undertake the challenges related to such constructions. Using the same technique, some new parameters of quantum MDS codes have been constructed here. One set of parameters obtained in this paper has achieved much larger distance than work done earlier. The remaining constructed parameters of quantum MDS codes have large minimum distance and were not explored yet.

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

    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.

  20. Effects of HAb18G/CD147 knockout on hepatocellular carcinoma cells in vitro using a novel zinc-finger nuclease-targeted gene knockout approach.

    Li, Hong-Wei; Yang, Xiang-Min; Tang, Juan; Wang, Shi-Jie; Chen, Zhi-Nan; Jiang, Jian-Li

    2015-03-01

    HAb18G/CD147 belongs to the immunoglobulin superfamily and predominantly functions as an inducer of matrix metalloproteinase secretion for tumor invasion and metastasis. This study was designed to investigate the effects of HAb18G/CD147 knockout on hepatocellular carcinoma cells using zinc-finger nuclease (ZFNs)-targeted gene knockout approach. The HCC cell line SMMC-7721 was used for ZFNs-targeted cleavage of the HAb18G/CD147 gene. RT-PCR and Western blot assays were used to detect HAb18G/CD147 expression. HAb18G phenotypic changes following HAb18G/CD147 knockout in SMMC-K7721 cells were assessed using tumor cell adhesion, invasion, migration and colony formation and flow cytometric assays. These data demonstrated that tumor cell adhesion, invasion, migration, and colony formation capabilities of SMMC-K7721 were significantly reduced compared to parental cells or SMMC-7721 with re-expression of HAb18G/CD147 protein transfected with HAb18G/CD147 cDNA. Moreover, knockout of HAb18G/CD147 expression also induced SMMC-K7721 cells to undergo apoptosis compared to SMMC-7721 and SMMC-R7721 (P CD147 reduced p53 levels in SMMC-R7721 cells, possibly through inhibition of the PI3K-Akt-MDM2 signaling pathway. The findings provide a novel insight into the mechanisms underlying HAb18G/CD147-induced progression of HCC cells.

  1. Genomic Knockout of Endogenous Canine P-Glycoprotein in Wild-Type, Human P-Glycoprotein and Human BCRP Transfected MDCKII Cell Lines by Zinc Finger Nucleases.

    Gartzke, Dominik; Delzer, Jürgen; Laplanche, Loic; Uchida, Yasuo; Hoshi, Yutaro; Tachikawa, Masanori; Terasaki, Tetsuya; Sydor, Jens; Fricker, Gert

    2015-06-01

    To investigate whether it is possible to specifically suppress the expression and function of endogenous canine P-glycoprotein (cPgp) in Madin-Darby canine kidney type II cells (MDCKII) transfected with hPGP and breast cancer resistance protein (hBCRP) by zinc finger nuclease (ZFN) producing sequence specific DNA double strand breaks. Wild-type, hPGP-transfected, and hBCRP-transfected MDCKII cells were transfected with ZFN targeting for cPgp. Net efflux ratios (NER) of Pgp and Bcrp substrates were determined by dividing efflux ratios (basal-to-apical / apical-to-basal) in over-expressing cell monolayers by those in wild-type ones. From ZFN-transfected cells, cell populations (ko-cells) showing knockout of cPgp were selected based on genotyping by PCR. qRT-PCR analysis showed the significant knock-downs of cPgp and interestingly also cMrp2 expressions. Specific knock-downs of protein expression for cPgp were shown by western blotting and quantitative targeted absolute proteomics. Endogenous canine Bcrp proteins were not detected. For PGP-transfected cells, NERs of 5 Pgp substrates in ko-cells were significantly greater than those in parental cells not transfected with ZFN. Similar result was obtained for BCRP-transfected cells with a dual Pgp and Bcrp substrate. Specific efflux mediated by hPGP or hBCRP can be determined with MDCKII cells where cPgp has been knocked out by ZFN.

  2. Combinatorial neural codes from a mathematical coding theory perspective.

    Curto, Carina; Itskov, Vladimir; Morrison, Katherine; Roth, Zachary; Walker, Judy L

    2013-07-01

    Shannon's seminal 1948 work gave rise to two distinct areas of research: information theory and mathematical coding theory. While information theory has had a strong influence on theoretical neuroscience, ideas from mathematical coding theory have received considerably less attention. Here we take a new look at combinatorial neural codes from a mathematical coding theory perspective, examining the error correction capabilities of familiar receptive field codes (RF codes). We find, perhaps surprisingly, that the high levels of redundancy present in these codes do not support accurate error correction, although the error-correcting performance of receptive field codes catches up to that of random comparison codes when a small tolerance to error is introduced. However, receptive field codes are good at reflecting distances between represented stimuli, while the random comparison codes are not. We suggest that a compromise in error-correcting capability may be a necessary price to pay for a neural code whose structure serves not only error correction, but must also reflect relationships between stimuli.

  3. Convolutional coding techniques for data protection

    Massey, J. L.

    1975-01-01

    Results of research on the use of convolutional codes in data communications are presented. Convolutional coding fundamentals are discussed along with modulation and coding interaction. Concatenated coding systems and data compression with convolutional codes are described.

  4. High Energy Transport Code HETC

    Gabriel, T.A.

    1985-09-01

    The physics contained in the High Energy Transport Code (HETC), in particular the collision models, are discussed. An application using HETC as part of the CALOR code system is also given. 19 refs., 5 figs., 3 tabs

  5. Code stroke in Asturias.

    Benavente, L; Villanueva, M J; Vega, P; Casado, I; Vidal, J A; Castaño, B; Amorín, M; de la Vega, V; Santos, H; Trigo, A; Gómez, M B; Larrosa, D; Temprano, T; González, M; Murias, E; Calleja, S

    2016-04-01

    Intravenous thrombolysis with alteplase is an effective treatment for ischaemic stroke when applied during the first 4.5 hours, but less than 15% of patients have access to this technique. Mechanical thrombectomy is more frequently able to recanalise proximal occlusions in large vessels, but the infrastructure it requires makes it even less available. We describe the implementation of code stroke in Asturias, as well as the process of adapting various existing resources for urgent stroke care in the region. By considering these resources, and the demographic and geographic circumstances of our region, we examine ways of reorganising the code stroke protocol that would optimise treatment times and provide the most appropriate treatment for each patient. We distributed the 8 health districts in Asturias so as to permit referral of candidates for reperfusion therapies to either of the 2 hospitals with 24-hour stroke units and on-call neurologists and providing IV fibrinolysis. Hospitals were assigned according to proximity and stroke severity; the most severe cases were immediately referred to the hospital with on-call interventional neurology care. Patient triage was provided by pre-hospital emergency services according to the NIHSS score. Modifications to code stroke in Asturias have allowed us to apply reperfusion therapies with good results, while emphasising equitable care and managing the severity-time ratio to offer the best and safest treatment for each patient as soon as possible. Copyright © 2015 Sociedad Española de Neurología. Published by Elsevier España, S.L.U. All rights reserved.

  6. Decoding Xing-Ling codes

    Nielsen, Rasmus Refslund

    2002-01-01

    This paper describes an efficient decoding method for a recent construction of good linear codes as well as an extension to the construction. Furthermore, asymptotic properties and list decoding of the codes are discussed.......This paper describes an efficient decoding method for a recent construction of good linear codes as well as an extension to the construction. Furthermore, asymptotic properties and list decoding of the codes are discussed....

  7. WWER reactor physics code applications

    Gado, J.; Kereszturi, A.; Gacs, A.; Telbisz, M.

    1994-01-01

    The coupled steady-state reactor physics and thermohydraulic code system KARATE has been developed and applied for WWER-1000 and WWER-440 operational calculations. The 3 D coupled kinetic code KIKO3D has been developed and validated for WWER-440 accident analysis applications. The coupled kinetic code SMARTA developed by VTT Helsinki has been applied for WWER-440 accident analysis. The paper gives a summary of the experience in code development and application. (authors). 10 refs., 2 tabs., 5 figs

  8. The path of code linting

    CERN. Geneva

    2017-01-01

    Join the path of code linting and discover how it can help you reach higher levels of programming enlightenment. Today we will cover how to embrace code linters to offload cognitive strain on preserving style standards in your code base as well as avoiding error-prone constructs. Additionally, I will show you the journey ahead for integrating several code linters in the programming tools your already use with very little effort.

  9. The CORSYS neutronics code system

    Caner, M.; Krumbein, A.D.; Saphier, D.; Shapira, M.

    1994-01-01

    The purpose of this work is to assemble a code package for LWR core physics including coupled neutronics, burnup and thermal hydraulics. The CORSYS system is built around the cell code WIMS (for group microscopic cross section calculations) and 3-dimension diffusion code CITATION (for burnup and fuel management). We are implementing such a system on an IBM RS-6000 workstation. The code was rested with a simplified model of the Zion Unit 2 PWR. (authors). 6 refs., 8 figs., 1 tabs

  10. Bar codes for nuclear safeguards

    Keswani, A.N.; Bieber, A.M. Jr.

    1983-01-01

    Bar codes similar to those used in supermarkets can be used to reduce the effort and cost of collecting nuclear materials accountability data. A wide range of equipment is now commercially available for printing and reading bar-coded information. Several examples of each of the major types of commercially available equipment are given, and considerations are discussed both for planning systems using bar codes and for choosing suitable bar code equipment

  11. Bar codes for nuclear safeguards

    Keswani, A.N.; Bieber, A.M.

    1983-01-01

    Bar codes similar to those used in supermarkets can be used to reduce the effort and cost of collecting nuclear materials accountability data. A wide range of equipment is now commercially available for printing and reading bar-coded information. Several examples of each of the major types of commercially-available equipment are given, and considerations are discussed both for planning systems using bar codes and for choosing suitable bar code equipment

  12. Quick response codes in Orthodontics

    Moidin Shakil

    2015-01-01

    Full Text Available Quick response (QR code codes are two-dimensional barcodes, which encodes for a large amount of information. QR codes in Orthodontics are an innovative approach in which patient details, radiographic interpretation, and treatment plan can be encoded. Implementing QR code in Orthodontics will save time, reduces paperwork, and minimizes manual efforts in storage and retrieval of patient information during subsequent stages of treatment.

  13. Multiple LDPC decoding for distributed source coding and video coding

    Forchhammer, Søren; Luong, Huynh Van; Huang, Xin

    2011-01-01

    Distributed source coding (DSC) is a coding paradigm for systems which fully or partly exploit the source statistics at the decoder to reduce the computational burden at the encoder. Distributed video coding (DVC) is one example. This paper considers the use of Low Density Parity Check Accumulate...... (LDPCA) codes in a DSC scheme with feed-back. To improve the LDPC coding performance in the context of DSC and DVC, while retaining short encoder blocks, this paper proposes multiple parallel LDPC decoding. The proposed scheme passes soft information between decoders to enhance performance. Experimental...

  14. Cinder begin creative coding

    Rijnieks, Krisjanis

    2013-01-01

    Presented in an easy to follow, tutorial-style format, this book will lead you step-by-step through the multi-faceted uses of Cinder.""Cinder: Begin Creative Coding"" is for people who already have experience in programming. It can serve as a transition from a previous background in Processing, Java in general, JavaScript, openFrameworks, C++ in general or ActionScript to the framework covered in this book, namely Cinder. If you like quick and easy to follow tutorials that will let yousee progress in less than an hour - this book is for you. If you are searching for a book that will explain al

  15. UNSPEC: revisited (semaphore code)

    Neifert, R.D.

    1981-01-01

    The UNSPEC code is used to solve the problem of unfolding an observed x-ray spectrum given the response matrix of the measuring system and the measured signal values. UNSPEC uses an iterative technique to solve the unfold problem. Due to experimental errors in the measured signal values and/or computer round-off errors, discontinuities and oscillatory behavior may occur in the iterated spectrum. These can be suppressed by smoothing the results after each iteration. Input/output options and control cards are explained; sample input and output are provided

  16. The FLIC conversion codes

    Basher, J.C.

    1965-05-01

    This report describes the FORTRAN programmes, FLIC 1 and FLIC 2. These programmes convert programmes coded in one dialect of FORTRAN to another dialect of the same language. FLIC 1 is a general pattern recognition and replacement programme whereas FLIC 2 contains extensions directed towards the conversion of FORTRAN II and S2 programmes to EGTRAN 1 - the dialect now in use on the Winfrith KDF9. FII or S2 statements are replaced where possible by their E1 equivalents; other statements which may need changing are flagged. (author)

  17. SPRAY code user's report

    Shire, P.R.

    1977-03-01

    The SPRAY computer code has been developed to model the effects of postulated sodium spray release from LMFBR piping within containment chambers. The calculation method utilizes gas convection, heat transfer and droplet combustion theory to calculate the pressure and temperature effects within the enclosure. The applicable range is 0-21 mol percent oxygen and .02-.30 inch droplets with or without humidity. Droplet motion and large sodium surface area combine to produce rapid heat release and pressure rise within the enclosed volume

  18. The FLIC conversion codes

    Basher, J C [General Reactor Physics Division, Atomic Energy Establishment, Winfrith, Dorchester, Dorset (United Kingdom)

    1965-05-15

    This report describes the FORTRAN programmes, FLIC 1 and FLIC 2. These programmes convert programmes coded in one dialect of FORTRAN to another dialect of the same language. FLIC 1 is a general pattern recognition and replacement programme whereas FLIC 2 contains extensions directed towards the conversion of FORTRAN II and S2 programmes to EGTRAN 1 - the dialect now in use on the Winfrith KDF9. FII or S2 statements are replaced where possible by their E1 equivalents; other statements which may need changing are flagged. (author)

  19. Code Generation with Templates

    Arnoldus, Jeroen; Serebrenik, A

    2012-01-01

    Templates are used to generate all kinds of text, including computer code. The last decade, the use of templates gained a lot of popularity due to the increase of dynamic web applications. Templates are a tool for programmers, and implementations of template engines are most times based on practical experience rather than based on a theoretical background. This book reveals the mathematical background of templates and shows interesting findings for improving the practical use of templates. First, a framework to determine the necessary computational power for the template metalanguage is presen

  20. Order functions and evaluation codes

    Høholdt, Tom; Pellikaan, Ruud; van Lint, Jack

    1997-01-01

    Based on the notion of an order function we construct and determine the parameters of a class of error-correcting evaluation codes. This class includes the one-point algebraic geometry codes as wella s the generalized Reed-Muller codes and the parameters are detremined without using the heavy...... machinery of algebraic geometry....

  1. Direct-semidirect (DSD) codes

    Cvelbar, F.

    1999-01-01

    Recent codes for direct-semidirect (DSD) model calculations in the form of answers to a detailed questionnaire are reviewed. These codes include those embodying the classical DSD approach covering only the transitions to the bound states (RAF, HIKARI, and those of the Bologna group), as well as the code CUPIDO++ that also treats transitions to unbound states. (author)

  2. Dual Coding, Reasoning and Fallacies.

    Hample, Dale

    1982-01-01

    Develops the theory that a fallacy is not a comparison of a rhetorical text to a set of definitions but a comparison of one person's cognition with another's. Reviews Paivio's dual coding theory, relates nonverbal coding to reasoning processes, and generates a limited fallacy theory based on dual coding theory. (PD)

  3. Strongly-MDS convolutional codes

    Gluesing-Luerssen, H; Rosenthal, J; Smarandache, R

    Maximum-distance separable (MDS) convolutional codes have the property that their free distance is maximal among all codes of the same rate and the same degree. In this paper, a class of MDS convolutional codes is introduced whose column distances reach the generalized Singleton bound at the

  4. Lattice polytopes in coding theory

    Ivan Soprunov

    2015-05-01

    Full Text Available In this paper we discuss combinatorial questions about lattice polytopes motivated by recent results on minimum distance estimation for toric codes. We also include a new inductive bound for the minimum distance of generalized toric codes. As an application, we give new formulas for the minimum distance of generalized toric codes for special lattice point configurations.

  5. Computer codes for safety analysis

    Holland, D.F.

    1986-11-01

    Computer codes for fusion safety analysis have been under development in the United States for about a decade. This paper will discuss five codes that are currently under development by the Fusion Safety Program. The purpose and capability of each code will be presented, a sample given, followed by a discussion of the present status and future development plans

  6. Geochemical computer codes. A review

    Andersson, K.

    1987-01-01

    In this report a review of available codes is performed and some code intercomparisons are also discussed. The number of codes treating natural waters (groundwater, lake water, sea water) is large. Most geochemical computer codes treat equilibrium conditions, although some codes with kinetic capability are available. A geochemical equilibrium model consists of a computer code, solving a set of equations by some numerical method and a data base, consisting of thermodynamic data required for the calculations. There are some codes which treat coupled geochemical and transport modeling. Some of these codes solve the equilibrium and transport equations simultaneously while other solve the equations separately from each other. The coupled codes require a large computer capacity and have thus as yet limited use. Three code intercomparisons have been found in literature. It may be concluded that there are many codes available for geochemical calculations but most of them require a user that us quite familiar with the code. The user also has to know the geochemical system in order to judge the reliability of the results. A high quality data base is necessary to obtain a reliable result. The best results may be expected for the major species of natural waters. For more complicated problems, including trace elements, precipitation/dissolution, adsorption, etc., the results seem to be less reliable. (With 44 refs.) (author)

  7. Separate Turbo Code and Single Turbo Code Adaptive OFDM Transmissions

    Lei Ye

    2009-01-01

    Full Text Available This paper discusses the application of adaptive modulation and adaptive rate turbo coding to orthogonal frequency-division multiplexing (OFDM, to increase throughput on the time and frequency selective channel. The adaptive turbo code scheme is based on a subband adaptive method, and compares two adaptive systems: a conventional approach where a separate turbo code is used for each subband, and a single turbo code adaptive system which uses a single turbo code over all subbands. Five modulation schemes (BPSK, QPSK, 8AMPM, 16QAM, and 64QAM are employed and turbo code rates considered are 1/2 and 1/3. The performances of both systems with high (10−2 and low (10−4 BER targets are compared. Simulation results for throughput and BER show that the single turbo code adaptive system provides a significant improvement.

  8. New quantum codes constructed from quaternary BCH codes

    Xu, Gen; Li, Ruihu; Guo, Luobin; Ma, Yuena

    2016-10-01

    In this paper, we firstly study construction of new quantum error-correcting codes (QECCs) from three classes of quaternary imprimitive BCH codes. As a result, the improved maximal designed distance of these narrow-sense imprimitive Hermitian dual-containing quaternary BCH codes are determined to be much larger than the result given according to Aly et al. (IEEE Trans Inf Theory 53:1183-1188, 2007) for each different code length. Thus, families of new QECCs are newly obtained, and the constructed QECCs have larger distance than those in the previous literature. Secondly, we apply a combinatorial construction to the imprimitive BCH codes with their corresponding primitive counterpart and construct many new linear quantum codes with good parameters, some of which have parameters exceeding the finite Gilbert-Varshamov bound for linear quantum codes.

  9. Quantum Codes From Cyclic Codes Over The Ring R 2

    Altinel, Alev; Güzeltepe, Murat

    2016-01-01

    Let R 2 denotes the ring F 2 + μF 2 + υ 2 + μυ F 2 + wF 2 + μwF 2 + υwF 2 + μυwF 2 . In this study, we construct quantum codes from cyclic codes over the ring R 2 , for arbitrary length n, with the restrictions μ 2 = 0, υ 2 = 0, w 2 = 0, μυ = υμ, μw = wμ, υw = wυ and μ (υw) = (μυ) w. Also, we give a necessary and sufficient condition for cyclic codes over R 2 that contains its dual. As a final point, we obtain the parameters of quantum error-correcting codes from cyclic codes over R 2 and we give an example of quantum error-correcting codes form cyclic codes over R 2 . (paper)

  10. Separate Turbo Code and Single Turbo Code Adaptive OFDM Transmissions

    Burr Alister

    2009-01-01

    Full Text Available Abstract This paper discusses the application of adaptive modulation and adaptive rate turbo coding to orthogonal frequency-division multiplexing (OFDM, to increase throughput on the time and frequency selective channel. The adaptive turbo code scheme is based on a subband adaptive method, and compares two adaptive systems: a conventional approach where a separate turbo code is used for each subband, and a single turbo code adaptive system which uses a single turbo code over all subbands. Five modulation schemes (BPSK, QPSK, 8AMPM, 16QAM, and 64QAM are employed and turbo code rates considered are and . The performances of both systems with high ( and low ( BER targets are compared. Simulation results for throughput and BER show that the single turbo code adaptive system provides a significant improvement.

  11. Converter of a continuous code into the Grey code

    Gonchar, A.I.; TrUbnikov, V.R.

    1979-01-01

    Described is a converter of a continuous code into the Grey code used in a 12-charged precision amplitude-to-digital converter to decrease the digital component of spectrometer differential nonlinearity to +0.7% in the 98% range of the measured band. To construct the converter of a continuous code corresponding to the input signal amplitude into the Grey code used is the regularity in recycling of units and zeroes in each discharge of the Grey code in the case of a continuous change of the number of pulses of a continuous code. The converter is constructed on the elements of 155 series, the frequency of continuous code pulse passing at the converter input is 25 MHz

  12. Supervised Transfer Sparse Coding

    Al-Shedivat, Maruan

    2014-07-27

    A combination of the sparse coding and transfer learn- ing techniques was shown to be accurate and robust in classification tasks where training and testing objects have a shared feature space but are sampled from differ- ent underlying distributions, i.e., belong to different do- mains. The key assumption in such case is that in spite of the domain disparity, samples from different domains share some common hidden factors. Previous methods often assumed that all the objects in the target domain are unlabeled, and thus the training set solely comprised objects from the source domain. However, in real world applications, the target domain often has some labeled objects, or one can always manually label a small num- ber of them. In this paper, we explore such possibil- ity and show how a small number of labeled data in the target domain can significantly leverage classifica- tion accuracy of the state-of-the-art transfer sparse cod- ing methods. We further propose a unified framework named supervised transfer sparse coding (STSC) which simultaneously optimizes sparse representation, domain transfer and classification. Experimental results on three applications demonstrate that a little manual labeling and then learning the model in a supervised fashion can significantly improve classification accuracy.

  13. Two-terminal video coding.

    Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

    2009-03-01

    Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

  14. The Art of Readable Code

    Boswell, Dustin

    2011-01-01

    As programmers, we've all seen source code that's so ugly and buggy it makes our brain ache. Over the past five years, authors Dustin Boswell and Trevor Foucher have analyzed hundreds of examples of "bad code" (much of it their own) to determine why they're bad and how they could be improved. Their conclusion? You need to write code that minimizes the time it would take someone else to understand it-even if that someone else is you. This book focuses on basic principles and practical techniques you can apply every time you write code. Using easy-to-digest code examples from different languag

  15. Sub-Transport Layer Coding

    Hansen, Jonas; Krigslund, Jeppe; Roetter, Daniel Enrique Lucani

    2014-01-01

    Packet losses in wireless networks dramatically curbs the performance of TCP. This paper introduces a simple coding shim that aids IP-layer traffic in lossy environments while being transparent to transport layer protocols. The proposed coding approach enables erasure correction while being...... oblivious to the congestion control algorithms of the utilised transport layer protocol. Although our coding shim is indifferent towards the transport layer protocol, we focus on the performance of TCP when ran on top of our proposed coding mechanism due to its widespread use. The coding shim provides gains...

  16. 75 FR 19944 - International Code Council: The Update Process for the International Codes and Standards

    2010-04-16

    ... documents from ICC's Chicago District Office: International Code Council, 4051 W Flossmoor Road, Country... Energy Conservation Code. International Existing Building Code. International Fire Code. International...

  17. Polynomial weights and code constructions

    Massey, J; Costello, D; Justesen, Jørn

    1973-01-01

    polynomial included. This fundamental property is then used as the key to a variety of code constructions including 1) a simplified derivation of the binary Reed-Muller codes and, for any primepgreater than 2, a new extensive class ofp-ary "Reed-Muller codes," 2) a new class of "repeated-root" cyclic codes...... of long constraint length binary convolutional codes derived from2^r-ary Reed-Solomon codes, and 6) a new class ofq-ary "repeated-root" constacyclic codes with an algebraic decoding algorithm.......For any nonzero elementcof a general finite fieldGF(q), it is shown that the polynomials(x - c)^i, i = 0,1,2,cdots, have the "weight-retaining" property that any linear combination of these polynomials with coefficients inGF(q)has Hamming weight at least as great as that of the minimum degree...

  18. Introduction of SCIENCE code package

    Lu Haoliang; Li Jinggang; Zhu Ya'nan; Bai Ning

    2012-01-01

    The SCIENCE code package is a set of neutronics tools based on 2D assembly calculations and 3D core calculations. It is made up of APOLLO2F, SMART and SQUALE and used to perform the nuclear design and loading pattern analysis for the reactors on operation or under construction of China Guangdong Nuclear Power Group. The purpose of paper is to briefly present the physical and numerical models used in each computation codes of the SCIENCE code pack age, including the description of the general structure of the code package, the coupling relationship of APOLLO2-F transport lattice code and SMART core nodal code, and the SQUALE code used for processing the core maps. (authors)

  19. Elements of algebraic coding systems

    Cardoso da Rocha, Jr, Valdemar

    2014-01-01

    Elements of Algebraic Coding Systems is an introductory text to algebraic coding theory. In the first chapter, you'll gain inside knowledge of coding fundamentals, which is essential for a deeper understanding of state-of-the-art coding systems. This book is a quick reference for those who are unfamiliar with this topic, as well as for use with specific applications such as cryptography and communication. Linear error-correcting block codes through elementary principles span eleven chapters of the text. Cyclic codes, some finite field algebra, Goppa codes, algebraic decoding algorithms, and applications in public-key cryptography and secret-key cryptography are discussed, including problems and solutions at the end of each chapter. Three appendices cover the Gilbert bound and some related derivations, a derivation of the Mac- Williams' identities based on the probability of undetected error, and two important tools for algebraic decoding-namely, the finite field Fourier transform and the Euclidean algorithm f...

  20. Physical Layer Network Coding

    Fukui, Hironori; Yomo, Hironori; Popovski, Petar

    2013-01-01

    of interfering nodes and usage of spatial reservation mechanisms. Specifically, we introduce a reserved area in order to protect the nodes involved in two-way relaying from the interference caused by neighboring nodes. We analytically derive the end-to-end rate achieved by PLNC considering the impact......Physical layer network coding (PLNC) has the potential to improve throughput of multi-hop networks. However, most of the works are focused on the simple, three-node model with two-way relaying, not taking into account the fact that there can be other neighboring nodes that can cause....../receive interference. The way to deal with this problem in distributed wireless networks is usage of MAC-layer mechanisms that make a spatial reservation of the shared wireless medium, similar to the well-known RTS/CTS in IEEE 802.11 wireless networks. In this paper, we investigate two-way relaying in presence...

  1. Concatenated quantum codes

    Knill, E.; Laflamme, R.

    1996-07-01

    One main problem for the future of practial quantum computing is to stabilize the computation against unwanted interactions with the environment and imperfections in the applied operations. Existing proposals for quantum memories and quantum channels require gates with asymptotically zero error to store or transmit an input quantum state for arbitrarily long times or distances with fixed error. This report gives a method which has the property that to store or transmit a qubit with maximum error {epsilon} requires gates with errors at most {ital c}{epsilon} and storage or channel elements with error at most {epsilon}, independent of how long we wish to store the state or how far we wish to transmit it. The method relies on using concatenated quantum codes and hierarchically implemented recovery operations. The overhead of the method is polynomial in the time of storage or the distance of the transmission. Rigorous and heuristic lower bounds for the constant {ital c} are given.

  2. Code des baux 2018

    Vial-Pedroletti, Béatrice; Kendérian, Fabien; Chavance, Emmanuelle; Coutan-Lapalus, Christelle

    2017-01-01

    Le code des baux 2018 vous offre un contenu extrêmement pratique, fiable et à jour au 1er août 2017. Cette 16e édition intègre notamment : le décret du 27 juillet 2017 relatif à l’évolution de certains loyers dans le cadre d’une nouvelle location ou d’un renouvellement de bail, pris en application de l’article 18 de la loi n° 89-462 du 6 juillet 1989 ; la loi du 27 janvier 2017 relative à l’égalité et à la citoyenneté ; la loi du 9 décembre 2016 relative à la transparence, à la lutte contre la corruption et à la modernisation de la vie économique ; la loi du 18 novembre 2016 de modernisation de la justice du xxie siècle

  3. GOC: General Orbit Code

    Maddox, L.B.; McNeilly, G.S.

    1979-08-01

    GOC (General Orbit Code) is a versatile program which will perform a variety of calculations relevant to isochronous cyclotron design studies. In addition to the usual calculations of interest (e.g., equilibrium and accelerated orbits, focusing frequencies, field isochronization, etc.), GOC has a number of options to calculate injections with a charge change. GOC provides both printed and plotted output, and will follow groups of particles to allow determination of finite-beam properties. An interactive PDP-10 program called GIP, which prepares input data for GOC, is available. GIP is a very easy and convenient way to prepare complicated input data for GOC. Enclosed with this report are several microfiche containing source listings of GOC and other related routines and the printed output from a multiple-option GOC run

  4. LDGM Codes for Channel Coding and Joint Source-Channel Coding of Correlated Sources

    Javier Garcia-Frias

    2005-05-01

    Full Text Available We propose a coding scheme based on the use of systematic linear codes with low-density generator matrix (LDGM codes for channel coding and joint source-channel coding of multiterminal correlated binary sources. In both cases, the structures of the LDGM encoder and decoder are shown, and a concatenated scheme aimed at reducing the error floor is proposed. Several decoding possibilities are investigated, compared, and evaluated. For different types of noisy channels and correlation models, the resulting performance is very close to the theoretical limits.

  5. Surface acoustic wave coding for orthogonal frequency coded devices

    Malocha, Donald (Inventor); Kozlovski, Nikolai (Inventor)

    2011-01-01

    Methods and systems for coding SAW OFC devices to mitigate code collisions in a wireless multi-tag system. Each device producing plural stepped frequencies as an OFC signal with a chip offset delay to increase code diversity. A method for assigning a different OCF to each device includes using a matrix based on the number of OFCs needed and the number chips per code, populating each matrix cell with OFC chip, and assigning the codes from the matrix to the devices. The asynchronous passive multi-tag system includes plural surface acoustic wave devices each producing a different OFC signal having the same number of chips and including a chip offset time delay, an algorithm for assigning OFCs to each device, and a transceiver to transmit an interrogation signal and receive OFC signals in response with minimal code collisions during transmission.

  6. Entanglement-assisted quantum MDS codes from negacyclic codes

    Lu, Liangdong; Li, Ruihu; Guo, Luobin; Ma, Yuena; Liu, Yang

    2018-03-01

    The entanglement-assisted formalism generalizes the standard stabilizer formalism, which can transform arbitrary classical linear codes into entanglement-assisted quantum error-correcting codes (EAQECCs) by using pre-shared entanglement between the sender and the receiver. In this work, we construct six classes of q-ary entanglement-assisted quantum MDS (EAQMDS) codes based on classical negacyclic MDS codes by exploiting two or more pre-shared maximally entangled states. We show that two of these six classes q-ary EAQMDS have minimum distance more larger than q+1. Most of these q-ary EAQMDS codes are new in the sense that their parameters are not covered by the codes available in the literature.

  7. An algebraic approach to graph codes

    Pinero, Fernando

    This thesis consists of six chapters. The first chapter, contains a short introduction to coding theory in which we explain the coding theory concepts we use. In the second chapter, we present the required theory for evaluation codes and also give an example of some fundamental codes in coding...... theory as evaluation codes. Chapter three consists of the introduction to graph based codes, such as Tanner codes and graph codes. In Chapter four, we compute the dimension of some graph based codes with a result combining graph based codes and subfield subcodes. Moreover, some codes in chapter four...

  8. Use of zinc-finger nucleases to knock out the WAS gene in K562 cells: a human cellular model for Wiskott-Aldrich syndrome

    Miguel G. Toscano

    2013-03-01

    Mutations in the WAS gene cause Wiskott-Aldrich syndrome (WAS, which is characterized by eczema, immunodeficiency and microthrombocytopenia. Although the role of WASP in lymphocytes and myeloid cells is well characterized, its role on megakaryocyte (MK development is poorly understood. In order to develop a human cellular model that mimics the megakaryocytic-derived defects observed in WAS patients we used K562 cells, a well-known model for study of megakaryocytic development. We knocked out the WAS gene in K562 cells using a zinc-finger nuclease (ZFN pair targeting the WAS intron 1 and a homologous donor DNA that disrupted WASP expression. Knockout of WASP on K562 cells (K562WASKO cells resulted in several megakaryocytic-related defects such as morphological alterations, lower expression of CD41ɑ, lower increments in F-actin polymerization upon stimulation, reduced CD43 expression and increased phosphatidylserine exposure. All these defects have been previously described either in WAS-knockout mice or in WAS patients, validating K562WASKO as a cell model for WAS. However, K562WASPKO cells showed also increased basal F-actin and adhesion, increased expression of CD61 and reduced expression of TGFβ and Factor VIII, defects that have never been described before for WAS-deficient cells. Interestingly, these phenotypic alterations correlate with different roles for WASP in megakaryocytic differentiation. All phenotypic alterations observed in K562WASKO cells were alleviated upon expression of WAS following lentiviral transduction, confirming the role of WASP in these phenotypes. In summary, in this work we have validated a human cellular model, K562WASPKO, that mimics the megakaryocytic-related defects found in WAS-knockout mice and have found evidences for a role of WASP as regulator of megakaryocytic differentiation. We propose the use of K562WASPKO cells as a tool to study the molecular mechanisms involved in the megakaryocytic-related defects observed in WAS

  9. Zinc finger nuclease mediated knockout of ADP-dependent glucokinase in cancer cell lines: effects on cell survival and mitochondrial oxidative metabolism.

    Susan Richter

    Full Text Available Zinc finger nucleases (ZFN are powerful tools for editing genes in cells. Here we use ZFNs to interrogate the biological function of ADPGK, which encodes an ADP-dependent glucokinase (ADPGK, in human tumour cell lines. The hypothesis we tested is that ADPGK utilises ADP to phosphorylate glucose under conditions where ATP becomes limiting, such as hypoxia. We characterised two ZFN knockout clones in each of two lines (H460 and HCT116. All four clones had frameshift mutations in all alleles at the target site in exon 1 of ADPGK, and were ADPGK-null by immunoblotting. ADPGK knockout had little or no effect on cell proliferation, but compromised the ability of H460 cells to survive siRNA silencing of hexokinase-2 under oxic conditions, with clonogenic survival falling from 21±3% for the parental line to 6.4±0.8% (p = 0.002 and 4.3±0.8% (p = 0.001 for the two knockouts. A similar increased sensitivity to clonogenic cell killing was observed under anoxia. No such changes were found when ADPGK was knocked out in HCT116 cells, for which the parental line was less sensitive than H460 to anoxia and to hexokinase-2 silencing. While knockout of ADPGK in HCT116 cells caused few changes in global gene expression, knockout of ADPGK in H460 cells caused notable up-regulation of mRNAs encoding cell adhesion proteins. Surprisingly, we could discern no consistent effect on glycolysis as measured by glucose consumption or lactate formation under anoxia, or extracellular acidification rate (Seahorse XF analyser under oxic conditions in a variety of media. However, oxygen consumption rates were generally lower in the ADPGK knockouts, in some cases markedly so. Collectively, the results demonstrate that ADPGK can contribute to tumour cell survival under conditions of high glycolytic dependence, but the phenotype resulting from knockout of ADPGK is cell line dependent and appears to be unrelated to priming of glycolysis in these lines.

  10. NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1

    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.

  11. Zinc finger nuclease mediated knockout of ADP-dependent glucokinase in cancer cell lines: effects on cell survival and mitochondrial oxidative metabolism.

    Richter, Susan; Morrison, Shona; Connor, Tim; Su, Jiechuang; Print, Cristin G; Ronimus, Ron S; McGee, Sean L; Wilson, William R

    2013-01-01

    Zinc finger nucleases (ZFN) are powerful tools for editing genes in cells. Here we use ZFNs to interrogate the biological function of ADPGK, which encodes an ADP-dependent glucokinase (ADPGK), in human tumour cell lines. The hypothesis we tested is that ADPGK utilises ADP to phosphorylate glucose under conditions where ATP becomes limiting, such as hypoxia. We characterised two ZFN knockout clones in each of two lines (H460 and HCT116). All four clones had frameshift mutations in all alleles at the target site in exon 1 of ADPGK, and were ADPGK-null by immunoblotting. ADPGK knockout had little or no effect on cell proliferation, but compromised the ability of H460 cells to survive siRNA silencing of hexokinase-2 under oxic conditions, with clonogenic survival falling from 21±3% for the parental line to 6.4±0.8% (p = 0.002) and 4.3±0.8% (p = 0.001) for the two knockouts. A similar increased sensitivity to clonogenic cell killing was observed under anoxia. No such changes were found when ADPGK was knocked out in HCT116 cells, for which the parental line was less sensitive than H460 to anoxia and to hexokinase-2 silencing. While knockout of ADPGK in HCT116 cells caused few changes in global gene expression, knockout of ADPGK in H460 cells caused notable up-regulation of mRNAs encoding cell adhesion proteins. Surprisingly, we could discern no consistent effect on glycolysis as measured by glucose consumption or lactate formation under anoxia, or extracellular acidification rate (Seahorse XF analyser) under oxic conditions in a variety of media. However, oxygen consumption rates were generally lower in the ADPGK knockouts, in some cases markedly so. Collectively, the results demonstrate that ADPGK can contribute to tumour cell survival under conditions of high glycolytic dependence, but the phenotype resulting from knockout of ADPGK is cell line dependent and appears to be unrelated to priming of glycolysis in these lines.

  12. 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.

    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

  13. Diagonal Eigenvalue Unity (DEU) code for spectral amplitude coding-optical code division multiple access

    Ahmed, Hassan Yousif; Nisar, K. S.

    2013-08-01

    Code with ideal in-phase cross correlation (CC) and practical code length to support high number of users are required in spectral amplitude coding-optical code division multiple access (SAC-OCDMA) systems. SAC systems are getting more attractive in the field of OCDMA because of its ability to eliminate the influence of multiple access interference (MAI) and also suppress the effect of phase induced intensity noise (PIIN). In this paper, we have proposed new Diagonal Eigenvalue Unity (DEU) code families with ideal in-phase CC based on Jordan block matrix with simple algebraic ways. Four sets of DEU code families based on the code weight W and number of users N for the combination (even, even), (even, odd), (odd, odd) and (odd, even) are constructed. This combination gives DEU code more flexibility in selection of code weight and number of users. These features made this code a compelling candidate for future optical communication systems. Numerical results show that the proposed DEU system outperforms reported codes. In addition, simulation results taken from a commercial optical systems simulator, Virtual Photonic Instrument (VPI™) shown that, using point to multipoint transmission in passive optical network (PON), DEU has better performance and could support long span with high data rate.

  14. Self-complementary circular codes in coding theory.

    Fimmel, Elena; Michel, Christian J; Starman, Martin; Strüngmann, Lutz

    2018-04-01

    Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016). A directed graph [Formula: see text] associated with any code X mirrors the properties of the code. In the present paper, we demonstrate a necessary condition for the self-complementarity of an arbitrary code X in terms of the graph theory. The same condition has been proven to be sufficient for codes which are circular and of large size [Formula: see text] trinucleotides, in particular for maximal circular codes ([Formula: see text] trinucleotides). For codes of small-size [Formula: see text] trinucleotides, some very rare counterexamples have been constructed. Furthermore, the length and the structure of the longest paths in the graphs associated with the self-complementary circular codes are investigated. It has been proven that the longest paths in such graphs determine the reading frame for the self-complementary circular codes. By applying this result, the reading frame in any arbitrary sequence of trinucleotides is retrieved after at most 15 nucleotides, i.e., 5 consecutive trinucleotides, from the circular code X identified in genes. Thus, an X motif of a length of at least 15 nucleotides in an arbitrary sequence of trinucleotides (not necessarily all of them belonging to X) uniquely defines the reading (correct) frame, an important criterion for analyzing the X motifs in genes in the future.

  15. Copper complexes as chemical nucleases

    Unknown

    anticancer drug famotidine has been shown as a better catalyst than CuCl2 for sulfite ... Effect of addition of bis-chelate copper(II) complexes (dpq, •; phen, ; ..... Reproduction, Development & Genetics for their help in the DNA cleavage studies ...

  16. Error correcting coding for OTN

    Justesen, Jørn; Larsen, Knud J.; Pedersen, Lars A.

    2010-01-01

    Forward error correction codes for 100 Gb/s optical transmission are currently receiving much attention from transport network operators and technology providers. We discuss the performance of hard decision decoding using product type codes that cover a single OTN frame or a small number...... of such frames. In particular we argue that a three-error correcting BCH is the best choice for the component code in such systems....

  17. Numerical Tokamak Project code comparison

    Waltz, R.E.; Cohen, B.I.; Beer, M.A.

    1994-01-01

    The Numerical Tokamak Project undertook a code comparison using a set of TFTR tokamak parameters. Local radial annulus codes of both gyrokinetic and gyrofluid types were compared for both slab and toroidal case limits assuming ion temperature gradient mode turbulence in a pure plasma with adiabatic electrons. The heat diffusivities were found to be in good internal agreement within ± 50% of the group average over five codes

  18. Ethical codes in business practice

    Kobrlová, Marie

    2013-01-01

    The diploma thesis discusses the issues of ethics and codes of ethics in business. The theoretical part defines basic concepts of ethics, presents its historical development and the methods and tools of business ethics. It also focuses on ethical codes and the area of law and ethics. The practical part consists of a quantitative survey, which provides views of selected business entities of business ethics and the use of codes of ethics in practice.

  19. QR code for medical information uses.

    Fontelo, Paul; Liu, Fang; Ducut, Erick G

    2008-11-06

    We developed QR code online tools, simulated and tested QR code applications for medical information uses including scanning QR code labels, URLs and authentication. Our results show possible applications for QR code in medicine.

  20. High Order Modulation Protograph Codes

    Nguyen, Thuy V. (Inventor); Nosratinia, Aria (Inventor); Divsalar, Dariush (Inventor)

    2014-01-01

    Digital communication coding methods for designing protograph-based bit-interleaved code modulation that is general and applies to any modulation. The general coding framework can support not only multiple rates but also adaptive modulation. The method is a two stage lifting approach. In the first stage, an original protograph is lifted to a slightly larger intermediate protograph. The intermediate protograph is then lifted via a circulant matrix to the expected codeword length to form a protograph-based low-density parity-check code.

  1. Semi-supervised sparse coding

    Wang, Jim Jing-Yan; Gao, Xin

    2014-01-01

    Sparse coding approximates the data sample as a sparse linear combination of some basic codewords and uses the sparse codes as new presentations. In this paper, we investigate learning discriminative sparse codes by sparse coding in a semi-supervised manner, where only a few training samples are labeled. By using the manifold structure spanned by the data set of both labeled and unlabeled samples and the constraints provided by the labels of the labeled samples, we learn the variable class labels for all the samples. Furthermore, to improve the discriminative ability of the learned sparse codes, we assume that the class labels could be predicted from the sparse codes directly using a linear classifier. By solving the codebook, sparse codes, class labels and classifier parameters simultaneously in a unified objective function, we develop a semi-supervised sparse coding algorithm. Experiments on two real-world pattern recognition problems demonstrate the advantage of the proposed methods over supervised sparse coding methods on partially labeled data sets.

  2. Programming Entity Framework Code First

    Lerman, Julia

    2011-01-01

    Take advantage of the Code First data modeling approach in ADO.NET Entity Framework, and learn how to build and configure a model based on existing classes in your business domain. With this concise book, you'll work hands-on with examples to learn how Code First can create an in-memory model and database by default, and how you can exert more control over the model through further configuration. Code First provides an alternative to the database first and model first approaches to the Entity Data Model. Learn the benefits of defining your model with code, whether you're working with an exis

  3. User manual of UNF code

    Zhang Jingshang

    2001-01-01

    The UNF code (2001 version) written in FORTRAN-90 is developed for calculating fast neutron reaction data of structure materials with incident energies from about 1 Kev up to 20 Mev. The code consists of the spherical optical model, the unified Hauser-Feshbach and exciton model. The man nal of the UNF code is available for users. The format of the input parameter files and the output files, as well as the functions of flag used in UNF code, are introduced in detail, and the examples of the format of input parameters files are given

  4. Semi-supervised sparse coding

    Wang, Jim Jing-Yan

    2014-07-06

    Sparse coding approximates the data sample as a sparse linear combination of some basic codewords and uses the sparse codes as new presentations. In this paper, we investigate learning discriminative sparse codes by sparse coding in a semi-supervised manner, where only a few training samples are labeled. By using the manifold structure spanned by the data set of both labeled and unlabeled samples and the constraints provided by the labels of the labeled samples, we learn the variable class labels for all the samples. Furthermore, to improve the discriminative ability of the learned sparse codes, we assume that the class labels could be predicted from the sparse codes directly using a linear classifier. By solving the codebook, sparse codes, class labels and classifier parameters simultaneously in a unified objective function, we develop a semi-supervised sparse coding algorithm. Experiments on two real-world pattern recognition problems demonstrate the advantage of the proposed methods over supervised sparse coding methods on partially labeled data sets.

  5. Consensus Convolutional Sparse Coding

    Choudhury, Biswarup

    2017-12-01

    Convolutional sparse coding (CSC) is a promising direction for unsupervised learning in computer vision. In contrast to recent supervised methods, CSC allows for convolutional image representations to be learned that are equally useful for high-level vision tasks and low-level image reconstruction and can be applied to a wide range of tasks without problem-specific retraining. Due to their extreme memory requirements, however, existing CSC solvers have so far been limited to low-dimensional problems and datasets using a handful of low-resolution example images at a time. In this paper, we propose a new approach to solving CSC as a consensus optimization problem, which lifts these limitations. By learning CSC features from large-scale image datasets for the first time, we achieve significant quality improvements in a number of imaging tasks. Moreover, the proposed method enables new applications in high-dimensional feature learning that has been intractable using existing CSC methods. This is demonstrated for a variety of reconstruction problems across diverse problem domains, including 3D multispectral demosaicing and 4D light field view synthesis.

  6. Coded aperture tomography revisited

    Bizais, Y.; Rowe, R.W.; Zubal, I.G.; Bennett, G.W.; Brill, A.B.

    1983-01-01

    Coded aperture (CA) Tomography never achieved wide spread use in Nuclear Medicine, except for the degenerate case of Seven Pinhole tomagraphy (7PHT). However it enjoys several attractive features (high sensitivity and tomographic ability with a statis detector). On the other hand, resolution is usually poor especially along the depth axis and the reconstructed volume is rather limited. Arguments are presented justifying the position that CA tomography can be useful for imaging time-varying 3D structures, if its major drawbacks (poor longitudinal resolution and difficulty in quantification) are overcome. Poor results obtained with 7PHT can be explained by both a very limited angular range sampled and a crude modelling of the image formation process. Therefore improvements can be expected by the use of a dual-detector system, along with a better understanding of its sampling properties and the use of more powerful reconstruction algorithms. Non overlapping multipinhole plates, because they do not involve a decoding procedure, should be considered first for practical applications. Use of real CA should be considered for cases in which non overlapping multipinhole plates do not lead to satisfactory solutions. We have been and currently are carrying out theoretical and experimental works, in order to define the factors which limit CA imaging and to propose satisfactory solutions for Dynamic Emission Tomography

  7. Mobile code security

    Ramalingam, Srikumar

    2001-11-01

    A highly secure mobile agent system is very important for a mobile computing environment. The security issues in mobile agent system comprise protecting mobile hosts from malicious agents, protecting agents from other malicious agents, protecting hosts from other malicious hosts and protecting agents from malicious hosts. Using traditional security mechanisms the first three security problems can be solved. Apart from using trusted hardware, very few approaches exist to protect mobile code from malicious hosts. Some of the approaches to solve this problem are the use of trusted computing, computing with encrypted function, steganography, cryptographic traces, Seal Calculas, etc. This paper focuses on the simulation of some of these existing techniques in the designed mobile language. Some new approaches to solve malicious network problem and agent tampering problem are developed using public key encryption system and steganographic concepts. The approaches are based on encrypting and hiding the partial solutions of the mobile agents. The partial results are stored and the address of the storage is destroyed as the agent moves from one host to another host. This allows only the originator to make use of the partial results. Through these approaches some of the existing problems are solved.

  8. Consensus Convolutional Sparse Coding

    Choudhury, Biswarup

    2017-04-11

    Convolutional sparse coding (CSC) is a promising direction for unsupervised learning in computer vision. In contrast to recent supervised methods, CSC allows for convolutional image representations to be learned that are equally useful for high-level vision tasks and low-level image reconstruction and can be applied to a wide range of tasks without problem-specific retraining. Due to their extreme memory requirements, however, existing CSC solvers have so far been limited to low-dimensional problems and datasets using a handful of low-resolution example images at a time. In this paper, we propose a new approach to solving CSC as a consensus optimization problem, which lifts these limitations. By learning CSC features from large-scale image datasets for the first time, we achieve significant quality improvements in a number of imaging tasks. Moreover, the proposed method enables new applications in high dimensional feature learning that has been intractable using existing CSC methods. This is demonstrated for a variety of reconstruction problems across diverse problem domains, including 3D multispectral demosaickingand 4D light field view synthesis.

  9. Coding, cryptography and combinatorics

    Niederreiter, Harald; Xing, Chaoping

    2004-01-01

    It has long been recognized that there are fascinating connections between cod­ ing theory, cryptology, and combinatorics. Therefore it seemed desirable to us to organize a conference that brings together experts from these three areas for a fruitful exchange of ideas. We decided on a venue in the Huang Shan (Yellow Mountain) region, one of the most scenic areas of China, so as to provide the additional inducement of an attractive location. The conference was planned for June 2003 with the official title Workshop on Coding, Cryptography and Combi­ natorics (CCC 2003). Those who are familiar with events in East Asia in the first half of 2003 can guess what happened in the end, namely the conference had to be cancelled in the interest of the health of the participants. The SARS epidemic posed too serious a threat. At the time of the cancellation, the organization of the conference was at an advanced stage: all invited speakers had been selected and all abstracts of contributed talks had been screened by the p...

  10. Consensus Convolutional Sparse Coding

    Choudhury, Biswarup; Swanson, Robin; Heide, Felix; Wetzstein, Gordon; Heidrich, Wolfgang

    2017-01-01

    Convolutional sparse coding (CSC) is a promising direction for unsupervised learning in computer vision. In contrast to recent supervised methods, CSC allows for convolutional image representations to be learned that are equally useful for high-level vision tasks and low-level image reconstruction and can be applied to a wide range of tasks without problem-specific retraining. Due to their extreme memory requirements, however, existing CSC solvers have so far been limited to low-dimensional problems and datasets using a handful of low-resolution example images at a time. In this paper, we propose a new approach to solving CSC as a consensus optimization problem, which lifts these limitations. By learning CSC features from large-scale image datasets for the first time, we achieve significant quality improvements in a number of imaging tasks. Moreover, the proposed method enables new applications in high-dimensional feature learning that has been intractable using existing CSC methods. This is demonstrated for a variety of reconstruction problems across diverse problem domains, including 3D multispectral demosaicing and 4D light field view synthesis.

  11. Computer code abstract: NESTLE

    Turinsky, P.J.; Al-Chalabi, R.M.K.; Engrand, P.; Sarsour, H.N.; Faure, F.X.; Guo, W.

    1995-01-01

    NESTLE is a few-group neutron diffusion equation solver utilizing the nodal expansion method (NEM) for eigenvalue, adjoint, and fixed-source steady-state and transient problems. The NESTLE code solve the eigenvalue (criticality), eigenvalue adjoint, external fixed-source steady-state, and external fixed-source or eigenvalue initiated transient problems. The eigenvalue problem allows criticality searches to be completed, and the external fixed-source steady-state problem can search to achieve a specified power level. Transient problems model delayed neutrons via precursor groups. Several core properties can be input as time dependent. Two- or four-energy groups can be utilized, with all energy groups being thermal groups (i.e., upscatter exits) is desired. Core geometries modeled include Cartesian and hexagonal. Three-, two-, and one-dimensional models can be utilized with various symmetries. The thermal conditions predicted by the thermal-hydraulic model of the core are used to correct cross sections for temperature and density effects. Cross sections for temperature and density effects. Cross sections are parameterized by color, control rod state (i.e., in or out), and burnup, allowing fuel depletion to be modeled. Either a macroscopic or microscopic model may be employed

  12. Joint source-channel coding using variable length codes

    Balakirsky, V.B.

    2001-01-01

    We address the problem of joint source-channel coding when variable-length codes are used for information transmission over a discrete memoryless channel. Data transmitted over the channel are interpreted as pairs (m k ,t k ), where m k is a message generated by the source and t k is a time instant

  13. Interrelations of codes in human semiotic systems.

    Somov, Georgij

    2016-01-01

    Codes can be viewed as mechanisms that enable relations of signs and their components, i.e., semiosis is actualized. The combinations of these relations produce new relations as new codes are building over other codes. Structures appear in the mechanisms of codes. Hence, codes can be described as transformations of structures from some material systems into others. Structures belong to different carriers, but exist in codes in their "pure" form. Building of codes over other codes fosters t...

  14. Further Generalisations of Twisted Gabidulin Codes

    Puchinger, Sven; Rosenkilde, Johan Sebastian Heesemann; Sheekey, John

    2017-01-01

    We present a new family of maximum rank distance (MRD) codes. The new class contains codes that are neither equivalent to a generalised Gabidulin nor to a twisted Gabidulin code, the only two known general constructions of linear MRD codes.......We present a new family of maximum rank distance (MRD) codes. The new class contains codes that are neither equivalent to a generalised Gabidulin nor to a twisted Gabidulin code, the only two known general constructions of linear MRD codes....

  15. MARS Code in Linux Environment

    Hwang, Moon Kyu; Bae, Sung Won; Jung, Jae Joon; Chung, Bub Dong [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    2005-07-01

    The two-phase system analysis code MARS has been incorporated into Linux system. The MARS code was originally developed based on the RELAP5/MOD3.2 and COBRA-TF. The 1-D module which evolved from RELAP5 alone could be applied for the whole NSSS system analysis. The 3-D module developed based on the COBRA-TF, however, could be applied for the analysis of the reactor core region where 3-D phenomena would be better treated. The MARS code also has several other code units that could be incorporated for more detailed analysis. The separate code units include containment analysis modules and 3-D kinetics module. These code modules could be optionally invoked to be coupled with the main MARS code. The containment code modules (CONTAIN and CONTEMPT), for example, could be utilized for the analysis of the plant containment phenomena in a coupled manner with the nuclear reactor system. The mass and energy interaction during the hypothetical coolant leakage accident could, thereby, be analyzed in a more realistic manner. In a similar way, 3-D kinetics could be incorporated for simulating the three dimensional reactor kinetic behavior, instead of using the built-in point kinetics model. The MARS code system, developed initially for the MS Windows environment, however, would not be adequate enough for the PC cluster system where multiple CPUs are available. When parallelism is to be eventually incorporated into the MARS code, MS Windows environment is not considered as an optimum platform. Linux environment, on the other hand, is generally being adopted as a preferred platform for the multiple codes executions as well as for the parallel application. In this study, MARS code has been modified for the adaptation of Linux platform. For the initial code modification, the Windows system specific features have been removed from the code. Since the coupling code module CONTAIN is originally in a form of dynamic load library (DLL) in the Windows system, a similar adaptation method

  16. Allele coding in genomic evaluation

    Christensen Ole F

    2011-06-01

    Full Text Available Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being

  17. MARS Code in Linux Environment

    Hwang, Moon Kyu; Bae, Sung Won; Jung, Jae Joon; Chung, Bub Dong

    2005-01-01

    The two-phase system analysis code MARS has been incorporated into Linux system. The MARS code was originally developed based on the RELAP5/MOD3.2 and COBRA-TF. The 1-D module which evolved from RELAP5 alone could be applied for the whole NSSS system analysis. The 3-D module developed based on the COBRA-TF, however, could be applied for the analysis of the reactor core region where 3-D phenomena would be better treated. The MARS code also has several other code units that could be incorporated for more detailed analysis. The separate code units include containment analysis modules and 3-D kinetics module. These code modules could be optionally invoked to be coupled with the main MARS code. The containment code modules (CONTAIN and CONTEMPT), for example, could be utilized for the analysis of the plant containment phenomena in a coupled manner with the nuclear reactor system. The mass and energy interaction during the hypothetical coolant leakage accident could, thereby, be analyzed in a more realistic manner. In a similar way, 3-D kinetics could be incorporated for simulating the three dimensional reactor kinetic behavior, instead of using the built-in point kinetics model. The MARS code system, developed initially for the MS Windows environment, however, would not be adequate enough for the PC cluster system where multiple CPUs are available. When parallelism is to be eventually incorporated into the MARS code, MS Windows environment is not considered as an optimum platform. Linux environment, on the other hand, is generally being adopted as a preferred platform for the multiple codes executions as well as for the parallel application. In this study, MARS code has been modified for the adaptation of Linux platform. For the initial code modification, the Windows system specific features have been removed from the code. Since the coupling code module CONTAIN is originally in a form of dynamic load library (DLL) in the Windows system, a similar adaptation method

  18. Coding in pigeons: Multiple-coding versus single-code/default strategies.

    Pinto, Carlos; Machado, Armando

    2015-05-01

    To investigate the coding strategies that pigeons may use in a temporal discrimination tasks, pigeons were trained on a matching-to-sample procedure with three sample durations (2s, 6s and 18s) and two comparisons (red and green hues). One comparison was correct following 2-s samples and the other was correct following both 6-s and 18-s samples. Tests were then run to contrast the predictions of two hypotheses concerning the pigeons' coding strategies, the multiple-coding and the single-code/default. According to the multiple-coding hypothesis, three response rules are acquired, one for each sample. According to the single-code/default hypothesis, only two response rules are acquired, one for the 2-s sample and a "default" rule for any other duration. In retention interval tests, pigeons preferred the "default" key, a result predicted by the single-code/default hypothesis. In no-sample tests, pigeons preferred the key associated with the 2-s sample, a result predicted by multiple-coding. Finally, in generalization tests, when the sample duration equaled 3.5s, the geometric mean of 2s and 6s, pigeons preferred the key associated with the 6-s and 18-s samples, a result predicted by the single-code/default hypothesis. The pattern of results suggests the need for models that take into account multiple sources of stimulus control. © Society for the Experimental Analysis of Behavior.

  19. Error-correction coding for digital communications

    Clark, G. C., Jr.; Cain, J. B.

    This book is written for the design engineer who must build the coding and decoding equipment and for the communication system engineer who must incorporate this equipment into a system. It is also suitable as a senior-level or first-year graduate text for an introductory one-semester course in coding theory. Fundamental concepts of coding are discussed along with group codes, taking into account basic principles, practical constraints, performance computations, coding bounds, generalized parity check codes, polynomial codes, and important classes of group codes. Other topics explored are related to simple nonalgebraic decoding techniques for group codes, soft decision decoding of block codes, algebraic techniques for multiple error correction, the convolutional code structure and Viterbi decoding, syndrome decoding techniques, and sequential decoding techniques. System applications are also considered, giving attention to concatenated codes, coding for the white Gaussian noise channel, interleaver structures for coded systems, and coding for burst noise channels.

  20. Distributed space-time coding

    Jing, Yindi

    2014-01-01

    Distributed Space-Time Coding (DSTC) is a cooperative relaying scheme that enables high reliability in wireless networks. This brief presents the basic concept of DSTC, its achievable performance, generalizations, code design, and differential use. Recent results on training design and channel estimation for DSTC and the performance of training-based DSTC are also discussed.

  1. NETWORK CODING BY BEAM FORMING

    2013-01-01

    Network coding by beam forming in networks, for example, in single frequency networks, can provide aid in increasing spectral efficiency. When network coding by beam forming and user cooperation are combined, spectral efficiency gains may be achieved. According to certain embodiments, a method...... cooperating with the plurality of user equipment to decode the received data....

  2. Building codes : obstacle or opportunity?

    Alberto Goetzl; David B. McKeever

    1999-01-01

    Building codes are critically important in the use of wood products for construction. The codes contain regulations that are prescriptive or performance related for various kinds of buildings and construction types. A prescriptive standard might dictate that a particular type of material be used in a given application. A performance standard requires that a particular...

  3. Accelerator Physics Code Web Repository

    Zimmermann, Frank; Bellodi, G; Benedetto, E; Dorda, U; Giovannozzi, Massimo; Papaphilippou, Y; Pieloni, T; Ruggiero, F; Rumolo, G; Schmidt, F; Todesco, E; Zotter, Bruno W; Payet, J; Bartolini, R; Farvacque, L; Sen, T; Chin, Y H; Ohmi, K; Oide, K; Furman, M; Qiang, J; Sabbi, G L; Seidl, P A; Vay, J L; Friedman, A; Grote, D P; Cousineau, S M; Danilov, V; Holmes, J A; Shishlo, A; Kim, E S; Cai, Y; Pivi, M; Kaltchev, D I; Abell, D T; Katsouleas, Thomas C; Boine-Frankenheim, O; Franchetti, G; Hofmann, I; Machida, S; Wei, J

    2006-01-01

    In the framework of the CARE HHH European Network, we have developed a web-based dynamic acceleratorphysics code repository. We describe the design, structure and contents of this repository, illustrate its usage, and discuss our future plans, with emphasis on code benchmarking.

  4. LFSC - Linac Feedback Simulation Code

    Ivanov, Valentin; /Fermilab

    2008-05-01

    The computer program LFSC (Code>) is a numerical tool for simulation beam based feedback in high performance linacs. The code LFSC is based on the earlier version developed by a collective of authors at SLAC (L.Hendrickson, R. McEwen, T. Himel, H. Shoaee, S. Shah, P. Emma, P. Schultz) during 1990-2005. That code was successively used in simulation of SLC, TESLA, CLIC and NLC projects. It can simulate as pulse-to-pulse feedback on timescale corresponding to 5-100 Hz, as slower feedbacks, operating in the 0.1-1 Hz range in the Main Linac and Beam Delivery System. The code LFSC is running under Matlab for MS Windows operating system. It contains about 30,000 lines of source code in more than 260 subroutines. The code uses the LIAR ('Linear Accelerator Research code') for particle tracking under ground motion and technical noise perturbations. It uses the Guinea Pig code to simulate the luminosity performance. A set of input files includes the lattice description (XSIF format), and plane text files with numerical parameters, wake fields, ground motion data etc. The Matlab environment provides a flexible system for graphical output.

  5. Interleaver Design for Turbo Coding

    Andersen, Jakob Dahl; Zyablov, Viktor

    1997-01-01

    By a combination of construction and random search based on a careful analysis of the low weight words and the distance properties of the component codes, it is possible to find interleavers for turbo coding with a high minimum distance. We have designed a block interleaver with permutations...

  6. Code breaking in the pacific

    Donovan, Peter

    2014-01-01

    Covers the historical context and the evolution of the technically complex Allied Signals Intelligence (Sigint) activity against Japan from 1920 to 1945 Describes, explains and analyzes the code breaking techniques developed during the war in the Pacific Exposes the blunders (in code construction and use) made by the Japanese Navy that led to significant US Naval victories

  7. Development status of TUF code

    Liu, W.S.; Tahir, A.; Zaltsgendler

    1996-01-01

    An overview of the important development of the TUF code in 1995 is presented. The development in the following areas is presented: control of round-off error propagation, gas resolution and release models, and condensation induced water hammer. This development is mainly generated from station requests for operational support and code improvement. (author)

  8. Accident consequence assessment code development

    Homma, T.; Togawa, O.

    1991-01-01

    This paper describes the new computer code system, OSCAAR developed for off-site consequence assessment of a potential nuclear accident. OSCAAR consists of several modules which have modeling capabilities in atmospheric transport, foodchain transport, dosimetry, emergency response and radiological health effects. The major modules of the consequence assessment code are described, highlighting the validation and verification of the models. (author)

  9. The nuclear codes and guidelines

    Sonter, M.

    1984-01-01

    This paper considers problems faced by the mining industry when implementing the nuclear codes of practice. Errors of interpretation are likely. A major criticism is that the guidelines to the codes must be seen as recommendations only. They are not regulations. Specific clauses in the guidelines are criticised

  10. Survey of coded aperture imaging

    Barrett, H.H.

    1975-01-01

    The basic principle and limitations of coded aperture imaging for x-ray and gamma cameras are discussed. Current trends include (1) use of time varying apertures, (2) use of ''dilute'' apertures with transmission much less than 50%, and (3) attempts to derive transverse tomographic sections, unblurred by other planes, from coded images

  11. ACCELERATION PHYSICS CODE WEB REPOSITORY.

    WEI, J.

    2006-06-26

    In the framework of the CARE HHH European Network, we have developed a web-based dynamic accelerator-physics code repository. We describe the design, structure and contents of this repository, illustrate its usage, and discuss our future plans, with emphasis on code benchmarking.

  12. Grassmann codes and Schubert unions

    Hansen, Johan Peder; Johnsen, Trygve; Ranestad, Kristian

    2009-01-01

    We study subsets of Grassmann varieties over a field , such that these subsets are unions of Schubert cycles, with respect to a fixed flag. We study such sets in detail, and give applications to coding theory, in particular for Grassmann codes. For much is known about such Schubert unions with a ...

  13. On Network Coded Filesystem Shim

    Sørensen, Chres Wiant; Roetter, Daniel Enrique Lucani; Médard, Muriel

    2017-01-01

    Although network coding has shown the potential to revolutionize networking and storage, its deployment has faced a number of challenges. Usual proposals involve two approaches. First, deploying a new protocol (e.g., Multipath Coded TCP), or retrofitting another one (e.g., TCP/NC) to deliver bene...

  14. Running codes through the web

    Clark, R.E.H.

    2001-01-01

    Dr. Clark presented a report and demonstration of running atomic physics codes through the WWW. The atomic physics data is generated from Los Alamos National Laboratory (LANL) codes that calculate electron impact excitation, ionization, photoionization, and autoionization, and inversed processes through detailed balance. Samples of Web interfaces, input and output are given in the report

  15. Dynamic benchmarking of simulation codes

    Henry, R.E.; Paik, C.Y.; Hauser, G.M.

    1996-01-01

    Computer simulation of nuclear power plant response can be a full-scope control room simulator, an engineering simulator to represent the general behavior of the plant under normal and abnormal conditions, or the modeling of the plant response to conditions that would eventually lead to core damage. In any of these, the underlying foundation for their use in analysing situations, training of vendor/utility personnel, etc. is how well they represent what has been known from industrial experience, large integral experiments and separate effects tests. Typically, simulation codes are benchmarked with some of these; the level of agreement necessary being dependent upon the ultimate use of the simulation tool. However, these analytical models are computer codes, and as a result, the capabilities are continually enhanced, errors are corrected, new situations are imposed on the code that are outside of the original design basis, etc. Consequently, there is a continual need to assure that the benchmarks with important transients are preserved as the computer code evolves. Retention of this benchmarking capability is essential to develop trust in the computer code. Given the evolving world of computer codes, how is this retention of benchmarking capabilities accomplished? For the MAAP4 codes this capability is accomplished through a 'dynamic benchmarking' feature embedded in the source code. In particular, a set of dynamic benchmarks are included in the source code and these are exercised every time the archive codes are upgraded and distributed to the MAAP users. Three different types of dynamic benchmarks are used: plant transients; large integral experiments; and separate effects tests. Each of these is performed in a different manner. The first is accomplished by developing a parameter file for the plant modeled and an input deck to describe the sequence; i.e. the entire MAAP4 code is exercised. The pertinent plant data is included in the source code and the computer

  16. Distributed source coding of video

    Forchhammer, Søren; Van Luong, Huynh

    2015-01-01

    A foundation for distributed source coding was established in the classic papers of Slepian-Wolf (SW) [1] and Wyner-Ziv (WZ) [2]. This has provided a starting point for work on Distributed Video Coding (DVC), which exploits the source statistics at the decoder side offering shifting processing...... steps, conventionally performed at the video encoder side, to the decoder side. Emerging applications such as wireless visual sensor networks and wireless video surveillance all require lightweight video encoding with high coding efficiency and error-resilience. The video data of DVC schemes differ from...... the assumptions of SW and WZ distributed coding, e.g. by being correlated in time and nonstationary. Improving the efficiency of DVC coding is challenging. This paper presents some selected techniques to address the DVC challenges. Focus is put on pin-pointing how the decoder steps are modified to provide...

  17. Non-Protein Coding RNAs

    Walter, Nils G; Batey, Robert T

    2009-01-01

    This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and ot...

  18. Reliability-Based Code Calibration

    Faber, M.H.; Sørensen, John Dalsgaard

    2003-01-01

    The present paper addresses fundamental concepts of reliability based code calibration. First basic principles of structural reliability theory are introduced and it is shown how the results of FORM based reliability analysis may be related to partial safety factors and characteristic values....... Thereafter the code calibration problem is presented in its principal decision theoretical form and it is discussed how acceptable levels of failure probability (or target reliabilities) may be established. Furthermore suggested values for acceptable annual failure probabilities are given for ultimate...... and serviceability limit states. Finally the paper describes the Joint Committee on Structural Safety (JCSS) recommended procedure - CodeCal - for the practical implementation of reliability based code calibration of LRFD based design codes....

  19. What Froze the Genetic Code?

    Lluís Ribas de Pouplana

    2017-04-01

    Full Text Available The frozen accident theory of the Genetic Code was a proposal by Francis Crick that attempted to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. Fifty years later, it is clear that variations to the universal Genetic Code exist in nature and that translation is not limited to twenty amino acids. However, given the astonishing diversity of life on earth, and the extended evolutionary time that has taken place since the emergence of the extant Genetic Code, the idea that the translation apparatus is for the most part immobile remains true. Here, we will offer a potential explanation to the reason why the code has remained mostly stable for over three billion years, and discuss some of the mechanisms that allow species to overcome the intrinsic functional limitations of the protein synthesis machinery.

  20. Verification of reactor safety codes

    Murley, T.E.

    1978-01-01

    The safety evaluation of nuclear power plants requires the investigation of wide range of potential accidents that could be postulated to occur. Many of these accidents deal with phenomena that are outside the range of normal engineering experience. Because of the expense and difficulty of full scale tests covering the complete range of accident conditions, it is necessary to rely on complex computer codes to assess these accidents. The central role that computer codes play in safety analyses requires that the codes be verified, or tested, by comparing the code predictions with a wide range of experimental data chosen to span the physical phenomena expected under potential accident conditions. This paper discusses the plans of the Nuclear Regulatory Commission for verifying the reactor safety codes being developed by NRC to assess the safety of light water reactors and fast breeder reactors. (author)

  1. What Froze the Genetic Code?

    Ribas de Pouplana, Lluís; Torres, Adrian Gabriel; Rafels-Ybern, Àlbert

    2017-04-05

    The frozen accident theory of the Genetic Code was a proposal by Francis Crick that attempted to explain the universal nature of the Genetic Code and the fact that it only contains information for twenty amino acids. Fifty years later, it is clear that variations to the universal Genetic Code exist in nature and that translation is not limited to twenty amino acids. However, given the astonishing diversity of life on earth, and the extended evolutionary time that has taken place since the emergence of the extant Genetic Code, the idea that the translation apparatus is for the most part immobile remains true. Here, we will offer a potential explanation to the reason why the code has remained mostly stable for over three billion years, and discuss some of the mechanisms that allow species to overcome the intrinsic functional limitations of the protein synthesis machinery.

  2. Tristan code and its application

    Nishikawa, K.-I.

    Since TRISTAN: The 3-D Electromagnetic Particle Code was introduced in 1990, it has been used for many applications including the simulations of global solar windmagnetosphere interaction. The most essential ingridients of this code have been published in the ISSS-4 book. In this abstract we describe some of issues and an application of this code for the study of global solar wind-magnetosphere interaction including a substorm study. The basic code (tristan.f) for the global simulation and a local simulation of reconnection with a Harris model (issrec2.f) are available at http:/www.physics.rutger.edu/˜kenichi. For beginners the code (isssrc2.f) with simpler boundary conditions is suitable to start to run simulations. The future of global particle simulations for a global geospace general circulation (GGCM) model with predictive capability (for Space Weather Program) is discussed.

  3. High efficiency video coding coding tools and specification

    Wien, Mathias

    2015-01-01

    The video coding standard High Efficiency Video Coding (HEVC) targets at improved compression performance for video resolutions of HD and beyond, providing Ultra HD video at similar compressed bit rates as for HD video encoded with the well-established video coding standard H.264 | AVC. Based on known concepts, new coding structures and improved coding tools have been developed and specified in HEVC. The standard is expected to be taken up easily by established industry as well as new endeavors, answering the needs of todays connected and ever-evolving online world. This book presents the High Efficiency Video Coding standard and explains it in a clear and coherent language. It provides a comprehensive and consistently written description, all of a piece. The book targets at both, newbies to video coding as well as experts in the field. While providing sections with introductory text for the beginner, it suits as a well-arranged reference book for the expert. The book provides a comprehensive reference for th...

  4. Detecting non-coding selective pressure in coding regions

    Blanchette Mathieu

    2007-02-01

    Full Text Available Abstract Background Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements.

  5. Identity of zinc finger nucleases with specificity to herpes simplex virus type II genomic DNA: novel HSV-2 vaccine/therapy precursors

    Wayengera Misaki

    2011-06-01

    Full Text Available Abstract Background Herpes simplex type II (HSV-2 is a member of the family herpesviridae. Human infection with this double stranded linear DNA virus causes genital ulcerative disease and existing treatment options only serve to resolve the symptomatology (ulcers associated with active HSV-2 infection but do not eliminate latent virus. As a result, infection with HSV-2 follows a life-long relapsing (active versus latent course. On the basis of a primitive bacterium anti-phage DNA defense, the restriction modification (R-M system, we previously identified the Escherichia coli restriction enzyme (REase EcoRII as a novel peptide to excise or irreversibly disrupt latent HSV-2 DNA from infected cells. However, sequences of the site specificity palindrome of EcoRII 5'-CCWGG-3' (W = A or T are equally present within the human genome and are a potential source of host-genome toxicity. This feature has limited previous HSV-2 EcoRII based therapeutic models to microbicides only, and highlights the need to engineer artificial REases (zinc finger nucleases-ZFNs with specificity to HSV-2 genomic-DNA only. Herein, the therapeutic-potential of zinc finger arrays (ZFAs and ZFNs is identified and modeled, with unique specificity to the HSV-2 genome. Methods and results Using the whole genome of HSV-2 strain HG52 (Dolan A et al.,, and with the ZFN-consortium's CoDA-ZiFiT software pre-set at default, more than 28,000 ZFAs with specificity to HSV-2 DNA were identified. Using computational assembly (through in-silico linkage to the Flavobacterium okeanokoites endonuclease Fok I of the type IIS class, 684 ZFNs with specificity to the HSV-2 genome, were constructed. Graphic-analysis of the HSV-2 genome-cleavage pattern using the afore-identified ZFNs revealed that the highest cleavage-incidence occurred within the 30,950 base-pairs (~between the genomic context coordinates 0.80 and 1.00 at the 3' end of the HSV-2 genome. At approximately 3,095 bp before and after the

  6. Coding for effective denial management.

    Miller, Jackie; Lineberry, Joe

    2004-01-01

    Nearly everyone will agree that accurate and consistent coding of diagnoses and procedures is the cornerstone for operating a compliant practice. The CPT or HCPCS procedure code tells the payor what service was performed and also (in most cases) determines the amount of payment. The ICD-9-CM diagnosis code, on the other hand, tells the payor why the service was performed. If the diagnosis code does not meet the payor's criteria for medical necessity, all payment for the service will be denied. Implementation of an effective denial management program can help "stop the bleeding." Denial management is a comprehensive process that works in two ways. First, it evaluates the cause of denials and takes steps to prevent them. Second, denial management creates specific procedures for refiling or appealing claims that are initially denied. Accurate, consistent and compliant coding is key to both of these functions. The process of proactively managing claim denials also reveals a practice's administrative strengths and weaknesses, enabling radiology business managers to streamline processes, eliminate duplicated efforts and shift a larger proportion of the staff's focus from paperwork to servicing patients--all of which are sure to enhance operations and improve practice management and office morale. Accurate coding requires a program of ongoing training and education in both CPT and ICD-9-CM coding. Radiology business managers must make education a top priority for their coding staff. Front office staff, technologists and radiologists should also be familiar with the types of information needed for accurate coding. A good staff training program will also cover the proper use of Advance Beneficiary Notices (ABNs). Registration and coding staff should understand how to determine whether the patient's clinical history meets criteria for Medicare coverage, and how to administer an ABN if the exam is likely to be denied. Staff should also understand the restrictions on use of

  7. ESCADRE and ICARE code systems

    Reocreux, M.; Gauvain, J.

    1992-01-01

    The French sever accident code development program is following two parallel approaches: the first one is dealing with ''integral codes'' which are designed for giving immediate engineer answers, the second one is following a more mechanistic way in order to have the capability of detailed analysis of experiments, in order to get a better understanding of the scaling problem and reach a better confidence in plant calculations. In the first approach a complete system has been developed and is being used for practical cases: this is the ESCADRE system. In the second approach, a set of codes dealing first with primary circuit is being developed: a mechanistic core degradation code, ICARE, has been issued and is being coupled with the advanced thermalhydraulic code CATHARE. Fission product codes have been also coupled to CATHARE. The ''integral'' ESCADRE system and the mechanistic ICARE and associated codes are described. Their main characteristics are reviewed and the status of their development and assessment given. Future studies are finally discussed. 36 refs, 4 figs, 1 tab

  8. The ZPIC educational code suite

    Calado, R.; Pardal, M.; Ninhos, P.; Helm, A.; Mori, W. B.; Decyk, V. K.; Vieira, J.; Silva, L. O.; Fonseca, R. A.

    2017-10-01

    Particle-in-Cell (PIC) codes are used in almost all areas of plasma physics, such as fusion energy research, plasma accelerators, space physics, ion propulsion, and plasma processing, and many other areas. In this work, we present the ZPIC educational code suite, a new initiative to foster training in plasma physics using computer simulations. Leveraging on our expertise and experience from the development and use of the OSIRIS PIC code, we have developed a suite of 1D/2D fully relativistic electromagnetic PIC codes, as well as 1D electrostatic. These codes are self-contained and require only a standard laptop/desktop computer with a C compiler to be run. The output files are written in a new file format called ZDF that can be easily read using the supplied routines in a number of languages, such as Python, and IDL. The code suite also includes a number of example problems that can be used to illustrate several textbook and advanced plasma mechanisms, including instructions for parameter space exploration. We also invite contributions to this repository of test problems that will be made freely available to the community provided the input files comply with the format defined by the ZPIC team. The code suite is freely available and hosted on GitHub at https://github.com/zambzamb/zpic. Work partially supported by PICKSC.

  9. Stability analysis by ERATO code

    Tsunematsu, Toshihide; Takeda, Tatsuoki; Matsuura, Toshihiko; Azumi, Masafumi; Kurita, Gen-ichi

    1979-12-01

    Problems in MHD stability calculations by ERATO code are described; which concern convergence property of results, equilibrium codes, and machine optimization of ERATO code. It is concluded that irregularity on a convergence curve is not due to a fault of the ERATO code itself but due to inappropriate choice of the equilibrium calculation meshes. Also described are a code to calculate an equilibrium as a quasi-inverse problem and a code to calculate an equilibrium as a result of a transport process. Optimization of the code with respect to I/O operations reduced both CPU time and I/O time considerably. With the FACOM230-75 APU/CPU multiprocessor system, the performance is about 6 times as high as with the FACOM230-75 CPU, showing the effectiveness of a vector processing computer for the kind of MHD computations. This report is a summary of the material presented at the ERATO workshop 1979(ORNL), supplemented with some details. (author)

  10. ETR/ITER systems code

    Barr, W.L.; Bathke, C.G.; Brooks, J.N.; Bulmer, R.H.; Busigin, A.; DuBois, P.F.; Fenstermacher, M.E.; Fink, J.; Finn, P.A.; Galambos, J.D.; Gohar, Y.; Gorker, G.E.; Haines, J.R.; Hassanein, A.M.; Hicks, D.R.; Ho, S.K.; Kalsi, S.S.; Kalyanam, K.M.; Kerns, J.A.; Lee, J.D.; Miller, J.R.; Miller, R.L.; Myall, J.O.; Peng, Y-K.M.; Perkins, L.J.; Spampinato, P.T.; Strickler, D.J.; Thomson, S.L.; Wagner, C.E.; Willms, R.S.; Reid, R.L. (ed.)

    1988-04-01

    A tokamak systems code capable of modeling experimental test reactors has been developed and is described in this document. The code, named TETRA (for Tokamak Engineering Test Reactor Analysis), consists of a series of modules, each describing a tokamak system or component, controlled by an optimizer/driver. This code development was a national effort in that the modules were contributed by members of the fusion community and integrated into a code by the Fusion Engineering Design Center. The code has been checked out on the Cray computers at the National Magnetic Fusion Energy Computing Center and has satisfactorily simulated the Tokamak Ignition/Burn Experimental Reactor II (TIBER) design. A feature of this code is the ability to perform optimization studies through the use of a numerical software package, which iterates prescribed variables to satisfy a set of prescribed equations or constraints. This code will be used to perform sensitivity studies for the proposed International Thermonuclear Experimental Reactor (ITER). 22 figs., 29 tabs.

  11. ETR/ITER systems code

    Barr, W.L.; Bathke, C.G.; Brooks, J.N.

    1988-04-01

    A tokamak systems code capable of modeling experimental test reactors has been developed and is described in this document. The code, named TETRA (for Tokamak Engineering Test Reactor Analysis), consists of a series of modules, each describing a tokamak system or component, controlled by an optimizer/driver. This code development was a national effort in that the modules were contributed by members of the fusion community and integrated into a code by the Fusion Engineering Design Center. The code has been checked out on the Cray computers at the National Magnetic Fusion Energy Computing Center and has satisfactorily simulated the Tokamak Ignition/Burn Experimental Reactor II (TIBER) design. A feature of this code is the ability to perform optimization studies through the use of a numerical software package, which iterates prescribed variables to satisfy a set of prescribed equations or constraints. This code will be used to perform sensitivity studies for the proposed International Thermonuclear Experimental Reactor (ITER). 22 figs., 29 tabs

  12. LFSC - Linac Feedback Simulation Code

    Ivanov, Valentin; Fermilab

    2008-01-01

    The computer program LFSC ( ) is a numerical tool for simulation beam based feedback in high performance linacs. The code LFSC is based on the earlier version developed by a collective of authors at SLAC (L.Hendrickson, R. McEwen, T. Himel, H. Shoaee, S. Shah, P. Emma, P. Schultz) during 1990-2005. That code was successively used in simulation of SLC, TESLA, CLIC and NLC projects. It can simulate as pulse-to-pulse feedback on timescale corresponding to 5-100 Hz, as slower feedbacks, operating in the 0.1-1 Hz range in the Main Linac and Beam Delivery System. The code LFSC is running under Matlab for MS Windows operating system. It contains about 30,000 lines of source code in more than 260 subroutines. The code uses the LIAR ('Linear Accelerator Research code') for particle tracking under ground motion and technical noise perturbations. It uses the Guinea Pig code to simulate the luminosity performance. A set of input files includes the lattice description (XSIF format), and plane text files with numerical parameters, wake fields, ground motion data etc. The Matlab environment provides a flexible system for graphical output

  13. Coded communications with nonideal interleaving

    Laufer, Shaul

    1991-02-01

    Burst error channels - a type of block interference channels - feature increasing capacity but decreasing cutoff rate as the memory rate increases. Despite the large capacity, there is degradation in the performance of practical coding schemes when the memory length is excessive. A short-coding error parameter (SCEP) was introduced, which expresses a bound on the average decoding-error probability for codes shorter than the block interference length. The performance of a coded slow frequency-hopping communication channel is analyzed for worst-case partial band jamming and nonideal interleaving, by deriving expressions for the capacity and cutoff rate. The capacity and cutoff rate, respectively, are shown to approach and depart from those of a memoryless channel corresponding to the transmission of a single code letter per hop. For multiaccess communications over a slot-synchronized collision channel without feedback, the channel was considered as a block interference channel with memory length equal to the number of letters transmitted in each slot. The effects of an asymmetrical background noise and a reduced collision error rate were studied, as aspects of real communications. The performance of specific convolutional and Reed-Solomon codes was examined for slow frequency-hopping systems with nonideal interleaving. An upper bound is presented for the performance of a Viterbi decoder for a convolutional code with nonideal interleaving, and a soft decision diversity combining technique is introduced.

  14. Coding and decoding for code division multiple user communication systems

    Healy, T. J.

    1985-01-01

    A new algorithm is introduced which decodes code division multiple user communication signals. The algorithm makes use of the distinctive form or pattern of each signal to separate it from the composite signal created by the multiple users. Although the algorithm is presented in terms of frequency-hopped signals, the actual transmitter modulator can use any of the existing digital modulation techniques. The algorithm is applicable to error-free codes or to codes where controlled interference is permitted. It can be used when block synchronization is assumed, and in some cases when it is not. The paper also discusses briefly some of the codes which can be used in connection with the algorithm, and relates the algorithm to past studies which use other approaches to the same problem.

  15. GAMERA - The New Magnetospheric Code

    Lyon, J.; Sorathia, K.; Zhang, B.; Merkin, V. G.; Wiltberger, M. J.; Daldorff, L. K. S.

    2017-12-01

    The Lyon-Fedder-Mobarry (LFM) code has been a main-line magnetospheric simulation code for 30 years. The code base, designed in the age of memory to memory vector ma- chines,is still in wide use for science production but needs upgrading to ensure the long term sustainability. In this presentation, we will discuss our recent efforts to update and improve that code base and also highlight some recent results. The new project GAM- ERA, Grid Agnostic MHD for Extended Research Applications, has kept the original design characteristics of the LFM and made significant improvements. The original de- sign included high order numerical differencing with very aggressive limiting, the ability to use arbitrary, but logically rectangular, grids, and maintenance of div B = 0 through the use of the Yee grid. Significant improvements include high-order upwinding and a non-clipping limiter. One other improvement with wider applicability is an im- proved averaging technique for the singularities in polar and spherical grids. The new code adopts a hybrid structure - multi-threaded OpenMP with an overarching MPI layer for large scale and coupled applications. The MPI layer uses a combination of standard MPI and the Global Array Toolkit from PNL to provide a lightweight mechanism for coupling codes together concurrently. The single processor code is highly efficient and can run magnetospheric simulations at the default CCMC resolution faster than real time on a MacBook pro. We have run the new code through the Athena suite of tests, and the results compare favorably with the codes available to the astrophysics community. LFM/GAMERA has been applied to many different situations ranging from the inner and outer heliosphere and magnetospheres of Venus, the Earth, Jupiter and Saturn. We present example results the Earth's magnetosphere including a coupled ring current (RCM), the magnetospheres of Jupiter and Saturn, and the inner heliosphere.

  16. SCALE Code System

    Jessee, Matthew Anderson [ORNL

    2016-04-01

    The SCALE Code System is a widely-used modeling and simulation suite for nuclear safety analysis and design that is developed, maintained, tested, and managed by the Reactor and Nuclear Systems Division (RNSD) of Oak Ridge National Laboratory (ORNL). SCALE provides a comprehensive, verified and validated, user-friendly tool set for criticality safety, reactor and lattice physics, radiation shielding, spent fuel and radioactive source term characterization, and sensitivity and uncertainty analysis. Since 1980, regulators, licensees, and research institutions around the world have used SCALE for safety analysis and design. SCALE provides an integrated framework with dozens of computational modules including three deterministic and three Monte Carlo radiation transport solvers that are selected based on the desired solution strategy. SCALE includes current nuclear data libraries and problem-dependent processing tools for continuous-energy (CE) and multigroup (MG) neutronics and coupled neutron-gamma calculations, as well as activation, depletion, and decay calculations. SCALE includes unique capabilities for automated variance reduction for shielding calculations, as well as sensitivity and uncertainty analysis. SCALE’s graphical user interfaces assist with accurate system modeling, visualization of nuclear data, and convenient access to desired results.SCALE 6.2 provides many new capabilities and significant improvements of existing features.New capabilities include:• ENDF/B-VII.1 nuclear data libraries CE and MG with enhanced group structures,• Neutron covariance data based on ENDF/B-VII.1 and supplemented with ORNL data,• Covariance data for fission product yields and decay constants,• Stochastic uncertainty and correlation quantification for any SCALE sequence with Sampler,• Parallel calculations with KENO,• Problem-dependent temperature corrections for CE calculations,• CE shielding and criticality accident alarm system analysis with MAVRIC,• CE

  17. Code-Mixing and Code Switchingin The Process of Learning

    Diyah Atiek Mustikawati

    2016-09-01

    Full Text Available This study aimed to describe a form of code switching and code mixing specific form found in the teaching and learning activities in the classroom as well as determining factors influencing events stand out that form of code switching and code mixing in question.Form of this research is descriptive qualitative case study which took place in Al Mawaddah Boarding School Ponorogo. Based on the analysis and discussion that has been stated in the previous chapter that the form of code mixing and code switching learning activities in Al Mawaddah Boarding School is in between the use of either language Java language, Arabic, English and Indonesian, on the use of insertion of words, phrases, idioms, use of nouns, adjectives, clauses, and sentences. Code mixing deciding factor in the learning process include: Identification of the role, the desire to explain and interpret, sourced from the original language and its variations, is sourced from a foreign language. While deciding factor in the learning process of code, includes: speakers (O1, partners speakers (O2, the presence of a third person (O3, the topic of conversation, evoke a sense of humour, and just prestige. The significance of this study is to allow readers to see the use of language in a multilingual society, especially in AL Mawaddah boarding school about the rules and characteristics variation in the language of teaching and learning activities in the classroom. Furthermore, the results of this research will provide input to the ustadz / ustadzah and students in developing oral communication skills and the effectiveness of teaching and learning strategies in boarding schools.

  18. Neural Decoder for Topological Codes

    Torlai, Giacomo; Melko, Roger G.

    2017-07-01

    We present an algorithm for error correction in topological codes that exploits modern machine learning techniques. Our decoder is constructed from a stochastic neural network called a Boltzmann machine, of the type extensively used in deep learning. We provide a general prescription for the training of the network and a decoding strategy that is applicable to a wide variety of stabilizer codes with very little specialization. We demonstrate the neural decoder numerically on the well-known two-dimensional toric code with phase-flip errors.

  19. Coding chaotic billiards. Pt. 3

    Ullmo, D.; Giannoni, M.J.

    1993-01-01

    Non-tiling compact billiard defined on the pseudosphere is studied 'a la Morse coding'. As for most bounded systems, the coding is non exact. However, two sets of approximate grammar rules can be obtained, one specifying forbidden codes, and the other allowed ones. In-between some sequences remain in the 'unknown' zone, but their relative amount can be reduced to zero if one lets the length of the approximate grammar rules goes to infinity. The relationship between these approximate grammar rules and the 'pruning front' introduced by Cvitanovic et al. is discussed. (authors). 13 refs., 10 figs., 1 tab

  20. Iterative nonlinear unfolding code: TWOGO

    Hajnal, F.

    1981-03-01

    a new iterative unfolding code, TWOGO, was developed to analyze Bonner sphere neutron measurements. The code includes two different unfolding schemes which alternate on successive iterations. The iterative process can be terminated either when the ratio of the coefficient of variations in terms of the measured and calculated responses is unity, or when the percentage difference between the measured and evaluated sphere responses is less than the average measurement error. The code was extensively tested with various known spectra and real multisphere neutron measurements which were performed inside the containments of pressurized water reactors